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Second-harmony generation studies of organic salts Patrick, Brian Olivier 1997

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SECOND-HARMONIC GENERATION STUDIES O ORGANIC SALTS by BRIAN OLIVIER PATRICK B.Sc. (Hons-Co-op), University of Waterloo, Waterloo, Ontario, A THESIS SUBMITTED IN P A R T I A L F U L F I L M E N T OF T H E REQUIREMENTS FOR T H E D E G R E E OF DOCTOR OF PHILOSOPHY in T H E F A C U L T Y OF G R A D U A T E STUDIES (DEPARTMENT OF CHEMISTRY) We accept this thesis as conforming to the required standard T H E UNIVERSITY OF BRITISH C O L U M B I A October 1997 © Brian Olivier Patrick, 1997 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Department The University of British Columbia Vancouver, Canada Date g.LUr 9./9fh DE-6 (2/88) Abstract R Second-harmonic generation (SHG) in the solid-state is N H \ restricted to materials that crystallize in non-C H J - C Q J H (1) R = H centrosymmetric space groups. Unfortunately, the vast (2) R= NOj majority of solids crystallize in centrosymmetric space N i I \ _ y N-CH, groups and are therefore SHG-inactive. The (3) X = CH requirement for solid-state asymmetry is addressed in (4) X = N two series of salts. Acid (1), SHG-inactive due to its centrosymmetric (Pi) packing, was coupled to six optically pure amines to form salts and/or complexes that, by virtue of their chiral counterion, crystallized in non-centrosymmetric space groups. The 1064 nm output from a N d : Y A G laser produced 532 nm SHG from each of the six salts, with three of the salts producing SHG-intensities at least an order of magnitude greater than that of our standard, urea. X-ray crystallographic analysis was carried out on five of the six salts, and an attempt was made to rationalize each salt's SHG-intensity based on the orientation of its molecular charge-transfer axis in the unit cell and on its chromophore density. A second series of salts and/or complexes was formed by coupling acid (2) to the same set of optically pure amines as were used in the first series. The second electron-withdrawing group in (2) permits additional directions of charge-transfer, rather than the unidirectional charge-transfer along the para amine-nitro axis of (1). As such, the macroscopic second-order susceptibilities of salts made from (2) depend on the ii orientations of the aromatic ring as a whole and not simply the above-mentioned charge-transfer axis. Once again, the parent acid of the series of salts crystallized in a centrosymmetric space group {P2\lc) and was SHG-inactive, while each of the six salts produced varied amounts of SHG. While none of the salts formed from (2) produce SHG with the same intensity as the best of the salts formed from acid (1), four of the six salts produced SHG-intensities that were at least twice that of urea. X-ray crystallographic analysis was carried out on each of the salts and an attempt was once again made to rationalize the SHG-intensities measured from each salt, this time based on the orientations of the respective aromatic rings and on the different chromophore densities. The SHG-intensities of the salts and complexes formed in the first two series appear to be limited, in part, by the decrease in NLO chromophore density produced by the salt formation. A means of increasing the chromophore density was achieved in a third series of salts, where acids (1) and (2) were coupled to amines (3) and (4). While the chromophore densities of the salts were indeed greater relative to those found in the first two series of materials, the salts were no longer constrained to pack in non-centrosymmetric space groups due to absence of optical purity in any of the acids or bases. As a result, none of the salts packed in non-centrosymmetric space groups and thus each salt was SHG-inactive. iii Table of Contents Abstract ii Table of Contents iv Table of Figures x List of Tables xvi Acknowledgement xxii Dedication xxiii Chapter 1 - Introduction 1 1.1. Introduction 1 1.2. Origins of Second-Harmonic Generation . 4 1.3. Modern description of SHG 9 1.4. Materials for Second-Order Nonlinear Optics 15 1.4.1. Overview 15 1.4.2. Inorganic Materials for Nonlinear Optics 18 1.4.3. Poled-Polymer Systems 22 1.4.4. Self-Assembled Multilayer Systems 26 1.4.5. Organic Crystals 28 1.5. Research Outline 34 Chapter 2 - Survey of the Cambridge Structural Database 38 2.1. Introduction 38 2.2. Packing trends of PNA and DNA analogs 42 iv 2.3. Discussion 46 Chapter 3 - p-Nitrophenylglycine and its salts - Results and discussion 48 3.1. Introduction 48 3.1.1. Macroscopic nonlinear susceptibility 48 3.1.2. Phase-matching 55 3.2. General synthesis 58 3.3. X-ray structural analyses 61 3.4. Estimation of second-order nonlinear susceptibilities 62 3.5. Second-order nonlinear optical properties 67 3.5.1. SHG results of the (IS, 2S)-(+)-pseudoephedrine salt of (1): l.eph 68 3.5.2. SHG results of the S-(-)-proline t-butyl ester salt of (1): l.pro-but 72 3.5.3. SHG results of the S-(-)-prolinol salt of (1): l.pro-ol 74 3.5.4. SHG results of the S-(-)-prolinamide salt of (1): l.pro-amide 76 3.5.5. SHG results of the S-(-)-proline methyl ester complex of (1): l.pro-meth 77 3.6. Phase-matching results 79 3.7. Discussion 82 Chapter 4 - 2,4-Dinitrophenylglycine and its salts - Results and discussion 84 4.1. Introduction 84 4.1.1. 2,4-Dinitroaniline systems and their quadratic hyperpolarizabilities 84 4.1.2. Orientation of the molecular plane 87 4.1.3. Orientation of the molecular reference frame 93 4.2. General synthesis 95 4.3. X-ray structural analyses 97 4.4. Estimation of second-order nonlinear susceptibilities 98 4.5. Second-order nonlinear optical properties 101 4.5.1. SHG results of the S-(-)-proline t-butyl ester salt of (2): 2.pro-but 104 4.5.2. SHG results of the S-(-)-prolinol salt of (2): 2.pro-ol 105 4.5.3. SHG results of the S-(-)-proline methyl ester complex of (2): 2.pro-meth 107 4.5.4. SHG results of the S-(-)-prolinamide salt of (2): 2.pro-amide 108 4.5.5. SHG results of the S-(-)-proline benzyl ester complex of (2): 2.pro-benz 109 4.5.6. SHG results of the (IS, 2S) - (+) - pseudoephedrine salt of (2): 2.eph 111 4.6. Phase-matching results 113 4.7. Discussion 115 Chapter 5 - Doubly chromophoric salts: NLO acids coupled to NLO amines - Results and discussion 117 5.1. Introduction 117 5.2. General synthesis 118 5.3. X-ray structural analyses 121 5.4. SHG results of l-(p-nitrophenyl)-4-methylpiperazine (3) 121 5.4. Discussion 123 Chapter 6 - Experimental (Organic Synthesis) 126 6.1. General Experimental 126 6.2. Synthesis and characterization 129 6.2.1. Synthesis of N-/?-nitrophenyl glycine (1) 129 vi 6.2.2. Synthesis of the (IS, 2S)-(+)-pseudoephedrine salt of (1): l.eph 130 6.2.3. Synthesis of the S-(-)-proline t-butyl ester salt of (1): l.pro-but 131 6.2.4. Synthesis of the S-(-)-proline methyl ester complex of (1): l.pro-meth 133 6.2.5. Synthesis of the S-(-)-prolinamide salt of (1): l.pro-amide 134 6.2.6. Synthesis of the S-(-)-prolinol salt of (1): l.pro-ol 135 6.2.7. Synthesis of the S-(-)-proline benzyl ester salt of (1): l.pro-benz 136 6.2.8. Synthesis of the (IS, 2S)-(+)-pseudoephedrine salt of (2): 2.eph 137 6.2.9. Synthesis of the S-(-)-proline t-butyl ester salt of (2): 2.pro-but 139 6.2.10. Synthesis of the S-(-)-proline methyl ester complex of (2): 2.pro-meth 140 6.2.11. Synthesis of the S-(-)-proline benzyl ester complex of (2): 2.pro-benz 141 6.2.12. Synthesis of the S-(-)-prolinol salt of (2): 2.pro-ol 143 6.2.13. Synthesis of the S-(-)-prolinamide salt of (2): 2.pro-amide 144 6.2.14. Synthesis of l-(p-nitrophenyl)-4-mefhylpiperazine (3) 145 6.2.15. Synthesis of l-methyl-4-(4-nitro-2-pyridyl)-piperazine (4) 146 6.2.16. Synthesis of the l-(p-nitrophenyl)-4-methylpiperazinium salt of (1): l.nitrophen 147 6.2.16. Synthesis of the l-methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (1): 1. nitropyr 148 6.2.17. Synthesis of the l-(p-nitrophenyl)-4-methylpiperazinium salt of (2): 2. nitrophen 149 6.2.18. Synthesis of the l-methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (2): 2.nitropyr 150 vii Chapter 7 - Experimental (SHG measurement) 152 7.1. Measurement of SHG Efficiency 152 Chapter 8 - Experimental (Crystallographic) 156 8.1. General Considerations 156 8.1.1. Data Collection 156 8.1.2. Data Reduction 158 8.1.3. Structure Solution 159 8.1.4. Structure Refinement 163 8.1.5. Treatment of disorder 165 8.1.6. Structure completion 166 8.2. p-Nitrophenylglycine (1) : 166 8.3. (lS,2S)-(+)-pseudoephedrinesaltof (1): l.eph 169 8.4. S-(-)-Proline f-butyl ester salt of (1): l.pro-but 174 8.5. S-(-)-Proline methyl ester salt of (1): l.pro-meth 186 8.6. S-(-)-Prolinamide salt of (1): l.pro-amide.... 189 8.7. S-(-)-Prolinol salt of (1): l.pro-ol.. 192 8.8. 2,4-Dinitrophenylglycine (2) 206 8.9. (IS, 2S)-(+)-pseudoephedrine salt of (2): 2.eph 208 8.10. S-(-)-Proline r-butyl ester salt of (2): 2.pro-but 211 8.11. S-(-)-Proline methyl ester salt of (2): 2.pro-meth 226 8.12. S-(-)-Proline benzyl ester salt of (2): 2.pro-benz 229 8.13. S-(-)-Prolinol salt of (2): 2.pro-ol 240 viii 8.14. S-(-)-Prolinamide salt of (2): 2.pro-amide 244 8.15. l-(p-Nitrophenyl)-4-methylpiperazine (3) 255 8.16. l-(p-Nitrophenyl)-4-methylpiperazinium salt of (1): l.nitrophen 258 8.17. l-(p-Nitrophenyl)-4-methylpiperazinium salt of (2): 2.nitrophen 260 8.18. 1 -(4-nitro-2-pyridyl)-4-methylpiperazine (4) 271 8.19. l-Methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (1): l.nitropyr 274 8.20. l-Methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (2): 2.nitropyr 277 References 289 ix Table of Figures Figure 1.1 Induced dipole (fi - ji0) as a function of field strength. Plot (a) represents {ji - ii0) as a linear function of field strength E, while in plot (b) {fi -Ho) is expressed as a quadratic function of E. Adapted from ref. [1] 2 Figure 1.2 Plots of the electric field of (a) an applied electromagnetic wave and (b) the induced dipole from a molecule with a centre of inversion. Adapted from ref. [1] 5 Figure 1.3 Plots of the electric field of (a) an applied electromagnetic wave and (b) the induced dipole in a second-order N L O material. Adapted from ref. [1] 6 Figure 1.4 Deconvolution of a polarization wave (a) of a second-order NLO material to give waves with both the fundamental (b) and second-harmonic (c) frequency, as well as a dc electric field (d). Adapted from ref. [1] 7 Figure 1.5 Time-ordered diagrams describing SHG, where col = co2 and co3 = 2col. Adapted from ref. [9] 10 Figure 1.6 Two resonance forms of PNA, a typical donor/acceptor system for second-order NLO materials 16 Figure 1.7 Distorted octahedral coordination of metal-oxides found in typical inorganic N L O materials 19 Figure 1.8 The periodic poling technique, (a) Application of a strong electric field induces a change in polarity in a typical inorganic chromophore. (b) Careful poling control creates domains of reversed polarity. Adapted from ref. [41] 21 Figure 1.9 Examples of (a) a side-chain poled-polymer (4-(dicyanovinyl)-4'-(diethylamino)azobenzene) linked to poly(methyl methacrylate), and (b) a main-chain poled-polymer (bisphenol A-Af,Af-nitroaniline). Adapted from refs. [46] and [62] 24 Figure 1.10 An example of a typical cross-linked epoxy host and a commonly used guest, DANS. Adapted from ref. [58] 25 Figure 1.11 An example of an NLO chromophore incorporated in a cross-linked epoxy host matrix. Adapted from ref.[67] 26 Figure 1.12 A self-assembled monolayer with a stilbazolium chromophore. Repeating steps 1-3 produces structurally rigid multilayers capable of SHG. Adapted from ref. [69] 27 Figure 1.13 Packing arrangement of NPAN 30 Figure 1.14 Resonance structures of POM 30 Figure 1.15 Af-p-nitrophenyl-L-prolinol (NPP) 31 Figure 1.16 Acid (1), p-nitrophenylglycine 35 Figure 1.17 Acid (2), 2,4-dinitrophenylglycine 36 Figure 1.18 Amines (3) and (4), l-(p-nitrophenyl)-4-methylpiperazine and 1-methyl-4-(4-nitro-2-pyridyl)-piperazine, respectively 37 Figure 2.1 Chemical structures considered in the CSD search for PNA analogs 42 Figure 2.2 Anti-parallel alignment of molecular dipoles in PNA analogs 43 Figure 2.3 Chemical structures considered in the CSD search for DNA analogs 44 Figure 2.4 Pseudo-centrosymmetric alignment of DNA analogs 45 Figure 3.1 p-Nitrophenylglycine (1) and the molecular axis system describing the orientation of the charge-transfer axis 48 Figure 3.2 Axis systems used to define the molecular (xyz) reference frame with respect to the crystal (XYZ) reference frame for point groups 2 and m 52 Figure 3.3 The crystal reference frame used to define the charge-transfer axis for PNA analogs crystallizing in point groups mm2 or 222. Crystal reference axes X , Y and Z coincide with unit cell axes a, b and c, respectively 54 Figure 3.4 Index ellipsoid of a uniaxial crystal, where s is the direction of propagation, and n 0 and n e are the ordinary and extraordinary components of the refractive index. Reproduced from ref. [75] 57 xi Figure 3.5 C H A R O N packing diagram of (1) 62 Figure 3.6 UV-vis spectra of (1), PNA and NPP in EtOH 66 Figure 3.7 ORTEP diagram of l.eph. Only the major disordered p-nitrophenylglycinate fragment is shown (50% probability ellipsoids) 69 Figure 3.8 Orientations of the disordered p-nitrophenylglycinate anion in l.eph. The major fragment, labeled without stars, makes an angle of Omaj = 76.7° to the &-axis, while the minor fragment, labeled with stars, makes an angle of Omin = 61.0° to the same axis 70 Figure 3.9 ORTEP packing stereodiagram of l.pro-but (50% probability ellipsoids) 74 Figure 3.10 ORTEP diagram of l.pro-ol (50% probability ellipsoids) 76 Figure 3.11 ORTEP diagram of l.pro-amide (50 % probability ellipsoids) 77 Figure 3.12 ORTEP diagram of l.pro-meth (50% probability ellipsoids) 78 Figure 3.13 Theoretical SHG behavior of phase-matchable and non phase-matchable materials.[153] The variables <r> and <lc> are the mean particle-size and mean coherence length of the material. The coherence length is defined as the distance between two points in the crystal where second-harmonic waves are generated 180° out of phase with each other 80 Figure 3.14 Change in SHG-intensity with particle size for NPP, l.eph and l.pro-but 81 Figure 4.1 Polarization throughout the aromatic plane of DNA, as shown by its resonance forms ., 85 Figure 4.2 Molecular reference frames describing DNA analogs 87 Figure 4.3 The relationship between an aromatic ring and a two-fold rotation axis for both PNA and DNA. In both (a) and (c) the aromatic rings are co-planar, while in (b) and (d) there is a dihedral angle between the two rings. This angle has no bearing on the direction of the lone charge-transfer axis in PNA, but in xii DNA this angle determines the orientation of the second electron-accepting N 0 2 group 88 Figure 4.4 The definition of the crystal and molecular reference frames for DNA-type molecules in point group 2. Adapted from ref. [129] 90 Figure 4.5 The axis system describing angle 0 for point group 222. Points 1 and 2 represent equivalent molecules related by the Z two-fold axis of rotation. Adapted from ref. [129] 91 Figure 4.6 Rotation of the (abc) reference axis onto the molecular (xyz) axis system 93 Figure 4.7 ORTEP packing diagram of acid (2) (50% probability ellipsoids). 98 Figure 4.8 ORTEP packing diagram of 2.pro-but (50% probability ellipsoids) 104 Figure 4.9 The relative orientations of the two chromophores in the asymmetric unit of 2.pro-ol 106 Figure 4.10 ORTEP diagram of 2.pro-meth. (50% probability ellipsoids) 108 Figure 4.11 ORTEP diagram of 2.pro-benz. (50% probability ellipsoids) 110 Figure 4.12 The axis system defining angles 0i and 02 for space group PI 112 Figure 4.13 Change in SHG-intensity with particle size for 2.pro-but, 2.pro-oI and2.eph 114 Figure 5.1 ORTEP packing stereodiagram of amine (3) (50% probability ellipsoids) 123 Figure 6.1 A typical DSC melting endotherm. The number to the left represents the onset melting temperature while the number to the right is the temperature at the endotherm peak 128 Figure 7.1 Experimental set-up for SHG measurements. B l , 2: boxcar averagers; BS: beamsplitter; F: sharp-cut filter; L I , 2: focusing lenses; M C : monochromator; ND1, 2: neutral density filters; PC: personal computer; PMT: photomultiplier tube; S: sample cell; U : urea reference cell 153 xiii Figure 8.1 A four-circle diffractometer with the angles (0, 26, % a n d y^as defined. Adapted from ref. [157] , 157 Figure 8.2 ORTEP diagram of acid (1) (50% probability ellipsoids) 168 Figure 8.3 ORTEP diagram of l.eph (50% probability ellipsoids). Only the major disordered fragment is shown 172 Figure 8.4 ORTEP packing stereodiagram of l.eph (50% probability ellipsoids). Only the major disordered fragment is shown 173 Figure 8.5 ORTEP diagram of l.pro-but (50% probability ellipsoids). Only the major disordered fragment is shown 176 Figure 8.6 C H A R O N packing diagram of l.pro-meth viewed down the c-axis 189 Figure 8.7 C H A R O N packing diagram of l.pro-amide viewed down the &-axis 192 Figure 8.8 ORTEP packing diagrams of (a) the p-nitrophenylglycinate anions and (b) the L-prolinol cations of l.pro-ol (50% probability ellipsoids). Only the major disordered fragment is shown 195 Figure 8.9 ORTEP of acid (2) (50% probability ellipsoids) 207 Figure 8.10 ORTEP diagram of 2.eph (50% probability ellipsoids) 210 Figure 8.11 C H A R O N packing diagram of 2.eph 211 Figure 8.12 ORTEP diagram of 2.pro-but (50% probability ellipsoids). Only the major disordered fragment is shown 214 Figure 8.13 C H A R O N packing diagram of 2.pro-meth 229 Figure 8.14 C H A R O N packing diagram of 2.pro-benz 232 Figure 8.15 ORTEP diagram of 2.pro-ol (50% probability ellipsoids). Only the major disordered fragment is shown 243 Figure 8.16 ORTEP packing stereodiagram of 2.pro-ol (50% probability ellipsoids). Only the major disordered fragment is shown 244 xiv Figure 8.17 ORTEP diagram of 2.pro-amide, with the MeOH and EtOH solvent molecules shown (50% probability ellipsoids). Only the major disordered fragments are shown 247 Figure 8.18 C H A R O N packing diagram of 2.pro-amide viewed down the c-axis.... 248 Figure 8.19 ORTEP diagram of (3) (50% probability ellipsoids) 257 Figure 8.20 ORTEP diagram of l.nitrophen (50% probability ellipsoids) 259 Figure 8.21 C H A R O N packing diagram of l.nitrophen viewed down the &-axis.... 260 Figure 8.22 ORTEP diagram of 2.nitrophen (50% probability ellipsoids) 262 Figure 8.23 C H A R O N packing diagram of 2.nitrophen 263 Figure 8.24 ORTEP diagram of (4) (50% probability ellipsoids) 273 Figure 8.25 ORTEP packing stereodiagram of acid (4) 274 Figure 8.26 ORTEP diagram of l.nitropyr (50% probability ellipsoids) 276 Figure 8.27 C H A R O N packing diagram of l.nitropyr viewed down the c-axis 277 Figure 8.28 ORTEP diagram of 2.nitropyr (50% probability ellipsoids) 279 Figure 8.29 C H A R O N packing diagram of 2.nitropyr 279 XV List of Tables Table 1.1 Properties of selected inorganic NLO compounds. Adapted from ref. [37] 20 Table 2.1 Packing trends of PNA and DNA analogs (cf. data for all organic structures from Mighell et al.) 41 Table 2.2 Survey of non-centrosymmetric PNA and DNA analogs 46 Table 3.1 Glossary of materials described in Chapter 3 60 Table 3.2 Space group, chromophore density (AO and orientational parameters (a, for the six salts made from (1) 65 Table 3.3 SHG results for (1) and all six salts containing the (1) chromophore.... 68 Table 4.1 Quadratic-hyperpolarizabilities calculated for various (3,^  tensor elements for PNA and DNA 86 Table 4.2 Glossary of materials described in Chapter 4 96 Table 4.3 Space group, chromophore density (A7) and orientational parameters (a, <]) and 9) for the six salts made from (2). 99 Table 4.4 SHG results for (2) and all six salts containing the (2) chromophore 103 Table 5.1 Glossary of materials described in Chapter 5 120 Table 5.1 Space group and chromophore density (AO for acids (1) and (2), amines (3) and (4) and the four salts 125 Table 8.1 Crystallographic data for (1), l.eph and l.pro-but 178 Table 8.2 Final atomic coordinates (fractional) and B(eq) (A2) of (1) 179 Table 8.3 Bond lengths (A) of (1) with estimated standard deviations 180 Table 8.4 Bond angles (°) of (1) with estimated standard deviations 180 xvi Table 8.5 Geometry of (1) hydrogen bonds and C — H - 0 interactions (A, °) 181 Table 8.6 Final atomic coordinates (fractional) and B(eq) (A2) of l.eph 181 Table 8.7 Bond lengths (A) of l.eph with estimated standard deviations 182 Table 8.8 Bond angles (°) of l.eph with estimated standard deviations 183 Table 8.9 Geometry of l.eph hydrogen bonds and C—H- • - O interactions (A, °) 183 Table 8.10 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-but 184 Table 8.11 Bond lengths (A) of l.pro-but with estimated standard deviations 185 Table 8.12 Bond angles (°) of l.pro-but with estimated standard deviations 185 Table 8.13 Geometry of l.pro-but hydrogen bonds and C — H - - 0 interactions (A, °) 186 Table 8.14 Crystallographic data for l.pro-meth, l.pro-amide and l.pro-ol 196 Table 8.15 Final atomic coordinates (fractional) and B(eq) (A)2 of l.pro-meth. 197 Table 8.16 Bond lengths (A) of l.pro-meth with estimated standard deviations 198 Table 8.17 Bond angles (°) of l.pro-meth with standard deviations 198 Table 8.18 Geometry of l.pro-meth hydrogen bonds and C — H - 0 interactions (A, °) 199 Table 8.19 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-amide 199 Table 8.20 Bond lengths (A) of l.pro-amide with estimated standard deviations 201 Table 8.21 Bond angles (°) of l.pro-amide with estimated standard deviations 201 Table 8.22 Geometry of l.pro-amide hydrogen bonds and C—H- • -O interactions (A, °) 202 xvii Table 8.23 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-ol 203 Table 8.24 Bond lengths (A) of l.pro-ol with estimated standard deviations 204 Table 8.25 Bond angles (°) of l.pro-ol with estimated standard deviations 204 Table 8.26 Geometry of l.pro-ol hydrogen bonds and C—H---0 interactions (A, °) 205 Table 8.27 Crystallographic data for (2), 2.eph and 2.pro-but 216 Table 8.28 Final atomic coordinates (fractional) and B(eq) (A2) of (2) 217 Table 8.29 Bond lengths (A) of (2) with estimated standard deviations 217 Table 8.30 Bond angles (°) of (2) with standard deviations 218 Table 8.31 Geometry of (2) hydrogen bonds and C — H - 0 interactions (A, °) 218 Table 8.32 Final atomic coordinates (fractional) and B(eq) (A2) of 2.eph 218 Table 8.33 Bond lengths (A) of 2.eph with estimated standard deviations 220 Table 8.34 Bond angles (°) of 2.eph with estimated standard deviations 221 Table 8.35 Geometry of 2.eph hydrogen bonds and C—H- • O interactions(A, °) 222 Table 8.36 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-but 222 Table 8.37 Bond lengths (A) of 2.pro-but with estimated standard deviations 224 Table 8.38 Bond angles (°) of 2.pro-but with estimated standard deviations 224 Table 8.39 Geometry of 2.pro-but hydrogen bonds (A, °) 225 Table 8.40 Crystallographic data for 2.pro-meth and 2.pro-benz 233 Table 8.41 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-meth 234 xviii Table 8.42 Bond lengths (A) of 2.pro-meth with estimated standard deviations 235 Table 8.43 Bond angles (°) of 2.pro-meth with estimated standard deviations 235 Table 8.44 Geometry of 2.pro-meth hydrogen bonds and C — H - - 0 interactions (A, °) 236 Table 8.45 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-benz 237 Table 8.46 Bond lengths (A) of 2.pro-benz with estimated standard deviations 238 Table 8.47 Bond angles (°) of 2.pro-benz with estimated standard deviations 239 Table 8.48 Geometry of 2.pro-benz hydrogen bonds and C — H - 0 interactions (A, °) 240 Table 8.49 Crystallographic data for 2.pro-ol and 2.pro-amide 249 Table 8.50 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-oI 250 Table 8.51 Bond lengths (A) of 2.pro-ol with estimated standard deviations 251 Table 8.52 Bond angles (°) of 2.pro-ol with estimated standard deviations 251 Table 8.53 Geometry of 2.pro-ol hydrogen bonds and C—H---0 interactions (A, °) 252 Table 8.54 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH 253 Table 8.55 Bond lengths (A) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH with estimated standard deviations 254 Table 8.56 Bond angles (deg) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH with estimated standard deviations : 254 Table 8.57 Geometry of 2.pro-arhide» 1/4 EtOH • 1/8 MeOH hydrogen bonds and C — H - 0 interactions (A, °) 255 Table 8.58 Crystallographic data for (3), l.nitrophen, and 2.nitrophen 264 xix Table 8.59 Final atomic coordinates (fractional) and B(eq) (A2) of (3) 265 Table 8.60 Bond lengths (A) of (3) with estimated standard deviations 265 Table 8.61 Bond angles (°) of (3) with estimated standard deviations 265 Table 8.62 Geometry of (3) C—H- • O interactions (A, °) 266 Table 8.63 Final atomic coordinates (fractional) and B(eq) (A2) of l.nitrophen 266 Table 8.64 Bond lengths (A) of l.nitrophen with estimated standard deviations 267 Table 8.65 Bond angles (°) of l.nitrophen with estimated standard deviations 268 Table 8.66 Geometry of l.nitrophen hydrogen bonds and C—H- • O interactions (A, °) 268 Table 8.67 Final atomic coordinates (fractional) and B(eq) (A2) of 2.nitrophen 269 Table 8.68 Bond lengths (A) of 2.nitrophen with estimated standard deviations 270 Table 8.69 Bond angles (°) of 2.nitrophen with estimated standard deviations 270 Table 8.70 Geometry of 2.nitrophen hydrogen bonds and C—H- • O interactions (A, °) 271 Table 8.71 Crystallographic data for (4), l.nitropyr and 2.nitropyr 280 Table 8.72 Final atomic coordinates (fractional) and B(eq) (A2) of (4) 281 Table 8.73 Bond lengths (A) of (4) with estimated standard deviations 281 Table 8.74 Bond angles (deg) of (4) with estimated standard deviations 282 Table 8.75 Geometry of (4) hydrogen bonds and C—H- • O interactions(A, °) 282 Table 8.76 Final atomic coordinates (fractional) and B(eq) (A2) of l.nitropyr 283 Table 8.77 Bond lengths (A) of l.nitropyr with estimated standard deviations 284 XX Table 8.78 Bond angles (deg) of l.nitropyr with estimated standard deviations 284 Table 8.79 Geometry of l.nitropyr hydrogen bonds and 0—•H-0 interactions (A, °) 285 Table 8.80 Final atomic coordinates (fractional) and B(eq) (A2) of 2.nitropyr 285 Table 8.81 Bond lengths (A) of 2.nitropyr with estimated standard deviations 287 Table 8.82 Bond angles (deg) of 2.nitropyr with estimated standard deviations 287 Table 8.83 Geometry of 2.nitropyr hydrogen bonds and C—H---0 interactions (A, °) 288 xxi Acknowledgement I would like to thank Professors James Trotter, John Scheffer and Alan Bree for their help, patience and guidance in my research. They each have a remarkable talent for teaching without making the student feel inadequate, which says something about the type of people they are. A grad student's life is hard enough without being stressed by the people he or she works with, so I would also especially like to thank Dr. Steve Rettig, Dr. Bozena Borecka-Bednarz, Dr. Gunnar Olovsson and Dr. Tony Fu of the X-ray crystallography lab for their help and encouragement these past years. They were all more than generous with their time, and perhaps more importantly they were all genuinely terrific to work with. The same can be said of members of the Scheffer lab, both past and present, and they are acknowledged for their help and good humour towards a novice synthetic chemist. Finally, I'd like to thank the people who made my life outside the lab as interesting, if not more so, than my life in the lab. To Bruce Todd, Mike Blades, Ken Wright, Len Lermer, Cam Patterson, and especially Ryan Males, thanks guys. xxii Dedication It has been my good luck to have made a wonderful collection of friends in my time here. I truly feel fortunate to say they are too numerous to mention individually. I would, however, like to thank them and dedicate this, in part, to them. Mostly, however, this work is dedicated to my family. To my father, whom I miss, and to my mother, whom I love, and to my brother, who was my first friend, thank you. xxiii Chapter 1 - Introduction 1.1. Introduction The study of nonlinear optical (NLO) phenomena has stimulated significant scientific investigation into the manner in which electromagnetic radiation interacts with matter. Unlike linear optical processes such as refraction and absorption, NLO processes change, very briefly, the properties of the material with which the electric field is interacting by generating an internal electric field that modifies the applied field. As described by Stucky et ai, " A process is nonlinear when the response to an input (i.e., the output) changes the process itself. Nonlinear behavior is not unusual, and for most physical processes a linear formulation is generally just the lowest-order approximation to the actual process". [1] The interaction between an electric field and a molecule can produce a redistribution of charge in the molecule, resulting in an induced dipole. As a first approximation the total dipole in a molecule can be expressed as a linear function of the applied field strength,[2, 3] where fi = jl0+a-E (1.1) where Ji is the total dipole, Jlo is the static dipole moment in the absence of the applied field, a is the linear polarizability of the molecule and E is the applied field. The term 1 a • E is refered to as the induced dipole. If the electric field oscillates, as it does in electromagnetic radiation, then electric charge in the molecule oscillates at the frequency of the applied field, re-emitting radiation of the same frequency as the incident radiation. At the simplest level, electrons in an atom or molecule can be viewed as charged particles bound to nuclei. Under the influence of a weak electric field, the restoring force returning the particle to its equilibrium position is linearly proportional to its displacement from that equilibrium position and is independent of the direction of displacement and the induced dipole of an atom or a molecule is adequately described by equation (1.1). However, as the magnitude of the applied field increases, the induced dipole deviates from linearity, as described in Figure 1.1. Figure 1.1 Induced dipole (/! - fi0) as a function of field strength. Plot (a) represents (/i - /l0) as a linear function of field strength E, while in plot (b) (/I - /l0) is expressed as a quadratic function of E• Adapted from ref. [1] i 2 Under these conditions of high applied field the total dipole is more accurately approximated by a Taylor series expansion of the polarizability,[2, 3] given by, fi = fia + a. E + j-;$.E.E + jjY* E.E.E+... (1.2a) where P and y are the second and third-order polarizabilities, or more commonly, the first and second-hyperpolarizabilities, respectively (in some instances these variables are also referred to as the quadratic- and cubic-hyperpolarizabilities). The factorial terms are often included in P and y to give the more simplified expression, fi = fi0+a*E + $*E*E + y. E*E*E+... (1.2b) Since, by definition, a, P and y are tensors that describe the various relationships between vector quantities p, and E, it is necessary to identify the direction of the induced dipole and of the applied electric field. As such, a more appropriate description of induced nonlinear polarization is given by, /x' = & + X UijEj + X p p Ej Ek+1 ym Ej Ek Ei+... (1 -2c) j j,k j,k,l where i, j , k and / describe the direction of polarization of all the interacting electric fields in the three orthogonal directions of the molecular frame of reference, JC, y and z-3 Just as the induced dipole in a molecule is a function of the electric field strength and the different polarizability terms, an analogous expression for the bulk polarization (P) of the material can be formulated. (1.3) where x > X a n ^ % a r e tensors representing the first, second and third-order macroscopic susceptibilities, respectively, for the ensemble of molecules making up the material. Once again, subscripts /, J, K and L describe the direction of polarization of the interacting electric fields in the three orthogonal directions of the material frame of reference, X , Y and Z. 1.2. Origins of Second-Harmonic Generation While the first NLO effects were recorded over 100 years ago, with Kerr's electric field-induced change in the refractive index of CS2,[4] followed by the same observation in quartz by Pockels [5] (historically referred to as the Kerr and Pockels effects, respectively), the first "all-optical" NLO effect (i.e., an effect brought about solely by strong electromagnetic fields, as opposed strong dc-electric fields) was not observed until shortly after the invention of the laser in 1960. [6] In 1961 Franken et al.[7] at the 4 University of Michigan first observed the frequency doubling of 694 nm ruby laser radiation by passing it through quartz, producing a weak 347 nm emission. As mentioned previously, as electromagnetic radiation travels through a medium, the polarization wave, produced by the oscillating charges in the material, re-emits light of the same frequency as the incident radiation. If the electric field is strong, like those found in lasers, then the induced polarization will no longer oscillate linearly with the applied field. Instead, the polarization wave is distorted, as shown in Figure 1.2, according to equation (1.2b). The example in Figure 1.2 shows the polarization of a molecule, benzene, that has a centre of inversion. In this case the restoring force returning displaced electron density is symmetric, therefore the magnitude of the induced dipole is equal in opposite directions, or, Figure 1.2 Plots of the electric field of (a) an applied electromagnetic wave and (b) the induced dipole from a molecule with a centre of inversion. Adapted from ref. [1] (1.4) +6 +6 5 If, however, the restoring force were dependent upon the direction of charge-displacement, then the induced polarization of the atom or molecule would no longer depend simply upon the magnitude of the applied field, but also upon the direction of the field. An example of this type of system is a metal-oxygen bond, where electron density is more easily shifted towards the oxygen than towards the metal, due to their different electronegativities. The interaction of a strong oscillating electric field with this type of system is shown in Figure 1.3. Once again, the induced polarization wave is distorted due to the nonlinear response. This time, however, the induced polarization is asymmetric, or, jii(E)-n0^-(iLi(-E)-ii0) (1.5) Time Figure 1.3 Plots of the electric field of (a) an applied electromagnetic wave and (b) the induced dipole in a second-order NLO material. Adapted from ref. [1] It is the nature of this asymmetric polarization wave that gives rise to second-order N L O effects. Deconvolution of the distorted wave in Figure 1.3 shows that it 6 contains elements of both the incident fundamental frequency (co) and the second-harmonic frequency (2(D), as well as a dc component, as depicted in Figure 1.4. Figure 1.4 Deconvolution of a polarization wave (a) of a second-order NLO material to give waves with both the fundamental (b) and second-harmonic (c) frequency, as well as a dc electric field (d). Adapted from ref. [1] These same results can be derived mathematically by introducing a cosinusoidal field expression into equation (1.3) to describe the oscillating electric field. The subscripts i,j, k and / have been omitted for brevity. /i(£) = fi0+aE0cos((at) + ^ Elcos2((at) + y Elcos3((at)+... (1.6) 7 where co is the frequency of the electric field. By truncating after the second term and applying the trigonometric identity cos2(x) = V2 + V2 cos(2x), equation (1.6) can be reduced to: H(E) = \ia + ( ^ p £ 2 ) + a£0cos(GX) + ^p£ 2,cos(2GX) (1.7) once again demonstrating that the introduction of the first hyperpolarizability term P produces a second-harmonic component in the resultant polarization wave. While the classical description of SHG appears to be straightforward, further examination reveals a set of strict conditions under which this process can take place. Since SHG originates from the asymmetry of the induced polarization wave (Figure 1.4), only materials capable of producing this asymmetric wave are capable of producing SHG, or any other second-order NLO process.[l] This can be shown using Figure 1.2 as an example. According to equation (1.4), for molecules with a centre of inversion, ( fi(E) - Ho) = -( l±(-E) - /Ho). Using the expanded form of the induced polarization in equation (1.2b) we get, (fi(E) -fi0) = aE + $EE + yEEE+.. =aE + $E2 + y £ 3 - h . . and, - (M-£ ) - jUo) = - « ( - £ ) - H-EX-E) - y(-E)(-E)(-E))+. ..= aE - P E2 + j £3+. Thus, the only way in which the relation in equation (1.4) can hold is by making |3 (and all subsequent even-order hyperpolarizability terms) identically equal to zero. This result shows that, while all even-order NLO processes (including SHG) are limited to materials lacking a centre of symmetry, all odd-order processes have no such symmetry restrictions. The second requirement that must be met in order for a material to produce SHG is an extension of the first requirement, and deals with the orientation of the molecules making up the N L O materials. The array of molecules making up the material must be arranged in a non-centrosymmetric manner, otherwise, like (3 in the previous example, % ( 2 ) must be zero.[8] This last restriction prevents materials in an isotropic environment, such as gases, liquids and centrosymmetric crystals, from producing SHG. 1.3. Modern description of SHG ... • The previous section described SHG in classical terms. That is, an electromagnetic wave shifts electron density back and forth, producing a time-dependent polarization which includes components of both the fundamental and second-harmonic frequencies. While this is a convenient way of describing SHG, the motion of electrons can also be described from a quantum mechanical perspective. According to Craig and Thirunamachandran,[9] "... generation of the nth harmonic frequency can be described as absorption of n photons of frequency (O and emission of one photon of frequency nco"; thus SHG involves the "absorption" of two 9 photons to produce a third photon of twice the frequency. The process is depicted in the Feynman diagrams (also known as time-ordered diagrams) in Figures 1.5(a)-(c). 003, i 3 2 (02 ,k r „ (02 ,k (01J (02,& COlJ (a) (b) (c) Figure 1.5 Time-ordered diagrams describing SHG, where col = C02 and (03 = 2coi. Adapted from ref. [9] The rules for interpreting these diagrams, according to Craig and Thirunamachandran, are as follows. First, time flows upwards. The vertical line represents the changes taking place in the molecule during the process, and the wavy lines represent photons. The state of the system (molecule + photons) can be read at any time along the vertical line, thus at time 1 the system consists of a molecule in initial state | o) and two photons, (Oi and 002. The energy of the system is (Eo + M M + han). At time 2 the system consists of the molecule in state | p) and photon (02. The energy of the system is (Ep + h(H2). According to Figure 1.5(a) then, SHG (where coi = (02 and (03 = coi + (02) involves the transition from initial state | o) to some intermediate state | p), brought about by the absorption of photon 01. Absorption of photon (02 moves the system from | p) to I q). Emission of photon (03 returns the system to its initial state | o). Two other means 10 of SHG are represented by Figures 1.5(b) and 1.5(c). Since the time in which the photons and molecule interact is exceedingly short, the three vertices (a)-(c) refer to near simultaneous events, [9] and thus all three processes should be included in a complete representation of SHG. Since neither of the two absorption processes involves transitions to real (i.e., stationary) excited-states of the system, intermediate states \p) and \q) are referred to as "virtual states", and the absorptions are called "virtual transitions".[9] These virtual states are usually treated as linear combinations of the ground- and excited-states of the undisturbed system, thus, y/p=lcp(n)y/M (1.8) n where \jfM is the wave function describing the n t h excited-state of the undisturbed system. This description of SHG also conforms to the symmetry restrictions arrived at from the classical description. The series of transitions that take place in SHG (i.e., \o) —> \P) ~* \q) \o) ) result in an overall change in parity for a centred system in the electric dipole approximation, and so the quadratic hyperpolarizability, P, (and all even-order hyperpolarizabilities) must be zero for centrosymmetric molecules. For odd-order processes, however, no overall change in parity is required between the initial and final states, therefore any molecule can have non-zero odd-order hyperpolarizabilities. 11 An expression for (3,^ , determined from time-dependent perturbation theory, can be derived directly from Figures 1.5(a)-(c). Recalling that the indices i,j and k refer to the polarization of photons (03, (0i and (02, respectively, and that in the case of SHG (01 = (02 = (0, and (03 = 2(0, Figures 1.5(a)-(c) yield the following, The (3 tensor for SHG must be j,k symmetric, that is, indices j and k may be freely interchanged so that Py*(-2(o;(0,G)) = P,x/(-2(o;(0,(0),[9] thus Figure 1.5 describing SHG should, in fact, contain six vertices, consisting of the three already shown and three new vertices with j and k interchanged. Including this j <-> k interchange in equation (1.9) and halving [i.e., (P^sym = Vi(Py* + Pay)] gives, > (°\^jU)(^i\p)(p\^k\°)} (Eq+hco)(Ep-hco) K1.9) (coq - 2o))((op - a) (aq - 2(0){(0p - (O) P SHG ijk 1 (1.10) 2% p,q {(Oq + 0))(0)p - CO) {COq + (0){(Op - CO) (coq + co){cop + 2co) (coq + co)(cop + 2co) 12 where / x^ i s the dipole moment along axis / for the transition between stationary states m and n, and com is the frequency of transition from the ground-state to state m. Rearranging and combining terms gives, ,SHG ijk ~ in1 p,q (ft)„ft)„ + 2co ) uoq(uqpupo + uqpupo) q p -(co -4a )(o) - G ) ) Ofl on no +fik9lifnpj (coqcop-co ) (ft) 2 , - f t > 2 ) ( & > 2 - ft)2) The expression in equation (1.11) shows that p will show significant resonant enhancement when either the fundamental frequency or the second-harmonic frequency is close to that of the excited state i / / ^ or y/q\ Oudar and Chemla[lQ, 11] showed that by restricting the summation in equation (1.11) to the ground state (g) and the charge-transfer excited-state (e), the expression reduces to, 8' k •egr^eg ' eg P ijk 2h (co2eg-4co2)(co2eg-co2) + (co2eg-(o2) (1.12) where jig and fie are the ground- and charge-transfer excited-state dipole moments, ^ieg is the transition dipole moment and coeg is the frequency of the electronic transition. If one 13 assumes that the charge-transfer direction is unidirectional (i.e., along one molecular axis) and that one tensorial component of (3 (P,,„ for example) dominates the response, equation (1.12) can be further reduced to, o S H G _ " H I — 2(A^2(col + 2(o2) 2h (co2g-4co2)(co2ei!-co2) eg ( A / / ) / 4 {(o]g-(o2) (1.13) Assuming that the system is near resonance with the second-harmonic frequency (i.e., (Oeg = 2co), equation (1.13) becomes, P SHG (A/i)/r to1 . eg eg 2h' (co2eg-4co2)(co2eg-co2) (1.14) The results from this two-level model reveal that the magnitude of P depends on factors such as the permanent (A^i) and transition (/j,eg) dipole moments and resonant frequencies (coeg) of the molecule that can be modified and optimized by changing the nature of the chromophore. 14 1.4. Materials for Second-Order Nonlinear Optics 1.4.1. Overview As mentioned earlier, the first observation of SHG occurred from the laser irradiation of quartz. From the time of that first observation in 1961 until 1970,[12] research into materials for second-order NLO processes was carried out almost exclusively on inorganic materials. In 1970 Davydov et al. [13] first determined a relationship between enhanced second-order NLO properties and the charge-transfer interactions in organic conjugated systems. In the nearly 30 years since then, extensive research has gone into the development of organic NLO chromophores with large quadratic-hyperpolarizabilities. As can be seen from Figurel.3, the magnitude of the second-order nonlinear response depends upon the ease with which electron density is redistributed, as well as on the extent of asymmetry that can be induced in the polarization wave. In organic molecules, easily polarized electrons such as those found in conjugated rc-systems are commonplace. There is also a wide variety of potential electron-donors and electron-acceptors that can be chemically linked to these conjugated 7i-systems to form molecules possessing the attributes described above. A simple example of this type of system is an aromatic ring para-substituted by an electron-donor and an electron acceptor, such as p-nitroaniline (PNA), shown in Figure 1.6. 15 Figure 1.6 Two resonance forms of PNA, a typical donor/acceptor system for second-order NLO materials. The easily polarized ^ -electron system, coupled with a highly asymmetric charge-transfer, has made P N A and its derivatives among the most extensively studied class of compounds for second-order NLO applications. The two-level model for (3, derived in the previous section, also predicts that P N A should be ideal for second-order N L O processes, based on its large value for A/i and /ieg.[H, 15] In addition, the resonant frequency of P N A approaches the doubled frequency of most industrially used infrared lasers, therefore (3,-,-f for P N A is likely to gain from significant resonant enhancement. Unfortunately P N A crystallizes in.the.centrosymmetric space group P2\ln [16] and is therefore SHG-inactive in the crystalline solid-state, a situation that is typical of many organic materials whose molecular architecture is well-suited for second-order N L O applications. Research into materials for second-order nonlinear optical processes has taken two distinct approaches, one concentrating on the development of large p chromophores (i.e., enhancement of molecular properties) , a second concentrating on the development of large % ( 2 ) materials (i.e., enhancement of macroscopic properties). The first approach combines the expertise of computational scientists, who identify the structural features of traditional NLO chromophores like P N A that can be modified in order to enhance P, 16 with the expertise of synthetic chemists, who devise new methods to alter the molecular architecture of these traditional chromophores. While a description of the modern quantum-chemical methods of deriving expressions for the quadratic hyperpolarizability, first formalized by Oudar,[10, 11] was given in Section 1.3., the methods for calculating values for p* beyond the simplified two-level model is beyond the scope of this discussion. Several review articles describing the different computational formalisms are available.[17, 18] The results of these investigations have provided valuable insight into the source of the large P's displayed by many NLO chromophores and the P's predicted by these computational methods are generally in good agreement with those determined experimentally. The synthesis of many new materials has been inspired by the computational predictions regarding various chemical modifications made to standard donor-acceptor systems, from the modification of the substituent donor and acceptor strengths, [19-24] and the effect of extended conjugation,[23-27] to bond length-alternation,[28-30] and the advantages of ethylenic vs. acetylenic bridging. [31] The second approach to research into NLO materials involves the development of new preparative methods for potential use in device applications. This field of research generally involves material scientists and synthetic chemists, and is less concerned with enhancing the molecular properties of the NLO chromophore than with presenting a collection of molecules or chromophores in a regular, acentric environment so as to maximize the desired macroscopic properties. As mentioned previously, considerable interest has been shown by material scientists and synthetic chemists in the design of 17 materials for use in second-order nonlinear optical processes. As early as Franken's first observation of SHG from quartz, and the subsequent discussion of its origins,[8] it was recognized that the magnitude of the second-order response depended critically upon the orientation of the oscillators in the material in addition to the molecular hyperpolarizability of the oscillators. In light of the requirement for bulk asymmetry, significant effort has been invested in developing methods that efficiently produce materials with non-centrosymmetric molecular alignments. Additionally, these materials must also possess the physical and chemical properties appropriate to the application for which they were designed, such as thermal, temporal and optical stability, as well as a wide range of optical transparency if the materials are to be used in frequency conversion devices. Due to the many potential applications of second-order NLO devices, the design of these materials has encompassed many synthetic disciplines, including inorganic, organic and polymer chemistry, each material developed to suit particular applications or to take advantage of particular NLO effects. In the ensuing sections some of the techniques used to produce materials for second-order NLO processes, and recent developments in the field will be discussed. 1.4.2. Inorganic Materials for Nonlinear Optics Inorganic materials are the most popular class of NLO compounds currently in use in commercial applications. The electro-optic properties of some inorganic compounds have been known for over 100 years;[4, 5] their well-established position in the 18 commercial field is likely due to their physical properties, such as excellent thermal and optical stabilities and their short wavelength transparency. An informal survey of the materials marketed for second-order frequency conversion and electro-optical applications reveals that these materials are almost exclusively inorganic in nature. This underlines perhaps the most significant advantages inorganic N L O materials hold over their organic counterparts: physical robustness leading to extremely long functional lifetimes and their wide range of visible transparency. Most inorganic NLO materials are composed of anionic metal oxides with alkali or alkali-earth counterions. The quadratic hyperpolarizability of these materials results, in general, from the distortion of the metal-oxygen bonds of the oxide groups,[32-35] as shown in Figure 1.7. While |3 for these bonds is small relative to the traditional n-electron bridged donor/acceptor systems found in organic materials,[36, 37] inorganic materials generally exhibit a greater range of transparency than organic materials like P N A , which allows for both frequency doubling and tripling of typical pulsed infrared lasers. Table 1.1 shows the physical characteristics of some representative inorganic N L O materials. Figure 1.7 Distorted octahedral coordination of metal-oxides found in typical inorganic NLO materials. o • = metal cation 19 Table 1.1 Properties of selected inorganic NLO compounds. Adapted from ref. [37] Compound Damage Thresholdb Cutoffc (xlO 9 esu) (MW/cm2) (nm) £ -BaB 2 0 4 rfxxx = 4.1 10,000 198 Ba2NaNb501 5 dzxx = 32 1 370 KH 2 P0 4 dzxy = 1 500 200 LiB 3 0 5 dzYY= 3.1 2,000 165 LiNb0 3 dzxx = 13 20 400 LiI0 3 dzxx = 10 50 300 KTiOP0 4 dXrz = 15 20,000 350 a The macroscopic susceptibility tensor is often replaced by the value d, where d = ^ tf2). b The radiation intensity threshold before optical damage such as streaking and clouding occurs. ° Short wavelength absorption cutoff. Since ions in an inorganic crystal lattice have a certain degree of mobility, researchers have recently taken advantage of their ability to displace ions in the lattice to develop a new class of inorganic NLO materials with enhanced macroscopic properties. A critical condition that must be met for any material developed for frequency conversion applications is that the input and output beams must maintain a fixed phase relationship as they traverse the crystal.[38] This "phase-matching" condition will be discussed in greater detail in Chapter 3. For the purposes of this introduction suffice it to say that should a fundamental and a second-harmonic wave lose their in-phase relationship, the intensity of the second-harmonic wave cannot build as it propagates through the crystal, due to destructive interference. Instead the intensity oscillates through zero and a small maximum intensity. Since two independent waves can maintain an in-phase relationship only i f they are traveling with the same velocity, and the velocities of the two waves are determined by the respective refractive indices at the two frequencies in question ( n w l and n f f l 2 ) , the phase-matching condition becomes: nwl =nw2. In birefringent 20 crystals, phase-matching is achieved by finding a direction of propagation through the crystal where this condition is met, usually with the planes of polarization of 0)1 and 0)2 at right angles to each other. A new preparative method that has elicited significant interest recently relaxes the above-mentioned phase-matching condition by creating regions of alternating polarity by periodic poling. In this technique, thin regions of an inorganic NLO crystal are subjected to a strong dc electric field. The influence of the field causes mobile metal ions to migrate to alternate positions in the oxide lattice, reversing the direction of the polarity of these domains, as depicted in Figure 1.8. With accurate control of the widths of these domains the intensity of the second-harmonic waves, rather than being periodically extinguished, builds as they travel through the periodically poled crystal.[39-41] © © © © © © 0 © 0 © (a) (b) Figure 1.8 The periodic poling technique, (a) Application of a strong electric field induces a change in polarity in a typical inorganic chromophore. (b) Careful poling control creates domains of reversed polarity. Adapted from ref. [41] One area of concern associated with inorganic NLO materials is the presence of crystal defects. These defects can take the form of ionic impurities, and can also arise 21 from the natural inclination for these materials to form non-stoichiometric crystals. The most damaging effect these defects cause is an increase in the ionic-conductivity of the material. While ionic displacement is a desirable property in the design of periodically-poled crystals, optical damage can result from the high electric fields associated with N L O applications. Control of the defect chemistry of these materials has been achieved by modifying the crystal growth process and by the choice and concentration of the non-stoichiometric impurity. [42, 43] 1.4.3. Poled-Polymer Systems Beginning in the early 1980's, the interest of many researchers turned to the incorporation of N L O chromophores into host matrices. As always, the need to induce a polar alignment of chromophores was required for use in second-order N L O applications. In addition, there was a desire to include materials with larger quadratic hyperpolarizabilities than those found in inorganic materials in order to function more efficiently. Poled polymers offered all the advantages that polymers traditionally held over crystalline materials, such as lower processing temperatures and greater structural flexibility, while at the same time permitting the incorporation of components whose chromophoric properties were tailored to specific applications. The approach used in poled polymers is straightforward and permits significant flexibility in the design of new materials. The earliest procedures involved dissolving N L O chromophores into a host polymer matrix, after which orientational order was established by heating the polymer above its glass transition temperature while in the 22 presence of a strong dc electric field. The polymer was cooled in the presence of the field, thus "locking" the aligned chromophores into place.[44-47] These systems, consisting mainly of donor/acceptor stilbene derivatives as the guest dissolved in poly(methyl methacrylate), exhibited two inadequacies associated with this approach. The first was the low chromophore number densities achievable before phase separation occurred. [48] Typical polymeric guest-host NLO materials had chromophore densities roughly an order of magnitude lower than crystalline NLO materials of the same chemical structure. [49, 50] The second problem was the relatively short functional lifetimes of these materials before structural relaxation destroyed the polar ordering of the chromophores. It was soon found that the degree of dipolar ordering could be improved by altering the poling technique, [46, 51] and the temporal stability was found to depend on factors such as chromophore volume [52-54] and the glass transition temperature of the host polymer matrix.[55-57] By adjusting the nature of both the guest and the host, researchers were able to improve upon both of the aforementioned factors. Unfortunately, the functional lifetimes of these materials, although improved, still did not rival those of crystalline materials. While the macroscopic susceptibilities of guest-host poled polymer systems approached and even surpassed those found in commercial inorganic materials,[58] the effective lifetimes of the guest-host systems were still only on the order of days. [54] Since the temporal stability of dipolar ordering was found to be a function of the chromophore mobility in the host-matrix, several approaches were developed to restrict the guest mobility once poled-ordering had taken place. One approach involved 23 chemically linking the NLO chromophores to the polymer backbone as both side-chain [46, 50, 59] and main-chain substituents.[60-62] Figure 1.9 shows examples of side-chain and main-chain poled polymer systems. Figure 1.9 Examples of (a) a side-chain poled-polymer (4-(dicyanovinyl)-4'-(diethylamino)azobenzene) linked to poly(methyl methacrylate), and (b) a main-chain poled-polymer (bisphenol A-N.N-nitroaniline). Adapted from refs. [46] and [62]. A second approach returned to guest-host systems, this time incorporating the N L O chromophore into a thermally cross-linked host matrix. Epoxy resins are commonly used in applications requiring high glass-transition temperatures, and have thus been investigated for use in poled polymer guest-host systems.[63] In these systems the NLO chromophore is dissolved in the epoxy material and poled. Addition of the cross-linking initiator occurs in the presence of the applied electric field, locking in the poled-order. An example of a cross-linked guest-host epoxy system is shown in Figure 1.10. While such systems again showed considerably greater temporal stability, with lifetimes on the 2(H 2 C) 24 order of 1000 h,[63, 64] the effective macroscopic nonlinearities were once again limited by low chromophore densities, brought about by low chromophore solubilities. O H + H 2 N — R - N H 2 N H — R ' - N H 2 O H N H — R ' — N H -O H O Z A etc. > O H H 3 C \ I / N' H 3 C N 0 2 N,N-Dimethylamino-nitrostilbene Figure 1.10 An example of a typical cross-linked epoxy host and a commonly used guest, DANS. Adapted from ref. [58]. As with the original guest-host poled-polymer systems, the problem of low chromophore density in cross-linked systems was addressed by incorporating the NLO chromophore into the cross-linked polymer backbone. [65, 66] One approach, [67] shown in Figure 1.11, involved the use of amine-containing NLO chromophores to initiate the ring opening of the epoxy-based polymer backbone. While the poling must be maintained throughout the high temperature curing and subsequent cooling, the resultant 25 macroscopic susceptibilities rivaled those of some inorganic materials, with no noticeable relaxation of the polar-ordering after 500 h. O H O H - - C H 2 — C H - C H 2 C H 2 - C H — C H 2 - O -\ O H •o+-C H 2 C H — C H 2 + C H 2 C H - C H 2 - O O H Figure 1.11 An example of an NLO chromophore incorporated in a cross-linked epoxy host matrix. Adapted from ref. [67]. While poled-polymer systems were successful in incorporating high P chromophores into host-matrices, the insufficient orientational lifetimes of these materials have limited their usefulness. Self-assembled multilayers (SAMS), typified by the work carried out by Marks [68, 69] and L i , [70-73] represent a relatively new technique for controlling the molecular assembly of N L O chromophores. The technique, described in Figure 1.12, involves the build-up, in a layer-by-layer fashion, of an acentric chromophoric superlattice through the formation of chemical bonds. The most common approach begins with the chemisorption of an alkyl halide containing trichlorosilane onto a hydroxyiated surface, like Si02- In the second step a 1.4.4. Self-Assembled Multilayer Systems 26 thin layer of the NLO chromophore, usually a hydroxy-functionalized stilbazole, is added to the substrate surface, where heating effects the quaternization of the chromophore. The final step, addition of a "capping agent", provides structural rigidity to the substrate, as well as a regeneration of the hydroxy-terrninated surface, so that additional layers can be deposited. OH OH Figure 1.12 A self-assembled monolayer with a stilbazolium chromophore. Repeating steps 1-3 produces structurally rigid multilayers capable of SHG. Adapted from ref. [69]. The results from this new preparative technique show that SAMS not only produces structurally rigid, acentric superlattices, but that the bulk nonlinear susceptibility of these materials is enhanced by increased chromophore densities, relative to poled-polymer systems. The long-range ordering of these multilayer systems, where as many as 10 monolayers have been deposited, is such that X-ray reflectivity studies reveal Bragg peaks from scattering by individual layers. This is in contrast to poled-polymer systems 27 where the field induced alignment is only a mean orientational ordering in the direction of the field. 1.4.5. Organic Crystals The last type of material surveyed in this section is simple organic crystals. In terms of structural stability and chromophore density, these types of systems are ideal in that there is little loss of ordering in the crystal lattice, and the density does not depend upon the chromophore's solubility in the host-matrix . The ease with which an organic chromophore can be chemically modified is also advantageous when considering the relative merits of organic systems versus inorganic systems. Of course, the most significant drawback to organic crystalline materials is their natural inclination to pack in centrosymmetric space groups. While this point will be explored more thoroughly in Chapter 2, it is this point alone that has excluded many potentially effective materials from use in second-order NLO processes. It is this same point, however, that has encouraged extensive research into the development of methods that facilitate non-centrosymmetric packing. This area of research, labeled "crystal engineering", attempts to introduce factors other than the typical van der Waals interactions and dipolar-interactions, such as hydrogen-bonding and ionic interactions, that help determine the packing pattern of the material. Several reviews are available that provide surveys of the best results obtained from organic crystalline materials, [12, 74-76] either for SHG purposes or for other second-order NLO applications. Many of the best early results appear to have been 28 arrived at in a somewhat haphazard manner, that is, many of the materials were chosen for study because they were excellent chromophores for SHG that happened to crystallize in non-centrosymmetric space groups. One means of structural modification that has successfully produced materials in non-centric environments is to control the polar nature of the chromophore moiety. By virtue of their donor/acceptor architectures, most materials for SHG are highly polar and thus tend to pack so as to maximize their dipolar interaction. The synthesis of N-(4-nitrophenyl)-N-methylaminoacetonitrile (NPAN) by Barzoukas et al. [77] was described as an attempt to counter the intermolecular dipolar attraction between the p-substituted donor and acceptor by the addition of a second polar group sterically removed from the charge-transfer chromophore. The solid-state structure of NPAN [78] is such that neighboring cyano groups are aligned so as to maximize their dipolar interaction, while the two charge-transfer portions of the neighboring molecules are aligned as shown in Figure 1.13. 29 N02 H 3 C C I I 2 - C = N N ^ N=C-CH2 C H 3 Figure 1.13 Packing arrangement of NPAN The approach was successful, with NPAN crystallizing in the non-centrosymmetric space group Fdd2, and the material producing a strong SHG signal. Another example of controlling the polar nature of the material used a reduction in the polarity of the chromophore to effect a non-centrosymmetric packing structure. In this case, 3-methyl-4-nitropyridine-l-oxide (POM), [79] shown in Figure 1.14, has virtually zero ground-state dipole moment, thus intermolecular dipole interactions are eliminated. The material crystallizes in a non-centrosymmetric space group (P2j2i2i); however, its SHG signal is not particularly strong. G 0 Figure 1.14 Resonance structures of POM. 30 The simplest way to modify a material structurally that will ensure its non-centrosymmetric packing is to introduce chirality to the structure. Optically pure molecules cannot pack in anything other than non-centrosymmetric space groups, therefore the requirement for both molecular and bulk asymmetry is met. Perhaps the most extensively studied organic material for SHG (apart from PNA) is Ar-/?-nitrophenyl-L-prolinol (NPP),[80] shown in Figure 1.15. The optical purity of the material ensures its non-centrosymmetric packing (space group P2\), while strong intermolecular hydrogen-bonding leads to a structure that is virtually optimal for SHG. Figure 1.15 Af-p-nitrophenyl-L-prolinol (NPP). While there have been several reports of optical purity producing strongly SHG-active materials,[80-82] chirality alone is insufficient when considering efficient SHG-production. The orientation of the NLO chromophore and the magnitude of its molecular second-order nonlinearity determine the extent to which SHG is produced, and while molecular chirality ensures bulk asymmetry, it does not ensure an SHG-optimized chromophore orientation. 31 Several methods have been devised that take a more active approach to the induction of solid-state asymmetry, that is, methods that combine the N L O chromophore with a second component, be it by co-crystallization, inclusion, or some other means, to encourage asymmetric packing. Okamoto et al.[83] were successful in co-crystallizing PNA with several of its 7V-alkyl derivatives. In each case both PNA (crystallizing in P2\/n) and its derivative were either SHG-inactive or very feebly active on their own, but upon co-crystallization became strongly SHG-active. The intensity of the second-harmonic was found to vary as a function of the weight ratios of the compounds. Channel-forming materials have also been investigated for use in N L O applications by making guest-host systems. Several studies have been conducted wherein N L O chromophores were included in the lattice of a host structure, forming polar inclusion compounds.[84-87] Recently, Hulliger et al.[88] have grown SHG-active inclusion compounds in which NLO chromophores were included into parallel channels formed by a racemic host lattice, (±)-perhydrotriphenylene (PHTP). In a series of 20 guest chromophores, 18 formed inclusion compounds that exhibited some degree of SHG. Salt formation has been suggested as another means of engineering asymmetric packing arrangements. From a physicochemical point of view, the Coulombic interactions in ionic compounds are expected to form higher melting materials, which are advantageous in device applications. Apart from that, however, the large variety of organic acids and amines has allowed for extensive study into the packing tendencies of 32 ionic materials, thus enabling the researcher to make predictions as to the likelihood of asymmetric packing. Studies by Etter et al. [89-92] and Lehn et al. [93, 94] have investigated the hydrogen-bonding patterns of non-centrosymmetric, ionic lattices. In work by Aakeroy et al. [95-98] and others,[99-102] anionic hydrogen-bonded host-lattices were successfully coupled to NLO chromophores to form SHG-active materials. In all of these cases the chromophores in question did not have particularly large quadratic hyperpolarizabilities (i.e., none approached that of PNA) and thus only weak SHG-intensities were observed. This again underscores the need for larger quadratic hyperpolarizability along with bulk asymmetry and optimized chromophore orientations for efficient SHG production. In light of the above observations, organic salts have been prepared by coupling high (3 ionic chromophores to some form of organic counterion. Studies by Nakanishi et a/.[103-107] and Marder et a/.[108-115] have shown that employing a high p* ionic chromophore and forming salts with a variety of counterions is a highly successful approach to engineering a variety of materials with large macroscopic optical nonlinearities. While the reason behind the success of the organic salt approach in forming non-centrosymmetric structures is not entirely clear, it has been suggested that the strength of the Coulombic interactions between the anion and cation is sufficient to overcome the dipolar-interactions between neighboring chromophores,[116] allowing the counterions to shield the N L O chromophores from one another. 33 1.5. Research Outline. The main goal of this research project was to apply the strategy used by Prof. J. Scheffer and his research group in their studies of solid-state photochemical asymmetric induction,[117-122] in order to produce SHG-active materials. In this approach an achiral acid or amine is coupled to an optically active amine or acid to produce a salt that, in the solid-state, must crystallize in a non-centrosymmetric space group. If the product of the photolysis of the achiral starting material is chiral, solution photolysis leads to the equal production of both enantiomers. In the solid state, however, photolysis often leads to photoproducts with large enantiomeric excesses. In terms of this project, three series of organic salts were synthesized and investigated, each salt containing one or more NLO chromophores. In the first series of salts the chiral ionic auxiliary approach described above was employed to create optically pure organic salts capable of SHG-activity. An achiral acid (pictured in Figure 1.16) containing the PNA chromophore was synthesized. Although originally SHG-inactive (due to the centrosymmetric space group in which it crystallizes), coupling of the acid to a series of optically pure amines activated the second-order N L O properties of the chromophore by forcing each of the resultant salts to crystallize in a non-centrosymmetric space group. The SHG-intensity of each salt was measured using the Kurtz and Perry powder method, using urea as a standard. 34 v OH (1) Figure 1.16 Acid (1), p-nitrophenylglycine. According to Kurtz and Perry[74] the observed SHG-intensities of the salts should be proprtional to the square of their macroscopic second-order susceptibilities, that is, / ( 2 F F L ) « (M£»¥»>)2 (1.15) where N is the chromophore density, b(*®*is the phase-matching component of the crystalline nonlinearity per molecule and fm) is the intensity of the incident fundamental radiation. An expression describing the relationship between p\ the first hyperpolarizability tensor, and b, the macroscopic susceptibility tensor, will be introduced. Where possible X-ray structural analyses were carried out on the salts and an attempt was made to rationalize the observed SHG-intensities of each salt based on its chromophore orientation and chromophore density derived from its structural analysis. A second series of salts was also synthesized employing the chiral ionic auxiliary approach. In this case, however, the acid contained the 2,4-dinitroaniline (DNA) chromophore. This chromophore contains two electron-withdrawing substituents, which allows for polarization throughout the aromatic ring of the molecule. The same optically pure amines that were used in the first series of salts were also coupled to this acid. Once 35 again the second-order NLO properties of the previously SHG-inactive parent acid were activated once each of the salts was forced to crystallize in a non-centrosymmetric space group. An X-ray structural analysis was carried out on each of the salts, and the chromophore orientation and density were used to rationalize each of the observed SHG-intensities. Figure 1.17 Acid (2), 2,4-dinitrophenylglycine. A third series of salts was synthesized which coupled either acid (1) or (2) to one of two N L O chromophore containing amines (pictured in Figure 1.18). Neither the acid nor the amine were optically active, thus the chiral ionic auxiliary approach was not employed in this series. This series was prepared in hopes of obtaining results similar to those of Okamoto et al. [83], who coupled two SHG-inactive components to form strongly SHG-active co-crystals. The SHG-intensities of the acids, amines and salts were measured and an X-ray structural analysis was carried out on each of the materials used in this series. The information contained in the crystal structures was used to rationalize the observed SHG-intensities of each material, if any. P O H (2) 36 H 3 C — r / \ — / \ N02 H 3 C — l / \ — ^ \ N02 (3) ( 4 ) Figure 1.18 Amines (3) and (4), l-(p-nitrophenyl)-4-methylpiperazine and l-methyl-4-(4-nitro-2-pyridyl)-piperazine, respectively. To begin, Chapter 2 presents a survey of the Cambridge Structural Database. While it is often claimed that the vast majority of organic materials crystallize in centrosymmetric space groups (a fact that has been confirmed in several broad surveys of available structural databases), a much narrower survey was conducted on the class of material encountered in this project, in order to have a rough estimate of the probability of these materials crystallizing in non-centrosymmetric space groups. In Chapters 3, 4 and 5 the study of the three series of salts is presented. The synthetic methods are described and the results from the measurement of each salt's SHG-activity (if any) are presented. In addition, an attempt is made to rationalize the SHG-intensities produced by each salt based on structural information derived from their X-ray structural analysis. Complete details of the synthesis and characterization of each material in this project are found in Chapter 6, while a detailed description of the SHG measurement technique is found in Chapter 7. Finally, complete descriptions of each of the X-ray crystal structures determined in this project as well as fractional coordinates, bond lengths, bond angles and hydrogen-bonding geometries are found in Chapter 8. 37 Chapter 2 - Survey of the Cambridge Structural Database 2.1. Introduction Several statistical surveys of crystallographic databases have been carried out in the past, each with the goal of determining the percentage of non-centrosymmetric space groups occurring in the total population of organic structures.[123-127] While the results of these surveys vary somewhat, the more recent results,[126, 127] drawn from larger populations, tend to agree that the percentage of non-centrosymmetric structures is roughly 25-30%. In addition to determining the overall percentage of non-centrosymmetric space groups, the frequencies with which the various space groups appear were also examined. Of the 32 three-dimensional point groups, 21 are non-centrosymmetric. In the following chapters it will be shown that the bulk nonlinear susceptibilities of the materials under investigation in this thesis depend on the orientation of the molecules within the unit cell. The bulk nonlinear susceptibility arises from a contribution from each individual molecule in the unit cell, and from the spatial relationship between the molecules, as determined by the various symmetry elements present in the unit cell. Of the 21 non-centrosymmetric point groups, the collection of symmetry elements found in three of these (422, 432 and 622) act to cancel out any macroscopic susceptibility entirely, making any material crystallizing in those point groups unable to produce SHG. [128] Of the remaining 18, those found in point groups 1, 2, m and mm2 are the most desirable for producing SHG. While materials in other point groups are capable of SHG-production, 38 under optimal orientation conditions the materials in the aforementioned point groups produce SHG more efficiently.[129] In the more recent of two studies by Mighell et al. [127] (the results of which are found in Table 2.1), 29,059 organic structures were surveyed. Of these, 8,601 (29.6%) were found in non-centrosymmetric space groups. Point group 222 proved to be the most populated point group, followed by point groups 2, mm2, m and 1 in descending order. These point groups accounted for 90% of all acentric structures. The remaining 10% of non-centrosymmetric structures were distributed over the other 16 point groups, none of which contained more than 1.5% of the total. Of importance to note is that none of these surveys make mention of the number of optically active materials present in the populations that were surveyed. Since all enantiomerically pure materials must crystallize in non-centrosymmetric space groups, the actual percentage of achiral, non-centrosymmetric structures must be even lower. While the results of the Mighell survey suggest that the likelihood of encountering an organic N L O material in one of the more favorable non-centrosymmetric point groups (i.e., 1, 2, m and mm2) is small, the probability of finding an inorganic material with the same features is even smaller. In a comparison between the previously mentioned survey and an earlier survey of the most populated space groups for inorganic materials by Mighell,[126, 127] 7.7% of all organic structures crystallized in point group 2, while for inorganic materials less than 1% were found in this point group. The same trend was evident for point group 222, the point group in which 12.6% of all organic materials 39 crystallized. Once again, this point group was found in less than 1% of all inorganic materials. A l l of the surveys suggest, first, the need for further investigation into methods that encourage non-centrosymmetric packing. The number of naturally occurring asymmetric structures is already quite low, particularly in those space groups capable of efficient SHG. Several methods for preparing asymmetric packing arrangements were discussed in Chapter 1. Second, these surveys suggest that in addition to the various chemical advantages organics hold over inorganic materials (more highly polarizable, ease of synthesis, etc.), organic materials are also significantly more likely to pack in non-centrosymmetric space groups. In light of the results of the previously mentioned surveys, a survey of the Cambridge Structural Database (CSD) was undertaken in order to examine the packing trends of materials that are structurally similar to those included in this study. Various researchers have claimed that highly polar materials tend to orient themselves so as to minimize their electrostatic dipole-dipole interaction energies.[116] This anti-parallel side-by-side alignment of dipoles results in the cancellation of their molecular hyperpolarizabilities, leaving a negligible macroscopic nonlinear susceptibility. At the time of this writing, the CSD contained all of the pertinent crystallographic data such as space groups, unit cell parameters and fractional coordinates for over 160,000 organic and organometallic structures, or virtually all structures determined through the first half of 1996, and is therefore an ideal resource to investigate this generally accepted observation. In some cases no fractional coordinates were available, as the journal in which the 40 structure was originally published did not submit this information. In the vast majority of cases, however, all of the above-mentioned information was downloaded directly from the database. As discussed in Section 1.3, the natural bias towards centrosymmetric packing will exclude many compounds from use as crystalline SHG materials. The goal of this survey was to determine the number of structures containing either the p-nitroaniline (hereafter referred to as PNA analogs) or the 2,4-dinitroaniline chromophore (DNA analogs) and to see how many pack non-centrosymmetrically. The results of this survey, as well as the results compiled from the Mighell survey are presented in Table 2.1. Table 2.1 Packing trends of PNA and DNA analogs (cf. data for all organic structures from Mighell et al.) Mighell[127] PNA a DNA a total numbers 29,059 119 117 centrosymmetric 20,458 89 90 non-centrosymmetric 8,601 (29.6%) 30 (25.2%) 27 (23.1%) point group 222 3,665 (12.6) 10 (8.4) 10 (8.6) 2 2,241 (7.7) 8 (6.7) 13 (11.1) mm2 1,125 (3.9) 7 (5.9) 2 (1.7) m 402 (1.4) 2 (1.7) 0 (0.0) 1 305 (1.1) 0 (0.0) 2 (1.7) 422 166 (0.6) 2 (1.7) 0 (0.0) 4 145 (0.5) 1 (0.8) 0 (0.0) a Results compiled from the Cambridge Structural Database (1996). 41 2.2. Packing trends of PNA and DNA analogs The CSD allows searches by chemical structure, and therefore restrictions were imposed that limited the search to materials of the same chemical nature. In the case of PNA analogs, the survey was conducted on materials that were unsubstituted at the 2,3,5 and 6 positions (Figure 2.1). This restriction was put in place in order to preserve the character of the dipole moment along the charge-transfer axis. Substituents at these positions on the aromatic ring, particularly if they are strong electron donors or acceptors, can influence the nature and direction of the dipole moment. [82] A second restriction was added to exclude the structure of any material whose conjugation extended beyond the amine nitrogen. Materials whose conjugation extends beyond the aromatic ring, such as stilbenes and azobenzenes, are expected to have larger dipole moments [20, 22, 24, 26, 130] due to the greater extent of charge separation, and therefore differ significantly from the materials synthesized in this study. H3v ,H2 R 3 , « 2 H H R 2 , R 3 , R 5 or R 6 not H Conjugation extends beyond aromatic ring Included Excluded Excluded Figure 2.1 Chemical structures considered in the CSD search for PNA analogs. 42 On the whole, PNA analogs tend to pack in non-centrosymmetric space groups with a slightly lower frequency than the overall population of organic materials. Of the 119 materials found in the CSD search, 30 (25.2% vs. 29.6% for the general population of organic structures) crystallized in non-centrosymmetric space groups, including 14 materials that were optically pure. Complete point group distributions for PNA analogs are shown in Table 2.1. In order to examine the packing geometries of the molecules within each unit cell, the angle between the charge-transfer axes of the various symmetry related molecules was calculated. Any two molecules with their charge-transfer axes separated by 175° or more were considered to be in an anti-parallel alignment. The same strategy was employed for pairs of molecules not related by any formal symmetry (i.e., cases where there was more than one molecule per asymmetric unit). PNA anti-parallel Figure 2.2 Anti-parallel alignment of molecular dipoles in PNA analogs. 43 The results of this examination showed that 9 of the 30 non-centrosymmetric PNA structures were oriented with this anti-parallel alignment of dipoles, including 5 of the 10 in point group 222,[131-135] both materials in point group 422,[135, 136] and the lone material in point group 4.[137] Of the other two most populated point groups, only one of the 8 in point group 2 [138] and none of the 7 in point group mm2 crystallized in this manner. With these results in mind, the 30 original non-centrosymmetric structures were reduced to 21 in terms of those whose bulk nonlinear susceptibility is not cancelled out by virtue of symmetry or unfavorable alignment. (Table 2.2.) In the case of DNA analogs, the survey was conducted with the same restrictions as for PNA analogs, except for allowing substitution by a nitro group at the position ortho to the amine group. R 3 , R 5 or Rft not H Conjugation extends beyond aromatic ring Included Excluded Excluded Figure 2.3 Chemical structures considered in the CSD search for DNA analogs. 44 Once again, the frequency of non-centrosymmetric DNA type structures is slightly lower than that of the overall population of organic materials. Of the 117 DNA analogs found in the CSD search, 27 (23.1% vs. 29.6% for the general population of organic structures) crystallized in non-centrosymmetric space groups, with the majority of these (23) being optically pure. Complete point group distributions for DNA analogs are shown in Table 2.1. For SHG purposes, the most unfavorable alignment for DNA analogs to adopt involves a pseudo-centre of inversion between adjacent DNA chromophores. In this orientation the nitro groups both ortho and para to the aniline nitrogen are in an anti-parallel alignment with another molecule in the unit cell (Figure 2.4). DNA N0 2 pseudo-centrosymmetric Figure 2.4 Pseudo-centrosymmetric alignment of DNA analogs. 45 The results of this examination showed that 9 of the 27 non-centrosymmetric D N A structures were oriented with this pseudo-centre of inversion , including 4 of the 13 in point group 2[139-142] and 5 of the 10 in point group 222.[143-147] As a result, of the original 27 non-centrosymmetric D N A structures, only 18 do not have their macroscopic nonlinear susceptibility canceled out by virtue of symmetry or unfavorable alignment (Table 2.2). Table 2.2 Survey of non-centrosymmetric PNA and DNA analogs. non-centrosymmetric PNA chiral achiral 14 16 DNA chiral achiral 23 4 total anti-parallel/ pseudo-centric total 30 7 2 9 27 9 0 9 potential SHG compounds 21 18 2.3. Discussion Although the sample sizes of P N A and D N A analogs reflect only a small percentage of the population surveyed by Mighell, the results are instructive just the same. The combined frequencies of the more advantageous point groups (i.e., 1, 2, m, mm2), ~ 14%, are almost exactly the same as in the general population of organic materials. Examination of the population of non-centrosymmetric materials showed several differences. Nearly half of all non-centrosymmetric DNA-type structures packed 46 in point group 2, while only one quarter of the general population of non-centrosymmetric organic structures packed in point group 2. In addition, nearly one quarter of the non-centrosymmetric PNA-type structures packed in point group mm2, while only about one structure in eight from the general population of non-centrosymmetric structures packed in point group mm2. The comparison between chiral and achiral materials seems to suggest that the presence of a chiral centre by itself is not enough to prevent anti-parallel or pseudo-centric orientation of P N A and D N A analogs. That is not to say that the addition of chirality does nothing to discourage these unfavorable orientations. Of the 119 P N A analogs found in the search, 105 were achiral. Of these, only 14 (13.3%) were oriented non-centrosymmetrically, without the anti-parallel alignment, while 50% of the optically pure P N A analogs were oriented without an anti-parallel alignment. A similar trend was seen with the D N A analogs, where only 4 of the 94 achiral D N A analogs (4.3%) were not truly centric or had a pseudo-centre of inversion; 14 of the 23 chiral D N A analogs (60.9%) were oriented without a pseudo-centre of inversion. In light of these results it would appear that the probability of producing materials capable of efficient SHG-production is greatly enhanced by the addition of some optically active component to the material, either by way of a covalent linkage to the NLO chromophore, or via an ionic chiral auxiliary. 47 Chapter 3 - /j-Nitrophenylglycine and its salts - Results and discussion. 3.1. Introduction 3.1.1. Macroscopic nonlinear susceptibility Each of the materials investigated in this chapter contains p-nitrophenylglycine (1), which belongs to the family of PNA analogs. Figure 3.1 shows the structure of (1) and the molecular axis system used in describing its hyperpolarizability. The v-direction is chosen to coincide with the molecular charge-transfer axis, while the jc-direction is perpendicular to y in the plane of the aromatic ring. The z-direction is perpendicular to the aromatic ring. This axis system was chosen to coincide with the axis system described in ref. [82] (1) Figure 3.1 p-Nitrophenylglycine (1) and the molecular axis system describing the orientation of the charge-transfer axis. The quadratic hyperpolarizability, (3yvt, is a third-rank tensor describing the influence of the three waves involved in SHG, including the two incident fundamental 48 waves with frequency co and the second-harmonic wave with frequency 2 CO. The indices i, j and k refer to the direction of polarization of these three waves in the molecular frame of reference (i.e., (3^ refers to the hyperpolarizability tensor element for an x-polarized second-harmonic wave produced from two j-polarized fundamental waves.). According to the axis system described in Figure 3.1, waves polarized in the x- and ^-directions are expected to have a negligible influence on the polarization of the material relative to y-polarized waves, since ^-polarization is assisted by the presence of the electron-donating and accepting groups. As a result, the only tensor elements expected to contribute to the overall hyperpolarizability are derived from y-polarized light (i.e., $ i y y , where i = x, y, or z). Numerous theoretical investigations calculating the various py* elements have been carried out. [24, 81, 148] While the calculated magnitudes of these elements vary, depending on the formalism under which the calculation was carried out and the frequency of the incident fundamental radiation used in the calculation, there is general agreement that each of the p,^ elements, is negligible with respect to the one predominant element, $ y y y . This result agrees well with the two-level model derived in section 1.3, where the dominant P,^  tensor was said to fall along the molecular charge-transfer axis. Just as the molecular quadratic hyperpolarizability is described by a third-rank tensor, the second-order macroscopic susceptibility, %(f]K, is also a third-rank tensor which takes into account the contribution from each of the 27 p,^ tensor elements, recalling, of course, that p w is the only significant contributor to the overall molecular hyperpolarizability for PNA-type systems such as those described in this chapter. Since 49 $ m is directed along the charge-transfer axis of the molecule, the bulk properties of these materials are expect to be a function of the orientation of this charge-transfer axis. In 1982 Zyss and Oudar[82, 129] devised a system for systematically defining the orientation of the SHG-chromophore in the unit cell, and determining the macroscopic nonlinear susceptibility based on the contribution from each oscillator in the unit cell. The following is a brief review of this system, with derivations that are relevant to the crystal structures reported in this chapter. Recalling equation (1.3) from Chapter 1, P1 = + Ej + ±Zxl&EjgK + ± Zx1&lEj.EKEL+... (1.3) where x ( n ) is the n-th order macroscopic susceptibility. For convenience, the second-order susceptibility term, y %ffK, is routinely referred to as dux, where, Xui = 2dUK (3.1) Zyss and Oudar surmised that the second-order macroscopic susceptibility should be a function of the second-order hyperpolarizability, p, and the chromophore density, N. Taking into account the local electric fields from neighboring molecules, and also the orientation of the chromophores in the unit cell, they put forward the following relationship, 50 duK = ^ V ; / ; - Z X c o s ( / f iXs))cos(/,7Xs))cos(A:,fc(s))P^(^ ( 3- 2) <W = WFffffrtnc (3-3) where / is the Lorentz local-field factor used to correct for mutual polarization from neighboring molecules; n is the number of symmetry-related molecules in the unit cell (indexed by s); the cosine terms represent the rotation of the molecular reference frame from (i,j,k) onto the crystal reference frame (I,J,K); bjjK in equation (3.3) represents the crystalline nonlinearity per molecule. Equation (3.2) is tremendously simplified for P N A analogs if one assumes that P w is the only significant contributor to the crystalline nonlinearity. Figure 3.2 shows the axis system used to define the orientations of the charge-transfer axis of a typical chromophore crystallizing in point groups 2 and m. For materials crystallizing in point group 2, Y is chosen to coincide with the two-fold axis of rotation. Since this two-fold axis is the only symmetry element in this point group, Y is the only axis that needs to be restricted to one of the crystallographic axes. X and Z can be chosen arbitrarily. The Z-axis is defined as the line of intersection between the X Z plane and the plane containing both the Y and y-axes. In this way the angles the charge-transfer axis makes with the X , Y and Z axes are 90°, a and 90°- a, respectively. Materials crystallizing in point group m are defined in much the same way. The X Z plane is chosen to coincide with the mirror plane and is thus perpendicular to the Y -51 axis. The charge-transfer axis y is chosen to lie in the Y Z plane. In this way the angles the charge-transfer axis makes with the X , Y and Z crystal reference axes are the same as in the case of point group 2, that is 90°, a and 90° - a, respectively. Y =2 Y D D Z X Figure 3.2 Axis systems used to define the molecular (xyz) reference frame with respect to the crystal (XYZ) reference frame for point groups 2 and m. Using equation (3.2) and the orientational information derived from the crystal structure, the various buK elements can be determined for each material. For materials crystallizing in point group 2, the derivation of the 27 buK elements leads to only two non-zero results, brry and brzz, assuming that $ y y y is the only significant contributor to the molecular hyperpolarizability. The derivation of the relationship for byzz serves as an illustrative example: 1 " bUK = - yLJdcos{I ,i{s))cos{J, j{s))cos{K,k{s))^ n s=\ijk ijk (3.4) YZZ = - Icos(y, y(s))cos(Z, y(s))cos(Z, y(s))$ yyy (3.5) s=\ 52 = [cosacos2 (90 - a) + cos(- a)cos 2 (a - 90)](3 = ^ [cosasin 2a + cos(-a)sin 2 (-oojp^, = (cosasin 2 a)p w y Using the same approach, it can be shown that byrr = cos a $ y y y . The remaining 25 elements are zero. Of the two components of the overall bulk susceptibility, byyy is maximized for a = 0°, so that b{ffl = $m , while brzz is maximized for a = 54.7°, so that = 0.385pV An analogous situation arises for materials crystallizing in point group m. Once again, only two b\jK tensor elements are found to be non-zero; bzzz and bzw, where bzzz = sin3oc Pyyy and bzn = sina cos 2a $ m . For monoclinic systems 2 and m, the orientation of the charge-transfer axis is fully defined by the lone symmetry element. Defining the orientation of the charge-transfer axis becomes more complex for orthorhombic point groups mm2 and 222, due to the presence of multiple symmetry elements in the unit cell. Figure 3.3 shows the axis system used to define the orientation of the charge-transfer axis for point groups mm2 and 222. The crystal reference frame (XYZ), in this case, coincides with the three crystallographic axes (abc) of the unit cell. The angle a is defined as the angle the charge-transfer axis makes with the Z two-fold axis of rotation. A second angle, \jr, defines the orientation of the charge-transfer axis with respect to both the X and Y-axes, 53 and is taken as the angle between the Y-axis and the projection of the charge-transfer axis onto the X Y plane. z =2 Figure 3.3 The crystal reference frame used to define the charge-transfer axis for PNA analogs crystallizing in point groups mm2 or 222. Crystal reference axes X, Y and Z coincide with unit cell axes a, b and c, respectively. Deriving the various bun tensor elements for these two point groups (mm2 and 222) is made more complex because of the increased number of symmetry-related positions in the unit cell. Ultimately, the number of non-zero bjjx elements is reduced to three in the case of materials crystallizing in point group mm2 (&zzz> bzyy and bzxx) and one in the case of point group 222 (bxyz)-In the case of materials from point group mm2, bzzz - cos 3a $m (3.6) where b%£> = $yyy fora = 0°. bzxx = sin2\|/ cosa sin 2a $m (3.7) bzYY = cos2\j/ cosa sin 2a Pyyj, (3.8) 54 where b%g? = bffi = a 3 8 5 P O T for a = 54.7° and i | / = 90° and 0°, respectively. For materials from point group 222, bxYz = simj/ cosy cosa sin 2a $yyy (3.9) where b ^ = 0.193(3 m for a = 54.7° and y = 45°. A l l of the materials discussed in the following sections belong to either point group 2 or 222. Equation (3.3) will be used, with the help of information from the X-ray crystal structures defining the orientations of the charge-transfer axes, to rationalize the SHG-intensities produced by the various materials. 3.1.2. Phase-matching In addition to the requirements that both the molecule and the unit cell possess no centre of inversion, and the geometric considerations leading to efficient SHG-production discussed in the preceding section, there is a further condition that must be met before the material can produce SHG efficiently. As the driving frequency (cd) propagates through the medium, dipoles at molecular sites are driven at both the fundamental frequency co and the second-harmonic 55 frequency 2 ft). If there is a difference in the refractive index (n) of the material at these two frequencies (i.e., dispersion), the fundamental and second-harmonic waves will travel through the medium at different velocities. As a result, second-harmonic waves created at a site will be out-of-phase with those created at earlier sites, and destructive interference will decrease the intensity of the second-harmonic waves. In some crystalline media it is possible to achieve phase-matched propagation of the fundamental and second-harmonic waves. In uniaxial crystals (i.e., those with trigonal, tetragonal and hexagonal symmetries) and biaxial crystals (which include those with triclinic, monoclinic and orthorhombic symmetries) the refractive indices vary depending on the direction in which the electric-field of the wave is polarized. For uniaxial crystals, nx = ny * nz, while for biaxial crystals nx * ny * nz. Figure 3.4 describes the index ellipsoid of a uniaxial crystal. The surface of the ellipsoid defines the refractive index for a given direction of propagation and polarization. The axes nQ (= nx = ny) and ne (= nz) are termed the ordinary and extraordinary components of the refractive index, respectively. For a light wave propagating through the crystal at an arbitrary angle 0, the electric-field polarization can be divided into two components - one polarized along n 0 , the other polarized orthogonally to both the direction of propagation and n 0 . As indicated by the diagram, the value of the refractive index orthogonal to na is 0-dependent, and is designated ne(0). In order to achieve phase-matching, the crystal must be oriented in such a way that n 2 o ) (0) = n™ , or n 2 c o = n"(f?). If this is the case there will be constructive 56 interference and the second-harmonic intensity will increase as the fundamental wave passes through the crystal. z Figure 3.4 Index ellipsoid of a uniaxial crystal, where s is the direction of propagation, and n,, and ne are the ordinary and extraordinary components of the refractive index. Reproduced from ref. [75] One conclusion that can be drawn from the preceding discussion of phase-matching is that certain bim elements cannot contribute to phase-matched SHG. In order for phase-matching to occur the fundamental and second-harmonic waves must be polarized perpendicularly to one another; i.e., one along n 0 , the other along ne(0). As shown earlier, in the case of materials from point group 2 the bun tensor element that most takes advantage of p ^ is brm- This tensor element, however, cannot participate in phase-matching because, by definition, the polarization of both the fundamental and second-harmonic waves are in the Y-direction. By extension, no buK tensor elements with three identical indices can participate in phase-matched SHG. Thus, in the discussion of materials crystallizing in point group 2, bnz is the sole buK element capable of contributing to phase-matched SHG. 57 3.2. General synthesis A series of six salts containing the acid (1) was prepared by coupling the acid with various optically pure amines. The acid was prepared by slight modifications of the procedure described by Lantz and Obellianne,[149] and involved the substitution reaction between p-fluoronitrobenzene and glycine methyl ester hydrochloride, followed by acid hydrolysis of the ester to give the carboxylic acid in moderate yield (Scheme 3.1). Scheme 3.1 The salts were prepared by one of two methods. When the free amine was available, as was the case with pseudoephedrine, prolinamide, prolinol and proline jf-butyl ester, the addition of (1) to the amine in a nonpolar solvent usually resulted in the immediate precipitation of the desired salt. If precipitation was not immediate, evaporation of the solvent afforded the salt precipitate. In both cases the crude salt was produced in high yield (Scheme 3.2). 2 equiv (1) 58 Scheme 3.2 R = CQjNIfe, CH2OH, CChQCHjb When the amine was available only as the hydrochloride salt, as was the case with both the proline methyl ester and benzyl ester, the free amine was prepared by dissolving equimolar amounts of amine and K O H or NaOH in ethanol and precipitating out either KC1 or NaCl. The ethanol solution containing the free amine was then added to an ether solution containing the acid, then evaporated to dryness (Scheme 3.3). The benzyl ester salt, l.pro-benz, precipitated from solution during evaporation. The methyl ester containing solution gave a yellow oil on complete evaporation. The oil was readily dissolved in a small volume of acetone, and the addition of hexane afforded the unexpected 2:1 acid/amine complex, l.pro-meth. A list of each structure and shorthand notation appears in Table 3.1. Complete synthetic and characterization details are found in Chapter 6 - Experimental (Organic synthesis). 59 Scheme 3.3 (1) N R c i Q 1 eq. KOH EtOH K C I J R = C 0 2 C H 3 ) C0 2 CH 2 Ph (2) O 2 N — N H C H j C O i H B j O [ C H 2 C 0 2 e O L 1 X R H H acid / chiral auxiliary name / shorthand ° 2 N - < 0 ^ i H 2 _ / \ ) H p-nitrophenylglycine (1) Table 3.1 Glossary of materials described in Chapter 3 o f»J N H C H 3 C H 2 O H ' N H 2 . C H 3 N H N H pseudoephedrine salt l.eph proline t-butyl ester salt l.pro-but prolinol salt l.pro-ol prolinamide salt 1.pro-amide proline methyl ester complex l.pro-meth proline benzyl ester salt l.pro-benz 60 3.3. X-ray structural analyses Single crystals suitable for X-ray analysis were grown and the structures of the salts determined for all but l.pro-benz. No solvent system was found in which l.pro-benz would recrystallize in any form other than a fine powder. The parent acid, (1), crystallizes in space group PT and must therefore be SHG-inactive (Figure 3.5). Each salt crystallized in a non-centrosymmetric space group, as they all must, due to the chiral nature of the counterion. Three of the salts (l.eph, l.pro-but and l.pro-amide) crystallize in P2\, one of the most favorable space group for efficient SHG,[82] as described in section 3.1.1., while the remaining two, l.pro-ol and l.pro-meth, crystallize in P2i2i2 and P2\2{1\, respectively. The structure of l.eph contains significant structural disorder, with respect to the p-nitrophenylglycinate chromophore. In it, the p-nitrophenylglycinate adopts two positions, the major fragment adopting a much less favorable orientation for SHG than the minor fragment. Several of the other salts exhibit some degree of structural disorder; however, all of this disorder occurs in the conformation of the pyrrolidine ring and should have no effect on the NLO properties of the salts. Complete crystallographic data and detailed structural descriptions for each salt except l.pro-benz are found in Chapter 8 - Experimental (Crystallographic). 61 Figure 3.5 CHARON packing diagram of (1). 3.4. Estimation of second-order nonlinear susceptibilities. Using the axis conventions described in Figures 3.2 and 3.3, a and \j/ were determined (Table 3.2) and the values of the pertinent non-zero bun elements were calculated according to the model described by Zyss and Oudar.[1.29] Calculation of the various non-zero dJJK elements via equation (3.4), is somewhat problematic because it requires a knowledge of the refractive indices at both co and 2co in order to apply the local-field factor corrections. In the absence of large, high-quality crystals required for refractive index measurements, it is possible to estimate the ratio of SHG-intensities between two materials through equation (3.3), assuming they possess similar refractive indices and molecular hyperpolarizabilities. As each salt contains the same N L O 62 chromophore we can assume the magnitude of the molecular hyperpolarizabilities will be the same for each salt. The fact that the chromophore remains constant throughout the series of materials under investigation should also serve to minimize any difference in local field-factor corrections. Traditionally, the Lorentz form of the correction is employed where: f 2 ^ ni+2 (3.10) and n^ is the refractive index of the material at frequency co. Accordingly, any significant difference between the refractive indices of the two materials will be reflected in a difference in/0. Since the two materials exhibit similar absorption characteristics, as long as co and 2co are non-resonant frequencies it is reasonable to assume there will be no significant difference in their respective refractive indices.[77, 150] The calculated ratio of the SHG-intensities between two materials can therefore be given by: [77, 150] 7 2 t»(l) 7 2 w(2) «*//JC(2) 2 f A W , i n 2 UK (3.11) where d/JK (and biJK) refers to the predominant d (and b) tensor for phase-matched SHG, dyzz for materials crystallizing in point group 2, and dxyz for those in point group 222. 63 The SHG-intensity for each salt was compared with that of a known NLO material, l-(4-nitrophenyl)-L-prolinol (NPP).[80] NPP is widely considered to be the model compound for SHG, due to the optimized orientation of its N L O chromophore (a = 58.6° vs. 54.7° for by%£}). Studies calculating and measuring the molecular hyperpolarizability of p-nitroaniline (PNA) and its derivatives have consistently shown that those with tertiary amines, like NPP, possess greater molecular hyperpolarizabilities than P N A , and than PNA derivatives with secondary amines.[21, 22, 151] In addition, the absorption spectrum of NPP differs significantly from those of P N A and (1) (Figure 3.6); thus one should expect some difference in refractive indices (and subsequently in the calculated local-field factor corrections). As a result, direct comparison of each salt's SHG-response to that of NPP cannot be completely accurate. However, barring extreme differences in local-field factors and molecular hyperpolarizabilities, this type of comparison remains instructive when discussing the effect of chromophore density and orientation on the observed SHG-response. 64 Table 3.2 Space group, chromophore density (AO and orientational parameters (a, \|/) for the six salts made from (1). acid/salt space group a ( ° ) a v ( ° ) (1) PI 4.75 N / A b N/A l.eph « i 2.17 76.7, 61.0 N/A l.pro-but F2, 2.17 50.3 N/A l.pro-benz undetermined l.pro-ol P2,2,2 2.72 64.8, -117.1 80.2, -98.8 l.pro-amide />2, 2.84 47.6, -131.5 N/A l.pro-meth P2,2,2, " 3.20 -92.7, 88.9 170.7, -11.1 Entries with more than one angle correspond to structures containing more than one asymmetric chromophore per unit cell. N/A : not applicable. 65 25000 20000 15000 10000 5000 1 r 250 275 300 325 350 375 400 425 450 475 500 X (nm) Figure 3.6 UV-visible absorption spectra of (1), NPP and PNA in EtOH. 66 3.5. Second-order nonlinear optical properties Once a salt was isolated it was screened for SHG-activity at 1064 nm by the Kurtz and Perry powder method. [74] In addition to providing a test for SHG-activity, this semiquantitative technique may also be used to rank the salts based on their SHG-efficiencies and to test for phase-matchability.[75] The SHG-activity of each salt was measured relative to crystalline powder samples of both urea and NPP. Details concerning the apparatus and the measurement technique employed are found in Chapter 7 - Experimental (SHG measurements). Of the six salts made from (1), three (l.eph, l.pro-but and l.pro-benz) had SHG-intensities greater than 10 times that of urea, whereas the parent acid, (1) was SHG-inactive. While the remaining salts (l.pro-ol, l.pro-amide and l.pro-meth) all displayed some smaller degree of SHG-activity, each was several orders of magnitude lower than that of urea. None of the salts proved to be as efficient a producer of SHG as the second reference, NPP (SHG vs. urea = 53 ± 5). 67 Table 3.3 SHG results for (1) and all six salts containing the (1) chromophore. acid/salt SHG vs. urea (1) n — > CH2-C02H 0 l.eph (1) + H 3 C CH3 18 ± 2 l.pro-but (1) + \ , / \ OC(CH3)3 1 " H 13 ± 2 l.pro-benz (1) + 1 " H 11 ± 2 l.pro-ol (1) + ^ " ^ . C H 2 O H 1 " H 0.010 + 0.004 l.pro-amide (1) + 1 H H 0.012 + 0.008 l.pro-meth + (1) + 1 h H 0.022 ± 0.005 Forms 2:1 acid/amine complex. 3.5.1. SHG results of the (IS, 2S)-(+)-pseudoephedrine salt of (1): l.eph. Salt l.eph, with an SHG-intensity of ~ 18 times that of urea, displays the greatest efficiency of the six salts in the series, but, it is still considerably weaker than that of our second standard, NPP. The reduced chromophore density (2.17 x 10"3 A"3) compared with that of NPP (3.68 x 10"3 A"3) acts to reduce its SHG-intensity significantly. A 68 second factor influencing the SHG-efficiency is the relatively unfavorable orientation adopted by the chromophore. l.eph, like NPP, crystallizes in space group P2\, therefore byzz, the phase-matching buK tensor, depends solely on the angle the molecular charge-transfer axis makes with the two-fold axis of rotation. The /j-nitrophenylglycinate anion in l.eph is considerably disordered, adopting two distinct orientations. The major and minor fragments, with relative populations of 0.75 and 0.25 respectively, are oriented so that their charge-transfer axes are offset by approximately 16°, with the major fragment adopting an orientation with OW) = 76.7°, and the minor fragment adopting an orientation with a^n = 61.0° (Figures 3.7 and 3.8). Figure 3.7 ORTEP diagram of l.eph. Only the major disordered p-nitrophenylglycinate fragment is shown (50% probability ellipsoids). 69 C7* 03 C1 N 1 pg--j C4« 03* Figure 3.8 Orientations of the disordered p-nitrophenylglycinate anion in l.eph. The major fragment, labeled without stars, makes an angle of o^aj = 76.7° to the fc-axis, while the minor fragment, labeled with stars, makes an angle of (Xm^ = 61.0° to the same axis. The effective byzz element for the disordered structure, taking into account the relative populations of each fragment, is then: byzz (l.eph) = (0.75 COSOmaj sin2Omaj + 0.25 COSOmin sin2G!min) Pyyy = 0.256 fiyyy (3.12) The value of a for NPP is 58.7°, close to the orientation ( o w = 54.7°) required to maximize the bulk nonlinear susceptibility according to the relationship described in equation (3.3). This orientation of the NLO chromophore leads to a byzz element of: bYZZ (NPP) = 0.379 fiyyy (3.13) 70 Taking into account the different chromophore densities of the two materials and assuming equivalent local-field factor terms, the NPP : l.eph ratio of SHG-intensities is estimated to be: I2(0 (l.eph) / 2 f t )(NPP) {estimated) = ^ (l.eph) , ^ ( N P P ) , = 0.16 (3.14) In fact, the measured ratio appears to be approximately twice the estimated ratio. One possible explanation for the surprisingly high SHG-response of l.eph relative to NPP is a contribution to the overall molecular hyperpolarizability from the optically active counterion. This is unlikely, however, since the counterion is not expected to contribute significantly to the hyperpolarizability. Experimental measurements of the molecular hyperpolarizability of structurally similar materials such as alkyl-substituted benzenes reveal values several orders of magnitude lower than those of PNA.[22] There is no reason to believe the pseudoephedrinium counterion contributes to the molecular hyperpolarizability of the salt to any appreciable extent. A second explanation for the high SHG-response of l.eph relative to NPP is the invalidity of the assumption made in equation (3.11), where the refractive indices of each I2{0 (l.eph) / 2 < B(NPP) (measured) = 0.34 + 0.07 (3.15) 71 material were taken to be approximately equal, leading to equivalent local-field factor correction terms. These terms are intended to account for any contribution to the polarization of the chromophores from their immediate surroundings (i.e., neighboring molecules), and are assumed to be consistent throughout the crystal. The considerable fraction of disordered chromophores (30%) may have an additional influence on the refractive indices of the salt. Without direct measurement of the refractive indices for both wavelengths in question, the extent to which the disorder contributes to the increased SHG-response of l.eph is unclear. 3.5.2. SHG results of the S-(-)-proline t-butyl ester salt of (1): l.pro-but. times that of urea. Unlike l.eph, l.pro-but's SHG-response is more readily rationalized from its crystal structure. Salt l.pro-but crystallizes in space group P2\, and is therefore subject to the same orientational and density considerations as NPP and l.eph. In this case a, the angle between the molecular charge-transfer axis and the two-fold b-axis, is 50.1° (Figure 3.9) and the chromophore density is 2.17 x 10"3 A" 3 . On this basis, and on the basis of assumptions concerning the local-field factors and molecular hyperpolarizabilities outlined earlier, equation (3.11) yields the following estimated ratio of SHG-intensities, Like l.eph, l.pro-but produced a significant SHG-response, roughly 13 Il(0 (l.pro-but) / 2 ( B ( N P P ) r dYZZ (l.pro-but) V (estimated) = = 0.34 (3.16) V dvzzCNPP) ) 72 The observed ratio of SHG-intensities was, I2o) (l.pro-but) (measured) = 0.25 ± 0.05 (3.17) 72<0(NPP) The estimated ratio of SHG-intensities using equation (3.11), is quite possibly lower if the molecular hyperpolarizability of NPP is indeed greater than that of the (1) chromophore found in l.pro-but. Comparing the measured and estimated SHG ratios of l.eph to l.pro-but, one again finds that the SHG-response of l.eph is underestimated by equation (3.11). With identical space groups, chromophores and chromophore densities, the salt with the greater SHG-response should be that with the more favorably oriented chromophores, assuming similar local-field factor correction terms. On the basis of a, the angle that defines the orientation of the charge-transfer axis, l.pro-but packs more favorably than l.eph does for SHG; however, the SHG-response is roughly 40% greater in l.eph. / 2 ( 0 (l.pro-but), . fdy^q.pro-but^ 2 / 2 ( 0 (l.eph) •(estimated) = d^ (l.eph) = 2.0 (3.18) / 2 w ( l .pro-but) (measured) = 0.7 ± 0.2 (3.19) 7 2 w (l.eph) 73 Figure 3.9 ORTEP packing stereodiagram of l.pro-but (50% probability ellipsoids). 3.5.3. SHG results of the S-(-)-prolinol salt of (1): l.pro-ol. Salt l.pro-ol produces a very small but measurable amount of SHG. The packing consists of two formula units per asymmetric unit, with the two p-nitrophenylglycinate moieties related by a pseudo-centre of inversion (Figure 3.10). According to the space group in which l.pro-ol crystallizes (P2]2i2), the only non-zero buK tensor element is bxYz, which depends both on angles a and \|/, as defined in Figure 3.3. In the case of l.pro-ol, the angular parameters for each asymmetric p-nitrophenylglycinate unit (Table 3.2) lead to an almost complete cancellation of their individual bXyz tensors: 74 fcre(l) = 0.058 p\ 'yyy, bxrz (2) = -0.055 p\ 'yyy bxrz (tot) = bXYz(l) + bxrz (2) = 0.003 p\ 'yyy (3.20) Estimation of the ratio of SHG-intensities between l.pro-ol and NPP requires a slight modification to the previous examples. Equations (3.2) and (3.3) assume that each chromophore in the unit cell is related to all others by the space group symmetry, where N is the number of chromophores per unit cell volume, and bIJK is the contribution to the macroscopic nonlinearity for one chromophore. In cases such as l.pro-ol, where there is more than one molecule in the asymmetric unit, N now becomes the number of symmetry related positions (four in this case) per unit cell volume, and bun is the combined macroscopic nonlinearity of the two (or more) molecules in the asymmetric unit. The ratio of SHG-intensities between l.pro-ol and NPP, according to equation (3.11), is estimated to be ~ 8.6 x 10"6 : 1. This ratio is considerably lower than the measured ratio of (2 ± 1) x 10'4 : 1. The "high" ratio could be the result of a small contribution to the quadratic-hyperpolarizability from some tensor other than $ y y y (which are assumed to be zero), or, more likely, it is the result of some small amount of dark current or drift in the signal from the photomultiplier. The model is, however, correct in predicting a very small SHG-response based on the anti-parallel alignment of the chromophores. 75 Figure 3.10 ORTEP diagram of l.pro-ol (50% probability ellipsoids). 3.5.4. SHG results of the S-(-)-prolinamide salt of (1): l.pro-amide. Salt l.pro-amide, like l.pro-ol in the previous example, crystallizes with two N L O chromophores related by a pseudo-center of inversion (Figure 3.11). Individually, each p-nitrophenylglycinate moiety in the asymmetric unit is favorably oriented for SHG, according to the P2i space group in which the salt crystallizes. However, addition of the two byzz tensor elements (with oc(l) = 47.6° and a(2) = -131.5°), leads to their nearly complete cancellation: byzz (1) = 0.368 p w , byzz (2) = -0.372 $ m 76 byzz (tot) = byzz (1) + byzz (2) = -0.004 p. (3.21) Estimation of the ratio of SHG-intensities between l.pro-amide and NPP leads to an estimated ratio of ~ 1.7 x 10"5 : 1, while the actual ratio of intensities is an order of magnitude higher, at (2.3 ± 1.5) x 10"4 : 1. Once again, as with l.pro-ol, the unfavorable chromophore orientation predicts little or SHG-intensity, and the "high" measured intensity may be the result of some small instrument error, as discussed earlier. Figure 3.11 ORTEP diagram of l.pro-amide (50 % probability ellipsoids). 3.5.5. SHG results of the S-(-)-proline methyl ester complex of (1): l.pro-meth. The l.pro-meth complex crystallizes with the two p-nitrophenylglycinate moieties oriented in an anti-parallel manner (Figure 3.12). While there is no pseudo-center of inversion between the chromophores, the two charge-transfer axes are separated by almost 180° (a(l) = 88.9°, a(2) = -92.7° , =11.1°, \|/(2) = -170.7°). According to the space group in which the salt crystallizes, P2\2{2\, neither of the two chromophores is favorably oriented for SHG. Addition of the two bxyz tensors gives: 77 bxYz(l) = 0.004 p> y >„ bXYZ(2) = -0.008 $ m , bxrzm = bXYZ(l) + bxrzV) = -0.004 $m (3.22) Estimation of the SHG-ratio between l.pro-meth and NPP predicts a ratio of approximately 2 x 10 s : 1 while the measured ratio is approximately (4 ± 1) x 10"4 : 1. Once again the actual ratio is significantly higher than the predicted ratio. As is also the case for all the samples with chromophores oriented in an anti-parallel fashion, however, there is agreement between both the predicted and measured ratios, in that the SHG-response should be almost negligible. Figure 3.12 ORTEP diagram of l.pro-meth (50% probability ellipsoids). 78 3.6. Phase-matching results. Where possible, salts displaying significant SHG-activity [i.e., SHG(salt) > SHG(urea)] were tested for phase-matchability. Phase-matchable materials can be distinguished from non phase-matchable materials by their different behavior with increasing particle size.[74, 152] The SHG-intensity of a phase-matchable material is expected to increase with increasing particle size to a maximum before leveling off to a relatively constant intensity. This saturation is due to the reduced number of large particles in the path of the beam. Non phase-matchable materials are expected to show a linear increase in SHG-intensity until the average particle size exceeds the coherence length of the material, after which the intensity drops off significantly with increasing particle size. Figure 3.13. shows the typical SHG behavior of phase-matchable and non phase-matchable materials. In order to carry out this test, a large quantity (~ 1 g) of crystalline material was powdered and passed through a series of sieves, separating the grains into several particle size ranges. The SHG-intensity for each range was then measured and plotted against particle size. In the cases where the observed SHG-intensity was less than that of urea (i.e., l.pro-meth, l.pro-ol and l.pro-amide), no test for phase-matchability was carried out. In the case of l.pro-benz, recrystallization produced only a microcrystalline powder, therefore no test for phase-matchability was carried out. The results for NPP, l.eph arid l.pro-but suggest that all three are phase-matchable. 79 phase motchoble «>/<*> Figure 3.13 Theoretical SHG behavior of phase-matchable and non phase-matchable materials.[153] The variables <r> and <lc> are the mean particle-size and mean coherence length of the material. The coherence length is defined as the distance between two points in the crystal where second-harmonic waves are generated 180° out of phase with each other. The phase-matching analysis of both l.eph and l.pro-but reveals a maximum SHG-intensity in the 125-149 | im range before decreasing slightly with larger particle sizes and leveling off to a constant intensity (Figure 3.14). These results would appear to indicate that both are phase-matchable. The behavior of NPP, a known phase-matchable material,[154] was similar to the behavior displayed by the two salts when subjected to the same analysis. The decrease in SHG-intensity for larger particle sizes is likely due to a decrease in the amount of material exposed to the incident radiation. The larger sized particles are likely to occupy the volume in the sample cell less efficiently than smaller particles, producing voids containing no sample. In addition, crystal morphology may limit the number of orientations a particle may adopt in the sample cell, possibly excluding the orientations best suited for phase-matching. •80 1 1 1 ! , <125 125-149 149-177 177-250 >250 particle size (|im) Figure 3.14. Change in SHG-intensity with particle size for NPP, l.eph and l.pro-but 81 3.7. Discussion It would appear from the results reported in the preceding sections that the coupling of chiral ionic auxiliaries to SHG chromophores not only ensures non-centrosymmetric packing, but also significantly improves the potential for packing that leads to large SHG-efficiencies compared to achiral compounds and non-ionic systems. Of the six salts prepared from the otherwise SHG-inactive parent acid (1), three displayed significant SHG-activity on coupling with the chiral auxiliary. While no structural information is as yet available for l.pro-benz (SHG vs. urea ~ 11) it seems reasonable to surmise, based on the magnitude of its SHG-response, that addition of the proline benzyl ester has allowed the p-nitrophenylglycinate chromophore to align in a favorable orientation for SHG. Examination of the SHG results reveals that none of the salts, even those with favorably oriented chromophores, approach the SHG-efficiency of NPP. The most likely explanation is the reduced chromophore densities associated with the salts. This is as expected since the chiral counterion is responsible only for inducing a acentric packing environment, and should have a negligible contribution to the hyperpolarizability (/j) of the salt. Also of note is the seemingly conflicting relationship between chromophore density and SHG-activity. In the case of salts with significant SHG-activity (whose crystal structures were determined) both chromophore densities were ~ 2.2 x io-3 A"3, whereas the three salts and parent acid that showed little or no SHG-activity (l.pro-ol, 82 l.pro-amide, l.pro-meth and (1)) had chromophore densities of 2.7 x 10~3 A" 3 or greater. The three most strongly SHG-active salts contained the three bulkiest counterions. These bulky counterions may be more adept at separating the polar chromophores, thus diminishing the electrostatic attraction that leads to anti-parallel packing. This, however, limits the maximum possible SHG-efficiency by "diluting" the chromophore density. 83 Chapter 4 - 2,4-Dinitrophenylglycine and its salts - Results and discussion 4.1. Introduction 4.1.1. 2,4-Dinitroaniline systems and their quadratic hyperpolarizabilities In the preceding chapter it was shown how the SHG-intensity produced by a material containing the /?-nitroaniline chromophore depended greatly upon the spatial orientation of the molecular charge-transfer axis in the unit cell. Contributions to the crystalline nonlinearity, biJK, from the various (3,^  components were assumed to be negligible for all but $ y y y . The addition of a second electron-accepting substituent to the aromatic ring can, however, allow the chromophore to be polarized throughout the aromatic plane, and not only along the para (amine-nitro) charge-transfer axis, as shown in Figure 4.1. As a result, unlike PNA analogs, materials containing the 2,4-dinitroaniline chromophore (DNA analogs) have multiple non-zero py* elements that can contribute to the crystalline nonlinearity. Since DNA-type materials are polarizable throughout the aromatic plane, but not into or out of this plane, it is assumed that only x-polarized and y-polarized light can contribute to any induced polarization. Thus, only those py* tensor with a z subscript are assumed to be zero. This restriction reduces the number of pp elements from 27 to 8. In addition, according to Kleinman [128], at non-resonant frequencies, energy is simply exchanged between the interacting fields, therefore 84 the different $ijk(-2co;co,co) tensor elements are identical under index permutation (as they also are for bUK and duK), therefore, only four independent fiuk elements,gamely $yyy, p ^ , fiyxx (= fixyx = Pxry) and P w (= $yxy = $yyx) remain. Figure 4.1 Polarization throughout the aromatic plane of DNA, as shown by its resonance forms. While there has been limited computational investigation into the magnitude of the different P ^ elements of D N A analogs, those few that have been done reveal that, as expected, p^, is no longer the lone non-zero component of the quadratic-hyperpolarizability and the assumptions made earlier are valid. The results of two computational studies into the magnitude of some of the P,y* components, carried out by Oudar and Zyss [82] and Dirk et al. [81] are shown in Table 4.1. 85 Table 4.1 Quadratic-hyperpolarizabilities calculated for various (3,^  tensor elements for PNA and DNA PNA a DNA a DNA fiyyy (x 10"30 esu) 37.0 26.2 -6.33 $xxx -14.8 -0.43 $yxx -2.1 -8.4 2.07 $xyy 3.5 0.34 a Ref.[81], calculated for (0 corresponding to 1064 nm b Ref. [82], calculated for co=0. The difference in magnitudes of the $ y y y values between the two studies for D N A is likely due to the different frequencies at which the calculations were carried out. The most significant difference between the two studies is in the magnitude of p ^ , where Dirk et al. found the value of p ^ to be better than half that of p ^ , while Oudar et al. calculated P ^ to be more than an order of magnitude smaller than P w . Both studies suggest, however, that unlike PNA analogs with only one non-zero Py* element, the contributions from other p,^ elements of D N A analogs are not negligible. At this stage it is important to define the various axis systems that will be used to orient the molecular plane in the crystal. As in Chapter 3, the crystal frame of reference will be defined by an orthogonal (XYZ) system that is based on the point group of the material. The quadratic-hyperpolarizability (P) will be defined by the same orthogonal (xyz) system as in Chapter 3, with the y-direction along the para (amine-nitro) axis and x perpendicular to y in the molecular plane. Unlike in Chapter 3, a third orthogonal axis system, (abc), will be employed where the ab plane is co-planar with the xy plane described above, as shown in Figure 4.2. The orientation of axes a and b will be defined 86 individually for each structure, and an angle 6 will be determined that rotates the a and b axes on to the molecular axes x and y. 0 Figure 4.2 Molecular reference frames describing DNA analogs. 4.1.2. Orientation of the molecular plane. In the same way that the bulk second-order properties of PNA-type materials depend on the orientation of the molecular charge-transfer axis, the same properties of D N A analogs will now depend on the orientation of the aromatic plane. This can be shown in Figure 4.3, where in PNA, the orientation of the ring does not influence § y y y because the molecular charge-transfer axis is always in the same orientation with respect to the two-fold axis, regardless of the orientation of the ring, and thus has no influence on its macroscopic nonlinearity. In the case of DNA, the orientation of the ortho-nitro group does depend on the orientation of the ring, and thus its contribution to the macroscopic nonlinearity will depend on this orientation. 87 ( Y : t ^ ^ N H 2 a) = 2 k (1 Y : i ^ ^ N H 2 b) = 2 k ( Y = t c)  2 k 0 Y = t ^ ^ N H 2 i)  2 k 0 2N / ^ / N ° 2 K ^ N ' " ^ ^ Figure 4.3 The relationship between an aromatic ring and a two-fold rotation axis for both PNA and DNA. In both (a) and (c) the aromatic rings are co-planar, while in (b) and (d) there is a dihedral angle between the two rings. This angle has no bearing on the direction of the lone charge-transfer axis in PNA, but in DNA this angle determines the orientation of the second electron-accepting N0 2 group. The relationships between dUK and (described in equations (3.2) and (3.3) and reproduced here for convenience) still hold. dm = A^2V"/"-iZcos(/,/(s))cos(/,7Xs))cos(/C,/:(s))P.,(s) n j=i ijk (3.2) dUK = N f l fj fK bIJK (3.3) 88 Determining the different dux elements, however, is no longer as straightforward for D N A analogs as it was for P N A analogs, due to the additional P,^  elements present in the former. As with the determination of the crystalline nonlinear susceptibility elements of PNA-type materials discussed in Chapter 3, Zyss and Oudar [82, 129] devised a method for relating the molecular reference frame to a crystal reference frame in order to determine the various dUK elements for DNA-type materials (in fact, the method was first applied to D N A analogs, and subsequently to P N A analogs by changing the molecular reference frame from the aromatic ring to the charge-transfer axis). In this method they strove to find some crystalline symmetry element within the molecular (aromatic) plane that could be related to both the crystal and molecular reference frames. For brevity, only those point groups that will be encountered in the discussion of results in this chapter will be outlined here. For point group 2, the two-fold axis of rotation is once again defined as the Y-axis in the crystal reference frame, and the plane perpendicular to Y is the X Z plane. Since Y contains the only symmetry element in the point group, axes X and Z can be assigned arbitrarily. In order to define an axis common to both the crystal reference frame and the molecular reference frame, Zyss and Oudar chose to define the crystal reference axis X as the line of intersection between the molecular plane and the X Z plane, and subsequently this axis was chosen to coincide with molecular reference axis b, as described in Figure 4.4. It should be noted that the molecular axis labels used in this discussion are not those used by Zyss and Oudar. This is for the sake of consistency with Chapter 3. 89 Y = 2 Figure 4.4 The definition of the crystal and molecular reference frames for DNA-type molecules in point group 2. Adapted from ref. [129] Molecular axis a is in the plane of the ring, perpendicular to b, while molecular axis c is normal to the molecular plane. Polarization in the c direction need not be considered, as we have already assumed all polarization occurs in the plane of the ring. Angle a is defined as half the dihedral angle between the two symmetry related planes. Thus, the angles b makes with X, Y and Z are 0°, 90° and 90°, respectively, while the angles a makes with X, Y and Z are 90°, a, and 90° + a, respectively. The orientation of the molecular plane in point group 4 is determined in much the same way, this time with the Z-axis defined as the four-fold axis of rotation. Axis b is defined as the line of intersection between the molecular plane and the X Y plane, coinciding with crystal reference axis X. Axis a is in the molecular plane, perpendicular to b. In this case, b makes the angles 0°, 90°, and 90° with X, Y and Z, respectively, while a makes the angles 90°, 90° + a, and a, with X, Y and Z, respectively. For point group 222, a second angle is required to describe fully the orientation of the molecular plane in the crystal reference frame. The crystal frame is chosen to coincide with the conventional crystallographic axes. In this case, angle a is defined as 90 half the dihedral angle between the molecular planes related by the Z two-fold axis. Looking down the Z-axis, as shown in Figure 4.5, we define a new angle, </>. This angle is defined as that between the molecular plane and the X Y crystal plane. Molecular axis b is defined as this line, thus <p is the angle between b and X . Molecular axis a is, as always, perpendicular to b, in the plane of the aromatic ring. Figure 4.5 The axis system describing angle <p for point group 222. Points 1 and 2 represent equivalent molecules related by the Z two-fold axis of rotation. Adapted from ref. [129] Now that the crystal reference frame has been set, the different bim tensors can be determined. From equations (3.3) and (3.4) we can see that, b1JK = \lZ I cos(/,i(s))cos(/,y(s))cos(^,fc(s))P^ (4.1) ijks=\ where the cosine terms represent the projection of molecular axes i, j and k(= a, b and c) onto the crystal reference axes I, J and K(=X, Y and Z), and n is the number of symmetry X 91 related molecules in the unit cell. With PNA-type molecules the calculation was greatly simplified by simply assuming that (3^ was the only non-zero element. In the case of D N A analogs there are eight possible py* contributors to each bim element. This adds to the complexity of the analysis, but fortunately many of these bjjx elements have cosine terms with cos (90°) and thus are zero. For point group 2, equation (4.1) yields the following four non-zero bux elements. bm = cos 3a p a a a (4-2) byxx = cos a $abb (4'3^ byzz = cos OL sin 2a % a a bxYZ = -cos a sin a $baa (4-5) For point group 4, equation (4.1) yields two bux elements. bzzz = cos 3a p a f l f l bzxx = cos a(sin 2a p a f l a + p a M)/2 For point group 222, equation (4.1) yields only one bjjx element. bxrz = sin 2<|> cos a(%bb -sin 2a p a a a) - cos 2<|> sin 2a $baa (4.8) (4.6) (4.7) 92 Equations (4.2)-(4.8) illustrate how complex the analysis becomes upon addition of a third substituent to the aromatic ring. It also illustrates, however, that the SHG can have contributions from more than one bim component. For example, consider a D N A analog crystallizing in point group 2. If a were close to 0°, according to equations (4.2)-(4.5) one would still expect some SHG to be observed even though both byzz and bxvz (each proportional to sin a) approach zero, because the susceptibility tensor byxx (proportional to cos a) is non-zero. 4.1.3. Orientation of the molecular reference frame As was referred to in section 4.1.1., three axis systems were defined to describe the orientation of the molecular plane in the crystal. The (XYZ) system has already been related to the (abc) system by angles a and <|), now the (abc) system can be related to the molecular (xyz) system by defining a new angle, 6. Now that axis b has been defined, 9 is the angle that rotates b onto x, as shown in Figure 4.6, while the angle between y and b is 90° + e. Figure 4.6 Rotation of the {abc) reference axis onto the molecular (xyz) axis system. 93 Just as a vector in the a-direction (in Figure 4.6) can be said to consist of contributions from both the x- and y-directed vectors, the pp elements where i, j, and k are in the (abc) axis system must contain contribution from the various s listed in Table 4.1. The transformation from the (abc) system to the (xyz) system gives: P a a a = cos39 fiyyy + sin30 p * ^ + 3cos6 sin"9 P ^ + 3sin 9 cos26 p w (4.9) $abb = cos0 sin20 P w + sinG cos29 p ^ + (cos30 - 2cos0 sin29) $ y x x + (sin39 - 2sin0 cos29) p w (4.10) Pfc«a = -sin9 cos29 $yyy + cos9 sin29 p x « + (-sin39 -2sin9 cos29) $ y x x + (cos39 - 2cos9 sin29) % y (4.11) $ b b b = -sin39 $yyy + cos39 p ^ - 3sin9 cos29 $ y x x + 3cos9 sin29 $ x y y (4.12) Clearly, the expressions above are complicated and reflect the contributions from the different quadratic-hyperpolarizabilities present as a result of the potential for polarization throughout the aromatic plane, instead of simply along one charge-transfer axis. Their relationship to the PNA axis system described in Chapter 3 can be displayed by a simple example. Consider an orientation where molecular reference axis b coincides with x in the molecular plane (i.e., 9 = 0°). In this case equations (4.9)-(4.12) are reduced to p a a a = $ y y y , $ b b b = p ^ , and $ a b b = § b a a = 0. Substitution of these expressions into equations (4.2)-(4.5) for a system in point group 2 yields, 94 bYYY = COS 3 a fiyyy byxx=0 byzz= cosa sin 2a $ y y y bxrz = 0 These expressions are analogous to the expressions derived for P N A analogs in point group 2, but reflect the orientation of the molecular plane rather than the charge-transfer axis. Now that the expressions for buK have been derived, it should be possible to apply the information from a crystal structure of a D N A analog to equations (4.2)-(4.12) to determine the magnitude of the various second-order macroscopic nonlinearity tensors. 4.2. General synthesis A series of six optically pure salts containing the 2,4-dinitroaniline (DNA) chromophore was prepared by coupling the acid 2,4-dinitrophenylglycine (2) to the six chiral amines described in the previous chapter. The syntheses of these salts were carried out via the same procedures (Schemes 3.2 and 3.3) as outlined in Chapter 3. A l l the materials prepared from free amines (i.e., pseudoephedrine, prolinol, proline ?-butyl ester and prolinamide) resulted in 1:1 salts, while both materials prepared from protected amines (i.e., the hydrochloride salts of proline methyl ester and proline benzyl ester) resulted in 2:1 acid/amine complexes (Table 4.2) 95 Table 4.2 Glossary of materials described in Chapter 4. acid / chiral auxiliary name / shorthand 0 2 0 2 N OH (2) 2,4-dinitrophenylglycine O f 1 * NH C H 3 o NH C H 2 O H NH NH , C H 3 JCH2 pseudoephedrine salt 2.eph proline f-butyl ester salt 2.pro-but prolinol salt 2.pro-ol prolinamide salt 2.pro-amide proline methyl ester complex 2.pro-meth proline benzyl ester complex 2.pro-benz 96 4.3. X-ray structural analyses Single crystals suitable for X-ray analysis were grown for acid (2) as were each of the six salt/complexes. The parent acid crystallized in space group P2i/c and is therefore SHG-inactive (Figure 4.3). Once again, the optically pure counterion ensured that each salt or complex crystallized in a non-centrosymmetric space group. Three materials crystallized in space group P2\ (2.pro-but, 2.pro-ol and 2.pro-meth) while there was one salt or complex in each of PI , P2{2{L\ and PA (2.eph, 2.pro-benz and 2.pro-amide, respectively). None of the structures contained any significant structural disorder other than the disorder found by the pyrrolidine ring adopting two conformations, however, the 2.pro-amide structure included solvent (both MeOH and EtOH) in the lattice. Neither the disorder nor the presence of solvent is expected to influence the N L O properties of these materials. Complete crystallographic data for each salt and complex appear in Chapter 8. 97 Figure 4.7 ORTEP packing diagram of acid (2) (50% probability ellipsoids). 4.4. Estimation of second-order nonlinear susceptibilities Using the axis conventions described in Figures 4.4, 4.5 and 4.6, angles a, <|> and 6 were determined (Table 4.3) and the expressions for the pertinent non-zero bux elements were determined. The strategy used to determine these elements was carried out in two or three steps. First, the contributions from the quadratic-hyperpolarizability terms in the xyz axis system (i.e., p y j t, where i,j and k = x or y) to (3^, $abb and $ b a a were determined based on angle 0. Examination of equations (4.2)-(4.8) shows that $ b b b is not a factor in any of the non-zero bIJK elements and therefore was not determined. Next, the pertinent bUK tensors for each material were determined based on angles a (and § in the case of 98 point group 222) using equations (4.2)-(4.8) and the expressions derived for % a a , $ a b b and $ b a a . Last, if there were more than one NLO chromophore in the asymmetric unit, the appropriate bux tensor elements were determined separately, then combined, as they were in certain instances in Chapter 3. Table 4.3 Space group, chromophore density (AO and orientational parameters (a, if and 9) for the six salts made from (2). acid/salt space group N(x 10' 3/A 3) < x ( ° ) a <t>(°) 0 ( ° ) (2) P2x/c 4.19 N / A b N/A 2.pro-but P2i 1.98 39.5, 40.7 N/A -8.4, 1.0 2.pro-ol P2i 2.53 1.9, 2.6 N/A 15.6, 164.8 2.pro-meth P2X 2.57 13.6, 16.3 N/A -1.5, 183.7 2.pro-amide PA 2.30 44.1 N/A 60.0 2.pro-benz P2i2,2i 2.98 4.7, 2.7 87.0, 72.4 -18.3, 191.3 2.eph PI 2.05 N/A N/A N/A a Entries with more than one angle correspond to structures containing more than one molecule per asymmetric unit. b N/A : not applicable. A few points should be noted before a discussion of the analysis is begun. First, the conditions for phase-matching apply to these systems as they did to the materials in Chapter 3, therefore it is not useful to determine values for byn (in point group 2) and bzzz (in point group 4), since they are unlikely to contribute to phase-matched SHG. Second, since the goal of this structural analysis is simply to examine the orientations of each chromophore and predict whether a particular material should be capable of 99 producing a strong SHG-intensity or not (and, of course, testing this prediction with the powder SHG measurements), it should suffice to examine the magnitude of the various bjjK elements and base the predictions on them. Estimating intensity ratios cannot be done as readily, as can be seen from the following. According to Kurtz and Perry [74], and i{2co) - {Nb^i^y ( i . i5) I(2m) Nz b2 ———(estimated) = T (2OJ ) v — / 2 , 2 *(2) I V ( 2 ) ° ( 2 ) where is the chromophore density of material i, bp2^ is the phase-matchable bim coefficient and is the intensity of the incident fundamental radiation. It was noted earlier that materials crystallizing in certain point groups have several phase-matchable bjm elements, therefore their SHG-intensity will come as a result of contributions from each of them, assuming the orientation of the crystals in the sample is random. In addition, each bUK tensor contains contributions from each of $yyy, P ^ , $yxx and P ^ . According to Table 4.1, there is some disagreement over the magnitude of these elements, therefore it is difficult to gauge what contribution each element makes to the overall susceptibility. This was not the case for the P N A systems encountered in Chapter 3, where $ y y y was assumed to be the sole non-zero py* element and no direct knowledge of its magnitude was required in order to estimate ratios of SHG-intensities. 100 Since an accurate understanding of these (3,^  elements and of the relative contributions from each bux element is not possible from the powder SHG-intensities, the analyses in the following sections stop short of estimating SHG-intensity ratios. Instead, the various bim elements are presented in the form of, A fixXX + B fiyyy + C $yxx + D fixyy. where coefficients A, B, C, and D represent the influence of the molecular orientation. 4.5. Second-order nonlinear optical properties. Once a salt or complex was isolated it was screened for SHG-activity at 1064 nm by the Kurtz and Perry powder method. The SHG-activity of each salt was measured relative to a crystalline powder sample of urea. Details of the apparatus and the measurement technique employed are found in Chapter 7 - Experimental (SHG measurement). Of the six salts made from (2), four (2.pro-but, 2.pro-ol, 2.pro-eph and 2.pro-amide) produced SHG-intensities between 6 and 2 times that of the urea standard, while the two complexes (2.pro-meth and 2.pro-benz) both produced SHG-intensities lower than the urea standard (Table 4.4). None of the salts proved to be as efficient a producer of SHG as any of the better materials examined in Chapter 3. 101 While it was noted earlier in Chapter 3, it should be repeated that this powder technique of measuring SHG-intensities is only semi-quantitative. The measured SHG-intensities are subject to significant error due to factors such as crystal morphology and preferred particle orientations in the sample holder that are difficult to control. 102 Table 4.4 SHG results for (2) and all six salts containing the (2) chromophore. acid/salt SHG vs. urea N O 2 (2) 0 2.pro-but (2) + 1 H H 5.8 ± 1.4 2.pro-ol (2) + ^"A^.CH2OH 1 " H 3.8 ±0 .7 2.eph (2) + H 3 C C H 3 2.7 ± 0.3 2.pro-amide (2) + i H H 1.8 ± 0 . 4 2.pro-benz+ (2) + 1 " H 0.4 ±0.1 2.pro-meth + (2) + i h H 0.12 ±0 .03 Forms 2:1 acid/amine complex. 103 4.5.1. SHG results of the S-(-)-proline t-butyl ester salt of (2): 2.pro-but. The salt 2.pro-but produces the strongest SHG-intensity of the six materials examined in this chapter, with an intensity ~ 6 times that of urea. Crystallizing in space group P2\, it is almost isostructural to the same salt made from acid (1), l.pro-but (Figure 4.8). + c +c Figure 4.8 ORTEP packing diagram of 2.pro-but (50% probability ellipsoids). 104 The following bjjx values were determined from the orientational data in Table 4.3. bvxx (total) = -0.097 (3^ + 0.017 $ m + 1.472 $ y x x + 0.192 p w b¥ZZ (total) = -0.001 p ^ + 0.624 $ y y y + 0.020 p ^ - 0.117 p ^ bXYZ (total) = -0.011 p ^ - 0.062 p y y > - 0.125 $ y x x - 0.948 % y The strong contributions from p ^ in byxx, $m in byzz and p w in &XKZ appear to be responsible for the strong SHG-intensity observed from this salt. It should be noted that each of these bux elements represent the contribution from the two chromophores in the asymmetric unit. For a material crystallizing in point group 2, a = 54.7° and 6 = 0° produces a contribution of 0.385 p ^ per chromophore for byzz, whereas 2.pro-but has a contribution of 0.312 $yyy per chromophore in byzz- Thus, although not optimized for SHG, its orientation is still very favorable, and this is reflected in the fact it produces the largest SHG-intensities of the series. 4.5.2. S H G results of the S-(-)-prolinol salt of (2): 2.pro-oI. The salt 2.pro-oI produces the next strongest SHG-intensity of the six materials in this series, with an intensity approximately 4 times that of the urea standard. Like 2.pro-but, 2.pro-ol crystallizes in space group P2\ with two chromophores in the asymmetric 105 unit. In this case, however, the two para (amine-nitro) axes are oriented ~ 150° apart, as described by Figure 4.9. N 2.pro-ol Figure 4.9 The relative orientations of the two chromophores in the asymmetric unit of 2.pro-ol. The orientational data in Table 4.3 yield the following bim values, brxx (total) = -0.493 p ^ + 0.003 $ m - 0.011 $ y x x - 0.949 p w byzz (total) = 0.000 P^ - 0.001 § m + 0.000 $ y x x + 0.002 p w bxrz (total) = 0.001 p ^ + 0.019 $ y y y + 0.040 $ y x x + 0.010 p w Examination of the various bux tensors reveals that there is virtually no contribution from byzz and bxvz whatsoever, whereas byxx consists of strong components of both P^ rjr and P^y, thus this salt's moderately high SHG-intensity (relative to the other materials in this series) must result strictly from byxx-A second factor that favors 2.pro-ol for SHG over some of the other materials in this series is its chromophore density. Compared with 2.pro-but, 2.pro-oI has a 106 chromophore density -1.25 as large. The result of this is that 2.pro-ol's less than favorable orientation is partially compensated by its greater chromophore density. 4.5.3. SHG results of the S-(-)-proline methyl ester complex of (2): 2.pro-meth. The complex 2.pro-meth crystallizes in space group P2\, with two chromophores in the asymmetric unit, just like 2.pro-but and 2.pro-ol. The SHG-intensity produced by 2.pro-meth, however, is the weakest of the six materials in the series, with a value of ~0.1 relative to the urea standard. byxx (total) = -0.087 - 0.003 $ y y y + 0.024 $ y x x + 0.174 p. byzz (total) = 0.000 p ^ - 0.021 $ m - 0.001 p ^ + 0.019 p^, bxrz (total) = 0.001 p*^ - 0.023 $ m - 0.047 § y x x + 0.037 p^ The feeble SHG-intensity results both from the orientations of the chromophores in the asymmetric unit (i.e., relative to one another), and from the highly unfavorable orientation of each asymmetric unit for SHG. The two chromophores are oriented so that their para (amine-nitro) axes are almost 180° apart, as shown in Figure 4.10. 107 05 Figure 4.10 ORTEP diagram of 2.pro-meth. (50% probability ellipsoids) Examination of the bux components reveals only one susceptibility tensor with even a modest contribution from one of the quadratic-hyperpolarizability tensors, with byxx having a contribution of 0.174 (3^. Since pV^ is the smallest of the non-zero py* tensors (according to both the Oudar [82] and Dirk studies [81]), it is not surprising that 2.pro-meth produces very little SHG. 4.5.4. SHG results of the S-(-)-prolinamide salt of (2): 2.pro-amide. The salt 2.pro-amide crystallizes in space group PA and produces an SHG-intensity approximately twice that of the urea standard. Point group 4 allows for only one non-zero bjJK component that can contribute to phase-matched SHG; bzxx-bzxx = 0.191 P^ + 0.156 P^ - 0.029 § y x x + 0.191 (3^ 108 Examination of the contributions to bzxx reveals three modest contributions from fiyyy, pxxx and In the previous discussion of the complex 2.pro-meth, it was shown that a modest contribution from P w led to little or no SHG-intensity, therefore it seems reasonable that this should be the same for 2.pro-amide, and thus any SHG-intensity must be the result of the contributions from ^ y y y and P.^  only. In the case of both 2.pro-but and 2.pro-ol (the two materials with the largest SHG-intensities) their contributions to byzz from $yyy (2.pro-but) and to byxx from (2.pro-ol) were larger than those in 2.pro-amide, and therefore it is not surprising that 2.pro-amide's SHG-intensity is somewhat lower than both 2.pro-but and 2.pro-ol. 4.5.5. SHG results of the S-(-)-proline benzyl ester complex of (2): 2.pro-benz. The complex 2.pro-benz crystallizes in space group P2]2i2i with two chromophores in the asymmetric unit. The orientation of the two chromophores is similar to that of the other 2:1 acidVamine complex, 2.pro-meth. In this case the two chromophores are oriented with their para (amine-nitro) axes approximately 170° apart (Figure 4.11). The complex is only feebly SHG-active, with an SHG-intensity of approximately 0.4 relative to the urea standard. 109 OS Figure 4.11 ORTEP diagram of 2.pro-benz. (50% probability ellipsoids) Examination of 2.pro-benz's lone non-zero biJK tensor, bxrz, reveals modest contributions from both P ^ and $ y x x. bxrz (total) = -0.122 p ^ + 0.048 p ^ - 0.313 p > x c - 0.086 p; These contributions are responsible for what little SHG-intensity is produced, along with (by far) the largest chromophore density of any of the materials in this series. 110 4.5.6. SHG results of the (IS, 2S) - (+) - pseudoephedrine salt of (2): 2.eph. The discussion of 2.eph was kept for last because its crystal packing is unique in that it crystallizes in space group PI , with two chromophores in the asymmetric unit, and therefore requires a different approach to determining the bulk second-order nonlinearities. Since there are no symmetry elements about which the aromatic plane must be oriented, the simplest means of describing the chromophore orientation relative to some crystal reference axis system is to have the crystal axis (XYZ) coincide with the molecular reference axis (xyz). Thus, for one chromophore, byYY = fiyyy bxxx ~ PXM byXX = fiyxx bxYY = fixyy Since phase-matched SHG is unlikely from byYY or bxxx, any significant SHG-intensity must be derived from byxx and bxYY- In the case of 2.eph, with the two chromophores in the asymmetric unit, they must share a common crystal reference axis that coincides with the molecular (xyz) axes sets of one the chromophores, then two angles, 61 and 62 are defined that relate the orientation of the second molecular y-axis with respect to Y , and the second *-axis with respect X , as shown in Figure 4.12. (4.13) (4.14) (4.15) (4.16) i l l Figure 4.12 The axis system defining angles 0] and 82 for space group PI. In the case of 2.eph, 9i and 02 are 173.4° and 6.6°, respectively. Using equation (4.1) to determine the contributions from p ^ , p ^ , p ^ and p w to byxx and bxrr results in, byxx (total) = -0.0133 p ^ + 0.133 p ^ + 0.020 p y x t + 0.002 p w and, bxvY (total) = 0.133 p ^ + 0.013 p ^ + 0.002 p y x x + 1.980 P ^ Thus, the SHG-intensity produced by 2.eph (2.7 times that of urea) must result from the small contributions from P ^ (in bxw) and P ^ (in byxx) and the large contribution from p w to bXyy, all other contributions being negligibly small. It is interesting to note that 2.eph produces a stronger SHG-intensity than 2.pro-amide, despite the fact that both contributions from P ^ and P ^ are smaller, as is the chromophore density, thus it is possible that a significant fraction of the SHG-intensity is 112 derived from pV^, even though it is likely to be much smaller in magnitude than $ y y y (or fyxxx, according to Dirk et al.). 4.6. Phase-matching results. Once again, where possible, those salts displaying SHG-activity greater than urea were tested for phase-matchability. The SHG-intensity for a material was measured as a function of particle size and plotted. The results for 2.pro-but, 2.pro-oI and 2.eph are shown in Figure 4.13. The phase-matchability of 2.pro-amide was not measured since there was insufficient crystalline material to provide a large enough sample in each of the particle ranges. If anything, the results show a relatively constant SHG-intensity throughout the different particle-size ranges (if one takes into account the error bars associated with each data point). The lack of any drastic decrease in SHG-intensity (i.e., down to zero intensity) suggest that each of the three materials tested are indeed phase matchable. 113 1 1 1 1 1 <125 125-149 149-177 177-250 >250 particle size (um) Figure 4.13 Change in SHG-intensity with particle size for 2.pro-but, 2.pro-ol, and 2.eph 114 4.7. Discussion As with the results from Chapter 3, the use of the ionic chiral auxiliary approach, has produced materials capable of SHG from a previously SHG-inactive precursor. Four of the six materials prepared in this series have SHG-intensities greater than the urea standard, although none approach the SHG-intensity produced by NPP, or even the intensities produced by the better salts from acid (1), examined in Chapter 3. An attempt has been made to rationalize the relative SHG-intensities produced (or not produced, as the case may be) by these materials by relating the orientations of the chromophores in the crystal lattice to their crystalline second-order nonlinearity per molecule. It is evident from the expressions derived for the crystalline nonlinearity that the chromophores in those materials producing very little SHG are very unfavorably aligned for SHG. It should be noted that both of the feebly SHG-active materials (2.pro-meth and 2.pro-benz) were materials that formed 2:1 acid/amine complexes and were prepared from protected amines (i.e., the amine was originally in the form of a hydrochloride salt), thus an extra preparative step was needed to produce the free amine before it was coupled to the NLO acid (2). It is possible that in this extra step some amine was lost, or conversion to the free amine was incomplete, and this in some way led to the production of the complex rather than the salt. Whatever the reason, the chromophores in these complexes (including the 2:1 complex, l.pro-meth, from Chapter 3) are each aligned in an anti-parallel alignment, in order to maximize the interaction 115 between the two acid groups and this alignment is unfavorable for SHG-production. The details of the crystal packing are found in Chapter 8 - Experimental (Crystallographic). A second point to note is that none of the measured SHG-intensities in this chapter approached those of the best materials made from acid (1) in Chapter 3. The reasons for this appear to be two-fold. First, according to the study carried out by Dirk et al. [81], P N A analogs have a significantly greater $ y y y value than do D N A analogs. Second, a comparison of chromophore densities reveals lower values for materials with acid (2) than for the analogous material with acid (1). Thus, for a salt like 2.pro-but, with both of these factors working against it, its measured SHG-intensity is only roughly half that of l.pro-but, even though they have very similar crystal structures. 116 Chapter 5 - Doubly chromophoric salts: NLO acids coupled to NLO amines - Results and discussion. 5.1. Introduction. In Chapters 3 and 4 it was shown that the chiral ionic auxiliary method of salt formation ensured a non-centrosymmetric crystallization of the product. In many instances, even though both parent acids (1) and (2) were SHG-inactive, the optically pure salt produced significant SHG-intensity. The counterion, however, did not contribute to the overall molecular hyperpolarizability of the material and thus, even for those structures with near-ideal chromophore orientations, only served to decrease the chromophore density, limiting the salt's potential for SHG-production. One potential solution was to include in the counterion a chromophore that could contribute to the molecular hyperpolarizability, and thus produce salts where both the anion and cation had the capacity for SHG. In light of the structural survey carried out in Chapter 2, where it was shown that achiral materials containing the p-nitroaniline or the 2,4-dinitroaniline chromophore tend to crystallize in centrosymmetric space groups, it was of interest to see if any of these doubly chromophoric salts would crystallize non-centrosymmetrically. If any did, the expected increase in chromophore density might then translate into greater SHG-intensities, depending on the individual chromophore orientations. Since the materials investigated in this chapter are all achiral there was nothing to ensure the salts would crystallize non-centrosymmetrically. 117 5.2. General synthesis. Four salts were prepared by coupling an NLO-acid containing either p-nitrophenylglycine (1) or 2,4-dinitrophenylglycine (2) to one of two NLO-amines. The preparation of (1) is outlined in Section 3.2. and its characterization is outlined in detail in Chapter 6 - Experimental (Organic Synthesis). Acid (2) was used as purchased without further purification. The amines were prepared by Heather Peters, a summer undergraduate student, by way of a substitution reaction between either p-chloronitrobenzene or 2-chloro-5-nitropyridine and A/-methylpiperazine to produce l-(p-nitrophenyl)-4-methylpiperazine, (3), and l-methyl-4-(4-nitro-2-pyridyl)-piperazine, (4), (Scheme 5.1). The molecular hyperpolarizabilities of the p-nitroaniline and 2,4-dinitroaniline chromophores have been discussed previously in Chapters 3 and 4. The calculated molecular hyperpolarizability of l-amino-4-nitropyridines such as (4) are similar to that of p-nitroaniline.[81] Scheme 5.1 C h N - ^ f \)—CI + r / V - C H a 0 2 N — / ~ Y - i / V - C H a + HC1 \ / reflux \ = v / \ / (3) X = CH (4) X = N The salts were prepared by dissolving equimolar amounts of acid and amine in a minimum of acetone, followed by the addition of a large volume of diethyl ether to 118 initiate precipitation of the salt. If precipitation did not occur, evaporation of the solvent afforded the salt precipitate. In all cases the crude salt was produced in high yield (Scheme 5.2). A list of each structure and shorthand notation appears in Table 5.1 Complete synthetic and characterization details appear in Chapter 6 - Experimental (Organic Synthesis). Scheme 5.2 X = C H , N Y=HN02 Lnitrophen X = C H , Y = H 1. nitropyr X = N, Y = H 2. nitrophen X = CH, Y = N 0 2 2.nitropyr X = N, Y = N Q 2 119 Table 5.1 Glossary of materials described in Chapter 5. Acid/amine/salt name/shorthand 0 2 N H / \ C H 2 - c o 2 H N 0 2 0 2 N H 3 C H 3C—f/ \ ^ \ N 0 2 0 2 N \ s CH2-CO2 N02 O 2 N 02N NOi \ = / CH2-COj€ CH2-C0f. H * V ~ \ _ / ~ \ _ K9 Z 1 — \ / — N ° 2 HjC 1/® \)—i v 0 2 N N 0 2 €02* ^f{a~^i—^"^y—N O j p-nitrophenylglycine (1) 2,4-dinitrophenylglycine (2) l-(p-nitrophenyl)-4-methylpiperazine (3) l-methyl-4-(4-nitro-2-pyridyl)-piperazine (4) l-(p-nitrophenyl)-4-methylpiperazinium salt of (1) l.nitrophen l-(p-nitrophenyl)-4-methylpiperazinium salt of (2) 2.nitrophen l-methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (1) l.nitropyr 1 -methy l-4-(4-nitro-2-py ridy 1)-piperazinium salt of (2) 2.nitropyr 120 5.3. X-ray structural analyses. Single crystals suitable for X-ray structural analysis were grown and the structures of the two parent acids, the two amines and of the four salts were determined. The structures of acids (1) and (2) are described elsewhere (Sections 8.2. and 8.8., respectively). Of the eight materials reported in this chapter, only one, amine (3), crystallizes in a non-centrosymmetric space group (Pna2i). The parent acids (1) and (2) and the other parent amine, (4), crystallize in P I , P2i/c and P2i/c respectively, while three of the salts, l.nitropyr, 2.nitrophen and 2.nitropyr, crystallize in P I . The remaining salt, l.nitrophen, crystallizes in C2/c. None of the materials is optically active and therefore obliged to crystallize in a non-centrosymmetric space group. This scarcity of non-centrosymmetric structures, while disappointing, is not unexpected, particularly in light of the results reported in Chapter 2. Complete crystallographic data and detailed structural descriptions for each acid, amine and salt are found in Chapter 8 - Experimental (Crystallographic). 5.4. SHG results of l-(/;-nitrophenyl)-4-methylpiperazine (3). Amine (3) produces an SHG intensity of -0.1 relative to urea. Despite the fact that it crystallizes in space group Pna2i, one of the better crystal classes for SHG, the orientation of the NLO chromophore is extremely unfavorable for SHG. According to the 121 model presented by Zyss and Oudar, there are two non-zero macroscopic nonlinear susceptibility tensors for PNA-type materials crystallizing in point group mm2, [129] given by: bzYY = (sin2\j/ cos6 sin29) (3^ (4.2) and bzxx = (cos2\j/ cosG sin20) [3yyy (4.3) where \|/ and 9 are as defined in Figure 3.3 (reproduced here for the reader's convenience). The maximum possible values of bZYY and bzxx are therefore the same as for point group 2; 0.385 Pyyy, where 9 = 54.7° and \\f = 90° and 0°, respectively. z =2 Figure 3.3 The crystal reference frame used to define the charge-transfer axis for PNA analogs crystallizing in point groups mm2 or 222. Crystal reference axes X, Y and Z coincide with unit cell axes a, b, and c, respectively. In the case of amine (3), the charge-transfer axis of the molecule lies almost in the ab plane of the unit cell (Figure 5.1), with 9 = 89.97° and Y|/ = 54.2°. Thus, rotation about the two-fold c-axis places a second symmetry-related molecule in an orientation almost 122 directly anti-parallel to the first. The resulting values of bzn and bzxx are exceedingly small, suggesting that little or no SHG should be expected. Figure 5.1 ORTEP packing stereodiagram of amine (3) (50% probability ellipsoids). 5.4. Discussion. The salts investigated in this section were designed to improve upon the salts with chiral auxiliaries (Chapters 3 and 4) by including an NLO chromophore in both the anion and the cation. In each of the preceding two chapters the SHG response of even the most favorably oriented material was limited by a low chromophore density, since the chiral ionic auxiliary contributes negligibly to the molecular hyperpolarizability. By allowing the counterion to contribute to the molecular hyperpolarizability, it was hoped that one or 123 more of the salts might achieve an asymmetric packing arrangement and take advantage of the increased chromophore density to produce a substantial second-harmonic response. Unfortunately, all four of the salts crystallized centrosymmetrically and were therefore SHG-inactive, as were three of the starting materials. The lone non-centrosymmetric material, (3), is oriented so as to be virtually SHG-inactive. While these results were disappointing, they do reinforce the point that highly polar materials are likely to crystallize centrosymmetrically, and that some form of intervention is required, be it by the addition of an optically active component to the material or by shielding neighboring chromophores with bulky, non-polar counterions, in order to induce an asymmetric crystal packing arrangement. The increased chromophore densities found for each structure (relative to those found in the materials discussed in Chapters 3 and 4) may even have encouraged centrosymmetric or anti-parallel packing, as every anion and cation is highly polar, and thus neighboring moieties within the unit cell are likely to orient themselves so as to maximize their mutual dipolar attraction. 124 Table 5.1 Space group and chromophore density (AO for acids (1) and (2), (3) and (4) and the four salts. material space group JV/(10"3/A3) (1) PI 4.75 (2) P2,/c 4.19 (3) />na2, 3.50 (4) P2,/c 3.64 l.nitrophen (1) + (3) C2/c 4.11 l.nitropyr (1) + (4) PI 4.13 2.nitrophen (2)+ (3) PI 3.89 2.nitropyr (2)+ (4) PI 3.92 125 Chapter 6 - Experimental (Organic Synthesis) 6.1. General Experimental Infrared (IR) Spectra Infrared spectra were recorded on a Perkin-Elmer 1710 Fourier transform infrared spectrometer. A l l samples were prepared by grinding a small amount of material (~5 mg) into ~ 200 mg of KBr. The powdered mixture was then compressed to 17000 psi in a Perkin-Elmer evacuable die (186-0002) with a Carver laboratory press (Model B). Absorption bands characteristic of amines, carboxylic acids, carboxylates and esters are listed in reciprocal centimeters (cm"1). The abbreviations used in describing the relative strength of the absorption bands are as follows: s = strong, m = medium, w = weak. Mass Spectra (MS) Low resolution electron impact mass spectra (EIMS) were obtained for all acids and amines using a Kratos MS 50 mass spectrometer with 70 eV electron bombardment. Liquid secondary-ion mass spectra (LSIMS), both positive and negative, were obtained for all salts using an AEI MS 9 mass spectrometer. Each of these methods was performed by the mass spectrometry laboratory of the U B C Chemistry Department. The mass to charge ratio (m/e) followed by the relative abundance in parentheses is given for the most abundant fragments in each spectrum. 126 Ultraviolet/Visible (UV/VIS) Spectra Spectra were recorded on a Perkin-Elmer Lambda 4B UV/VIS spectrophotometer using a 1 cm quartz cell. HPLC grade (BDH) solvent was used without further purification. Wavelengths (k) in nanometers (nm) are reported and the extinction coefficients (e, M " 1 cm'1) are given in brackets. Nuclear Magnetic Resonance (NMR) Spectra Proton nuclear magnetic resonance (*H NMR) spectra were recorded on a Briiker AC-200 (200 MHz) or a Briiker WH-400 (400 MHz) spectrometer in either CDC1 3 , C D 3 O D , acetone-d6 or DMSO-d6. Chemical shifts (8) are given in parts per million (ppm) with the multiplicity, number of protons, and assignments in parentheses following the position. The abbreviations used in describing the signal multiplicity are as follows: s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet. Microanalysis Carbon, hydrogen and nitrogen elemental analyses were performed by Mr. P. Borda of the microanalysis lab in the U B C Chemistry Department. Chromatography A Hewlett Packard 5890A gas chromatograph fitted with a flame ionization detector and a Hewlett Packard 3392 A integrator was employed for gas liquid chromatography analysis. Samples dissolved in acetone were injected (2 uX) into a 15 m 127 x 0.25 mm DB1 column (J & W Scientific Inc.) with helium as a gas carrier. Column head pressure was maintained at 15 psi. Solvents and Reagents A l l solvents and reagents were used as supplied by either Aldrich, B D H , Fischer Scientific or Sigma. Melting Point Determinations Melting points (MP) were determined on a DSC 91 OS Differential Scanning Calorimeter connected to the Thermal Analyst 2000 System (TA Instruments). Melting point ranges are reported between the onset and peak of the melting endotherm. Figure 6.1 shows a typical melting endotherm. Figure 6.1 A typical DSC melting endotherm. The number to the left represents the onset melting temperature while the number to the right is the temperature at the endotherm peak. 128 6.2. Synthesis and characterization 6.2.1. Synthesis of N-p-nitrophenyi giycine (1). H 0 2 N C H 2 - C 0 2 H (1) Following the procedure of Lantz and Obellianne [149], 2.80 g of p-fluoronitrobenzene (19.8 mmol, Aldrich) was dissolved in 20 mL of ethanol. The hydrochloride salt of glycine methyl ester (2.77 g, 22.0 mmol, Sigma) and 3.99 g of NaHC03 (47.4 mmol, Aldrich) were added to a 100 mL round bottomed flask. The fluoronitrobenzene solution was added to the round bottomed flask, as well as 20 mL of H 2 0 and several boiling chips. The flask was then equipped with a reflux condenser and the mixture was refluxed overnight, after which the now orange solution was acidified with 5 mL of 1M HC1, causing the immediate precipitation of a yellow solid. The crude product was allowed to settle and was then vacuum filtered, dried in air and recrystallized from methanol to afford yellow prisms (2.15 g, 11.0 mmol, 55% yield). M P : >230 °C (decomposed) (229 °C), ref.[149] IR (KBr disc): v (cm 1) 3363 (s, N - H str), 1736 (s, C=0 str), 1289 (C-0 str I O-H def) 129 EIMS: m/e (relative intensity) 196 (M, 25.7), 151 (100), 150 (67.7), 149 (34.3), 138 (28.7), 120 (54.0) *H NMR (acetone-de, 200 MHz): 5 2.9 (broad s, 1H, NHCH 2 ) , 4.1 (d, 2H, J = 3 Hz, NHCHa), 6.6 (broad s, 1H, OH), 6.8 (d, 2H, / = 9 Hz, aromatic H), 8.1 (d, J = 9 Hz, 2H, aromatic H) ppm. UV/Vis (EtOH): Xmax = 363 nm (e = 16400 M " 1 cm"1) Anal, calculated for (1), C 8 H 8 N 2 04 : C, 48.98; H , 4.11; N , 14.28;. Found: C, 48.75; H , 4.19; N , 14.50. 6.2.2. Synthesis of the (IS, 2S)-(+)-pseudoephedrine salt of (1): l.eph. 0 2 N / \ H / N \ e C H 2 - C 0 2 C H 3 H 3 C H H O l.eph Acid (1) (81.8 mg, 0.417 mmol) was dissolved in 150 mL of diethyl ether. The amine (IS, 2S)-(+)-pseudoephedrine (67.8 mg, 0.410 mmol, Sigma) was dissolved in 20 mL of diethyl ether and added to the solution of (1). A light yellow precipitate formed immediately. The solution was stirred for 0.5 h then gravity filtered and dried in air. The crude product was recovered (120.0 mg, 0.332 mmol, 81% yield) and recrystallization from ethanol produced long needle-like crystals. MP: 171.6-178.2 °C 130 IR (KBr disc): v (cm 1) 3377 (s, N - H str.) 1605 (s, C-0 str.) -LSIMS: m/e (relative intensity) 391(2 x M - +1, 20), 195 ( M _ , 100), 179 (6.7) +LSIMS: m/e (relative intensity) 166 ( M + , 100), 148 (29) *H NMR (CD 3 OD, 400 MHz): 5 1.09 (d, 3 H , J = 7 Hz, CHCH3), 2.74 (s, 3 H , NH2CH3), 3.50 (m, 1H, CHCH 3 ) , 3.82 (s, 2H, N H C H 2 ) , 4.65 (d, 1H, J = 9 Hz, CHOH), 6.59 (d, 2H, J = 9 Hz, aromatic H), 7.42 (m, 5 H , aromatic H), 8.06 (d, 2H, J = 9 Hz, aromatic H) ppm. Anal, calculated for l.eph, C 1 8 H 2 3N30 5 : C, 59.82; H , 6.41; N , 11.63. Found: C, 59.51; H , 6.48; N , 11.66. 6.2.3. Synthesis of the S-(-)-proline t-butyl ester salt of (1): l.pro-but. 0 2 N H \ e CH2-CO2 O FH3 \\ r ' . . .nCH 3 v^-o CII, l.pro-but Acid (1) (52.1 mg, 0.266 mmol) was dissolved in 200 mL of diethyl ether with stirring. Once the solid was completely dissolved, 50 \iL S-(-)-proline t-butyl ester (50 mg, 0.292 mmol, Sigma) was added to the ether solution and stirred. The solution was concentrated to approximately 25 mL by rotary evaporation and was left to stand, stoppered, overnight. A yellow precipitate was gravity filtered, dried in air, then 131 recrystallized from an acetone/hexane mixture as long needles (72.3 mg, 0.197 mmol, 74% yield). M P : 115.9-122.3 °C IR (KBr disc): v (cm 1) 3289 (s, N - H str.), 1726 (s, C=0 str.), 1602 (s, C-0 str.) -LSIMS: m/e (relative intensity) 195 (100, M") +LSIMS: m/e (relative intensity) 172 (M + , 91), 116 (100) X H N M R (CD 3 OD, 400 MHz): 5 1.5 (s, 9 H , C(CHa) 3), 2.0-2.4 (m, 4 H , C H 2 ) , 3.35 (m, 3 H , N H 2 C H 2 + NH 2 CH), 3.78 (s, 2H, N H C H 2 ) , 6.61 (d, 2H, / = 9 Hz, aromatic H), 8.08 (d, 2H, J = 9 Hz, aromatic H) ppm. Anal , calculated for l.pro-but, C17H25N3O6: C, 55.58; H , 6.86; N , 11.44. Found: C, 55.83; H , 6.99; N , 11.62. 132 6.2.4. Synthesis of the S-(-)-proline methyl ester complex of (1): l.pro i-meth. • \ H H O \\ / C H 3 H 0 2 N N \ e / N C H 2 - C 0 2 H 0 2 C - H 2 C / \ N 0 2 l.pro-meth The hydrochloride salt of S-(-)-proline methyl ester (54.4 mg, 0.329 mmol, Sigma) and 13.2 mg of NaOH (0.330 mmol, BDH) were dissolved in approximately 10 mL of ethanol, producing a cloudy precipitate (NaCl). The solution was centrifuged for 30 minutes then added to a flask containing 66.2 mg of (1) (0.337 mmol) dissolved in approximately 150 mL of diethyl ether. The resultant bright yellow solution was rotary evaporated to near dryness producing a yellow oil. Approximately 10 mL of acetone was added to the flask, then hexane was added until the solution became faintly cloudy. Over the course of several hours a light yellow solid precipitated along the walls of the flask. Recrystallization from a supersaturated ethanol solution produced rod-like crystals (27.3 mg, 0.026 mmol, 15.5% yield). M P : two overlapping endotherms, the first with an onset temperature of 113 °C, peaking at 132.2 °C, the second peaking at 138.2 °C . IR (KBr disc): v (cm 1) 3377 (s, N - H str.), 1746 (s, C=0 str.), 1607 (s, C-0 str.) 133 -LSIMS: m/e (relative intensity) 391 (2 x M " + 1, 38), 195 (M" , 100), 179 (5.6) +LSIMS: m/e (relative intensity) 130 (M + , 100), 70 (24) *H NMR (D 20, 400 MHz): 8 2.0-2.5 (m, 4H, CHj), 3.4(m, 3H, N H 2 C H + N H 2 C H 2 ) , 3.83 (s, 4H, N H Q L J , 3.85 (s, 3H, OCH3), 6.61 (d, 4H, J = 9 Hz, aromatic H), 8.09 (d, 4H, 7 = 9 Hz, aromatic H) ppm. Anal, calculated for l.pro-meth, C 2 2 H 2 7 N 5 O i o : C, 50.67; H , 5.22; N , 13.43. Found: C, 50.63; H , 5.17; N , 13.42. 6.2.5. Synthesis of the S-(-)-prolinamide salt of (1): l.pro-amide. l.pro-amide Acid (1) (47.0 mg, 0.240 mmol) was dissolved in 125 mL of diethyl ether with stirring. The amine S-(-)-prolinamide (29.4 mg, 0.258 mmol, Aldrich) was added to the ether solution, immediately producing a bright yellow precipitate. The solution was stirred for 0.5 h, then gravity filtered and dried in air. The crude product (59.0 mg, 0.190 mmol, 79% yield) was recrystallized from an acetone/hexane mixture. MP: 166.6-172.3 °C IR (KBr disc): v (cm"1) 3285 (s, N - H str.), 1687 (s, C=0 str./N-K def.), 1600 (s, C-O str.) 134 -LSIMS: m/e (relative intensity) 391 (2 x M " + 1, 17), 195 (M ", 100), 179 (6.7) +LSIMS: m/e (relative intensity) 115 (M + , 100), 70 (22) *H NMR (CD 3 OD, 400 MHz): 6 2.0-2.5 (m, 4 H , C H 2 ) , 3.39 (m, 3 H , N H 2 C H 2 + NH 2 CH) , 3.83 (s, 2H, N H C H 2 ) , 6.61 (d, 2H, J = 9 Hz, aromatic H), 8.08 (d, 2H, J = 9 Hz, aromatic H) ppm. Anal, calculated for l.pro-amide, C i 3 H 1 8 N 4 0 5 : C, 50.32; H , 5.85; N , 18.06. Found: C, 50.16; H,5.65;N, 18.06. 6.2.6. Synthesis of the S-(-)-prolinol salt of (1): l.pro-ol. 0 2 N t W H \ e CH2-CO2 H 2 - O H H H l.pro-ol Acid (1) (97.6 mg, 0.498 mmol) was dissolved in 10 mL of acetone. Once the solid was completely dissolved, 50 | i L of S-(-)-prolinol (50 mg, 0.495 mmol, Aldrich) was added to the acetone solution. This solution was stirred briefly then concentrated to approximately 5 mL. Approximately 20 mL of diethyl ether was added to the acetone solution, immediately producing a bright yellow precipitate. The crude product was 135 gravity filtered and dried in air. Recrystallization from a 1:1 acetone/ethanol mixture produced large rectangular crystals (125 mg, 0.420 mmol, 85% yield). MP: 161.8-166.2 °C IR (KBr disc): v (cm 1) 3300 (s, N - H str.), 1612 (s, C-0 str.) -LSIMS: m/e (relative intensity) 391 (2 x M " + 1, 10), 195 (M ", 100), 179 (7.5) +LSIMS: m/e (relative intensity) 102 (M + , 100) X H NMR (acetone-d6, 200 MHz): 5 1.5-2.0 (m, 4 H , C H 2 ) , 2.5 (m, 1H, OH), 3.1 (t, 2H, J = 9 Hz, C H 2 C H 2 ) , 3.6 (m, 5 H , N H C H 2 + C H 2 ) , 6.7 (d, 2H, J = 9 Hz, aromatic H), 7.1 (t, 1H, J = 7 Hz, NHCH 2 ) , 8.0 (d, 2H, J = 9 Hz, aromatic H) ppm. Anal, calculated for l.pro-ol, C13H19N3O5: C, 52.52; H, 6.44; N , 14.13. Found: C, 52.23; H , 6.32; N , 13.96 6.2.7. Synthesis of the S-(-)-proiine benzyl ester salt of (1): l.pro-benz. l.pro-benz The hydrochloride salt of S-(-)-proline benzyl ester (120.9 mg, 0.500 mmol, Sigma) and 32.4 mg of crushed K O H (0.579 mmol, Aldrich) were dissolved in 30 mL of ethanol, producing a white solid precipitate (KC1). The solution was centrifuged for 10 min after which the liquid was decanted and added to a solution of acid (1) (95.9 mg, 136 0.489 mmol) in 20 mL of ethanol. The resultant solution was rotary evaporated to dryness leaving a bright yellow precipitate which was dried under vacuum. The crude product (180.6 mg, 0.450 mmol, 92% yield) was recrystallized from methanol as irregular prisms. MP: 120.1-130.5 °C IR (KBr disc): v (cm 1) 3277 (s, N-H str.), 1732 (s, C=0 str.), 1603 (s, C-0 str.) -LSIMS: m/e (relative intensity) 391 (2 x M ' + 1, 50), 195 (M ", 100) +LSIMS: m/e (relative intensity) 206 (M + , 100), 91 (51), 70 (24) 1 H NMR (CD 3 OD, 400 MHz): 8 2.0-2.5 (m, 4H, C H 2 ) , 3.4 (m, 2H, N H 2 C H 2 ) , 3.83 (s, 2H, N H C H 2 ) , 4.5 (t, 1H, J = 9 Hz, CH 2 CH), 5.30 (m, 2H, CHaPh), 6.61 (d, 2H, J = 9 Hz, aromatic H), 7.45 (s, 5H, aromatic H), 8.08 (d, 2H, J = 9 Hz, aromatic H) ppm. Anal, calculated for l.pro-benz, C 2oH23N 30 6: C, 59.84; H, 5.78; N , 10.47. Found: C, 59.60; H , 5.85; N , 10.54. 6.2.8. Synthesis of the (IS, 2S)-(+)-pseudoephedrine salt of (2): 2.eph. 2.eph Acid (2) (49.3 mg, 0.204 mmol, Sigma) was dissolved in 100 mL of diethyl ether with stirring. The amine (IS, 2S)-(+)-pseudoephedrine (33.8 mg, 0.205 mmol, Sigma) 137 was dissolved in 5 mL of diethyl ether and then added to the acid-containing solution, producing a yellow precipitate. The solution was stirred for 0.5 h, then gravity filtered. The clear yellow filtrate was concentrated to ~ 15 mL and allowed to sit overnight, when further precipitation occurred. The crude precipitate (70.5 mg, 0.173 mmol, 85% yield) was recrystallized from acetone. M P : 179.0-182.7 °C (decomposed) IR (KBr disc): v (cm 1) 3320 (s, N - H str.), 1630 (s, C-O str.) -LSIMS: m/e (relative intensity) 481 (2 x M " + 1, 26), 240 (M \ 100), 224 (6.7) +LSIMS: m/e (relative intensity) 166 (M + , 100), 148 (27) *H N M R (D 2 0, 400 MHz): 5 1.08 (d, 3H, J = 1 Hz, CHCH3), 2.74 (s, 3H, NCH3), 3.50 (m, 1H, CHCH 3 ) , 4.04 (s, 2H, NCFLJ, 4.65 (d, 1H, J = 3 Hz, CHPh), 6.88 (d, 1H, J = 10 Hz, aromatic H), 7.42 (s, 5H, aromatic H), 8.25 (d, 1H, J = 10 Hz, aromatic H), 9.06 (s, 1H, aromatic H) ppm. Anal , calculated for 2.eph, C18H22N4O7: C, 53.20; H , 5.46; N , 13.79. Found: C, 53.12; H , 5.51; N , 13.86 138 6.2.9. Synthesis of the S-(-)-proIine t-butyl ester salt of (2): 2.pro-but. CH 2—COV / 2 N H H H 2.pro-but Acid (2) (49.3 mg, 0.240 mmol, Sigma) was dissolved in 15 mL of acetone. 50 | i L of S-(-)-proline t-butyl ester (50 mg, 0.292 mmol, Sigma) was added to the acetone solution and stirred for 1 h. The solution was rotary evaporated to dryness, leaving a yellow precipitate along the walls of the flask. The contents of the flask were washed with diethyl ether and then gravity filtered. The crude product was recrystallized from an acetone/hexane mixture (70.0 mg, 0.170 mmol, 71% yield). MP: 203.6-207.3 °C (decomposed) IR (KBr disc): v (cm"1) 3342 (s, N - H str.), 1722 (s, C=0 str.), 1622 (s, C-O str.) -LSIMS: m/e (relative intensity) 481 (2 x M " + 1, 12), 240 (M" , 100) +LSIMS: m/e (relative intensity) 172 (M + , 80), 116 (100) *H NMR (DMSO-d 6 , 400 MHz): 8 1.42 (s, 9 H , C(CHj) 3), 1.7-2.1 (m, 4 H , C H 2 ) , 3.90 (m, 1H, CH 2 CH), 3.94 (d, 2H, J = 5 Hz, N H C H 2 ) , 7.05 (d, 1H, J = 9 Hz, aromatic H), 8.24 (dd, 1H, J} = 9 Hz, J2 = 3 Hz, aromatic H), 8.87 (d, 1H, J = 3 Hz, aromatic H), 9.23 (broad s, 1H, NH) ppm. Anal, calculated for 2.pro-but, C17H24N4O5: C, 49.51; H , 5.87; N , 13.59. Found: C, 49.50; H , 5.95; N , 13.67 139 6.2.10. Synthesis of the S-(-)-proline methyl ester complex of (2): 2.pro-meth. H H N 0 2 0 2 N 0 2 N \ © / C H 2 - C 0 2 H 0 2 C - H 2 C H H N 0 2 2.pro-meth The hydrochloride salt of S-(-)-proline methyl ester (54.3 mg, 0.328 mmol, Sigma) and 12.0 mg of NaOH (0.301 mmol, BDH) were dissolved in 10 mL of ethanol, producing a white precipitate (NaCl). The solution was centrifuged for 30 min and then decanted into a flask containing 79.2 mg of acid (2) (0.328 mmol, Sigma) dissolved in a minimum of ethanol. The resultant solution was rotary evaporated to dryness, leaving a yellow precipitate. The precipitate was gravity filtered and washed with diethyl ether. The filtrate was then collected and rotary evaporated to dryness, leaving behind a yellow oil. This oil was dissolved in approximately 10 mL of acetone, then hexane was added until the solution became faintly cloudy and a yellow precipitate began to grow along the walls of the flask. The crude product (49.2 mg, 0.081 mmol, 49.3% yield) was combined and recrystallized from an acetone/hexane mixture, producing a small amount of X-ray quality crystals. Integration of the N M R spectrum of the crude product indicated a 2:1 140 aciaVamine stoichiometry. X-ray structural analysis unambiguously determined the acid/amine ratio in the crystals to be 2:1 (Chapter 8 - Experimental (Crystallographic)). MP: 118.8-138.5 °C (decomposed) IR (KBr disc): v (cm"1) 3355 (s, N - H str.), 1716 (s, C=0 str.), 1615 (s, C-O str.) -LSIMS: m/e (relative intensity) 481 (2 x M " + 1, 20), 240 (M \ 100) +LSIMS: m/e (relative intensity) 130 (M + , 100) *H NMR (CD 3 OD, 400 MHz): 8 2.0-2.5 (m, 4 H , CHg), 3.30 (s, 3 H , O C H 3 ) , 3.35-3.45 (m, 2H, C H 2 ) , 4.11 (s, 4 H , N C H 2 ) , 4.39 (m, 1H, CH 2 CH), 7.01 (d, 2H, J = 10 Hz, aromatic H), 8.29 (dd, 2H, J, = 10 Hz, J2 = 3 Hz, aromatic H), 9.05 (d, 2H, J = 3 Hz, aromatic H) ppm. 6.2.11. Synthesis of the S-(-)-proline benzyl ester complex of (2): 2.pro-benz. The hydrochloride salt of S-(-)-proline benzyl ester (48.0 mg, 0.199 mmol, Sigma) and 18.6 mg of NaHCC<3 (0.221 mmol, Aldrich) were dissolved in 2 mL of H 2 O . \ e / CH2-CO2 H 0 2 C - H 2 C 2.pro-benz 141 Approximately 30 mL of acetone were added to the solution producing a white precipitate (NaCl). The solution was dried over MgS04, then gravity filtered into a flask containing 45.4 mg of acid (2) (0.188 mmol, Sigma) dissolved in 10 mL acetone. The resultant solution was rotary evaporated to dryness, leaving a yellow oil along the walls of the flask. Diethyl ether was added to the flask (50 mL), after which small clusters of yellow product precipitated along the walls. The crude product was recrystallized from a 1:1 methanol/H20 solution (28.9 mg, 0.042 mmol, 45% yield). M P : 159.4-163.7 °C (decomposed) IR (KBr disc): v (cm 1) 3327 (s, N - H str.), 1737 (s, C=0 str.), 1627 (s, C -0 str.) -LSIMS: m/e (relative intensity) 481 (2 x M " + 1, 18), 240 (M \ 100) +LSIMS: m/e (relative intensity) 206 (M + , 100) *H N M R (DMSO-d 6 , 400 MHz): 5 1.7-2.2 (m, 4H, CfLJ, 4.11 (d, 4H, / = 5 Hz, NHCH 2 ) , 5.18 (m, 2H, CHaPh), 7.07 (d, 2H, J = 10 Hz, aromatic H), 7.38 (d, 5H, J = 4 Hz, aromatic H), 8.25 (dd, 2H, Jj = 10 Hz, J2 = 3 Hz, aromatic H), 8.87 (d, 2H, J = 3 Hz, aromatic H), 9.12 (broad t, 2H, J = 4 Hz, NHCH 2 ) ppm. Anal , calculated for 2.pro-benz, C 2 o H 2 2 N 4 0 8 : C, 48.91; H , 4.25; N , 14.26. Found: C, 48.89; H, 4.18; N , 14.21 142 6.2.12. Synthesis of the S-(-)-prolinol salt of (2): 2.pro-ol. 0 2 N = \ C H 2 - C O 2 0 N \ y \ H H H , C H 2 ^ O H 2.pro-ol Acid (2) (60.0 mg, 0.249 mmol, Sigma) was dissolved in 10 mL of acetone. 50 \iL S-(-)-prolinol (50 mg, 0.495 mmol, Aldrich) was added to the acetone solution which was then concentrated to ~ 3 mL. Approximately 20 mL of diethyl ether was added to the acetone solution producing a yellow precipitate. The crude product (61.7 mg, 0.179 mmol, 72% yield) was gravity filtered and dried in air. M P : 152.6-158.7 °C (decomposed) IR (KBr disc): v (cm"1) 3310 (s, N - H str.), 1606 (s, C-0 str.) -LSIMS: m/e (relative intensity) 481 (2 x M + 1, 11), 240 (M ", 100) +LSIMS: m/e (relative intensity) 102 (M + , 100) *H N M R (CD 3 OD, 400 MHz): 5 1.7-2.2 (m, 4H, C H 2 ) , 3.31 (t, 2H, J = 8 Hz, C H C H 2 ) , 3.6-3.9 (m, 3H, N H 2 C H + N H 2 C H 2 ) , 4.03 (s, 2H, NHCH 2 ) , 6.86 (d, 1H, J = 10 Hz, aromatic H), 8.23 (dd, 1H, Jj = 10 Hz, J2 = 3 Hz, aromatic H), 9.03 (d, 1H, / = 3 Hz, aromatic H) ppm. Anal , calculated for C i 3 H i 8 N 4 0 7 : C, 45.61; H, 5.30; N , 16.37. Found: C, 45.64; H , 5.31; N , 16.44 143 6.2.13. Synthesis of the S-(-)-prolinamide salt of (2): 2.pro-amide. 2.pro-amide The amine S-(-)-prolinamide (30.1 mg, 0.264 mmol, Aldrich) was dissolved in 100 mL of diethyl ether with stirring. Acid (2) (62.2 mg, 0.258 mmol, Sigma) was dissolved in 100 mL of diethyl ether. The prolinamide solution was added to the solution of (2) and stirred for 1 h, then left to stand, stoppered, overnight. A light yellow precipitate was collected by gravity filtration (86.7 mg, 0.245 mmol, 95% yield). X-ray quality crystals were grown from a 1:1 ethanol/methanol mixture. Evidence from the ! H N M R spectrum suggested that both EtOH and MeOH were trapped in the crystal lattice. Subsequent X-ray structural analysis on the same batch of crystals (Chapter 8 -Experimental (Crystallographic)) clearly determined the positions of the two solvents in the lattice, with the EtOH and MeOH populations refined to 0.25 and 0.125 equivalents, respectively. MP: loss of solvent at 110 °C and 165 °C, melting between 172.1-176.7 °C (decomposed) IR (KBr disc): v (cm 1) 3334 (s, N - H str.), 1704 (s, C=0 str.I N - H def.), 1626 (s, C-0 str.) -LSIMS: m/e (relative intensity) 481 (2 x M " + 1, 9.3), 240 (M \ 100) 224 (12.8) +LSIMS: m/e (relative intensity) 115 ( M + , 100) 144 *H N M R (D 2 0, 400 MHz): 8 1.17 (t, ~ 0.75 H , J = 1 Hz, CH2CH3.), 2.0-2.5 (m, 4H, C H 2 ) , 3.40 (m, 3H, N H 2 C H + N H 2 C H 2 ) , 3.62 (q, ~ 0.5 H , J = 7 Hz, CH2 .CH 3 ) , 4.71 (s, ~ 0.5 H , O C H 3 ) , 6.89 (d, 1H, J = 10 Hz, aromatic H), 8.26 (dd, 1H, / , = 10 Hz, J2 = 3 Hz, aromatic H), 9.09 (d, 1H, 7=3 Hz, aromatic H) ppm. Anal , calculated for 2.pro-amide, C13H17N5O7 • 1/4 C 2 H 5 O H • 1/8 C H 3 O H : C, 44.14; H , 5.16; N , 18.89. Found: C, 44.05; H, 5.20; N , 19.44 6.2.14. Synthesis of l-(p-nitrophenyl)-4-methylpiperazine (3). This compound was prepared by summer student Heather Peters following the procedure of Wagner-Jauregg and Zirngibl.[155] Ethanol was dried by distilling over CaO for six and a half hours under nitrogen, then reacted with magnesium turnings and a few drops of CCI4 to produce anhydrous ethanol. The amine 1-methylpiperazine (11.0 g, 110 mmol, Aldrich), p-chloronitrobenzene (8.7 g, 55 mmol, Aldrich) and 15 mL of anhydrous ethanol were refluxed until gas chromatography showed a constant product/reactant ratio (44 h). On standing overnight, 4.7 g (21.2 mmol) of product crystallized out of solution. The mother liquor was concentrated and another 1.0 g of product was isolated by column chromatography (silica gel, acetone eluent) A total of 5.7 g (25.8 mmol, 47% yield) was obtained. (3) M P : 102.4-106.4°C (103.5-104.5), ref. [155] 145 EIMS: m/e (relative intensity) 221 (M, 100), 150 (39.2), 71 (59.7), 70 (51.4) J H NMR (DMSO-d 6 , 200 MHz): 8 2.2 (s, 3H, CH 3 ) , 2.4 (t, 4H, CH 2 ) , 3.4 (t, 4H, CH 2 ) , 7.0 (d, 2H, aromatic H), 8.0 (d, 2H, aromatic H) UV/Vis (EtOH): Xmax 375 nm (e = 17300 M " 1 cm"1) 6.2.15. Synthesis of l-methyl-4-(4-nitro-2-pyridyl)-piperazine (4). The amine 1-methylpiperazine (5.0 g, 50.0 mmol, Aldrich), 2-chloro-5-nitropyridine (3.96 g, 5 mmol, Aldrich) and 20 mL of anhydrous ethanol were refluxed for 30 h until gas chromatography showed a constant product/reactant ratio. On cooling the product precipitated from solution and was gravity filtered and washed with cold ethanol. The filtrate was concentrated by rotary evaporation and more product was isolated by column chromatography using acetone as the eluent. A total of 3.98 g (17.9 mmol, 72% yield) of product was obtained. MP: two overlapping endotherms, the first with an onset temperature of 96 °C, peaking at 102.3 °C, the second peaking at 107.4 °C. EIMS: m/e (relative intensity) 222 (M, 33.3), 152 (29.9) 124 (34.5), 83 (55.2), 70 (100) •N (4) 146 *H NMR (CDC1 3 ) 200 MHz): 5 2.3 (s, 3H, CH 3 ) , 2.5 (t, 4H, CH 2 ) , 3.8 (t, 4H, CH 2 ) , 6.5 (d, 1H, aromatic H), 8.2 (m, 1H, aromatic H), 9.0 (d, 1H, aromatic H) UV/Vis (EtOH): 367 nm (e = 21000 M " 1 cm"1) 6.2.16. Synthesis of the l-(p-nitrophenyl)-4-methylpiperazinium salt of (1): l.nitrophen. l.nitrophen Acid (1) (19.7 mg, 0.100 mmol) and amine (3) (22.4 mg, 0.101 mmol) were dissolved with gentle heating in 5 mL of acetone. The solution was concentrated to approximately 3 mL then 70 mL of diethyl ether were added to the solution. No precipitate was apparent therefore the solution was rotary evaporated to dryness, leaving a yellow precipitate along the walls of the flask. This crude product was recrystallized from hot methanol leaving 29.6 mg of product (0.071 mmol, 71% yield). MP: 174.5-179.9 °C IR (KBr disc): v (cm"1) 3362 (m, N - H str.), 1593 (s, C-0 str.) -LSIMS: m/e (relative intensity) 195 ( M " , 100), 179 (12), 151 (20) +LSIMS: m/e (relative intensity) 222 (M + , 100), 206 (18) *H NMR (CD 3 OD, 400 MHz): 8 2.51 (s, 3H, NCH3), 2.81 (t, 4H, J = 5 Hz, C H 2 C H 2 ) , 3.54 (t, 4H, / = 5 Hz, CH 2CHa), 3.88 (s, 2H, NCELJ, 6.61 (d, 2H, / = 9.3 Hz, aromatic 147 H), 7.00 (d, 2H, J = 9.4 Hz, aromatic H), 8.04 (d, 2H, J = 9.3 Hz, aromatic H), 8.12 (d, 2H, J = 9.4 Hz, aromatic H) ppm. Anal, calculated for l.nitrophen, Ci 9 H23N 5 0 6 : C, 54.67; H , 5.55; N , 16.78. Found: C, 54.65; H , 5.48; N , 16.54 6.2.16. Synthesis of the l-methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (1): l.nitropyr. 0 2 N t W H \ e C H 2 - C O 2 H 3 C \ r ~ \ N© N N N 0 2 l.nitropyr Acid (1) (19.5 mg, 0.100 mmol) and amine (4) (22.2 mg, 0.100 mmol) were dissolved with gentle heating in 5 mL of acetone and concentrated to 3 mL by rotary evaporation. Approximately 20 mL of diethyl ether were added to the solution and within 30 minutes a fine yellow precipitate began to grow along the walls of the flask. The solution was stoppered and left to sit overnight. The precipitate was collected by gravity filtration and recrystallized from methanol (31.1 mg, 0.074 mmol, 74.3 % yield). MP: 189.1-195.2 °C IR (KBr disc): v (cm 1) 3375 (m, N - H str.), 1594 (s, C-0 str.) -LSIMS: m/e (relative intensity) 195 ( M \ 100), 151 (20) +LSIMS: m/e (relative intensity) 223 (M + , 100), 207 (21), 166 (16), 133 (32) 148 *H N M R (DMSO-de, 400 MHz): 5 2.21 (s, 3 H , NCH3), 2.40 (t, 4 H , J = 5 Hz, CH2CH2), 3.75 (t, 4 H , J = 5 Hz, C H 2 C H ; , ) , 3.95 (d, 2H, J = 6 Hz, N H C H 2 ) , 6.65 (d, 2H, J = 9.1 Hz, aromatic H), 6.95 (d, 1 H , J = 9.7 Hz, aromatic H), 7.40 (t, 1 H , J = 6 Hz, NHCH 2 ) , 8.00 (d, 2H, J = 9.2 Hz, aromatic H), 8.20 (dd, 1 H , Ji = 9.6 Hz, J2 = 3 Hz, aromatic H), 8.95 (d, 1 H , J = 3 Hz, aromatic H) ppm. Anal, calculated for l.nitropyr, C i 8 H 2 2 N 6 0 6 : C, 51.67; H , 5.30; N , 20.09. Found: C, 51.90; H , 5 . 3 5 ; N , 19.95 6.2.17. Synthesis of the l-(p-nitrophenyl)-4-methylpiperazinium salt of (2): 2.nitrophen. r ,NO 2 T 1 2.nitrophen Acid (2) (97.9 mg, 0.406 mmol, Sigma) was dissolved in 5 mL of acetone and added to approximately 100 mL of diethyl ether. Amine (3) (90.9 mg, 0.409 mmol) was dissolved in 10 mL of diethyl ether and then added to the acid-containing solution. The resultant solution was rotary evaporated to dryness, leaving a yellow precipitate along the walls of the flask. The crude product was recrystallized from hot methanol leaving a total of 107.7 mg (0.233 mmol, 57% yield). M P : 177.7-182.4 °C (decomposed) IR (KBr disc): v (cm 1) 3320 (m, N-H str.), 1623 (s, C-O str.) 149 -LSIMS: m/e (relative intensity) 240 (M \ 100), 213 (27) +LSIMS: m/e (relative intensity) 222 (M + , 100), 206 (17.8) 133 (13.3) *H N M R (CD 3 OD, 400 MHz): 5 2.70 (s, 3 H , N C H 3 ) , 3.07 (t, 4 H , J = 5 Hz, C H 2 C H 2 ) , 3.61 (t, 4 H , J = 5 Hz, C H 2 C H 2 ) , 4.06 (s, 2H, N C H 2 ) , 7.00 (d, 1H, J = 9.6 Hz, aromatic H), 7.05 (d, 2H, J = 9.5 Hz, aromatic H), 8.13 (d, 2H, J = 9.4 Hz, aromatic H), 8.28 (dd, 1H, J 1 = 9.5 Hz, J2 = 3 Hz, aromatic H), 9.04 (d, 1H, J = 3 Hz, aromatic H) ppm. Anal, calculated for 2.nitrophen, C i ^ N g O g : C, 49.35; H , 4.80; N , 18.17. Found: C, 49.54; H , 4.76; N , 17.96 6.2.18. Synthesis of the l-methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (2): 2.nitropyr. r ,NO, lr 1 2.nitropyr Acid (2) (101.3 mg, 0.420 mmol, Sigma) was dissolved in 5 mL of acetone and then added to 100 mL of diethyl ether. Amine (4) (92.8 mg, 0.418 mmol) was dissolved in 10 mL of diethyl ether and then added to the acid-containing solution. The resultant solution immediately turned cloudy and a yellow solid began to precipitate. After stirring for 30 min the precipitate was collected by gravity filtration and recrystallized from hot methanol (132 mg, 0.285 mmol, 68.2 % yield). M P : 186.2-191.2 °C (decomposed) 150 IR (KBr disc): v (cm 1) 3316 (m, N - H str.), 1624 (s, C-0 str.) -LSIMS: m/e (relative intensity) 240 ( M Y 100), 213 (39.5) +LSIMS: m/e (relative intensity) 223 (M + , 100), 207 (17.1) *H N M R (CD 3 OD, 400 MHz): 5 2.62 (s, 3H, NCH3), 2.93 (t, 4H, J = 5 Hz, C H 2 C H 2 ) , 3.93 (broad s, 4H, CH2.CH2), 4.07 (s, 2H, NCH2), 6.91 (d, 1H, J = 9.7 Hz, aromatic H), 7.00 (d, 1H, J = 9.6 Hz, aromatic H), 8.28 (m, 2H, aromatic H), 8.99 (d, 1H, / = 2.7 Hz, aromatic H), 9.05 (d, 1H, J = 2.7 Hz, aromatic H) ppm. Anal , calculated for 2.nitropyr, Cig^iNrOg: C, 46.65; H , 4.57; N , 21.16. Found: C, 46.75; H , 4.66; N , 21.09 151 Chapter 7 - Experimental (SHG measurement) 7.1. Measurement of SHG Efficiency Measurements were made using the Kurtz and Perry powder method. [74] Approximately 50 mg of material were loaded into the sample cell, which was formed between two Pyrex 25 x 75 x 1 mm microscope slides (Canlab). Two strips of masking tape with a 2 cm diameter hole cut through the centre were placed 3 cm from one end of one of the slides. The circular window was filled with a thin layer of sample (-20 u.m thick). A second microscope slide was clipped onto the first, sandwiching the sample between the slides. A Q-switched N d : Y A G laser (Quanta Ray) produced an 8 nsec, 1064 nm fundamental light pulse with an energy up to 100 mJ. A beam splitter directed a portion of this light onto a reference cell containing urea, producing a second-harmonic signal, and a portion of this 532 nm second-harmonic was focused onto a photomultiplier tube (RCA IP28). Between the urea and the photomultiplier tube were placed a sharp cut filter (Corning 527) designed to eliminate any stray visible light from the laser flash pump, and several neutral density filters (Wratten, 0.30 + 0.70) designed to attenuate the second-harmonic. The major part of the fundamental beam was directed onto a second cell containing the sample to be measured. Any second-harmonic produced was passed through a series of Wratten neutral density filters (1.0 + 0.7) then focused into a monochromator (Beckman D U Spectrophotometer, Model 2400), in order to discriminate 152 between SHG light and any stray visible and IR light. Monochromatic 532 nm light was then directed onto a second photomultiplier tube (RCA IP28) for measurement. The signals from each photomultiplier tube were measured with gated integrators and boxcar averagers (Stanford Research Systems, Model SR 250) and the output signals from each were directed through a computer interface (Stanford Research Systems, Model SR 245) and transmitted to the serial port of a personal computer for final processing. Figure 7.1. shows the optical system used, to measure the second-harmonic signal. PC Bl B2 Nd:YAG 1064 nm PMT1 K NDl BS A 1 H to MC L2 ' ND2 532 nm 532 nm L l F Figure 7.1 Experimental set-up for SHG measurements. B l , 2: boxcar averagers; BS: beamsplitter; F: sharp-cut filter; L l , 2: focusing lenses; MC: monochromator; NDl, 2: neutral density filters; PC: personal computer; PMT: photomultiplier tube; S: sample cell; U: urea reference cell. In order to measure the SHG efficiency of a given material accurately, urea was first placed in both the sample and reference cells and the relative SHG intensities were 153 measured. The relative amounts of light directed onto the two photomultiplier tubes by the same material were then used to normalize subsequent measurements of relative intensities between a given material and urea. To gauge the accuracy of our experimental set-up, the relative efficiency of an established SHG material, N-(4-nitrophenyl)-L-prolinol (NPP),[80] was measured. The frequency doubled signal was averaged over at least 600 laser pulses allowing for reproducibility to within ±10% with respect to the urea reference sample. This same measurement was recorded between 5-10 times, and the quoted value of the SHG-intensity relative to the urea standard was the average of those 5-10 measurements. Precautions were taken to avoid temperature fluctuations around the samples and photomultiplier tubes. NPP and urea easily form large crystals, which can be crushed to a powder and passed through sieves in order to isolate the desired range of particle size. Using particles within the 125-149 (im diameter range for both urea and NPP, NPP's relative SHG efficiency of 53 ± 5 was close to the relative efficiency of 60 previously reported. [80] The SHG efficiencies of the acids, amines and salts were first measured in the form of unsized powders. Single crystals large enough to be crushed into a wide range of particle sizes (i.e., from ~ 250 \im to less than 125 urn in diameter) were grown (if possible) of any material displaying significant SHG-intensity (approximately that of urea). These were then crushed and isolated on the basis of their particle size. SHG measurements were made over a series of particle size ranges in order to test for phase-matchability. The SHG efficiencies quoted hereafter, however, represent the measurements made with particles in the 125-149 um diameter range. 154 The errors associated with each measurement were determined from the following relationship; ± error = 3 X (7.1) where n is the number of measurements over which the average was calculated and a is the standard deviation of those n measurements. 155 Chapter 8 - Experimental (Crystallographic) 8.1. General Considerations 8.1.1. Data Collection A l l structures reported in this thesis were obtained using intensity measurements from a Rigaku AFC6 diffractometer equipped with a sealed tube Cu X-ray source. Typically, a crystal of appropriate dimensions and optical quality was glued to the tip of a glass fiber mounted on an AFC6 goniometer and centered in the X-ray beam at a distance of 285 mm from the detector. The detector was equipped with horizontal and vertical apertures fixed at 6.0 mm by manually insertable slits. Data collection procedures were controlled by the T E X R A Y software, supplied by Molecular Structure Corporation.[156] This software includes a collection of routines designed to carry out the data collection automatically. First, reciprocal space was systematically searched for up to 25 reflections. This working list of reflections was used to index a primitive unit cell and calculate an orientation matrix. The primitive cell was reduced and transformed to that of the highest possible symmetry. Laue symmetry, defined as the symmetry of the reciprocal lattice, was then determined for all but the triclinic cells by measuring equivalent reflections and the data collection limits were determined based on the selected Laue group and the unit cell volume. Three reflections were chosen as standards based on their intensity and spatial distribution in x (Figure 8.1 defines the four angular settings; co, 26, % and 0, measured 156 for each reflection.). Once the unit cell and orientation matrix were determined the detector was moved to the correct position to scan for a given reflection. The scan width in ft), determined from the standard reflections, is expressed as A + B tan0, where A depends on the mosaic spread of the crystal and B tan0 depends on the K 0 i - K 0 2 splitting of the source radiation. The scan speed, either 8, 16, or 32 ° min."1 in 0) was chosen based on the average intensity of the reflections in the working list. Figure 8.1 A four-circle diffractometer with the angles CO, 29, % and iff as defined. Adapted from ref. [157] Data were collected in two shells, the first with 20 < 120°, the second out to 155° in 2d . Weaker reflections (I < 40.0 a(I)) were rescanned up to 8 times and the counts accumulated to improve the counting statistics. Reflections were tagged as unobserved if I < 3.00(1). Stationary background measurements were made at the beginning and end of each scan with a scan-to-background counting time ratio of 2:1. The three standard reflections were monitored after every 200th reflection in order to correct for crystal re-orientation and decay. In cases where the deviation in any of the angular settings was 157 greater than preset deviation limits, all the reflections in the working list were re-centered and a new orientation matrix was calculated. At the end of the data collection more accurate cell dimensions were calculated using the positions of strong reflections with high 26 values. Up to 25 reflections from the data collected that satisfied the requirement Fobs > 50.0 were re-centered and used. Finally, three strong reflections with % n e a r 90° were selected for i/f-scans, which were subsequently used to correct for absorption. 8.1.2. Data Reduction The raw intensity data were then processed using the T E X S A N software provided by the Molecular Structure Corporation. [158] Intensities were corrected for background, and the standard deviations, 0(1), were calculated from the following expressions: I = C-2(b i+b 2 ) (8.1) o2(I) = [C + 4(b 1+b 2) + (pI)2] (8.2) where C is the total scan counts, bi and b 2 are the background counts on either side of the reflection, and p is a factor used to correct for the underestimation of 0(1)'s for the strong reflections. The corrected intensities were then used to calculate the observed structure factor amplitudes, | F0 \. \F0\=(l/Lpf2 (8.3) where Lp refers to Lorentz-polarization factors. The Lorentz factor occurs as a result of the different amount of time each reflection spends in its diffracting position over the 158 course of a scan. The polarization factor occurs as a result of the partial polarization of the incident X-ray beam from either the crystal monochromator or from the sample crytal itself, which can affect subsequent reflections from the crystal under study. If necessary, empirical absorption and decay corrections were applied to the individual reflections based on transmission factors calculated from the i/A-scans and the change in intensity of the three standard reflections over time, respectively. The intensities of each reflection were used to estimate initial isotropic temperature and scale factors, via a Wilson analysis.[159] The lattice was determined to be centrosymmetric or non-centrosymmetric based on a statistical analysis of the distribution of intensities (E-statistics).[160] The space group was selected based on the centricity of the unit cell and the Laue group, as well as an examination of the systematic absences, if any. 8.1.3. Structure Solution Each reflection has associated with it not only a structure factor amplitude, I Fhki I ,but also a phase angle, 0/,*/. In general the structure factor for a particular reflection (hkl) can be expressed as: Fhki= I Fhki | exip(27ti(l)hki) (8.4) and the electron density at any point (x,y,z) in the unit cell can be described as: 1 , , p(x, y, z) = — X11\F h ki\zxv[-2m(hx + ky + lz)- <phkl ] (8.5) V h k I 159 where V is the unit cell volume. In order to obtain structural information from the diffracted intensities of each reflection the phase of each reflection must be derived. This is known as the phase problem, and several methods have been developed to extract this information from the available data. A l l the structures in this thesis were solved using one of two direct methods routines, either SHELX-86 [161] or SIR-92.[162] A brief outline of phasing by direct methods is presented here. First, the structure factor amplitudes of all reflections were normalized, [163] via equation 8.6, in order to bring each class of reflection to a common basis. (8.6) where fi is the scattering factor of atom j and e is an integer that is generally 1, but which may assume different values for special sets of reflections that are related to the symmetry elements present in the unit cell. The scattering factor, fi, was corrected for isotropic thermal motion by: fi = / / exp(-B sin 20 / A 2) (8.7) where fi" is the scattering power of atom j given by an equivalent number of electrons located at the position of the atomic nucleus.[164] B is an isotropic temperature factor given by: 160 B = 8 7 t V (8.8) where u 2 is the mean-square vibrational amplitude of atom j. After normalizing the reflections, special sets of three reflections were chosen based on the magnitudes of | E | . These "triplets" are special in that the sum of their indices is zero, for example: M + /I2 + ( M + /I2) = 0 where hi = hi, k\, l\ and hi = h2, k2, l2. The relationship between the phases of these reflections, called the £2 relationship, is <j)M + §hl + <)>(W + h2) = 0(M,/i2) = 0 Each £2 relationship is given a weight, K(M,/I2), that is proportional to the product of the IEI's participating in the relationship. Once a sufficient number of £2 relationships was established, the list was scanned for reflections that participate in a large number of triples. These reflections were assigned phases, and the phases of all other reflections in the data set are derived from Karle and Hauptman's "tangent formula": [165] 161 tan[<|)(/i)] I,. K(h, H) sin[<b(fe' ) + ^ (h-h')] I „ . K(/l,/»') COs[<|>( # ) + - # ) ] (8.9) After a complete set of phases has been established new phase sets are determined by assigning new phases to the starting set, then establishing the new phases for the data set via (8.9). Each phase set is evaluated using several methods and these results are used to determine a combined figure of merit (CFOM) for that phase set. Finally, an electron density map of the unit cell can be obtained via (8.5) using the phase set with the largest C F O M . A correct solution to the phase problem will result in the appearance of electron density peaks corresponding to some or all of the atoms in the molecule under investigation. If only a partial structure was found from the electron density map, a second program called DIRDIF [166] was used to expand the trial structure. DIRDIF uses the starting phases from the known partial structure to calculate the difference between the observed and calculated structure factors, Fa - Fc. This difference synthesis represents the difference between the actual electron density and that of the model used to calculate Fc: (8.10) 162 where AFHU = (F0> hu - Fc, hkd- Missing atoms appear as peaks in the difference map, while smaller peaks, both positive and negative, can be indicative of a partially disordered structure. DIRDIF is used until all of the non-hydrogen atoms are located. 8.1.4. Structure Refinement At this stage all non-hydrogen atoms in the structure are defined by three positional variables and one isotropic thermal parameter. These variables now undergo a full-matrix least-squares refinement designed to minimize the function: [167] where w is the weight given to each reflection and is derived from the counting statistics and k is a factor used to scale the calculated structure factors to match the observed structure factors. Once an initial isotropic refinement has been accomplished subsequent refinements are carried out with anisotropic thermal parameters for all non-hydrogen hkl X w Fo\-k\Fc\j by: (8.11) 163 atoms. The general anisotropic temperature factor expression for a given set of reflections (hkl) is given by (8.12): exp -2K2 ^Unh2a*2 +U22k2b*2 +U33l2c*2 + 2Ul2hkab^ y+2Ul3hla c + 2U23klb c (8.12) where the [/y are the thermal parameters expressed in terms of mean-square vibrational amplitudes. The a*, b* and c* are the parameters defining the reciprocal lattice edges. Neutral atom scattering factors for all atoms and anomalous dispersion corrections for the non-hydrogen atoms are taken from the International Tables for X-ray Crystallography. [168] A secondary extinction coefficient (g) may also be refined, where: \FoC0"\ = \F0eM\(l+g\Fc\2Lp) (8.13) where | F 0 e x t | i s the structure factor amplitude with secondary extinction, | F c | i s the calculated structure factor amplitude and hp are the Lorentz-polarization correction terms. Hydrogen atoms are sometimes found as residual electron density peaks; however, it is also possible to calculate the theoretical positions of the hydrogens based on the geometry of the surrounding atoms and to fix these hydrogens in idealized positions. In some cases hydrogen atoms are refined with isotropic thermal parameters, particularly those that are suspected of being in non-ideal positions, such as those participating in hydrogen-bonds. 164 The anisotropic refinement is carried out over a preset number of cycles, or until the refinement has converged. The refinement is considered converged when the shift in any of the parameters being refined is negligible compared to its standard deviation. Three measures of the reliability of the model structure are provided in this thesis: (1) the fl-factor, R s ( k l - k l ) Lhkl Lhkl (2) the weighted /^-factor, wR = zw(\FO\-\F\)2 /i:W\FO\2 .hkl I hkl 1/2 (3) the goodness of fit (GOF), 5 = - | l /2 M | F j - | F c f ) / ( m - „ ) .hkl where m and n are the number of observations and variables, respectively. The closer the R-values are to zero, the better the model structure describes the actual structure, while S is ideally equal to 1. 8.1.5. Treatment of disorder Minor structural disorder was discovered in many of the structures reported here. Disorder can occur when two or more molecular conformations have equivalent or near-equivalent energy minima. Dynamic disorder refers to large atomic movements or oscillations between the different minima, with the diffraction data reflecting a time-average of the contents of the unit cell. Static disorder occurs when two or more conformations are adopted throughout the crystal, but oscillation between the two 165 conformations does not occur. The diffraction data therefore reflects a space-average of the unit cell. In general the disorder, if any, was usually evidenced by abnormally large thermal motion about the suspect atom, and by large residual electron density peaks at geometrically reasonable positions near the suspect atom. These peaks were labeled as atoms, with the occupancies of the new atom or atoms and the original suspect atom summing to one. The atoms were refined isotropically with their occupancies adjusted manually until the isotropic thermal parameters were roughly equivalent. This new model was then refined with anisotropic thermal parameters. In cases where the anisotropic refinement brought about unreasonable geometries, rigid body refinements and restraints were used. 8.1.6. Structure completion After the refinement was judged to have converged, all bond lengths and angles were derived from the final atomic positions and their standard deviations were estimated Molecular structures were drawn using ORTEP [169] with 50% probability ellipsoids or with CHARON.[170] 8.2. p-Nitrophenylglycine (1) A crystal of approximate dimensions 0.18 x 0.20 x 0.25 mm was chosen for data collection. Crystallographic data for (1) appear in Table 8.1. A triclinic cell with 166 Z = 4 (assuming a density of 1.55 g/cm3) was indicated by preliminary measurements. 3641 reflections were collected, of which 3434 were unique and 2148 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 24 reflections with 20 = 75.4 - 99.9°. The data for (1) were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on a statistical analysis of the intensity distributions and a successful solution and refinement, the space group was determined to be PI. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were found from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 1.14 xlO"6). Neutral atom scattering factors and the values of AV and A?' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms, were included in Fcaic.[172] The refinement converged at R = 0.040, Rw = 0.044 for 318 variables (GOF = 2.33; including zeros: R = 0.092, Rw = 0.049), with a negligible parameter shift in the final refinement cycle. The final difference map showed electron density between -0.18 and 0.20 e/A3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.2-4, respectively. 167 The structure of (1) is shown in Figure 8.2. The packing of (1) (Figure 3.5, reproduced here for convenience) consists of two molecules per asymmetric unit. The carboxylic acid proton of each molecule is linked via intermolecular O—H---0 hydrogen bonds to the N 0 2 oxygens directly behind it. A second set of hydrogen bonds, in this case intermolecular N—H---0 bonds, links each molecule to its symmetry related neighbor, forming an infinite chain of oppositely oriented dimer pairs. Complete hydrogen bond and C—H - --0 interaction details are given in Table 8.5. Figure 8.2 ORTEP diagram of acid (1) (50% probability ellipsoids). 168 Figure 3.5 CHARON packing diagram of (1). 8.3. (lS,2S)-(+)-pseudoephedrine salt of (1): l.eph. A crystal of approximate dimensions 0.07 x 0.20 x 0.50 mm was chosen for data collection. Crystallographic data for l.eph appear in Table 8.1. A monoclinic cell with Z = 2 (assuming a density of 1.30 g/cm3) was indicated by preliminary measurements. 2179 reflections were collected, of which 2083 were unique and 1788 observed (I > 3.0 o(I))- The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 75.2 - 98.8°. The data for l.eph were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. 169 Based on systematic absences of (OkO: k -t 2n) the space group was determined to be P2\. The structure was solved by direct-methods [162] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen-bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H o = 0.98 A, B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 2.04 xlO"5). Neutral atom scattering factors and the values of AT and AT' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.042, Rw = 0.053 for 330 variables (GOF = 3.62; including zeros: R = 0.054, Rw = 0.053), with the largest parameter shift in the final refinement cycle being 0.1 OCT. The final difference map showed electron density between -0.15 and 0.14 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.6-8, respectively. The structure and packing of l.eph are shown in Figures 8.3 and 8.4, respectively. The /?-nitrophenylglycinate moiety is disordered such that it adopts two separate orientations. The minor fragment is related to the major fragment by rotating it about its charge-transfer axis by 180°. The directions of the charge-transfer axes of the major and minor fragments are offset by = 15°. The orientations of both fragments are shown in Figure 3.8 (reproduced here for conveniece). A l l of the atoms in the minor fragment were eventually found from large peaks on the difference maps. This fragment, however, was 170 severely distorted, particularly the aromatic ring, therefore the ring was modeled as a rigid body with idealized positions and bond lengths of 1.39 A. With this type of modeling each atom in the ring is given the same, isotropically refined, thermal parameter. The relative populations of the major and minor fragments were 0.75 and 0.25 respectively. There is no evidence of disorder in the pseudoephedrinium moiety. The packing within the crystal is greatly influenced by hydrogen-bonding. Each anion is linked to three cations via either intermolecular N—H---0 or intermolecular O—H---0 hydrogen-bonds, with the carboxylate oxygens acting as acceptors in each case. In turn each cation behaves as a hydrogen-bond donor to three anions. This network of hydrogen-bonded anions and cations propagates through the crystal along the b-axis. None of these strong interactions (i.e., N—H- • -O or O—H- • -O) involve the N O 2 oxygens. Complete hydrogen bond and C—H- • -O interaction details are given in Table 8.9. 171 0 5 172 Figure 8.4 ORTEP packing stereodiagram of l.eph (50% probability ellipsoids). Only the major disordered fragment is shown. 8.4. S-(-)-Proline t-butyl ester salt of (1): l.pro-but. A crystal of approximate dimensions 0.25 x 0.20 x 0.10 mm was chosen for data collection. Crystallographic data for l.pro-but appear in Table 8.1. A monoclinic cell with Z = 2 (assuming a density of 1.32 g/cm3) was indicated by preliminary measurements. 2167 reflections were collected, of which 1969 were unique and 1672 observed (I > 3.0 o(T)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 20 = 55.3 - 89.9°. The data for l.pro-but were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences of (OkO: k * 2n) the space group was determined to be P2\. The structure was solved by direct-methods [162] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen-bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 6.78 xlO"6). Neutral atom scattering factors and the values of AT and AF were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.037, Rw = 0.039 for 255 variables (GOF = 2.68; including zeros: R = 0.053, Rw = 0.041), with the largest parameter shift in the final 174 refinement cycle being 0.02(7. The only disorder in the structure occurs in the proline ring where C ( l l ) adopts both positions of the "envelope" conformation. The population of the major C( l 1) fragment was found to be 0.79 by varying the populations of the two fragments until their anisotropic thermal parameters were approximately equal. The final difference map showed electron density between -0.14 and 0.16 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.10-12, respectively. The structure and crystal packing of l.pro-but are shown in Figures 8.5 and 3.9 (reproduced here for convenience), respectively. The packing consists of alternating layers of cations and anions stacking one upon the other along the b-axis of the unit cell. Each layer of anions is an infinite chain formed by intermolecular N — H - 0 hydrogen-bonds between N(l)—H(5) and the carboxylate 0(3) of the adjacent anion. The proline t-butyl ester cations comprising the cation layer are linked to each other, while the proline NH's are linked to the anion layer above, also via N—H---0 hydrogen-bonds. Complete hydrogen bond and C — H - 0 interaction details are given in Table 8.13. 175 Ol Figure 8.5 ORTEP diagram of l.pro-but (50% probability ellipsoids). Only the major disordered fragment is shown. 176 Figure 3.9 ORTEP stereodiagram of l.pro-but packing. (50% probability ellipsoids) Only the major disordered fragment is shown. 177 Table 8.1 Crystallographic data for (1), l.eph and l.pro-but. (1) l.eph l.pro-but Formula C 8 H 8 N 2 0 4 C 1 8H 2 3N 305 C 1 7 H 2 5 N 3 0 6 196.16 361.40 367.40 Crystal system triclinic monoclinic monoclinic Space group PI P2i P2i a, A 9.687(1) 11.646(1) 5.4759(5) b, A 10.089(1) 5.7799(8) 28.160(3) c A 9.328(1) 13.846(1) 6.0041(7) «(") 107.00(1) 90 90 PC) 100.67(1) 99.121(6) 94.116(8) 7(°) 97.07(1) 90 90 V 841.3(2) 920.2(2) 923.5(2) z 4 2 2 Pealed, g/cm3 1.55 1.30 1.32 F(000) 408 384 392 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) fi, cm'1 10.90 7.6 8.0 Crystal size, mm 0.18x0.20x0.25 0.07 x 0.20 x 0.50 0.25x0.20x0.10 Transmission factors 0.91-1.00 0.87-1.00 0.95-1.00 Scan type co-20 £0-20 co-IB Scan range, ° in co 1.10+ 0.20 tan 0 1.00+ 0.20 tan 9 1.00+ 0.20 tan 9 Scan speed, °/min 32 16 16 Data collected +h, ±k, ±1 +h, +k, ±1 +h, +k, ±1 9 ft o 155.2 155.4 155.3 Crystal decay -0.3% -0.2% -1.3% Total reflections 3641 2179 2167 Total unique 3434 2083 1969 Emerge 0.025 0.021 0.017 No. of reflections 2148 1788 1672 with / >3o(7) No. of variables 318 330 255 p-factor 0.002 0.011 0.003 R 0.040 0.042 0.037 Rw 0.044 0.053 0.039 Goodness of fit 2.33 3.62 2.68 Max. A/a (final 0.00 0.10 0.02 Residual density e/A3 -0.18 to +0.20 -0.14 to+ 0.15 -0.14 to+ 0.16 178 Table 8.2 Final atomic coordinates (fractional) and B(eq) (A2) of (1). atom X v z B(ea) 0(1) 0.2127(2) 0.5890(2) -0.0957(2) 4.90(5) 0(2) 0.2743(2) 0.7924(2) -0.1211(2) 4.98(5) 0(3) 1.0432(2) 0.8976(2) 0.6153(2) 4.12(5) 0(4) 1.0136(2) 0.6958(2) 0.6696(2) 4.36(5) 0(5) 0.3768(2) 0.5942(2) 0.5855(3) 6.22(6) 0(6) 0.5111(2) 0.7945(2) 0.6290(2) 4.94(5) 0(7) -0.1646(2) 0.8950(2) -0.1019(2) 4.69(5) 0(8) -0.3134(2) 0.6876(2) -0.1789(2) 4.35(5) N(l) 0.7977(2) 0.8108(2) 0.3925(3) 3.53(5) N(2) 0.2972(2) 0.7010(2) -0.0590(3) 3.60(5) N(3) 0.0159(2) 0.8165(2) 0.1074(3) 3.53(5) N(4) 0.4001(2) 0.7056(2) 0.5595(3) 3.82(6) C(l) 0.6736(3) 0.7836(3) 0.2848(3) 2.93(5) C(2) 0.5747(3) 0.6578(3) 0.2446(3) 3.01(6) C(3) 0.4514(3) 0.6302(3) 0.1316(3) 3.06(6) C(4) 0.4249(3) 0.7285(3) 0.0591(3) 3.16(6) C(5) 0.5206(3) 0.8547(3) 0.0990(4) 3.96(7) C(6) 0.6434(3) 0.8819(3) 0.2103(3) 3.80(7) C(7) 0.8343(3) 0.7186(3) 0.4790(4) 3.30(6) C(8) 0.9759(3) 0.7839(3) 0.5943(3) 3.19(6) C(9) 0.1074(2) 0.7886(3) 0.2188(3) 2.76(5) C(10) 0.0850(3) 0.6595(3) 0.2465(3) 3.08(6) C(ll) 0.1797(3) 0.6327(3) 0.3592(3) 3.13(6) C(12) 0.2991(3) 0.7355(3) 0.4459(3) 2.97(6) C(13) 0.3217(3) 0.8646(3) 0.4220(3) 3.40(6) C(14) 0.2281(3) 0.8915(3) 0.3106(3) 3.32(6) C(15) -0.1083(3) 0.7157(3) 0.0085(4) 3.25(6) C(16) -0.1961(3) 0.7790(3) -0.0948(3) 3.29(6) H(l) 0.592(2) 0.591(2) 0.294(3) 2.2(5) H(2) 0.389(3) 0.549(3) 0.105(3) 5.0(8) H(3) 0.495(3) 0.920(3) 0.049(3) 3.8(6) H(4) 0.707(3) 0.966(3) 0.240(3) 5.6(8) H(5) 0.853(3) 0.889(3) 0.417(3) 3.2(6) H(6) 0.842(3) 0.633(3) 0.418(3) 4.8(8) H(7) 0.767(3) 0:709(3) 0.539(3) 3.1(6) H(8) 1.102(4) 0.739(4) 0.734(4) 8(1) H(9) 0.001(3) 0.589(3) 0.186(3) 3.3(6) H(10) 0.159(3) 0.548(3) 0.374(3) 5.2(8) H(ll) 0.405(3) 0.932(3) 0.489(3) 3.5(6) H(12) 0.248(3) 0:977(3) 0.290(3) 4.8(7) H(13) 0.033(3) 0.895(3) 0.093(3) 3.5(7) H(14) -0.081(3) 0.639(3) -0.053(3) 3.2(6) H(15) -0.164(3) 0.688(3) 0.068(3) 3.9(7) H(16) -0.368(3) 0.729(3) -0.235(3) 5.1(8) 179 Table 8.3 Bond lengths (A) of (1) with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.227(3) 0(2) N(2) 1.246(3) 0(3) C(8) 1.191(3) 0(4) C(8) 1.329(3) 0(5) N(4) 1.221(3) 0(6) N(4) 1.243(3) 0(7) C(16) 1.196(3) 0(8) C(16) 1.321(3) N(l) C(l) 1.356(3) N(l) C(7) 1.434(3) N(2) C(4) 1.433(3) N(3) C(9) 1.355(3) N(3) C(15) 1.439(3) N(4) C(12) 1.431(3) C(l) C(2) 1.400(3) C(l) C(6) 1.397(4) C(2) C(3) 1.376(3) C(3) C(4) 1.378(4) C(4) C(5) 1.387(3) C(5) C(6) 1.365(4) C(7) C(8) 1.513(3) C(9) C(10) 1.399(3) C(9) C(14) 1.410(3) C(10) C(ll) 1.375(3) C(ll) C(12) 1.391(3) C(12) C(13) 1.383(4) C(13) C(14) 1.361(3) C(15) C(16) 1.500(4) Table 8.4 Bond angles (°) of (1) with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 123.3(2) N(l) C(7) C(8) 109.7(2) 0(1) N(2) 0(2) 121.6(2) 0(3) C(8) 0(4) 125.0(2) 0(1) N(2) C(4) 119.6(2) 0(3) C(8) C(7) 125.1(2) 0(2) N(2) C(4) 118.8(2) 0(4) C(8) C(7) 109.9(2) C(9) N(3) C(15) 122.7(2) N(3) C(9) C(10) 121.6(2) 0(5) N(4) 0(6) 121.5(2) N(3) C(9) C(14) 119.8(2) 0(5) N(4) C(12) 119.9(2) C(10) C(9) C(14) 118.6(2) 0(6) N(4) C(12) 118.6(2) C(9) C(10) C(ll) 120.8(2) N(l) C(l) C(2) 121.5(2) C(10) C(ll) C(12) 119.3(2) N(l) C(l) C(6) 119.7(2) N(4) C(12) C(ll) 119.2(2) C(2) C(l) C(6) 118.7(2) N(4) C(12) C(13) 120.0(2) C(l) C(2) C(3) 120.6(2) C(ll) C(12) C(13) 120.8(2) C(2) C(3) C(4) 119.4(2) C(12) C(13) C(14) 120.1(2) N(2) C(4) C(3) 120.0(2) C(9) C(14) C(13) 120.5(2) N(2) C(4) C(5) 119.3(2) N(3) C(15) C(16) 111.1(2) C(3) C(4) C(5) 120.8(2) 0(7) C(16) 0(8) 124.5(2) C(4) C(5) C(6) 119.9(3) 0(7) C(16) C(15) 125.3(2) C(l) C(6) C(5) 120.5(3) 0(8) C(16) C(15) 110.3(2) 180 Table 8.5 Geometry of (1) hydrogen bonds and C—H- • O interactions (A, °). n—H...4 D—H n-A / n—U--.A 0(4 ) -H (8) -0 ( l ) 0.92(3) 2.67(3) 3.162(3) 114(3) 0(4 ) -H (8)-0(2) 0.92(3) 1.85(3) 2.756(3) 167(3) 0(8)-H(16)---0(5) 0.90(3) 2.66(3) 3.221(3) 121(2) 0(8)-^i(16)-0(6) 0.90(3) 1.89(3) 2.778(3) 173(3) N(l)-H(5)-0(3) 0.84(3) 2.33(2) 2.708(3) 108(2) N(l)-^I(5)---0(3)(i) 0.84(3) 2.39(3) 3.176(3) 156(2) N(3)-^J(13)---0(7)(i> 0.84(3) 2.31(3) 3.104(3) 158(2) N(3)-^i(13)---0(7) 0.84(3) 2.39(2) 2.735(3) 106(2) C(2)-^l(l)---0(5)(i) 0.93(2) 2.47(3) 3.401(3) 176(2) C(6)-H(4)---0(3)(i) 0.92(3) 2.55(3) 3.347(3) 146(3) C(10)-4I(9)---O(l)(i) 0.96(2) 2.41(3) 3.352(3) 166(2) C(14)-^I(12)---0(7)(i) 0.94(3) 2.54(3) 3.338(3) 143(2) Symmetry Codes: (i) -x, -y, -z Table 8.6 Final atomic coordinates (fractional) and B(eq) (A2) of l.eph. atom X V z B(ea) occ 0(1) 0.6030(5) 0.0917 -0.3098(4) 6.6(1) 0.75 0(1*) 0.530(2) -0.350(4) -0.230(2) 8.5(6) 0.25 0(2*) 0.562(2) -0.038(4) -0.309(2) 8.0(5) 0.25 0(2) 0.5305(9) -0.233(2) -0.2651(7) 10.3(3) 0.75 0(3) 0.7783(4) 0.211(1) 0.3407(3) 6.26(9) 0.75 0(3*) 0.783(1) 0.611(3) 0.253(1) 9.2(4) 0.25 0(4*) 0.8127(9) 0.329(4) 0.3743(9) 7.9(4) 0.25 0(4) 0.8483(3) 0.562(1) 0.3322(2) 5.21(8) 0.75 0(5) 0.9326(2) 0.977(1) 0.5745(2) 6.07(6) N(l) 0.7179(4) 0.172(1) 0.1486(3) 5.2(1) 0.75 N(l*) 0.7403(9) 0.311(2) 0.1093(8) 4.7(3) 0.25 N(2) 0.5803(5) -0.048(2) -0.2441(4) 5.2(1) 0.75 N(2*) 0.558(2) -0.164(5) -0.243(2) 6.0(6) 0.25 N(3) 0.7485(2) 0.822(1) 0.4525(2) 4.50(6) C(l) 0.6850(4) 0.124(1) 0.0529(3) 4.37(10) 0.75 C(l*) 0.696(2) 0.194(5) 0.030(1) 11.289 0.25 C(2) 0.7067(4) 0.275(1) -0.0203(4) 4.9(1) 0.75 C(2*) 0.647(2) -0.026(5) 0.031(1) 11.289 0.25 C(3) 0.6727(4) 0.225(1) -0.1186(4) 5.1(1) 0.75 C(3*) 0.599(2) -0.131(3) -0.057(2) 11.289 0.25 C(4) 0.6136(5) 0.019(1) -0.1442(4) 4.4(1) 0.75 C(4*) 0.602(2) -0.017(5) -0.146(1) 11.289 0.25 C(5) 0.5904(6) -0.133(1) -0.0727(4) 4.9(1) 0.75 181 C(5*) 0.652(2) 0.202(5) -0.146(1) 11.289 0.25 C(6) 0.6239(5) -0.082(1) 0.0242(3) 5.0(1) 0.75 C(6*) 0.699(2) 0.308(3) -0.058(2) 11.289 0.25 C(7) 0.7768(4) 0.377(1) 0.1845(3) 4.9(1) 0.75 C(7*) 0.743(1) 0.220(3) 0.207(1) 5.3(4) 0.25 C(8) 0.798(1) 0.368(2) 0.2950(7) 3.9(2) 0.75 C(8*) 0.795(3) 0.442(6) 0.290(3) 5.8(7) 0.25 C(9) 0.9182(2) 0.697(1) 0.7043(2) 3.71(5) C(10) 0.8817(2) 0.848(1) 0.7693(2) 4.40(6) C(ll) 0.8984(3) 0.799(1) 0.8686(2) 5.21(8) C(12) 0.9536(3) 0.599(1) 0.9027(2) 5.52(8) C(13) 0.9920(3) 0.449(1) 0.8393(3) 5.95(8) C(14) 0.9742(3) 0.496(1) 0.7392(2) 5.07(7) C(15) 0.8961(2) 0.748(1) 0.5955(2) 4.06(6) C(16) 0.7676(2) 0.737(1) 0.5560(2) 4.00(6) C(17) 0.7188(3) 0.498(1) 0.5624(3) 6.43(9) C(18) 0.6255(3) 0.863(1) 0.4103(3) 7.5(1) H(5) 0.702(4) 0.09(1) 0.201(4) 5(1) H(14) 0.991(4) 0.98(1) 0.587(3) 10(1) H(19) 0.783(3) 0.702(8) 0.419(3) 5.7(9) H(20) 0.784(2) 0.941(6) 0.447(2) 3.1(6) Table 8.7 Bond lengths (A) of l.eph with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.275(9) C(2) C(3) 1.385(8) 0(1*) N(2*) 1.15(4) C(2*) C(3*) 1.40(3) 0(2*) N(2*) 1.18(4) C(3) C(4) 1.39(1) 0(2) N(2) 1.23(2) C(3*) C(4*) 1.40(3) 0(3) C(8) 1.15(1) C(4) C(5) 1.38(1) 0(3*) C(8*) 1.11(4) C(4*) C(5*) 1.40(2) 0(4*) C(8*) 1.32(5) C(5) C(6) 1.368(8) 0(4) C(8) 1.33(1) C(5*) C(6*) 1.40(2) 0(5) C(15) 1.430(9) C(7) C(8) 1.51(1) N(l) C(l) 1.348(6) C(7*) C(8*) 1.76(4) N(l) C(7) 1.42(1) C(9) C(10) 1.369(7) N(l*) C(7*) 1.45(2) C(9) C(14) 1.380(8) N(2) C(4) 1.428(3) C(9) C(15) 1.516(4) N(3) C(16) 1.498(5) C(10) C(ll) 1.387(4) N(3) C(18) 1.477(4) C(ll) C(12) 1.368(9) C(l) C(2) 1.390(9) C(12) C(13) 1.361(7) C(l*) C(2*) 1.40(2) C(13) C(14) 1.396(5) C(l) C(6) 1.41(1) C(15) C(16) 1.511(4) C(l*) C(6*) 1.40(2) C(16) C(17) 1.505(9) 182 Table 8.8 Bond angles (°) of l.eph with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 124.2(6) C(4*) C(5*) C(6*) 120(1) C(l*) N(l*) C(7*) 124(4) C(l) C(6) C(5) 120.7(6) O(l) N(2) 0(2) 121.7(7) C(l*) C(6*) C(5*) 120(1) 0(1*) N(2*) 0(2*) 139(3) N(l) C(7) C(8) 108.6(6) 0(1) N(2) C(4) 117.8(7) N(l*) C(7*) C(8*) 107(2) 0(1*) N(2*) C(4*) 114(2) 0(3) C(8) 0(4) 124.5(8) 0(2) N(2) C(4) 120.6(8) 0(3*) C(8*) 0(4*) 147(4) C(16) N(3) C(18) 114.7(3) 0(3) C(8) C(7) 124.7(9) N(l) C(l) C(2) 122.1(6) 0(3*) C(8*) C(7*) 109(3) N(l*) C(l*) C(2*) 118(1) 0(4) C(8) C(7) 110.8(8) N(l) C(l) C(6) 120.2(6) 0(4*) C(8*) C(7*) 102(2) N(l*) C(l*) C(6*) 122(1) C(10) C(9) C(14) 118.9(3) C(2) C(l) C(6) 117.7(4) C(10) C(9) C(15) 120.4(5) C(2*) C(l*) C(6*) 120(1) C(14) C(9) C(15) 120.7(4) C(l) C(2) C(3) 122.0(6) C(9) C(10) C(ll) 120.9(5) C(l*) C(2*) C(2*) 120(1) C(10) C(ll) C(12) 119.8(5) C(2) C(3) C(4) 118.7(6) C(ll) C(12) C(13) 120.1(4) C(2*) C(3*) C(4*) 120(1) C(12) Q13) C(14) 120.2(5) N(2) C(4) C(3) 121.6(6) C(9) C(14) C(13) 120.0(5) N(2*) C(4*) C(3*) 121(2) 0(5) C(15) C(9) 112.0(4) N(2) C(4) C(5) 118.0(7) 0(5) C(15) C(16) 105.9(4) N(2*) C(4*) C(5*) 119(2) C(9) C(15) C(16) 110.7(2) C(3) C(4) C(5) 120.3(5) N(3) C(16) C(15) 108.7(3) C(3*) C(4*) C(5*) 120(1) N(3) C(16) C(17) 111.0(3) C(4> C(5) C(6) 120.6(7) C(15) C(16) C(17) 112.3(4) Table 8.9 Geometry of l.eph hydrogen bonds and C — H - 0 interactions (A, °). n—u... 4 D—H H . - 4 D--A / D—H---/4 0(5)-H(14)- •0(4)(i) 0.67(5) • 2.080(5) 2.717(4) 158(6) 0(5)-H(14).. O(4*)0) 0.67(5) 2.431(5) 3.06(1) 156(7) N(l)-H(5)- •0(3) 0.92(6) 2.116(5) 2.651(6) 116(4) N(l*)—H(5*)- ••0(3*) 0.98(1) 2.243(2) 2.62(2) 102(1) N(3)-^I(19)- •0(3*) 0.96(4) 2.359(4) 3.10(2) 134(3) N(3)-^I(19)- ••0(4) 0.96(4) 1.724(4) 2.646(6) 160(4) N(3}-^(19)- •0(4*) 0.96(4) 2.286(5) 3.18(2) 156(3) N(3)-fl(20)- •0(4*) 0.81(3) 2.505(4) 3.25(2) 154(2) N(3)-H(20)- -0(3) 0.81(3) 2.143(3) 2.781(8) 136(2) N(3)-H(20)- -0(5) 0.81(3) 2.276(3) 2.664(4) 110(2) C(7*)-^(6*)-- •0(l*)( i) 0.98 2.30 3.26(3) 167 C(16)-^I(15) -0(1) 0.98 2.55 3.53(1) 175 183 C(16)—H(15)- ••0(2*) 0.98 2.60 3.51(2) 155 C(17)-H(18)- ••0(4*) 0.98 2.28 3.14(1) 145 C(18)—H(22)- •0(l) ( i ) 0.98 2.48 3.21(1) 131 C(18)—H(22)- •0(2*)(i) 0.98 2.49 3.34(2) 144 C(18)-H(23)" •0(l*)(i) 0.98 2.54 3.29(2) 134 C(18)-H(23) ••0(3) 0.98 . 2.49 2.95(1) 108 Symmetry Codes: (i) -x, 'A+y, -z Table 8.10 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-but. atom X V z B(ea) O(l) 0.0840(4) 0.6158 0.2968(5) 8.45(7) 0(2) 0.1700(5) 0.6447(1) 0.6244(4) 9.75(8) 0(3) 1.0791(3) 0.4380(1) 1.1467(2) 4.28(3) 0(4) 0.7539(3) 0.43862(9) 0.9054(2) 3.93(3) 0(5) 0.1666(3) 0.3212(1) 1.0380(3) 6.06(4) 0(6) 0.4539(2) 0.26792(9) 0.9564(2) 3.65(3) N(l) 0.9884(3) 0.4897(1) 0.5932(3) 4.10(4) N(2) 0.2054(5) 0.6165(1) 0.4743(5) 6.75(6) N(3) 0.5168(3) 0.3864(1) 1.1846(3) 3.05(3) C(l) 0.7979(4) 0.5208(1) 0.5701(3) 3.51(4) C(2) 0.6606(4) 0.5239(1) 0.3654(3) 4.10(4) C(3) 0.4665(4) 0.5546(1) 0.3342(4) 4.46(5) C(4) 0.4109(4) 0.5838(1) 0.5094(4) 4.60(5) C(5) 0.5442(5) 0.5821(1) 0.7109(4) 5.04(5) C(6) 0.7351(5) 0.5509(1) 0.7442(4) 4.42(5) C(7) 1.1159(4) 0.4776(1) 0.8027(4) 4.20(5) C(8) 0.9707(4) 0.4487(1) 0.9644(3) 3.21(4) C(9) 0.5893(3) 0.3366(1) 1.1356(3) 2.87(3) C(10) 0.6918(4) 0.3163(1) 1.3579(3) 4.25(5) C(ll*) 0.565(2) 0.3509(3) 1.526(1) 4.8(1) C(ll) 0.7750(6) 0.3585(1) 1.4947(4) 3.96(6) C(12) 0.5727(4) 0.3950(1) 1.4283(3) 4.24(4) C(13) 0.3754(3) 0.3082(1) 1.0358(3) 3.26(4) C(14) 0.2835(3) 0.2286(1) 0.8785(3) 3.48(4) C(15) 0.1028(4) 0.2466(1) 0.6945(4) 4.93(5) C(16) 0.4565(4) 0.1927(1) 0.7906(5) 6.08(7) C(17) 0.1594(5) 0.2101(1) 1.0739(4) 5.32(6) H(5) 1.019(4) 0.4723(8) 0.473(4) 4.5(5) H(8) 0.617(5) 0.409(1) 1.064(5) 7.8(7) H(9) 0.363(5) 0.3932(8) 1.135(4) 5.4(6) 184 Table 8.11 Bond lengths (A) of l.pro-but with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.215(6) 0(2) N(2) 1.226(6) 0(3) C(8) 1.244(4) 0(4) C(8) 1.247(4) 0(5) C(13) 1.201(4) 0(6) C(13) 1.314(3) 0(6) C(14) 1.500(4) N(l) C(l) 1.362(4) N(l) C(7) 1.435(5) N(2) C(4) 1.457(5) N(3) C(9) 1.493(4) N(3) C(12) 1.493(4) C(l) C(2) 1.397(5) C(l) C(6) 1.406(5) C(2) C(3) 1.374(5) C(3) C(4) 1.386(5) C(4) C(5) 1.368(6) C(5) C(6) 1.369(6) C(7) C(8) 1.532(4) C(9) C(10) 1.521(4) C(9) C(13) 1.507(4) C(10) C(ll*) 1.60(1) C(10) C(ll) 1.496(6) C(ll*) C(12) 1.37(1) C(ll) C(12) 1.542(6) C(14) C(15) 1.516(5) C(14) C(16) 1.506(5) C(14) C(17) 1.492(5) Table 8.12 Bond angles (°) of l.pro-but with estimated standard deviations. atom atom atom angle atom atom atom angle C(13) 0(6) C(14) 122.5(2) 0(4) C(8) C(7) 117.9(3) C(l) N(l) C(7) 124.3(3) N(3) C(9) C(10) 105.4(2) 0(1) N(2) 0(2) 123.3(4) N(3) C(9) C(13) 111.5(2) 0(1) N(2) C(4) 119.0(4) C(10) C(9) C(13) 112.2(3) 0(2) N(2) C(4) 117.6(5) C(9) C(10) C(ll*) 100.1(5) C(9) N(3) C(12) 107.9(2) C(9) C(10) C(ll) 105.2(3) N(l) C(l) C(2) 119.2(3) C(10) C(ll*) C(12) 104.7(8) N(l) C(l) C(6) 122.5(3) C(10) C(ll) C(12) 101.6(3) C(2) C(l) C(6) 118.2(3) N(3) C(12) C(ll*) 105.1(6) C(l) C(2) C(3) 121.4(3) N(3) C(12) C(ll) 103.8(3) C(2) C(3) C(4) 118.7(4) 0(5) C(13) 0(6) 127.1(3) N(2) C(4) C(3) 118.3(4) 0(5) C(13) C(9) 123.2(3) N(2) C(4) C(5) 120.5(4) 0(6) C(13) C(9) 109.7(2) C(3) C(4) C(5) 121.1(4) 0(6) C(14) C(15) 109.8(3) C(4) C(5) C(6) 120.4(3) 0(6) C(14) C(16) 102.2(2) C(l) C(6) C(5) 120.1(3) 0(6) C(14) C(17) 108.8(3) N(l) C(7) C(8) 116.1(3) C(15) C(14) C(16) 111.2(3) 0(3) C(8) 0(4) 125.4(3) C(15) C(14) C(17) 112.3(3) 0(3) C(8) C(7) 116.7(3) C(16) C(14) C(17) 112.0(3) 185 Table 8.13 Geometry of l.pro-but hydrogen bonds and C — H - 0 interactions (A, °). n—H...4 D—R n—A / D—H---4 N(l)-H(5)-0(3) 0.90(4) 2.23(4) 3.122(4) 172(3) N(3)-^(8)---0(3) 1.14(5) 2.67(5) 3.428(4) 123(3) N(3)HH(8)---0(4) 1.14(5) 1.51(5) 2.641(3) 179(4) N(3)-^I(9)---0(3) 0.89(4) 2.01(4) 2.799(3) 147(3) N(3)-H(9)-0(5) 0.89(4) 2.35(4) 2.753(4) 108(3) C(9)-^I(10)---O(5) 0.98 2.49 3.285(4) 138 C(17)-^i(23)---0(5) 0.98 2.55 3.137(5) 118 Symmetry Codes: (i) -x, V2+y, -z 8.5. S-(-)-Proline methyl ester salt of (1): l.pro-meth. A crystal of approximate dimensions 0.25 x 0.20 x 0.40 mm was chosen for data collection. Crystallographic data for l.pro-meth appear in Table 8.14. An orthorhombic cell with Z = 4 (assuming a density of 1.38 g/cm3) was indicated by preliminary measurements. 2972 reflections were collected, of which 2094 were observed (I > 3.0 o(I)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 51.3 - 93.6°. The data for l.pro-meth were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences (MX): h * 2n, 0k0: k * 2n, 00/:, I * 2n), the space group was determined to be P2i2i2i. The structure was solved by direct-methods [162] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from 186 E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen-bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bonded atom). A secondary extinction coefficient correction was applied (final coefficient = 1.31 xlO"6). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.042, Rw = 0.041 for 351 variables (GOF = 2.83; including zeros: R = 0.076, Rw = 0.042), with the largest parameter shift in the final refinement cycle being 0.02a. The final difference map showed electron density between -0.21 and 0.21 e /A 3 . Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.15-17, respectively. l.pro-meth forms a 2:1 acid/amine complex rather than the expected 1:1 salt. A diagram of the structure is reproduced from Figure 3.12 for convenience. A diagram of the crystal packing of this complex is given in Figure 8.6. The two p-nitrophenylglycine moieties share one proton via a strong O — H - 0 hydrogen-bond between their respective carboxylate groups so that the two charge-transfer axes are anti-parallel to each other. The position of the shared proton was refined and the difference in O—H distances (1.18 A vs. 1.39 A) suggests that the proton is more strongly held to 0(4) than to 0(8). The proline ring is linked to one carboxylate group via a strong N—H- • -O hydrogen-bond. 187 The p-nitrophenylglycine units (i.e., those with the shorter O—H distances) are oriented in an infinite chain linked via N — H - 0 hydrogen-bonds from the glycine N H to an N O 2 oxygen directly behind it, propagating through the crystal along the a-axis. Complete hydrogen-bonding geometries are given in Table 8.18. Figure 3.12 ORTEP diagram of l.pro-meth (50% probability ellipsoids). 188 Figure 8.6 CHARON packing diagram of l.pro-meth viewed down the c-axis. 8.6. S-(-)-Prolinamide salt of (1): l.pro-amide. A crystal of approximate dimensions 0.45 x 0.18 x 0.10 mm was chosen for data collection. Crystallographic data for l.pro-amide appear in Table 8.14. A monoclinic cell with Z = 4 (assuming a density of 1.46 g/cm3) was indicated by preliminary measurements. 3279 reflections were collected, of which 3173 were unique and 2151 189 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 29 = 41.0 - 67.8°. The data for l.pro-amide were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences of (OkO: k * 2n) the space group was determined to be P2\. The structure was solved by direct-methods [162] and expanded using Fourier techniques. [166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen-bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 3.58 xlO"6). Neutral atom scattering factors and the values of A f and A f were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.042, Rw = 0.046 for 456 variables (GOF = 2.82; including zeros: R = 0.094, Rw = 0.061), with the largest parameter shift in the final refinement cycle being 0.03 o. Both proline rings were found to be disordered by adopting the two "envelope" conformations. The populations of the major fragments, C( 10) and C(24), were refined to 0.7 and 0.5 respectively. The final difference map showed electron density between -0.16 and 0.17 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.19-21, respectively. 190 The two ^-nitrophenylglycinate moieties in the unit cell are related by a pseudo-center of symmetry. The structure of l.pro-amide is shown in Figure 3.11, reproduced here for convenience. A network of hydrogen-bonds form an infinite chain of l.pro-amide dimers that propagate through the crystal diagonally between the a and c-axes (Figure 8.7). Any hydrogen-bonding in the p-nitrophenylglycinate moiety occurs via the glycine fragment (i.e., the amine N H and carboxylate O's) while no significant interactions involve the N 0 2 oxygens. Complete details of hydrogen-bonding geometries are given in Table 8.22. Figure 3.11 ORTEP diagram of l.pro-amide (50% probability ellipsoids). Only the major disordered fragments are shown. 191 Figure 8.7 CHARON packing diagram of l.pro-amide viewed down the fo-axis. 8.7. S-(-)-Prolinol salt of (1): l.pro-ol. The diffraction data were collected and the structure solved by Dr. Bozena Borecka-Bednarz, a post-doctoral fellow in Prof. J. Trotter's lab, and is included herein 192 with her permission. A crystal of approximate dimensions 0.15 x 0.15 x 0.20 mm was chosen for data collection. Crystallographic data for l.pro-ol appear in Table 8.14. An orthorhombic cell with Z = 8 (assuming a density of 1.34 g/cm3) was indicated by preliminary measurements. 3575 reflections were collected, of which 2240 were observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 46.3 - 72.1°. The data for l.pro-ol were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences (hOO: h •£ 2n, OkO: Jc * 2n), the space group was determined to be P2i2i2. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen-bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A, B H = 1.2 x Bonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 1.16 xlO"6). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.043, Rw = 0.041 for 408 variables (GOF = 2.74; including zeros: R = 0.096, Rw = 0.044), with the largest parameter shift in the final refinement cycle being 0.92a. The final difference map showed electron density between -0.16 and 0.14 e/A3. Final atomic coordinates and 193 equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.23-25, respectively. The two p-nitrophenylglycinate moieties in the unit cell are related by a pseudo-center of inversion (Figure 3.10, reproduced here for convenience) and both l.pro-ol units are linked by a pair of N—H---0 hydrogen-bonds between the glycine N H and carboxylate O to form a dimer. In turn each dimer is linked to its neighbor to form an infinite chain of dimers that propagates through the crystal along the a-axis (Figure 8.7). Complete hydrogen-bonding geometries are given in Table 8.26. Figure 3.10 ORTEP diagram of l.pro-ol (50% probability ellipsoids). 194 195 Table 8.14 Crystallographic data for l.pro-meth, l.pro-amide and l.pro-ol. l.pro-meth l.pro-amide l.pro-ol Formula C22H27N5O10 C 1 3H 1 8N 405 C l 3 H i 9 N 3 0 5 fw 521.48 310.31 297.31 Crystal system orthorhombic monoclinic orthorhombic Space group P2i P2{2{1 a, A 14.595(1) 16.653(2) 13.280(3) b,k 24.152(2) 4.869(1) 26.182(3) c, A 7.103(2) 17.585(2) 8.464(6) an 90 90 90 pn 90 99.17(1) 90 m 90 90 90 V 2503.9(5) 1407.6(4) 2942(2) z 4 4 8 Pealed, g/cm3 1.38 1.46 1.34 F(000) 1096 656 1264 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) /X, cm"1 9.5 9.7 8.3 Crystal size, mm 0.25 x 0.20 x 0.40 0.45x0.18x0.10 0.15x0.15x0.20 Transmission factors 0.94-1.00 0.94-1.00 0.97-1.00 Scan type co-20 co-28 co-29 Scan range, ° in co 1.05+ 0.20 tan 6 0.94 + 0.20 tan 6 0.94 + 0.20 tan 6 Scan speed, °/min 32 8.0 8.0 Data collected +h, +k, +1 +h, +k, ±1 +h, +k, +1 Of) ° 155.2 155.3 155.2 Crystal decay -1.7% -0.8% +0.3% Total reflections 2972 3279 3575 Total unique 3173 Emerge 0.022 No. of reflections 2094 2151 2240 with/>3o(7) No. of variables 351 456 408 p-factor 0.001 0.005 0.004 R 0.042 0.042 0.043 Rw 0.041 0.046 0.041 Goodness of fit 2.83 2.82 2.74 Max. A/a (final 0.02 0.37 0.92 Residual density e/A3 -0.21 to +0.21 -0.16 to 0.17 -0.16 to +0.14 196 Table 8.15 Final atomic coordinates (fractional) and B(eq) (A)2 of l.pro-meth. atom X V z B(ea) 0(1) 1.4594(2) -0.1569(1) 0.5960(6) 8.2(1) 0(2) 1.4355(2) -0.2331(1) 0.4488(7) 8.1(1) 0(3) 0.8503(2) -0.1439(1) 0.5227(6) 6.97(9) 0(4) 0.8474(2) -0.0595(1) 0.6498(5) 5.23(7) 0(5) 0.0677(2) 0.0416(1) 0.4823(6) 8.1(1) 0(6) 0.0918(2) 0.1172(1) 0.6331(6) 7.6(1) 0(7) 0.6621(2) 0.0164(1) 0.6843(5) 5.55(8) 0(8) 0.6810(2) -0.0634(1) 0.5360(4) 4.92(7) 0(9) 0.6109(2) 0.1403(1) 0.5620(6) 7.7(1) 0(10) 0.6474(2) 0.2291(1) 0.5907(6) 7.6(1) N(l) 1.0311(2) -0.1542(1) 0.5659(6) 4.60(8) N(2) 1.4077(2) -0.1916(1) 0.5279(7) 5.7(1) N(3) 0.4937(2) 0.0308(1) 0.5715(6) 4.19(8) N(4) 0.1194(2) 0.0750(2) 0.5566(6) 5.4(1) N(5) 0.7774(2) 0.1043(1) 0.6846(5) 4.61(8) C(l) 1.1227(2) -0.1641(1) 0.5633(6) 3.75(8) C(2) 1.1572(2) -0.2134(1) 0.4871(6) 4.21(9) C(3) 1.2497(3) -0.2225(1) 0.4742(7) 4.5(1) C(4) 1.3092(2) -0.1827(1) 0.5425(7) 4.22(9) C(5) 1.2781(3) -0,1344(2) 0.6222(6) 4.30(9) C(6) 1.1849(2) -0.1246(1) 0.6306(6) 4.12(9) C(7) 0.9895(2) -0.1037(2) 0.6278(6) 4.6(1) C(8) 0.8883(3) -0.1045(2) 0.5952(7) 4.7(1) C(9) 0.4026(2) 0.0412(1) 0.5621(6) 3.55(8) C(10) 0.3684(2) 0.0919(1) 0.6323(6) 4.10(9) C(ll) 0.2767(3) 0.1028(1) 0.6279(6) 4.4(1) C(12) 0.2165(2) 0.0643(1) 0.5528(6) 4.02(9) C(13) 0.2480(3) 0.0150(1) 0.4803(6) 4.05(9) C(14) 0.3406(2) 0.0035(1) 0.4836(6) 3.85(9) C(15) 0.5362(2) -0.0203(2) 0.5161(7) 4.45(9) C(16) 0.6348(2) -0.0211(2) 0.5846(6) 4.08(9) C(17) 0.7606(3) 0.1651(2) 0.6707(7) 5.2(1) C(18) 0.8356(4) 0.1853(2) 0.541(1) 10.4(2) C(19) 0.8632(4) 0.1401(2) 0.4309(9) 9.8(2) C(20) 0.8461(3) 0.0888(2) 0.5376(8) 6.5(1) C(21) 0.6647(3) 0.1753(2) 0.6021(7) 5.3(1) C(22) 0.5548(4) 0.2444(2) 0.527(1) 9.2(2) H(5) 0.998(2) -0.181(1) 0.535(5) 3.5(8) H(8) 0.771(4) -0.057(2) 0.60(1) 14(1) H(13) 0.532(2) 0.053(1) 0.634(6) 5(1) H(23) 0.718(3) 0.083(2) 0.673(8) 8(1) H(24) 0.7872 0.0986 0.8090 8.4 197 Table 8.16 Bond lengths (A) of l.pro-meth with estimated standard deviations. atom atom distance • atom atom distance 0(1) N(2) 1.228(4) C(l) C(2) 1.400(5) 0(2) N(2) 1.219(5) C(l) C(6) 1.401(5) 0(3) C(8) 1.218(5) C(2) C(3) 1.371(5) 0(4) C(8) 1.299(4) C(3) C(4) 1.385(5) 0(5) N(4) 1.224(4) C(4) C(5) 1.373(5) 0(6) N(4) 1.223(4) C(5) C(6) 1.382(5) 0(7) C(16) 1.217(4) C(7) C(8) 1.494(5) 0(8) C(16) 1.272(4) C(9) C(10) 1.413(5) 0(9) C(21) 1.188(5) C(9) C(14) 1.401(5) 0(10) C(21) 1.326(5) C(10) C(ll) 1.364(5) 0(10) C(22) 1.472(6) C(ll) C(12) 1.388(5) N(l) C(l) 1.359(4) C(12) C(13) 1.376(5) N(l) C(7) 1.432(5) C(13) C(14) 1.380(5) N(2) C(4) 1.456(5) C(15) C(16) 1.518(5) N(3) C(9) 1.355(4) C(17) C(18) 1.511(6) N(3) C(15) 1.436(5) C(17) C(21) 1.501(6) N(4) C(12) 1.441(4) C(18) C(19) 1.404(7) N(5) C(17) 1.494(5) C(19) C(20) 1.474(7) N(5) C(20) 1.494(6) Table 8.17 Bond angles (°) of l.pro-meth with standard deviations. atom atom atom angle atom atom atom angle C(21) 0(10) C(22) 116.1(4) N(3) C(9) C(10) 119.3(3) C(l) N(l) C(7) 124.9(3) N(3) C(9) C(14) 122.2(3) 0(1) N(2) 0(2) 122.6(4) C(10) C(9) C(14) 118.5(3) 0(1) N(2) C(4) 118.5(4) C(9) C(10) C(ll) 120.4(3) 0(2) N(2) C(4) 118.9(4) C(10) C(ll) C(12) 120.1(3) C(9) N(3) C(15) 124,8(3) N(4) C(12) C(ll) 119.7(3) 0(5) N(4) 0(6) 122.6(4) N(4) C(12) C(13) 119.4(4) 0(5) N(4) C(12) 118.6(4) C(ll) C(12) C(13) 120.8(3) 0(6) N(4) C(12) 118.8(4) C(12) C(13) C(14) 119.7(3) C(17) N(5) C(20) 108.1(4) C(9) C(14) C(13) 120.6(3) N(l) C(l) C(2) 120.6(3) N(3) C(15) C(16) 109.5(3) N(l) C(l) C(6) 120.8(3) 0(7) C(16) 0(8) 125.5(4) C(2) C(l) C(6) 118.6(3) 0(7) C(16) C(15) 119.2(4) C(l) C(2) C(3) 121.1(3) 0(8) C(16) C(15) 115.2(4) C(2) C(3) C(4) 118.9(3) N(5) C(17) C(18) 103.8(4) N(2) C(4) C(3) 119.4(3) N(5) C(17) C(21) 109.6(3) N(2) C(4) C(5) 118.8(3) C(18) C(17) C(21) 115.2(5) C(3) C(4) C(5) 121.7(3) C(17) C(18) C(19) 107.2(4) 198 C(4) C(5) C(l) C(6) N(l) C(7) 0(3) C(8) 0(3) C(8) 0(4) C(8) C(6) 119.4(3) C(5) 120.3(3) C(8) 111.2(3) 0(4) 124.8(4) C(7) 121.7(4) C(7) 113.5(4) C(18) C(19) N(5) C(20) 0(9) C(21) 0(9) C(21) 0(10) C(21) C(20) 108.5(5) C(19) 105.3(4) 0(10) 123.8(5) C(17) 125.3(4) C(17) 111.0(4) Table 8.18 Geometry of l.pro-meth hydrogen bonds and C — H - O interactions (A, °). A D - H H.-4 n-A / r>—H-A 0(4)-H(8)- •0(7) 1-18(6) 2.45(6) 3.276(4) 125(4) 0(4)-H(8)- •0(8) 1-18(6) 1.39(6) 2.561(4) 170(5) N(l)-H(5)" 0(2)(ii) 0.84(3) 2.27(3) 3.060(4) 158(3) N(l)-H(5)- •0(3) 0.84(3) 2.34(3) 2.669(4) 104(2) N(3)-H(13) -0(7) 0.89(4) 2.13(4) 2.610(4) 113(3) N(3)-H(13) -0(9) 0.89(4) 2.46(3) 3.152(4) 135(3) N(5)-H(23) ••0(7) 1-00(5) 1.81(5) 2.708(4) 147(4) N(5)-^(23) -0(9) 1.00(5) 2.23(5) 2.724(4) 108(3) N(5)-^i(24)- •0(3)(i) 0.91(1) 2.74(1) 3.188(5) 111(1) N(5)-^(24)- •0(8)(i) 0.91(1) 1.88(2) 2.753(5) 161(1) C(17)—H(16)- -0(3) ( i ) 0.98 2.54 3.022(6) 110 C(18)-^l(17)- •0(10) 0.98 2.60 2.964(6) 101 Symmetry Codes: (i) 'A-x, -y, 'A+z (ii) 'A+x, 'A-y, -z (iii) -x, 'A+y, 'A-z Table 8.19 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-amide. atom X V z B(eq) occ 0(1) -0.3287(1) -0.115(2) 0.3202(2) 6.49(8) 0(2) -0.3491(2) -0.075(2) 0.4375(2) 7.31(9) 0(3) 0.0707(1) 0.480(2) 0.3952(1) 3.17(5) 0(4) 0.0794(1) 0.791(2) 0.3055(1) 3.58(5) 0(5) 0.1996(2) 0.540(2) 0.1615(2) 5.55(6) 0(6) 0.8332(1) 0.838(2) 0.1823(2) 6.18(8) 0(7) 0.8593(2) 0.778(2) 0.0679(2) 6.78(9) 0(8) 0.4311(1) 0.254(2) 0.1028(2) 4.87(7) 0(9) 0.4339(2) -0.018(2) 0.2033(1) 4.77(6) 0(10) 0.2971(1) 0.753(2) 0.3381(1) 4.68(6) N(l) -0.0624(1) 0.758(2) 0.4426(1) 2.77(6) N(2) -0.3117(2) -0.013(2) 0.3846(2) 4.38(7) N(3) 0.0757(2) 0.273(2) 0.2252(1) 2.89(6) N(4) 0.2603(2) 0.132(2) 0.1488(2) 4.30(7) N(5) 0.5659(2) -0.030(2) 0.0583(2) 3.80(7) 199 N(6) 0.8197(2) 0.730(2) 0.1190(2) 4.62(7) N(7) 0.4210(2) 0.477(2) 0.2787(2) 3.50(6) N(8) 0.2359(2) 0.347(2) 0.3564(2) 3.58(6) C(l) -0.1232(2) 0.571(2) 0.4269(2) 2.64(6) C(2) -0.1423(2) 0.440(2) 0.3552(2) 2.97(6) C(3) -0.2030(2) 0.248(2) 0.3421(2) 3.11(7) C(4) -0.2471(2) 0.185(2) 0.4000(2) 3.28(6) C(5) -0.2304(2) 0.312(2) 0.4712(2) 3.37(6) C(6) -0.1691(2) 0.499(2) 0.4847(2) 3.23(7) C(7) -0.0195(2) 0.870(2) 0.3841(2) 2.73(6) C(8) 0.0480(2) 0.696(2) 0.3609(2) 2.48(6) C(9) 0.1250(2) 0.131(2) 0.1721(2) 3.65(7) C(10) 0.0648(5) 0.075(3) 0.1016(4) 5.1(1) C(10*) 0.069(1) 0.206(7) 0.0860(9) 11.1(7) C(ll) -0.0011(3) 0.283(2) 0.0995(2) 6.1(1) C(12) -0.0084(2) 0.319(2) 0.1823(2) 4.54(8) C(13) 0.1994(2) 0.293(2) 0.1619(2) 3.27(6) C(14) 0.6270(2) 0.154(2) 0.0744(2) 3.19(7) C(15) 0.6441(2) 0.290(2) 0.1455(2) 3.34(7) C(16) 0.7056(2) 0.477(2) 0.1594(2) 3.61(7) C(17) 0.7536(2) 0.532(2) 0.1035(2) 3.51(7) C(18) 0.7392(2) 0.398(2) 0.0335(2) 4.42(8) C(19) 0.6776(2) 0.211(2) 0.0186(2) 4.09(8) C(20) 0.5219(2) -0.134(2) 0.1171(2) 3.53(8) C(21) 0.4574(2) 0.053(2) 0.1418(2) 3.44(7) C(22) 0.3732(2) 0.343(2) 0.3332(2) 3.76(7) C(23) 0.4323(2) 0.320(2) 0.4072(2) 7.8(1) C(24*) 0.4946(7) 0.481(3) 0.4036(6) 6.3(2) C(24) 0.5162(6) 0.352(3) 0.3867(6) 5.3(2) C(25) 0.5078(2) 0.502(2) 0.3175(2) 5.7(1) C(26) 0.2969(2) 0.505(2) 0.3418(2) 3.13(6) H(5) -0.063(2) 0.83(1) 0.488(2) 6.2(9) H(8) 0.101(2) 0.47(1) 0.251(2) 7(1) H(9) 0.074(3) 0.16(1) 0.276(3) 11(1) H(17) 0.259(2) -0.080(9) 0.148(2) 5.2(9) H(18) 0.304(2) 0.217(9) 0.139(2) 6(1) H(23) 0.558(2) -0.106(8) 0.016(2) 3.4(7) H(26) 0.419(2) 0.363(9) 0.231(2) 4.5(7) H(27) 0.403(2) 0.66(1). 0.255(2) 5.8(9) H(35) 0.247(2) 0.166(8) 0.356(2) 3.2(7) H(36) 0.187(2) 0.42(1) 0.368(2) 7(1) 200 Table 8.20 Bond lengths (A) of l.pro-amide with estimated standard deviations. atom atom distance atom atom distance O(l) N(2) 1.228(6) C(2) C(3) 1.368(6) 0(2) N(2) 1.237(6) C(3) C(4) 1.382(7) 0(3) C(8) 1.241(6) C(4) C(5) 1.385(7) 0(4) C(8) 1.265(5) C(5) C(6) 1.361(7) 0(5) C(13) 1.201(6) C(7) C(8) 1.514(6) 0(6) N(6) 1.218(6) C(9) C(10) 1.49(1) 0(7) N(6) 1.219(6) C(9) C(10*) 1.69(3) 0(8) C(21) 1.238(7) C(9) C(13) 1.502(7) 0(9) C(21) 1.255(6) C(10) C(ll) 1.49(1) 0(10) C(26) 1.209(6) C(10*) C(ll) 1.28(4) N(l) C(l) 1.356(6) C(ll) C(12) 1.491(8) N(l) C(7) 1.448(5) C(14) C(15) 1.402(7) N(2) C(4) 1.437(7) C(14) C(19) 1.419(6) N(3) C(9) 1.505(6) C(15) C(16) 1.362(7) N(3) C(12) 1.499(6) C(16) C(17) 1.391(7) N(4) C(13) 1.331(6) C(17) C(18) 1.380(7) N(5) C(14) 1.354(7) C(18) C(19) 1.362(8) N(5) C(20) 1.449(6) C(20) C(21) 1.521(7) N(6) C(17) 1.455(7) C(22) C(23) 1.507(8) N(7) C(22) 1.489(6) C(22) C(26) 1.522(6) N(7) C(25) 1.502(6) C(23) C(24*) 1.31(2) N(8) C(26) 1.332(6) C(23) C(24) 1.50(2) C(l) C(2) 1.404(6) C(24*) C(25) 1.57(2) C(l) C(6) 1.410(6) C(24) C(25) 1-41(2) Table 8.21 Bond angles (°) of l.pro-amide with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 123.0(4) C(10*) C(ll) C(12) 116(1) 0(1) N(2) 0(2) 121.7(5) N(3) C(12) C(ll) 105.0(5) 0(1) N(2) C(4) 120.1(5) 0(5) C(13) N(4) 125.8(6) 0(2) N(2) C(4) 118.2(5) 0(5) C(13) C(9) 121.9(5) C(9) N(3) C(12) 108.3(4) N(4) C(13) C(9) 112.2(5) C(14) N(5) C(20) 122.0(5) N(5) C(14) C(15) 122.6(5) 0(6) N(6) 0(7) 123.2(5) N(5) C(14) C(19) 119.6(5) 0(6) N(6) C(17) 118.7(5) C(15) C(14) C(19) 117.8(5) 0(7) N(6) C(17) 118.0(5) C(14) C(15) C(16) 121.0(5) C(22) N(7) C(25) 108.6(4) C(15) C(16) C(17) 120.2(5) N(l) C(l) C(2) 122.9(4) N(6) C(17) C(16) 119.9(5) N(l) C(l) C(6) 119.5(4) N(6) C(17) C(18) 120.1(5) C(2) C(l) C(6) 117.6(5) C(16) C(17) C(18) 120.0(5) 201 C(l) C(2) C(3) 121.2(4) C(17) C(18) C(19) 120.4(5) C(2) C(3) C(4) 119.6(5) C(14) C(19) C(18) 120.6(5) N(2) C(4) C(3) 118.7(5) N(5) C(20) C(21) 117.2(5) N(2) C(4) C(5) 120.5(5) 0(8) C(21) 0(9) 124.3(5) C(3) C(4) C(5) 120.7(5) 0(8) C(21) C(20) 121.2(5) C(4) C(5) C(6) 119.7(4) 0(9) C(21) C(20) 114.5(5) C(l) C(6) C(5) 121.2(5) N(7) C(22) C(23) 104.2(4) N(l) C(7) C(8) 116.9(4) N(7) C(22) C(26) 112.2(4) 0(3) C(8) 0(4) 123.6(4) C(23) C(22) C(26) 113.3(5) 0(3) C(8) C(7) 121.6(4) C(22) C(23) C(24*) 109.1(9) 0(4) C(8) C(7) 114.8(4) C(22) C(23) C(24) 106.8(7) N(3) C(9) C(10) 103.9(6) C(23) C(24*) C(25) 109(1) N(3) C(9) C(10*) 100(1) C(23) C(24) C(25) 107(1) N(3) C(9) C(13) 112.1(4) N(7) C(25) C(24*) 99.1(8) C(10) C(9) C(13) 117.1(5) N(7) C(25) C(24) 107.8(8) C(10*) C(9) C(13) 97(1) 0(10) C(26) N(8) 126.6(5) C(9) C(10) C(ll) 106.8(8) 0(10) C(26) C(22) 120.1(5) C(9) C(10*) C(ll) 107(2) N(8) C(26) C(22) 113.2(4) C(10) C(ll) C(12) 103.2(6) Table 8.22 Geometry of l.pro-amide hydrogen bonds and C — H - 0 interactions (A, °). D—H...4 D—H H---4 D---4 / D—H---4 N(l)-^l(5)---0(3)(i) 0.89(6) 2.19(6) 3.075(5) 174(7) N(3)-^I(8)---0(3) 1.10(7) 2.66(7) 3.169(5) 107(4) N(3)—H(8)---0(4) 1.10(7) 1.92(7) 2.889(6) 145(5) N(3)-^(8)---0(5) 1.10(7) 2.47(7) 2.817(5) 97(4) N(3)-^I(9)---0(3) 1.05(9) 2.63(9) 3.169(5) 111(7) N(3)-H(9)---0(4) 1.05(9) 1.9(1) 2.732(6) 138(7) N(4>-41(17)---0(5) 1.03(7) 2.13(6) 3.075(8) 151(4) N(4)-+l(18)---0(8) 0.88(6) 2.31(6) 3.136(6) 156(6) N(4)-^I(18)---0(9) 0.88(6) 2.54(6) 2.988(6) 112(5) N(5)-^l(23)---0(8)(i) 0.83(5) 2.23(5) 3.028(6) 163(4) N(7)-fl(26)---0(8) 1.00(6) 2.36(5) 3.308(6) 158(5) N(7)-^l(26)---0(9) 1.00(6) 1.94(6) 2.775(7) 139(5) N(7)-^l(27)---0(9) 1.01(7) 1.92(7) 2.819(7) 146(5) N(7)-^I(27)---O(10) 1.01(7) 2.50(6) 2.801(6) 96(4) N(8)-^I(35)---O(10) 0.90(6) 2.21(6) 3.099(6) 167(4) N(8)-+l(36)---0(3) 0.94(6) 2.09(6) 3.010(5) 165(6) N(8)-41(36)---0(4) 0.94(6) 2.66(7) 3.396(6) 136(5) C(6)-^i(4)---0(3)(i) 0.98 2.57 3.525(6) 141 C(9)-^H(10)---O(5) 0.98 2.29 3.155(6) 150 C(10*)-^(11*)---O(7)(i) 0.98 2.45 3.15(3) 134 C(10*)-^l(ll*)---O(5) 0.98 2.58 2.86(3) 99 C(20)-^l(24)---O(8) 0.98 2.42 3.333(7) 158 C(22)-^I(28)---O(10) 0.98 2.20 3.148(6) 147 202 C(24)-^I(32)-0(2) 0^ 98 230 3.08(2) 135 Symmetry Codes: (i) -x, '/2+y, -z Table 8.23 Final atomic coordinates (fractional) and B(eq) (A2) of l.pro-ol. atom X V z B(ea) O(l) -0.2463(3) 0.5213(2) 0.4290(6) 9.1(2) 0(2) -0.1206(3) 0.4908(1) 0.5589(6) 8.2(1) 0(3) -0.0799(3) 0.7803(1) 0.5426(4) 5.1(1) 0(4) -0.2095(3) 0.8282(1) 0.6062(5) 5.7(1) 0(5) -0.0357(3) 0.7928(2) 0.1141(6) 8.3(1) 0(6) 0.2541(3) 0.9828(2) 1.0776(6) 8.4(2) 0(7) 0.1203(3) 1.0112(1) 0.9645(6) 8.0(1) 0(8) 0.0877(3) 0.7261(1) 0.9520(4) 4.76(9) 0(9) 0.2093(3) 0.6732(1) 0.8895(4) 4.80(9) 0(10) 0.0532(4) 0.7142(2) 1.3798(6) 9:1(1) N(l) -0.1129(3) 0.7161(2) 0.8039(6) 4.5(1) N(2) -0.1770(4) 0.5259(2) 0.5232(7) 6.0(1) N(3) -0.1432(3) 0.8644(1) 0.2970(6) 3.67(9) N(4) 0.1237(3) 07892(1) 0.6937(6) 4.3(1) N(5) 0.1802(4) 0.9766(2) 0.9926(6) 5.8(1) N(6) 0.1499(3) 0.6377(2) 1.1836(6) 4.2(1) C(l) -0.1293(3) 0.6711(2) 0.7324(6) 3.8(1) C(2) -0.2114(4) 0.6622(2) 0.6309(7) 4.4(1) C(3) -0.2252(4) 0.6151(2) 0.5639(6) 4.9(1) C(4) -0.1605(4) 0.5756(2) 0.5962(7) 4.4(1) C(5) -0.0780(4) 0.5824(2) 0.6954(7) 4.5(1) C(6) -0.0635(3) 0.6295(2) 0.7600(6) 4.1(1) C(7) -0.1718(4) 0.7616(2) 0.7803(6) 4.4(1) C(8) -0.1508(4) 0.7913(2) 0.6307(7) 3.9(1) C(9) -0.0496(3) 0.8769(2) 0.2066(6) 4.1(1) C(10) -0.0070(4) 0.9219(2) 0.2971(9) 6.4(2) C(ll) -0.0905(5) 0.9444(2) 0.3908(8) 6.9(2) C(12) -0.1828(4) 0.9146(2) 0.3514(7) 5.4(1) C(13) 0.0177(3) 0.8313(2) 0.1944(6) 5.2(1) C(14) 0.1381(4) 0.8333(2) 0.7734(6) 3.9(1) C(15) 0.2219(4) 0.8425(2) 0.8697(7) 4.6(1) C(16) 0.2352(3) 0.8892(2) 0.9411(6) 4.5(1) C(17) 0.1656(4) 0.9275(2) 0.9187(7) 4.5(1) C(18) 0.0824(4) 0.9188(2) 0.8262(8) 4.6(1) C(19) 0.0672(4) 0.8726(2) 0.7552(6) 4.3(1) C(20) 0.1837(4) 0.7434(2) 0.7166(6) 4.3(1) C(21) 0.1582(3) 0.7126(2) 0.8640(7) 3.6(1) C(22) 0.0401(4) 0.6374(2) 1.2268(6) 4.6(1) C(23) 0.0127(4) 0.5811(2) 1.2258(9) 7.5(2) C(24) 0.0916(5) 0.5552(2) 1.1293(9) 7.0(2) 203 C(25) 0.1828(4) 0.5837(2) 1.1678(8) 5.6(1) C(26) 0.0229(4) 0.6632(2) 1.3825(8) 7.0(2) H(5) -0.065(2) 0.722(1) 0.851(5) 1-8(9) H(8) -0.127(4) 0.840(2) 0.389(7) 7(1) H(9) -0.179(3) 0:848(1) 0.222(5) 3(1) H(19) 0.004(3) 0.770(2) 0.084(6) 6(1) H(24) 0.067(4) 0.789(2) 0.608(8) 9(1) H(27) 0.169(4) 0.653(2) 1.074(7) 8(1) H(28) 0.197(4) 0.654(2) 1.254(6) 5(1) Table 8.24 Bond lengths (A) of l.pro-ol with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.224(6) 0(2) N(2) 1.223(6) 0(3) C(8) 1.235(6) 0(4) C(8) 1.259(5) 0(5) C(13) 1.407(6) 0(6) N(5) 1.227(6) 0(7) N(5) 1.229(5) 0(8) C(21) 1.247(5) 0(9) C(21) 1.253(5) 0(10) C(26) 1.394(6) N(l) C(l) 1.344(6) N(l) C(7) 1.439(5) N(2) C(4) 1.458(7) N(3) C(9) 1.496(6) N(3) C(12) 1.489(6) N(4) C(14) 1.352(6) N(4) C(20) 1.453(5) N(5) C(17) 1.443(6) N(6) C(22) 1.503(6) N(6) C(25) 1.486(6) C(l) C(2) 1.408(7) C(l) C(6) 1.416(5) C(2) C(3) 1.370(8) , C(3) C(4) 1.372(7) C(4) C(5) 1.392(7) C(5) C(6) 1.363(6) C(7) C(8) 1.511(7) C(9) C(10) 1.514(7) C(9) C(13) 1.497(6) C(10) C(H) 1.486(8) C(ll) C(12) 1.491(7) C(14) C(15) 1.400(6) C(14) C(19) 1.403(5) C(15) C(16) 1.375(8) C(16) C(17) 1.376(6) C(17) C(18) 1.373(7) C(18) C(19) 1.366(6) C(20) C(21) 1.523(7) C(22) C(23) 1.519(6) C(22) C(26) 1.499(7) C(23) C(24) 1.492(8) C(24) C(25) 1.459(7) Table 8.25 Bond angles (°) of l.pro-ol with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 125.2(5) C(10) C(9) C(13) 115.6(4) 0(1) N(2) 0(2) 123.2(6) C(9) C(10) C(ll) 107.4(4) 0(1) N(2) C(4) 118.5(6) C(10) C(ll) C(12) 106.7(5) 0(2) N(2) C(4) 118.3(6) N(3) C(12) C(ll) 104.0(4) C(9) N(3) C(12) 104.9(4) 0(5) C(13) C(9) 107.7(4) 204 C(14) N(4) C(20) 124.2(4) N(4) C(14) C(15) 123.4(5) 0(6) N(5) 0(7) 122.2(6) N(4) C(14) C(19) 118.5(5) 0(6) N(5) C(17) 118.6(6) C(15) C(14) C(19) 118.0(5) 0(7) N(5) C(17) 119.1(6) C(14) C(15) C(16) 120.8(5) C(22) N(6) C(25) 107.7(4) C(15) C(16) C(17) 120.0(5) N(l) C(l) C(2) 123.1(5) N(5) C(17) C(16) 119.9(5) N(l) C(l) C(6) 120.1(5) N(5) C(17) C(18) 120.2(5) C(2) C(l) C(6) 116.9(5) C(16) C(17) C(18) 120.0(5) C(l) C(2) C(3) 120.3(5) C(17) C(18) C(19) 121.0(5) C(2) C(3) C(4) 120.9(5) C(14) C(19) C(18) 120.2(5) N(2) C(4) C(3) 119.7(5) N(4) C(20) C(21) 115.1(4) N(2) C(4) C(5) 119.3(5) 0(8) C(21) 0(9) 122.5(5) C(3) C(4) C(5) 121.1(5) 0(8) C(21) C(20) 120.4(4) C(4) C(5) C(6) 118.0(5) 0(9) C(21) C(20) 117.1(5) C(l) C(6) C(5) 122.8(5) N(6) C(22) C(23) 103.6(4) N(l) C(7) C(8) 116.2(4) N(6) C(22) C(26) 111.1(5) 0(3) C(8) 0(4) 123.4(5) C(23) C(22) C(26) 113.9(5) 0(3) C(8) C(7) 121.9(5) C(22) C(23) C(24) 106.1(5) 0(4) C(8) C(7) 114.7(5) C(23) C(24) C(25) 103.2(5) N(3) C(9) C(10) 102.9(4) N(6) C(25) C(24) 105.2(5) N(3) C(9) C(13) 110.9(4) 0(10) C(26) C(22) 111.9(5) Table 8.26 Geometry of l.pro-ol hydrogen bonds and C — H - 0 interactions (A, °). n—H...4 D—H H---4 n-A / n—H-.-4 0(5)-^(19)---0(8) 0.84(4) 1.94(5) 2.760(5) 163(5) N(l)-H(5)--0(8) 0.76(3) 2.21(3) 2.956(6) 168(4) N(3)-^I(8)---0(3) 1.02(5) 2.14(5) 3.141(6) 168(4) N(3)-H(8)-0(4) 1.02(5) 2.16(4) 2.919(6) 129(4) N(3)-H(9)-0(5) 0.90(4) 2.56(4) 2.818(6) 97(3) N(3)-^(9)--0(9)(ii) 0.90(4) 1.84(4) 2.701(6) 158(4) N(4)-H(24)---0(3) 1.04(6) 2.04(3) 3.001(5) 152(5) N(4)-^I(24)---O(10) 1.04(6) 2.75(6) 3.433(7) 123(4) N(6)-^(27)--0(8) 1.04(6) 2.43(6) 3.145(6) 174(5) N(6)-^(27)--0(9) 1.04(6) 1.73(6) 2.772(6) 125(4) N(6)-^I(28)---0(4)(ii) 0.97(5) 1.77(5) 2.729(6) 168(4) N(6)-^(28)---O(10) 0.97(5) 2.69(5) 2.901(6) 93(3) C(12)-HH(15)---0(4) 0.98 2.56 3.145(6) 119 Symmetry Codes: (i) -x, -y, z (ii) 'A+x, 'h-y, -z (iii) '/2-x, '/2+y, -z 205 8.8. 2,4-DinitrophenyIglycine (2) The acid 2,4-dinitrophenylglycine, (2) (Sigma), was recrystallized from methanol forming rod-like crystals. A crystal of approximate dimensions 0.20 x 0-20 x 0.30 mm was chosen for data collection. Crystallographic data for (2) appear in Table 8.27. An monoclinic cell with Z = 4 (assuming a density of 1.68 g/cm3) was indicated by preliminary measurements. 2296 reflections were collected, of which 2060 were unique and 1478 were observed (I > 3.0 o(T))- The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 93.9 -109.6°. The data for (2) were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences (hOl: I * 2n, OkO: k * 2n), the space group was determined to be P2i/c. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were found from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 3.68 xlO"5). Neutral atom scattering factors and the values of Af and Af" were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.035, Rw = 0.041 for 183 variables (GOF = 2.69; including zeros: R = 0.063, Rw = 0.046), with a negligible parameter shift in the 206 final refinement cycle. The final difference map showed electron density between -0.16 and 0.21 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.28-30, respectively. The structure of (2) is shown in Figure 8.9. The packing of (2) (Figure 4.7, reproduced here for convenience) consists of a dimer pair linked by an intermolecular O — H - O hydrogen bond, with the two molecules related by a center of inversion. In addition, each molecule also participates in two more intermolecular N — H - O hydrogen bonds, forming a two-dimensional network of molecules running parallel to the (100) plane of the crystal. Complete hydrogen bond and C—H- • 0 interaction details are given in Table 8.31. Figure 8.9 ORTEP of acid (2) (50% probability ellipsoids). 207 Figure 4.7 ORTEP packing diagram of (2) (50% probability ellipsoids). 8.9. (IS, 2S)-(+)-pseudoephedrine salt of (2): 2.eph. A crystal of approximate dimensions 0.25 x 0.20 x 0.15 mm was chosen for data collection. Crystallographic data for 2.eph appear in Table 8.27.' A triclinic cell with Z = 2 (assuming a density of 1.39 g/cm3) was indicated by preliminary measurements. 4172 reflections were collected, of which 3962 were unique and 3410 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 24 reflections with 28 = 93.7 - 111.1°. The data for 2.eph were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. 208 Based on a statistical analysis of the intensity distributions and a successful solution and refinement, the space group was determined to be PI . The structure was solved by direct-methods [161] and expanded using Fourier techniques. [166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions ( C — H = 0.98 A, B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 1.06 xlO"6). Neutral atom scattering factors and the values of AT and A?' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fc aic.[172] The refinement converged at R = 0.035, Rw = 0.037 for 556 variables (GOF = 2.64; including zeros: R = 0.048, Rw = 0.038), with the largest parameter shift in the final refinement cycle being 0.02a The final difference map showed electron density between -0.15 and 0.12 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.32-34, respectively. There are two 2.eph moieties in the asymmetric unit (Figure 8.10). The packing (Figure 8.11) consists of layers of 2,4-dinitrophenylglycinate anions and pseudoephedrinium cations, each alternating along the b-axis. Neighboring 2,4-dinitrophenylglycinate anions are oriented such that the charge-transfer axes between the glycine nitrogen and the para-nitro group are aligned anti-parallel to each other. The meta-nitro groups, however, are all oriented in the same direction. 209 The cation and anion layers are linked via both N — H - O and O — H - 0 hydrogen bonds. Each moiety, cation or anion, participates in hydrogen bonding with its counterion layers directly above and below it. Complete hydrogen bond and C — H - 0 interaction details are given in Table 8.35. Figure 8.10 ORTEP diagram of 2.eph (50% probability ellipsoids). 210 Figure 8.11 CHARON packing diagram of 2.eph. 8.10. S-(-)-Proline t-butyl ester salt of (2): 2.pro-but. A crystal of approximate dimensions 0.45 x 0.11 x 0.20 mm was chosen for data collection. Crystallographic data for 2.pro-but appear in Table 8.27. A monoclinic cell with Z = 4 (assuming a density of 1.36 g/cm3) was indicated by preliminary measurements. 4608 reflections were collected, of which 4329 were unique and 2957 211 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 24 reflections with 26 = 53.4 - 61.7°. The data for 2.pro-but were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences of (OkO: k * 2n) the space group was determined to be P2\. The structure was solved by direct-methods [162] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 8.87 xlO" ). Neutral atom scattering factors and the values of AT and Af were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.055, Rw = 0.054 for 574 variables (GOF = 3.54; including zeros: R = 0.100, Rw = 0.057), with the largest parameter shift in the final refinement cycle being 0.0 lo . Both proline rings were found to be partially disordered. In each case the rings were found to adopt the two "envelope" conformations. The populations of C ( l l ) and C(28) were both found to be 0.72. 0(15), the carbonyl oxygen of one of the ester groups was also found to be disordered. The refined position of 0(15*) leads to a short (1.01 A) C—O double bond, however the bond angles around C(30) do not differ significantly from those around the other ester group, where no 212 evidence of disorder was detectable. The final difference map showed electron density between -0.18 and 0.35 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.36-38, respectively. There are two 2.pro-but moieties per asymmetric unit (Figure 8.12), and the molecular orientations within the cell are very similar to that found in the p-nitroaniline salt l.pro-but, as discussed in section 8.4. The packing (Figure 4.8, reproduced here for convenience) consists of alternating 2,4-dinitrophenylglycinate anion and proline t-butyl ester cation layers. Each proline t-butyl ester cation is coordinated to two 2,4-dinitrophenylglycinate anions directly above it via N — H - 0 hydrogen bonds. Neighboring 2,4-dinitrophenylglycinate anions have their meta-nitro groups oriented in opposite directions while the para-nitro groups in each layer are oriented in the same direction, roughly along the b-axis. Complete hydrogen bond and C — H - 0 interaction details are given in Table 8.39. 213 214 Figure 4.8 ORTEP packing stereodiagram of 2.pro-but (50% probability ellipsoids). Only the major disordered fragment is shown. 215 Table 8.27 Crystallographic data for (2), 2.eph and 2.pro-but. (2) 2.eph 2.pro-but Formula C 8 H v N 3 0 6 C 1 8 H 2 2 N 4 0 7 C 1 7 H 2 4 N 4 0 8 fw 241.16 406.39 412.40 Crystal system monoclinic triclinic monoclinic Space group P2,/c PI Pit a, A 5.118(2) 11.000(2) 7.978(1) b, A 12.763(1) 13.018(2) 30.195(2) c A 14.7484(9) 7.9314(8) 8.4303(5) an 90 99.34(1) 90 PC) 97.72(1) 106.89(1) 95.598(8) YC) 90 110.42(1) 90 V 954.7(3) 973.5(2) 2021.1(3) z 4 2 4 Pcakd, g/cm3 1.68 1.39 1.36 F(000) 496 428 872 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) H, cm" 6.1 8.7 8.8 Crystal size, mm 0.20x0.20x0.30 0.25 x 0.20x0.15 0.45x0.11 x0.20 Transmission factors 0.97-1.00 0.94-1.00 0.78-1.00 Scan type co-26 co-20 co-26 Scan range, ° in co 1.00+ 0.20 tan 9 0.84 + 0.20 tan 6 1.05+ 0.20 tan 9 Scan speed, °/min 32.0 32.0 8.0 Data collected +h, +k, ±1 +h, ±k, ±1 +h, +k, ±1 154.9 155.1 155.3 Crystal decay -0.6% +0.2% +0.4% Total reflections 2296 4172 4608 Total unique reflections 2060 3962 4329 ^merge 0.021 0.025 0.066 No. of reflections with / >3o(/) 1475 3410 2957 No. of variables 183 556 574 p-factor 0.00 0.001 0.003 R 0.035 0.035 0.055 Rw 0.041 0.037 0.054 Goodness of fit (GOF) 2.64 2.64 3.54 Max A/a (final cycle) 0.00 0.02 0.01 Residual density e/A3 -0.16 to+0.21 -0.15 to +0.12 -0.18 to +0.35 216 Table 8.28 Final atomic coordinates (fractional) and B(eq) (A2) of (2). atom X v z B(ea) 0(1) 0.2960(3) 0.2692(1) 0.8235(1) 5.28(4) 0(2) 0.6334(3) 0.1933(1) 0.8969(1) 4.57(4) 0(3) 1.1037(3) -0.0714(1) 0.7637(1) 4.85(4) 0(4) 1.1073(4) -0.0707(1) 0.6175(1) 5.56(5) 0(5) 0.1916(3) 0.4341(1) 0.4511(1) 3.53(3) 0(6) 0.4738(3) 0.4184(1) 0.5796(1) 3.85(3) N(l) 0.2076(3) 0.2574(1) 0.6433(1) 3.20(4) N(2) 0.4891(3) 0.2115(1) 0.8258(1) 3.44(4) N(3) 1.0246(4) -0.0384(1) 0.6865(1) 3.72(4) C(l) 0.4152(4) 0.1915(1) 0.6547(1) 2.83(4) C(2) 0.5484(4) 0.1623(1) 0.7422(1) 2.86(4) C(3) 0.7450(4) 0.0875(2) 0.7523(1) 3.03(4) C(4) 0.8201(4) 0.0414(1) 0.6762(1) 3.04(4) C(5) 0.7081(4) 0.0722(2) 0.5888(1) 3.42(4) C(6) 0.5131(4) 0.1448(2) 0.5791(1) 3.37(4) C(7) 0.1039(4) 0.3040(2) 0.5563(1) 3.27(4) C(8) 0.2767(4) 0.3913(1) 0.5307(1) 2.88(4) H(l) 0.834(4) 0.072(2) 0.807(1) 3.4(5) H(2) 0.767(4) 0.041(2) 0.538(2) 4.7(5) H(3) 0.439(4) 0.160(2) 0.526(2) 4.5(5) H(4) 0.164(5) 0.288(2) 0.692(2) 4.9(6) H(5) 0.074(4) 0.256(2) 0.508(1) 3.5(5) H(6) -0.065(4) 0.334(2) 0.561(1) 3.8(5) H(7) 0.318(5) 0.487(2) 0.438(2) 6.9(7) Table 8.29 Bond lengths (A) of (2) with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.229(2) N(3) C(4) 1.454(3) 0(2) N(2) 1.221(2) C(l) C(2) 1.426(2) 0(3) N(3) 1.230(2) C(l) C(6) 1.414(3) 0(4) N(3) 1.225(2) C(2) C(3) 1.380(3) 0(5) C(8) 1.314(2) C(3) C(4) 1.368(3) 0(6) C(8) 1.210(2) C(4) C(5) 1.395(3) N(l) C(l) 1.348(3) C(5) C(6) 1.356(3) N(l) C(7) 1.448(2) C(7) C(8) 1.502(3) N(2) C(2) 1.452(2) 217 Table 8.30 Bond angles (°) of (2) with standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 123.8(2) C(l) C(2) C(3) 122.1(2) 0(1) N(2) 0(2) 122.0(2) C(2) C(3) C(4) 119.3(2) 0(1) N(2) C(2) 119.6(2) N(3) C(4) C(3) 119.5(2) 0(2) N(2) C(2) 118.4(2) N(3) C(4) C(5) 119.7(2) 0(3) N(3) 0(4) 123.1(2) C(3) C(4) C(5) 120.8(2) 0(3) N(3) C(4) 118.7(2) C(4) C(5) C(6) 119.7(2) 0(4) N(3) C(4) 118.2(2) C(l) C(6) C(5) 122.6(2) N(l) C(l) C(2) 123.3(2) N(l) C(7) C(8) 111.7(2) N(l) C(l) C(6) 121.4(2) 0(5) C(8) 0(6) 124.3(2) C(2) C(l) C(6) 115.3(2) 0(5) C(8) C(7) 113.4(2) N(2) C(2) C(l) 121.8(2) 0(6) C(8) C(7) 122.2(2) N(2) C(2) C(3) 116.1(2) Table 8.31 Geometry of (2) hydrogen bonds and C—H- • • 0 interactions (A, °) D—H H - •A n—A / n—H-.4 0 (5 )—H(7) -0 (6 ) ° > 0.98(3) 1.65(3) 2.626(2) 177(3) N(l)-H(4)-0(1) 0.88(2) 1.98(2) 2.640(2) 131(2) N(l)-H(4)-0(3) ( > 0.88(2) 2.40(2) 3.128(3) 141(2) C(5)—ii(2y--0(4f > 0.94(2) 2.49(2) 3.305(3) 146(2) Symmetry Codes: (i) -x, '/2+y, '/2-z (ii) -x, -y, -z (iii) x, Vz-y, Vi+z Table 8.32 Final atomic coordinates (fractional) and B(eq) (A2) of 2.eph. atom X V z B(ea) 0(1) 0.2670(8) 0.1159(7) 0.275(1) 5.70(7) 0(2) 0.2818(8) 0.2767(6) 0.417(1) 5.97(8) 0(3) 0.6337(8) 0.6322(6) 0.480(1) 5.21(7) 0(4) 0.8049(8) 0.6383(6) 0.398(1) 6.35(8) 0(5) 0.4967(8) -0.1446(6) -0.044(1) 4.42(6) 0(6) 0.3375(8) -0.1198(6) 0.058(1) 5.45(7) 0(7) 0.3655(8) 0.3187(6) 0.875(1) 5.45(7) 0(8) 0.2166(8) 0.1581(6) 0.869(1) 5.93(8) 0(9) 0.1989(8) -0.1989(6) 0.583(1) 5.88(7) 0(10) 0.3634(8) -0.2030(6) 0.490(1) 6.59(8) 0(11) 0.8554(8) 0.5773(6) 0.798(1) 4.07(5) 0(12) 0.6782(8) 0.5510(6) 0.892(1) 5.06(6) 218 0(13) 0.7536(8) 0.9292(7) -0.071(1) 5.00(7) 0(14) 0.0597(8) 0.5284(7) -0.262(1) 4.42(6) N(l) 0.4774(8) 0.1052(6) 0.185(1) 3.76(6) N(2) 0.3270(8) 0.2209(6) 0.335(1) 4.13(7) N(3) 0.6946(8) 0.5847(7) 0.413(1) 4.43(7) N(4) 0.5862(8) 0.3274(7) 0.797(1) 3.72(7) N(5) 0.3176(8) 0.2133(7) 0.836(1) 4.04(7) N(6) 0.3070(8) -0.1512(7) 0.559(1) 4.77(7) N(7) 0.8841(8) 0.7938(6) -0.144(1) 3.59(6) N(8) 0.3282(8) 0.6330(7) -0.228(1) 3.59(6) C(l) 0.5261(8) 0.2192(7) 0.242(1) 3.31(6) C(2) 0.4571(8) 0.2799(7) 0.313(1) 3.43(7) C(3) 0.5126(8) 0.3991(7) 0.368(1) 3.53(7) C(4) 0.6357(8) 0.4602(7) 0.352(1) 3.67(7) C(5) 0.7083(8) 0.4061(7) 0.286(1) 4.22(8) C(6) 0.6558(9) 0.2893(7) 0.235(1) 4.07(8) C(7) 0.5471(8) 0.0424(7) 0.116(1) 3.71(7) C(8) 0.4509(8) -0.0847(7) 0.039(1) 3.85(7) C(9) 0.5165(8) 0.2133(7) 0.742(1) 3.33(7) C(10) 0.3850(8) 0.1531(7) 0.754(1) 3.50(7) C(ll) 0.3168(8) 0.0352(7) 0.695(1) 3.71(7) C(12) 0.3772(8) -0.0261(7) 0.619(1) 3.91(7) C(13) 0.5044(9) 0.0273(7) 0.605(1) 4.45(9) C(14) 0.5732(8) 0.1430(7) 0.666(1) 4.16(8) C(15) 0.7204(8) 0.3894(7) 0.789(1) 3.81(7) C(16) 0.7524(8) 0.5169(7) 0.831(1) 3.53(7) C(17) 0.8574(8) 0.9719(7) 0.264(1) 3.59(7) C(18) 0.7637(8) 0.8951(7) 0.319(1) 4.23(8) C(19) 0.7546(9) 0.9290(7) 0.488(1) 5.0(1) C(20) 0.8361(9) 1.0385(8) 0.601(1) 6.0(1) C(21) 0.9295(9) 1.1160(7) 0.547(1) 6.4(1) C(22) 0.9405(9) 1.0825(7) 0.380(1) 5.08(9) C(23) 0.8688(8) 0.9383(7) 0.080(1) 3.62(7) C(24) 0.8874(8) 0.8274(7) 0.048(1) 3.43(7) C(25) 1.0172(9) 0.8313(7) 0.189(1) 5.3(1) C(26) 1.0078(9) 0.8606(7) -0.181(1) 4.68(9) C(27) 0.1142(8) 0.4952(7) 0.039(1) 3.61(7) C(28) 0.0808(9)' 0.3793(7) -0.006(1) 5.2(1) C(29) 0.0347(9) 0.3146(7) 0.101(1) 6.7(1) C(30) 0.0220(9) 0.3658(8) 0.258(1) 6.5(1) C(31) 0.0555(9) 0.4810(8) 0.305(1) 5.6(1) C(32) 0.1020(9) 0.5451(7) 0.197(1) 4.36(8) C(33) 0.1628(8) 0.5667(6) -0.080(1) 3.49(7) C(34) 0.2924(8) 0.5616(7) -0.106(1) 3.80(7) C(35) 0.4162(8) 0.6008(7) 0.073(1) 5.4(1) C(36) 0.4085(8) 0.6002(7) -0.331(1) 5.0(1) H(l) 0.392(4) 0.060(3) 0.196(5) 5.2(9) H(7) 0.559(3) 0.367(3) 0.842(4) 2.4(7) H(19) 0.688(4) 0.908(3) -0.050(5) 3.5(8) H(24) 0.791(5) 0.797(4) -0.234(7) 8(1) 219 H(25) 0.873(4) 0.716(4) -0.162(5) 4.7(9) H(35) 1.001(6) 0.540(5) -0.250(7) 7(1) H(40) 1.248(5) 0.627(4) -0.309(6) 6(1) H(41) 1.377(4) 0.705(4) -0.156(6) 4.8(9) Table 8.33 Bond lengths (A) of 2.eph with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.228(4) C(3) C(4) 1.363(5) 0(2) N(2) 1.221(4) C(4) C(5) 1.387(5) 0(3) N(3) 1.226(4) C(5) C(6) 1.364(5) 0(4) N(3) 1.223(4) C(7) C(8) 1.519(5) 0(5) C(8) 1.265(4) C(9) C(10) 1.426(4) 0(6) C(8) 1.235(4) C(9) C(14) 1.425(4) 0(7) N(5) 1.232(4) C(10) C(ll) 1.377(5) 0(8) N(5) 1.221(4) C(ll) C(12) 1.372(5) 0(9) N(6) 1.220(4) C(12) C(13) 1.375(5) 0(10) N(6) 1.230(4) C(13) C(14) 1.353(5) O(ll) C(16) 1.262(4) C(15) C(16) 1.528(5) 0(12) C(16) 1.227(4) C(17) C(18) 1.393(5) 0(13) C(23) 1.421(4) C(17) C(22) 1.385(5) 0(14) C(33) 1.429(4) C(17) C(23) 1.510(5) N(l) C(l) 1.333(4) C(18) C(19) 1.383(5) N(l) C(7) 1.446(4) C(19) C(20) 1.366(6) N(2) C(2) 1.446(4) C(20) C(21) 1.387(7) N(3) C(4) 1.453(4) C(21) C(22) 1.379(6) N(4) C(9) 1.336(4) C(23) C(24) 1.518(4) N(4) C(15) 1.440(4) C(24) C(25) 1.515(5) N(5) C(10) 1.451(4) C(27) C(28) 1.380(5) N(6) C(12) 1.460(5) C(27) C(32) 1.383(5) N(7) C(24) 1.503(4) C(27) C(33) 1.505(5) N(7) C(26) 1.477(4) C(28) C(29) 1.369(6) N(8) C(34) 1.490(4) C(29) C(30) 1.383(7) N(8) C(36) 1.485(4) C(30) C(31) 1.371(7) C(l) C(2) 1.428(4) C(31) C(32) 1.371(6) C(l) C(6) 1.423(5) C(33) C(34) 1.519(4) C(2) C(3) 1.392(5) C(34) C(35) 1.509(5) 220 Table 8.34 Bond angles (°) of 2.eph with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 125.2(3) C(10) C(ll) C(12) 118.7(3) 0(1) N(2) 0(2) 121.7(3) N(6) C(12) C(ll) 118.9(3) 0(1) N(2) C(2) 119.2(3) N(6) C(12) C(13) 119.4(3) 0(2) N(2) C(2) 119.1(3) C(ll) C(12) C(13) 121.7(3) 0(3) N(3) 0(4) 122.4(3) C(12) C(13) C(14) 120.1(3) 0(3) N(3) C(4) 119.3(3) C(9) C(14) C(13) 122.0(3) 0(4) N(3) C(4) 118.3(3) N(4) C(15) C(16) 109.1(3) C(9) N(4) C(15) 125.2(3) 0(11) C(16) 0(12) 126.3(3) 0(7) N(5) 0(8) 121.7(3) 0(11) C(16) C(15) 114.8(3) 0(7) N(5) C(10) 119.4(3) 0(12) C(16) C(15) 118.9(3) 0(8) N(5) C(10) 118.8(3) C(l 8) C(17) C(22) 119.0(3) 0(9) N(6) 0(10) 123.4(3) .. C(18) C(17) C(23) 121.7(3) 0(9) N(6) C(12) 119.5(3) C(22) C(17) C(23) 119.4(3) 0(10) N(6) C(12) 117.1(3) C(17) C(18) C(19) 120.3(4) C(24) N(7) C(26) 117.7(3) C(18) C(19) C(20) 120.3(4) C(34) N(8) C(36) 114.5(3) C(19) C(20) C(21) 120.1(4) N(l) C(l) C(2) 124.5(3) C(20) C(21) C(22) 120.0(4) N(l) C(l) C(6) 120.3(3) C(17) C(22) C(21) 120.4(4) C(2) C(l) C(6) 115.2(3) 0(13) C(23) C(17) 113.1(2) N(2) C(2) C(l) 121.9(3) 0(13) C(23) C(24) 109.6(3) N(2) C(2) C(3) 116.2(3) C(17) C(23) C(24) 111.9(3) C(l) C(2) C(3) 121.9(3) N(7) C(24) C(23) 108.8(3) C(2) C(3) C(4) 119.3(3) N(7) C(24) C(25) 111.3(3) N(3) C(4) C(3) 119.1(3) C(23) C(24) C(25) 114.5(3) N(3) C(4) C(5) 119.5(3) C(28) C(27) C(32) 118.0(3) C(3) C(4) C(5) 121.4(3) C(28) C(27) C(33) 121.7(3) C(4) C(5) C(6) 119.6(3) C(32) C(27) C(33) 120.3(3) C(l) C(6) C(5) 122.5(3) C(27) C(28) C(29) 121.3(4) N(l) C(7) C(8) 110.2(3) C(28) C(29) C(30) 119.9(4) 0(5) C(8) 0(6) 126.3(3) C(29) C(30) C(31) 119.5(4) 0(5) C(8) C(7) 114.5(3) C(30) C(31) C(32) 120.1(4) 0(6) C(8) C(7) 119.1(3) C(27) C(32) C(31) 121.1(4) N(4) C(9) C(10) 124.5(3) 0(14) C(33) C(27) 112.1(3) N(4) C(9) C(14) 120.2(3) 0(14) C(33) C(34) 105.2(2) C(10) C(9) C(14) 115.3(3) C(27) C(33) C(34) 112.7(3) N(5) C(10) C(9) 121.4(3) N(8) C(34) C(33) 107.7(2) N(5) C(10) C(ll) 116.3(3) N(8) C(34) C(35) 110.4(3) C(9) C(10) C(ll) 122.3(3) C(33) C(34) C(35) 113.8(3) 221 Table 8.35 Geometry of 2.eph hydrogen bonds and 0—H- - O interactions(A, °). D—H— 4 D—H H--4 0(13)-^(19) -0(5) 0.75(4) 1.99(4) 2.733(4) 168(4) 0(14)—H(35)-•0(11) 0.74(5) 1.95(5) 2.686(3) 176(6) N(l)-H(l)- •0(1) 0.96(4) 1.96(4) 2.650(4) 127(3) N(l)-H(l)- •0(6) 0.96(4) 2.20(4) 2.638(4) 107(3) N(4)-H(7)" •0(7) 0.77(3) 2.10(3) 2.644(4) 128(3) N(4)-H(7)" 0(12) 0.77(3) 2.20(3) 2.618(4) 115(3) N(7)—H(24)- ••0(3) 1.08(5) 2.50(5) 3.168(4) 119(3) N(7)-^J(24)- •0(13) 1.08(5) 2.22(5) 2.725(4) 106(3) N(7)—H(25)- 0(11) 0.96(4) 1.71(4) 2.670(4) 178(4) N(7)-H(25)" •0(12) 0.96(4) 2.65(4) 3.298(4) 125(3) N(8)-H(40)- ••0(9) 0.90(5) 2.71(5) 3.326(4) 127(4) N(8)-^I(40)- •0(14) 0.90(5) 2.19(4) 2.693(4) 114(3) N(8)—H(41)- -0(5) 0.89(4) 1.82(4) 2.693(4) 168(4) C(24)-H(20)- -0(12) 0.98 2.56 3.301(4) 132 C(26)-H(28) -0(6) 0.98 2.54 3.468(5) 163 C(36)-fl(42)- -0(12) 0.98 2.54 3.315(5) 137 C(36)-H(43)- -0(10) 0.98 2.45 3.236(5) 136 Table 8.36 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-but. atom X v z B(ea) 0(1) -0.0482(6) 0.4353 0.1935(6) 6.1(1) 0(2) -0.1546(5) 0.3851(2) 0.0324(6) 7.0(1) 0(3) 0.1827(8) 0.2928(2) -0.2578(7) 7.8(2) 0(4) 0.4508(7) 0.3010(2) -0.2471(7) 7.5(2) 0(5) 0.4960(6) 0.5208(2) 0.5062(5) 5.6(1) 0(6) 0.2242(6) 0.5149(2) 0.4249(5) 5-9(1) 0(7) 1.1935(6) 0.6243(2) 0.3627(6) 6.8(1) 0(8) 1.0936(5) 0.6734(2) 0.1756(5) 4.6(1) 0(9) 1.2238(5) 0.4485(2) 0.7263(6) 5.8(1) 0(10) 1.3255(6) 0.4015(2) 0.5633(6) 6.7(1) 0(11) 0.9824(7) 0.3035(2) 0.2494(6) 7.0(2) 0(12) 0.7137(8) 0.2983(3) 0.2700(7) 8.2(2) 0(13) 0.6827(6) 0.5291(2) 0.9836(6) 6.3(1) 0(14) 0.9540(6) 0.5141(2) 0.9724(5) 5.3(1) 0(15*) 0.665(6) 0.629(2) 0.847(4) 8.3(6) 0(15) 0.674(4) 0.630(1) 0.897(2) 6.6(4) 0(16) 0.5726(5) 0.6783(2) 0.6882(5) 4.5(1) N(l) 0.2767(6) 0.4520(2) 0.2184(6) 4.8(1) N(2) -0.0327(7) 0.4051(2) 0.0935(7) 5.1(1) N(3) 0.3125(9) 0.3110(2) -0.2047(7) 5.6(2) 222 N(4) 0.9677(7) 0.5615(2) 0.2461(7) 4.1(1 N(5) 0.8960(7) 0.4550(2) 0.7466(7) 4.7(1 N(6) 1.2025(7) 0.4179(3) 0.6243(7) 4.9(1 N(7) 0.8536(9) 0.3138(2) 0.3088(7) 5.6(2 N(8) 0.4420(8) 0.5673(2) 0.7624(7) 4.3(1 C(l) 0.2797(7) 0.4167(3) 0.1182(7) 4.0(1 C(2) 0.1372(7) 0.3940(3) 0.0548(7) 4.0(1 C(3) 0.1474(8) 0.3589(3) -0.0490(7) 4.6(2 C(4) 0.3008(8) 0.3463(3) -0.0925(7) 4.2(1 C(5) 0.4470(8) 0.3668(3) -0.0300(8) 4.7(2 C(6) 0.4369(7) 0.4019(3) 0.0739(8) 4.9(2 C(7) 0.4235(8) 0.4737(3) 0.2895(8) 4.8(2 C(8) 0.3731(9) 0.5062(3) 0.4182(7) 4.6(2 C(9) 0.9413(7) 0.6086(2) 0.1974(6) 3.8(1 C(10) 0.7864(9) 0.6232(3) 0.2754(9) 6.3(2 C(ll*) 0.679(3) 0.5854(9) 0.286(4) 6.4(8 C(ll) 0.784(2) 0.5906(4) 0.414(1) 7.0(3 C(12) 0.8352(9) 0.5488(3) 0.3491(8) 5.9(2 C(13) 1.0925(8) 0.6362(3) 0.2541(7) 4.4(1 C(14) 1.2221(8) 0.7089(2) 0.2214(7) 4.1(1 C(15) 1.3981(8) 0.6918(3) 0.2182(8) 5.5(2 C(16) 1.187(1) 0.7273(3) 0.3825(8) 5.8(2 C(17) 1.179(1) 0.7431(3) 0.0906(9) 6.6(2 C(18) 0.8919(7) 0.4203(3) 0.6412(7) 4.3(1 C(19) 1.0329(7) 0.4022(3) 0.5787(7) 4.0(1 C(20) 1.0201(8) 0.3676(3) 0.4721(7) 4.3(1 C(21) 0.8671(9) 0.3504(3) 0.4266(7) 4.6(2 C(22) 0.7217(8) 0.3658(3) 0.4831(8) 5.2(2 C(23) 0.7371(8) 0.4017(3) 0.5900(8) 5.2(2 C(24) 0.7509(8) 0.4735(3) 0.8040(8) 5.2(2 C(25) 0.801(1) 0.5092(3) 0.9301(7) 4.7(2 C(26) 0.4230(7) 0.6136(3) 0.7035(6) 3.8(1 C(27) 0.2569(7) 0.6288(3) 0.7649(8) 5.0(2 C(28*) 0.242(3) 0.5945(9) 0.908(3) 5.2(6 C(28) 0.159(1) 0.5879(5) 0.781(2) 7.5(4 C(29) 0.287(1) 0.5543(3) 0.8346(9) 5.8(2 C(30) 0.5723(8) 0.6413(3) 0.7689(8) 4.3(2 C(31) 0.7018(7) 0.7136(3) 0.7291(7) 4.0(1 C(32) 0.8745(9) 0.6948(3) 0.719(1) 6.6(2 C(33) 0.679(1) 0.7316(3) 0.8866(9) 6.9(2 C(34) 0.660(1) 0.7469(3) 0.598(1) 8.2(2 H(4) 0.162(7) 0.467(2) 0.289(7) 4(1) H(7) 1.063(6) 0.559(2) 0.283(6) 2(1) H(8) 0.995(9) 0.539(2) 0.164(9) 8(2) H(28) 0.992(7) 0.469(2) 0.771(7) 3(1) H(31) 0.538(8) 0.563(2) 0.791(7) 4(1) H(32) 0.455(6) 0.551(2) 0.686(6) 3(1) 223 Table 8.37 Bond lengths (A) of 2.pro-but with estimated standard deviations. atom atom distance atom atom distance O(l) N(2) 1.256(7) C(l) C(2) 1.391(8) 0(2) N(2) 1.216(7) C(l) C(6) 1.416(8) 0(3) N(3) 1.218(7) C(2) C(3) 1.381(8) 0(4) N(3) 1.230(7) C(3) C(4) 1.365(9) 0(5) C(8) 1.251(7) C(4) C(5) 1.379(8) 0(6) C(8) 1.224(7) C(5) C(6) 1.381(8) 0(7) C(13) 1.213(7) C(7) C(8) 1.545(9) 0(8) C(13) 1.305(7) C(9) C(10) 1.521(8) 0(8) C(14) 1.507(7) C(9) C(13) 1.504(8) 0(9) N(6) 1.262(7) C(10) C(ll*) 1.44(3) 0(10) N(6) 1.253(7) C(10) C(ll) 1.53(1) 0(11) N(7) 1.226(7) C(ll) C(12) 1.45(1) 0(12) N(7) 1.225(8) C(14) C(15) 1.498(9) 0(13) C(25) 1.239(8) C(14) C(16) 1.518(9) 0(14) C(25) 1.250(8) C(14) C(17) 1.525(9) 0(15*) C(30) 1.01(3) C(18) C(19) 1.399(8) 0(15) C(30) 1.33(2) C(18) C(23) 1.387(8) 0(16) C(30) 1.310(7) C(19) C(20) 1.376(8) 0(16) C(31) 1.499(6) C(20) C(21) 1.348(8) N(l) C(l) 1.361(7) C(21) C(22) 1.378(9) N(l) C(7) 1.423(8) C(22) C(23) 1.407(9) N(2) C(2) 1.464(7) C(24) C(25) 1.538(9) N(3) C(4) 1.436(8) C(26) C(27) 1.539(8) N(4) C(9) 1.492(8) C(26) C(30) 1.514(8) N(4) C(12) 1.483(8) C(27) C(28*) 1.60(3) N(5) C(18) 1.373(8) C(27) C(28) 1.47(1) N(5) C(24) 1.412(8) C(28*) C(29) 1.42(2) N(6) C(19) 1.450(7) C(28) C(29) 1.48(1) N(7) C(21) 1.482(8) C(31) C(32) 1.501(9) N(8) C(26) 1.486(8) C(31) C(33) 1.462(9) N(8) C(29) 1.482(9) C(31) C(34) 1.506(9) Table 8.38 Bond angles (°) of 2.pro-but with estimated standard deviations. atom atom atom angle atom atom atom angle C(13) 0(8) C(14) 121.4(5) 0(8) C(13) C(9) 111.1(5) C(30) 0(16) C(31) 121.6(5) 0(8) C(14) C(15) 111.4(5) C(l) N(l) C(7) 123.9(5) 0(8) C(14) C(16) 108.0(5) 0(1) N(2) 0(2) 121.2(6) 0(8) C(14) C(17) 101.4(5) 0(1) N(2) C(2) 118.1(5) C(15) C(14) C(16) 113.4(5) 0(2) N(2) C(2) 120.7(6) C(15) C(14) C(17) 111.3(6) 224 0(3) N(3) 0(4) 122.5(6) C(16) C(14) C(17) 110.6(6) 0(3) N(3) C(4) 118.1(7) N(5) C(18) C(19) 125.0(6) 0(4) N(3) C(4) 119.4(6) N(5) C(18) C(23) 118.3(6) C(9) N(4) C(12) 108.6(5) C(19) C(18) C(23) 116.7(6) C(18) N(5) C(24) 123.8(6) N(6) C(19) C(18) 122.4(6) 0(9) N(6) 0(10) 120.6(5) N(6) C(19) C(20) 115.5(6) 0(9) N(6) C(19) 118.7(5) C(18) C(19) C(20) 122.1(6) 0(10) N(6) C(19) 120.7(6) C(19) C(20) C(21) 119.1(6) 0(11) N(7) 0(12) 124.9(7) N(7) C(21) C(20) 118.8(6) O(ll) N(7) C(21) 117.0(6) N(7) C(21) C(22) 118.4(6) 0(12) N(7) C(21) 117.8(7) C(20) C(21) C(22) 122.7(6) C(26) N(8) C(29) 109.0(5) C(21) C(22) C(23) 117.3(6) N(l) C(l) C(2) 124.2(5) C(18) C(23) C(22) 122.0(6) N(l) C(l) C(6) 118.8(5) N(5) C(24) C(25) 110.4(5) C(2) C(l) C(6) 117.0(6) 0(13) C(25) 0(14) 126.5(6) N(2) C(2) C(l) 122.7(6) 0(13) C(25) C(24) 116.0(6) N(2) C(2) C(3) 115.5(6) 0(14) C(25) C(24) 117.5(6) C(l) C(2) C(3) 121.7(6) N(8) C(26) C(27) 103.3(5) C(2) C(3) C(4) 119.5(6) N(8) C(26) C(30) 110.2(5) N(3) C(4) C(3) 120.0(6) C(27) C(26) C(30) 112.7(5) N(3) C(4) C(5) 118.6(6) C(26) C(27) C(28*) 101(1) C(3) C(4) C(5) 121.3(6) C(26) C(27) C(28) 105.2(6) C(4) C(5) C(6) 119.1(6) C(27) C(28*) C(29) 101(1) C(l) C(6) C(5) 121.2(6) C(27) C(28) C(29) 104.4(8) N(l) C(7) C(8) 109.2(5) N(8) C(29) C(28*) 101.8(9) 0(5) C(8) 0(6) 127.3(6) N(8) C(29) C(28) 105.6(6) 0(5) C(8) C(7) 113.5(6) 0(15*) C(30) 0(16) 127(2) 0(6) C(8) C(7) 119.3(6) 0(15*) C(30) C(26) 123(2) N(4) C(9) C(10) 104.9(5) 0(15) C(30) 0(16) 127(1) N(4) C(9) C(13) 110.7(5) 0(15) C(30) C(26) 124(1) C(10) C(9) C(13) 111.3(5) 0(16) C(30) C(26) 108.8(6) C(9) C(10) C(ll*) 108(1) 0(16) C(31) C(32) 109.4(5) C(9) C(10) C(ll) 102.4(7) 0(16) C(31) C(33) 109.2(5) C(10) C(ll) C(12) 104.2(7) 0(16) C(31) C(34) 102.0(5) N(4) C(12) C(ll) 103.8(6) C(32) C(31) C(33) 112.8(6) 0(7) C(13) 0(8) 126.8(6) C(32) C(31) C(34) 110.6(6) 0(7) C(13) C(9) 122.0(6) C(33) C(31) C(34) 112.2(6) Table 3.39 Geometry of 2.pro-but hydrogen bonds (A, °). D - H H-.-4 D.-A / /V-H.-4 N(l)-H(4)-0(1) 1.22(6) 2.03(6) 2.628(7) 105(3) N(l)-^I(4)-"0(6) 1.22(6) 1.88(6) 2.637(7) 114(4) N(4)-^(7)-0(6) 0.79(5) 2.13(5) 2.799(7) 141(5) N(4)-H(7)-0(7) 0.79(5) - 2.30(5) 2.733(7) 115(4) N(4)-4i(8)--0(14) 1.01(7) 1.78(7) 2.707(4) 151(6) N(5)-«(28)- - -0(9) 0.88(6) 2.02(6) 2.645(7) 128(5) 225 N(5)-H(28)" •0(14) 0.88(6) 2.23(4) 2.619(7) 107(4) N(8)-H(31)" •0(13) 0.79(6) 2.15(4) 2.793(7) 138(6) N(8)-fl(31)-- 0(15) 0.79(6) 2.44(6) 2.81(2) 110(5) N(8)-^l(31)- 0(15*) 0.79(6) 2.29(7) 2.63(4) 107(5) N(8)—H(32)- ••0(5) 0.83(5) ' 1.82(6) 2.646(4) 173(5) C(5)-H(2)- •0(2) 0.98 2.45 3.218(7) 132 C(9)-H(9)- 0(15) 0.98 2.46 3.22(2) 133 C(10)-^i(ll)- ••0(15) 0.98 2.52 3.24(2) 128 C(12*)-H(12* )-0(5) 0.98 2.52 3.15(3) 118 C(ll)—H(13) -0(5) 0.98 2.51 3.27(1) 126 C(ll*)-4i(13*) -0(13) 0.98 2.43 3.07(3) 129 C(12)-H(15)- •0(13) 0.98 2.59 3.256(9) 125 C(15)-H(18) -0(7) 0.98 2.32 2.948(8) 121 C(16)-H(20) ••0(7) 0.98 2.49 3.113(9) 120 C(22)—H(26)--0(12) 0.98 2.45 2.713(9) 94 C(23)-^(27)- ••0(10) 0.98 2.49 3.269(7) 134 C(24)-H(30) ••0(5) 0.98 2.40 3.389(8) 179 C(26)-H(33) ••0(7) 0.98 2.47 3.268(7) 140 C(29)-HH(39) •0(9) 0.98 2.44 3.347(9) 155 C(32)HH(42)- -0(15) 0.98 2.36 3.01(3) 125 C(32)-HH(42)" •0(15*) 0.98 2.28 2.86(5) 119 C(33)-^J(44)- -0(15) 0.98 2.42 3.06(3) 122 C(33)—H(44)-•0(15*) 0.98 2.59 3.11(5) 113 C(34)-^l(46)- •0(ll) ( i ) 0.98 2.60 3.463(9) 148 Symmetry codes: (i) -x, y+'A, -z. 8.11. S-(-)-ProIine methyl ester salt of (2): 2.pro-meth. A crystal of approximate dimensions 0.25 x 0.10 x 0.70 mm was chosen for data collection. Crystallographic data for 2.pro-meth appear in Table 8.40. A monoclinic cell with Z = 2 (assuming a density of 1.51 g/cm3) was indicated by preliminary measurements. 3025 reflections were collected, of which 2803 were unique and 2163 observed (I > 3.0 o(I)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 82.1 -95.1°. The data for 226 2.pro-meth were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences of (OkO: k * 2n), the space group was determined to be P2\. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A, B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 3.45 xlO"6). Neutral atom scattering factors and the values of AT and AS" were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.041, Rw = 0.046 for 407 variables (GOF = 2.58; including zeros: R = 0.067, Rw = 0.058), with the largest parameter shift in the final refinement cycle being 0.11a. The final difference map showed electron density between -0.19 and 0.24 e/A3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.41-43, respectively. 2.pro-meth (Figure 4.10, reproduced for convenience) forms a 2:1 acid/amine complex (rather than the expected 1:1 salt) that is similar in nature to the p-nitroaniline salt, l.pro-meth, as discussed in section 8.6. In this case the acid proton H(7) is shared almost evenly between 0(5) and 0(11) [0(5)—H(7) = 1.21(7) A, 0(11)---H(7) = 1.30(7) A] by means of a strong O—H---0 hydrogen bond. The refined position of H(14), the 227 second acid proton, suggests that in the solid state it has undergone only partial dissociation to the proline nitrogen N(7) [0(12)—H(14) = 1.3(1) A , N(7)---H(14) = 1.4(1) A] . The proline ring is coordinated to both carboxylic acid groups via both N — H - O and O—H---N hydrogen bonds. The orientation of the two chromophores has their para-nitro groups anti-parallel to each other while the two meta-nitro groups in each complex are aligned in the same direction. By virtue of the 2-fold screw axis, however, each meta-nitro group is oppositely oriented with respect to its symmetry related unit. Unlike most of the structures discussed in this study, there is no network of hydrogen bonds propagating throughout the crystal. Instead, all the hydrogen bonding takes place within the same 2:1 complex. Each 2.pro-meth unit, along with its symmetry related unit, forms two layers of 2,4-dinitrophenylglycines "sandwiching" a layer of proline methyl ester (Figure 8.13). Complete hydrogen bond and C — H - 0 interaction details are given in Table 8.44. 05 Figure 4.10 ORTEP diagram of 2.pro-meth (50% probability ellipsoids). 228 Figure 8.13 CHARON packing diagram of 2.pro-meth. 8.12. S-(-)-ProIine benzyl ester salt of (2): 2.pro-benz. A crystal of approximate dimensions 0.30 x 0.20 x 0.15 mm was chosen for data collection. Crystallographic data for 2.pro-benz appear in Table 8.40. An orthorhombic cell with Z = 4 (assuming a density of 1.47 g/cm3) was indicated by preliminary measurements. 3690 reflections were collected, of which 1672 were observed (I > 3.0 o(I)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 28 = 51.4 - 81.2°. The data for 2.pro-benz were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. 229 Based on systematic absences (h00:h * 2n, OkO: k * 2n, 00/: / * 2n) the space group was determined to be P2i2i2i. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 2.28 xlO"6). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.049, Rw = 0.047 for 468 variables (GOF = 3.00; including zeros: R = 0.096, Rw = 0.049), with the largest parameter shift in the final refinement cycle being 0.07 a. C(19) of the proline ring was found to be partially disordered by adopting the two "envelope" conformations. The population of the major fragment was found to be 0.87. The final difference map showed electron density between -0.20 and 0.18 e/A 3 . Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.45-8.47, respectively. 2.pro-benz (Figure 4.11, reproduced for convenience) forms a 2:1 acid/amine complex rather than the expected 1:1 salt. In this case there is a strong O — H - 0 hydrogen bond between the two carboxylate groups, with the refined position of H(13) showing that it is more strongly associated to O ( l l ) than to 0(5) [0(11)—H(13) = 230 0.90(6) A , 0(5)--H(13) = 1.59(6) A] . The para-nitro groups are aligned anti-parallel to each other while the meta-nitro groups are oriented in the same direction. The complex propagates through the crystal by alternating layers of 2,4-dinitrophenylglycine and proline benzyl ester along the direction of the a-axis (Figure 8.14). By virtue of the 2-fold screw axis parallel to the c-axis, layers Of 2,4-dinitrophenylglycine dimers stack one upon the other. The proline benzyl ester orients itself so that its two NH's are in position to act as hydrogen bond donors to two carboxylate oxygens, one above the NH's, one below. The meta-nitro groups of these stacked dimers are oriented oppositely to one another. Complete hydrogen bond and C—H- • O interaction details are given in Table 8.48. Figure 4.11 ORTEP diagram of 2.pro-benz (50% probability ellipsoids). Only the major disordered fragment is shown. 231 Figure 8.14 CHARON packing diagram of 2.pro-benz. 232 Table 8.40 Crystallographic data for 2.pro-meth and 2.pro-benz. 2.pro-meth 2.pro-benz Formula C22H25N7O14 C28H29N7O14 fw 611.48 687.58 Crystal system monoclinic orthorhombic Space group P2i P2i2 ,2 , a , k 7.242(1) 21.289(2) b,k 11.845(1) 21.314(2) c, A 15.8743(9) 6.8603(5) « ( ° ) 90 90 PC) 99.35(1) 90 m 90 90 V 1343.6(2) 3112.8(5) z 2 4 Pealed, g/cm3 1.51 1.47 F(000) 636 1432 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A = 1.54178 A) H, cm"1 11.1 10.3 Crystal size, mm 0.25 x 0.10x0.70 0.30x0.20x0.15 Transmission factors 0.81-1.00 0.92-1.00 Scan type co-26 co-26 Scan range, ° in co 1.05 + 0.20 tan 6 0.89 + 0.20 tan 9 Scan speed, °/min 32.0 16.0 Data collected +h, +k, ±1 +h, +k, +1 155.3 155.3 Crystal decay +28.6% -1.4% Total reflections 3025 3690 Total unique reflections 2803 Emerge 0.027 No. of reflections with / >2>a{I) 2163 2343 No. of variables 407 468 p-factor 0.01 0.002 R 0.041 0.049 /?w 0.046 0.047 Goodness of fit (GOF) 2.358 3.00 Max A/a (final cycle) 0.01 0.07 Residual density c/A3 -0.19 to+0.24 -0.20 to +0.18 233 Table 8.41 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-meth. atom X V z B(ea) 0(1) 0.3882(6) 0.1999 0.6452(2) 6.9(1) 0(2) 0.3243(7) 0.3631(4) 0.5892(2) 7.2(1) 0(3) 0.1335(6) 0.6705(4) 0.7371(2) 6.8(1) 0(4) 0.1095(6) 0.6587(4) 0.8703(3) 6.8(1) 0(5) 0.4567(5) -0.0924 0.9220(2) 4.96(8) 0(6) 0.4857(6) -0.0437(4) 0.7898(2) 5.70(9) 0(7) 0.7523(6) 0.4333(4) 0.6659(2) 6.4(1) 0(8) 0.8657(6) 0.2809(4) 0.6242(2) 6.6(1) 0(9) 0.9552(6) -0.0451(4) 0.7952(2) 6.5(1) 0(10) 0.9242(6) -0.0392(4) 0.9280(2) 5.92(9) 0(11) 0.5861(5) 0.7131(4) 0.9237(2) 5.44(8) 0(12) 0.5971(5) 0.6627(4) 0.7897(2) 5.09(8) 0(13) 0.7115(6) 0.9911(4) 0.5993(2) 6.6(1) 0(14) 0.9712(6) 0.8988(4) 0.5821(3) 7.0(1) N(l) 0.3724(5) 0.1653(4) 0.8075(2) 3.86(8) N(2) 0.3407(6) 0.2987(4) 0.6502(2) 5.06(10) N(3) 0.1485(5) 0.6182(4) 0.8043(3) 4.76(10) N(4) 0.7384(5) 0.4639(4) 0.8299(2) 3.69(8) N(5) 0.8105(6) 0.3376(4) 0.6796(2) 4.47(9) N(6) 0.9207(5) 0.0059(4) 0.8576(3) 4.44(9) N(7) 0.5558(7) 0.8117(5) 0.6633(3) 5.4(1) C(l) 0.3222(5) 0.2744(4) 0.8059(2) 3.26(9) C(2) 0.3032(6) 0.3434(4) 0.7312(2) 3.62(9) C(3) 0.2480(6) 0.4544(5) 0.7313(3) 3.9(1) C(4) 0.2116(6) 0.5019(5) 0.8057(3) 3.68(9) C(5) 0.2300(6) 0.4393(4) 0.8802(2) 3.63(9) C(6) 0.2848(6) 0.3286(4) 0.8806(2) 3.40(9) C(7) 0.3873(6) 0.0937(4) 0.8822(3) 3.61(9) C(8) 0.4462(6) -0.0219(4) 0.8591(3) 3.8(1) C(9) 0.7847(5) 0.3554(4) 0.8349(3) 3.25(9) C(10) 0.8169(6) 0.2885(4) 0.7640(2) 3.41(9) C(ll) 0.8600(6) 0.1749(4) 0.7715(3) 3.64(9) C(12) 0.8764(6) 0.1249(5) 0.8502(3) 3.63(9) C(13) 0.8504(6) 0.1861(4) 0.9218(3) 3.64(9) C(14) 0.8068(6) 0.2981(4) 0.9149(2) 3.50(9) C(15) 0.7050(6) 0.5347(4) 0.9007(2) 3.46(9) C(16) 0.6238(6) 0.6465(4) 0.8683(3) 3.72(9) C(17) 0.7473(8) 0.7986(5) 0.6430(3) 4.6(1) C(18) 0.7366(9) 0.6965(5) 0.5841(3) 5.3(1) C(19) 0.5368(9) 0.6621(6) 0.5675(3) 6.5(2) C(20) 0.4269(9) 0.7631(6) 0.5875(4) 6.7(2) C(21) 0.807(1) 0.9069(5) 0.6052(3) 5.2(1) C(22) 1.045(1) 0.9970(7) 0.5438(5) 10.0(2) H(l) 0.391(7) 0.124(5) 0.763(4) 7(1) H(7) 0.512(7) -0.188(5) 0.913(3) 6(1) 234 H(8) 0.727(7) 0.504(4) 0.792(3) 4(1) H(14) 0.55(2) 0.75(1) 0.738(7) 21(2) H(15) 0.534(6) 0.884(5) 0.667(3) 4(1) Table 8.42 Bond lengths (A) of 2.pro-meth with estimated standard deviations. atom atom distance atom atom distance O(l) N(2) 1.226(5) 0(2) N(2) 1.223(5) 0(3) N(3) 1.222(5) 0(4) N(3) 1.226(5) 0(5) C(8) 1.294(5) 0(6) C(8) 1.208(5) 0(7) N(5) 1.216(5) 0(8) N(5) 1.225(5) 0(9) N(6) 1.221(5) 0(10) N(6) 1.237(5) O(ll) C(16) 1.244(5) 0(12) C(16) 1.246(5) 0(13) C(21) 1.207(6) 0(14) C(21) 1.307(7) 0(14) C(22) 1.455(8) N(l) C(l) 1.342(6) N(l) C(7) 1.447(5) N(2) C(2) 1.457(5) N(3) C(4) 1.450(6) N(4) C(9) 1.328(6) N(4) C(15) 1.453(5) N(5) C(10) 1.454(5) N(6) C(12) 1.445(6) N(7) C(17) 1.483(7) N(7) C(20) 1.512(7) C(l) C(2) 1.428(5) C(l) C(6) 1.413(5) C(2) C(3) 1.375(6) C(3) C(4) 1.372(6) C(4) C(5) 1.384(6) C(5) C(6) 1.370(6) C(7) C(8) 1.497(6) C(9) C(10) 1.427(6) C(9) C(14) 1.425(5) C(10) C(ll) 1.383(6) C(ll) C(12) 1.370(6) C(12) C(13) 1.387(6) C(13) C(14) 1.364(6) C(15) C(16) 1.506(6) C(17) C(18) 1.523(6) C(17) C(21) 1.508(7) C(18) C(19) 1.485(8) C(19) C(20) 1.499(9) Table 8.43 Bond angles (°) of 2.pro-meth with estimated standard deviations. atom atom atom angle atom atom atom angle C(21) 0(14) C(22) 118.2(5) 0(13) C(21) C(17) 122.6(6) C(l) N(l) C(7) 124.3(4) 0(14) C(21) C(17) 112.3(5) 0(1) N(2) 0(2) 122.5(4) C(4) C(5) C(6) 120.3(4) 0(1) N(2) C(2) 119.8(4) C(l) C(6) C(5) 121.8(4) 0(2) N(2) C(2) 117.7(4) N(l) C(7) C(8) 108.7(3) 0(3) N(3) 0(4) 123.2(4) 0(5) C(8) 0(6) 124.8(4) 0(3) N(3) C(4) 118.5(4) 0(5) C(8) C(7) 112.7(4) 0(4) N(3) C(4) 118.3(4) 0(6) C(8) C(7) 122.5(4) 235 C(9) N(4) C(15) 125.8(4) N(4) C(9) C(10) 124.2(4) 0(7) N(5) 0(8) 121.8(4) N(4) C(9) C(14) 120.4(4) 0(7) N(5) C(10) 119.7(4) C(10) C(9) C(14) 115.4(4) 0(8) N(5) C(10) 118.5(4) N(5) C(10) C(9) 121.4(4) 0(9) N(6) 0(10) 122.9(4) N(5) C(10) C(ll) 116.2(4) 0(9) N(6) C(12) 119.3(4) " C(9) C(10) C(ll) 122.4(4) 0(10) N(6) C(12) 117.8(4) C(10) C(ll) C(12) 119.0(4) C(17) N(7) C(20) 105.4(4) N(6) C(12) C(ll) 118.7(4) N(l) C(l) C(2) 123.8(4) N(6) C(12) C(13) 120.1(4) N(l) C(l) C(6) 120.7(4) C(ll) C(12) C(13) 121.2(4) C(2) C(l) C(6) 115.5(4) C(12) C(13) C(14) 120.2(4) N(2) C(2) C(l) 121.3(4) C(9) C(14) C(13) 121.8(4) N(2) C(2) C(3) 116.4(4) N(4) C(15) C(16) 110.3(3) C(l) C(2) C(3) 122.4(4) O(ll) C(16) 0(12) 126.5(4) C(2) C(3) C(4) 119.3(4) 0(11) C(16) C(15) 115.7(4) N(3) C(4) C(3) 118.7(4) 0(12) C(16) C(15) 117.8(4) N(3) C(4) C(5) 120.6(4) . N(7) C(17) C(18) 105.1(4) C(3) C(4) C(5) 120.7(4) N(7) C(17) C(21) 109.5(4) C(18) C(19) C(20) 106.2(5) C(18) C(17) C(21) 114.9(4) N(7) C(20) C(19) 101.1(5) C(17) C(18) C(19) 106.1(5) 0(13) C(21) 0(14) 125.1(6) Table 8.44 Geometry of 2.pro-meth hydrogen bonds and C—H- • -O interactions (A, °). D—H H---4 D--A 0(5)-H(7)-0(ll) 1.21(7) 1.30(7) 2.482(5) 163(5) 0 (12) -« (14) - - -0 (6 ) 1.3(1) 2.7(1) 3.578(6) 122(6) 0(12)-«(14)- - -N(7) 1.3(1) 1.4(1) 2.654(6) 160(8) N(l)-H(l)-0(1) 0.87(6) 2.03(5) 2.634(6) 125(5) N(l)-H(l)-0(6) 0.87(6) 2.19(6) 2.637(6) 112(4) N(4)-+l(8)---0(7) 0.77(5) 2.15(5) 2.650(6) 122(5) N(4)-4I(8)---0(12) 0.77(5) 2.14(5) 2.609(6) 119(4) N(7)-fl(15)--0(6) 0.89(6) 2.22(5) 2.755(6) 118(4) N(7)-+l(15)---0(13) 0.89(6) 2.17(5) 2.672(8) 116(4) C(5)-H(3)---O(10) 0.98 2.53 3.412(7) 150 C(6)—H(4)---0(ll)(i) 0.98 2.43 164 C(13)-H(10)---O(4) 0.98 2.39 3.278(7) 150 C(17)-41(16)-"0(3) 0.98 2.53 3.322(7) 137 C(18)-H(17)---0(2)(i) 0.98 2.59 3.367(7) 136 Symmetry codes: (i) -x, 'A+y, -z 236 Table 8.45 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-benz. atom X v z B(eq) O(l) -0.01178(9) 0.44433(8) 0.0167(5) 5.92(6) 0(2) 0.08843(9) 0.43740(9) 0.0308(5) 7.38(7) 0(3) 0.2218(1) 0.6138(1) 0.0630(7) 11.9(1) 0(4) 0.1837(1) 0.7058(1) 0.0731(7) 11.1(1) 0(5) -0.23026(8) 0.57973(9) -0.0495(4) 5.41(6) 0(6) -0.17232(8) 0.49391(9) -0.0046(4) 5.86(5) 0(7) 0.52828(9) 0.33531(9) 0.0215(5) 7.03(6) 0(8) 0.4432(1) 0.28334(9) 0.0306(6) 9.25(9) 0(9) 0.2445(1) 0.3748(1) 0.0627(8) 13.8(1) 0(10) 0.2337(1) 0.4733(1) 0.055(1) 15.7(2) O(H) 0.65690(8) 0.55934(9) -0.0060(5) 5.41(5) 0(12) 0.65086(8) 0.45510(9) -0.0039(5) 5.49(5) 0(13) 0.8162(1) 0.7058(1) 0.6373(4) 6.95(7) 0(14) 0.8339(1) 0.7242(1) 0.3158(4) 5.94(6) N(l) -0.0662(1) 0.5546(1) -0.0028(5) 4.13(6) N(2) 0.0412(1) 0.4688(1) 0.0244(5) 4.92(6) N(3) 0.1783(1) 0.6496(2) 0.0575(6) 7.99(9) N(4) 0.5258(1) 0.4576(1) 0.0113(5) 4.30(6) N(5) 0.4710(1) 0.3328(1) 0.0244(6) 6.00(7) N(6) 0.2653(1) 0.4279(2) 0.0489(9) 10.1(1) N(7) 0.7276(1) 0.6197(1) 0.5668(5) 5.09(7) C(l) -0.0075(1) 0.5757(1) 0.0110(6) 3.86(6) C(2) 0.0467(1) 0.5362(1) 0.0231(6) 3.96(6) C(3) 0.1064(1) 0.5604(1) 0.0350(6) 4.67(7) C(4) 0.1145(1) 0.6239(1) 0.0381(6) 5.35(7) C(5) 0.0638(1) 0.6644(1) 0.0281(6) 5.21(8) C(6) 0.0044(1) 0.6417(1) 0.0141(6) 4.74(7) C(7) -0.1221(1) 0.5929(1) -0.0237(6) 4.20(7) C(8) -0.1792(1) 0.5511(1) -0.0240(6) 4.34(6) C(9) 0.4635(1) 0.4499(1) 0.0187(5) 3.81(6) C(10) 0.4345(1) 0.3901(1) 0.0280(6) 4.29(6) C(ll) 0.3702(1) 0.3840(1) 0.0361(7) 5.67(8) C(12) 0.3334(1) 0.4352(1) 0.0408(7) 5.99(8) C(13) 0.3591(1) 0.4950(1) 0.0298(7) 5.45(8) C(14) 0.4225(1) 0.5018(1) 0.0230(6) 4.25(6) C(15) 0.5573(1) 0.5171(1) 0.0076(6) 4.30(6) C(16) 0.6275(1) 0.5062(1) -0.0028(6) 4.37(6) C(17) 0.7560(1) 0.6526(1) 0.3973(5) 4.63(7) C(18) 0.7025(2) 0.6874(2) 0.2915(7) 6.9(1) C(19) 0.6431(2) 0.6603(2) 0.3907(8) 6.9(1) C(19*) 0.677(2) 0.701(1) 0.467(6) 7.4(7) C(20) 0.6650(2) 0.6493(2) 0.5961(7) 6.9(1) C(21) 0.8064(2) 0.6958(2) 0.4714(6) 5.00(7) C(22) 0.8769(1) 0.7755(1) 0.3685(6) 5.42(8) C(23) 0.9076(2) 0.7958(1) 0.1825(6) 4.90(7) 237 C(24) 0.9724(2) 0.8029(1) 0.1765(7) 6.27(9) C(25) 1.0007(2) 0.8221(2) 0.0040(8) 7.5(1) C(26) 0.9654(2) 0.8351(2) -0.1566(7) 7.5(1) C(27) 0.9009(2) 0.8289(2) -0.1457(7) 7.6(1) C(28) 0.8727(2) 0.8101(2) 0.0209(7) 6.6(1) H(4) -0.074(1) 0.517(1) 0.021(6) 6.2(8) H(10) 0.549(1) 0.432(1) 0.021(6) 4.7(8) H(13) 0.699(2) 0.559(2) -0.019(8) 10(1) H(15) 0.717(2) 0.577(2) 0.483(6) 9(1) Table 8.46 Bond lengths (A) of 2.pro-benz with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.243(4) C(l) C(6) 1.431(6) 0(2) N(2) 1.209(4) C(2) C(3) 1.374(6) 0(3) N(3) 1.202(6) C(3) C(4) 1.366(7) 0(4) N(3) 1.207(6) C(4) C(5) 1.384(7) 0(5) C(8) 1.259(5) C(5) C(6) 1.358(6) 0(6) C(8) 1.234(5) C(7) C(8) 1.508(6) 0(7) N(5) 1.220(5) C(9) C(10) 1.418(6) 0(8) N(5) 1.209(5) C(9) C(14) 1.408(6) 0(9) N(6) 1.219(7) C(10) C(ll) 1.378(6) O(10) N(6) 1.180(7) C(ll) C(12) 1.343(7) 0(11) C(16) 1.294(5) C(12) C(13) 1.390(7) 0(12) C(16) 1.197(5) C(13) C(14) 1.359(6) 0(13) C(21) 1.177(7) C(15) C(16) 1.515(6) 0(14) C(21) 1.359(7) C(17) C(18) 1.542(8) 0(14) C(22) 1.472(6) C(17) C(21) 1.502(7) N(l) C(l) 1.332(5) C(18) C(19) 1.55(1) N(l) C(7) 1.450(5) C(18) C(19*) 1.35(7) N(2) C(2) 1.442(5) C(19) C(20) 1.50(1) N(3) C(4) 1.471(6) C(19*) C(20) 1.44(6) N(4) C(9) 1.337(5) C(22) C(23) 1.498(8) N(4) C(15) 1.436(5) C(23) C(24) 1.388(8) N(5) C(10) 1.447(6) C(23) C(28) 1.369(9) N(6) C(12) 1.458(6) C(24) C(25) 1.39(1) N(7) C(17) 1.485(7) C(25) C(26) 1.36(1) N(7) C(20) 1.488(7) C(26) C(27) 1.38(1) C(l) C(2) 1.429(6) C(27) C(28) 1.351(9) 238 Table 8.47 Bond angles (°) of 2.pro-benz with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 126.0(4) C(ll) C(10) C(9) 121.2(4) 0(2) N(2) O(l) 121.6(4) C(ll) C(10) N(5) 117.1(4) 0(2) N(2) C(2) 118.9(4) C(9) C(10) N(5) 121.6(4) 0(1) N(2) C(2) 119.4(4) C(12) C(ll) C(10) 120.3(5) 0(3) N(3) 0(4) 123.7(5) C(ll) C(12) C(13) 120.9(4) 0(3) N(3) C(4) 118.5(5) C(ll) C(12) N(6) 119.6(5) 0(4) N(3) C(4) 117.7(5) C(13) C(12) N(6) 119.4(5) C(9) N(4) C(15) 125.0(4) C(14) C(13) C(12) 119.4(5) 0(8) N(5) 0(7) 121.9(4) C(13) C(14) C(9) 122.2(4) 0(8) N(5) C(10) 118.1(4) N(4) C(15) C(16) 109.1(4) 0(7) N(5) C(10) 120.0(4) 0(12) C(16) 0(11) 126.6(4) 0(10) N(6) 0(9) 123.5(5) 0(12) C(16) C(15) 123.3(4) 0(10) N(6) C(12) 118.7(6) 0(11) C(16) C(15) 110.0(4) 0(9) N(6) C(12) 117.6(6) N(7) C(17) C(21) 108.4(5) C(17) N(7) C(20) 105.8(5) N(7) C(17) C(18) 107.1(5) N(l) C(l) C(2) 124.3(4) C(21) C(17) C(18) 113.1(5) N(l) C(l) C(6) 119.9(4) C(17) C(18) C(19) 102.5(5) C(2) C(l) C(6) 115.8(4) C(19*) C(18) C(17) 89(2) C(l) C(2) N(2) 121.4(4) C(20) C(19) C(18) 102.6(6) C(3) C(2) C(l) 121.9(4) C(18) C(19*) C(20) 117(3) C(3) C(2) N(2) 116.6(4) N(7) C(20) C(19) 102.5(5) C(4) C(3) C(2) 119.4(4) C(19*) C(20) N(7) 94(2) C(3) C(4) C(5) 121.2(4) 0(13) C(21) 0(14) 127.0(6) C(3) C(4) N(3) 119.2(5) 0(13) C(21) C(17) 124.4(6) C(5) C(4) N(3) 119.5(5) 0(14) C(21) C(17) 108.4(5) C(6) C(5) C(4) 120.5(4) 0(14) C(22) C(23) 106.1(5) C(5) C(6) C(l) 121.1(4) C(28) C(23) C(24) 119.4(7) N(l) C(7) C(8) 109.2(4) C(28) C(23) C(22) 121.1(5) 0(6) C(8) 0(5) 126.6(4) C(24) C(23) C(22) 119.4(6) 0(6) C(8) C(7) 119.2(4) C(23) C(24) C(25) 119.3(7) 0(5) C(8) C(7) 114.1(4) C(26) C(25) C(24) 120.6(6) N(4) C(9) C(14) 121.3(4) C(25) C(26) C(27) 119.0(7) N(4) C(9) C(10) 122.9(4) C(28) C(27) C(26) 121.0(8) C(14) C(9) C(10) 115.8(4) C(27) C(28) C(23) 120.7(6) 239 Table 8.48 Geometry of 2.pro-benz hydrogen bonds and C — H - 0 interactions (A, "). D—H H-.-4 D--A / D—M--A 0(ll)-H(13)-0(5) 0.90(6) 1.59(6) 2.460(4) 163(6) N(l)-H(4)-0(1) 0.83(5) 2.05(5) 2.625(5) 127(4) N(l)-H(4)-0(6) 0.83(5) 2.16(5) 2.603(5) 114(4) N(4)-H(10)-O(7) 0.75(4) 2.10(4) 2.608(5) 126(4) N(4)—H(10)-O(12) 0.75(4) 2.23(4) 2.666(5) 118(4) N(7)-H(14)—0(5) 1.17(5) 1.913(5) 2.909(7) 140(1) N(7)-H(14)•••0(12)(i, 1.17(5) 2.633(4) 3.078(5) 101(1) N(7)-H(14)-0(13) 1.17(5) 2.331(4) 2.676(6) 94(1) N(7)—H(15)---0(6)(i) 1.11(6) 1.78(6) 2.738(5) 142(6) C(3)-H(l)-O(10) 0.98 2.31 3.288(8) 175 C(13)-H(8)---O(10) 0.98 2.43 2.714(6) 96 C(17)-H(16)---0(5) 0.98 2.59 3.499(9) 143 C(19*)-^J(19*)---0(8)(iii) 0.98 2.00 3.11(5) 168 C(19)-^(20)---O(8)(iii) 0.98 2.34 3.248(8) 153 C(19*)-^I(20*)"-O(13) 0.98 2.55 3.18(5) 114 C(20)-^i(21)---O(ll) 0.98 2.58 3.340(9) 132 C(22)-41(23)---0(9)(iii) 0.98 2.51 3.374(7) 148 C(22>-H(24)---O(7)0) 0.98 2.47 3.279(7) 139 Symmetry Codes: (i) 'A-x, -y, 'A+z (ii) 'A+x, 'A-y, -z (iii) -x, 'A+y, 'A-z 8.13. S-(-)-ProlinoI salt of (2): 2.pro-ol. A crystal of approximate dimensions 0.20 x 0.11 x 0.18 mm was chosen for data collection. Crystallographic data for 2.pro-ol appear in Table 8.49. A monoclinic cell with Z = 4 (assuming a density of 1.44 g/cm3) was indicated by preliminary measurements. 3613 reflections were collected, of which 3313 were unique and 1827 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 29 = 45.1 - 56.2°. The data for 240 2.pro-ol were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences of (OkO: k * 2n), the space group was determined to be P2\. The structure was solved by direct-methods [161] and expanded using Fourier techniques. [166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 4.26 xlO"6). Neutral atom scattering factors and the values of Af and Af were taken from the International Tables for X-ray Crystallography. [168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.037, Rw = 0.036 for 472 variables (GOF = 1.80; including zeros: R = 0.111, Rw = 0.044), with the largest parameter shift in the final refinement cycle being 0.03 a. The only disorder in the structure occurs in the proline ring where C ( l l ) adopts both positions of the "envelope" conformation. The population of the major fragment was found to be 0.53. The final difference map showed electron density between -0.12 and 0.11 e/A 3 . Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.50-52, respectively. The 2.pro-oI structure (Figure 8.15) consists of two moieties per asymmetric unit. The two 2,4-dinitrophenylglycinate moieties are oriented so that the angle between the two para (amine-nitro) charge-transfer axes is 149°. Alternating layers of 2,4-241 dinitrophenylglycinate anions and prolinol cations stack one upon the other along the direction of the b-axis. A series of N—H- • O and O—H- • O hydrogen bonds coordinates each prolinol to two 2,4-dinitrophenylglycinate anions. The anions are aligned such that the meta-nitro groups in each layer are oriented in the same direction. By virtue of the 2-fold screw axis, however, successive layers of anions have their meta-nitro groups oriented in opposite directions. Figure 8.16 shows the crystal packing of the salt. Complete hydrogen bond and C — H - O interaction details are given in Table 8.53. 242 Figure 8.15 ORTEP diagram of 2.pro-ol (50% probability ellipsoids). Only the major disordered fragment is shown 243 Figure 8.16 ORTEP packing stereodiagram of 2.pro-oI (50% probability ellipsoids). Only the major disordered fragment is shown. 8.14. S-(-)-Prolinamide salt of (2): 2.pro-amide. A crystal of approximate dimensions 0.20 x 0.15 x 0.25 mm was chosen for data collection. Crystallographic data for 2.pro-amide appear in Table 8.49. A monoclinic 244 cell with Z = 4 (assuming a density of 1.43 g/cm3) was indicated by preliminary measurements. 2085 reflections were collected, of which 1970 were unique and 1421 observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 20 =50.1 - 63.2°. The data for 2.pro-amide were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on a statistical analysis of the intensity distributions and a successful solution and refinement, the space group was determined to be PA. The structure was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Only those hydrogens involved in hydrogen bonding were found from difference Fourier syntheses and refined isotropically, all others were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bbondedatom). A secondary extinction coefficient correction was applied (final coefficient = 4.12 xlO"6). Neutral atom scattering factors and the values of Af and AF were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in F c ai c.[172] The refinement converged at R = 0.038, Rw = 0.040 for 256 variables (GOF = 2.53; including zeros: R = 0.072, Rw = 0.043), with the largest parameter shift in the final refinement cycle being 0.66a. C ( l l ) of the proline ring was found to be partially disordered by adopting the two "envelope" conformations. The population of the major fragment was found to be 0.90. The crystal lattice was also found to contain solvent from which the 245 salt was recrystallized. Ethanol is found at the centre of the unit cell, with C(14) residing on the 4-fold symmetry axis, while the methanol is found at the cell edge, with 0(9) residing on the b 4-fold axis. In subsequent refinements the two solvents were refined isotropically. The presence of solvent in the lattice is supported by the ' H - N M R spectrum which has peaks at chemical shifts associated with both methanol and ethanol. Refinement of the two solvents showed that the population of methanol was significantly less than 0.25, which one would expect from its position on a 4-fold axis. Instead, the best model had a methanol population of 0.125. Since methanol is the more volatile of the two solvents it was thought that perhaps the trapped methanol was diffusing from the lattice. The same batch of crystals was gently heated under reduced pressure in an effort to remove the solvent from the lattice; however, both the ' H - N M R data and newly collected X-ray data revealed no change in the composition of the crystal. The final difference map showed electron density between -0.14 and 0.16 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.54-56, respectively. The structure of 2.pro-amide is shown in Figure 8.17. The 2.pro-amide packing (Figure 8.18) consists of a series of intermolecular N—H---0 hydrogen bonds forming a tetramer of anions and cations centered about a 4-fold axis. Each prolinamide acts as both a hydrogen bond donor and a hydrogen bond acceptor with its neighboring prolinamides, in addition to being coordinated to two 2,4-dinitrophenylglycinates, one above the amine NH's and one from below to form a channel of tetramers directed along the c-axis. The methanol resides within this channel of prolinamides. Difference Fourier 246 syntheses were able to locate neither the methanolic nor the ethanolic proton, however the distances of both 0(9) and 0(10), the methanol and ethanol oxygens respectively, to the next nearest hydrogen bond acceptor are short enough to suggest that hydrogen bonding may explain the presence of these solvents in the lattice. Complete hydrogen bond and C—H- -O interaction details are given in Table 8.57. Figure 8.17 ORTEP diagram of 2.pro-amide, with the MeOH and EtOH solvent molecules shown (50% probability ellipsoids). Only the major disordered fragments are shown. 247 Figure 8.18 CHARON packing diagram of 2.pro-amide viewed down the c-axis. 248 Table 8.49 Crystallographic data for 2.pro-ol and 2.pro-amide. 2.pro-ol 2.Dro-amide • 1/4 EtOH • 1/8 MeOH Formula C 1 3 H 1 8 N 4 0 7 C13.63H19N5O7.3g fw 342.31 374.33 Crystal system monoclinic tetragonal Space group P2i PA a, A 6.233(2) 19.336(2) b,k 33.054(8) c, A 7.662(1) 4.6429(8) 90 90 p n 91.05(2) 90 y(°) 90 90 V 1578.3(7) 1735.8(4) z 4 4 Pealed, g/cm3 1.44 1.43 F(000) 720 786 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) ft, cm"1 9.7 10.2 Crystal size, mm 0.20x0.11 x 0.18 0.20x0.15 x 0.25 Transmission factors 0.95-1.00 0.95-1.00 Scan type co- 26 co-28 Scan range,0 in co 1.00 + 0.20 tan 0 0.89 + 0.20 tan 9 Scan speed, °/min 16 16 Data collected +h, +k, ±1 +h, +k, +1 Of) 0 155.4 154.5 Crystal decay -0.1% -0.2% Total reflections 3613 2085 Total unique reflections 3313 1970 Emerge 0.016 0.015 No. of reflections with / ^3o(/) 1827 1421 No. of variables 472 256 p-factor 0.011 0.004 R 0.037 0.038 /J w 0.036 0.040 Goodness of fit (GOF) 1.80 2.53 Max A/a (final cycle) 0.03 0.66 Residual density e/A3 -0.12 to+0.11 -0.14 to+0.16 249 Table 8.50 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-ol. atom X V z B(ea) 0(1) 0.3380(5) 0.1774 0.2851(5) 6.7(1) 0(2) 0.2870(6) 0.2417(2) 0.2593(5) 6.8(1) 0(3) 0.7528(7) 0.3382(2) 0.5132(6) 8.4(1) 0(4) 1.0570(8) 0.3196(2) 0.6269(6) 9.1(1) 0(5) 0.8264(6) 0.0451(2) 0.4567(7) 8.3(1) 0(6) 0.5305(5) 0.0781(1) 0.3756(5) 6.27(9) 0(7) -0.1073(5) -0.0369(1) 0.4249(6) 8.3(1) 0(8) 0.3446(5) 0.1878(1) 0.7880(5) 6.2(1) 0(9) 0.2997(6) 0.1241(2) 0.7458(5) 6.3(1) 0(10) 0.7876(8) 0.0264(2) 0.9711(6) 9.9(1) O(ll) 1.0958(8) 0.0456(2) 1.0729(6) 8.8(1) 0(12) 0.8044(5) 0.3195(1) 1.0074(6) 7.0(1) 0(13) 0.5208(5) 0.2862(1) 0.9095(5) 5.83(9) 0(14) 0.6120(6) 0.3930(2) -0.0594(7) 9.1(1) N(l) 0.3921(7) 0.2126(2) 0.3107(5) 4.85(9) N(2) 0.883(1) 0.3123(2) 0.5548(6) 6.5(1) N(3) 0.6861(6) 0.1494(2) 0.4365(5) 4.33(9) N(4) 0.2520(7) 0.0202(2) 0.4761(5) 4.68(9) N(5) 0.4058(7) 0.1521(2) 0.8074(6) 5.0(1) N(6) 0.913(1) 0.0524(2) 1.0169(6) 7.0(1) N(7) 0.6884(7) 0.2154(2) 0.9504(6) 4.43(9) N(8) 0.2250(6) 0.3424(1) 0.0192(5) 4.45(9) C(l) 0.7314(7) 0.1888(2) 0.4623(6) 3.9(1) C(2) 0.5891(8) 0.2203(2) 0.4093(6) 3.93(9) C(3) 0.6410(8) 0.2607(2) 0.4433(6) 4.5(1) C(4) 0.8315(9) 0.2705(2) 0.5235(6) 4.7(1) C(5) 0.9738(8) 0.2404(2) 0.5744(6) 4.5(1) C(6) 0.9270(8) 0.2012(2) 0.5455(6) 4.1(1) C(7) 0.8274(7) 0.1162(2) 0.4794(6) 4.1(1) C(8) 0.7182(8) 0.0765(2) 0.4336(7) 5.4(1) C(9) 0.2719(7) -0.0227(2) 0.4145(7) 5.2(1) C(10) 0.3323(8) -0.0461(2) 0.5793(7) 6.8(1) C(ll*) 0.262(2) -0.0219(4) 0.730(2) 6.5(3) C(ll) 0.396(2) -0.0135(4) 0.709(2) 7.7(3) C(12) 0.289(1) 0.0212(2) 0.6657(8) 8.3(2) C(13) 0.0767(9) -0.0374(2) 0.3198(7) 7.1(1) C(14) 0.7338(7) 0.1763(2) 0.9626(6) 3.82(9) C(15) 0.6018(8) 0.1443(2) 0.9002(6) 4.08(9) C(16) 0.6564(8) 0.1039(2) 0.9220(6) 4.6(1) C(17) 0.8488(9) 0.0953(2) 0.9989(6) 4.8(1) C(18) 0.9888(8) 0.1251(2) 1.0562(6) 4.8(1) C(19) 0.9306(7) 0.1646(2) 1.0397(6) 4.4(1) C(20) 0.8247(7) 0.2489(2) 1.0034(6) 4.3(1) C(21) 0.7040(8) 0.2882(2) 0.9674(7) 4.8(1) C(22) 0.2262(7) 0.3834(2) -0.0650(6) 4.9(1) 250 C(23) 0.1883(8) 0.4124(2) 0.0822(7) 6.6(1) C(24) 0.1473(9) 0.3875(2) 0.2404(7) 7.5(2) C(25) 0.2641(9) 0.3490(2) 0.2078(7) 6.4(1) C(26) 0.4274(8) 0.3902(2) -0.1656(7) 7.1(1) Table 8.51 Bond lengths (A) of 2.pro-ol with estimated standard deviations. atom atom distance atom atom distance 0(1) N(l) 1.226(7) N(8) C(25) 1.477(9) 0(2) N(l) 1.224(7) C(l) C(2) 1.424(8) 0(3) N(2) 1.220(8) C(l) C(6) 1.426(8) 0(4) N(2) 1.230(8) C(2) C(3) 1.397(8) 0(5) C(8) 1.247(8) C(3) C(4) 1.366(9) 0(6) C(8) 1.245(8) C(4) C(5) 1.385(9) 0(7) C(13) 1.413(8) C(5) C(6) 1.345(8) 0(8) N(5) 1.247(7) C(7) C(8) 1.518(9) 0(9) N(5) 1.227(7) C(9) C(10) 1.522(9) 0(10) N(6) 1.209(8) C(9) C(13) 1.487(9) 0(11) N(6) 1.230(8) C(10) C(ll*) 1.47(2) 0(12) C(21) 1.246(7) C(10) C(ll) 1.51(2) 0(13) C(21) 1.219(7) C(ll*) C(12) 1.52(2) 0(14) C(26) 1.400(8) C(ll) C(12) 1.36(2) N(l) C(2) 1.452(8) C(14) C(15) 1.417(8) N(2) C(4) 1.436(9) C(14) C(19) 1.405(8) N(3) C(l) 1.344(8) C(15) C(16) 1.388(8) N(3) C(7) 1.442(7) C(16) C(17) 1.357(9) N(4) C(9) 1.501(8) C(17) C(18) 1.382(9) N(4) C(12) 1.47(1) C(18) C(19) 1.362(8) N(5) C(15) 1.426(8) C(20) C(21) 1.524(8) N(6) C(17) 1.481(9) C(22) C(23) 1.502(9) N(7) C(14) 1.325(8) C(22) C(26) 1.501(8) N(7) C(20) 1.450(8) C(23) C(24) 1.49(1) N(8) C(22) 1.500(8) . C(24) C(25) 1.49(1) Bond angles (°) of 2.pro-ol with estimated standard deviations. Table 8.52 atom atom atom angle O(l) N(l) 0(2) 123.3(6) 0(1) N(l) C(2) 118.5(6) 0(2) N(l) C(2) 118.1(6) 0(3) N(2) 0(4) 123.8(7) 0(3) N(2) C(4) 118.9(8) 0(4) N(2) C(4) 117.3(8) atom atom atom angle N(4) C(9) C(13) 113.0(5) C(10) C(9) C(13) 115.3(6) C(9) C(10) C(ll*) 107.5(8) C(9) C(10) C(ll) 104.1(8) C(10) C(ll*) C(12) 103(1) C(10) C(ll) C(12) 108(1) 251 C(l) N(3) C(9) N(4) 0(8) N(5) 0(8) N(5) 0(9) N(5) 0(10) N(6) 0(10) N(6) 0(11) N(6) C(14) N(7) C(22) N(8) N(3) C(l) N(3) C(l) C(2) C(l) N(l) C(2) N(l) C(2) C(l) C(2) C(2) C(3) N(2) C(4) N(2) C(4) C(3) C(4) C(4) C(5) C(l) C(6) N(3) C(7) 0(5) C(8) 0(5) C(8) 0(6) C(8) N(4) C(9) C(7) 125.3(6) C(12) 108.6(6) 0(9) 120.4(7) C(15) 119.2(6) C(15) 120.4(7) 0(11) 124.2(8) C(17) 118.7(8) C(17) 117.1(8) C(20) 127.0(6) C(25) 106.6(5) C(2) 122.6(6) C(6) 121.4(6) C(6) 116.0(6) C(l) 122.4(6) C(3) 117.1(6) C(3) 120.4(6) C(4) 120.5(6) C(3) 119.6(7) C(5) 120.2(7) C(5) 120.2(6) C(6) 120.7(6) C(5) 122.2(6) C(8) 109.7(6) 0(6) 126.1(8) C(7) 116.6(7) C(7) 117.3(7) C(10) 103.8(5) N(4) C(12) N(4) C(12) 0(7) C(13) N(7) C(14) N(7) C(14) C(15) C(14) N(5) C(15) N(5) C(15) C(14) C(15) C(15) C(16) N(6) C(17) N(6) C(17) C(16) C(17) C(17) C(18) C(14) C(19) N(7) C(20) 0(12) C(21) 0(12) C(21) 0(13) C(21) N(8) C(22) N(8) C(22) C(23) C(22) C(22) C(23) C(23) C(24) N(8) C(25) 0(14) C(26) C(H*) 106.4(9) C(ll) 107.0(9) C(9) 112.5(6) C(15) 125.5(6) C(19) 118.7(6) C(19) 115.7(6) C(14) 121.3(6) C(16) 116.1(7) C(16) 122.5(7) C(17) 117.9(7) C(16) 118.5(7) C(18) 119.0(7) C(18) 122.4(7) C(19) 119.3(7) C(18) 122.1(7) C(21) 108.4(6) 0(13) 126.7(7) C(20) 114.8(6) C(20) 118.4(6) C(23) 104.5(5) C(26) 111.6(5) C(26) 115.7(6) C(24) 106.9(5) C(25) 104.1(6) C(24) 102.5(6) C(22) 113.4(6) Table 8.53 Geometry of 2.pro-ol hydrogen bonds and C — H - 0 interactions (A, °). \ D—H n-A / n—H--,4 0(7)-4I(18)- •0(5) 0.95(9) 2.00(9) 2.753(7) 135(7) 0(14)-^J(36)- •0(12) 0.77(8) 2.02(8) 2.753(7) 150(10) N(3)-H(4)- 0(1) 1.12(8) 1.94(8) 2.611(7) 115(5) N(3)-H(4)- •0(6) 1.12(8) • 1.97(8) 2.588(7) 111(5) N(4)-H(8)- •0(5) 0.92(5) 1.87(5) 2.779(8) 167(4) N(4)-^I(8)- •0(7) 0.92(5) 2.66(5) 2.949(7) 99(3) N(7)—H(22)- •0(8) 0.78(4) 2.03(4) 2.622(8) 133(4) N(7)-^H(22)- 0(13) 0.78(4) 2.18(4) 2.580(7) 112(4) N(8)-H(25)-- •0(13) 0.88(5) 1.89(5) 2.761(7) 169(5) N(8>-^(26)-- •0(12) 1.12(7) 1.63(7) 2.729(7) 164(5) C(6)-H(3)- •0(8) 0.98 2.49 3.201(8) 128 C(10)-^i(ll) -0(7) 0.98 2.60 2.980(8) 104 C(13)-^(16)- 0(11) 0.98 2.49 3.336(9) 147 C(19)-fl(21) ••0(1) 0.98 2.48 3.160(8) 127 Symmetry Codes: (i) -x, 'A+y, -z Table 8.54 Final atomic coordinates (fractional) and B(eq) (A2) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH. atom X V z B(eq) occ 0(1) 0.11606(8) 0.41516(8) 1.061(2) 6.35(5) 0(2) 0.1115(1) 0.52291(9) 0.954(2) 7.89(6) 0(3) 0.25256(9) 0.62562(9) 0.262(2) 7.62(6) 0(4) 0.3336(1) 0.5682(1) 0.047(2) 8.38(7) 0(5) 0.23555(9) 0.15482(8) 0.967(2) 5.13(4) 0(6) 0.16517(9) 0.23377(8) 1.152(2) 5.59(5) 0(7) 0.15418(9) 0.02471(8) 0.761(2) 5.98(5) 0(8) 0.5488 0.4863 0.8203 30 0.25 0(9) 1 0 0.1788 13 0.125 N(l) 0.1361(1) 0.4648(1) 0.921(2) 5.12(5) N(2) 0.2846(1) 0.5721(1) 0.215(2) 5.92(6) N(3) 0.20745(9) 0.3330(1) 0.812(2) 4.00(5) N(4) 0.2558(1) 0.07749(9) 0.438(2) 4.04(4) N(5) 0.1524(1) -0.0796(1) 0.542(2) 5.89(7) C(l) 0.2246(1) 0.3909(1) 0.671(2) 3.79(5) C(2) 0.1923(1) 0.4562(1) 0.716(2) 4.29(5) C(3) 0.2129(1) 0:5142(1) 0.566(2) 4.60(6) C(4) 0.2650(1) 0.5101(1) 0.371(2) 4.67(6) C(5) 0.2984(1) 0.4484(1) 0.318(2) 4.91(6) C(6) 0.2790(1) 0.3904(1) 0.466(2) 4.59(6) C(7) 0.2409(1) 0.2662(1) 0.775(2) 4.12(5) C(8) 0.2100(1) 0.2143(1) 0.984(2) 4.19(5) C(9) 0.2413(1) 0.0015(1) 0.409(2) 3.97(5) C(10) 0.3077(1) -0.0323(1) 0.521(2) 5.24(7) C(ll) 0.3643(2) 0.0175(2) 0.437(2) 6.20(9) 0.90 C(ll*) 0.348(1) 0.017(1) 0.64(1) 5.8(7) 0.10 C(12) 0.3320(1) 0.0867(1) 0.475(2) 5.38(6) C(13) 0.1773(1) -0.0167(1) 0.587(2) 4.45(5) C(14) 0.5 0.5 0.6188 31 0.25 C(15) 0.4656 0.4595 0.5388 24 0.25 C(16) 1.0689 0.0324 0.1715 7 0.125 H(4) 0.177(1) 0.335(1) 0.952(6) 3.5(5) H(7) 0.243(2) 0.117(2) 0.22(1) 10.0(9) H(8) 0.236(1) 0.094(1) 0.591(6) 2.7(5) H(16) 0.172(1) -0.102(1) 0.418(7) 5.0(7) H(17) 0.101(2) -0.099(2) 0.70(1) 20(1) 253 Table 8.55 Bond lengths (A) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH with estimated standard deviations. atom atom distance atom atom distance 0(1) N(l) 1.222(4) N(5) C(13) 1.325(5) 0(2) N(l) 1.230(4) C(l) C(2) 1.424(5) 0(3) N(2) 1.226(4) C(l) C(6) 1.419(6) 0(4) N(2) 1.229(5) C(2) C(3) 1.378(5) 0(5) C(8) 1.255(4) C(3) C(4) 1.359(6) 0(6) C(8) 1.228(5) C(4) C(5) 1.379(5) 0(7) C(13) 1.224(5) C(5) C(6) 1.368(5) 0(8) C(14) 1.3555(1) C(7) C(8) 1.518(6) 0(9) C(16) 1.4724(1) C(9) C(10) 1.530(5) N(l) C(2) 1.455(5) C(9) C(13) 1.529(5) N(2) C(4) 1.449(5) C(10) C(ll) 1.506(7) N(3) C(l) 1.339(5) C(10) C(ll*) 1.36(5) N(3) C(7) 1.455(4) C(ll) C(12) 1.489(7) N(4) C(9) 1.502(4) C(ll*) C(12) 1.56(5) N(4) C(12) 1.494(5) C(14) C(15) 1.093 Table 8.56 Bond angl 2S (deg) of 2.pro-amide • 1/4 EtOH • 1/8 MeOH with estimated standard deviations. atom atom atom angle atom atom atom angle 0(1) N(l) 0(2) 121.9(4) C(l) C(6) C(5) 122.4(3) O(l) N(l) C(2) 119.7(3) N(3) C(7) C(8) 109.6(4) 0(2) N(l) C(2) 118.4(4) 0(5) C(8) 0(6) 126.9(4) 0(3) N(2) 0(4) 123.6(4) 0(5) C(8) C(7) 114.2(4) 0(3) N(2) C(4) 118.6(4) 0(6) C(8) C(7) 118.9(3) 0(4) N(2) C(4) 117.8(4) N(4) C(9) C(10) 103.4(3) C(l) N(3) C(7) 125.0(4) N(4) C(9) C(13) 109.1(3) C(9) N(4) C(12) 108.1(3) C(10) C(9) C(13) 113.5(4) N(3) C(l) C(2) 124.1(4) C(9) C(10) C(ll) 104.5(4) C(2) C(l) C(6) 115.4(3) C(9) C(10) C(ll*) 108(2) N(3) C(l) C(6) 120.5(3) C(10) C(ll) C(12) 103.8(4) N(l) C(2) C(l) 121.6(4) C(10) C(ll*) C(12) 107(4) N(l) C(2) C(3) 116.9(3) N(4) C(12) C(ll) 107.0(3) C(l) C(2) C(3) 121.5(4) N(4) C(12) C(ll*) 98(1) C(2) C(3) C(4) 120.2(3) 0(7) C(13) N(5) 124.9(4) N(2) C(4) C(3) 118.6(4) 0(7) C(13) C(9) 120.2(3) N(2) C(4) C(5) 120.2(4) N(5) C(13) C(9) 114.8(4) C(3) C(4) C(5) 121.2(4) 0(8) C(14) C(15) 121.190(3) C(4) C(5) C(6) 119.4(4) 254 Table 8.57 Geometry of 2.pro-amide* 1/4 EtOH • 1/8 MeOH hydrogen bonds and C-HH---0 interactions (A, °). £>-« n—A n—A / D—H--4 N(3>-H(4)-0(l) 0.88(4) 2.01(3) 2.641(4) 128(3) N(3)-H(4)-0(6) 0.88(4) 2.18(3) 2.617(4) 110(3) N(4)-H(7)-0(5) 1.30(7) 1.38(7) 2.679(5) 173(4) N(4)-H(8)-0(5) 0.86(4) 2.10(4) 2.900(5) 153(3) N(4)-^I(8)—0(7) 0.86(4) 2.22(3) 2.675(5) 112(3) N(5)—H(16)-0(6) 0.81(4) 2.11(4) 2.912(5) 170(4) N(5)-^I(17)-0(7) 1.33(9) 1.82(8) 3.036(5) 149(7) C(6>-H(3)---0(3)(ii) 0.98 2.42 3.376(5) 166 C(7)-H(6)-0(6) 0.98 2.44 3.298(6) 153 C(16)-H(25)-0(7) 0.98 2.28 3.20(1) 157 Symmetry Codes: (i) -x, -y, z (ii) y, -x, z (iii) -y, x, z 8.15. l-(p-Nitrophenyl)-4-methylpiperazine (3) The diffraction data were collected and the structure solved by Dr. Steven J. Rettig, the U B C staff crystallographer, and is included herein with his permission. A crystal of approximate dimensions 0.30 x 0.35 x 0.35 mm was chosen for data collection. Crystallographic data for (3) appear in Table 8.58. An orthorhombic cell with Z = 4 (assuming a density of 1.29 g/cm3) was indicated by preliminary measurements. 1414 reflections were collected, of which 1156 were observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 28 = 88.3 - 108.6°. The data for (3) were processed and corrected for Lorentz and polarization effects, as well as for absorption. 255 Based on systematic absences (Okl: k + I * 2n, hOl: h * 2n), a statistical analysis of the intensity distributions and a successful solution and refinement, the space group was determined to be Pna2i. The structure (Figure 8.19) was solved by direct-methods [173] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Hydrogens were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 4.23 xlO"5). Neutral atom scattering factors and the values of AT and AF were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic-[172] The refinement converged at R = 0.029, Rw = 0.029 for 145 variables (GOF = 2.78), with the largest parameter shift in the final refinement cycle being 0.03a. The final difference map showed electron density between -0.09 and 0.09 e /A 3 . Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.59-61, respectively. The packing of (3) (Figure 5.1, reproduced here for convenience) consists of chains of symmetry equivalent molecules, related by the 2i screw axis, aligned with their molecular charge-transfer axes oriented anti-parallel to each other. These pairs of molecules propagate through the crystal in a "herringbone" manner along the a-axis of the unit cell. As there are no NH's or OH's to act as hydrogen bond donors, the crystal packing appears to most influenced by electrostatic (dipole-dipole) interactions and 256 weaker C — H - 0 interactions. Complete C — H - 0 bonding details are given in Table 8.16. l-(p-Nitrophenyl)-4-methylpiperazinium salt of (1): l.nitrophen. A crystal of approximate dimensions 0.40 x 0.30 x 0.20 mm was chosen for data collection. Crystallographic data for l.nitrophen appear in Table 8.58. • A monoclinic cell with Z = 8 (assuming a density of 1.42 g/cm3) was indicated by preliminary measurements. 4319 reflections were collected, of which 4193 were unique and 2811 were observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 24 reflections with 26 = 91.9 - 103.6°. The data for l.nitrophen were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences (hkl: h + k* 2n, hOl: I * 2n), a statistical analysis of intensity distributions and the successful solution and refinement of the structure, the space group was determined to be C2/c. The structure (Figure 8.20) was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were determined from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 7.46 xlO"7). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.035, Rw = 0.041 258 for 290 variables (GOF = 2.38; including zeros: R = 0.059, Rw = 0.043), with a negligible parameter shift in the final refinement cycle. The final difference map showed electron density between -0.12 and 0.14 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.63-65, respectively. The crystal packing of l.nitrophen is shown in Figure 8.21. The piperazine ring is oriented perpendicularly to its benzene ring, allowing the protonated amine, N(5)—H(16), to participate in a bifurcated N — H - O hydrogen bond with the two carboxylate oxygens, 0(3) and 0(4). The piperazine ring conformation also allows for weak C — H - - 0 interactions with the p-NC>2 group of a symmetry related neighbor [C(16)—H(5)---0(5) and C(17)—H(18)- -0(6)], forming oppositely oriented salt dimers with each charge-transfer axis oriented roughly along the c-axis of the unit cell. Complete hydrogen bond and C—H- • O interaction details are given in Table 8.66. Figure 8.20 ORTEP diagram of l.nitrophen (50% probability ellipsoids). 259 8.17. l-(p-Nitrophenyl)-4-methylpiperazinium salt of (2): 2.nitrophen. A crystal of approximate dimensions 0.12 x 0.06 x 0.25 mm was chosen for data collection. Crystallographic data for 2.nitrophen appear in Table 8.58. A triclinic cell with Z = 2 (assuming a density of 1.50 g/cm ) was indicated by preliminary measurements. 4400 reflections were collected, of which 4195 were unique and 2351 were observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 20 reflections with 26 = 37.8 - 54.3°. The data for 2.nitrophen were processed and corrected for Lorentz and polarization effects, as well as for absorption. 260 Based on a statistical analysis of intensity distributions and the successful solution and refinement of the structure, the space group was determined to be P I . The structure (Figure 8.22) was solved by direct-methods [162] and expanded using Fourier techniques. [166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were determined from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 2.71 xlO"6). Neutral atom scattering factors and the values of AT and Af were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fc aic.[172] The refinement converged at R = 0.041, Rw = 0.043 for 387 variables (GOF = 2.23; including zeros: R = 0.106, Rw = 0.049), with the largest parameter shift in the final refinement cycle being 0.03cr The final difference map showed electron density between -0.16 and 0.16 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.67-69, respectively. The crystal packing of 2.nitrophen is shown in Figure 8.23. The piperazine ring is oriented perpendicularly to its benzene ring, allowing the protonated amine, N(6)—H(15), to participate in a bifurcated N — H - 0 bond with the two carboxylate oxygens, 0(5) and 0(6). The piperazine ring conformation also allows for weak C—H---0 interactions with the P - N O 2 group of its symmetry related neighbor [C(16>—H(13)---0(7) and C(17>—H(16)---0(8)], forming oppositely oriented salt dimers 261 centered about the a-axis of the unit cell. Complete hydrogen bond and C—H-interaction details are given in Table 8.70. Figure 8.22 ORTEP diagram of 2.nitrophen (50% probability ellipsoids). 262 Figure 8.23 CHARON packing diagram of 2.nitrophen. 263 Table 8.58 Crystallographic data for (3), l.nitrophen, and 2.nitrophen. (3) l.nitrophen 2.nitrophen Formula C„H 1 S N 3 02 C 1 9 H 2 3 N 5 0 6 C 1 9 H 2 2 N 6 0 8 fw 221.26 417.42 462.42 Crystal system orthorhombic monoclinic triclinic Space group Pna2i C2/c PI a, A 16.913(1) 20.773(2) 12.116(2) b,k 8.815(1) 7.581(2) 14.744(2) c A 7.658(2) 26.250(2) 6.2136(8) 93.63(1) p o • 109.629(6) 92.36(1) y(°) 111.64(1) V 1141.8(6) 3893(1) 1027.2(2) z 4 8 2 Pealed, g/cm3 1.29 1.42 1.50 F(000) 472 . 1760 484 Radiation Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) fi, cm"1 7.1 8.6 10.14 Crystal size, mm 0.30 x 0.35 x 0.35 0.40 x 0.30 x 0.20 0.12x0.06x0.25 Transmission factors 0.85-1.00 0.90- 1.00 0.91 - 1.00 Scan type co-29 co-26 co-29 Scan range, ° in co 1.00 + 0.20 tan 6 0.94 + 0.20 tan 6 0.94 + 0.20 tan 9 Scan speed, °/min 32.0 32.0 8.0 Data collected +h, +k, +1 +h, +k, ±1 +h, ±k, ±1 155.2 155.3 155.5 Crystal decay negligible -0.3% negligible Total reflections 1414 4319 4400 Total unique 4193 4195 Emerge 0.015 0.045 No. of reflections 1156 2811 2351 with/>3o(/) No. of variables 145 364 387 p-factor 0.00 0.009 0.009 R 0.029 0.035 0.041 Rw 0.029 0.041 0.043 Goodness of fit 2.78 2.38 2.23 Max A/a (final cycle) 0.03 0.00 0.03 Residual density e/A3 -0.09 to + 0.09 -0.12 to+0.14 -0.16 to+0.16 264 Table 8.59 Final atomic coordinates (fractional) and B(eq) (A2) of (3). atom X V z B(ea) 0(1) 0.6066(1) 0.0894(2) 0.2973 7.2(1) 0(2) 0.5261(1) -0.0223(2) 0.1228(5) 8.2(1) N(l) 0.3513(1) 0.6030(2) 0.2117(4) 4.06(7) N(2) 0.5454(1) 0.0861(2) 0.2113(4) 5.3(1) N(3) 0.2474(1) 0.8559(2) 0.2535(4) 4.67(7) C(l) 0.3973(1) 0.4723(2) 0.2189(4) 3.61(7) C(2) 0.4638(1) 0.4632(2) 0.3289(4) 4.35(9) C(3) 0.5116(1) 0.3363(2) 0.3265(4) 4.49(9) C(4) 0.4941(1) 0.2181(2) 0.2161(4) 4.11(8) C(5) 0.4283(1) 0.2225(2) 0.1078(4) 4.27(8) C(6) 0.3801(1) 0.3488(2) 0.1109(4) 4.06(8) C(7) 0.2653(1) 0.5873(2) 0.1887(4) 4.46(9) C(8) 0.2280(1) 0.7342(3) 0.1324(4) 5.0(1) C(9) 0.3325(1) 0.8759(2) 0.2559(4) 4.67(9) C(10) 0.3733(1) 0.7340(2) 0.3182(5) 4.50(9) C(ll) 0.2077(2) 0.9954(3) 0.2017(5) 6.9(1) Table 8.60 Bond lengths (A) of (3) with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.227(2) C(l) C(2) 1.408(3) 0(2) N(2) 1.217(3) C(l) C(6) 1.398(3) N(l) C(l) 1.390(2) C(2) C(3) 1.380(3) N(l) C(7) 1.472(2) C(3) C(4) 1.375(3) N(l) C(10) 1.462(3) C(4) C(5) 1.389(3) N(2) C(4) 1.452(2) C(5) C(6) 1.380(3) N(3) C(8) 1.456(3) C(7) C(8) 1.504(3) N(3) C(9) 1.450(3) C(9) C(10) 1.506(3) N(3) C(ll) 1.457(3) Table 8.61 Bond angles (°) of (3) with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 118.7(1) C(l) C(2) C(3) 120.5(2) C(l) N(l) C(10) 119.3(2) C(2) C(3) C(4) 119.7(2) C(7) N(l) C(10) 113.1(2) N(2) C(4) C(3) 119.6(2) 0(1) N(2) 0(2) 123.0(2) N(2) C(4) C(5) 119.1(2) O(l) N(2) C(4) 118.1(2) C(3) C(4) C(5) 121.3(2) 0(2) N(2) C(4) 118.9(2) C(4) C(5) C(6) 119.0(2) 265 C(8) N(3) C(9) 108.8(2) C(l) C(6) C(5) 121.1(2) C(8) N(3) C(ll) 110.1(2) N(l) C(7) C(8) 111.6(2) C(9) N(3) C(ll) 111.0(2) N(3) C(8) C(7) 110.9(2) N(l) C(l) C(2) 121.2(2) N(3) C(9) C(10) 111.0(2) N(l) C(l) C(6) 120.4(2) N(l) C(10) C(9) 111.3(2) C(2) C(l) C(6) 118.4(2) Table 8.62 Geometry of (3) C—H-• O interactions (A, °). D—H---/4 D—ti H - A n—A />—H-..4 C(6)—H(9)-N(2) 0.98 2.56 3.213(3) 158 Symmetry Codes: Table 8.63 Final atomic coordinates (fractional) and B(eq) (A2) of l.nitrophen. atom X V z B(ea) 0(1) -0.02082(8) 0.3535(2) 0.31581(6) 6.53(4) 0(2) -0.11898(8) 0.4386(2) 0.31782(6) 6.50(4) 0(3) 0.03130(7) 0.1626(2) 0.66168(5) 6.24(4) 0(4) 0.13102(7) 0.0251(2) 0.67979(5) 5.49(4) 0(5) 0.32674(8) 0.5228(2) 1.06381(5) 6.28(4) 0(6) 0.22420(8) 0.5898(2) 1.05936(6) 6.07(4) N(l) 0.01713(8) 0.2171(2) 0.55945(6) 4.17(4) N(2) -0.06160(8) 0.3770(2) 0.33973(6) 4.79(4) N(3) 0.17006(7) 0.3641(2) 0.81792(6) 4.01(3) N(4) 0.26548(9) 0.5397(2) 1.03830(6) 4.42(4) N(5) 0.14612(8) 0.0051(2) 0.78218(6) 4.04(3) C(l) -0.00149(9) 0.2502(2) 0.50590(7) 3.46(4) C(2) 0.03989(9) 0.2047(2) 0.47524(7) 3.53(4) C(3) 0.01974(9) 0.2443(2) 0.42083(7) 3.68(4) C(4) -0.04120(9) 0.3308(2) 0.39645(7) 3.66(4) C(5) -0.08343(9) 0.3753(3) 0.42546(8) 4.07(4) C(6) -0.06391(9) 0.3338(3) 0.47919(8) 4.04(4) C(7) 0.0791(1) 0.1338(3) 0.59161(7) 3.89(4) C(8) 0.0793(1) 0.1065(3) 0.64942(7) 4.23(4) C(9) 0.19407(8) 0.4071(2) 0.87215(6) 3.44(4) C(10) 0.26306(9) 0.3892(3) 0.90358(8) 4.18(4) C(ll) 0.28629(9) 0.4315(3) 0.95743(8) 4.09(4) C(12) 0.24151(9) 0.4977(2) 0.98128(6) 3.52(4) C(13) 0.17378(9) 0.5239(3) 0.95120(7) 3.86(4) C(14) 0.15010(9) 0.4771(3) 0.89752(7) 3.89(4) C(15) 0.1001(1) 0.2992(3) 0.79235(8) 4.64(5) C(16) 0.0973(1) 0.1037(3) 0.80220(7) 4.47(5) C(17) 0.2163(1) 0.0798(3) 0.80436(7) 4.13(4) C(18) 0.2147(1) 0.2751(3) 0.79358(8) 4.25(5) C(19) 0.1465(2) -0.1861(4) 0.7951(1) 6.15(7) H(l) 0.0815(8) 0.143(2) 0.4911(7) 3.8(4) H(2) 0.0470(8) 0.208(2) 0.3999(7) 3.8(4) H(3) -0.1272(9) 0.433(3) 0.4073(7) 4.7(4) H(4) -0.0937(9) 0.356(3) 0.4991(8) 5.4(5) H(5) -0.008(1) 0.238(3) 0.5785(8) 6.8(6) H(6) 0.1210(9) 0.202(2) 0.5949(7) 4.2(4) H(7) 0.0865(8) 0.011(3) 0.5773(7) 4.3(4) H(8) 0.2957(9) 0.346(2) 0.8882(7) 4.8(4) H(9) 0.335(1) 0.418(3) 0.9787(7) 5.4(5) H(10) 0.1442(9) 0.577(3) 0.9685(7) 5.1(5) H(ll) 0.1027(9) 0.496(3) 0.8767(8) 5.3(5) H(12) 0.0862(9) 0.319(3) 0.7516(8) 5.3(5) H(13) 0.069(1) 0.358(3) 0.8072(8) 5.8(5) H(14) 0.052(1) 0.052(3) 0.7827(8) 5.4(5) H(15) 0.1115(8) 0.079(2) 0.8422(7) 4.4(4) H(16) 0.131(1) 0:015(3) 0.739(1) 8.1(6) H(17) 0.2443(9) 0.014(3) 0.7869(8) 5.4(5) H(18) 0.2337(9) 0.055(3) 0.8437(8) 4.7(4) H(19) 0.1933(9) 0.295(3) 0.7525(8) 5.3(5) H(20) 0.2597(9) 0.326(3) 0.8059(7) 4.5(4) H(21) 0.100(1) -0.218(3) 0.779(1) 7.7(7) H(22) 0.171(1) -0.255(4) 0.777(1) 9.9(9) H(23) 0.164(1) -0.200(3) 0.8360(9) 7.2(6) Table 8.64 Bond lengths (A) of l.nitrophen with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.225(2) C(l) C(2) 1.404(2) 0(2) N(2) 1.229(2) C(l) C(6) 1.401(3) 0(3) C(8) 1.222(2) C(2) C(3) 1.380(2) 0(4) C(8) 1.263(2) C(3) C(4) 1.377(2) 0(5) N(4) 1.230(2) C(4) C(5) 1.383(3) 0(6) N(4) 1.226(2) C(5) C(6) 1.367(3) N(l) C(l) 1.350(2) C(7) C(8) 1.530(2) N(l) C(7) 1.428(2) C(9) C(10) 1.400(2) N(2) C(4) 1.448(2) C(9) C(14) 1.403(2) N(3) C(9) 1.380(2) C(10) C(ll) 1.369(3) N(3) C(15) 1.467(2) C(ll) C(12) 1.379(2) N(3) C(18) 1.458(2) C(12) C(13) 1.377(2) N(4) C(12) 1.445(2) C(13) C(14) 1.374(2) N(5) C(16) 1.490(2) C(15) C(16) 1.509(3) 267 N(5) C(17) 1.488(2) C(17) C(18) 1.505(3) N(5) C(19) 1.488(3) Table 8.65 Bond angles (°) of l.nitrophen with estimated standard deviations. atom atom atom angle atom atom atom angle C(l) N(l) C(7) 125.7(2) C(4) C(5) C(6) 119.3(2) O(l) N(2) 0(2) 123.0(2) C(l) C(6) C(5) 121.6(2) O(l) N(2) C(4) 118.6(2) N(l) C(7) C(8) 110.3(2) 0(2) N(2) C(4) 118.4(2) 0(3) C(8) 0(4) 126.9(2) C(9) N(3) C(15) 120.7(1) 0(3) C(8) C(7) 118.9(2) C(9) N(3) C(18) 119.9(1) 0(4) C(8) C(7) 114.2(2) C(15) N(3) C(18) 108.9(2) N(3) C(9) C(10) 121.9(2) 0(5) N(4) 0(6) 122.6(2) N(3) C(9) C(14) 120.8(2) 0(5) N(4) C(12) 118.3(2) C(10) C(9) C(14) 117.2(2) 0(6) N(4) C(12) 119.0(2) C(9) C(10) C(ll) 121.5(2) C(16) N(5) C(17) 111.4(1) C(10) C(ll) C(12) 119.8(2) C(16) N(5) C(19) 111.1(2) N(4) C(12) C(ll) 120.0(2) C(17) N(5) C(19) 110.6(2) N(4) C(12) C(13) 119.5(2) N(l) C(l) C(2) 122.3(2) C(ll) C(12) C(13) 120.5(2) N(l) C(l) C(6) 119.9(2) C(12) C(13) C(14) 119.7(2) C(2) C(l) C(6) 117.8(2) C(9) C(14) C(13) 121.2(2) C(l) C(2) C(3) 120.6(2) N(3) C(15) C(16) 109.9(2) C(2) C(3) C(4) 119.8(2) N(5) C(16) C(15) 111.2(2) N(2) C(4) C(3) 119.9(2) N(5) C(17) C(18) 110.2(2) N(2) C(4) C(5) 119.1(2) N(3) C(18) C(17) 110.4(2) C(3) C(4) C(5) 121.0(2) Table 8.66 Geometry of l.nitrophen hydrogen bonds and C — H - 0 interactions (A, °). D—H...A D - H D-.-A D—H-..4 N(l)-H(5)- 0(3) 0.85(2) 2.14(2) 2.632(2) 117(2) N(5)-^(16)-- •0(3) 1.08(2) 2.61(2) 3.471(2) 136(2) N(5)—HaeV- •0(4) 1.08(2) 1.55(2) 2.604(2) 164(2) C O S T - ^ ^ - ••0(3) 1.02(2) 2.54(3) 3.404(2) 142(2) CaeT-^iOS)- -0(5) 1.01(2) 2.49(2) 3.471(2) 164(2) C(17)-H(18)- •0(6) 0.99(2) 2.64(2) 3.607(2) 166(2) 268 Table 8.67 Final atomic coordinates (fractional) and B(eq) (A2) of 2.nitrophen. atom X V z B(ea) 0(1) 0.5163(2) 0.1677(2) 0.2321(3) 5.36(6) 0(2) 0.4026(2) 0.1696(2) -0.0416(4) 5.35(6) 0(3) 0.1465(2) 0.3449(2) 0.0222(4) 5.43(6) 0(4) 0.1298(2) 0:4161(2) 0.3234(4) 5.44(6) 0(5) 0.2244(2) 0.5921(2) 0.7925(3) 5.69(6) 0(6) 0.3384(2) 0.6241(2) 1.0994(3) 5.15(6) 0(7) -0.0033(2) 0.1744(2) 0.3556(4) 6.43(7) 0(8) 0.0788(2) 0.1894(2) 0.6766(4) 7.41(8) N(l) 0.3032(2) 0.4614(2) 0.6322(4) 3.67(6) N(2) 0.4434(2) 0.1961(2) 0.1448(4) 3.89(6) N(3) 0.1779(2) 0.3721(2) 0.2121(4) 3.82(6) N(4) 0.0636(2) 0.1578(2) 0.4873(5) 4.78(7) N(5) 0.2937(2) -0.0924(2) 0.2087(4) 4.03(6) N(6) 0.1802(2) -0.2999(2) 0.2295(4) 3.82(6) C(l) 0.3327(2) 0.3964(2) 0.5146(4) 3.07(6) C(2) 0.4261(2) 0.3677(2) 0.5910(5) 3.47(7) C(3) 0.4604(2) 0.3028(2) 0.4747(5) 3.58(7) C(4) 0.4055(2) 0.2639(2) 0.2700(4) 3.21(6) C(5) 0.3146(2) 0.2882(2) 0.1865(5) 3.24(6) C(6) 0.2777(2) 0.3524(2) 0.3074(4) 3.17(6) C(7) 0.3608(3) 0:5119(2) 0.8350(5) 3.51(7) C(8) 0.3017(3) 0.5826(2) 0.9124(5) 3.81(7) C(9) 0.1276(2) . 0.0965(2) 0.4149(5) 3.63(7) C(10) 0.2034(3) 0.0766(2) 0.5581(5) 4.13(8) C(ll) 0.2595(3) 0.0153(2) 0.4894(5) 4.13(8) C(12) 0.2398(2) -0.0289(2) 0.2772(4) 3.34(6) C(13) 0.1663(3) -0.0025(2) 0.1352(5) 4.01(7) C(14) 0.1114(3) 0.0598(2) 0.2038(5) 4.02(8) C(15) 0.3385(3) -0.1429(3) 0.3640(6) 4.53(8) C(16) 0.2386(3) -0.2328(2) 0.4254(5) 3.98(8) C(17) 0.1435(3) -0.2483(2) 0.0575(5) 4.08(8) C(18) 0.2465(3) -0.1579(3) 0.0101(5) 4.45(9) C(19) 0.0765(4) -0.3852(3) 0.2877(8) 5.7(1) H(l) 0.464(2) 0.391(2) 0.732(4) 2.8(5) H(2) 0.519(2) 0.282(2) 0.531(4) 4.1(6) H(3) 0.275(2) 0.262(2) 0.043(4) 3.9(6) H(4) 0.249(3) 0.477(2) 0.580(5) 5.2(8) H(5) 0.357(2) 0.468(2) 0.953(4) 3.9(6) H(6) 0.444(3) 0.548(2) 0.827(5) 5.2(8) H(7) 0.216(2) 0.103(2) 0.712(4) 4.6(7) H(8) 0.306(2) 0.003(2) 0.582(4) 4.0(7) H(9) 0.156(2) -0.025(2) -0.017(5) 4.7(7) H(10) 0.066(2) 0.078(2) 0.101(4) 4.4(7) H(ll) 0.376(3) -0.104(2) 0.506(5) 6.1(8) H(12) 0.400(3) -0.162(2) 0.302(4) 4.9(7) 269 H(13) 0.176(2) -0.217(2) 0.493(4) 3.7(6) H(14) 0.268(2) -0.269(2) 0.522(4) 4.6(7) H(15) 0.237(3) -0.327(2) 0.171(5) 8(1) H(16) 0.078(2) -0.230(2) 0.108(4) 4.2(6) H(17) 0.120(2) -0.293(2) -0.077(4) 4.4(7) H(18) 0.226(3) -0.122(2) -0.099(5) 5.0(8) H(19) 0.312(3) -0.177(2) -0.041(4) 4.9(7) H(20) 0.014(3) -0.363(3) 0.331(5) 8(1) H(21) 0.104(3) -0.418(2) 0.407(5) 6.7(9) H(22) 0.055(3) -0.432(3) 0.147(6) 8(1) Table 8.68 Bond lengths (A) of 2.nitrophen with estimated standard deviations. atom atom distance atom atom distance O(l) N(2) 1.230(3) 0(2) N(2) 1.221(3) 0(3) N(3) 1.220(3) 0(4) N(3) 1.222(3) 0(5) C(8) 1.226(3) 0(6) C(8) 1.261(3) 0(7) N(4) 1.227(3) 0(8) N(4) 1.218(3) N(l) C(l) 1.329(3) N(l) C(7) 1.433(4) N(2) C(4) 1.444(3) N(3) C(6) 1.456(3) N(4) C(9) 1.453(4) N(5) C(12) 1.380(3) N(5) C(15) 1.459(4) N(5) C(18) 1.472(4) N(6) C(16) 1.490(4) N(6) C(17) 1.494(4) N(6) C(19) 1.490(4) C(l) C(2) 1.422(3) C(l) C(6) 1.424(3) C(2) C(3) 1.356(4) C(3) C(4) 1.395(4) C(4) C(5) 1.370(3) C(5) C(6) 1.382(4) C(7) C(8) 1.532(4) C(9) C(10) 1.374(4) C(9) C(14) 1.365(4) C(10) C(ll) 1.374(4) C(ll) C(12) 1.404(4) C(12) C(13) 1.399(4) C(13) C(14) 1.376(4) C(15) C(16) 1.513(5) C(17) C(18) 1.508(5) Bond angles (°) of 2.nitrophen with estimated standard deviations. Table 8.69 atom atom atom angle C(l) N(l) C(7) 126.1(2) O(l) N(2) 0(2) 122.8(2) 0(1) N(2) C(4) 117.9(2) 0(2) N(2) C(4) 119.3(2) 0(3) N(3) 0(4) 122.5(2) 0(3) N(3) C(6) 118.3(2) 0(4) N(3) C(6) 119.2(2) 0(7) N(4) 0(8) 123.5(3) atom atom atom angle C(3) C(4) C(5) 120.8(2) C(4) C(5) C(6) 119.2(3) N(3) C(6) C(l) 121.4(2) N(3) C(6) C(5) 116.2(2) C(l) C(6) C(5) 122.3(2) N(l) C(7) C(8) 109.4(2) 0(5) C(8) 0(6) 127.1(3) 0(5) C(8) C(7) 118.5(3) 270 0(7) N(4) C(9) 118.5(3) 0(6) C(8) C(7) 114.4(3) 0(8) N(4) C(9) 118.1(3) N(4) C(9) C(10) 120.0(3) C(12) N(5) C(15) 120.7(2) N(4) C(9) C(14) 119.1(3) C(12) N(5) C(18) 120.0(2) C(10) C(9) C(14) 120.9(3) C(15) N(5) C(18) 108.9(2) C(9) C(10) C(ll) 119.3(3) C(16) N(6) C(17) 112.1(2) C(10) C(ll) C(12) 121.7(3) C(16) N(6) C(19) 110.5(3) N(5) C(12) C(ll) 122.0(3) C(17) N(6) C(19) 110.8(3) N(5) C(12) C(13) 121.3(3) N(l) C(l) C(2) 120.4(3) C(ll) C(12) C(13) 116.7(3) N(l) C(l) C(6) 124.2(2) C(12) C(13) C(14) 121.4(3) C(2) C(l) C(6) 115.3(2) C(9) C(14) C(13) 119.8(3) C(l) C(2) C(3) 122.3(3) N(5) C(15) C(16) 110.4(2) C(2) C(3) C(4) 119.9(3) N(6) C(16) C(15) 110.5(3) N(2) C(4) C(3) 119.9(2) N(6) C(17) C(18) 110.7(3) N(2) C(4) C(5) 119.3(2) N(5) C(18) C(17) 110.3(3) Table 8.70 Geometry of 2.nitrophen hydrogen bonds and C — H - 0 interactions (A, °). n—R-A D—H Vt--A D-A D—H---,4 N(l)-H(4)-0(3) 0.83(3) 2.03(3) 2.648(3) 131(3) N(l)-H(4)-0(5) 0.83(3) 2.20(3) 2.609(3) 111(2) N(6)-^i(15)---0(5) 0.99(4) 2.54(3) 3.225(3) 126(3) N(6)-^(15)---0(6) 0.99(4) 1.69(4) 2.679(2) 174(3) C(7)-H(5)-0(3) 1.00(3) 2.60(3) 3.171(4) 116(2) C(10)-^i(7)---O(2) 0.99(3) 2.52(3) 3.244(4) 130(2) C(15)-H(ll)---0(l) ( i ) 1.01(3) 2.48(3) 3.123(4) 121(2) C(16)-^(13)---0(7)(i) 0.98(3) 2.59(3) 3.564(4) 176(2) C(17)-^(16)---0(8)(i) 0.99(3) 2.59(3) 3.557(4) 167(2) C(17)-^I(17)---0(5) 1.00(3) 2.57(3) 3.249(4) 126(2) C(18)-^i(19)---0(l)(i) 0.99(3) 2.40(3) 3.344(4) 158(3) C(19)-^I(21)---0(4) 1.02(3) 2.60(3) ,3.243(4) 121(3) Symmetry Codes: (i) -x, -y, -z 8.18. l-(4-nitro-2-pyridyl)-4-methylpiperazine (4) A crystal of approximate dimensions 0.20 x 0.15 x 0.20 mm was chosen for data collection. Crystallographic data for (4) appear in Table 8.71. A monoclinic cell with Z 271 •3 = 8 (assuming a density of 1.35 g/cm ) was indicated by preliminary measurements. 5189 reflections were collected, of which 4988 were unique and 1853 were observed (I > 3.0 0(1)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 20 = 50.6 - 64.7°. The data for (4) were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on systematic absences (hOl: I ^ 2n, OkO: k * 2n), the space group was determined to be P2i/c. The structure (Figure 8.24) was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. Hydrogens were included in idealized positions (C—H = 0.98 A , B H = 1.2 x Bbonded atom)- A secondary extinction coefficient correction was applied (final coefficient = 1.32 xlO"5). Neutral atom scattering factors and the values of AT and Af were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.039, Rw = 0.039 for 290 variables (GOF = 1.86; including zeros: R = 0.156, Rw = 0.054), with a negligible parameter shift in the final refinement cycle. The final difference map showed electron density between -0.11 and 0.12 e /A 3 . Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.72-74, respectively. The unit cell of (4), shown in Figure 8.25 consists of two molecules in the asymmetric unit, with their charge-transfer axes parallel to each other and their pyridine 272 rings co-planar to the other. The symmetry related positions produce columns of pyridine rings stacked one upon the other along the direction of the a-axis. As there are no NH's or OH's to act as hydrogen bond donors the molecular packing appears to be driven primarily by electrostatic interactions, producing an anti-parallel orientation of the charge-transfer axes; however, there are several intermolecular C—H---0 interactions that also contribute to the packing, in particular C(20)—H(28)--0(l), between an N -methyl hydrogen and an N O 2 oxygen. Complete C—H---0 interaction details are given in Table 8.75. C 8 Q - P C I O 9rP C20 Figure 8.24 ORTEP diagram of (4) (50% probability ellipsoids). 273 Figure 8.25 ORTEP packing stereodiagram of acid (4). 8.19. l-Methyl-4-(4-nitro-2-pyridyI)-piperazinium salt of (1): l.nitropyr. A crystal of approximate dimensions 0.18 x 0.07 x 0.25 mm was chosen for data collection. Crystallographic data of l.nitropyr appear in Table 8.71. A triclinic cell with Z = 2 (assuming a density of 1.43 g/cm3 was indicated by preliminary measurements. 4184 reflections were collected, of which 3962 were unique and 1989 were observed (I > 274 3.0 o(T)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 29 = 51.5 - 85.6°. The data for l.nitropyr were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on a statistical analysis of intensity distributions and the successful solution and refinement of the structure, the space group was determined to be P I . The structure (Figure 8.26) was solved by direct-methods [161] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were determined from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 3.29 xlO"6). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fc aic.[172] The refinement converged at R = 0.046, Rw = 0.047 for 360 variables (GOF = 2.13; including zeros: R = 0.140, Rw = 0.058), with the largest parameter shift in the final refinement cycle being 0.03<t. The final difference map showed electron density between -0.22 and 0.16 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.76-78, respectively. The crystal packing of l.nitropyr is shown in Figure 8.27 The piperazine ring is oriented roughly perpendicularly to its pyridine ring, allowing the protonated amine, N(4)—H(14), to participate in a bifurcated N—H---0 bond with the two carboxylate 275 oxygens, 0(5) and 0(6). The piperazine ring conformation also allows for weak C — H - O interactions with the P -NO2 group of its symmetry related neighbor [C(15}-H(13)—0(7) and C(16)—H(16)--.-0(8)], forming oppositely oriented salt dimers about the centre of inversion. Complete hydrogen bond and C—H- • O interaction details are given in Table 8.79. Figure 8.26 ORTEP diagram of l.nitropyr (50% probability ellipsoids). 276 Figure 8.27 CHARON packing diagram of l.nitropyr viewed down the c-axis. 8.20. l-Methyl-4-(4-nitro-2-pyridyl)-piperazinium salt of (2): 2.hitropyr. A crystal of approximate dimensions 0.48 x 0.28 x 0.25 mm was chosen for data collection. Crystallographic data of 2.nitropyr appear in Table 8.71. A triclinic cell with Z = 2 (assuming a density of 1.51 g/cm3 was indicated by preliminary measurements. 4343 reflections were collected, of which 4144 were unique and 2897 were observed (I > 3.0 o(I)). The final unit cell parameters were obtained from a least-squares refinement using the setting angles of 25 reflections with 26 = 96.6 - 110.3°. The data for 2.nitropyr 277 were processed and corrected for Lorentz and polarization effects, as well as for absorption and decay. Based on a statistical analysis of intensity distributions and the successful solution and refinement of the structure, the space group was determined to be P I . The structure was solved by direct-methods [162] and expanded using Fourier techniques.[166] Non-hydrogen atoms were determined from E-maps or from subsequent difference Fourier syntheses and were refined with anisotropic thermal parameters. A l l hydrogens were determined from difference Fourier syntheses and refined isotropically. A secondary extinction coefficient correction was applied (final coefficient = 5.44 xlO"6). Neutral atom scattering factors and the values of Af and Af' were taken from the International Tables for X-ray Crystallography.[168, 171] Anomalous dispersion corrections for the non-hydrogen atoms were included in Fcaic.[172] The refinement converged at R = 0.046, Rw = 0.047 for 383 variables (GOF = 3.49; including zeros: R = 0.079, Rw = 0.050), with the largest parameter shift in the final refinement cycle being 0.02a The final difference map showed electron density between -0.17 and 0.21 e/A 3. Final atomic coordinates and equivalent isotropic thermal parameters, bond lengths and bond angles appear in Tables 8.80-82, respectively. Figure 8.28 shows an ORTEP diagram of 2.nitropyr. The crystal packing of 2.nitropyr is shown in Figure 8.29. The piperazine ring is oriented roughly perpendicularly to its pyridine ring, allowing the protonated amine, N(4)—H(14), to participate in a bifurcated N — H - 0 bond with the two carboxylate oxygens, 0(5) and 0(6). The piperazine ring conformation also allows for weak C — H - O interactions with 278 the /7-NO2 group of its symmetry related neighbor [C(15)—H(13)---0(7) and C(16>—H(16>--0(8)], forming oppositely oriented salt dimers about the centre of inversion. Complete hydrogen-bonding details are given in Table 8.83. Figure 8.28 ORTEP diagram of 2.nitropyr (50% probability ellipsoids). +a Figure 8.29 CHARON packing diagram of 2.nitropyr. 279 Table 8.71 Crystallographic data for (4), l.nitropyr and 2.nitropyr. (4) l.nitropyr 2.nitropvr Formula C 0 H H N 4 O 2 C 1 8 H 2 2 N 6 0 6 C 1 8 H 2 1 N 7 0 8 fw 222.25 418.41 463.41 Crystal system monoclinic triclinic triclinic Space group P2,/c P\ P\ a, A 13.430(1) 10.670(1) 12.051(2) b , k 6.1537(5) 13.327(2) 14.856(2) c, A 27.324(2) 7.4369(5) 6.0806(8) a(a) 90.702(9) 91.67(1) PC) 103.858(7) 99.921(8) 91.58(1) r o 68.59(1) 110.16(1) V 2195.5(3) 968.3(2) 1020.7(2) z 8 2 2 Pealed, g/cm3 1.35 1.43 1.51 F(000) 944 440 484 Radiation Cu-Ka(A = 1.54178 A) Cu-Ka(A= 1.54178 A) Cu-Ka(A= 1.54178 A) jU, cm"1 7.7 8.8 9.9 Crystal size, mm 0.20x0.15 x 0.20 0.18x0.07x0.25 0.48 x 0.28 x 0.25 Transmission factors 0.86-1.00 0.86-1.00 0.93 - 1.00 Scan type co-26 co-26 co-26 Scan range, ° in co 1.10+ 0.20 tan d 0.94 + 0.20 tan 6 1.10+ 0.20 tan 6 Scan speed, °/min 32.0 32.0 32.0 Data collected +h, +k, ±1 +h, ±k, ±1 +h, dk, ±1 155.3 155.5 155.2 Crystal decay -0.9% -0.2% +0.1% Total reflections 5189 4184 4343 Total unique 4988 3962 4144 Emerge 0.032 0.019 0.043 No. of reflections 1853 1989 2897 with / >3o(/) No. of variables 290 360 383 p-factor 0.009 0.007 0.00 R 0.039 0.046 0.046 Rw 0.039 0.047 0.047 Goodness of fit 1.86 2.13 3.49 Max A/a (final cycle) 0.00 0.03 0.02 Residual density elk3 -0.11 to+0.12 -0.22 to +0.16 -0.17 to +0.21 280 Table 8.72 Final atomic coordinates (fractional) and B(eq) (A2) of (4). atom X v z B(ea) O(l) 0.7595(2) 0.5505(5) -0.1283(1) 8.8(1) 0(2) 0.8051(2) 0.8860(6) -0.1191(1) 8.43(9) 0(3) 0.2853(2) 0.6191(5) 0.4094(1) 7.89(9) 0(4) 0.3377(2) 0.2996(5) 0.3954(1) 7.51(8) N(l) 0.9360(2) 0.6576(5) 0.1993(1) 5.39(8) N(2) 0.9645(2) 0.5909(4) 0.1005(1) 5.66(8) N(3) 0.9251(2) 0.8077(4) 0.0312(1) 5.20(8) N(4) 0.7995(2) 0.7034(7) -0.1018(1) 6.3(1) N(5) 0.5964(2) 0.2385(5) 0.7255(1) 5.22(8) N(6) 0.4659(2) 0.2878(4) 0.6272(1) 5.42(8) N(7) 0.4334(2) 0.1705(4) 0.5451(1) 5.13(8) N(8) 0.3263(2) 0.4451(6) 0.4243(1) 5.68(9) C(l) 0.9206(2) 0.6102(5) 0.0515(1) 4.63(9) C(2) 0.8736(3) 0.4336(5) 0.0219(1) 5.30(9) C(3) 0.8341(3) 0.4621(6) -0.0280(1) 5.5(1) C(4) 0.8405(2) 0.6653(6) -0.0485(1) 4.9(1) C(5) 0.8862(3) 0.8313(6) -0.0179(1) 5.2(1) C(6) 1.0139(3) 0.7722(6) 0.1316(1) 6.4(1) C(7) 0.9504(3) 0.8384(6) 0.1671(1) 6.1(1) C(8) 0.8885(3) 0.4743(6) 0.1679(1) 5.7(1) C(9) 0.9510(3) 0.4062(6) 0.1314(1) 5.8(1) C(10) 0.8732(3) 0.7235(7) 0.2337(1) 7.5(1) C(ll) 0.4305(2) 0.3345(5) 0.5784(1) 4.44(9) C(12) 0.3934(2) 0.5399(5) 0.5613(1) 4.84(9) C(13) 0.3598(2) 0.5767(5) 0.5117(1) 5.14(9) C(14) 0.3623(2) 0.4106(6) 0.4781(1) 4.51(9) C(15) 0.4000(3) 0.2126(6) 0.4962(1) 4.96(9) C(16) 0.5047(3) 0.0745(5) 0.6457(1) 5.6(1) C(17) 0.6054(3) 0.0972(6) 0.6840(1) 5.5(1) C(18) 0.5620(3) 0.4500(6) 0.7056(1) 6.1(1) C(19) 0.4606(3) 0.4361(6) 0.6685(1) 6.4(1) C(20) 0.6940(3) 0.2542(7) 0.7626(1) 7.6(1) Table 8.73 Bond lengths (A) of (4) with estimated standard deviations. atom atom distance atom atom distance 0(1) N(4) 1.229(4) N(6) C(16) 1.457(4) 0(2) N(4) 1.228(4) N(6) C(19) 1.465(4) 0(3) N(8) 1.228(3) „ N(7) C(ll) 1.365(4) 0(4) N(8) 1.227(3) N(7) C(15) 1.329(4) N(l) C(7) 1.460(4) N(8) C(14) 1.450(4) N(l) C(8) 1.468(4) C(l) C(2) 1.412(4) 281 N(l) C(10) 1.462(4) N(2) C(l) 1.332(4) N(2) C(6) 1.462(4) N(2) C(9) 1.454(4) N(3) C(l) 1.344(4) N(3) C(5) 1.325(4) N(4) C(4) 1.447(4) N(5) C(17) 1.457(4) N(5) C(18) 1.444(4) N(5) C(20) 1.455(4) N(6) C(ll) 1.336(4) C(2) C(3) 1.350(4) C(3) C(4) 1.381(4) C(4) C(5) 1.369(4) C(6) C(7) 1.493(5) C(8) C(9) 1.509(5) C(ll) C(12) 1.397(4) C(12) C(13) 1.341(4) C(13) C(14) 1.381(4) C(14) C(15) 1.366(4) C(16) C(17) 1.506(4) C(18) C(19) 1.493(5) Table 8.74 Bond angles (deg) of (4) with estimated standard deviations. atom atom atom angle atom atom atom angle C(7) N(l) C(8) 109.6(3) C(l) C(2) C(3) 119.6(3) C(7) N(l) C(10) 110.8(3) C(2) C(3) C(4) 118.7(3) C(8) N(l) C(10) 110.6(3) N(4) C(4) C(3) 120.6(4) C(l) N(2) C(6) 123.1(3) N(4) C(4) C(5) 120.1(3) C(l) N(2) C(9) 124.5(3) C(3) C(4) C(5) 119.3(3) C(6) N(2) C(9) 111.2(3) N(3) C(5) C(4) 123.1(3) C(l) N(3) C(5) 118.2(3) . N(2) C(6) C(7) 109.6(3) 0(1) N(4) 0(2) 122.2(4) N(l) C(7) C(6) 111.2(3) 0(1) N(4) C(4) 118.4(4) N(l) C(8) C(9) 111.5(3) 0(2) N(4) C(4) 119.4(4) N(2) C(9) C(8) 109.5(3) C(17) N(5) C(18) 108.8(3) N(6) C(ll) N(7) 116.5(3) C(17) N(5) C(20) 110.6(3) N(6) C(ll) C(12) 122.8(3) C(18) N(5) C(20) 110.9(3) N(7) C(H) C(12) 120.7(3) C(ll) N(6) C(16) 123.5(3) C(ll) C(12) C(13) 119.8(3) C(ll) N(6) C(19) 124.3(3) C(12) C(13) C(14) 119.4(3) C(16) N(6) C(19) 112.0(3) N(8) C(14) C(13) 120.8(3) C(ll) N(7) C(15) 118.0(3) N(8) C(14) C(15) 120.2(3) 0(3) N(8) 0(4) 122.6(4) C(13) C(14) C(15) 119.0(3) 0(3) N(8) C(14) 118.5(4) N(7) C(15) C(14) 123.0(3) 0(4) N(8) C(14) 118.8(3) N(6) C(16) C(17) 110.1(3) N(2) C(l) N(3) 116.3(3) N(5) C(17) C(16) 111.7(3) N(2) C(l) C(2) 122.6(3) N(5) C(18) C(19) 111.2(3) N(3) C(l) C(2) 121.1(3) N(6) C(19) C(18) 110.7(3) Table 8.75 Geometry of (4) hydrogen bonds and C—H- • O interactions(A, °). D—R--A D-H H---4 D---4 D-^H-A C(6)-H(5)-N(3) 0.98 - 2.29 2.727(5) 109 C(16)-4i(19)-N(7) 0.98 2.31 2.749(5) 106 282 C(20)-^i(28)---O(l)(iii) 0 19J 2^ 53 3.426(5) 152 Symmetry Codes: (i) -x, 'A+y, 'A-z (ii) x, 'A-y, 'A+z (Hi) -x, -y, -z Table 8.76 Final atomic coordinates (fractional) and B(eq) (A2) of l.nitropyr. atom X V z B(eq) O(l) 0.3759(3) 1.8797(2) -0.1545(4) 5.36(7) 0(2) 0.1875(3) 1.8689(2) -0.2918(5) 6.86(9) 0(3) 0.5818(3) 1.1221(2) -0.3710(4) 5.22(7) 0(4) 0.7391(2) 1.1781(2) -0.2146(4) 5.29(7) 0(5) 1.1869(3) 0.4034(2) 0.4035(4) 5.84(8) 0(6) 0.9976(3) 0.3819(2) 0.2992(4) 6.35(9) N(l) 0.5738(3) 1.3820(2) -0.2415(4) 3.86(8) N(2) 0.3095(3) 1.8269(2) -0.2253(4) 4.52(8) N(3) 0.7490(3) 0.9241(2) -0.3517(4) 3.93(7) N(4) 0.8207(3) 0.8553(2) 0.0263(4) 3.67(7) N(5) 0.8128(3) 0.6899(2) 0.0937(4) 3.86(7) N(6) 1.0683(3) 0.4372(2) 0.3213(4) 4.38(8) C(l) 0.5077(3) 1.4900(3) -0.2398(4) 3.20(8) C(2) 0.5779(4) 1.5545(3) -0.1593(5) 3.61(9) C(3) 0.5143(4) 1.6632(3) -0.1549(5) 3.60(9) C(4) 0.3770(4) 1.7114(3) -0.2319(5) 3.51(8) C(5) 0.3047(4) 1.6506(3) -0.3134(5) 3.94(9) C(6) 0.3693(4) 1.5414(3) -0.3200(5) 3.81(9) C(7) 0.5148(4) 1.3064(3) -0.3191(6) 3.58(9) C(8) 0.6233(4) 1.1923(3) -0.2974(5) 3.80(9) C(9) 0.8871(3) 0.7532(3) 0.0994(4) 3.43(8) C(10) 1.0267(4) 0.7152(3) 0.1860(5) 3.82(9) C(ll) 1.0858(4) 0.6124(3) 0.2591(5) 3.97(9) C(12) 1.0085(3) 0.5478(3) 0.2467(5) 3.53(8) C(13) 0.8733(4) 0.5901(3) 0.1662(5) 3.93(9) C(14) 0.6783(4) 0.8899(3) -0.0694(5) 3.69(9) C(15) 0.6756(4) 0.8662(3) -0.2662(5) 3.80(9) C(16) 0.8897(4) 0.9014(3) -0.2457(6) 4.4(1) C(17) 0.8899(4) 0.9187(3) -0.0459(6) 4.1(1) C(18) 0.7535(6) 0.8975(4) -0.5454(7) 5.8(1) H(l) 0.674(4) 1.518(3) -0.097(5) 5.6(9) H(2) 0.565(3) 1.705(3) -0.098(5) 5.2(9) H(3) 0.218(4) 1.682(3) -0.372(5) 5(1) H(4) 0.321(3) 1.502(2) -0.383(4) 3.6(8) H(5) 0.650(4) 1.353(3) -0.185(5) 5(1) H(6) 0.441(3) 1.304(3) -0.263(5) 4.3(9) H(7) 0.481(4) 1.326(3) -0.453(5) 6(1) H(8) 1.080(3) 0.761(2) 0198(4) 4.0(8) H(9) 1.173(3) 0.586(3) 0.327(5) 5.1(9) H(10) 0.821(3) 0.547(2) 0.167(4) 2.8(7) 283 H(ll) 0.640(3) 0.970(3) -0.050(4) 3.8(7) H(12) 0.633(3) 0.851(3) -0.010(5) 4.8(9) H(13) 0.583(4) 0.887(3) -0.342(5) 6(1) H(14) 0.719(3) 0.791(2) -0.288(4) 3.1(7) H(15) 0.679(4) 1.019(3) -0.356(5) 7(1) H(16) 0.919(3) 0.952(3) -0.301(5) 4.8(9) H(17) 0.944(3) 0.826(3) -0.272(5) 4.8(8) H(18) 0.841(3) 1.000(3) -0.028(4) 5.5(9) H(19) 0.982(4) 0.898(3) 0.022(5) 5.0(9) H(20) 0.795(5) 0.946(4) -0.611(7) 9(1) H(21) 0.661(5) 0.914(4) -0.613(7) 10(1) H(22) 0.799(4) 0.823(3) -0.555(5) 6(1) Table 8.77 Bond lengths (A) of l.nitropyr with estimated standard deviations. atom atom distance atom atom distance O(l) N(2) 1.225(3) N(5) C(13) 1.321(4) 0(2) N(2) 1.227(4) N(6) C(12) 1.449(4) 0(3) C(8) 1.255(4) C(l) C(2) 1.400(4) 0(4) C(8) 1.230(4) C(l) C(6) 1.405(4) 0(5) N(6) 1.226(4) C(2) C(3) 1.360(5) 0(6) N(6) 1.225(4) C(3) C(4) 1.386(5) N(l) C(l) 1.353(4) C(4) C(5) 1.379(5) N(l) C(7) 1.438(4) C(5) C(6) 1.369(5) N(2) C(4) 1.446(4) C(7) C(8) 1.528(5) N(3) C(15) 1.495(5) C(9) C(10) 1.419(4) N(3) C(16) 1.495(5) C(10) C(ll) 1.356(5) N(3) C(18) 1.484(5) C(ll) C(12) 1.386(5) N(4) C(9) 1.353(4) C(12) C(13) 1.369(5) N(4) C(14) 1.466(4) C(14) C(15) 1.491(5) N(4) C(17) 1.467(5) C(16) C(17) 1.501(6) N(5) C(9) 1.349(4) Bond angles (deg) of l.nitropyr with estimated standard deviations. Table 8.78 Atom atom atom angle C(l) N(l) C(7) 126.0(3) O(l) N(2) 0(2) 122.1(3) 0(1) N(2) C(4) 119.1(3) 0(2) N(2) C(4) 118.8(3) C(15) N(3) C(16) 111.7(3) C(15) N(3) C(18) 111.2(3) C(16) N(3) C(18) 110.9(4) atom atom atom angle C(3) C(4) C(5) 120.8(3) C(4) C(5) C(6) 119.8(4) C(l) C(6) C(5) 120.7(3) N(l) C(7) C(8) 110.2(3) 0(3) C(8) 0(4) 127.0(3) 0(3) C(8) C(7) 114.1(3) 0(4) C(8) C(7) 118.8(3) 284 C(9) N(4) C(14) 120.4(3) N(4) C(9) N(5) 116.8(3) C(9) N(4) C(17) 123.1(3) N(4) C(9) C(10) 122.0(3) C(14) N(4) C(17) 109.9(3) N(5) C(9) C(10) 121.1(3) C(9) N(5) C(13) 118.7(3) C(9) C(10) C(ll) 118.7(4) 0(5) N(6) 0(6) 123.1(3) C(10) C(ll) C(12) 119.1(4) 0(5) N(6) C(12) 118.6(3) N(6) C(12) C(ll) 120.8(3) 0(6) N(6) C(12) 118.3(3) N(6) C(12) C(13) 119.9(3) N(l) C(l) C(2) 120.1(3) C(ll) C(12) C(13) 119.3(3) N(l) C(l) C(6) 122.0(3) N(5) C(13) C(12) 123.0(3) C(2) C(l) C(6) 117.9(3) N(4) C(14) C(15) 109.5(3) C(l) C(2) C(3) 121.5(3) N(3) C(15) C(14) 110.3(3) C(2) C(3) C(4) 119.4(3) N(3) C(16) C(17) 112.2(3) N(2) C(4) C(3) 119.1(3) N(4) C(17) C(16) 109.7(3) N(2) C(4) C(5) 120.0(3) Table 8.79 Geometry of l.nitropyr hydrogen bonds and C—H- • -O interactions (A, °). \ D—H H--4 D—A D—H--A N(l)-H(5)- • 0(4) 0.80(4) 2.19(4) 2.631(3) 115(3) N(3)-^I(15)- •0(3) 1-21(4) 1.38(4) 2.580(3) 171(3) N(3)-^I(15)- •0(4) 1-21(4) 2.59(4) 3.494(4) 130(2) C(10)—H(8)- 0(4)(i) 0.98(3) 2.33(3) 3.273(4) 162(3) c(uy-n(iiy •0(l)( i ) 1-01(3) 2.48(3) 3.383(4) 149(3) C(U)—ii(l2) ..N(5) 0.97(3) 2.33(3) 2.706(5) 102(3) C(15)-^I(13)- • O(3)0) 0.99(3) 2.56(4) 3.463(5) 153(3) C(15)-H(14)- •0(5)(i) 2.61(3) 170(3) C(16)-^(17)- •0(6)(i) 2.62(4) 157(3) C(17)-fl(18) -0(4) 1-03(3) 2.53(4) 3.386(5) 140(3) Symmetry Codes: (i) -x, -y, -z Table 8.80 Final atomic coordinates (fractional) and B(eq) (A2) of 2.nitropyr. atom X V z B(ea) 0(1) 0.3700(2) 0.0838(1) 1.6739(4) 6.05(6) 0(2) 0.3501(2) 0.1536(2) 1.9758(3) 5.83(5) 0(3) 0.0965(2) 0.3343(1) 2.0266(3) 5.68(5) 0(4) -0.0211(2) 0.3340(1) 1.7532(3) 5.70(5) 0(5) 0.1542(2) -0.1315(1) 0.9232(3) 5.60(5) 0(6) 0.2733(2) -0.0945(2) 1.2222(3) 6.02(6) 0(7) 0.4094(2) -0.6878(2) 0.3011(4) 8.15(8) 0(8) 0.4999(2) -0.6762(2) 0.6153(4) 7.13(7) N(l) 0.1948(2) 0.0380(2) 1.3701(4) 4.15(5) 285 N(2) 0.3197(2) 0.1274(2) 1.7852(4) 4.15(5) N(3) 0.0538(2) 0.3069(2) 1.8419(4) 4.22(5) N(4) 0.3211(2) -0.2031(2) 0.7966(4) 4.25(5) N(5) 0.2201(2) -0.4070(2) 0.8135(3) 4.29(5) N(6) 0.3442(2) -0.4955(2) 0.8644(4) 4.59(5) N(7) 0.4310(2) -0.6568(2) 0.4911(4) 5.03(6) C(l) 0.1655(2) 0.1047(2) 1.4822(4) 3.45(5) C(2) 0.2209(2) 0.1485(2) 1.6860(4) 3.47(5) C(3) 0.1829(2) 0.2130(2) 1.8043(4) 3.50(5) C(4) 0.0925(2) 0.2384(2) 1.7181(4) 3.55(5) C(5) 0.0380(2) 0.2001(2) 1.5148(4) 3.92(6) C(6) 0.0729(2) 0.1349(2) 1.4018(4) 3.86(6) C(7) 0.1353(2) -0.0138(2) 1.1719(4) 3.71(6) C(8) 0.1938(2) -0.0863(2) 1.1020(4) 4.18(6) C(9) 0.2679(2) -0.4712(2) 0.7302(4) 3.70(5) C(10) 0.2385(3) -0,5112(2) 0.5191(5) 4.43(7) C(ll) 0.2902(3) -0.5723(2) 0.4382(5) 4.69(7) C(12) 0.3711(2) -0.5941(2) 0.5727(4) 3.84(6) C(13) 0.3943(2) -0.5565(2) 0.7830(5) 4.38(6) C(14) 0.2696(3) -0.3493(2) 1.0161(5) 4.63(7) C(15) 0.3645(2) -0.2569(2) 0.9634(4) 4.30(7) C(16) 0.2626(3) -0.2649(2) 0.5996(4) 4.48(7) C(17) 0.1676(3) -0.3548(2) 0.6678(5) 4.80(7) C(18) 0.4195(3) -0.1167(3) 0.7333(8) 6.17(10) H(l) 0.219(2) 0.236(2) 1.939(4) 3.5(5) H(2) -0.022(2) 0.218(2) 1.457(4) 5.0(6) H(3) 0.031(2) 0.110(2) 1.269(4) 4.4(6) H(4) 0.250(3) 0.026(2) 1.417(5) 6.8(9) H(5) 0.135(2) 0.027(2) 1.052(4) 3.1(5) H(6) 0.050(2) -0.049(2) 1.192(4) 3.7(5) H(7) 0.188(2) -0.503(2) 0.440(5) 5.4(7) H(8) 0.276(2) -0.597(2) 0.291(5) 6.0(7) H(9) 0.444(2) -0.575(2) 0.882(4) 5.2(6) H(10) 0.199(2) -0.337(2) 1.085(4) 4.5(6) H(ll) 0.297(2) -0.386(2) 1.117(4) 4.7(6) H(12) 0.391(2) -0.215(2) 1.097(4) 4.5(6) H(13) 0.433(2) -0.264(2) 0.892(4) 4.8(6) H(14) 0.260(3) -0.178(2) 0.864(5) 8.5(9) H(15) 0.230(2) -0.227(2) 0.495(4) 5.0(6) H(16) 0.324(2) -0.277(2) 0.523(4) 4.5(6) H(17) 0.106(2) -0.338(2) 0.760(4) 5.7(7) H(18) 0.128(2) -0.394(2) 0.542(5) 5.7(7) H(19) 0.443(3) -0.079(3) 0.875(6) 10(1) H(20) 0.388(3) -0.090(2) 0.619(5) 7.0(9) H(21) 0.490(3) -0.135(2) 0.677(5) 8.0(9) 286 Table 8.81 Bond lengths (A) of 2.nitropyr with estimated standard deviations. atom atom distance atom atom distance 0(1) N(2) 1.230(3) N(5) C(17) 1.461(3) 0(2) N(2) 1.217(3) N(6) C(9) 1.358(3) 0(3) N(3) 1.220(3) N(6) C(13) 1.341(3) 0(4) N(3) 1.227(3) N(7) C(12) 1.445(3) 0(5) C(8) 1.252(3) C(l) C(2) 1.419(3) 0(6) C(8) 1.230(3) C(l) C(6) 1.418(3) 0(7) N(7) 1.218(3) C(2) C(3) 1.388(3) 0(8) N(7) 1.219(3) C(3) C(4) 1.366(3) N(l) C(l) 1.336(3) C(4) C(5) 1.392(3) N(l) C(7) 1.442(3) C(5) C(6) 1.359(3) N(2) C(2) 1.451(3) C(7) C(8) 1.534(3) N(3) C(4) 1.457(3) C(9) C(10) 1.383(4) N(4) C(15) 1.498(3) C(10) C(ll) 1.355(4) N(4) C(16) 1.490(3) C(ll) C(12) 1.384(4) N(4) C(18) 1.485(4) C(12) C(13) 1.363(4) N(5) C(9) 1.366(3) C(14) C(15) 1.503(4) N(5) C(14) 1.468(3) C(16) C(17) 1.507(4) Table 8.82 Bond angles (deg) of 2.nitropyr with estimated standard deviations. Atom atom atom angle atom atom atom angle C(l) N(l) C(7) 125.9(2) C(2) C(3) C(4) 119.2(2) 0(1) N(2) 0(2) 122.2(2) N(3) C(4) C(3) 118.9(2) 0(1) N(2) C(2) 119.0(2) N(3) C(4) C(5) 120.1(2) 0(2) N(2) C(2) 118.9(2) C(3) C(4) C(5) 121.0(2) 0(3) N(3) 0(4) 123.3(2) ^ C(4) C(5) C(6) 119.9(2) 0(3) N(3) C(4) 119.2(2) C(l) C(6) C(5) 122.2(2) 0(4) N(3) C(4) 117.5(2) N(l) C(7) C(8) 109.2(2) C(15) N(4) C(16) 112.2(2) 0(5) C(8) 0(6) 126.7(2) C(15) N(4) C(18) 110.4(2) 0(5) C(8) C(7) 114.8(2) C(16) N(4) C(18) 111.2(3) 0(6) C(8) C(7) 118.4(2) C(9) N(5) C(14) 121.2(2) N(5) C(9) N(6) 117.3(2) C(9) N(5) C(17) 120.9(2) N(5) C(9) C(10) 121.4(2) C(14) N(5) C(17) 110.3(2) N(6) C(9) C(10) 121.3(2) C(9) N(6) C(13) 118.0(2) C(9) C(10) C(ll) 120.2(3) 0(7) N(7) 0(8) 123.4(2) C(10) C(ll) C(12) 118.4(3) 0(7) N(7) C(12) 118.0(3) N(7) C(12) C(ll) 120.2(2) 0(8) N(7) C(12) 118.6(2) N(7) C(12) C(13) 120.0(2) N(l) C(l) C(2) 123.8(2) C(ll) C(12) C(13) 119.8(2) N(l) C(l) C(6) 120.5(2) N(6) C(13) C(12) 122.3(3) C(2) C(l) C(6) 115.7(2) N(5) C(14) C(15) 110.4(2) 287 N(2) C(2) C(l) 122.1(2) N(4) C(15) C(14) 111.7(2) N(2) C(2) C(3) 115.9(2) N(4) C(16) C(17) 110.5(2) C(l) C(2) C(3) 122.0(2) N(5) C(17) C(16) 109.3(2) Table 8.83 Geometry of 2.nitropyr hydrogen bonds and C — H - 0 interactions (A, °). D—H ¥f--A n—A D—H---/4 N(l)-H(4)---0(1) 0.79(3) 2.05(3) 2.656(3) 133(3) N(l)-H(4)--0(6) 0.79(3) 2.22(3) 2.609(3) 111(3) N(4)-^l(14)---0(5) 1.03(3) 1.69(3) 2.699(3) 169(3) N(4)-^l(14)---0(6) 1.03(3) 2.45(3) 3.180(3) 128(2) C(ll)-^l(8)---0(3) 0.95(3) 2.55(3) 3.299(4) 136(3) C(14)-41(10)---O(4)(i) 1.03(2) 2.40(3) 3.416(3) 171(2) C(14)—H(ll)---N(6) 0.95(3) 2.42(3) 2.766(3) 101(2) C(15)-^I(13)---0(7)(i) 0.98(3) 2.55(3) 3.521(3) 171(2) C(16)-«(15)-- -0(6) 1.02(3) 2.53(3) 3.439(4) 148(2) C(16)-^l(16)---0(8)(i) 0.95(3) 2.60(3) 3.540(3) 169(2) C(17)-41(18)---0(4)(i) 1.04(3) . 2.54(3) 3.153(4) 122(2) Symmetry Codes: (i) -x, -y, -z 288 References 1. G. D. Stucky, S. R. Marder and J. E. Sohn, Materials for Nonlinear Optics: Chemical Perspectives (Editors: S. R. Marder, J. E. Sohn and G. D. Stucky), ACS Symposium Series 455; American Chemical Society, Washington, D.C., 1991. 2. J. F. Ward, Rev. Mod. Phys., 37, 1 (1965). 3. B. J. Orr and J. F. Ward, Molec. Phys., 20, 513 (1971). 4. J. Kerr, Phil. 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