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X-ray crystallographic studies of eight organic compounds 1981

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X-RAY CRYSTALLOGRAPHIC STUDIES OF EIGHT ORGANIC COMPOUNDS by RICHARD ALEXANDER PAUPTIT B.Sc, University of Cape Town, 1975. Sc., University of B r i t i s h Columbia, 1978. THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES DEPARTMENT OF CHEMISTRY we accept t h i s thesis as conforming to the required standard The University of B r i t i s h Columbia November, 1 98 1 . © Richard Alexander Pauptit. In presenting t h i s thesis i n p a r t i a l f u l f i l m e n t of the requirements f o r an advanced degree at the University of B r i t i s h Columbia, I agree that the Library s h a l l make i t f r e e l y a v a i l a b l e for reference and study. I further agree that permission for extensive copying of t h i s thesis for s c h o l a r l y purposes may be granted by the head of my department or by his or her representatives. It i s understood that copying or p u b l i c a t i o n of t h i s thesis for f i n a n c i a l gain s h a l l not be allowed without my written permission. Department of The University of B r i t i s h Columbia 2075 Wesbrook Place Vancouver, Canada V6T 1W5 Da te CVMO za ] \^&~^ ABSTRACT Part one of th i s thesis contains the x-ray c r y s t a l structure analyses of six compounds related to natural product chemistry. The f i r s t three analyses were performed in order to identif y two isomers, separated by chromatography, that were potential intermediates in the syntheses, of stemodin. and ap h i d i c o l i n , and d i f f e r e d only in the orientation of a cyclobutyl moiety. The f i r s t eluted isomer was shown to be a p-cyclobutyl t r i c y c l i c enone ( C 2 2 H 3 2 0 3 » monoclinic, space group P2 1/n, a = 11.832(1), b = 11.423(1), c = 14.637(1) A, fi = 98.71(2)°, Z = 4, solved by d i r e c t methods and refined to R = 0.034 for 2052 observed r e f l e c t i o n s ) . The second eluted isomer was the c-cyclobutyl species ( C 2 2 H 3 2 O 3 , monoclinic, space group P2 1/n, a = 15.722(4), b = 7.463(2), c = 17.213(6) A, I =- 1 04 . 67 ( 1 ) 0 , Z = 4, solved' by direct methods- and- refined to- R = 0.040 for 702 observed r e f l e c t i o n s ) . The t h i r d analysis was of the p-bromobenzoate derivative of the second eluted isomer, and confirmed the c-cyclobutyl structure ( C 2 9H 3 7BrO„, t r i c l i n i c , space group PT , a = 11.023(2), b = 11.877(1), c = 10.900(1) A, o = 90.461(8), 0 = 111.57(1), 7 = 80.51(1)°, Z = 2, solved by Patterson methods and refined to R = 0.032 for 2715 observed r e f l e c t ions). The fourth structure was also a p-bromobenzoate derivative of a system involving a four-membered ring, and was undertaken to v e r i f y the 1,4-homoenol structure of camphor-1,4-homoenol p- bromobenzoate (C , 7H , 9Br.Q2,. orthorhombic.,. space group P2 12. 12 1, a = 6.875(1), b = 8.522(2), c = 26.658(6) A, Z = 4, solved by both direct and Patterson methods and refined to R =0.045 for 697 observed r e f l e c t i o n s ) . The l a s t two structures of t h i s part proved to be c r y s t a l l o g r a p h i c a l l y d i f f i c u l t . One was the previously unknown structure of raucubaine, an indole a l k a l o i d isolated from the plant Rauwolfia s a l i c i f o l i a griseb. (C 2 0H 2 t tN 20 3, monoclinic, space group P2,, a = 7.2179(3), b = 12.8169(7), c = 9.1996(2) A, fi = 93.040(3)°, 1 = 2, solved by di r e c t methods (with great d i f f i c u l t y ) and refined to R = 0.046 for 1700 observed r e f l e c t i o n s ) . The other was a sugar that had remained unsolved for fourteen years (C 2«H 2„C1 20 B, monoclinic, space group P2,, a = 5.752(3), b = 15.436(3), c = 13.698(3) A, fi = 93.74(3)°, Z = 2, solved by dire c t methods (with great d i f f i c u l t y ) and refined to R = 0.042 for 898 observed r e f l e c t i o n s ) . Part two contains two o p t i c a l l y active structures as part of a project concerning spontaneous resolution in binaphthyl systems: the f i r s t being naphthidine ( C 2 0H 1 6N 2, tetragonal, space group P4!2,2 or P4 32,2, a = 7.945(1), c = 24.264(5) A, Z = 4, solved by dire c t methods and refined to R = 0.068 for 548 ref l e c t i o n s ) and the other 1 , 1 '-binaphthyl (C 2 0H 1 1 (, tetragonal, space group P4,2,2 or P4 32,2, a = 7.164(2), c = 27.70(1) A, Z = 4, solved by dire c t methods and refined to R = 0.030 for 562 observed r e f l e c t i o n s ) . These structures are compared to those of several related compounds. iv TABLE OF CONTENTS T i t l e page i Abstract i i Table of contents . . iv L i s t of tables . . . . v i i L i s t of figures x i i Acknowledgement xv Dedication xvi CHAPTER 1 : INTRODUCTION 1 Part one 10 CHAPTER 2: STEMODIN INTERMEDIATES 11 I. A 0-cyclobutyl t r i c y c l i c enone 12 Introduction and preparation 12 Experimental 14 Results and discussion 19 II. An c-cyclobutyl t r i c y c l i c enone 31 Introduction 31 Experimental 33 Results and discussion 37 II I . The p-bromobenzoate derivative of the second eluted i somer 49 Introduction 49 Experimental 49 Results and discussion 54' Comparison of the three structures 59 CHAPTER 3: THE CRYSTAL STRUCTURE OF CAMPHOR-1,4-HOMOENOL P- V BROMOBENZOATE 72 Introduction and preparation. 73 Experimental ... 74 Results and discussion 80 CHAPTER 4: DIFFICULT P2, STRUCTURES 92 I. Crystal structure of raucubaine 93 Introduction 93 Data c o l l e c t i o n 93 Solution 95 Post-solution analysis. 104 Refinement 106 Discussion 112 II. Crystal structure of methyl 3-C-(carbomethoxy- methyl)-4,6-di-0-p-chlorobenzoyl-2,3-dideoxy-c-D- ribo-hexopyranoside 122 Introduction and previous attempts at solution .... 122 Experimental 124 Solution 124 Refinement 129 Post-solution analysis 131 Discussion 135 Part two 144 CHAPTER 5: SPONTANEOUS RESOLUTION IN BINAPHTHYL SYSTEMS ... 145 Introduction 146 Experimental 146 A. Opt i c a l l y act i ve' 4,4" -di'amino- 1,1' -binaphthyl 1 46 B. O p t i c a l l y active 1,1'-binaphthyl 152 v i Results 153 Discussion . . 165 Half-normal pr o b a b i l i t y plots 169 Summary 173 References 175 APPENDIX: STRUCTURE FACTOR TABLES •• 181 v i i LIST OF TABLES Chapter 1 1 Chapter 2 11 I. Crystal data for molecule 4 15 II . E - s t a t i s t i c s after renormalization 18 I I I . Atomic p o s i t i o n a l and isotropic thermal parameters of molecule 4 20 IV. Anisotropic thermal parameters of molecule 4 . 22 V. Mean planes in the v i c i n i t y of the cyclobutyl ring in molecule _4 24 VI. Bond lengths ( A ) of the non-hydrogen atoms in molecule A 25 VII. Bond lengths( A ) involving hydrogen atoms in molecule 4 26 VIII. Bond angles(°) of non-hydrogen atoms in molecule 4̂  28 IX. Bond angles(°) involving hydrogen atoms in molecule 4 29 X. Crystal data for molecule 5 35 XI. Atomic p o s i t i o n a l and isotropic thermal parameters of molecule 5 38 XII. Anisotropic thermal parameters of molecule 5 . 40 XIII. Mean planes in the v i c i n i t y of the cyclobutyl ring in molecule 5 4'2 XIV. Bond lengths( A ) of the non-hydrogen atoms in molecule 5 43 v i i i XV. Bond lengths( A ) involving hydrogen atoms in molecule 5_ . ... .......... 44 XVI. Bond angles(°) of non-hydrogen atoms in molecule 5 45 XVII. Bond angles(°) involving hydrogen atoms in molecule 5_ 46 XVIII. Crystal data for derivative 9 50 XIX. Atomic p o s i t i o n a l and isotropic thermal parameters for molecule 9 55 XX. Anisotropic thermal parameters in molecule 9 . 57 XXI. Mean, planes in the v i c i n i t y of the cyclobutyl ring in molecule 9 60 XXII. Bond lengths( A ) of non-hydrogen atoms in molecule 9 61 XXIII. Bond angles(°) of non-hydrogen atoms in molecule 9 62 XXIV. Bond lengths( A ) of hydrogen atoms in molecule 9 63 XXV. Bond angles(°) involving hydrogen atoms in molecule 9 64 XXVI. Comparisons of equivalent bond lengths( A ) in molecules 4, 5, and 9 66 XXVII. Comparison of bond angles(°) in molecules 4 ,5 and 9 68 XXVIII. Mean planes of the p-bromobenzoate moiety in molecule 9 71 Chapter 3 72 XXIX. Crystal data for camphor-p-bromobenzoate 75 ix XXX. Posit i o n a l and isotropic thermal parameters of camphor-1 ,.4-homo.enol. p-bromobenzoate. ........... 81 XXXI. Anisotropic thermal parameters of camphor p- bromobenzoate 82 XXXII. Bond lengths ( A ) of the non-hydrogen atoms in camphor homoenol p-bromobenzoate 84 XXXIII. Bond lengths ( A ) involving hydrogen atoms in camphor homoenol p-bromobenzoate 85 XXXIV. Mean planes of the p-bromobenzoate moiety in camphor homoenol p-bromobenzoate 86 XXXV. Bond angles (°) of non-hydrogen atoms in camphor homoenol p-bromobenzoate 87 XXXVI. Bond angles (°) involving hydrogen atoms in camphor homoenol p-bromobenzoate 90 Chapter 4 92 XXXVII. Crystal data for raucubaine 94 XXXVIII. Origin and symbol sets for raucubaine 97 XXXIX. Posit i o n a l and iso t r o p i c thermal parameters for raucubaine 109 XL. Anisotropic thermal parameters for raucubaine 111 XLl. Mean plane calculations in raucubaine 115 XLlI. Bond lengths of non-hydrogen atoms in raucubaine 116 XLIII. Bond lengths involving hydrogen atoms in raucubaine 117 XLIV. Bond" angles of the non-hydrogen atoms in raucubaine 119 XLV. Bond • angles involving hydrogen atoms in X raucubaine 120 XLVI . Crystal data for the pyranoside . ...... 125 XLVII. Positional and isotropic thermal parameters for the pyranoside 132 XLVIII. Anisotropic temperature factors of the pyranoside 134 XLIX. Interannular torsion angles for the sugar ring 137 L. Non-hydrogen bond lengths of the pyranoside .. 138 LI. Non-hydrogen bond angles of the pyranoside ... 139 LI I. Bond lengths of the hydrogen atoms of the pyranoside 140 LIII. Bond angles involving hydrogen atoms in the pyranoside 141 Chapter 5 145 LIV. Crystal data for o p t i c a l l y active naphthidine 147 LV. Positional and isotropic thermal parameters of o p t i c a l l y active naphthidine 150 LVI. Anisotropic thermal parameters for o p t i c a l l y active naphthidine 151 LVII. Crystal data for o p t i c a l l y active 1,1'-binaphthyl 152 LVI11. Positional and isotropic thermal parameters of o p t i c a l l y active 1,1'-binaphthyl 154 LIX. Anisotropic thermal parameters of o p t i c a l l y active 1,1'-binaphthyl 155 LX. Bond lengths and angles' in o p t i c a l l y acti've naphthidine 158 xi LXI. Bond lengths and angles in o p t i c a l l y active 1 , 1' -binap.hth.yl. ..... 159. LXII. Naphthalene unit bond length comparison ( A ) 160 LXIII. Mean planes in o p t i c a l l y active naphthidine .. 161 LXIV. Mean planes in o p t i c a l l y active 1,1'-binaphthyl 162 LXV. Comparison of binaphthyl-type structures 166 LIST OF FIGURES Chapter 1 1 Chapter 2 . ... 11 1 . Scheme 1 13 2. A K-curve showing the minimum p r o f i l e ....... 16 3. A stereoview of molecule 4 23 4. Stereo packing diagram for compound 4 30 5. Scheme 2 32 6. Stereoview of the examined c r y s t a l of 5 .... 36 7. A stereoview of molecule 5_ 41 8. Stereo packing diagram for compound 5 47 9. Crystal shape of the p-bromobenzoate derivative 52 10. Stereoview of the p-bromobenzoate derivative 58 11. Packing diagram of the p-bromobenzoate derivative 65 Chapter 3 72 12. Crystal shape of camphor homoenol p- bromobenzoate 76 13. The camphor homoenol p-bromobenzoate molecule 83 14. Dihedral angles in the cyclobutyl moiety ... 89 15. Packing diagram for camphor homoenol p- bromobenzoate 91 Chapter 4 92 xi i i 16. Raucubaine: structure and atomic l a b e l l i n g scheme ........ . 113 "17. Stereoview of the raucubaine molecule 114 18. Stereo packing diagram for raucubaine 121 1 9 . The pyranoside molecule 136 20. Stereo packing diagram for the pyranoside .. 142 21. The unit c e l l viewed down b, showing the proximity of the p-chlorobenzene groups to the (103) planes (dashed) 143 Chapter 5 145 22. Molecular views of o p t i c a l l y active naphthidine (above) and 1,1'-binaphthyl (below) 157 23. Packing diagram for o p t i c a l l y active naphthidine 163 24. Packing diagram for o p t i c a l l y active 1 , 1'-binaphthyl 164 25. A half-normal probability plot 171 xiv Something there i s so appealing about a path The way i t i s worn around the rocks And through the grass. Something in i t s neatness leads you on The path i s the smooth way, The easy way along. Off the path i s up and down Boulders and brambles l i t t l e pain Danger and f r u s t r a t i o n , And rivers after r a i n . Stay on the path, you w i l l get somewhere And you w i l l never know a l l the places That you miss around you as you go. Get off the path, and you can have More than a l i f e t i m e to spend 'Cause off the path You don't ever have to reach an end. 'Path', by Michael Kennedy. XV ACKNOWLEDGEMENT I would very much l i k e to thank Prof. James Trotter for a l l his d i l i g e n t proofreading, help and. guidance during the l a s t f i v e years. I am grateful to Drs. J.P. Kutney, T. Money, E. Piers and R.E. Pincock for supplying c r y s t a l s and background information. I am indebted to my co-workers, from whom I have learned a great deal. I would also l i k e to thank a l l my friends for helping me maintain my sanity come 5.00 p.m. DEDICATION I would l i k e to dedicate t h i s thesis to my father, Gerry, for whom a major goal in l i f e i s f u l f i l l e d by th i s achievement. Cheers, Dad. 1 CHAPTER 1 INTRODUCTION 2 This thesis describes x-ray crystallographic investigations of the structures of, eight organic compounds. It. is. divided into two parts: the f i r s t deals with the analyses of six compounds related to natural product chemistry and the second i s concerned with two structures related to a project in spontaneous resolution of binaphthyl systems. Each structure analysis i s treated in a separate section which includes a general introduction to the compound and i t s preparation ( i t should perhaps be emphasized that no preparative work was ca r r i e d out for this thesis; a l l c r y s t a l s used were prepared by other research workers). In part one, the interest in the f i r s t four compounds l i e s in the nature of their four- membered ring systems. The next two compounds, both of space group P2,, proved to be c r y s t a l l o g r a p h i c a l l y d i f f i c u l t structures, and the main concern there l i e s in the methods of solution. Part two contains the work to date with respect to the spontaneous resolution project, followed by the structure analyses of two binaphthyl compounds. Comparisons of these structures with those of other binaphthyl systems and some general conclusions are presented in a f i n a l section. The background theory of x-ray crystallography is readily available in various t e x t s 1 " 5 , and a l l nomenclature, symbols and conventions used in th i s thesis are consistent with those described in International Tables for X-ray Crystallography 6. There are, however, various aspects of data c o l l e c t i o n and structure refinement that should" be c l a r i f red" here . The data for a l l structures (except one in chapter 4) were co l l e c t e d on an Enraf-Nonius CAD-4 diffractometer. This machine 3 allows the user to select various data-collection parameters. The values chosen w i l l appear in the experimental section of each structure, and a brief description of the more important parameters follows below. The distance d(hkl) between sets of planes of indices hkl is related to the d i f f r a c t i o n angle theta (the angle between the incident beam and the r e f l e c t i n g plane that w i l l give r i s e to d i f f r a c t i o n ) by Bragg's law, 2d(hkl)sin6 = nx, where V i s the wavelength and n is an integer. The intensity I(hkl) of a beam of x-rays d i f f r a c t e d from a p a r t i c u l a r set of planes i s measured by scanning across the intensity p r o f i l e and measuring the x-ray count with a suitable detector. In front of the detector i s an aperture which has a manually insertable s l i t of variable height (4mm has been found adequate for most structures) and a width which i s varied during data c o l l e c t i o n to account for the widening of the r e f l e c t i o n due to 0 , - 0 2 s p l i t t i n g in 6 at higher angles. The intensity p r o f i l e i s scanned by moving either the c r y s t a l alone (u-scan) or by moving the c r y s t a l and the detector ( 0 - 6 scan). The r a t i o of c r y s t a l to detector movement determines the d i r e c t i o n through which the intensity p r o f i l e is scanned. This i s important as r e f l e c t i o n s may streak out in a p a r t i c u l a r d i r e c t i o n and a representative measurement of the background i s desirable. The o-scan angle must be large enough to ensure that the entire intensity p r o f i l e i s scanned — t h i s parameter depends on c r y s t a l mosaic spread and divergence of the primary beam. The o-scan angle i s also widened at higher angles d'uring data c o l l e c t i o n , and i s usually extended by 25% on each side for background measurements. 4 The estimated standard deviations (e.s.d.'s.or c's) of the i n t e n s i t i e s are : ff{I(hkl)} = d/Lp)(S + 4B + ( 0 . 0 4 S ) 2 ) 1 / 2 , where S and B are the scan and background counts, (1/Lp) is the Lorentz - p o l a r i z a t i o n correction factor, and 0.04 is an additional error factor included to allow for instrument i n s t a b i l i t y . A r e f l e c t i o n i s normally considered observed i f i t s intensity i s greater than, say, three standard deviations (l>3*(I)). The speed with which a r e f l e c t i o n i s scanned may also be. varied. As a compromise between speed and accuracy, the scan speed i s calculated to give a desired value of <r(I)/I, normally in the range 0.01 to 0.05. In order to calculate the scan speed, a fast pre-scan i s performed. The pre-scan speed i s , however, chosen to be s u f f i c i e n t l y slow such that the majority of r e f l e c t i o n s w i l l already have the *( I ) / I requirement s a t i s f i e d . A pre-scan acceptance parameter i s also chosen : i f tf(l)/I i s greater than t h i s parameter during the pre-scan, the r e f l e c t i o n i s flagged unobserved. A time-- l i m i t of the order of 60 to 100 seconds i s normally imposed on the f i n a l scan time. As data c o l l e c t i o n often takes several days, a few r e f l e c t i o n s are chosen as standards and are checked at regular inter v a l s for intensity and orientation. The r e f l e c t i o n s chosen for intensity control should be f a i r l y strong. If their i n t e n s i t i e s vary systematically during data c o l l e c t i o n , the data are scaled accordingly. The r e f l e c t i o n s chosen for orientation control should i d e a l l y be strong and should preferably have scattering vectors that are as close to being mutually 5 perpendicular as possible. If during orientation control i t i s found that these scattering vectors d i f f e r from, their calculated positions by more than a user-selected amount, reorientation occurs. In general, the numeric values selected for data c o l l e c t i o n parameters w i l l depend mainly on c r y s t a l size and q u a l i t y . A few expressions used in the solution and refinement are defined in the following brief description. From the c o l l e c t e d i n t e n s i t i e s , the structure amplitudes may be derived, |F(hkl)| = { k l ( h k l ) / ( L p ) } 1 / 2 , where Lp i s the geometric Lorentz - polarization correction and k i s a proportionality constant. However, the sign (or phase) of these structure factors i s unknown at t h i s stage, and the d i r e c t methods procedure, which was used for most of the structures solved, begins here. By comparing the structure to i t s square, Sayre 7 showed that F(h,k,l) = *(h,k,l) EEE F ( h ' , k ' , l ' ) . F(h-h' ,k-k' , 1-1') where *(h,k,l) is a calculable scaling term and the summations are over a l l h',k', and 1'. A structure factor F(h,k,l) may hence be derived from the products of a l l the pairs of indices that add to give (h,k,l). This seems to imply that a l l F(h',k',l') and F(h-h' ,k-k' ,1-1' ) need be known before the phase of F(h,k,l) can be calculated, but in fact, should F(h,k,l) be large, the summations must tend strongly in one d i r e c t i o n (+1 or -1, in the centrosymmetric case), and a reasonable approximation of the phase may be made by considering only the larger contributors. 6 One problem that arises is that the structure factors decrease considerably with an increase in 6 (higher angle r e f l e c t i o n s w i l l be weaker as r e f l e c t i o n s from d i f f e r e n t parts of the electron cloud w i l l be increasingly out of phase), and r e l a t i v e l y strong high-angled r e f l e c t i o n s would have structure factors that would hardly contribute to the above r e l a t i o n . For t h i s reason the structure factors are normalized. Unitary structure factors are calculated such that U(hkl) = F(hkl)/F(000), where F(000) is the structure factor of the unobservable 0 0 0 r e f l e c t i o n and corresponds to the number of electrons in the unit c e l l , and so -1 < U < +1. Karle and Hauptmann8 introduced a normalized structure factor E such that E 2 = U 2/U(mean) 2. There exist various numerical methods of scaling the E's, including K-curves and Wilson plots (see for example page 15). The E's have the same phase as their respective F's and U's, but their magnitudes are more representative of their r e l a t i v e r e f l e c t i o n strength. Symmetry related' i n t e n s i t y considerations- are-also taken into account in- the determination of the E's. Although t h e o r e t i c a l l y independent of the size and content of the unit c e l l , the d i s t r i b u t i o n of the E's does depend on the presence or absence of a centre of symmetry (see Table II, page 18). In practice, the presence of a centre of symmetry may be established by examination of the E - s t a t i s t i e s . It i s the larger E's that are expected to be the predominant contributors responsible for determining the phase of a r e f l e c t i o n by Sayre's rel a t ionships. 7 A s h i f t in unit c e l l o r i g i n i s associated with a change of phase of r e f l e c t i o n s of parity depending on the di r e c t i o n of s h i f t . The or i g i n is therefore fixed by assigning phases to some r e f l e c t i o n s (three in general). Should these r e f l e c t i o n s have strong E's, they may be used to calculate the probable phases of other r e f l e c t i o n s using a relationship very similar in nature to that of Sayre: *(h,k,l) = *(h',k',l') + *(h-h',k-k',1-1') where 0(h,k,l) is the new phase to be calculated from the phases $(h',k',l') and 0'(h-h', k-k' , 1-1' ) . This r e l a t i o n s h i p is known as a r 2 _ r e l a t i o n s h i p as i t depends on the sum of two phases. Adding to t h i s i n i t i a l set of 'known' phases may be various phases determined from 1,-relationships (a special case of a I 2 - relatio n s h i p , where *(2h,2k,21) = <r>(h,k,l) + * ( h , k , l ) ) . From t h i s starting set, the phasing may continue using E 2- relationships u n t i l further phasing i s only made possible through the introduction of a few symbols for the unknown phases. These symbols, through their extensive use in E 2- relationships, w i l l hopefully become involved in a number of equ a l i t i e s that w i l l allow their evaluation. This is known as the symbolic addition procedure, and was f i r s t suggested by W.H. Zachariasen 9. The determined phase values may be refined (before they are used for further phase determination) by the tangent formula 1 0; E Q sin{*(h',k',1') + *(h-h',k-k',1-1')} tan *(h,k,l) = I Q c c s U ( h ' ,k" ,1' ) + *(h-h' , k - k " , l - l ' )} where the sine and cosine portions are obtained from s p l i t t i n g the exponential form of Sayre's r e l a t i o n , the Q terms involve 8 the E magnitudes, and the summation i s over a l l available terms. There are consistency parameters that describe the correctness of phases thus determined and enforce acceptance or rejection of these new phases. The speed of the phasing procedure may be greatly enhanced by assigning i n i t i a l phase values to the symbols, and carrying out multiple sets of phase determinations. There are computer programmmes available to perform this phasing, including TANS 1 1 (named after the tangent formula) and MULTAN12 (from 'MULtiple TANgent refinement programming). These multiple phasings result in a number of possible sets of phases, and a Fourier synthesis using the E's as c o e f f i c i e n t s (an 'E-map') w i l l produce electron density peaks corresponding to the positions of the larger atoms i f the phases are correct. This discussion i s only intended to introduce some of the terms used in th i s thesis and to remove a l i t t l e of the mystery often associated with direct methods for the u n i n i t i a t e d reader. For a more in-depth analysis of dire c t methods, the reader is referred to the more standard texts on the s u b j e c t 1 3 . Patterson and Fourier methods were also successful in chapters 2 and 3 and w i l l be b r i e f l y described therein. The refinement was based on the minimization of the function E(w(|Fo|-|scale x F c | ) 2 ) , where Fo and Fc are the observed and calculated structure factors and w is a weighting factor. The structure amplitudes were corrected for thermal vibrations using the anisotropic temperature factors' Ui'j i"n f = f °exp{-27r2 (U, 1 h 2 a * 2 + U 2 2 k 2 b * 2 + U 3 3 l 2 c * 2 + 2U 1 2hka*b* + 2U, 3 h l a * c * + 2U 2 3klb*c*)} 9 where f° and f are the tabulated and corrected structure factors respectively. Isotropic thermal, parameters have the form, f = f °exp{-B( sinS/x.)} where B = 8 i r 2 U 2 (U 2 is the mean-square displacement of the atom from i t s mean po s i t i o n ) . The scattering vectors used for the non-hydrogen atoms were obtained from reference 14, and those used for the hydrogen atoms were obtained from reference 15. Anomalous dispersion corrections, when used, were obtained from reference 16. In the temperature factor and a l l other tables, e.s.d.'s, i f present, are given in parentheses and correspond to the least s i g n i f i c a n t d i g i t or d i g i t s . The correctness of the f i n a l structure may be measured in terms of the agreement between the observed and the calculated structure factors. The agreement factors used here are the R and the weighted Rw in R = E {|Fo|-|scale x Fc|}/l|Fo| and Rw = {E[w(|Fo|-|scale x Fc|)] 2/Ew|Fo| 2} 1/ 2. More extensive d e t a i l s of data c o l l e c t i o n and refinement are discussed in the individual chapters. Structure factor tables appear in the appendix. 10 PART ONE 1 T CHAPTER 2 STEMODTN INTERMEDIATES 1 2 I. A p-CYCLOBUTYL TRICYCLIC ENONE Introduction and preparation Recent work by Dr. E. Piers and co-workers 1 7" 1 8 directed towards the t o t a l synthesis of t h e t e t r a c y c l i c diterpenoids a p h i d i c o l i n and stemodin (2) (see scheme 1) included the photochemically-induced cycloaddition of allene to the c y c l i c enone 3. Irra d i a t i o n (low-pressure mercury lamp, 4.5 hours) of a cold solution of racemic 3_ and allene in dry deoxygenated tetrahydrofuran gave a mixture of two isomeric photoadducts, presumably 4 and 5_, which were separated by column chromatography on s i l i c a gel (elution with 10:5:2 cyclohexane- hexane-ethylacetate). The f i r s t eluted diastereomer (39% yield) exhibited m.p. 132-133-GC, while: the- second (4>2%~ yield.) had- mvpv 134-135°C. It was thought that one of these isomers would be useful as an intermediate in the synthesis of stemodin, while the other might be useful in aph i d i c o l i n synthesis. In order to determine which adduct was which, an x-ray d i f f r a c t i o n study was undertaken on the compound that yielded the better c r y s t a l s : the f i r s t eluted isomer. 13 F i g u r e 1. Scheme 1 14 Experimental From preliminary photography, r e f l e c t i o n s of type OkO where k i s odd and hOl where h+1 i s odd were found to be systematically absent, indicating a twofold screw axis p a r a l l e l to b and a glide plane perpendicular to b of di r e c t i o n (a+c)/2 ( i . e . , [101]). The cr y s t a l s are monoclinic and thus of space group P2,/n. This space group i s in fact equivalent to that most often found in organic c r y s t a l s , P2,/c, and may be converted to P2,/c by using [101] as the a x i a l d i r e c t i o n instead of [001]. The intensity data were co l l e c t e d using graphite- monochromatized MoKa radiation (X = 0.71073 A) and an o-8 scan technique with an o-scan angle of (1.0+0.35 tan 6)°. The v e r t i c a l and horizontal aperture widths were 4 mm and (2.5 + tan 6)mm, respectively. The i n t e n s i t i e s of three standard r e f l e c t i o n s (-2 5-1, -1 6 -2, and -1 6 -3) were checked every one hour of x-ray exposure time and showed no s i g n i f i c a n t v a r i a t i o n . The same three r e f l e c t i o n s were checked for orientation every 100 ref lections', and reorientation' occurred- i f the difference between observed and calculated scattering vectors was greater than 0.05°. During the data c o l l e c t i o n , i t was noticed that this difference was often between 0.05 and 0.06°, and so the reorientation condition was relaxed to 0.07°, after which reorientation occurred far less often (thereby saving considerable time). In the range 0 < 6 < 25°, 2052 of the 3432 r e f l e c t i o n s c o l l e c t e d (59.8%) had l/tf(I) > 3.0 and were considered observed. The c e l l parameters were refined by least-squares methods with 15 the sinS / X values of 25 r e f l e c t i o n s within the l i m i t s 9 < 6 <18°, and are. l i s t e d with other c r y s t a l data in. Table I. *********************************************************** TABLE I. CRYSTAL DATA FOR MOLECULE 4 C 2 2 H 3 2 0 3 f.w. = 344.5 Monoclinic Z = 4 space group = P2 1/n a = 11.832(1) b = 1 1 .423(1 ) F(00'0) = 536 c = 14.637(1) A X = 0.71073 A /» = 98.71(2),° D C = 1 . 1 7 g/cc V = 1955.5 A 3 o = 0.7 cm"1 Lorentz and p o l a r i z a t i o n factors were applied as usual, and the c r y s t a l was s u f f i c i e n t l y small to render absorption effects n e g l i g i b l e . The structure was solved by d i r e c t methods. Figure 2 shows the minimum profile- oi- the K-curve-that: was- used: to- place--the^ the data on an absolute scale. As the r e l a t i v e i n t e n s i t i e s decrease with s i n 2 6 / X 2 , they are averaged within concentric s h e l l s in reciprocal space such that t h i s variation i s small. The r a t i o (K) of r e l a t i v e to absolute i n t e n s i t i e s is calculated within each s h e l l and plotted against s i n 2 6 / X 2 (s) to give the K-curve. The o v e r a l l scale factor may be determined from the value of K when s = 0. A Wilson plot would also y i e l d an o v e r a l l temperature factor, however i t assumes Gaussian-type temperature factors, which may not always be accurate. The E values are  1 7 generally obtained from the minimum p r o f i l e of the K-curve. This often produces |E| 2 values, greater than 1.0, especially in the presence of a large 'hump' (as in figure 2) due to the abnormal intensity averages produced by non-random c h a r a c t e r i s t i c s of a pa r t i c u l a r structure. E - s t a t i s t i c s (Table II) indicate a centrosymmetric structure, agreeing with the chosen space group. The 500 highest E's were input into the MULTAN programme i n i t i a l l y without success. MULTAN had produced two wrong sets of phased E's. However, i t was noted that MULTAN had accepted the phases of three r e f l e c t i o n s determined through 1,-relations as their p r o b a b i l i t i e s of being correct (determined from number of contributors) were greater than 0.95. A fourth r e f l e c t i o n , 0 0 14, had a 0.949 prob a b i l i t y of having phase t r , and this phase was i n i t i a l l y rejected, and later determined to have a phase of 0. This was unlikely to be correct, so the pro b a b i l i t y c r i t e r i o n of acceptance was relaxed to 0.94. Now four phases were accepted as known from E,-relations: 0 0 14 and 6 0 -10 (phase v), and 6 0-8 and 4 0 -12 (phase 0). In order to f i x the o r i g i n , the r e f l e c t i o n s 3 7 -5, 5 2 10 and 1 2 7 were assigned a phase of 0. The 2 8-4 r e f l e c t i o n , used as a symbol with i n i t i a l phase assignments of 0 and rr, completed the s tarting set of known phases, and MULTAN now produced two sets of phases (one for each value of the symbol), one of which was correct. The resulting E-map revealed the positions of a l l the non-hydrogen atoms. After three isotropic and three- a n i s o t r o p i c full-matrix least-squares refinement cycles, a difference map revealed the positions of 31 of the 32 hydrogens, and the remaining hydrogen TABLE II. E-STATISTICS AFTER RENORMALIZATION *********************** OBSERVED THEORETICAL non-centro. c e n t r e mean |E| 2 mean |E| mean | JE| 2~1| 1.000 1.000 1.000 0.799 0.866 0.798 1.010 0.736 0.968 re f l e c t i o n s with: E > 1.5 12.38 10.54 13.40 E > 1.75 7.96 4.67 8.00 E > 2.0 4.92 1.83 4.56 E > 2.5 1.61 0.19 1.24 *********************** 19 position was calculated geometrically. An additional two refinement cycles with isotropic temperature factors for the hydrogens and anisotropic temperature factors for the non-hydrogen atoms, with a polynomial weighting scheme 1 9 with c o e f f i c i e n t s that were updated after every cycle, resulted in the f i n a l R and Rw values of 0.034 and 0.046 respectively. After several more cycles the hydrogen atom parameters had converged. F i n a l p o s i t i o n a l and thermal parameters are given in Tables III and IV. The hydrogen atoms are i d e n t i f i e d by three-digit numbers; the f i r s t two d i g i t s refer to the label of the atom to which they are bound, and the t h i r d refers to the number of the hydrogen on that atom. The f i n a l c o e f f i c i e n t s used in the polynomial weighting scheme were A = 0.2818, B = -0.00981, C = 0.000278, and D = 0.000024, where w = 1/(A + B|Fo| + C|Fo| 2 + D|Fo| 3). Results and discussion The f i r s t eluted isomer has been shown to be the racemate of the p-cyclobutyl species i, and has since been used as an intermediate in the projected synthesis of stemodin. A stereoview showing the molecular structure and the atomic l a b e l l i n g scheme i s presented in Figure 3. Table V l i s t s the results of some mean plane calculations of planes in the v i c i n i t y of the four-membered ring. A comparison of the mean planes to similar ones in the next structures w i l l be presented at the end of t h i s chapter (page 59). Bond lengths are l i s t e d in 20 TABLE III . ATOMIC POSITIONAL AND ISOTROPIC THERMAL PARAMETERS OF MOLECULE 4 (fr a c t i o n a l x 10" ,. H. x 103 , U. x 103 A 2). Atom X 1 z Ueq/Uiso 0(1 ) 3520(2) -3497(2) 8453(1) 1 03 0(2) 3527(1) -579(1) 4657(1 ) 39 0(3) 2338(1) -455(1) 3236(1) 45 CO ) 2995(2) -3078(2) 4720(2) 45 C(2) 2851(2) -2282(2) 3875(2) 48 C(3) 2542(2) -1046(2) 4102(1) 37 C(4) 1500(2) -1025(2) 4599(1) 40 C(5) 1635(2) -1840(2) 5437 ( 1 ) 36 C(6) 594(2) -1791(2) 5940(2) 50 C(7) 803(2) -2508(2) 6819(2) 55 C(8) 1179(2) -3772(2) 6700(1) 47 C(9) 2139(2) -3843(2) 6096(1) 42 C ( 1 0). 1925(2) -3113(2) 5199(1) 38 C( 1 1 ) 3270(2) -3631(2) 6790(2) 52 C(12) 2928(2) -3754(2) 7742(2) 64 C( 1 3) 1726(2) -4234(3) 7644(2) 63 C( 1 4) 2574(2) -5112(2) 5953(2) 62 C( 1 5) 3716(2) -4782(2) 6474(2) 65 C( 1 6) 4758(3) -5232(4) 6566(3) 101 C( 1 7) 929(2) -3683(3) 4554(2) 57 • C( 18) 3498(2) 659(2) 4782(1) 43 C( 19) 3334(2) 1302(2) 3862(1) 45 C(20) 2259(2) 784(2) 3307(2) 46 C(21 ) 4358(2) 1101(3) 3362(2) 58 C(22) 3149(3) 2597(2) 4022(3) 74 H(011 ) 366(2) -282(2) 515(1) 48(6) H(012) 318(2) -389(2) 455(2) 61 (6) H(021 ) 354(2) -224(2) r 360(1) 54- (6) H(022) 224(2) -258(2) 340(2) 69(7) H(041) 138(2) -25(2) 483(1) 47(6) H(042) 84(2) -127(2) 416(2) 53(6) H(051) 229(2) -156(2) 587(1) 33(5) H(061) 46(2) -94(2) 607(2) 64(7) H(062) -8(2) -212(2) 552(2) 62(7) H(071) 146(2) -210(2) 728(2) 76(8) H(0~72) 13(2) -255(2) 712(2) 70(7) H(081) 53(2) -423(2) 645(1) 53(6) H( 1 1 1 ) 374(2) -293(2) 673(1) 54(6) H(131 ) 179(2) -515(3) 764(2) 83(8) H(132) 134(2) -394(2) 815(2) 73(8) H(141 ) 218(2) -573(2) 623(2) 78(8) H(142) 257(2) -535(2) 530(2) 75(8) continued... 21 H(161 ) 542(4) -478(4) 693(3) 157(18) H(162) 473(3) -603(4) 630(3) 122(14) H( 1 7.1 ) 23(2) -384(2) 489(2) 77( 8) H(172) 67(2) -320(2) 400(2) 83( 8) H( 173) 119(3) -438(3) 431(2) 94(10) H ( 1 8 1 ) 289(2) 91(2) 513(1) 38( 5) H( 182) 424(2) 85(2) 515(1) 51 ( 6) H(201) 217(2) 105(2) 267(2) 49( 6) H(202) 159(2) 102(2) 360(2) 55( 6) H ( 2 1 1 ) 429(2) 156(2) 281(2) 78( 8) H(212) 506(2) 133(2) 377(2) 78 ( 8) H(213) 443(2) 25(3) 321(2) 92(10) H(221 ) 304(3) 305(3) 346(3) 115(12) H(222) 246(3) 272(3) 434(2) 101(11) H(223) 380(3) 290(3) 438(2) 106(11) 22 TABLE IV. ANISOTROPIC THERMAL PARAMETERS OF MOLECULE 4 (Uij x 10" A 2) Atom 1 U 2 2 u 3 3 2 3 U 2 3 0(1) 783( 13) 1 677 ( 23) 547( 1 1 ) -209( 14) -1 71 ( 10) 1 26( 13) 0(2) 314( 7) 467( 8) 363( 7) -8( 6) -10( 5) 30( 6) 0(3) 494( 8) 51 0( 9) 324( 7) -85( 6) -21 ( 6) 61 ( 6) C(1 ) 505( 13) 393( 12) 478( 12) 63( 10) 1 38( 10) -1 9( 10) C(2) 564( 14) 478( 13) 4 1 7 ( 12) -24( 1 1 ) 1 59 ( 1 1 ) -30( 10) C(3) 35.0( 10) 44>9( 1 1 ) 301 ( 9). -1 2( 8) -9( 8) 37( 8) C(4) 31 6( 1 1 ) 427( 12) 455 ( 12) 9( 9) 30 ( 9) 58 ( 10) C(5) 297( 10) 41 0( 1 1 ) 379( 10) -1 ( 8) 47( 8) 6( 9) C(6) 406( 12) 551 ( 15) 587( 14) 66( 10) 1 69( 1 1 ) 51 ( 1 1 ) C(7) 482( 13) 681 ( 15) 530( 13) 6( 1 1 ) 232( 1 1 ) 27( 12) C(8) 4 1 0 ( 12) 540( 13) 460( 12) -94( 10) 51 ( 9) 70( 10) C(9) 399( 1 1 ) 379( 1 1 ) 468( 1 1 ) -32( 9) 26( 9) 28( 9) C(10) 384( 10) 374( 1 1 ) 372( 10) -33( 8) 27( 8) -6( 8) C(1 1 ) 396( 12) 562( 14) 560( 13) -37( 10) -191 10) 1 72 ( 1 1 ) C( 12) 551 ( 14) 829 ( 18) 509( 14) -34( 13) -32( 12) 181 ( 13) C( 13) 606( 15) 771 ( 19) 507( 14) -70( 13) 80( 12) 1 85 ( 13) C( 14) 731 ( 17) 379( 13) 781 ( 19) 36( 12) 1 85 < 14) 1 06 ( 13) C(15) 544( 14) 633( 16) 802( 17) 1 49( 12) 1 69 < 12) 335( 13) C( 16) 780( 23) 1 01 7 ( 29) 1267( 32) 344( 22) 273 22) 472( 26) C(17) 624( 16) 584( 16) 467( 13) - 1 77 ( 12) -17 ,12) -45( 12) C(18) 404( 12) 498( 13) 368( 1 1 ) -45( 10) 35 M 0 ) -28( 9) C(19) 428( 1 1 ) 471 ( 12) 433( 1 1 ) -37( 9) 45 [ 9) 40( 9) C(20) 398( 12) 548( 15) 431 ( 12) -7( 10) 16 (10) 1 60( 10) C ( 2 1 ) 44,7 ( 13) 794( 1-9-)- 49 & ( •V4)- -1 1 4( 1.2) 68 (•11 ) 1 4.4: ( 14) C(22) 943( 24) 493( 16) 774( 21 ) -53( 15) 63 (19) 29( 14) 23 F i g u r e 3 . A stereoview of molecule 4 TABLE V. MEAN PLANES IN THE VICINITY OF THE CYCLOBUTYL RING IN MOLECULE 4 Equat ions of planes (!X+mY+nZ=p) plane 1 2 3 4 0.3622 0.5727 -0.0488 0.3664 m 0.4486 0.3236 0.9982 -0.8221 -0 -0 -0 -0 n 8170 7532 0347 ,4358 -9.0314 -7.3883 -4.6835 -0.7156 Deviations from planes, ( A ) atom C(8) C(9) C(1 1 ) C( 12) C(13) C( 14) C(15) C( 16) 0( 1 ) 0.283(2) 0.000(2)* 0.000(3)* 0.000(3)* 0. 100(5) 000(2)* 000(2)* 0.000(3)* 0.261(3) 0.689(5) 0.051(2)* •0.062(2)* 0.086(2)* -0.071(3)* -0.545(3) 0.160(3) 0.000(2)* 0.913(2) 0.711(2) 0.000(3)* 0.000(3)* •0.491(2) *atoms included in plane calculations Angles between, normals, to the.- planes planes (1) and (2) planes (2) and (3) planes (3) and (4) 14.5° 108.7° 34.6° 25 TABLE VI. BOND LENGTHS ( A ) OF THE NON-HYDROGEN ATOMS IN MOLECULE 4 Bond Distance Bond Di stance 0(1 ) -C(12) 1.199(3) C(8) -C(13) 1 .528(3) 0(2) -C(3) 1.420(2) C(9) -COO) 1.544(3) 0(2) -C(18) 1.428(3) C(9) - c ( n ) 1.571(3) 0(3) -C(3) 1.424(2) C(9) -CO 4) 1 .563(3) 0(3) -C(20) 1.423(3) C(10)-C(17) 1.538(3) C(1 ) -C(2) 1.524(3) CO 1 )-C(l2) 1 .515(4) co: -COO) 1.538(3) CO 1 )-CO 5) 1.515(4) C(2] -C(3) 1.509(3) C( 12)-C(13) 1.511(4) C(3) »-C(4) 1.523(3) CO 4)-CO 5) 1.496(4) C U 1 -C(5) . 1.529(3) CO 5)-CO 6) 1.324(4) C(5 >-C(6) 1.529(3) C(18)-C(19) 1.521(3) C(5 l-COO) 1.546(3) C(19)-C(20) 1 .521(3) C(6 l-C(7) 1.514(3) CO 9)-C(21 ) 1.525(3) C(7 )-C(8) 1 .528(3) C(19)-C(22) 1.518(4) C(8 >-C(9) 1.544(3) 26 TABLE VII. BOND LENGTHS( A ) INVOLVING HYDROGEN ATOMS IN MOLECULE 4 Bond Distance Bond Distance C(1) -H(011) 0.98(2) C( 1 4) -H(142) 0.99(3) C( 1 ) -H(012) 0.99(2) C( 16) -H(161) 1 .01(5) C(2) -H(021) 0.96(2) C( 1 6) -H062) 0.99(4) C(2) -H(022) 0.99(3) C( 17) -H(171) 1.04(3) C(4) -H(041) 0.96(2) C(17) -H(172) 0.99(3) C(4) -H(042) 0.97(2) C( 17) -H(173) 0.95(3) C(5) -H(051 ) 0.98(2) C( 18) -H(181) 0.98(2) C(6) -H(061) 1.01(2) C( 18) -H(182) 0.98(2) C(6) -H(062) 1.00(2) C(20) -H(201) 0.97(2) C(7) -H(071) 1.06(3) C(20) -H(202) 1.00(2) C(7) -H(072) 0.97(3) C(21 : -H(211 ) 0.95(3) C(8) -H(081) 0.96(2) C(21 ; -H(212) 0.98(3) C(11)-H(111) 0.98(2) C(21 >-H(213) 1.00(3) C(13)-H(131 ) 1.05(3) C(22 >-H(221) 0.96(4) C(13)-H(132) 0.99(3) C(22 )-H(222) 1.01(4) C(14)-H(141). 0.97(3) C(22 )-H(223) 0.94(4) 27 Tables VI and VII and are representative of those expected for C-C, C=C, C-0, C=0 and C-H bonds. Bond angles (Tables VIII, and IX ) are f a i r l y close to values expected for 4-, 5-, and 6- membered rings, with some deviations due to s t r a i n in the pol y c y c l i c molecule. These angles and deviations, as well as those for the next two structures, w i l l be examined more closely at the end of thi s chapter. A packing diagram i s shown in Figure 4. There are no exceptionally short intermolecular distances; the c r y s t a l i s held together by van der Waals forces. 2 8 TABLE VIII. BOND ANGLES(0) OF NON-HYDROGEN ATOMS IN MOLECULE 4 Bonds Angle Bonds Angle C ( 3 ) - 0 ( 2 ) - C ( 1 8 ) 1 1 4 . 3 ( 1 ) C ( 1 ) - c ( 1 0 ) - c ( 5 ) 1 0 7 . 7 ( 2 ) C ( 3 ) - 0 ( 3 ) - C ( 2 0 ) 1 1 4 . 3 ( 2 ) C ( 1 ) - c ( 1 0 ) - c ( 9 ) 1 1 1 . 1 ( 2 ) C ( 2 ) - C O ) - C ( 1 0 ) 1 1 2 . 8 ( 2 ) C ( 1 ) - c ( 1 0 ) - c ( 1 7 ) 1 0 9 . 7 ( 2 ) C ( 1 ) - C ( 2 ) - C ( 3 ) 1 1 2 . 4 ( 2 ) C ( 5 ) -c( 1 0 ) - c ( 9 ) 1 0 9 . 3 ( 2 ) 0 ( 2 ) - C ( 3 ) - 0 ( 3 ) 1 1 0 . 2 ( 1 ) C ( 5 ) - c ( 10) - c ( 1 7 ) 1 1 1 . 2 ( 2 ) 0 ( 2 ) - C ( 3 ) - C ( 2 ) 1 0 5 . 8 ( 2 ) C ( 9 ) - c ( 10) - c ( 1 7 ) 1 0 7 . 8 ( 2 ) 0 ( 2 ) - C ( 3 ) - C ( 4 ) 1 1 2 . 0 ( 2 ) C ( 9 ) - c ( 11) - c ( 1 2 ) 1 0 5 . 1 ( 2 ) 0 ( 3 ) - C ( 3 ) - C ( 2 ) 1 0 5 . 1 ( 2 ) C ( 9 ) - c ( 11) - c ( 1 5 ) 8 8 . 3 ( 2 ) 0 ( 3 ) - C ( 3 ) - C ( 4 ) 1 1 2 . 2 < 2 ) C ( 1 2 ) - c ( 1 D - c ( 1 5 ) 1 1 0 . 8 ( 2 ) C ( 2 ) - C ( 3 ) - C ( 4 ) 1 1 1 . 2 ( 2 ) 0 ( 1 ) - c ( 12) - c ( 11) 1 2 5 . 0 ( 2 ) C ( 3 ) - C(4) - C ( 5 ) 1 1 2 . 3 ( 2 ) 0 ( 1 ) - c ( 12) -C( 1 3 ) 1 2 6 . 1 ( 2 ) C ( 4 ) - C ( 5 ) - C ( 6 ) 1 1 1 . 7 ( 2 ) C O 1 ) - c ( 12) - c < 1 3 ) 1 0 8 . 9 ( 2 ) C ( 4 ) - C ( 5 ) - C ( 1 0 ) 1 1 3 . 1 ( 2 ) C ( 8 ) - c ( 13) - C l 1 2 ) 1 0 3 . 0 ( 2 ) C ( 6 ) - C ( 5 ] - C ( 1 0 ) 1 1 1 . 4 ( 2 ) C ( 9 ) - c ( 14) - c < 1 5 ) 8 9 . 3 ( 2 ) C ( 5 ) - C ( 6 l - C ( 7 ) 1 1 0 . 5 ( 2 ) C O D - C ( 15) - c 1 4 ) 9 2 . 6 ( 2 ) C ( 6 ) -C(7' - C ( 8 ) 1 1 5 . 3 ( 2 ) C O D -Ci 15) - c , 1 6 ) 1 3 1 . 9 ( 4 ) C ( 7 ) - C ( 8 - C ( 9 ) 111:. 5 ( 2 ) C ( 1 4 ) - c < 1'5] - c , 1 6 ) - 1 35-, 2;( 4 ) C ( 7 ) - C ( 8 ) - C ( 1 3 ) 1 0 8 . 3 ( 2 ) 0 ( 2 ) - c 18] - c ( 1 9 ) 1 1 1 . 6 ( 2 ) C ( 9 ) - C ( 8 I - C ( 1 3 ) 1 0 4 . 6 ( 2 ) C ( 1 8 ) - c 1 9 1 - c ( 2 0 ) 1 0 5 . 6 ( 2 ) C ( 8 ) - C ( 9 ) - C ( 1 0 ) 1 1 4 . 7 ( 2 ) C ( 1 8 ) - c 19 - c (21 ) 1 1 0 . 3 ( 2 ) C ( 8 ) - C ( 9 ) - c d 1) 1 0 4 . 5 ( 2 ) C ( 1 8 ) - c 19 - c ( 2 2 ) 1 0 9 . 6 ( 2 ) C ( 8 ) - C ( 9 ) - C ( 1 4 ) 1 1 4 . 3 ( 2 ) C ( 2 0 ) - c [ 1 9 >-c (21 ) 1 1 0 . 3 ( 2 ) C ( 1 0 ) - C ( 9 ) - c d 1 ) 1 1 8 . 8 ( 2 ) C ( 2 0 ) - c ( 1 9 >-c ( 2 2 ) 1 0 9 . 5 ( 2 ) C ( 1 0 ) - C ( 9 ) - C ( 1 4 ) 1 1 3 . 7 ( 2 ) C ( 2 1 ) - c ( 1 9 ) - C ( 2 2 ) 1 1 1 . 4 ( 2 ) C ( 1 1 ) - C ( 9 ) - C ( 1 4 ) 8 8 . 0 ( 2 ) 0 ( 3 ) - c ( 2 0 ) - C 0 9 ) 1 1 1 . 5 ( 2 ) 29 TABLE IX. BOND ANGLES(0) INVOLVING HYDROGEN ATOMS IN MOLECULE 4 Bonds Angle Bonds Angle c ( 2) - C O ) - H ( 0 1 1 ) 1 09( 1 ) c ( 2) - C O ) -H(012) 1 1 1 ( 1 ) c ( 10) - C O ) -H(011) 1 1 1 ( 1 ) c ( 10) - C O ) -H(012 ) 1 08 ( 1 ) H( 011) - C O ) -H(012) 1 05( 2) C( 1 ) - C ( 2 ) -H(021) 1 1 1 ( 1 ) c ( 1 ) - C ( 2 ) -H(022) 1 10( 1 ) c ( 3) - C ( 2 ) -H(021) 1 07 ( 1 ) c ( 3) - C ( 2 ) -H(022) 1 07 ( 1 ) H( 021 ) - C ( 2 ) -H(022) 1 08 ( 2) C( 3) - C ( 4 ) -H(041) 1 1 1 ( 1 ) C( 3) - C ( 4 ) -H(042) 1 08 ( 1 ) C< 5) - C ( 4 ) -H(041) 1 07( 1 j C< 5) - C ( 4 ) -H(042) 1 1 0( 1 j H( 041 ) - C ( 4 ) -H(042) 1 1 0 < 2) C< 4) - C ( 5 ) -H(051) 1 07 < 1; C l 6) - C ( 5 ) -H(051) 1 07 ( 1; C< 10) - C ( 5 ) -H(051) 106) 1; C< 5) - C ( 6 ) -H(061) 1 07 < 1 C< 5) - C ( 6 ) -H(062) 1 08( 1 c [7) - C ( 6 ) -H(061) 1 1 2 1 c [7) - C ( 6 ) -H(062) 1 1 0 1 H [061 ) - C ( 6 ) -H(062) 1 10 ,2 C [6) - C ( 7 ) -H(071) 108 11 C (6) - C ( 7 ) -H(072) 1 1 2 [ 1 C [8) - C ( 7 ) -H(071 ) 1 07 i 1 C (8) - C ( 7 ) -H(072) 1 06 [ 1 H (071 ) - C ( 7 ) -H(072) 108 (2 C (7) - C ( 8 ) -H(081) 109 ( 1 c (9) - C ( 8 ) -H(081) 1 1 1 ( 1 c ( 13 ) - C ( 8 ) -H(081) 1 1 2 ( 1 c (9 ) -C (11) -H(111) 120 ( 1 c ( 12 ) - C O 1 ) -H(111) 1 1 3 ( 1 c ( 15 ) - C O D - H ( 1 1 1 ) 1 1 7 ( 1 c (8 ) - C O 3) -H(1 3 D 1 1 1 ( 1 c (8 ) - C O 3) -H(132) 1 1 2 (2 c ( 12 ) - C 0 3 ) -H(131) 107 ( 1 c ( 12 ) - C ( 1 3 ) -H(132) 110 (2 H( 131) - c ( 13) -H( 1 32) 112 ( 2 ) C( 9) - c ( 14) -H( 141 ) 115 ( 2 ) C( 9) - c ( 14) -H( 142) 116 ( 2 ) C( 15) - c ( 14) -H( 141) 1 1 5 ( 2 ) C( 15) - c ( 14) -H( 1 42) 115 ( 2 ) H( 141) - c ( 14) -H( 1 42) 106 ( 2 ) C.( 15) - c ( 16) -H( 161 ) 119(3) C( 15) - c ( 16) -H( 1 62) 1 1 0 ( 2 ) H( 161) - c ( 16) -H( 1 62) 131 ( 3 ) C( 10) - c ( 17) -H( 171) 112 ( 2 ) C( 10) - c ( 17) -H( 172) 112 ( 2 ) C( 10) - c ( 17) -H( 173) 109 ( 2 ) H( 171) - c ( 17) -H( 1 72) 108 ( 2 ) H( 171 ) - c ( 17) -H( 1 73) 1 1 1 ( 2 ) H( 1 72) - c ( 17) -H( 173) 1 0 4 ( 2 ) 0 ( 2 ) - c ( 18) -H( 181 ) 113 ( 1 ) 0 ( 2 ) - c ( 18) -H( 182) 105(1 ) C( 19) - c ( 18) -H( 181) 108(1) C< 19) - c ( 18) -H( 182) 111(1) H< 181) - c ( 18) -H( 182) 109(2) O 3) - c ( 20) -H< 201 ) 104(1 ) O 3) - c ( 20) -H( 202) 111(1) C M9) - c ( 20) -H( 201 ) 1 1 1 O ) C [19) -c< 20 1 -H< 202) 109(1) H-[201 ) - c ( 20 -H 202) 1 1 1 (-2--) C [19) -C( 21 )-H 211) 111(2) C [19) -C( 21 I-H 212) 109(2) c 09) -c< 21 )-H [213) 110(2) H [211) -c< 21 )-H [212) 109(2) H (211) - c 21 )-H [213) 110(2) H (212) - c 21 )-H [213) 108(2) C 09) - c [ 2 2 )-H [221 ) 113(2) C 0 9 ) - c , 2 2 )-H ( 2 2 2 ) 111(2) c 09) - c [ 2 2 )-H (223) 109(2) H (221) - c [ 2 2 )-H ( 2 2 2 ) 108(3) H (221 ) - c [ 2 2 )-H (223) 106(3) H ( 2 2 2 ) - c [ 2 2 )-H (223) 110(3) F i g u r e 4 . Stereo packing diagram f o r compound 31 II. AN c-CYCLOBUTYL TRICYCLIC ENONE Introduct ion The results of the last section indicated that the f i r s t eluted isomer was the cis-fused p-cyclobutyl adduct (4_ in scheme 1). This allowed the assignment of the cis-fused c- cyclobutyl adduct 5 to the second eluted isomer, and the problem as i n i t i a l l y stated was solved. However, some doubt was cast on the structure of 5 when the next step in the synthesis yielded i d e n t i c a l products from both isomers 2 0. Ozonolysis (0 3, CH2Cl2-MeOH, -78°C; Me2S) (see Figure 5: scheme 2) of the adduct 4, followed by treatment of the resultant cyclobutanone with NaOMe/MeOH produced the expected keto ester 6. Surprisingly, subjection of the second photoadduct (expected to be 5) to the same sequence of reactions produced the same keto ester 6. Clearly, the expected product was the isomeric keto ester This result seemed to imply that the only difference between the two adducts must l i e in the orientation of the bond that was broken during the ring opening: C(11)— C(15). In other words, rather than possessing the cis-fused structure 5, i t appeared that the second eluted isomer might have the more unlikely and highly strained trans-fused structure 8.  33 In order to investigate t h i s i n t r i n s i c a l l y fascinating possible trans-fused adduct, and. al.so to establish the. identity of the second eluted isomer, an x-ray study was undertaken. Unfortunately, the material did not c r y s t a l l i z e as e a s i l y as the f i r s t eluted isomer, and the quality of the c r y s t a l s even after various r e c r y s t a l l i z a t i o n s was poor. Considerable e f f o r t was required in selecting a c r y s t a l which was suitable for analysis. Crystals that were apparently well-formed were shown to be multiple p l a t e l e t s by examination on a po l a r i z i n g microscope, or if t h i s f a i l e d , by photography. Eventually, by selecting a s u f f i c i e n t l y thin p l a t e l e t (0.05 x 0.42 x 0.35 mm3),, a single c r y s t a l was located. Experimental Preliminary photography showed the c r y s t a l to be monoclinic, but because of the poor c r y s t a l quality assignment of the axes and hence determination* of systematic' a-bsences from- the photographs was d i f f i c u l t . C e l l parameters were determined on the CAD4 dif f T a c t o m e t e r , and systematic absences became apparent a f t e r the data c o l l e c t i o n and indicated the space group P2 1/n. The intensity data were co l l e c t e d using an O-(1/3)8 scan technique and graphite-monochromatized MoKa radiation. The o - scan angle was (1.2 + 0.35 tan 6)° and the aperture was (2.50 + tan 8)mm wide and 4 mm high. The i n t e n s i t i e s of three standard r e f l e c t i o n s (7 0 -5, 1 -1 4 and 5 0-1) were measured every hour and showed no v a r i a t i o n . The 7 0-5, 1 1-4, and 34 4 0 4 r e f l e c t i o n s were checked every 100 r e f l e c t i o n s for orientation, and reorientation, occurred, i f the difference between observed and calculated scattering vectors was greater than 0.06°. Of the 3836 r e f l e c t i o n s c o l l e c t e d within the range 0 < 6 < 25°, only 749 (19.5%) had I/*(I) > 3.0, and so a l l r e f l e c t i o n s with a theta value greater than 19.5° were removed from the data set. Between 19.5 and 25°, only 47 of the 1865 (2.5%) r e f l e c t i o n s measured were observed, so by removing this data we are not making a great s a c r i f i c e in the amount of information available, but we are s i g n i f i c a n t l y reducing the amount of computer storage space needed to handle the problem. Of the remaining data, 702 out of 1784 (39%) r e f l e c t i o n s have I / e r(I) > 3.0 and were considered observed. The unit c e l l parameters were refined by least-squares methods with the sinO/X. values of 18 r e f l e c t i o n s in the 6 range 9 to 18°. They appear together with other c r y s t a l data in Table X. It was thought that because of the anisotropic nature of the c r y s t a l shape (Figure 6), absorption effects could perhaps be s i g n i f i c a n t . However, the calculated transmission factors varied from 0.971 to 0.997, indicating that absorption is n e g l i g i b l e , and the corrections were not applied. Lorentz and p o l a r i z a t i o n corrections were applied as usual. The structure was solved by dir e c t methods. 342 E's > 1.2 were obtained from a K-curve and, together with the 50 lowest E's, were input into the MULTAN programme1. No E, - r e l a t ions' were accepted, and the three largest E's (4 5 7, 8 2-11 and 5 1 5) were assigned a phase of zero in order to f i x the o r i g i n . Four 35 ********************************************* TABLE X. CRYSTAL DATA FOR MOLECULE 5 C 2 2 H 3 2 O 3 . f.w. = 344.5 Monoclinic Z = 4 space group = P2 1/n a = 15.722(4) b = 7.463(2) o F(000) = 536 c = 17.213(1) A X = 0.71073 A ^ = 104.67(1) 0 Dc = 1.17 g/cc V = 1951.4 A 3 „ = 0.7 cm"1 **************************************************************** symbols (2 0 2, 7 0 -5, 12 0 0, and 1 1 1 ) were assigned i n i t i a l phases of 0 and i r, thereby generating sixteen sets of phased E's. One set stood out as being correct, and from the E-map the positions of a l l 25 non-hydrogen atoms could be determined. After three isotropic and seven anisotropic least-squares refinement cycles, a l l the hydrogen atoms could be located on a difference map. A • single least-sq.ua res cycle- including.'all the hydrogens fixed in their located positions and using sigma weights was run p a r a l l e l with a cycle wherein the hydrogen atoms were in fixed calculated positions. The hydrogen atomic parameters were not refined as the amount of data was i n s u f f i c i e n t . The cycle using calculated hydrogen positions refined to R and Rw values of 0.046 and 0.052 respectively, whereas the cycle using located hydrogen positions refined to R and Rw values of 0.064 and 0.073, and so the hydrogen atoms were fixed in their calculated positions. Attempts to refine the p l a n e 0 0 0 0 - -2 2 2 -2 - -1 0 1 0 - v e r t i c e s 1 ,2,3,4 5,6,7,8 1,2,5,6 3,4,7,8 1 ,2,5,7 2,4,6,8 d i s t a n c e from c e n t r e (nun) 0.175 0.175 0.225 0.200 0.025 0.025 c r y s t a l volume = 0.0100 mm: F i g u r e 6. S t e r e o v i e w of t h e examined c r y s t a l of 5 37 hydrogen thermal parameters proved unsuccessful, and each hydrogen was. assigned a temperature factor 10% greater than that of the carbon to which i t i s bound (25% for methyl hydrogens). The structure converged after three more least-squares cycles using a Hughes' weighting scheme 2 1 where (w) 1/ 2 = 1.0 for |Fo| < F* and (w) 1/ 2 = F*/|Fo| for |Fo| > F*, and F* = 21.0. The weighting scheme could be s l i g h t l y improved so three more cycles were run with F* = 20.0. The f i n a l R values are R = 0.040 (0.169 including the unobserved r e f l e c t i o n s ) and Rw = 0.053. Fi n a l p o s i t i o n a l and thermal parameters appear in Tables XI and XII. Results and discussion Contrary to the expectations from the ozonolysis results, the structure is that which was f i r s t assumed for the second eluted isomer: the cis-fused c-cyclobutyl species 5. A stereoview of the molecule is shown in Figure 7. Atomic l a b e l l i n g is the same- as- in the f i r s t eluted isomer.. Mean- planes, bond lengths and bond angles (Tables XIII, XIV, XV, XVI, and XVII) are very similar to those of the f i r s t eluted isomer, and w i l l be compared at the end of this chapter. A packing diagram i s presented in Figure 8; there are no unusually short intermolecular distances. Confidence in the chemical evidence was s u f f i c i e n t to suggest that the c r y s t a l chosen for examination might have been one of an impurity - a minor t h i r d product. The v a l i d i t y of such a suggestion i s d i f f i c u l t to e s t a b l i s h . A structure 38 TABLE XI. ATOMIC POSITIONAL AND ISOTROPIC THERMAL PARAMETERS OF MOLECULE 5 (fr a c t i o n a l x 10", H x 10J , U x 103 A 2) Atom X z Ueg/Uiso 0( 1 ) 1489(4) 755( 9) 2764(4) 82 0(2) 3008(3) 2381( 8) -1 409(3) 53 0(3) 4525(3) 1907( 8) -1025(3) 56 C(1 ) 3037(5) 300802) 324(5) 54 C(2) 3814(5) 3193(12) -42(5) 58 C(3) 3738(5) 1937(14) -756(5) 53 C(4) 3586(6) 41(12) -533(5) 55 C(5) 2813(5) -154(1 1 ) -153(5) 46 C(6) 2625(6) -2089(13) 13(5) 65 C(7) 1812(6) -2312(13) 342(5) 64 C(8) 1933(5) -1105(12) 1072(5) 55. C(9) 2057(5) 847(12) 855(4) 44 COO) 2909(5) 1083(12) 588(4) 46 CO 1 ) 1874(5) 1946(12) 1578(5) 52 C( 12) 1514(5) 561(12) 2062(6) 59 CO 3) 1247(5) -1075(14) 1567(5) 66 CO 4) 1206(5) 1708(12) 300(5) 59 C( 15) 1079(6) 2827(12) 1000(5) 59 C( 16) 524(6) 405803) 1109(6) 81 C( 17) 3708(5) 572(12) 1285(5) 66 C( 1 8 ) 3112(5) 4039(14) -1790(5) 61 C( 19) 3949(5) 4064(14) -2107(5) 60 C(20) 4691(5) 3521(13) -1393(5) 61 C(21 ) 4092(6) 5927(15) -2390(6) 85 C(22) 3880(6) 2690(15) -2778(5) 85 H(01 1) 312 387 80 70 H(012) 251 345 -4 70 H(021) 437 302 36 65 H(022) 386 44-2- -25 65 H(041 ) 348 -81 -100 74 H(042) 410 -54 -15 74 H(051 ) 227 26 -55 65 H(061 ) 256 -283 -48 75 H(062) 314 -261 39 75 H(071) 1 29 -203 -4 81 H(072) 1 74 -360 49 81 H(081 ) 248 -1 56 1 45 72 HO 1 1 ) 235 272 188 66 H( 131) 65 -110 1 17 87 HO 32) 1 24 -226 185 87 HO 41 ) 1 32 235 -16 73 HO 42) 75 85 6 73 continued... H(161) 46 535 161 100 H(162) -13 506 59 100 H(171) 366 -66 1 45 99 H(172) 425 71 1 1 5 99 H(173) 373 131 1 76 99 H(181) 259 444 -220 99 H( 182) 317 51 1 -1 38 99 H(201) 475 453 -99 68 H(202) 525 351 -1 52 68 H(211) 418 677 -1 92 . 1 06 H(212) 459 607 -260 1 06 H(213) 358 639 -277 106 H(221) 372 1 53 -260 1 04 H(222) 339 301 -324 1 04 H(223) 439 257 -296 1 04 TABLE XII. ANISOTROPIC THERMAL PARAMETERS OF MOLECULE 5 (Uij x .103 A 2) Atom On u 2 2 U 3 3 U,2 U, 3 u 2 3 0(1 ) 90(5) 111(6) 56(4) 5(4) 40(4) 0(4) 0(2) 38(3) 68(4) 51 (3) -3(3) 4(3) 0(4) 0(3) 40(3) 80(5) 54(4) 7(3) 20(3) 1 1(4) CO ) 60(6) 53(7) 56(5) -11(5) 28(5) -1 3.(6) C(2) 57(6) 76(7) 43(5) -21(5) 17(4) -13(6) C(3) 40(6) 76(9) 45(6). -3(5) 16(5) 3(6) C(4) 65(6) 53(7) 48(5) 8"(6) 16(5) -13(5) C(5) 39(5) 59(7) 43(5) 6(5) 14(4) 0(6) C(6) 82(7) 58(8) 61 (6) -1(6) 32(5) -3(6) C(7) 77(6) 58(8) 57(6) -16(6) 19(5) -5(6) C(8) 61 (6) 62(8) 44(5) -11(5) 15(5) -4(5) C(9) 41 (5) 53(7) 34(5) 3(5) 1(4) 2(5) COO) 39(5) 60(7) 37(5) -7(5) 8(4) -10(5) CO 1 ) 56(6) 58(6) 45(5) -11(6) 20(5) -5(5) C(12) 51 (6) 65(8) 63(7) 10(6) 19(5) 2(7) CO 3) 69(7) 70(8) 60(6) -20(6) 17(5) 0(6) C(14) 50(6) 73(7) 59(6) -10(5) 20(5) 9(6) C(15) 56(7) 57(7) 71(6) 13(6) 26(5) 24(7) C(16) 73(7) 54(6) 129(9) 13(7) 48(6) 1 1 (7) C07) 53(6) 92(7) 50(5) 1 (6) 8(5) -1 (5) C(18) 43(6) 79(8) 61 (6) 4(5) 13(5) 9(6) C(19) 55(6) 74(7) 52(6) 0(6) 16(5) 12(6) C(20) 45(6) 87(8) 55(6) -1(5) 19(5) 7(6) C(21 ) 66(7) 96(8) 95(7) -6( 60- 2 5.(6) 20 (7) C(22) 81 (7) 127(9) 53(6) 2(7) 28(5) -17(7) F i g u r e 7 . A stereoview of molecule TABLE XIII. MEAN PLANES IN THE VICINITY OF THE CYCLOBUTYL RING IN MOLECULE 5 Equations of planes (!X+mY+nZ=p) plane 1 2 3 4 m 0.6728 0.6183 -0.8246 -0.3664 0.7079 0.7583 0.0874 0.5520 n -0.2151 -0.2066 -0.5589 -0.7079 1.9814 1.9536 -3.1499 -2.8512 Deviations from planes ( A ) atom C(8) C(9) C ( 1 1 ) C( 12) C(13) C( 14) C( 15) C(16) 0(1 ) 0.084(8) 0.000(8)* 0.000(8)* 0.000(9)* •0.01(1) 0.000(8)* 0.000(9)* 0.000(8)* 0.080(9) 0.17(1 ) •0.040(8)* 0.051(7)* •0.054(8)* 0.047(9)* 0.570(9) 0.000(8) 0.932(8) 0.797(8) 0.00(1 )* 0.000(9) - 0 . 3 0 9 ( 6 ) - 0 . 5 9 6 ( 6 ) *atoms included in plane calculations Angles between normals to the planes planes (1) and (2) planes (2) and (3) planes (3) and (4) 4.2° 109.2° 36.2° 43 TABLE XIV. BOND LENGTHS( A ) OF THE NON-HYDROGEN ATOMS IN MOLECULE 5 Bond Distance Bond Distance 0(1 ) -C(12) 1.229(09) C(8) -C(13) 1.534(11) 0(2) -C(3) 1.428(09) C(9) -COO) 1.532(10) 0(2) -C(18) 1.428(10) C(9) - c ( n ) 1.577(10) 0(3) -C(3) 1.427(08) C(9) -C(14) 1.571(10) 0(3) -C(20) 1.415(09) C(10)-C(17) 1.549(10) C(1 ] -C(2) 1.515(10) CO 1 )-C0 2) 1.523(10) c d ; -COO) 1.536(11 ) CO D-CO 5) 1.534(11) C(2) -C(3) 1.526(1 1 ) C(12)-C(13) 1.487(12) C(3' -C(4) 1.501 (1 1 ) C(14)-C(15) 1.521(11) C U 1 >-C(5) 1.526(10) C(15)-C(16) 1.312(11) C(5 )-C(6) 1.516(11) C(18)-C(19) 1.546(10) C(5 l-COO) 1.550(10) C(19)-C(20) 1.520(11) C(6 )-C(7) 1.533(10) C(19)-C(21) 1.510(13) C(7 )-C(8) 1.519(11) C(19)-C(22) 1 ..529(1 2) C(8 )-C(9) 1.528(1 1 ) 44 TABLE XV. BOND LENGTHS( A ) INVOLVING HYDROGEN ATOMS IN MOLECULE 5 Bond Distance Bond Distance C(1) -H(011) 1 .02 C( 14)-H(142) 0.98 C( 1 ) -H(012) 0.96 C(16)-H(161) 1 .3.2 C(2) -H(021) 0.98 C(16)-H(162) 1 .40 C(2) -H(022) 0.99 C(17)-H(171) 0.97 C(4) -H(041) 1.01 C(17)-H(172) 0.94 C(4) -H(042) 1 .00 C(17)-H(173) 0.98 C(5) -H(051) 1 .00 C(18)-H(181) 0.98 C(6) -H(061) 0.99 C(18)-H(182) 1 .05 C(6) -H(062) 0.98 C(20)-H(201) 1 .02 C(7) -H(071) 0.94 C(20)-H(202) 0.96 C(7) -H(072) 1.01 C(21)-H(211) 1 .00 C(8) -H(081) 1 .00 C(21)-H(212) 0.94 C(11)-H(111) 0.99 C(21)-H(213) 0.97 C(13)-H(131 ) 1.01 C(22)-H(221) 0.97 C( 13)-H(132) 1.01 C(22)-H(222) 0.99 C(14)-H(141) 0.99 C(22)-H(223) 0.93 45 TABLE XVI. BOND ANGLES(0) OF NON-HYDROGEN ATOMS IN MOLECULE 5 Bonds Angle Bonds Angle C(3) -0(2) -C(18) 1 1 3 .6(6) CO ) -c( 10) -c( 5) 1 07 .8(6) C(3) -0(3) -C(20) 1 1 3 .9(7) CO) -c( 10) -c( 9) 1 12 .8(7) C(2) -CO ) -COO) 112 .9(8) CO ) -c( 10) -c( 17) 108 .6(7) CO ) -C(2) -C(3) 1 1 1 .8(7) C(5) -c( 10) -c( 9) 1 05 .6(6) 0(2) -C(3) -0(3) 109 .7(6) C(5) -c( 10) -c( 17) 1 12 .4(6) 0(2) -C(3) -C(2) 1 1 2 .0(7) C(9) -c( 10) -c( 17) 109 .8(6) 0(2) -C(3) -C(4) 1 05 .8(7) C(9) -c( 11) -C( 12) 1 04 .2(7) 0(3) -C(3) -C(2) 1 1 2 .0(7) C(9) -c( 11) -c< 15) 89 .6(6) 0(3) -C(3) -C(4) 1 06 .0(8) C( 12) -c( 11) -Cl 15) 1 06 .9(7) C(2) -C(3) -C(4) 1 1 1 .0(7) 0(1 ) -c( 12) -c< 1 1 ) 124 .5(9) C(3) -C(4) -C(5) 1 1 3 .3(7) 0(1 ) -c( 12) -Cl 13) 1 25 .9(8) C(4) -C(5) -C(6) 1 1 2 .7(7) C O D -C( 12) -Cl 13) 109 .5(7) C(4) -C(5) -COO) 1 12 .0(6) C(8) -c( 13) -c 12) 101 .1(7) C(6) -C(5) -COO) 1 1 3 .3(6) C(9) -C( 14) -c [15) 90 .3(6) C(5) -C(6) -C(7) 1 1 3 .2(8) C O D -c< 15) -c [14) 91 .7(6) C(6) -C(7) -C(8) 1 07 .5(7) CO 1) -Cl 151 -c (16) 1 32 .0(9) C(7) -C(8 1 -C(9) 1 1 1 ..my GO 40 -c 15 -C (160 1 3'6 . 3(9) C(7) -C(8' -C(13) 1 20 .7(8) 0(2) -c 18 l-C (19) 1 1 2 .2(8) C(9) -C(8 1 -CO 3) 1 05 .9(7) C( 18) -c [19 )-C (20) 105 .1(7) C(8) -C(9 >-C(10) 1 1 1 .0(7) C( 18) -c [19 l-C (21 ) 109 .6(9) C(8) -C(9 >-C(11) 1 04 .0(6) C( 18) -c [ 1 9 >-c (22) 1 10 .8(8) C(8) -C(9 >-C(14) 1 1 3 .4(7) C(20) -c [19 )-C (21) 1 1 1 .1(8) COO) -C(9 »-CO 1) 121 .7(7) C(20) -c [19 )-c (22) 109 .0(8) COO) -C(9 )-C(14) 1 1 6 .4(7) C(21 ) -c 09 )-c (22) 1 1 1 .2(8) CO 1 ) -C(9 >-CO 4) 88 .3(6) 0(3) -c (20 )-c 09) 1 1 3 .4(7) 46 TABLE XVII. BOND ANGLES(0) INVOLVING HYDROGEN ATOMS IN MOLECULE 5 Bonds Angle Bonds Angle c( 2) - c ( i ) -H(011) 109 H( 131 ) -c( 13) -H( 1 32) 101 c( 2) -CO ) -H(012) 1 1 1 C( 9) -c( 14) -H( 141) 1 1 3 c( 10) -CO ) -H(011) 110 C( 9) -c( 14) -H( 1 42) 1 1 4 c( 10) -CO ) -H(012) 1 1 1 C( 15) -c( 1 4) -H( 141) 1 18 H( 011) -CO ) -H(012) 1 03 C( 15) -c( 14) -H( 1 42) 1 1 7 c( 1 ) -C(2) -H(021) 1 1 1 H( 141) -c( 14) -H( 1 42) 1 04 c( 1 ) -C(2) -H(022) 112 C( 15) -c( 16) -H( 161) 1 40 C( 3) -C(2) -H(021) 1 1 1 C( 15) -c( 16) -H( 1 62) 1 34 c( 3) -C(2) -H(022) 1 06 H( 161 ) -c( 16) -H( 1 62) 82 H( 021 ) -C(2) -H(022) 1 04 C( 10) -c( 17) -H( 171) 1 10 C( 3) -C(4) -H(041) 1 1 3 C( 10) -c( 17) -H( 1 72) 1 1 3 c( 3) -C(4) -H(042) 115 C( 10) -c( 17) -H( 1 73) 1 1 1 c( 5) -C(4) -H(041) 1 07 H( 171) -c( 17) -H( 172) 1 09 c( 5) -C(4) -H(042) 1 06 H( 171) -c( 17) -H( 1 73) 1 06 H( 041 ) -C(4) -H(042) 101 H( 172) -c( 17) -H( 1 73) 1 07 C< 4) -C(5) -H(051) 1 08 0< 2) -c( 18) -H( 181) 1 1 5 C( 6) -C(5) -H(051) 1 04 0< 2) -c( 18) -H( 182) 1 1 1 C( 10) -C(5) -H(051) 105 C( 19) -c( 18) -H( 181) 1 1 2 c< 5) -C(6) -H(061) 1 1 1 C( 19) -c( 18) -H( 182) 1 06 c< 5) -C(6) -H(062) 109 H< 181 ) -C( 18) -H( 182) 99 c< 7) -C(6) -H(061) 1 10 0< 3) -C( 20) -H( 201 ) 1 09 c ,7) -C(6) -H(062) 1 10 O 3) -C( 20) -H< 202) 1 1 2 H [061 ) -C(6) -H(062) 1 04 C 19) -Cl 20 -H< 201 ) 106 C [6) -C(7) -H(071) 112 C (19) -Cl 20 )-H( 202) 1 1 2 c [6) -C(7) -HC072) 1 1 1 H' (201) -c •20 ) -Hi 202) V0.3' c (8) -C(7) -H(071) 1 1 1 C (19) -c 21 >-H< 211) 109 c (8) -C(7) -H(072) 1 10 C (19) -c ,21 )-H< 212) 1 16 H (071 ) -C(7) -H(072) 105 c 09) -c (21 )-H ,213) 1 1 3 C (7) -C(8) -H(081) 1 04 H (211) -c (21 )-H ,212) 1 06 c (9) • -C(8) -H(081) 1 1 0 H (211) -c (21 )-H (213) 1 04 c (13) -C(8) -H(081) 1 05 H (212) -c (21 )-H (213) 109 c (9) -COD -HO 1 1 ) 1 1 7 C 09) -c (22 )-H (221) 1 1 0 c (12) -COD -H(111) 1 1 7 C 09) -c (22 ) -H (222) 1 1 0 c (15) -CO 1) -H(111) 1 1 9 c 09) -c (22 )-H (223) 1 1 4 c (8) -C(13) -H(131) 1 07 H (221) -c (22 )-H (222) 105 c (8) -C(13) -H(132) 1 10 H (221) -c (22 )-H (223) 109 c (12) -CO 3) -H(131) 1 1 9 H (222) -c (22 )-H (223) 1 08 c (12) -C03) -H(132) 1 19 F i g u r e 8. S t e r e o p a c k i n g diagram f o r compound 5 48 determination on another c r y s t a l in the batch would be expensive, time consuming,, and only conclusive i f i t produced di f f e r e n t r e s u l t s . Also, the c r y s t a l s were s u f f i c i e n t l y poor that locating another single c r y s t a l of reasonable quality would have been a major task in i t s e l f . An x-ray analysis of a derivative of the second eluted isomer that produces high quality c r y s t a l s should solve t h i s ambiguity. 49 I I I . THE P-BROMOBENZOATE DERIVATIVE OF THE SECOND ELUTED ISOMER Introduct ion The p-bromobenzoate d e r i v a t i v e (9) (see scheme 2, page 32) of the second e l u t e d isomer (5) was prepared by Dr. P i e r s and co-workers, and y i e l d e d high q u a l i t y c r y s t a l s . The x-ray a n a l y s i s of t h i s d e r i v a t i v e should f i r m l y and f i n a l l y e s t a b l i s h the second e l u t e d isomer's s t r u c t u r e . Experimental A s i n g l e c r y s t a l of p r o p o r t i o n s 0.33 x 0.37 x 0.42 mm3 was s e l e c t e d f o r study. The c r y s t a l ' s good q u a l i t y and w e l l - d e f i n e d faces more than compensated f o r i t ' s s l i g h t l y l a r g e s i z e . P r e l i m i n a r y photography showed that the c r y s t a l i s t r i c l i n i c (no systematic absences) and, as the d e r i v a t i v e i s a racemate, of the centrosymmetric space group P1. The data were c o l l e c t e d using an o-(4/3)6 scan technique and graphite-monochromatized MoKc r a d i a t i o n . The o-scan angle was (0.70 + 0.35 tan 6)° and the ape r t u r e was (2.50' + tan 6) mm* wide and 4 mm h i g h . The i n t e n s i t i e s of three standard r e f l e c t i o n s (-2 -1 5, -1 -2 4 and -2 1 5) were measured every 50 one hour and showed a linear decay of 2% over the data c o l l e c t i o n . The data were scaled accordingly.. Three, r e f l e c t i o n s (-2 -1 5, -3 -6 0 and 6 2 1) were checked for orientation every 100 r e f l e c t i o n s , and reorientation occurred i f . the difference between observed and calculated scattering vectors was greater than 0.05°. Of the 4549 r e f l e c t i o n s c o l l e c t e d in the range 0 < 6 < 25°, 2715 (59.7%) had > 3.0 and were considered observed. The c e l l parameters were refined by least-squares methods with the sin6/X values of 24 r e f l e c t i o n s in the 6 range 15 to 19°, and" appear together with other c r y s t a l data in Table XVIII. The *************************************** TABLE XVI11. CRYSTAL DATA FOR DERIVATIVE 9 C 2 gHs^BrOn f . w. = 344.5 T r i c l i n i c z = = 2 space group = = PI a = 11.832(1) b = 11 .877(1) . F(000). = =• 536- c = 10.900(1) A X = = 0.71073 A c = 90.461(8) Dc = = 1 .32 g/cc B = 111.57(1) V = = 1306.8 A 3 r = 80.51(1) 0 f = = 15.86 cm"1 **************************************************************** large value of the linear absorption c o e f f i c i e n t v (15.8 cm - 1), due mainly to the presence of bromine in the unit c e l l , indicates that an absorption correction is in order unless the c r y s t a l i s extremely small. In order to accomplish t h i s i t i s necessary to measure the distances from the indexed faces to an 51 a r b i t r a r y centre of the c r y s t a l such that the shape of the c r y s t a l is defined. It then, becomes, possible to determine the x- ray path length through the c r y s t a l for any r e f l e c t i n g position, and the attenuation due to absorption may be calculated as a transmission factor. The transmission factor A i s given by : where V i s the c r y s t a l volume, » the linear absorption c o e f f i c i e n t , and Ri and Rd the incident and d i f f r a c t e d path lengths. A i s evaluated numerically by Gaussian integration. Sampling points are set up in a Gaussian grid to approximate the shape of the c r y s t a l - the number and spacing of these points are determined by experience; computing time per r e f l e c t i o n increases sharply with the number of sampling points, but after a certain number no great increase in accuracy i s obtained. In t h i s c r y s t a l the shape i s determined by six faces (see Figure 9). 144 sampling points are used with an average spacing of 0.076 mm for a c r y s t a l volume of 0.0568 mm3, and the resulting transmission factors varied from 0.569 for the -12 -4 4 r e f l e c t i o n to 0.0631 for 5 -1 9. The i n t e n s i t i e s were thus corrected for absorption, as well as for Lorentz and polarization e f f e c t s . The structure was solved by Patterson techniques. A three- dimensional Patterson map i s calculated from the structure amplitudes. The peaks in a Patterson map may be regarded as the heads of a l l the interatomic vectors grouped such that the t a i l s are at a common o r i g i n . For n atoms in the unit c e l l , there" w i l l be n 2-n peaks in the Patterson plus a large peak at the o r i g i n representing the sum of a l l the vectors from each atom to A = (l/V)exp[-„(Ri+Rd)]dV 52 p l a n e v e r t i c e s d i s t a n c e from c e n t r e (mm) 0 -1 0 1,2,3,4 0.1 50 0 1 0 5,6,7,8 0.180 0 0 -1 1,2,5,6 0.220 0 0 1 3,4,7,8 0. 150 -1 0 0 1,3,5,7 0. 175 1 0 0 2,4,6,8 0.250 c r y s t a l volume = 0.0546 mm: F i g u r e 9. C r y s t a l shape of the p-bromobenzoate d e r i v a t i v e 53 i t s e l f . The peak heights depend on the product of the number of electrons of each atom contributing to. the vector. Thus a Br-Br peak should be larger than a C-C peak by a factor of ( 3 5 ) 2 / ( 6 ) 2 , or about 34. In practice these factors are s l i g h t l y lower because of a smearing of the vector peak due to thermal motion. Patterson maps are thus more useful for structures containing heavy atoms. In t h i s structure, there are two bromines in the unit c e l l related by a centre of symmetry. If one bromine has f r a c t i o n a l coordinates (x,y,z), the other w i l l have coordinates (-x,-y,-z), and the interatomic vector is the difference between them, or (2x,2y,2z). The Patterson map contains one outstanding non- o r i g i n peak at (0.1542,0.3450,0.9215) which establishes the position of the bromines at ±(0.0771,0.1725,0.4608). Three cycles of full-matrix least-squares refinement including only the bromine with isotropic temperature factors resulted in an R value of 0.46, at which stage a difference map revealed the positions of twelve other atoms. Three more refinement cycles with anisotropic temperature factors for the bromine and isotropic temperature factors for the other twelve atoms lowered R to 0.39 and the remaining non-hydrogen atoms could be located on a difference map. After three least-squares cycles with a l l atoms except the bromine having isotropic temperature factors, followed by two cycles with a l l atoms having anisotropic temperature factors, a difference map revealed the positions of a l l ' 37 hydrogen atoms'. Four refinement cycles (hydrogen atoms with isotropic temperature factors, non-hydrogen atoms with anisotropic temperature factors) using a 54 polynomial weighting scheme followed by two cycles that included an anomalous dispersion correction f.or the bromine lowered R and Rw to their f i n a l values of 0.032 and 0.036 (0.083 and 0.076 including the unobserved r e f l e c t i o n s ) respectively. The f i n a l c o e f f i c i e n t s used in the polynomial weighting scheme were A = 0.3074, B = 0.0464, C = -0.00511 and D = 0.000129. In the l a s t cycle, the mean and maximum parameter s h i f t s were 0.046 and 0.474 respectively. A f i n a l difference map was calculated and showed two peaks of 0.4 electrons/A 3. One is in the v i c i n i t y of the bromine and could perhaps be due to a lone pair interaction, but the other i s near the ring containing the two oxygens for no obvious reason. Interestingly enough, bond lengths and bond angles involving 0(2) and C(18) show some s l i g h t deviations (see comparison section). F i n a l p o s i t i o n a l and thermal parameters are l i s t e d in Tables XIX and XX. Results and discussion A stereoview of the molecule i s presented in Figure 10. With the exception of the p-bromobenzoate group, the atomic l a b e l l i n g is as before. The p-bromobenzoate derivative contains the four-membered ring cis-fused to the cyclopentanone ring. Therefore the previous structure solved was not an impurity, but was indeed the second eluted isomer. The fact that both isomers give the same product upon ozonolysis followed by treatment with methoxide implies that they are both potential intermediates in 55 TABLE XIX. ATOMIC POSITIONAL AND ISOTROPIC THERMAL PARAMETERS FOR MOLECULE 9 (f r a c t i o n a l x 10", Br x 10", H x 10 3, U x 103 A 2) Atom X 1 z Ueq/Ui so Br 92418( 5) -17003{ 4) -46120( 4) 88 0(1 ) 7636( 2) 653( 2) 389( 2) 54 0(2) 1 527 ( 2) 4669( 2) 1 602( 2) 54 0(3) 2222( 2) 5980( 2) 3229( 2) 52 0(4) 8288( 2) 21 82 ( 2) -21 1 ( 2) 61 CO) 4 1 49 ( 4) 4344( 3) 1 408( 3) 47 C(2) 3501 ( 4) 5345( 3) 1 976( 4) 53 C(3) 2636( 3) 4983( 2) 2644( 3) 47 C(4) 3389( 4) 4000( 3) 3666( 3) 50 C(5) 4020( 3) 2991 ( 2) 3094( •3) 45 C(6) 4697 ( 4) 1968( 3) 41 03 ( 3) 60 C(7) 5298( 4) 935( 3) 3533( 4) 61 C(8) 61 75 ( 3) 1 3 1 6 ( 3) 2874( 3) 52 C(9) 5397( 3) 2278( 2) 1 8 1 4 ( 3) 41 COO) 4943 ( 3) 3359( 2) 2435( 3) 41 CO 1 ) 6229( 3) 2327( 3) 921 ( 3) 43 C(12)• 7333( 4) 1 283 ( 3) 1 41 9( 3) 52 CO 3) 6879( 4) 485( 3) 2181 ( 4) 60 C( 14) 4296( 3) 1 874 ( 3) 601 ( 3) 47 CO 5) 5031 ( 3) 2 1 24 ( 2) -261 ( 3) ' 46 C(16) 4722( 5) 2227( 3) -1545( 4) 66 C( 17) 6161 ( 4) 3777 ( 4) 3434( 4) 58 C( 18) 407< 3) 4606( 3) 1 909 ( 4) 58 C( 19) -65I 3) 5692( 2) 2462( 3) 48 C(20) 1 1 31 ( 3) 591 4( 3) 3622( 3) 53 C(21 ) -574! 4) 6684( 3) 1 4 1 2 ( 4) 66 C(22) -1163 < 5) 5491 ( 5) 2932( 5) 79 C(23) 80921 3) 12091 3) -366( 3) 48 C(24) 83 30 3) 4-9-2-( 2.) -1404( : 3) 46: C(25) 8391 4) 1 023 ( 3) -2502< 3) 62 C(26) 8636 ' 4) 377< 3) -3464( 4) 68 C(27) 8857 k 3) -794( 3) -3307I 3) 57 C(28) 881 1 [ 3) -13341 3) -2222< 4) 59 C(29) 8527 [ 3) -684< 3) -1278 < ' 3) 53 H ( 0 1 1 ) 473( 3) 462( 2) 1 02( 3) 54( 8) H(012) 349( 3) 41 0( 2) 71 ( 3) 47( 8) H(021) 294( 3) 593( 3) 1 26 ( 3) 55( 8) H(022) 41 6( 3) 570( 3) 259( 3) 63(10) H(041) 409( 3) 430( 2) 438( 3) 52( 8) H(042) 287( 3) 370( 3) 404( 3) 66(10) H(051) 331 ( 3) 275( 2) 239( 3) 35( 7) H(061) 545( 3) 225( 3) 491 ( 3) 63( 9) cont inue'd". H( 062) 400( 4) 1 76( 3) 446( 4) 84( 11) H( 071 ) 460( 3) 59( 3) 293( 3) 63( 10) H( 072) 581 ( 3) 36( 3) 424( 3) 69( 10) H( 081 ) 688( 3) 1 62( 3) 351 ( 3) 61 ( 10) H( 111) 657( 3) 302( 2) 85( 2) 42( 7) H( 121 ) 806( 3) 1 54( 3) 192 ( 3) 56( 10) H( 131) 624( 4) 4( 3) 1 55( 4) 75( 1 1 ) H( 1 32) 757( 4) -1 ( 3) 275( 3) 65( 10) H( 141) 426( 3) 1 0 5 ( 3) 73( 3) 55( 8) H( 1 42) 345( 3) 228 ( 2) 38( 2) 35( 7) H( 161 ) 534( 3) 245( 3) -1 94( 3) 69( 10) H( 1 62) 386( 4) 2 1 0 ( 3) -2 1 5 ( 3) 71 ( 10) H( 171) 653( 4) 334( 4) 426( 5) 1 03 ( 15) H( 172) 597( 4) 459( 4) 359( 4) 92( 12) H< 1 73) 684( 4) 373( 3) 3 1 2 ( 3) 73( 1 1 ) H< 181 ) -33( 3) 443( 2) 1 08 ( 3) 59( 8) H 182) 67( 3) 390( 3) 264 ( 4) 83( 1 1 ) H [201 ) 1 33( 3) 528( 2) 432( 3) 50< 8) H [202) 91 ( 3) 666 ( 3) 399( 3) 68 9) H (211) -83( 4) 481 ( 4) 351 ( 4) 89 ,14) H [212) -1 47 ( 5) 61 9 ( 4) 335( 5) 1 1 9 (16) H (213) -1 86 ( 5) 522( 4) 2 1 7 ( 5) 1 09 [15) H (221 ) 19( 4) 682( 3) 1 13( 3) 79 (11) H (222) -88( 3) 728( 3) 1 84 ( 3) 57 ( 9) H (223) -1 33 ( 4) 651 ( 3) 62( 4) 89 (12) H (251 ) 821 ( 3) 1 82 ( 3) -256( 3) 61 ( 9) H (261 ) 871 ( 3) 73( 3) -4 1 9 ( 4) 82 (11) H (281 ) 896( 3) -2 1 3 ( 3) -2 1 0 ( 3) 68 (10) H (291 ) 854( 3) -1 06 ( 2) -52( 3) 54 ( 9) TABLE XX. ANISOTROPIC THERMAL PARAMETERS IN MOLECULE 9. (Uij x 10" A*) Atom 1 u 2 2 u 3 3 U i 2 U i 3 u 2 3 Br 1 1 45( 4) 873( 3) 708( 3) -78( 2) 476( 2) -205( 2) 0( 1 ) 557( 13) 464( 1 1 ) 681 ( 13) -27( 10) 355( 1 1 ) -38( 10) 0( 2) 470( 13) 641 ( 13) 51 6( 12) -91 ( 10) 184 ( 11) -21 1 ( 10) o( 3) 487( 12) 540( 12) 548( 12) -60( 10) 2 1 7 ( 10) -1 98 ( 10) 0( 4) 631 ( 15) 480( 13) 794( 15) -1 04 ( 11) 358( 12) -89( 11) C( 1) 476( 19) 481 ( 18) 496 ( 18) -5,9( 15) 225 ( 17) -44( 15) c( 2) 527( 21 ) 471 ( 18) 61 4( 21 ) -39( 17) 266( 18) -47( 17) c( 3) 446( 18) 476( 17) 489( 17) -74( 14) 1 84 ( 15) - 1 54 ( 14) c( 4) 51 8 ( 20) 575( 19) 491 ( 18) -1 27 ( 16) 258( 17) -1 1 6( 16) c( 5) 425( 18) 483( 17) 451 ( 17) -77 ( 14) 1 77( 15) -39( 14) c( 6) 661 ( 23) 632( 21 ) 589( 21 ) -36( 18) 341 ( 20) 42( 17) C( 7) 666( 24) 532< 20) 641 ( 22) 1 5( 19) 31 5( 20) 1 24( 19) C( 8) 497( 20) 520( 18) 530( 18) 2( 15) 223( 17) 38( 15) C( 9) 386( 16) 426( 16) 432( 15) -49( 12) 1 65( 13) -18( .12) C( 10) 350( 16) 456< 16) 424( 15) -70( 12) 1 42( 13) -56( 12) c( 1 1 ) 397( 17) 4 1 2 ( 16) 524( 17) -57( 14) 221 ( 14) -26( 13) C( 12) 460( 20) 516 J B ) 588( 19) -1 6( 16) 228( 17) -57( 16) c( 13) 601 ( 23) 515 19) 648( 22) 1 03( 19) 271 ( 20) 1 06( 18) c( 14) 390( 19) 487 119) 524( 18) -84( 15) 1 50( 15) -98( 14) c( 15) 462( 18) 419 (16) 492( 18) -48( 13) 1 83 ( 15) -30( 13) c( 16) 696( 27) 717 (24) 554( 22) -1 71 ( 20) 21 3( 22) -22( 17) c( 17) 461 ( 21 ) 694 (24) 593( 22) -1 67( 18) 1 77 ( 18) -200( 19) C( 18) 493( 21 ) 643 (22) 604( 21 ) -1 26 ( 17) 1 82 ( 18) -1 78( 18) C( 19) 452( 18) 529 (18) 496 ( 1 7) -7'5( 14) 209'< J 5 ) -80 ( -1 4) C( 20) 505( 21 ) 603 (21 ) 508( 19) -33( 16) 235< 17) -1 45( 17) c< 21 ) 561 ( 24) 601 (23) 706( 25) 34( 19) 1 46( 22) -55( 19) c< 22) 676( 28) 979 (35) 859< 30) -1 80 ( 26) 423( 26) -82( 28) c 23) 368( 17) 434 (18) 61 3( 19) 27( 14) 1 83 < 15) 23( 15) c 24) 358( 17) 446 (17) 575( 18) -30( 13) 1 83 ( 14) 2( 14) c (25) 769( 25) 456 (20) 658< 22) -86< 17) 297< 19) 7( 17) c [26) 855< 27) 647 (24) 605I 22) - 1 23 < 19) 337 20) 38( 18) c (27) 566< 20) 625 (21 ) 5291 19) -59< 16) 239 16) - 1 1 3 < 16) c 128) 633 22) 448 (19) 736 23) -42( 16) 339 (18) -67( 17) c (29) 545 20) 463 (18) 640 21 ) -1 4< 15) 312 (17) 44( 16) 58 F i g u r e 10. S t e r e o v i e w of the p-bromobenzoate d e r i v a t i v e 59 the synthesis of stemodin, and their separation was apparently unnecessary. Of interest now is, the rearrangement mechanism that allows both isomers to y i e l d the same compound, but t h i s is beyond the scope of this thesis. Mean plane ca l c u l a t i o n s , bond lengths and bond angles are l i s t e d in Tables XXI, XXII, XXIII, XXIV, and XXV. A packing diagram i s shown in Figure 11. The c r y s t a l i s held together by van der Waals forces. Comparison of the three structures Whenever the structures of three molecules as similar as those presented so far are solved, i t i s of interest to compare derived quantities, e.g. bond lengths, bond angles and molecular geometry. Bond lengths for these three structures are compared in Table XXVI. Upon inspection of t h i s table, i t is immediately obvious that the estimated standard deviations (e.s.d.'s) in molecule 5 are about three times as great as: those in molecules 4_ and 9. This i s not surprising; the c r y s t a l structure of 5_ i s the least accurate of the three, mainly as the c r y s t a l was so poor that only 20% of the c o l l e c t e d r e f l e c t i o n s could be considered observed (as opposed to 60% in the other two structures). Consistent with t h i s , the R values for the structure of molecule 5 are s l i g h t l y larger than those for 4 and 9, especially when the unobserved r e f l e c t i o n s are included. The bond lengths compare extremely well with each other. Only one pair shows a s i g n i f i c a n t difference ( i . e . , has a TABLE XXI. MEAN PLANES IN THE VICINITY OF THE CYCLOBUTYL RING IN MOLECULE 9 Equations of planes (!X+mY+nZ=p) plane 1 2 3 4 -0.2436 -0.2024 -0.4777 -0.6224 m 0.9697 0.9377 -0.6437 -0.0055 n -0.0669 -0.2825 -0.5979 -0.7827 0.9328 -0.9354 -5.6270 -5.9661 Deviations f rom planes ( A ) atom C(8) C(9) C ( 1 1 ) C( 12) C( 13) C( 14) C( 15) C( 16) 0.248(3) 0.000(3)* 0.000(4)* 0.000(3)* 0.084(4) 0.000(3)* 0.000(3)* 0.000(3)* 0.230(3) 0.601(4) 0.036(3)* 0.036(3)* •0.041(3)* 0.038(4)* •0.610(4) 0.000(4) 0.985(3) 0.894(3) 0.000(4) 0.000(4) *atoms included in plane cal c u l a t i o n s Angles between- normals- to- the- planes- planes (1) and (2) planes (2) and (3) planes (3) and (4) 14.5° 108.7° 34.6° 61 TABLE XXII. BOND LENGTHS( A ) OF NON-HYDROGEN ATOMS IN MOLECULE 9 Bond Distance Bond Distance Br -C(27) 1.906(3) C(9) -COD 1 .57.1 (4) 0(1 ) -CO 2) 1.453(4) C(9) -CO 4) 1 .566(4) 0(1 ) -C(23) 1.336(4) COO) -CO 7) 1.540(4) 0(2) -C(3) 1.430(3) c d 1) -CO 2) 1 .529(4) 0(2) -C(18) 1 .40.6(4) C( 1 1 ) -C(15) 1 .520(4) 0(3) -C(3) 1.429(3) C(12) -C(13) 1 .521(5) 0(3) -C(20) 1.431(3) C( 14) -C05) 1.507(4) 0(4) -C(23) 1.209(3) CO 5) -C(16) 1 .315(5) C(1 ) -C(2) 1.530(4) C( 18) -C(19) 1 .515(4) c ( i ) -COO) 1.533(4) C( 19] -C(20) 1 .513(4) C(2) -C(3) 1.508(4) C( 19) -C(21) 1.531(5) C(3) -C(4) 1.521(5) C(19) -C(22) 1.529(5) C(4) -C(5) 1.530(4) C(23) -C(24) 1 .484(4) C(5) -C(6) 1.537(4) C(24' -C(25) 1.386(4) C(5) -COO) 1.560(4) C(24 >-C(29) 1.377(4) C(6) -C(7) 1.533(5) C(25 )-C(26) 1.373(5) C{7y -C(8) 1.520(5) C(26 )-C(27) 1.374(5) C(8 -C(9) 1'.532(4) C(27 )-C(28) 1.370(5) C(8 >-C(13) 1 .521(4) C(28 }-C(29) 1.378(4) C(9 )-C(10) 1 .542(4). 62 TABLE XXIII. BOND ANGLES(0) OF NON-HYDROGEN ATOMS IN MOLECULE 9 Bonds Angle Bonds Angle C( 12) - 0 ( 1 ) - c ( 2 3 ) 1 1 7 . 0 ( 2 ) C ( 9 ) - c ( 11) - c ( 12) 1 0 4 . 1 (2 ) C ( 3 ) - 0 ( 2 ) - c ( 18) 116.1(2) C ( 9 ) - c ( 11) - c ( 15) 8 8 . 6 ( 2 ) C (3 ) - 0 ( 3 ) - c ( 2 0 ) 1 1 4 . 6 ( 2 ) C ( 1 2 ) - c ( 11) - c ( 15). 1.1 4 . 3(3.) C ( 2 ) -C(1 ) - c ( 10) 1 1 3 . 2 ( 3 ) 0 ( 1 ) - c ( 12) - c ( 1 1 ) 1 1 4 . 9 (3 ) C (1 ) - C ( 2 ) - c ( 3) 1 1 2 . 6 ( 3 ) 0 ( 1 ) - c ( 12) - c ( 13) 1 0 8 . 3 ( 3 ) 0 ( 2 ) - C ( 3 ) - o ( 3) 1 1 0 . 3 ( 2 ) C O D - c ( 12) - c ( 13) 1 0 6 . 7 ( 3 ) 0 ( 2 ) - C ( 3 ) - c ( 2) 1 0 5 . 4 ( 2 ) C ( 8 ) - c ( 13) - c ( 12) 1 0 2 . 4 ( 3 ) 0 ( 2 ) - C ( 3 ) - C ( 4) 1 1 2 . 2 ( 2 ) C ( 9 ) - c ( 14) - c ( 15) 8 9 . 2 ( 2 ) 0 ( 3 ) - C ( 3 ) - c < 2) 1 0 5 . 5 ( 2 ) C O D - c ( 15) - c ( 14) 9 2 . 5 ( 2 ) 0 ( 3 ) -C (3) - c< 4) 1 1 1 . 9 ( 2 ) C O 1) - c ( 15) - c ( 16) 1 3 3 . 2 ( 3 ) C ( 2 ) - C ( 3 ) - c ( 4) 1 1 1 . 1 ( 3 ) C ( 1 4 ) - c ( 15) - c ( 16) 1 3 4 . 1 ( 3 ) C ( 3 ) - C ( 4 ) - C ( 5) 1 1 2 . 6 ( 2 ) 0 ( 2 ) - c ( 18) - c ( 19) 1 1 2 . 8 ( 3 ) C ( 4 ) - C ( 5 ) - c< 6) 1 1 2 . 4 ( 2 ) C ( 1 8 ) - c ( 19) - c ( 2 0 ) 1 0 5 . 4 ( 3 ) C (4) - C ( 5 ) -c< 10) 1 1 2 . 0 ( 2 ) C ( 1 8 ) - c ( 19) - c ( 2 1 ) 1 1 0 . 5 ( 3 ) C (6) - C ( 5 ) - C l 10) 1 1 3 . 0 ( 3 ) C ( 1 8 ) - c ( 19) - c ( 2 2 ) 1 0 9 . 0 ( 3 ) C ( 5 ) - C ( 6 ) - c : 7 ) 1 1 3 . 1 ( 3 ) C ( 2 0 ) - c ( 19) - C l 21 ) 1 1 1 . 2 ( 3 ) C ( 6 ) - C ( 7 ) - c , 8 ) 1 0 9 . 5 ( 3 ) C ( 2 0 ) - c ( 19) - C l 2 2 ) 1 1 0 . 2 ( 3 ) C ( 7 ) - C ( 8 ) - c [9) 1 1 0 . 9 ( 3 ) C ( 2 1 ) - c< 19) - C l 22) 1 1 0 . 3 ( 3 ) C ( 7 ) - C ( 8 ) - c [13) 1 2 1 . 8 ( 3 ) 0 ( 3 ) - c< 2 0 1 - C l 19) 1 1 1 . 2 ( 2 ) C ( 9 ) - C ( 8 ) - c [13) 1 0 3 . 5 ( 2 ) 0 ( 1 ) - C l 23 - 0 1 4) 1 2 3 . 5 ( 3 ) C (8) - C ( 9 ) - c [10) 1 11: . .012) 0 ( 1 ) - c i 23 >-G< 2 4 ) 1 1 2 . 1 ( 3 ) C ( 8 ) - C ( 9 ) - c [ 1 1 ) 1 0 5 . 9 ( 2 ) 0 ( 4 ) -c< 23 >-c 2 4 ) 1 2 4 . 3 ( 3 ) C ( 8 ) - C ( 9 ) - c 0 4 ) 1 1 2 . 9 ( 2 ) C ( 2 3 ) -c< 24 l - C 2 5 ) 1 1 8 . 9 ( 3 ) C( 10) - C ( 9 ) - c 0 1) 1 2 1 . 1 ( 2 ) C ( 2 3 ) - c 24 ) - c 2 9 ) 121 . 4 ( 3 ) C( 10) - C ( 9 ) - c 0 4 ) 1 1 5 . 7 ( 2 ) C ( 2 5 ) - c 24 >-c [29) 1 1 9 . 7 ( 3 ) C ( 1 1 ) - C ( 9 ) - c 0 4 ) 8 8 . 3 ( 2 ) C ( 2 4 ) - c ' 2 5 ) - c [26) 1 2 0 . 0 ( 3 ) C ( 1 ) - C ( 1 0 ) - c (5) 1 0 8 . 4 ( 2 ) C ( 2 5 ) - c , 2 6 ) - c [27) 1 1 9 . 4 ( 3 ) C ( 1 ) - C ( 1 0 ) - c (9 ) 1 1 2 . 8 ( 2 ) Br - c [27 ) - c [26) 1 1 9 . 8 ( 3 ) C (1 ) - C ( 1 0 ) - c 0 7 ) 1 0 8 . 0 ( 3 ) Br - c [27 ) - c [28) 1 1 8 . 8 ( 2 ) C ( 5 ) - C O O ) - c (9 ) 1 0 5 . 3 ( 2 ) C ( 2 6 ) - c [27 ) - c [ 2 8 ) 1 2 1 . 3 ( 3 ) C ( 5 ) - C O O ) - c 0 7 ) 1 1 2 . 7 ( 3 ) C ( 2 7 ) - c [28 ) - c [ 2 9 ) 1 1 9 . 1 ( 3 ) C ( 9 ) - C O O ) - c 0 7 ) 1 0 9 . 6 ( 2 ) C ( 2 4 ) - c [29 ) - c [ 2 8 ) 1 2 0 . 4 ( 3 ) 63 TABLE XXIV. BOND LENGTHS( A ) OF HYDROGEN ATOMS IN MOLECULE 9 Bond Distance Bond Distance C(1) -H(011) 0.98(3) C(16)-H(162) 0.97(4) C(1) -H(012) 0.92(3) C(17)-H(171) 0.95(4) C(2) -H(021) 0.98(3) C(17)-H(172) 0.98(4) C(2) -H(022) 0.94(3) C(17)-H(173) 0.92(4) C(4) -H(041) 0.98(3) C(18)-H(181) 1.01(3) C(4) -H(042) 0.92(3) C(18)-H(182) 1.08(4) C(5) -H(051) 0.95(3) C(20)-H(201) 1.01(3) C(6) -H(061) 1 .05(3) C(20)-H(202) 1.00(3) C(6) -H(062) 1.04(4) C(21)-H(211) 1.03(4) C(7) -H(071) 0.96(4) C(21)-H(212) 0.93(3) C(7) -H(072) 0.97(4) C(21)-H(213) 1.00(4) C(8) -H(081) 0.95(3) C(22)-H(221) 0.96(4) C(11)-H(111) 0.97(3) C(22)-H(222) 1.01(5) C <12)-H(12 1 ) ,0.88(3) C(22)-H(223) 0.99(5) C(13)-H(131) 1 .00(4) C(25)-H(251) 0.93(3) C(13)-H(132) 0.90(4) C(26)-H(261) 0.93(4) C(14)-H(141) 0.99(3) C(28)-H(281) 0.93(3) C(14)-H(142) 0.92(3) C(29)-H(291) 0.93(3) C(16)-H(161) 0.99(3) TABLE XXV. BOND ANGLES(0) INVOLVING HYDROGEN ATOMS IN MOLECULE 9 Bonds Angle C( 2) - c ( 1) -H( 011) 1 09( 2). C( 2) - c ( 1) -H( 012) 1 08 ( 2) C( 10) - c ( 1) -H( 01 1 ) 1 10( 2) C( 10) - c ( 1) -H( 012) 1 1 1 ( 2) H( 011) - c ( 1) -H( 012) 1 06( 2) C( 1 ) - c ( 2) -H( 021 ) 1 10( 2) C( 1 ) - c ( 2) -H( 022) 1 10( 2) C( 3) - c ( 2) -H( 021 ) 1 08 ( .2) C( 3) - c ( 2) -H( 022) 1 09 ( 2) H( 021 ) - c ( 2) -H( 022) 1 07( 3) C( 3) - c ( 4) -H< 041 ) 1 07( 2) C( 3) - c ( 4) -H( 042) 1 1 4( 2) C( 5) - c ( 4) -H( 041 ) 1 09< 2) C( 5) - c ( 4) -H( 042) 1 06( 2) H( 041 ) - c ( 4) -H( 042) 1 08I 3) C( 4) - c ( 5) -H( 051 ) 1 06< 1 ) C( 6) - c ( 5) -Hi 051 ) 1 081 1 ) C< 10) - c ( 5) -Hi 051 ) 1 051 1 ) C( 5) - c ( 6) -H( 061 ) 1 07 2) Cl 5) -C( 6) -H< 062) 1 07 (2) Cl 7) - c ( 6) -H< 061 ) 1 10 (2) Cl 7) - c ( 6) -H 062) 1 1 2 (2) H 061 ) -c< 6) -H (062) 1 07 (3) C ' 6 ) - c 7) -H (071 ) 1 09 (2) c I6) - c 7) -H (072) 1 09 (2) c (8) - c 7) -H (071 ) 1 1 2 (2) c (8) - c (7) -H (072) 1 10 (2) H (071 ) - c (7) -H (072) 106 (3) c (7) - c (8) -H (081 ) 1 10 (2) c (9) - c (8) -H (081 ) 1 06 (2) c (13) - c (8) -H (081 ) 1 03 (2) c (9) - c ( 1 1 )-H (111) 1 20 (2) c (12) - c ( 1 1 )-H (111) 1 1 2 (2) c (15) - c ( 1 1 )-H (111) 1 1 6 (2) 0 (1 ) - c ( 1 2 )-H (121) 1 07 (2) c (11) - c ( 1 2 )-H (121) 1 07 (2) c (13) - c ( 1 2 )-H ( 121 ) 1 1 3 (2) c (8) - c ( 1 3 )-H (131) 110 (2) c (8) - c (13 )-H ( 1 32) 1 13 (2) c (12) - c (13 )-H (131) 1 10 (2) c (12) - c ( 1 3 )-H (1 32) 1 1 2 (2) H (131) - c ( 1 3 )-H (132) 1 09 (3) c (9) - c ( 1 4 )-H (141) 1 1 1 (2) Bonds Angle c( 9) - c ( 14) -H( 1 42) 1 1 7( 2) c( 15) - c ( 14) -H( 141 ) 1 1 5( 2) c( 15) - c ( 14) -H( 1 42) 1 17( 2) H( 141) - c ( 14) -H( 1 42) 1 07( 2) c( 15) - c ( 16) -H( 161 ) 1 22 ( 2) c( 15) - c ( 16) -H( 1 62) 1 20( 2) H( 161 ) - c ( 16) -H( 1 62) 1 18( 3) c( 10) - c ( 17) -H( 171) 1 1 3 ( 3) C( 10) -c'( 17) -H'( 1 72) 1 12( 2) C( 10) - c ( 17) -H( 1 73) 1121 2) H( 171 ) - c ( 17) -H( 1 72) 1 09 ( 3) H( 171) - c ( 17) -H( 1 73) 1061 3) H( 1 72) - c ( 17) -H( 1 73) 1 041 3) 0( 2) - c ( 18) -H( 181 ) 1091 2) 0( 2) - c ( 18) -H( 1 82) 1081 2) C( 19) - c ( 18) -H( 181 ) 1 101 2) C< 19) - c ( 18) -H( 182) 1091 2) H( 181 ) - c ( 18) -H( 1 82) 109 3) 0< 3) - c ( 20) -H( 201 ) 1 1 4 2) 0< 3) - c ( 20) -H( 202) 1 07 (2) C< 19) - c ( 20) -H( 201 ) 107 (2) Cl 19) -c< 20) -H( 202) 1 10 (2) H 201 ) -C( 20) -HI 202) 1 08 (2) C , 19) -c< 21; -Hi 211) 109 (2) C I 19) -Cl 21; -HI 212) 1 03 (2) c ( 19) - e '21 ' -H>< 213) 11 1-('20 H (21 1 ) - c 21 -HI 212) 1 1 5 (3) H (211 ) - c ,21 >-H 213) 1 10 (3) H (212) - c ,21 -H 213) 1 10 (3) C (19) - c (22 >-H 221 ) 1 07 (2) C (19) - c (22 )-H 222) 1 1 1 (3) C (19) - c (22 >-H (223) 107 (3) H (221 ) - c (22 )-H (222) 1 14 (3) H (221 ) - c (22 )-H (223) 101 (3) H (222) - c (22 )-H (223) 1 1 6 (3) C (24) - c (25 )-H (251 ) 1 1 7 (2) C (26) - c (25 )-H (251 ) 123 (2) C (25) - c (26 )-H (261 ) 1 20 (2) c (27) - c (26 )-H (261 ) 1 20 (2) c (27) - c (28 )-H (281 ) 122 (2) c (29) - c (2'8" )-H (281 ) 1 19 (2) c (24) - c (29 )-H (291 ) 121 (2) c (28) - c (29 )-H (291 ) 118 (2) 65 F i g u r e 1 1 . P a c k i n g diagram of t h e p-bromobenzoate d e r i v a t i v e TABLE XXVI. COMPARISONS OF EQUIVALENT BOND LENGTHS( A ) IN MOLECULES 4 , 5 , AND 9 Bond 4 5 9 0(1)-C(12) 1.199(3) 1.229( 09) 0(2)-C(3) 1.420(2) 1.428( 09) 1.430(3) 0(2)-C(18) 1.428(3) 1.428( 10) 1.406(4) 0(3)-C(3) 1.424(2) 1.427( 08) 1.429(3) O(3)-C(20) 1.423(3) 1.415( 09) 1 .431(3) C(1)-C(2) 1 .524(3). 1.515( 10). 1.530(4) C(1)-C(10) 1 .538(3) 1 . 5 3 6 ( 1 1 ) 1.533(4) C(2)-C(3) 1.509(3) 1.526( 1 1 ) 1.508(4) C(3)-C(4) 1.523(3) 1.501( 1 1 ) 1.521(5) C(4)-C(5) 1.529(3) 1.526< 10) 1.530(4) C(5)-C(6) 1.529(3) 1 . 5 1 6 < 11) 1.537(4) C(5)-C(10) 1.546(3) 1.550( 10) 1.560(4) C(6)-C(7) 1.514(3) 1.533( 10) 1.533(5) C(7)-C(8) 1.528(3) 1 . 51 9 < 1 1 ) 1.520(5) C(8)-C(9) 1.544(3) 1 .528 1 1 ) 1.532(4) C(8)-C(13) 1.528(3) 1 .538 ,11) 1.521(4) C(9)-C(10) 1.544(3) 1 .532 n o ) 1.542(4) C(9)-C(11) 1.571(3) 1 .577 M0) 1.571(4) C(9)-C(14) 1.563(3) 1 .571 o o ) 1.566(4) C(10)-C(17) 1.538(3) 1 .549 O o ) 1.540(4) CO 1 )-C( 1 2) 1.515(4) 1 .523 O 0 ) 1.529(4) CO 1 )-C( 15) 1.515(4) 1 .534 (11) 1.520(4) C(12)-C(13) 1.511(4) 1 .487 0 2 ) 1.521(5) CO 4)-C( 1 5) 1.496(4) 1 .521 (11) 1.507(4) C(15)-C(16) 1.324(4) 1.312 (11) 1.315(5) C(18)-C(19) 1.521(3) 1 .546 (10) 1.515(4) C(19)-C(20) 1 .521(3) 1 .520 O D 1.513(4) C(19)-C(21) 1.525(3) 1.510 0 3 ) 1.531(5) C( 19)-C(22) 1.518(4) 1 .529 0 2 ) 1.529(5) • 67 difference greater than 3.0 0(2)-C(l8) has lengths 1.428(3) (in 4) and 1.406.(4) A (in 9) , a difference of only 0.022 A (about 4.5«y) and so of l i t t l e importance. The largest absolute difference i s for C(18)-C(19), which has lengths 1.546(10) (in 5) and 1.515(4) A (in 9), a difference of 0.031 A, but th i s only corresponds to about 3.0<*. More interesting trends may be found by comparing the bond angles (Table XXVII). Because of the larger e.s.d.'s in 5, the closest match is most often found between the values from 4̂  and 9. However, bond angles involving 0(2) and C(18) in 9_ again show s i g n i f i c a n t but most probably unimportant deviations. This might be related to the s l i g h t electron density (0.4 electrons/A 3) located near t h i s ring. Important deviations do occur when we examine bond angles in the v i c i n i t y of the four-membered ring. Angles involving atoms in the six-membered ring closest to the cyclobutyl ring are very similar in 5 and 9 but very d i f f e r e n t in 4. It seems very l i k e l y that the magnitudes of these angles are affected by the orientation of the four-membered ring. This effect is especially pronounced in the angles marked with an asterisk (*) in Table XXVII. In examining the angles in the five-membered ring, one notices that t h i s time the odd angles seem to come from the p-bromobenzoate derivative, 9. This is not too surprising as the hybridization of C(12) is d i f f e r e n t in 9. The angles that are affected by t h i s are marked with a plus sign (+) in Table XXVII. The cyclobutyl angles are a l l f a i r l y similar and do not deviate greatly from' the free cyclobutyl' a n g l e 2 2 , 89.3°. Mean plane calculations have been presented for planes in 6 8 TABLE XXVII. COMPARISON OF BOND ANGLES(0) IN MOLECULES 4 , 5 AND 9 Bonds 4 5 9 C ( 3 > - o ( 2 ) - C d 8 ) 1 1 4 . 3 ( 1 ) 1 1 3 . 6 ( 6 ) 1 1 6 . 1 ( 2 ) C ( 3 > - o ( 3 ) - C ( 2 0 ) • 1 1 4 - 3 ( 2 ) 1 1 3 . 9 ( 7 ) 1 1 4 . 6 ( 2 ) C ( 2 ) - c ( 1 ) - C O 0 ) 112.8( 2 ) 1 1 2 . 9 ( 8 ) 1 1 3 . 2 ( 3 ) C ( 1 > - c ( 2 ) - C ( 3 ) 1 1 2 . 4 ( 2 ) 1 1 1 . 8 ( 7 ) 1 1 2 . 6 ( 3 ) 0 ( 2 ) - c ( 3 ) - 0 ( 3 ) 1 1 0 . 2 ( 1 ) 1 0 9 . 7 ( 6 ) 1 1 0 . 3 ( 2 ) 0 ( 2 ) - c ( 3 ) - C ( 2 ) 1 0 5 . 8 ( 2 ) 1 1 2 . 0 ( 7 ) 1 0 5 . 4 ( 2 ) 0 ( 2 ) - c ( 3 ) - C ( 4 ) 1 1 2 . 0 ( 2 ) 1 0 5 . 8 ( 7 ) 1 1 2 . 2 ( 2 ) 0 ( 3 ) - c ( 3 ) - C ( 2 ) 1 0 5 . 1 ( 2 ) 1 1 2 . 0 ( 7 ) 1 0 5 . 5 ( 2 ) 0 ( 3 ) - c ( 3 ) - C ( 4 ) 1 1 2 . 2 ( 2 ) 1 0 6 . 0 ( 8 ) 1 1 1 . 9 ( 2 ) C ( 2 ) - c ( 3 ) - C ( 4 ) 1 1 1 . 2 ( 2 ) 1 1 1 . 0 ( 7 ) 1 1 1 . 1 ( 3 ) C ( 3 ) - c ( 4 ) - C ( 5 ) 1 1 2 . 3 ( 2 ) 1 1 3 . 3 ( 7 ) 1 1 2 . 6 ( 2 ) C ( 4 ) - c ( 5 ) - C ( 6 ) 1 1 1 . 7 ( 2 ) 1 1 2 . 7 ( 7 ) 1 1 2 . 4 ( 2 ) C ( 4 ) - c ( 5 ) - C O 0 ) 1 1 3 . 1< 2 ) * 1 1 2 . 0 ( 6 ) 1 1 2 . 0 ( 2 ) C ( 6 ) - c ( 5 ) - C ( 1 0 ) 111.41 2 ) * 1 1 3 . 3 ( 6 ) 1 1 3 . 0 ( 3 ) C ( 5 ) - c ( 6 ) - C ( 7 ) 1 1 0 . 5 1 2 ) * 1 1 3 . 2 ( 8 ) 1 1 3 . 1 ( 3 ) C ( 6 ) - c < 7 ) - C ( 8 ) 1 1 5 . 3 < 2 ) * 1 0 7 . 5 ( 7 ) 1 0 9 . 5 ( 3 ) C ( 7 ) - c ( 8 ) - C ( 9 ) 111.51 2 ) 1 1 1 . 1 ( 7 ) 1 1 0 . 9 ( 3 ) C ( 7 ) - c < 8 ) - C 0 3 ) 1 0 8 . 3 2 ) * 1 2 0 . 7 ( 8 ) 1 2 1 . 8 ( 3 ) C ( 9 ) - c < 8 ) - C O 3 ) 1 0 4 . 6 2 ) 1 0 5 . 9 ( 7 ) 1 0 3 . 5 ( 2 ) + C ( 8 ) - c , 9 ) - C O 0 ) 1 1 4 . 7 [ 2 ] * 1 1 1 . 0 ( 7 ) 1 1 1 . 0 ( 2 ) C ( 8 ) - c [ 9 ) - C ( 1 1 ) 1 0 4 . 5 [ 2 ] 1 0 4 . 0 ( 6 ) 1 0 5 . 9 ( 2 ) + C ( 8 ) - c ( 9 ) - C O 4 ) 1 1 4 . 3 (2 ) 1 1 3 . 4 ( 7 ) 1 1 2 . 9 ( 2 ) C ( 1 o ) - c ( 9 ) - C ( 1 1 ) 1 1 8 . 8 [2] * 1 2 1 . 7 ( 7 ) 1 2 1 . 1 ( 2 ) C ( 1 o ) - c ( 9 ) - C ( 1 4 ) 1 1 3 . 7 [2] * 1 1 6 . 4 ( 7 ) 1 1 5 . 7 ( 2 ) C ( 1 1 ) - c ( 9 ) - C ( 1 4 ) 8 8 . 0 (2 8 8 . 3 ( 6 ) 8 8 . 3 ( 2 ) C ( 1 ) - c 0 0 ) - C ( 5 ) 1 0>7\ 7 (-.2. 1 0 7 . 8 ( 6 ) 1 0 8 . 4 ( 2 ) C O ) - c O 0 ) - C ( 9 ) 1 1 1 . 1 (2 * 1 1 2 . 8 ( 7 ) 1 1 2 . 8 ( 2 ) C O ) - c ( 1 0 ) - C ( 1 7 ) 1 0 9 . 7 (2 1 0 8 . 6 ( 7 ) 1 0 8 . 0 ( 3 ) C ( 5 ) - c O 0 ) - C ( 9 ) 1 0 9 . 3 (2 * 1 0 5 . 6 ( 6 ) 1 0 5 . 3 ( 2 ) C ( 5 ) - c O 0 ) - C ( 1 7 ) 111.2 (2 * 1 1 2 . 4 ( 6 ) 1 1 2 . 7 ( 3 ) C ( 9 ) - c ( 1 0 ) - C ( 1 7 ) 1 0 7 . 8 ( 2 i * 1 0 9 . 8 ( 6 ) 1 0 9 . 6 ( 2 ) C ( 9 ) - c (11)-C(12) 1 0 5 . 1 ( 2 i * 1 0 4 . 2 ( 7 ) 1 0 4 . 1 ( 2 ) C ( 9 ) - c (11)-C(15) 8 8 . 3 ( 2 8 9 . 6 ( 6 ) 8 8 . 6 ( 2 ) C O 2 ) - C ( 1 1 ) - C ( 1 5 ) 1 1 0 . 8 ( 2 1 0 6 . 9 ( 7 ) 1 1 4 . 3 ( 3 ) 0 ( 1 ) - c (12) -C( 1 1 ) 1 2 5 . 0 ( 2 1 2 4 . 5 ( 9 ) - 0 ( 1 ) - c ( 1 2 ) - C ( 1 3 ) 1 2 6 . 1 ( 2 1 2 5 . 9 ( 8 ) - C O 1 ) - c 0 2 ) - C ( 1 3 ) 1 0 8 . 9 ( 2 1 0 9 . 5 ( 7 ) 1 0 6 . 7 ( 3 ) + C ( 8 ) - c (1 3 ) - C O 2 ) 1 0 3 . 0 ( 2 1 0 1 . 1 ( 7 ) 1 0 2 . 4 ( 3 ) C ( 9 ) - c ( 1 4 ) - C O 5 ) 8 9 . 3 ( 2 9 0 . 3 ( 6 ) 8 9 . 2 ( 2 ) C O D - c ( 1 5 ) - C ( 1 4 ) 9 2 . 6 ( 2 9 1 . 7 ( 6 ) 9 2 . 5 ( 2 ) C O 1 ) - c (1 5 ) - C ( 1 6 ) 1 3 1 . 9 " ('4 1 3 2 . 0 ( 9 ) 1 3 3 . 2 ( 3 ) Continued... 69 C ( 1 4 ) -C(15) -C(16) 135 .2(4) 1 36. 3(9) 134 .1(3) 0(2) -C(18) -C ( 1 9 ) 1 1 1 .6(2) 113. 4(7) 1 12 .8(3) C ( 1 8 ) -C(19) -C(20) 1 05 .6(2) 105. 1(7) 105 .4(3) C( 18) -C(19) -C(21) 110 .3(2) 109. 6(9) 1 1 0 .5(3) C( 18) -C(19) -C(22) 109 .6(2) 110. 8(8) 109 .0(3) C(20) -C(19) -C(21) 1 1 0 .3(2) 111. 1(8) 1 1 1 .2(3) C(20) -C(19) -C(22) 1 09 .5(2) 1 09. 0(8) 1 1 0 .2(3) C(21 ) -C(19) -C(22) 1 1 1 .4(2) 111. 2(8) 1 10 .3(3) 0(3) -C(20) -C(19) 1 1 1 .5(2) 112. 2(8) 1 1 1 .2(2) 70 the v i c i n i t y of the cyclobutyl ring for a l l three structures. The envelope t i p of the 5-membered ring is always, ori.e.nted in the same di r e c t i o n as the cyclobutyl ring. The change of hybridization at C(12) in the p-bromobenzoate derivative a f f e c t s the geometry of the 5-membered ring only s l i g h t l y - the envelope t i p i s bent down 35 and 36° in 4 and 5, and 39° in 9. When 0(1) is doubly bound to C(12) i t i s on the opposite side of. plane 3 (the 5-membered ring) to the envelope t i p . The cyclobutyl ring is folded away from the envelope t i p along the C(11)..,C(14) axis in every structure, although the degree of folding varies - 14°, 4.3° and 12.7° in 4, 5, and 9 respectively. The angle between the cyclobutyl and 5-membered rings is about 109° for a l l three structures. For the p-bromobenzoate derivative, the phenyl group i s oriented at 22° to the carboxyl moiety (Table XXVIII). The bromine l i e s in the phenyl plane. With the determination of these three c r y s t a l structures, the i d e n t i t i e s of 4̂  and 5 have been firmly established. After three structures the conclusion was e s s e n t i a l l y the same as after one, but the value of investigating the possible trans- fused adduct should not be underestimated. As well as determining the structure of the second eluted isomer, the last two structures also confirmed the existence of an unusual rearrangement mechanism which i s s t i l l under investigation. 71 TABLE XXVI11. MEAN PLANES OF THE P-BROMOBENZOATE MOIETY IN MOLECULE 9 Equations of planes (lX+mY+nZ=p) plane 1 m 1 -0.8726 -0.0174 -0.4881 -7.8953 2 -0.7206 0.3002 -0.6250 -6.0556 Deviations from planes. ( A ) atom 1 2 0(1) 0.368(2) 0.000(2)* 0(4) -0.464(2) 0.000(2)* C(23) -0.067(3) 0.001(3)* C(24) -0.007(3)* 0.000(4)* C(25) -0.009(4)* 0.421(4) C(26) 0.018(4)* 0.405(4) C(27) 0.007(4)* -0.069(4) C(28) -0.002(4)* -0.500(4) C(29) 0.009(4)* -0.446(4) Br -0.0002(5)* -0.1398(5) *atoms included in plane calculations Angles between normals to the planes planes (1) and (2) : 21.8° CHAPTER 3 THE CRYSTAL STRUCTURE OF CAMPHOR-1,4-HOMOENOL P-BROMOBENZOATE 73 I n t r o d u c t i o n and p r e p a r a t i o n In i n v e s t i g a t i o n s of homoenolization of b i c y c l i c k e t o n e s 2 3 , i t was noted that the C(3), C(6), C(8) and C(10) hydrogen atoms i n camphor underwent exchange (prolonged treatment with KOBu/HOBu, 185-250°C, s e a l e d tube), and the intermediacy of a h i g h l y s t r a i n e d 1,4-homoenol was proposed to account f o r the exchange at the C(8) p o s i t i o n . During recent attempts to extend the use of camphor i n m o n o t e r p e n o i d 2 * " 2 6 and s e s q u i t e r p e n o i d 2 7 s y n t h e s i s , a new compound was obt a i n e d (treatment of 8- bromocamphor with Ca/NH 3/CH 3OH, -78°C, y i e l d 45%, camphor 33%) which had s p e c t r a l p r o p e r t i e s 2 8 i n d i c a t i v e of the 1,4-homoenol s t r u c t u r e (J_, R = H). In order to v e r i f y t h i s s t r u c t u r e , an x- ray a n a l y s i s was performed on the p-bromobenzoate d e r i v a t i v e , camphor-1 ,4-homoen'ol p-bromobenzoate (J_, R = COC 6H sBr). 9 8 " The p-bromobenzoate d e r i v a t i v e was p r e p a r e d 2 8 by s t i r r i n g a s o l u t i o n of camphor-1 ,4-homoenol (]_„ R = H, 250 mg) and p- bromobenzoyl c h l o r i d e (1.0 g) i n 2 mis of dry methylphosphoramide (under N 2, 20°C, 24 h r s ) . A f t e r d i l u t i o n with water, e x t r a c t i o n with e t h e r , and washing of the e x t r a c t with sodium bicar b o n a t e s o l u t i o n , d r y i n g and eva p o r a t i o n 74 produced a yellow semi-solid. P u r i f i c a t i o n of t h i s by chromatography over alumina yielded a colorless o i l which, c r y s t a l l i z e d from petroleum ether to give the desired product. Spectral and a n a l y t i c a l properties of this derivative agreed with the proposed s t r u c t u r e 2 8 . Experimental X-ray photography showed, that along the hOO,. OkO, and 001 axes r e f l e c t i o n s were systematically absent when h, k, and 1 were respectively odd, indicating the presence of three mutually perpendicular twofold screw axes, and hence that the c r y s t a l must be of the orthorhombic space group P2,2 12 l. The intensity data were co l l e c t e d using graphite- monochromatized MoKc radiation and an u-(4/3)8 scan technique with an o-scan angle of (0.8 + 0.35 tan 6)°. The v e r t i c a l and horizontal aperture widths were 4 mm and (2.5 + tan 6)mm, respectively. The' i n t e n s i t i e s of- three standard', reflections; (2 0 -7, -1 1 -7, and 2 0 -3) were measured every one hour of x- ray exposure time and were used to scale the data although variations were small. The orientations of another three r e f l e c t i o n s (2 1 -10, 0 4 -8, and 2 0 -8) were checked every 100 re f l e c t i o n s , and reorientation occurred i f the difference between observed and calculated scattering vectors was greater than 0.05°. In the range 0 < 6 < 25°, 700 out of 1645 re f l e c t i o n s c o l l e c t e d had l/tf(I) > 3.0 and were considered observed. In the refinement, only the r e f l e c t i o n s in the range 75 0 < 6 < 23° were used, where 697 out of 1300 (53.6%) were observed. The c e l l parameters were refined by leas.t-sq.ua.res methods using the sin6/X. values of 25 re f l e c t i o n s in the range 6 < 0 < 14°, and appear with other c r y s t a l data in Table XXIX. The linear absorption c o e f f i c i e n t v is f a i r l y large and an ***************************************** TABLE XXIX. CRYSTAL DATA FOR CAMPHOR-P-BROMOBENZOATE C l 7 H 1 9 B r 0 2 f.w. = 344.5 Orthorhombic Z = 4 space group = P2,2 12, a = 6.875(1) F(000) = 688 b = 8.522(2) . X = 0.71073 A c = 26.658(6) A „ = 25.5 cm"1 V = 1562 A 3 Dc = 1.32 g/cc **************************************************************** absorption correction i s in order. The c r y s t a l shape was approximated by 11 faces (see figure 12). 184 sampling points were used with air average - spac ing of - 5.0- x 1 0" 3 cm- in a c r y s t a l of volume 0.0205 mm3 and the resulting transmission factors ranged from 0.450 to 0.633. The i n t e n s i t i e s were corrected for absorption, as well as for Lorentz and pola r i z a t i o n e f f e c t s . The structure was solved by Patterson and di r e c t methods. Direct methods were used because of an eagerness to elucidate the structure, and the Patterson map was i n i t i a l l y miscalculated. Later a correct Patterson map was used to arrive at the same set of bromine positions. The 500 highest E's obtained by following the minimum p l a n e v e r t i c e s d i s t a n c e from c e n t r e (mm) 1 0 0 1,2,3,4,5 0. 200 0 1 0 6,7,8,9,10 0. 1 50 0 0 1 1,2,6,7,11 0. 100 0 1 -1 8,9,12,13,14,15 0. 1 40 0 -1 1 1,3,11,16 17 0. 100 -2 1 2 6,10,11,16 0. 175 1 1 -2 4,5,12,13 0. 200 2 1 0 2,4,7,8,12 0. 210 -1 1 0 14,15,18 0. 175 -2 1 0 8,10,14,16,17 , 1 8 0. 175 0 0 -1 3,5,13,15,17,18 0. 125 F i g u r e 12. C r y s t a l shape of camphor homoenol p-bromobenzoate 77 p r o f i l e of a K-curve were input into the MULTAN programme. Four phases were accepted as known from their E!-relationships (4 0 10 and 4 0 0 had phase n, 4 4 0 and 0 8 0 had phase 0). The or i g i n determining phase assignments were ir/2 for 0 5 18, rr/2 for 0 7 5 and JT/4 for 3 5 2. The 3 5 2 phase assignment also fixed the enantiomorph. The highest E (2 7 0) was used as a symbol and was assigned i n i t i a l phases of 0 and j r . Two sets of phases were generated and both proved to be correct. E-maps were calculated for each set, and one high peak appeared in both cases and could be assigned to the bromine. The positions of the peaks in the second set were related to those in the f i r s t by the symmetry operation (l/2-x,y,z), i . e . , the two sets are enantiomorphic. The r e s t r i c t i o n on the phase assignment of (3 5 2) f a i l e d to f i x the enantiomorph. The f i r s t set was a r b i t r a r i l y chosen placing the bromine at the f r a c t i o n a l coordinates (0.3886, -0.6046, 0.0100). If we have a bromine at (x,y,z) in the space group P2 12,2 1, then we w i l l also have bromines at : (1/2-x,-y,1/2+z) (1/2+x,1/2-y,-z) (-x,1/2+y,1/2-y). The bromine interatomic vectors we would expect to find on a Patterson map are then : (1/2,l/2±2y,±2z) (±2x,1/2,1/2±2z) ( l/2±2x,±-2y, 1/2) . These are known as the Harker sections at X=1/2, y=l/2 and Z=1/2 respectively. As an interatomic vector may originate at either 78 of the two atoms i t connects, a Patterson map is always centrosymmetric. If the o r i g i n a l space group i s not centrosymmetric, the Patterson then has an additional symmetry element, and the unique volume w i l l be half that of the o r i g i n a l space group. In P2,2,2, the unique volume i s a quarter of the unit c e l l and so only an eighth of the Patterson need be examined. In t h i s eighth, there were three large outstanding peaks, one on each Harker section, due to the bromine-bromine interatomic vectors : (0.2209,0.5000,0.4939), corresponding to the Harker section -2x,1/2,1/2-2z and solving to x = 0.3895 and z = 0.0030; (0.5000,0.2840,0.0186), corresponding to the Harker section 1/2,1/2-2y,+2z and solving to y = 0.6080 and z = 0.0093; and (0.2692,0.2141,0.5000), corresponding to the Harker section l/2+2x,+2y,1/2 and solving to x = 0.3846 and y = 0.6070. These average to give the one out of four solutions (the other three are symmetry related) that places the bromine at (0.3870,0.6075,0.0062) in agreement with the d i r e c t methods re s u l t . Obtaining the same solution from both methods i s always reassuring. It i s also of interest to see that d i r e c t methods, a s t a t i s t i c a l technique based on the assumption that the electron density i s d i s t r i b u t e d randomly throughout the unit c e l l , can also work for heavy-atom structures. A difference map calculated after re f i n i n g the bromine for three least-squares cycles revealed -the' posrtions of nine other' atoms, and nine more could be located on a map calculated after - r e f i n i n g the f i r s t 10 atoms for three cycles. A t h i r d difference 79 map, calculated after three more refinement cycles, revealed the positions of the remaining.two non-hydrogen atoms. A l l twenty non-hydrogen atoms were refined a n i s o t r o p i c a l l y for three cycles, lowering R to 0.062. A l l nineteen hydrogens could now be located on a difference map, but they would not refine, and better results were obtained by keeping the hydrogens fixed in calculated positions with fixed isotropic temperature factors (U = 0.057 A 2 ) . Hughes' weighting scheme was introduced ((w) 1/ 2 = 1 for |Fo| < F* and (w) 1/ 2 = F*/|Fo| for |Fo| > F*, F* = 23.5) and the structure was refined for four more cycles to an R value of 0.049. Anomalous dispersion corrections have d i f f e r e n t effects on the magnitudes of the structure factors F(hkl) and F ( - ( h k l ) ) , and i f these differences are s u f f i c i e n t l y large i t i s possible to determine the absolute configuration of a molecule by determining which observed set of data, Fo(hkl) or Fo(-(hkl)), gives better agreement with the calculated structure factors. Very often the F(-(hkl)) data are not c o l l e c t e d , so a l t e r n a t i v e l y i t may be determined which enantiomorph gives r i s e to the calculated strucure factors that have the best agreement with the Fo(hkl) data (with anomalous dispersion corrections applied). Anomalous dispersion corrections were applied to the bromine, carbon, and oxygen atoms, and the two enantiomers were each refined in three equivalent least-squares cycles. For the enantiomer o r i g i n a l l y chosen, the three' cycles" refined to R = 0.056 and Rw = 0.070; for the enantiomer obtained by changing the signs of x, y, and z, the three cycles refined to 80 R = 0.046 and Rw = 0.056. The l a t t e r is therefore the correct enantiomer (better agreement with the observed data) and was., used in further refinement. The structure was refined for four cycles before the weighting scheme was modified such that F* was now equal to 18.0. The weighting scheme needed further modification after four more least-squares refinement cycles; F* was now 17.8 and a factor G* was introduced such that when |Fo| < G*, (w) 1/ 2 = |Fo|/G* and G* = 11.5. A f i n a l least-squares cycle refined the structure to convergence with R and Rw values of 0.045 and 0.054 (0.123 and 0.054 including unobserved re f l e c t i o n s ) respectively. Positional and thermal parameters are given in Tables XXX and XXXI. Results and discussion Figure 13 shows a stereoview of the structure with the atomic l a b e l l i n g . The 1,4-homoenol structure is v e r i f i e d , and a l l bond lengths' (Tables XXXII. amd XXXIII')' agree- farrl-y well- with expected values. The C(1)-C(2) and C(1)-C(7) bond lengths (1.569 and 1.558 A) are s l i g h t l y longer than normal sp 3-sp 3 carbon-carbon bonds (1.53 A ) 2 9 , but this i s not surprising considering the strained nature of their environment. Mean plane calculations (Table XXXIV) show that the p-bromobenzoate group is not far from planar - there is an angle of 5° between the bromophenyl and carboxyl planes, as opposed to 21° in the p- bromobenzoate derivative in the l a s t chapter. Bond angles (Table XXXV) in the p-bromobenzoate group are normal. 81 TABLE XXX. POSITIONAL AND ISOTROPIC THERMAL PARAMETERS OF CAMPHOR-1,4-HOMOENOL P-BROMOBENZOATE (fr a c t i o n a l x 10", H x 10 3, U x 103 A 2) Atom X 1 z Ueq/Uiso Br -3868( 3) -6066( 2) -94(1) 84 0(1 ) 893(12) -268< 9) -1329(3) 56 0(2) 3485(13) -1 335 < 1 1 ) -954(4) 77 C(1 ) 931(17) 2325( 12) -1793(4) 49 C(2) 2068(17) 907( 15) -1558(4) 52 C(3) 3478(20) 436< 13) -1966(4) 64 C(4) 3889(19) 2 1 20 < 16) -2165(4) 65 C(5) 2471(25) 2396 16) -2601(5) 79 C(6) 509(20). 21 83 17) -2346(4) 65 C(7) 2988(20) 3074 14). -1739(4) 53 C(8) 3288(17) 21 00 ,16) -1259(4) 63 C(9) 3309(26) 4843 [17) -1747(6) 87 C( 10) -706(20) 291 4 117) -1480(6) 78 C( 1 1 ) 1762(19) -1316 [16) -1019(5) 61 C( 12) 339(17) -241 1 [13) -794(4) 47 C( 1 3) -1595(17) -2434 [14) -923(4) 53 C( 14) -2878(21 ) -3488 [15) -719(5) 56 C( 1 5) -2136(21) -4566 (13) -373(5) 56 C( 16) -228(22) -4572 (14) -236(4) 60 C( 1 7) 1055(21) • -3482 (13) -445(4) 59 H(031 ) 273 -29 -225 57 H(032) 470 -17 -183 57 H(04) 539 233 -225 57 H(051 ) 265 352 -275 57 H(052) 271 1 50 -289 57 H(061) -51 306 -248 57 H(062) -12 102 -244 57 H(081 ) 260 262' ' -93.- 57' H(082) 476 183 -118 57 H(091) 234 541 -1 46 57 H(092) 477 518 -1 66 57 H(093) 289 536 -21 1 57 H(101 ) -187 213 -1 42 57 H(102) -1 18 392 -1 67 57 H(103) -19 334 -110 57 H( 1 3) -216 -1 54 -117 57 H( 1 4) -443 -353 -85 57 H( 1 6) 33 -549 0 57 H( 1 7) 261 -347 -33 57 TABLE XXXI. ANISOTROPIC THERMAL PARAMETERS OF CAMPHOR P-BROMOBENZOATE ( U i j x 103 AM 82 Atom U i 1 U 2 2 y 3 3 2 u, 3 U 2 3 Br 1 12( 1) 64( 1 ) 77( 1) -26( 1) -6( 1) 15( 1 ) 0(1 ) 47( 5) 58( 4) 64( 5) -7( 5) -3( 5) 1 1 ( 4) 0(2) •52( 6) 76( 6) 1 03( 7) 15( 6) -10( 5) 29( 5) C(1 ) 45( 7) 42( 6) 58 ( 7) 8( 6) 1 ( 7) 3( 5) C(2) 39( 6) 61 ( 7) 55( 7) -4( 6) 2( 6) 2( 7) C(3) ' 65(10) 58( 7) 69( 8) 13( 7) 4( 7) -4( 6) C(4) 54( 8) 86( 9) 56( 8) -10( 8) 9( 8) 8( 7) C(5) 114(13) 67( 9) 55( 8) -13( 9) -1 ( 9) 4( 7) C(6) 68(10) 72( 8) 55( 8) -9( 8) -19( 6) 5( 7) C(7) 68( 9) 47( 7) 45( 8) -12( 7) 3( 7) 3( 6) C(8) 50( 9) 85( 9) 55( 8) 0( 7) -6( 6) -7( 7) C(9) 98(13) 69( 9) 93(10) -28( 9) 5( 9) -8( 8) C( 10) 55( 9) 80( 8) 99(11) 12( 8) 18( 8) 27( 9) C(11) 55(10) 66( 9) 63( 8) 27( 8) -6( 7) -11 ( 7) C( 12) 42( 8) 42( 6) 58( 7) -3( 6) 0( 5) 0( 6) C(13) 59(10) 54( 7) 46( 7) 0( 7) 0( 6) 2( 6) C( 1 4) 66( 9) 52( 7) 52( 8) 5( 7) -10( 6) 10( 6) C( 15) 60(10) 54( 8) 55( 7) -12( 6) 11 ( 7) -18( 7) C( 16) 73(10) 51 ( 7) 55( 9) 5( 7) -3( 7) 12( 6) C(17) 64 ( 8) 58 ( 7) 54( 7) 7"( 8J) -6( 8) 3( 6) i g u r e 13. The camphor homoenol p-bromobenzoate m o l e c u l e 84 TABLE XXXII. BOND LENGTHS ( A ) OF THE NON-HYDROGEN ATOMS IN CAMPHOR HOMOENOL P-BROMOBENZOATE Bond Distance Bond Di stance Br -CO 5) 1.898(12) C(4) -C(7) 1 .528(17) 0(1 ) -C(2) 1.424(14) C(5) -C(6) 1.522(21) 0(1 ) - C O D 1.354(15) C(7) -C(8) 1.541(16) 0(2) - C O D 1.197 (13) C(7) -C(9) 1.523(17) C(1 ) -C(2) 1 . 5 6 9 0 6 ) C O D -CO 2) 1 . 4 7 9 0 8 ) CO ) -C(6) 1.509(16) C( 12) -CO 3) 1 . 3 7 3 0 6 ) CO ) -C(7) 1.558(17) C( 12) - C 0 7 ) 1.394(16) C O ) -COO) 1 .487(17) C( 13) -CO 4) 1.371(17) C(2) -C(3) 1.511(16) C( 14) -C(15) 1.400(17) C(2) -C(8) 1.541(16) C( 15) -CO 6) 1 .361(18) C(3) -C(4) 1 . 5 5 6 0 7 ) C( 16) - C 0 7 ) 1 .397( 17) C(4) -C(5) 1.536(19) 85 TABLE XXXIII. BOND LENGTHS ( A ) INVOLVING HYDROGEN ATOMS IN CAMPHOR HOMOENOL P-BROMOBENZOATE Bond Distance Bond Distance C(3)-H(031) 1.11 C(9) -H(092) 1 .07 C(3)-H(032) 1 .05 C(9) -H(093) 1 .09 C(4)-H(04) 1.07 C( 10)-H(101) 1 .05 C(5)-H(051) 1 .05 C(10)-H(102) 1 .04 C(5)-H(052) 1 .09 C( 1 0)-H(103) 1.14 C(6)-H(061) 1 .09 C(13)-H(13) 1 .08 C(6)-H(062) 1.11 C( 14)-H(14) 1.12 C(8)-H(081) 1 .09 C(16)-H(16) 1 .09 C(8)-H(082) 1 .06 C(17)-H(17) 1.11 C(9)-H(091) 1.12 TABLE XXXIV. MEAN PLANES OF THE P-BROMOBENZOATE MOIETY IN CAMPHOR HOMOENOL P-BROMOBENZOATE Equations of planes (lX+mY+nZ=p) plane 1 m 1 0.2074 -0.6334 -0.7455 2.9216 2 0.1325 -0.6015 -0.7878 3.0019 Deviations from planes ( A ) atom 1 2 C(2) -0.02(1) -0.01(1)* 0( 1 ) -0.009(8) 0.007(8)* 0(4) 0.19(1) 0.006(9)* C(11) -0.07(1) -0.02(1)* C(12) 0.01(1)* -0.06(1) C(13) 0.00(1)* 0.04(1 ) C (1 4 )• -0.01(1 )* 0.04(1 ) C(15) -0.01(1)* -0.07(1) C(16) -0.01(1)* -0.17(1) C(17) 0.00( 1 )* -0.18(1) Br 0.000(1)* -0.036(1 ) *atoms included* in plane' calculations> Angles between normals to the planes planes (1) and (2) : 5.3° 8 7 TABLE XXXV. BOND ANGLES (°) OF NON-HYDROGEN ATOMS IN CAMPHOR HOMOENOL P-BROMOBENZOATE Bonds Angle C ( 2 ) - 0 ( 1 ) - C O r ) 1 18 . 3 ( 0 . 9 C ( 2 ) - C O ) - C ( 6 ) 1 1 5 . 0 ( 1 . 0 C ( 2 ) -cd) - C ( 7 ) 8 0 . 0 ( 0 . 8 C ( 2 ) - C O ) - C O O ) 1 14 . 5 ( 0 . 9 C ( 6 ) - C O ) - C ( 7 ) 1 07 . 3 ( 0 . 9 C ( 6 ) -cd) - C O O ) 1 15 . 4 ( 1 . 1 C ( 7 ) -cd) -coo) 1 19 . 8 ( 1 . 0 0 ( 1 ] - C ( 2 ) - C O ) 1 15 . 5 ( 0 . 9 0 ( 1 ! - C ( 2 ) - C ( 3 ) 1 19 . 1 ( 1 . 0 0 ( 1 ] - C ( 2 ) - C ( 8 ) 123 . 3 ( 0 . 9 co; - C ( 2 ) - C ( 3 ) 1 03 . 7 ( 0 . 9 c ( r - C ( 2 ) - C ( 8 ) 8 8 . 2 ( 0 . 9 C ( 3 - C ( 2 ) - C ( 8 ) 101 . 5 ( 0 . 9 C ( 2 > - C ( 3 ] - C ( 4 ) 9 6 . 7 ( 0 . 9 C ( 3 > - C ( 4 ] - C ( 5 ) 1 0 6 . 5 ( 1 . 1 C ( 3 > - C ( 4 - C ( 7 ) 9 9 . 5 ( 0 . 8 C ( 5 ) - C ( 4 > - C ( 7 ) 1 0 3 . 0 ( 1 . 2 C ( 4 ) - C ( 5 > - C ( 6 ) 101 . 9 ( 0 . 9 C O ) - C ( 6 ) - C ( 5 ) 1 0 4 . 9 ( 1 . 0 C O ) - C ( 7 ) - C ( 4 ) 94 . 7 ( 0 . 9 Bonds Angle CO ) - C ( 7 ) - C ( 8 ) 8 8 . 7 ( 0 . 9 ) c d ) - C ( 7 ) - C ( 9 ) 122 . 4 ( 1 . 2 ) C .(4) - C ( 7 ) - C ( 8 ) 1 0 6 . 0 ( 1 . 0 ) C ( 4 ) - C ( 7 ) - C ( 9 ) 1 1 7 . 3 ( 1 . 2 ) C ( 8 ) - C ( 7 ) - C ( 9 ) 121 . 7 ( 1 . 2 ) C ( 2 ) - C ( 8 ) - C ( 7 ) 81 . 5 ( 0 . 8 ) 0 ( 1 ) - C O D - 0 ( 2 ) 1 2 2 . 3 ( 1 . 3 ) 0 ( 1 ) -CO 1) -C( 1 2 ) 1 1 1 .80 .1 ) 0 ( 2 ) - c ( n ) -C( 1 2 ) 1 2 5 . 9 ( 1 . 3 ) C O D - C ( 1 2 ) -CO 3 ) 123 . 2 ( 1 . 1 ) c d D - C ( 1 2 ) -CO 7 ) 1 16 .80 . 1 ) C ( 1 3 ) - C ( 1 2 ) -CO 7 ) 1 2 0 . 0 ( 1 . 2 ) C ( 1 2 ) - C ( 1 3 ) -CO 4 ) 122 . 3 ( 1 . 2 ) C( 1 3 ) - C ( 1 4 ) -CO 5 ) 1 17 . 1 ( 1 . 3 ) Br - C ( 1 5 ) - C ( 1 4 ) 1 18 . 1 ( 1 . 1 ) Br -CO 5 ) - C ( 1 6 ) 1 1 9 . 8 ( 1 . 1 ) C( 1 4 ) - C ( 1 5 ) -CO 6 ) 122 . 0 ( 1 . 2 ) C ( 1 5 ) - C 0 6 ) - C ( 1 7 ) 1 2 0 . 0 ( 1 . 2 ) CO 2 ) - C ( 1 7 ) - C ( 1 6 ) 1 18 . 6 ( 1 . 2 ) 88 From Table XXXV i t can be seen that there i s evidence for considerable s t r a i n in. the v i c i n i t y of the cyclobutyl ring.. The. C-C-C angles in the four-membered ring are 80, 88, 81, and 89°, i . e . , two opposite angles are s i g n i f i c a n t l y smaller than the free cyclobutyl a n g l e 2 2 , 89.3°. These two angles, C(2)-C(1)-C(7) and C(2)-C(8)-C(7), also form the envelope t i p s of two f i v e - membered rings whose conformations are adapted to allow for the cyclobutyl ring. The C-C-C angles in the five-membered ring are lower than normal (97,99,101,81,106 and 97,99,104,95,80°) and the dihedral angles between the envelope flaps and the remainder of the ring are 117 and 110° (see figure 14), i . e . , quite small (plane C(2)-C(3)-C(4)-C(7) has equation -0.7953X + 0.0525Y - 0.6039Z = 1.3643, with atom displacements C(2) 0.05, C(3) -0.08, C(4) 0.09, C(7) -0.06, C(l)' 1.12, and C(8) -1.04(1) A). The envelope t i p of the C(1)C(2)C(3)C(4)C(7) ring has shifted from C(7) in the free camphor to C(1) in the 1,4-homoenol derivative. The cyclobutyl ring i s f a i r l y t i g h t l y folded; the dihedral angles (133 and 129°, see figure 14) are s i g n i f i c a n t l y smaller than the free cyclobutyl a n g l e 2 2 of 162.6°. Deviations from ideal bond angles are less pronounced further away from the four-membered ring. Bond angles involving hydrogen atoms in their fixed calculated positions are l i s t e d in Table XXXVI. Figure 15 presents a stereo packing diagram - there are no unusually short intermolecular contacts and the c r y s t a l is held together by van der Waals forces. F i g u r e 14. D i h e d r a l angles i n the c y c l o b u t y l moiety TABLE XXXVI. BOND ANGLES (°) INVOLVING HYDROGEN ATOMS IN CAMPHOR HOMOENOL P-BROMOBENZOATE Bonds Angle C(2) -C(3) -H(031) 1 10 C(2) -C(3) -H(032) 1 1 4 C(4) -C(3) -H(031) 1 1 1 C(4) -C(3) -H(032) 1 1 5 H(031) -C(3) -H(032) 109 C(3) -C(4) -H(04) 1 1 4 C(5) -C(4) -H(04) 1 1 5 C(7) -C(4) -H(04) 1 18 C(4) -C(5) -H(051) 1 1 1 C(4) -C(5) -H(052) 109 C(6) -C(5) -H(051) 1 1 2 C(6) -C(5) -H(052) 1 1 1 H(051) -C(5) -H(052) 1 1 1 C(1 ) -C(6) -H(061) 1 1 3 C(1) -C(6] -H(062) 1 1 1 C(5) -C(6) -H(061) 1 10 C(5) -C(6] -H(062) 1 1 1 H(061) -C(6) -H(062) 107 C(2) -C(8] -H(081) 1 17 C(2) -C(8] -H(082) 1 19 C(7) -C(8, -H(081) 1 1 3 C(7) -C(8 -H-(08«2) 1 1 4 Bonds Angle H( 081 ) - c < 8) - H i 082) 1 10 C( 7) - c l 9) - H i 091 ) 1 09 C( 7) - c < 9) -HI 092) 1 13 C< 7) - c i 9) - H i 093) 1 1 2 HI 091 ) - C l 9) - H i 092) 107 H( 091 ) - C l 9) - H i 093) 106 HI 092) - C l 9) -HI 093) 109 C l 1 ) - C l 10) -HI 101 ) 1 1 7 C l 1 ) - c 10) -HI 102) 1 04 C l 1 ) - c 10) -HI 103) 1 1 2 HI 101) - c 10) -HI 1 02) 1 1 1 HI 101 ) - c J O ) -HI 103) 107 HI 1 02) - c ,10) -H 103) 105 C l 12) - c : 1 3 ; -H 13) 119 C l 14) - c [131 -H 13) 118 C 13) - c [14] -H 14) 121 C 15) - c ( 1 41 -H 14) 1 22 C 15) - c [16] -H r16) 1 20 C 17) - c [ 161 -H r16) 119 C 12) - c [1 7 -H 117) 121 C 16) - c [ 1 7 I-H M7) 120 9 1 Figure 1 5 . Packing diagram for camphor homoenol p-bromobenzoate 92 CHAPTER 4 DIFFICULT P2, STRUCTURES 93 I. CRYSTAL STRUCTURE OF RAUCUBAINE Introduction. The leaves of the plant Rauwolfia s a l i c i f o l i a griseb., a species endemic to Cuba, y i e l d a new a l k a l o i d , rau.cuba.ine... The plant was c o l l e c t e d in Baracoa, a zone in the Guantanamo province. Spectroscopic d a t a 3 0 suggested structures of various fragments, but did not allow' complete st r u c t u r a l elucidation of the a l k a l o i d . In order to obtain the complete structure the compound was subjected to x-ray d i f f r a c t i o n analysis. Data c o l l e c t i o n . Preliminary photography showed the c r y s t a l to be monoclinic with the 0 k 0 r e f l e c t i o n s systematically absent when k i s odd, indicating the presence of a twofold screw axis and establishing the space group as P2 , (or P21/m, which could be disregarded as the material i s o p t i c a l l y a c t i v e ) . The intensity data were c o l l e c t e d using n i c k e l - f i l t e r e d CuKa radiation (X. = 1.54188 A) and an u-26 scan with an u scan angle of (0.9 + 0.15 tan 8)°. The horizontal and" v e r t i c a l aperture widths were (2.0 + 0.5 tan 6) mm and 4 mm respectively. The i n t e n s i t i e s of three standard r e f l e c t i o n s (-5 -2 6, -6 -3 4, 94 and -2 -3 7) were measured every one hour of x-ray exposure time and were used to scale the data. The, same three reflections,were checked for orientation every 100 r e f l e c t i o n s , and reorientation occurred i f the difference between observed and calculated scattering vectors was greater than 0.05°. Reorientation occurred only once during the data c o l l e c t i o n . Of the 1822 r e f l e c t i o n s measured in the range 2 < 0 < 75°, 1700 (93.3%) had I/*(I) > 3.0 and were considered observed. The c e l l parameters were refined by least-squares methods using the sinO/x. values of 25 r e f l e c t i o n s in the range 39 < 6 < 49° and are presented with other c r y s t a l data in Table XXXVII. Lorentz and p o l a r i z a t i o n corrections were applied. ************************************* TABLE XXXVII. CRYSTAL DATA FOR RAUCUBAINE C 2 0H 2 1 (N 203 Monoclinic Space group = P2, a = 7.2179(3) b = 12.8169(3) c = 9.1996(3) A fi = 93.040(3) 0 f.w. = 340.4 Z". =- 2 F(000) = 364 X = 1 .54188 oA V = 849.87 A 3 Dc = 1.33 gem'1 »/(Mo radn.) = 0.85 cm - 1 u(Cu radn.) = 6.8 cm - 1 **************************************************************** 95 Solution Attempts to solve the c r y s t a l structure of raucubaine spanned well over a year. Probably the simplest way of recounting these attempts is in a chronological fashion. A l l solution attempts involved the use of di r e c t methods, as the lack of heavy atoms in a molecule this size would render the Patterson map v i r t u a l l y uninterpretable. In the space group P2,, the conventional o r i g i n choice involves the assignment of phase 0 or n to two r e f l e c t i o n s in. the h 0 1 zone, thereby l i m i t i n g the o r i g i n to one of the four unique screw axes p a r a l l e l to b (at 0 y 0, 0.5 y 0, 0 y 0.5, or 0.5 y 0.5). A t h i r d general r e f l e c t i o n preferably of type h 1 1 i s assigned any phase in order to f i x the o r i g i n along the chosen screw axis. The o r i g i n determining r e f l e c t i o n s , or any additive combination of the o r i g i n determining r e f l e c t i o n s , may not have parity ggg (e.g. a parity permissible ori g i n set could be u 0 g, u 0 u, and g 1 u). The enantiomorph i s fixed by l i m i t i n g the phase of an additional' r e f l e c t i o n to the range 0 to t r . Further considerations in o r i g i n choice should be that the o r i g i n determining r e f l e c t i o n s have strong E's and be involved in as many E 2 - r e l a t i o n s h i p s with other strong E's as possible. The pr o b a b i l i t y of a phase $(h,k,l) being determined c o r r e c t l y from E 2 - r e l a t i o n s h i p s depends on the number of contributing E 2~ relationships, and on the strength of the (h',k',l') and (h- h' , k-k',1-1') contributors within each relationship. In order for the symbolic addition routine to phase other r e f l e c t i o n s c o r r e c t l y , i t i s especially important that the i n i t i a l E 2- 96 relationships used ( i . e . those involving the origi n and symbols) hold true. Unfortunately, i t is not always possible to find two strong h 0 1 r e f l e c t i o n s that are involved in many E 2 - r e l a t i o n s h i p s , as is required in P2,, and the elucidation could present immediate d i f f i c u l t i e s . In t h i s structure the f i r s t r e f l e c t i o n s chosen for the ori g i n were 1 0 6, 7 0 -3 and 4 1 5 (origin 1 in Table XXXVIII). If the E's are ranked according to magnitude, these r e f l e c t i o n s have ranks 44, 38 and 2, respectively. The strengths of the zonal r e f l e c t i o n s are somewhat lower than desirable; however these were the strongest h 0 1 re f l e c t i o n s available. This o r i g i n was discarded upon discovering that i t was not involved in any of the 77 E 2-relationships derived from the 50 strongest E's. Based on the 168 E 2 - r e l a t i o n s h i p s from the 65 strongest E's, the next o r i g i n chosen was o r i g i n 2 in Table XXXVIII. Working through the E 2 - r e l a t i o n s h i p s by hand, as many re f l e c t i o n s were phased from the o r i g i n as possible before the f i r s t symbol assignment was made to the r e f l e c t i o n with the most E 2-contributors of reasonable strength. Phasing was continued manually and the second and t h i r d symbols were selected in a similar manner to give a st a r t i n g symbol set of 1 9 -6 (rank 15), 1 2 -7 (rank 18), and 3 10 3 (rank 13) (symbol set 'a' in Table XXXVIII). Using two values for each of the symbols, and 9545 E 2 - r e l a t i o n s h i p s derived from the 261 strongest E's, eight sets of phases were generated which were in fact two enantiomorphic groups of four sets each, the enantiomorph being TABLE XXXVIII. ORIGIN AND SYMBOL SETS FOR RAUCUBAINE. Origins hkl rank hkl rank hkl rank 1 1 0 6 44 7 0 - 3 38 4 1 5 2 2 1 0 6 44 1 0 - 9 60 6 1 - 3 4 3 1 o , 6 44 1 0 - 9 60 4 1 5 2 4 1 0 6 44 1 0 - 9 60 5 1 4 30 5 2 9 3 15 1 .7 5 29 3 10 - 3 40 6 - 3 - 1 3 - 5 2 1 • -10 3 1 46 0 6 - 5 1 52 7 4 1 5 1 3 9 2 53 2 2 - 3 100 8 5 7 5 43 2 9 3 58 3 10 - 3 1 55 hkl rank Symbols hkl rank hkl rank a 1 9 - 6 1 5 1 2 - 7 18 3 10 3 1 3 b 1 9 9 7 6 3 - 4 8 3 10 3 1 3 c 3 10 3 1 3 1 2 - 7 18 0 7 6 6 d 6 1 - 3 4 1 2 - 7 18 0. 7 6 6 e 6 3 - 4 8 1 2 - 7 18 0 7 6 6 f 1 9 - 6 1 5 1 2 - 7 1 8 0 7 6 6 g 4 1 5 2 1 2 - 7 18 0 7 6 6 h 3 13 - 5 1 4 0 0 21 i 3 13 2 9 - 5 3 1 30 2 - 3 8 1 4 2 -S I 3 29 j 3 13 - 5 1 6 0 - 4 10 k 2 9 3 1 5 4 0 0 21 m 3 13 2 3 - 5 - 8 1 1 45 1 10 - 4 1 4 4 0 0 21 98 determined by the starting phase of the 1 9 -6 r e f l e c t i o n . For each set of. phases various, c r i t e r i a , exist that allow, discrimination of the correct set from the incorrect sets, including average consistencies, various R factors, the number of phases determined, and the number of E 2 - r e l a t i o n s h i p s actually used. For the correct set, the values for most i f not a l l of these c r i t e r i a should stand out s i g n i f i c a n t l y above those for the incorrect sets ( s i g n i f i c a n t l y below for the R f a c t o r s ) . The number of phases determined and one of the R factors (1R- Karle') are the more sensitive indicators. Of the eight sets of phases determined, none were obviously correct. In an attempt to improve the discrimination between the sets, the symbols were given four s t a r t i n g values rather than two (except for 1 9 -6, which was limited to two s t a r t i n g values within the range 0 to rr to determine the enantiomorph), and 32 sets of phases were generated, the best of which did not y i e l d any recognizable features on an E-map. At t h i s stage i t was thought that perhaps an i n s u f f i c i e n t number of E's (and hence an i n s u f f i c i e n t number of E 2- relationships) was being used to determine the structure c o r r e c t l y . With the same or i g i n and symbols, 380 E's greater than 1.25 were used to generate eight starting sets, but the E- map from the best set showed no improvement. The phasing procedure in the programme TANS involves incrementing the number of E's included in the various phase determining cycles. As i t was n'otieed that the i n i t i a l phasing was very slow ( i . e . few phases were succesfully assigned in the f i r s t ten of f i f t e e n cycles) a 'lump refinement' was attempted 99 in which a l l 380 E's were introduced at the f i r s t cycle. Although convergence was. more rapid, the, f i n a l results were, no better. As attempted e a r l i e r , the number of sets generated was increased to 32, but s t i l l no s i g n i f i c a n t discrimination between the sets could be observed. A few E-maps were calculated from the s l i g h t l y better sets without success. Before rejecting t h i s o r i g i n , i t was t r i e d with a d i f f e r e n t symbol set (set b in Table XXXVIII) but there were s t i l l no useful r e s u l t s . To check on the o r i g i n choice, a E 2 - l i s t i n g involving the highest 129 E's was inspected, using I {E (h, k, 1 )"E"(h' , k ' , 1' ) E (h- h',k-k',1-1')} as a parameter to indicate the strength and E 2- involvement of each r e f l e c t i o n . It was decided that the 4 1 5 r e f l e c t i o n was as good an o r i g i n choice as 6 1 -3, and i t was reused in origin/symbol set 3a (see Table XXXVIII) to generate 48 starting sets, none of which refined well. The 4 0 0 r e f l e c t i o n could be assigned phase i r from various E,-relationships and several attempts at solution including 4 0 0 in the s t a r t i n g set (starting sets 3c, 3d, 3e, 3f and 4g) gave no useful r e s u l t s . The above calculations were performed in May and June of 1978. In July, 1978, our laboratory group started using K-curves (see chapter two, page 15) as an alternate method of c a l c u l a t i n g E's, and in the hope that i t might make a difference, the raucubaine data were renormalized using a K-curve. Further attempts at solution were s t i l l in vain, but later an error in the m u l t i p l i c i t y of zonal r e f l e c t i o n s was discovered- in the renormalization procedure. This was corrected in January, 1979. At t h i s time our laboratory had also started using the MULTAN 100 programme for direct methods, which features automatic o r i g i n selection and i s in general more powerful with, more sensitive correctness c r i t e r i a than some other available programmes. 410 E's greater than 1.20 obtained from the K-curve were input into the MULTAN programme. The or i g i n MULTAN selected was unconventional: i t assigned phase 0 to 2 9 3 (rank 15), starting phases ± ir/4 to 1 7 5 (rank 29) and starting phase ir/4 to 3 10 - 3 (rank 40), with symbols 3 13 -5 and 4 0 0 (ranks 1 and 21), i. e . , s t a r t i n g set 5h in Table XXXVIII. Presumably i f the zonal r e f l e c t i o n s would have been s u f f i c i e n t l y strong they would have appeared in the MULTAN starting set. The rationale for being able to use general r e f l e c t i o n s as o r i g i n determining r e f l e c t i o n s l i e s in the following: a phase may l i e in one of four quadrants: quadrant 1, 2, 3, or 4. A s h i f t in o r i g i n (e.g. from one twofold screw axis to another) would result in the s h i f t i n g of a phase of a general r e f l e c t i o n from quadrant 1 to quadrant 3 or from quadrant 4 to quadrant 2. Res t r i c t i n g the phase of thi s general r e f l e c t i o n to quadrants 1 and 4 then renders i t o r i g i n determining. However, the phase may move from, say, quadrant 1 to quadrant 4 upon changing the enantiomorph. Res t r i c t i n g the phase to one quadrant therefore also determines the enantiomorph. This argument may also be extended to other space groups. In t h i s o r i g i n selected by MULTAN, the two zonal r e f l e c t i o n s have been replaced by 1 7 5, which is r e s t r i c t e d to quadrants 1 and 2, and' 3 10" -3, which is' restricted' to quadrant one and hence is also enantiomorph determining. The assignment of zero phase to a t h i r d r e f l e c t i o n of proper parity (2 9 3) 101 completes the or i g i n and enantiomorph d e f i n i t i o n . E-maps were calculated from the apparently mo.st, correct sets of phases generated, but each had only a single large peak and offered no structural information. A crystallographic device sometimes used to solve d i f f i c u l t structures i s the reduction of the symmetry of the system in which the structure is being solved, i . e . , e s s e n t i a l l y to ignore one of the symmetry elements present. This i s most often used when i t i s the symmetry element that i s the source of the d i f f i c u l t y (e.g. large parts of the structure lying near a mirror plane, pseudo centre of symmetry, etc.) and hence i t s removal might eliminate the confusion. It i s doubtful that the P2, axis was related to the source of trouble in raucubaine, but at t h i s stage (February 1979) i t seemed that trying to solve the structure in a lower symmetry space group might be worthwhile. The only symmetry element present in P2, i s the twofold screw axis, and i t s removal places the structure in the lowest symmetry space group, P1. PI i s t r i c l i n i c with one asymmetric unit, which would hopefully incorporate two molecules of raucubaine related by' a twofold screw. The (h,-k,l) r e f l e c t i o n s (which were not collected for the monoclinic system) were added to the data set with F(h,-k,l) = F( h , k , l ) . The highest 500 E's calculated by following the minimum p r o f i l e of a K-curve were input into the MULTAN programme. The or i g i n was selected by assigning zero phase to three r e f l e c t i o n s : 3 -13 -5 (rank 2), 1 -10 3 (rank 146) and- 0 6 -5 (rank 152); and four symbols were used: 3 13 -5, 2 -3 8, 2 -9 3 and 2 9 3 (origin/symbol set 6 i ) . A l l of the resultant sets of phases showed i d e n t i c a l values for 1 02 the correctness c r i t e r i a ( i . e . , no discrimination) and an E-map from one of the sets produced, only a, single large peak.. The ranks of the o r i g i n determining r e f l e c t i o n s were very high, so an o r i g i n and symbol set was chosen manually by examining a E 2 - l i s t i n g (-3-13 5, 0 -7 6 and 2 -9 3, with symbols 3 10 3, 4 0 0 and 2 -3 8), and with this o r i g i n set eight sets of phases were generated using the TANS programme, but once more the E-maps from the best two sets revealed nothing but single large peaks. With the lack of success in P1, i t was hard to pinpoint the area of d i f f i c u l t y . There could perhaps have been something inherently wrong with the E's, or with their renormalization. For this reason, a few attempts were made using unrenormalized E's. The R-curve was redone without the renormalization, and the 500 highest E's were input into MULTAN, which selected origin/symbol set 5j and accepted the 4 0 0 Z,-relationship as having phase IT, but the sets of phases produced showed poor values for the correctness c r i t e r i a , and the E-maps calculated produced single large peaks. Using t h i s same o r i g i n , TANS produced no better r e s u l t s . The highest E i s 3 13-5 and i t has value of about 3.8, which i s considerably larger than the next few E's. If there is some p e c u l i a r i t y among the E's, t h i s strongest E may well be affected, and were i t i n i t i a l l y i ncorrectly phased, i t would in turn af f e c t the phasing of the remaining E's. This was tested by omitting the strongest E i n - the" direct methods"procedure. Without the 3 13-5 r e f l e c t i o n , MULTAN chose origin/symbol set 7k, but no useful results were obtained. A TANS run with the 103 same o r i g i n was a l s o u n s u c c e s f u l . In continued e f f o r t s to i n v e s t i g a t e a l t e r n a t e E d i s t r i b u t i o n s , a set of E's was a l s o generated by f o l l o w i n g the K-curve i n s t e a d of using i t s minimum p r o f i l e , and was input i n t o MULTAN. MULTAN chose o r i g i n / s y m b o l set 8h, but there was no out s t a n d i n g s o l u t i o n . The c o r r e c t n e s s c r i t e r i a that MULTAN uses are a f i g u r e of merit (FOM) (which should approach u n i t y f o r the c o r r e c t set of phases), an R - f a c t o r , and a *(0) parameter (read ' p s i - z e r o ' ) , which i s e s s e n t i a l l y an R - f a c t d r based on the c l o s e n e s s of f i t of the lowest E's, and i s very s e n s i t i v e to the c o r r e c t s o l u t i o n . Up to t h i s stage ( J u l y 1979) the *(0) t e s t had not been i n c l u d e d . I n c o r p o r a t i n g the *(0) t e s t , 500 renormalized E's were input i n t o the MULTAN programme, which accepted phase n f o r the 4 0 0 L , - r e l a t i o n s h i p , and chose o r i g i n / s y m b o l set 5 j . The r e s u l t i n g set of phases with the lowest *(0) value was a l s o the set with the highest R and lowest FOM, and so was u n l i k e l y to be c o r r e c t . The run was repeated with f i f t y *(0) r e f l e c t i o n s being the f i f t y a b s o l u t e lowest E's ra t h e r than the lowest f i f t y of the 500 E's in p u t , and purposely not a c c e p t i n g the 4 0 0 r e f l e c t i o n as phased. T h i s time, using origin/symbol set 5h, a set of phases was generated that had not only the lowest *(0) va l u e , but a l s o the lowest R, yet the d i s c r i m i n a t i o n was not very good. In an attempt to improve t h i s d i s c r i m i n a t i o n , s t i l l u s i n g 500 E's and the f i f t y lowest E" s' f o r the *(0) t e s t , an i m p o s i t i o n on MULTAN f o r c e d i t to choose four r a t h e r than two symbols. The r e s u l t i n g o r i g i n / s y m b o l set was 5m i n Table 104 XXXVIII, and this time the lowest *(0) value s t i l l corresponded to the lowest. R and both stood out a l i t t l e better, than in the previous MULTAN run. An E-map calculated from this set revealed the chemically-reasonable positions of 25 non-hydrogen atoms, and the structure was f i n a l l y solved. Post-solution analysis. Once the structure was solved, the correct set of phases was examined with the hope of finding possible trouble spots that rendered the solution so d i f f i c u l t . The f i r s t oddity is that the 3 10-3 r e f l e c t i o n , which is supposedly enantiomorph determining, changed sign (or enantiomorph) from +45 to -83° in the refinement of phases. The significance of thi s i s not immediately obvious, however the results were affected. In the previous MULTAN run, the numeric values for the star t i n g set corresponding to those that produced the correct solution, produced a set of phases*• in< which- the- enantiomorph determining r e f l e c t i o n ( s t i l l 3 10 -3) did not f l i p - however th i s p a r t i c u l a r set of phases was incorrect. Also in this previous MULTAN run, the best set of phases (lowest *(0) and R) did not correspond to the correct set. It i s possible that the 3 10 -3 r e f l e c t i o n i s involved in some misleading E 2 _ r e l a t i o n s h i p s early in the phase determining procedure, and that by forcing numerical values on extra symbols, these misleading relationships are overcome. From the numerical values of the origin/symbol set. that led to the 105 correct solution (set 5m), the phases for other r e f l e c t i o n s were calculated manually from their T. 2-relationships,. It was found that two of the symbols were not involved in many I 2 - relationships and that the phasing proceeded rather slowly. The f i r s t r e f l e c t i o n to be assigned a phase completely dif f e r e n t to that in the f i n a l correct set was 2 3 8, and i t s phase was d i r e c t l y derived from that of 3 10 -3. The next few inconsistent phases were those of 1 10 3, also derived from 3 10 -3, and 4 6 -5, derived from 1 10 3. These are a l l r e l a t i v e l y strong r e f l e c t i o n s , and their being incorrectly phased would d e f i n i t e l y decrease the pr o b a b i l i t y of solving the structure. MULTAN uses a convergence tree (or map) from which i t determines the order in which the r e f l e c t i o n s are phased. The phasings of 25 r e f l e c t i o n s at the root of the convergence tree were examined using both the starting and flipped value of the 3 10-3 phase. A sensitive measure of consistency i s the parameter cos(#, + <t>2 ~ # 3 ) , where <t>\, 4>2, and * 3 are the phases involved in the I 2 - r e l a t i o n s h i p . This parameter should be 1.0 for a co r r e c t l y phased r e f l e c t i o n . It was found that for the phases that were dependent on the 3 10-3 phase, th i s consistency was generally greater than 0.95 i f the flipped value of the 3 10 -3 phase was used (-83°) and around 0.5 i f the sta r t i n g value (45°) was used. The d i f f i c u l t i e s a r i s i n g from this enantiomorph determining r e f l e c t i o n may not be the only reasons for the d i f f i c u l t i e s encountered with this- structure; there may have been more re f l e c t i o n s that were involved in poor I 2 - r e l a t i o n s h i p s , or perhaps there were not s u f f i c i e n t E 2 - r e l a t i o n s h i p s to allow 106 straightforward solution. In conclusion,, the circumstances, that led .to. success, in the solution of raucubaine were the use of a sensitive discriminator (the *(0) t e s t ) , the use of four symbols in MULTAN's symbolic addition routine (thereby e s s e n t i a l l y increasing computing power and discrimination), and perseverance. Ref inement A l l 25 non-hydrogen atoms were i n i t i a l l y assigned carbon scattering factors, and after three full-matrix least-squares refinement cycles, the atoms could' e a s i l y be i d e n t i f i e d as carbon, nitrogen, or oxygen from their temperature factors. Three additional isotropic least-squares cycles and a difference map confirmed the correctness of the atom-type assignment. After an anisotropic refinement cycle a difference map revealed a l l the hydrogen positions, and several more cycles with unit weights (hydrogens with isotropic temperature factors, non-hydrogens with anisotropic temperature factors) lowered R to 0.067. For several intense low-theta r e f l e c t i o n s the observed structure factors were consistently less than the calculated structure factors. When a least-squares cycle with a polynomial weighting scheme f a i l e d to change th i s s i t u a t i o n , the need for an extinction correction became apparent. There are two types of extinction, primary and secondary, both of which attenuate the d i f f r a c t e d x-ray beam when the c r y s t a l i s set at the Bragg angle for a r e f l e c t i o n . Primary 107 e x t i n c t i o n i s due to a t t e n u a t i o n of the i n c i d e n t beam i n s i d e the c r y s t a l as a r e s u l t of d e s t r u c t i v e i n t e r f e r e n c e from, m u l t i p l y r e f l e c t e d (and hence p e r f e c t l y out of phase) i n c i d e n t r a y s . Primary e x t i n c t i o n e f f e c t s are s i g n i f i c a n t i n c r y s t a l s that are very c l o s e to i d e a l l y p e r f e c t , and are n e g l i g i b l e i n most cases. Secondary e x t i n c t i o n i s more common in c r y s t a l s of high q u a l i t y (not i d e a l l y p e r f e c t ) , and occurs when a s t r o n g l y r e f l e c t i n g plane r e f l e c t s a s u b s t a n t i a l p o r t i o n of the i n c i d e n t beam from the f i r s t few l a t t i c e planes, thereby denying the r e s t of the c r y s t a l the f u l l i n c i d e n t i n t e n s i t y , and thus the d i f f r a c t e d beam i s a t t e n u a t e d . Secondary e x t i n c t i o n i s more pronounced at low angle r e f l e c t i o n s where the i n t e n s i t i e s are i n h e r e n t l y g r e a t e r . Often only a few r e f l e c t i o n s are s e r i o u s l y a f f e c t e d , and i n p r a c t i c e i t i s q u i t e common simply to exclude these from the refinement. I s o t r o p i c e x t i n c t i o n may be measured in terms of g, the secondary e x t i n c t i o n c o e f f i c i e n t , where Ic/Io = 1 + 2 g l c , and g i s c h a r a c t e r i s t i c of the c r y s t a l f o r a given r a d i a t i o n . A n i s o t r o p i c e x t i n c t i o n i s more d i f f i c u l t to handle, but i n raucubaine there i s no evidence f o r the e x t i n c t i o n being a n i s o t r o p i c . Four l e a s t - s q u a r e s refinement c y c l e s r e f i n i n g only g and the s c a l e f a c t o r lowered R from 0.054 to 0.049, showing that the e x t i n c t i o n e f f e c t i s d e f i n i t e l y a p p r e c i a b l e . The s t r u c t u r e was r e f i n e d u n t i l convergence using a polynomial weighting scheme with c o e f f i c i e n t s that were updated a f t e r every c y c l e . The f i n a l c o e f f i c i e n t s used are' A = -0.0493', B = 0.06254, C = -0.004685, and D = 0.000210. The f i n a l R and Rw are 0.046 and 0.066 r e s p e c t i v e l y (0.051 and 0.066 i n c l u d i n g the 108 unobserved r e f l e c t i o n s ) . The f i n a l g value is 1.627 x 10 3. E f f o r t s to determine the absolute configuration, were, unsuccessful, as might well be expected as the anomalous dispersion corrections for the atoms carbon, nitrogen, oxygen, and hydrogen are very small. P a r a l l e l refinements of both enantiomorphs with anomalous dispersion corrections applied, using the Fo data c o l l e c t e d , yielded no s i g n i f i c a n t differences in R values. Structure factors were calculated for both the enantiomorphs (including the anomalous dispersion corrections) and the twenty r e f l e c t i o n s that produced the greatest differences in Fc between the two enantiomorphs were recorded. The i n t e n s i t i e s of the F r i e d e l pairs of these twenty r e f l e c t i o n s were recollected very accurately. The signs of the differences between Fo(hkl) and Fo(-(hkl)) were compared to the signs of the differences between Fc(hkl) and Fc(-(hkl)) for these twenty r e f l e c t i o n s . Had the signs matched for each F r i e d e l pair, the o r i g i n a l enantiomorph chosen would probably have been correct. Had the signs been consistently opposite for each F r i e d e l pair, the correct enantiomer would have been enantiomorphic to that o r i g i n a l l y chosen. Unfortunately, in several attempts, about 50% of the F r i e d e l pairs had matched signs, and the remaining F r i e d e l pairs had opposite signs, o f f e r i n g no conclusion. F i n a l atomic and thermal parameters for the o r i g i n a l enantiomorph chosen appear in Tables XXXIX and XL. 109 TABLE XXXIX. POSITIONAL AND ISOTROPIC THERMAL PARAMETERS FOR RAUCUBAINE (f r a c t i o n a l x 10", H x, 10 3, U- x 10.3 A 2) Atom X I z Ueq/Uiso 0( 1 ) 1116(4) 4770 5140(3) 38 0(2) -1156(4) 5339(3) 6484(3) 46 C(1) -1066(6) 4300(5) 10212(5) 49 C(2) -1807(8) 4045(7) 11552(6) 67 C(3) -1200(8) 3173(7) 12299(6) 68 C(4) 202(8) 2559(5) 11811(5) 60 C(5) 972(6) 2813(4) 10507(4) 42 C(6) 289(6) 3677(4) 9696(4) 39 C(7) 1326(5) 3681(4) 8302(4) 34 C(8) 3134(5) 3189(4) 8898(4) 38 C(9) 3906(9) 1854(5) 10774(6) 59 N( 1 ) 2470(5) 2341(4) 9816(4) 46 C(10) 1795(5) 4769(4) 7657(4) 34 C(1 1 ) 3664(5) 4822(4) 6884(4) 38 C( 12) 5235(6) 4104(5) 7421(5) 45 C( 13) 4449(5) 3015(4) 7658(4) 42 N(2) 3488(5) 2647(4) 6267(4) 42 C( 14) 1704(7) 2160(4) 6513(5) 43 C( 15) 334(6) 2897(4) 7205(4) 39 C(16) 3473(6) 3382(4) 5020(5) 42 C( 1 7) 3089(5) 4547(4) 5306(4) 39 C( 18) 409( 5) 5021( 4) 6415 ( 4) 36 continued... 1 10 C( 19) 4037( 6) 5244( 4) 4204( 5) 46 0(3) 3684( 6.) 6299 ( 4) 4579(. 4) 55 C ( 2 0 ) 3340( 9) 5037( 6) 2640( 6) 59 H(1) -146( 7) 493( 5) 965( 6) 4 8 ( 1 3 ) H(2) -274(12) 466( 8) 1190( 9) 9 3 ( 2 4 ) H(3) 160(10) 293( 7) 1328( 8) 76(21 ) H(4) 67( 9) 1 93 ( 6) 1230( 7) 6 4 ( 1 7 ) H(8) 374( 6) 372( 4) 955( 5) 33 (11 ) H(91 ) 4 5 5 ( 1 0 ) 249( 6) 1137( 8) 7 5 ( 2 1 ) H(92) 352(10) 1 42 ( 7) 1150"( 8) 7 6 ( 2 1 ) H(93) 481 ( 11 ) 1 50 ( 7) 1020( 8) 8 0 ( 2 2 ) H( 10) 170( 5) 529( 3) 844( 4) 21 ( 9) H(1 1 ) 407( 6) 555( 4) 6 9 K 4) 25( 9) H(121 ) 573( 8) 444( 5) 828( 6) 5 0 ( 1 4 ) H(122) 628( 9) 4 1 0 ( 6) 670( 7) 68 (18) H( 13) 534( 8) 248( 5) 788( 6) 4 7 ( 1 4 ) H(141 ) 119( 7) 1 88 ( 5) 560( 6) 4 7 ( 1 4 ) H(142) 191( 7) 1 59( 5) 713( 5) 3 9 ( 1 2 ) H(151 ) - 3 0 ( 8) 322( 5) 648( 7) 50(14 ) H(152) -51( 7) 245( 4) 772( 6) 4 2 ( 1 3 ) H(161 ) 269( 7) 3 1 0 ( 5) 429( 6) 4 2 ( 1 2 ) H(162) 469( 9) 338( 5) 450( 7) 5 0 ( 1 5 ) H( 19) 536( 8) 51 3 ( 5) 443( 6) 5 5 ( 1 5 ) H(201 ) 396( 8) 549( 5) 189( 6) 56(15) H(202) 3 5 9 ( 1 3 ) 428( 8) 248( 9) 9 0 ( 2 5 ) H(203) 2 0 7 ( 1 0 ) 51 6 C 6)' 250( 6) 6 1 ( 1 7 ) H(O) 4 6 9 ( 1 4 ) 665( 9) 4 3 6 ( 1 0 ) 1 0 3 ( 3 0 ) 111 TABLE XL. ANISOTROPIC THERMAL PARAMETERS FOR RAUCUBAINE (Uij x 10 3 A 2) Atom U 1 1 u 2 2 U 3 3 U 1 2 U 1 3 U 2 0( 1 ) 37( 1) 40(1 ) 35(1) -2(1 ) - 1 ( 1 ) 0(1 0( 2) 38( 1 ) 50(2) 51(2) 7(1 ) 2(1 ) 6(1 C( 1 ) 41 ( 2) 63(3) 43(2) 1 (2) 2(2) -1 (2 C( 2) 54( 3) 99(5) 49(3) 0(3) 10(2) - 8 ( 3 C( 3) 62( 3) 99(5) 45(2) - 9 ( 3 ) 9(2) 8(3 C( 4) 72( 3) 64(3.) 42(2) -2.1 (.3) - 8 ( 2 ) 1 4.(2. C< 5) 49( 2) 37(2) 39(2) - 11 (2 ) -6(1 ) 4(2 C< 6) 42( 2) 42(2) 34(2) - 6 ( 2 ) - 1 ( 1 ) 0(1 c 7) 36( 2) 30(2) 34(2) 1(1) -3(1 ) 0(1 c 8) 41 ( 2) 34(2) 38(2) 4(2) -6(1 ) -1 (2 c 9) 74( 3) 48(3) 54(3) 7(3) - 16 ( 2 ) 13(2 N J ) 57( 2) 39(2) 40(2) 2(2) - 11 ( 1 ) 7(1 c ,10) 41 ( 2) 29(2) 33(2) -5(1 ) 0(1) -5(1 c [11) 40( 2) 32(2) 41(2) - 5 ( 2 ) -2(1 ) 0(2 c [12) 34( 2) 48(2) 52(2) - 4 ( 2 ) - 4 ( 2 ) - 5 ( 2 c [13) 38( 2) 44(2) 44(2) 9(2) -3(1 ) 1 (2 N (2) 48( 2) 35(2) 42(2) 4(1 ) K D -5(1 c [14) 56( 2) 28 (2) 45(2) - 9 ( 2 ) - 2 ( 2 ) - 5 ( 2 c [15) 44( 2) 36(2) 38(2) - 10 (2 ) -5(1 ) 0(2 c (16) 48( 2) 37(2) 40(2) 1(2) 1 (2) - 7 ( 2 c (17) 35( 2) 43(2) 38(2) - 1 ( 2 ) 4(1 ) - 4 ( 2 c (18) 41 ( 2) 27(2) 39(2) -2(1 ) 3(1 ) 1(1 c (19) 45( 2) 45(2) 49(2) - 12 ( 2 ) 10(2) 3(2 0 (3) 67( 2) 34(2) 6.5(2) -10(2-) V8*( 2) 4.(1 c (20) 71 ( 3) 61(3) 47(2) - 11 (3 ) 1 1 (2) 6(2 .112 Discussion. The molecular structure, shown in Figure 16 with the atomic l a b e l l i n g scheme, is a new type of indole a l k a l o i d with interesting biosynthetic aspects that w i l l not be discussed here. Figure 17 shows a stereoview of the molecule i l l u s t r a t i n g a cage-like framework. Excluding the dihydroindole group, the central cage consists of three six-membered rings and a f i v e - membered ring so connected as to form a 'bowl' of which the open face is the nine-membered r i n g C ( 7 )-C (1 5)-C (1 4)-N ( 2 )-C.( 1 6) - C(17)-0(1)-C(18)-C(10). The C(10)-C(11)-C(12)-C(13)-C(8)-C(7) ring has a s l i g h t l y distorted chair conformation, while the other two six-membered rings have s l i g h t l y skewed .boat conformations. Mean plane calculations (Table XLl) show that the f i v e - membered ring has a skew conformation: C(10) and C(11) are both 0.24 A away from the mean plane of the ring including 0(2), but on opposite sides. The dihydroindole group i s planar i f C(8) and C(9) are not included-. In this* way- the- greatest deviation- of any atom in the plane C(1)-C(7),N(1) from the mean plane i s 0.057 A for C(4), whereas C(8) and C(9) are 0.66 and 0.73 A away from the mean plane on the same side; i.e, the envelope t i p of the dihydroindole five-membered ring i s C(8). Bond distances are l i s t e d in Tables XLII and XLIII and have reasonable values. The C(7)-C(10) and C(7)-C(15) bonds have lengths that are s i g n i f i c a n t l y greater (1.559(5) and 1.570(5) A, respectively) than normal sp 3-sp 3 carbon-carbon bonds, but occurences such as these are not uncommon in strained systems. 1 1 3 F i g u r e 16. Raucubaine: s t r u c t u r e and atomic l a b e l l i n g scheme F i g u r e 17. Stereoview of the raucubaine molecule TABLE XLl. MEAN PLANE CALCULATIONS IN RAUCUBAINE Equation of plane: plane 1 1 -0.6517 2 0.2347 (!X+mY+nZ=p) m -0.5997 0.9641 n -0.4643 -0. 1241 P -6.7818 5.4737 Deviations from plane ( A ) plane 1 plane 2 0( 1 )* - 0 . 036 (1 ) CO ) * - 0 . 0 5 3 ( 5 ) 0 ( 2 ) * 0 . 1 1 5 ( 4 ) C (2) * - 0 . 0 3 9 ( 7 ) C ( 1 0 ) * - o . 2 3 8 ( 5 ) C (3) * 0 . 0 5 2 ( 7 ) C( 1 1 ) * 0 . 2 4 2 ( 5 ) C(4] * 0 . 0 5 7 ( 6 ) C ( 1 7 ) * 0 . 0 0 3 ( 5 ) C ( 5 ; * 0 . 0 1 4 ( 5 ) C ( 1 8 ) * - 0 . 0 0 5 ( 5 ) C (6 * - 0 . 0 0 8 ( 5 ) C (7 * 0 . 0 5 1 ( 4 ) C(8 - 0 . 6 5 6 ( 4 ) C(9 - 0 . 7 3 4 ( 6 ) N( 1 - 0 . 0 5 4 ( 4 ) *atoms included in mean plane cal c u l a t i o n 1 16 TABLE XLlI. BOND LENGTHS OF NON-HYDROGEN ATOMS IN RAUCUBAINE Bond LengthC A ) Bond Length( A ) 0(1)-C(17) 1.453(4) C(.8)-C( 1 3) 1 .538(6). 0(1)-C(18) 1.343(5) C(9)-N(1) 1 .464(6) 0(2)-C(18) 1.206(5) C(10)-C(11 ) 1 .559(5) C(1)-C(2) 1.408(7) C(10)-C(18) 1.513(5) C(1)-C(6) 1.366(7) C(11)-C(12) 1 .522(6) C(2)-C(3) 1.372(11) C(11)-C(17) 1.530(5) C(3)-C(4) 1.376(10) C(12)-C(13) 1 .527(7) C(4)-C(5) 1.387(7) C(13)-N(2) 1 .499(5) C(5)-C(6) 1.410(6) N(2)-C(14) 1.460(6) C(5)-N(1) 1.419(6) N(2)-C(16) 1.484(6) C(6)-C(7) 1.519(5) C( 14)-C(15) 1.531(6) C(7)-C(8) 1.526(5) C(16)-C(17) 1.544(6) C(7)-C(10) 1.559(5) C( 1 7)-C(19) 1.539(6) C(7)-C(15) 1.570(5) C( l9)-0(3)) 1.422(6) C(8)-N(1) 1.472(6) C(19)-C(20) 1.521(7) 1 17 TABLE XLIII. BOND LENGTHS INVOLVING HYDROGEN ATOMS IN RAUCUBAINE Bond Length( A ) Bond Length( A ) C(1)-H(1) 0.99(6) C(13) -H(13) 0.96(6) C(2)-H(2) 1.10(9) C( 1 4) -H(141) 0.97(6) C(3)-H(3) 1.01(8) C( 1 4) -H(142) 0.94(6) C(4)-H(4) 0.97(8) C( 15) -H(151 ) 0.89(6) C(8)-H(8) 0.99(5) C( 15) -H(152) 0.98(6) C(9)-H(91) 1.08(8) C( 16) -H(161 ) 0.93(6) C(9)-H(92) 0.92(8) C( 1 6) -H(162) 1.02(6) C(9)-H(93) 0.97(8) C( 19) -H(19) 0.98(6) C(10)-H(10) 0.99(4) 0(3)) -H(O) 0.89(11) C( 1 1)-H(11) 0.98(5) C(20) -H(201) 1.03(6) C( 12)-H(121) 0.96(6) C(20' -H(202) 1.00(10) C( 12)-H(122) 1 .03(7) C(20 -H(203) 0.93(7) 1 18 Bond angles (Tables XLIV and XLV) are as reasonable as could be expected given the constraints of the cage. A stereo packing diagram i s presented in Figure 1 8 . The molecules are strung together along the twofold screw axis (b) by 0(3)-H...N(2) hydrogen bonds. The hydrogen bond length 0(3)...N(2) i s 2.815(5) A. The structure is consistent with previous spectral d a t a 3 0 . 1.1.9 TABLE XLIV. BOND ANGLES OF THE NON-HYDROGEN ATOMS IN RAUCUBAINE Bonds Angle(deg) Bonds Angle(deg) C(17)-0(1 )-C0 8) 111. 8(3) CO 0)-C( 1 1 )-C( 1 2) 1 18 .2(3) C(2 >-C(1 ) -C(6) 118. 7(5) C(10)-C(11)-C(17) 103 .0(3) CO )-C(2) -C(3) 1 20. 1 (6) C(12)-C(11)-C(17) 109 .2(3) C(2 )-C(3) -C(4) 121. 6(5) CO 1 )-C0 2)-C( 13) 1 08 .8(3) C(3 )-C(4) -C(5) 118. 9(5) C(8)-C(13)-C(12) 1 02 .8(4) C(4 )-C(5) -C(6) 1 19. 8.(5) C(.8)-C(1 3.) -N(2) 11 3 .8(3) C(4 )-C(5) -NO ) 129. 6(4) C(12)-C(13)-N(2) 109 .0(3) C(6 )-C(5) -NO) 110. 6(4) C(13)-N(2)-C(14) 1 1 2 .0(3) CO )-C(6) -C(5) 1 20. 8(4) CO 3)-N(2)-C( 16) 1 16 .3(3) CO )-C(6) -C(7) 1 33. 2(4) CO 4)-N(2)-CO 6) 1 1 4 .9(3) C(5 )-C(6) -C(7) 1 06. 0(4) N(2)-C(14)-C(15) 1 1 3 .3(3) C(6 )-C(7) -C(8) 98. 4(3) C(7)-C(1 5)-C('l4) 1 12 .3(3) C(6 )-C(7) -COO) 116. 8(3) N(2)-C(16)-C(17) 1 18 .5(3) C(6 )-C(7) -C(15) 1 08. 2(3) 0(1 )-Cd7)-C( 1 1 ) 105 .6(3) C(8 )-C(7) -COO) 107. 9(3) 0( 1 )-C07)-C(l6) 1 10 .9(3) C(8 )-C(7) -C(15) 108. 6(3) 0( 1)-C(17)-C(19) 1 06 .5(3) CO D)-C(7)-C(15) 115. 4(3) CO 1 )-C07)-C(l6) 110 .0(3) C(7 )-C(8) -NO) 1 02. 3(3) CO 1 )-C(l7)-C09) 1 12 .6(3) C(7 )-C(8) -C(13) 110. 0(3) C(16)-C(17)-C(19) 1 1 1 .0(3) N( 1 )-C(8) -C(13) 1 23. 5(4) 0(1 )-CO8)-0(2) 121 .8(3) C(5 )-NO ) -C(8) 1 02. 8(3) 0( 1 )-C(18)-C(10) 1 10 .0(3) C(5 )-N(1) -C(9) 116. 4(4) 0(2)-C(18)-C(10) 1 28 .1(4) C(8 )-NO ) -C(9) 114. 7(4) C(l7)-C09)-0(3) ) 107 .5(4) C(7 )-C( 1 0)-C( H ) 115. 1 C3) C(17)-C(19)-C(20) 1 1 2 .7(4) C(7 )-C(lO)-C08) 109. 2(3) 0(3) )-CO9)-C(20) 109 .9(4) CO 1 )-CO0)-CO8) 101. 5(3) 120 TABLE XLV. BOND ANGLES INVOLVING HYDROGEN ATOMS IN RAUCUBAINE Bonds Angle(deg) Bonds Angle(deg) c ( 2)-C(1)-H(1) 122(3) C( 8)-C(l3)-H(13) 112(3) C( 6)-C(1)-H(1) 119(3) C( 12)-C(13)-H(13) 116(3) C( 1)-C(2)-H(2) 111(5) N( 2)-C(l3)-H(13) 103(3) c ( 3)-C(2)-H(2) 129(4) N( 2)-C(14)-H(141) 109(3) C( 2)-C(3)-H(3) 127(5) N( 2)-C( 1 4)-H(.1 42) 108(3) C( 4)-C(3)-H(3) 111(5) C( 15)-C(14)-H(141) 111(3) c( 3)-C(4)-H(4) 124(4) C( 15)-C(14)-H(142) 109(3) C( 5)-C(4)-H(4) 117(4) H( 141)-C(14)-H(142) 106(5) C( 7)-C(8)-H(8) 106(3) C( 7)-C(15)-H(151) 112(4) N( 1)-C(8)-H(8) 108(3) C( 7)-C(15)-H(152) 110(3) c< 13)-C(8)-H(8) 106(3) C< 14)-C(15)-H(151) 107(4) N( 1)-C(9)-H(9l) 105(4) C< 14)-C(15)-H(152) 106(3) N< 1)-C(9)-H(92) 118(5) H< 151)-C(15)-H(152) 109(5) N< 1)-C(9)-H(93) 110(5) N( 2)-C(16)-H(161 ) 107(4) H< 91)-C(9)-H(92) 103(6) N< 2)"C(16)-H(162) 113(3) H 91)-C(9)-H(93) 110(7) C< 17)-C(16)-H(161) 113(4) H 92)-C(9)-H(93) 111(7) C ,17)-C(16)-H(162) 104(4) C ,7)"C(10)-H(10) 107(2) H ,161)-C(16)-H(162) 100(5) C ; 11)-c(io)-H(io) 114(2) C ' 17)-C(19)-H(19) 104(4) C ;18)-C(10)-H(10) 110(2) 0 I 3))"C(19)-H(19) 106(4) C (10)-C(11)-H(11) 107(2) c I20)-C(19)-H(19) 116(3) C (12)-C(11)-H(11) 111(2) c [19)"0(3))-H(0) 105(7) C (17)-C(11)-H(11) 108(2) c M9)-C(20)-H(201 ) 1 14(3) c (11)-C(12)-H(121) 103(3) c •19)-C(20)-H(202) 105(5) c (11)-C(12)-H(122) 111(4) c ( 19)-C(20)-H(203) 1 12(4) c (13)-C(12)-H(121) 115(4) H (201)-C(20)-H(202) 111(6) c (13)-C(12)-H(122) 112(4) H (201)-C(20)-H(203) 106(5) H (121)-C(12)-H(122) 106(5) H (202)-C(20)-H(203) 109(7) F i g u r e 18. S t e r e o p a c k i n g diagram f o r r a u c u b a i n e 122 I I . CRYSTAL STRUCTURE OF METHYL 3-C~(CARBOMETHOXYMETHYL)~4,6~ O-p-CHLOROBENZQYL-2.3-DIDEOXY-o-D~RIBQ-HEXOPYRANOSIDE I n t r o d u c t i o n and p r e v i o u s a t t e m p t s a t s o l u t i o n A f t e r the s u c c e s s w i t h r a u c u b a i n e , i t seemed w o r t h w h i l e t o a p p l y any f r e s h l y g a i n e d e x p e r i e n c e t o a n o t h e r d i f f i c u l t P2, s t r u c t u r e - t h a t of the t i t l e compound (J_, R = C1C 6H,C0-). CHaCOzCHj OCH3 s' F o l l o w i n g i n i t i a l i n v e s t i g a t i o n s by Dr. D a v i d H u g h e s 3 1 i n 1967, t h i s s t r u c t u r e had remained u n s o l v e d f o r f o u r t e e n y e a r s . C o n s i d e r i n g the advances i n c o m p u t a t i o n a l methods over the l a s t decade, the problem was approached o p t i m i s t i c a l l y , however - the s o l u t i o n was not s t r a i g h t f o r w a r d . The compound was p r e p a r e d by R o s e n t h a l and C a t s o u l a c o s 3 2 . Branched c h a i n s u g a r s of t h i s t y pe were o f g r e a t i n t e r e s t a f t e r some a n t i b i o t i c s were found t o have branched c h a i n sugar s u b s t i t u e n t groups. The x- r a y s t r u c t u r e a n a l y s i s was at t e m p t e d i n o r d e r t o c o n f i r m s t r u c t u r a l a s s i g n m e n t s o b t a i n e d from 123 N.M.R. d a t a 3 2 . Details of elaborate attempts at structural elucidation., using both Patterson and dir e c t methods, are found in Dr. Hughes' Ph.D. t h e s i s 3 1 . His Patterson attempts were extensive, involving various methods of sharpening the Patterson map, and various structural postulations that placed the planar p-chlorobenzoate groups of the molecule in the more strongly r e f l e c t i n g planes of the c r y s t a l l a t t i c e . Although he often obtained not unreasonable positions for the chlorine atoms, the rest of the molecule never appeared in a difference map. Attempts at solution involving the Patterson function have been f a i r l y well exhausted, and there was l i t t l e point in repeating Dr. Hughes' e f f o r t s . The d i r e c t methods attempts by Dr. Hughes produced no outstanding sets of phases, and the E-maps that he calculated did not produce recognizable fragments of the molecule. Some peaks were persistent from one map to the other; however difference Fourier maps based on these peaks plus postulated attached molecular fragments produced no useful r e s u l t s . Hopefully the more powerful techniques available today in dire c t methods would f a c i l i t a t e the solution. These techniques include the use of K-curves and the *(0) test, and due to improvements in computing power large numbers of E's and symbols may be used (the programme Dr. Hughes was using was limited to only 200 E's and three symbols). 124 E x p e r i m e n t a l The d a t a were c o l l e c t e d by Dr. Hughes on a G.E. XRD-6 automated d i f f r a c t o m e t e r u s i n g a 6-26 scan t e c h n i q u e and n i c k e l - f i l t e r e d CuKc r a d i a t i o n . The scan speed was 1°/minute w i t h 40 second background measurements b e f o r e and a f t e r the scan. Of the 1028 r e f l e c t i o n s c o l l e c t e d i n the range 0 < 6 < 45°, 898 had l/<r(I) > 2.0 and were c o n s i d e r e d o b s e r v e d , where <y(I) was d e f i n e d a2{I) = S + B +(0.02S) 2 and S and B are the scan and background c o u n t s over the same range. The c r y s t a l examined was v e r y s m a l l (0.25 x 0.05 x 0.04 mm3) and no a b s o r p t i o n c o r r e c t i o n was n e c e s s a r y . L o r e n t z and p o l a r i z a t i o n c o r r e c t i o n s were a p p l i e d and the s t r u c t u r e a m p l i t u d e s c a l c u l a t e d . The c e l l d i m e n s i o n s were o b t a i n e d by a l e a s t - s q u a r e s r e f i n e m e n t based on the si n 6 / X v a l u e s of 30 r e f l e c t i o n s , and a r e l i s t e d t o g e t h e r w i t h o t h e r c r y s t a l d a t a i n T a b l e XLVI. A l i s t of the 1028 Fo's i s p r e s e n t e d i n Dr. Hughes' t h e s i s , and i t i s w i t h t h e s e d a t a t h a t the p r e s e n t i n v e s t i g a t i o n commenced.. S o l u t i o n The 238 h i g h e s t E's o b t a i n e d from a K-curve t o g e t h e r w i t h the 45 l o w e s t E's f o r use i n the *(0) t e s t were i n p u t i n t o the MULTAN programme. The o r i g i n s e l e c t e d by MULTAN was a c o n v e n t i o n a l P2, o r i g i n : the 1 0 3, 1 0 6', and 1" T 3' r e f l e c t i o n s ( r a n k s 1, 6, and 86, r e s p e c t i v e l y ) were a s s i g n e d phases of z e r o . U n l i k e the r a u c u b a i n e s t r u c t u r e , t h e r e was no problem f i n d i n g 125 ********************************************** TABLE XLVI. CRYSTAL DATA FOR THE PYRANOSIDE C 2 « H 2 U C 1 2 0 8 f .w. = 511 .26 Monoclinic Z = 2 Space group = P2, F(000) = 532 a = 5.752(3) X. = 1.54188 A b = 15.436(3) . V = 849.87 A 3 c = 13.698(3) A Dm = 1.43 gem"1 B = 93.74(3) 0 Dc = 1.40 gem"1 K(CU radn.) = 28.1 cm - 1 **************************************************************** two strong zonal r e f l e c t i o n s . The 2 0 6 r e f l e c t i o n could be assigned phase zero from several E,-relationships. Three symbols were chosen: 1 6 -4, 0 2 3, and 2 3 9 of ranks 2, 3, and 15, respectively, and ten sets of phases were generated. The best set of phases had the lowest R and *(0) values, but also had the lowest FOM, and the discrimination was not very good. The E-map of this set revealed 1 some unrecognizable fragments of a molecule, and attempts to refine these fragments f a i l e d . Because of the s t a t i s t i c a l nature of d i r e c t methods, i t is not always necessarily the set of phases with the best correctness c r i t e r i a that leads to the correct solution, especially when there are several sets that seem reasonable. With t h i s in mind, an E-map was calculated from the second best set, and a fragment including 22 atoms but no p-chlorobenzoate groups was revealed. Attempts to refine t h i s fragment also f a i l e d . 126 The MULTAN programme was rerun with the 500 highest and 50 lowest E's obtained from a Wilson plot, and with four rather than three symbols in an attempt to improve the discrimination between sets. The same or i g i n was selected, and the symbols were now 1 6 -4, 0 2 3, 1 7 -2, and 1 2 0, of ranks 2, 3, 11 and 26 respectively. The 2 0 6 r e f l e c t i o n was assigned phase 0 from I, - relatio n s h i p s . This phase had changed to TT in 5 of the 16 sets of phases generated. The set with the lowest *(0) value had a very high R value, and vice-versa, lending l i t t l e confidence to the correctness of any set. The E-maps that were calculated mostly showed a single large peak, although the E-map from the set with the lowest *(0) value produced two high peaks some distance apart: quite possibly the chlorine atoms. Attempts to refine these atoms and to obtain additional information from subsequent difference maps f a i l e d . The MULTAN programme contains a feature which involves the cal c u l a t i o n of spherically averaged group scattering factors for sections of the molecule of known geometry but of random orientation. This i s useful in the scaling in the renormalization procedure which otherwise assumes a random d i s t r i b u t i o n of the unit c e l l contents throughout the unit c e l l . A t h i r d MULTAN run included the stereochemical information of the four p-chlorobenzoate groups in the unit c e l l . The 500 largest and 50 smallest E's used were obtained from a K-curve. MULTAN selected the same or i g i n as before with symbols 1 6 -4, 0 2 3,. 1 3 6, and- 2 3 9 (ranks 2, 3, 5 strdr 1"5') . As the 2 0 6 r e f l e c t i o n changed phase several times in the previous MULTAN run, i t was not permitted to accept the phase of zero as 127 suggested by the I,-relationships, but was allowed to refine . The phase did, however, refine to phase zero in each of the 16 sets of phases generated. The set with the lowest *(0) value also had the highest R, and was unlikely to be correct. No recognizable molecular fragments could be located on the few E- maps that were calculated. In an attempt to improve discrimination, fi v e symbols were used in a fourth MULTAN run. As before, the maximum number of E's (obtained from a K-curve) and the stereochemical information of the p^-chlorobenzoate groups were used; The 2 0 6 r e f l e c t i o n was again allowed to accept phase zero from I,-relationships, and once again MULTAN selected the same o r i g i n , t h i s time with symbols 1 6 -4, 0 2 3, 1 3 6, 2 3 9 and 1 10 8 of ranks 2, 3, 5, 15, and 69 respectively. 25 sets of phases were generated of which none stood out s i g n i f i c a n t l y above the rest. MULTAN was run a f i f t h time, where the only difference from the fourth run was that only 400 E's were used. This can sometimes force MULTAN to choose a s l i g h t l y d i f f e r e n t starting set, and with luck this could lead to the solution. The same or i g i n was selected with symbols 1 6 -4, 0 2 3, 1 3 6, 2 3 9, and 1 12 5, of ranks 2, 3, 5, 15, and 61, but the results were no more useful. A f i n a l attempt was made including the 200 lowest E's for use in the *(0) test ( s t i l l trying for better discrimination between generated sets of phases) but the set with the lowest *(0) value had quite a high R value, and' the E-map from" t h i s set produced no str u c t u r a l information. At t h i s stage (January 1981) the problem was given lower 128 p r i o r i t y than other matters, and i t was l e f t aside u n t i l discussions with Dr. E... Subramanian, v i s i t i n g . professor, from, the University of Madras, India, renewed interest in thi s d i f f i c u l t structure. Dr. Subramanian recalled that in a recent problem structure that he had solved, he surmounted the d i f f i c u l t y by reducing the number of E's used to an absolute minimum rather than by using as many E's as possible. T r a d i t i o n a l l y 3 3 , the optimum number of E's to be used in the direct methods procedure i s approximately ten times the number of non-hydrogen atoms in the asymmetric unit. For problem structures, the trend has been to increase the number of E's in use, the philosophy being that the greater the number of i t s E 2 _ contributors, the greater p r o b a b i l i t y a certain phase has of being calculated c o r r e c t l y . Dr. Subramanian suggested that for problem structures the E's to atoms r a t i o should be much lower, approximately fiv e to one. The general philosophy here i s that t h i s should prevent weaker erroneous E's from contributing to the phase determining procedure. He also suggested that t h i s would force MULTAN to choose a stronger E for the t h i r d o r i g i n determining r e f l e c t i o n . Throughout the above attempts, the 1 1 3 r e f l e c t i o n (rank 86) had been used, which is indeed a l i t t l e weak. By t h i s time (July 1981) the laboratory group had started using the most recent version of the MULTAN programme, MULTAN- 80 3'. One of the differences between th i s and the previous version, MULTAN-78, i s that a user' s p e c i f i e d number of re f l e c t i o n s that are least l i k e l y to be phased accurately may be eliminated from the phase-determining procedure - i . e . , their 129 phases may be determined, but may not be used for the determination of. other phases. The worst. 1 2" relat ionships, may si m i l a r l y be rejected. This should prevent a l o t of spurious phasing. The 170 highest E's obtained from a K-curve were input into MULTAN, 50 of which were rejected from the phase-determining process. The 43 lowest E's were used for the *(0) test. The or i g i n included the two zonal r e f l e c t i o n s 1 0 3 and 1 0 6 as before but the t h i r d o r i g i n determining r e f l e c t i o n was 1 3 6 (rank 5), which had been previously used as a symbol. Four symbols were used: 0 2 3,1 6 -4, 1 2 3, and 1 0 -3 (ranks 2, 3, 7, and 125). The 2 0 6 r e f l e c t i o n was assigned phase zero. 18 sets of phases were generated, and the set that had the lowest *(0) value also had the lowest R value, and both values stood out s i g n i f i c a n t l y below those of other sets. From the E-map 27 non-hydrogen atoms could be located, and the structure was solved. Ref inement The 27 non-hydrogen atoms could e a s i l y be i d e n t i f i e d as carbon, chlorine or oxygen from their molecular geometry. Three isotropic least-squares refinement cycles followed by a difference map revealed the positions of 7 more non-hydrogen atoms. Three more isotropic refinement cycles and a difference map proved the position of one -0-Me group to be faulty, and this group could be relocated c o r r e c t l y on a difference map 130 following two additional least-squares cycles. With a l l non-hydrogen atoms included, R dropped to 0.124 after two more refinement cycles. Following two cycles with anisotropic temperature factors for the chlorine atoms which lowered R to 0.094, a difference map revealed the positions of 18 of the 24 hydrogen atoms. The hydrogen atoms were included in calculated positions, but were not refined because of i n s u f f i c i e n t data. After two cycles with anisotropic temperature factors for the chlorine and oxygen atoms a weighting scheme was introduced where (w) 1/ 2 = |Fo|/G* for | Fo | < G*, (wW 2 = 1 for G* < | Fo | < F*, and (w) 1/ 2 = F*/|Fo| for |Fo| > F*, and F* = 25.0 and G* = 5.0. After fi v e cycles with anisotropic temperature factors for a l l non-hydrogen atoms, the refinement had converged R = 0.043 and Rw = 0.048. In order to determine the correct enantiomorph, a p a r a l l e l refinement of both enantiomorphs with anomalous dispersion corrections applied to a l l non-hydrogen atoms was undertaken. After three refinement cycles, for the enantiomorph o r i g i n a l l y chosen, R and Rw had increased to 0.044 and 0.050, whereas in the enantiomorph obtained by changing the signs of x, y, and z, R and Rw had decreased to 0.042 and 0.048, respectively. Using Hamilton's r a t i o t e s t 3 5 , i t may be said with 99.5% confidence that the l a t t e r is therefore the correct isomer. This assignment is consistent with the chemically-known configuration. Two more least-squares cycles were s u f f i c i e n t to' refine - the' correct enantiomorph to convergence with R and Rw equal to 0.042 and 0.048 (0.053 and 0.048 including the unobserved r e f l e c t i o n s ) 131 respectively. Final atomic p o s i t i o n a l and thermal parameters appear in Tables XLVII and XLVIII. Post-solution analysis The structure was not solved using a large number of E's and a great amount of computing power, so in retrospect, of the experience gained in solving raucubaine only the *(0) test (and persevere.nce) were of use here. Credit must be. given to the experienced insight of Dr. Subramanian for d r a s t i c a l l y reducing the number of E's to 170. Clearly part of the d i f f i c u l t y was that the lower E's were given too much weight in the phase- determining procedure. This i s reflected in the f i r s t o r i g i n choice, which included one low E which persisted through six MULTAN runs but f a i l e d to produce the solution. The new r e f l e c t i o n weighting feature of MULTAN-80 must also have served to correct this problem. It might adsobe-' mentioned' that this- one to five' r a t i o of atoms to E's as suggested by Dr. Subramanian has since also been succesful in the solution of a phosphazene 3 6 that had remained unsolved for several years. A possible reason for the d i f f i c u l t y Dr. Hughes experienced in obtaining the chlorine positions from the Patterson map is that there exists considerable motion at the chlorine termini of the p-chlorobenzoate side chains. This is especially evident in the thermal parameters of C1(1) where U,, = 0.311 A 2 (see Table XLVIII) corresponding to the very large root mean square 1 32 TABLE XLVII. POSITIONAL AND ISOTROPIC THERMAL PARAMETERS FOR THE PYRANOSIDE (f r a c t i o n a l x 1 0 H x 10 3, U x 10 3 A 2) Atom X 1 z Ueq/Uiso C1(1 ) 408(11) -2322 . 6160( 3) 185 Cl(2) 5271( 7) 6067( 4) 4487( 3) 126 0(1 ) -2207( 1 1 ) 3526( 5) 8974( 5) 67 0(2) 1147(14) 3580( 6) 9998( 5) 68 0(3) 100(11) 1 1 22 ( 7) 11837( 5) 90 0(4) 3668(13) 1 1 33( 7 ) 11349( 5) 97 0(5) -2011(12) 1 2 1 5 ( 6) 8498( 5) 69 0(6) -5397(15) 571 ( 6) 8705( 6) 95 0(7) -1419(13) 3467( 6) 6936( 6) 74 0(8) 1313(15) 251 7( 8) 6618( 6) 95 C(1 ) -1282(22) 3566( 8) 9950( 9) 68 C(2) -2107(18) 281 1 ( 10) 10556( 8) 69 C(3) - 1724(15) 1941 ( 8) 10085( 7) 5'3 C(4) -2643(17) 1 989 ( 8) 9029( 8) 61 C(5) -1641(14) 2745( 8) 8487( 7) 56 C(6) 2094(23) 4285( 8) 9489( 10) 88 C(7) 818(17) 1 635 ( 7) 10214( 8) 59 C(8) 1396(19) 1 276 ( 7) 11226( 8) 58 C(9) 4443(20) 751 ( 1 1 ) 12262( 10) 108 C( 10) -3509(22) 565( 9) 8375( 8) 64 C( 1 1 ) -2518(23) -1 35 ( 8) 7832( 8) 62 C( 1 2) -3657(22) -926( 1 1 ) 7777( 9) 81 C( 13) -2745(37) -1600( 9) 7235( 1 1 ) 1 04 C( 1 4) -731(38) -1477( 13) 6801 ( 10) 109 C( 1 5) 374(29) -71 1( 14). 6861 ( 10) 1 06 C( 1 6) -472(24) -36( 9) 7375( 9) 81 C( 1 7) -2635(18) 2821 ( 10) 7454( 8) 75 C( 18) 529(24) 3234( 1 1 ) 6550( 8) 70 C( 19) 1624(20) 3960( 10) 6037( 8) 62 C(20) 3640(22) 3794( 8) 5558( 9) 74 C(21 ) 4721(24) 4450( 12) 5095( 10) 91 C(22) 3818(24) 5255( 10) 51 00 ( 9) 79 C(23) 1851(25) 5443( 9) 5558( 12) 99 C(24) 782(21) 4780( 1 1 ) 6024( 10) 85 continued'. . . 1 33 H( 011) -1 94 409 1 027 82 HC021 ) -375 285 1066 73 H(022) -128 281 1118 73 H(031 ) -264 1 53 1 042 61 H'(041 ) -438 204 899 69 H(051 ) 5 266 847 62 H(061 ) 216 413 879 77 H(062) 359 444 973 77 H(063) 1 07 478 949 77 H(071 ) 186 208 1 004 57 H(072) 1 04 1 17 972 57 H(091 ) 528 21 1220 1 05 H(092) 325 65 1 269 105 H(093) 559 1 1 4 1 261 1 05 H(121 ) -520 -1 02 810 79 H(131 ) -366 -218 717 102 H(151 ) 185 -67 647 117 H(161 ) 31 50 747 81 H(171 ) -427 298 746 68 H( 1 72) -259 227 71 1 68 H(201 ) 430 319 553 79 H(21 1 ) 618 432 477 83 H(231 ) 119 605 547 1 03 H(241 ) -53 490 639 91 134 TABLE X L V I I I . ANISOTROPIC TEMPERATURE FACTORS OF THE PYRANOSIDE ( U i j x 10 3 A 2 ) Atom U i 1 U 2 2 U 3 3 y 1 2 y 1 3 y 2 3 C l ( 1 ) 31 1 ( 7) 1 17( 3) 1 23( 3) 1 07 ( 4) -7( 4) -33( 3) C l ( 2 ) 1 24( 3) 1 17( 3) 1 35( 3) -39( 3) -4( 2) 35( 3) 0(1 ) 60( 4) 69( 5) 72( 6) 1 4( 4) -2( 4) • -1 ( 5) 0(2) 59( 6) 60 ( 5) 84( 6) -5( 4) -6( 4) -6( 4) 0(3) 61 ( 4) 1 43( 7) 69( 5) 0( 5) 30( 4) 31 ( 6) 0(4) 52( 5) 1 52( 8) 86( 6) 14( 6) 8( 4) 52( 6) 0(5) 57( 4) 70( 5) 81 ( 5)' -1 2( 5) 21 ( 4) -24( 5) 0(6) 68( 5) 1 04 ( 6) 1 1 5( 6) -25( 5) 30( 5) -31 ( 5) 0(7) 55( 4) 97( 6) 70( 5) 6( 5) 1 1 ( 4) 8( 5) 0(8) 1 08 ( 7) 78( 7) 1 02 ( 6) 1 4( 6) 42( 5) 9( 5) C( 1 ) 74( 1 1 ) 69( 8) 62( 9) 1 3( 7) 6( 7) -1 4( 7) C(2) 56( 7) 86( 9) 67( 7) 10( 7) 19( 6) -22( 8) C(3) 41 ( 6) 67( 8) 52( 7) -4( 5) 10( 5) -5( 6) C(4) 43( 6) 65( 8) 76( 8) -4( 6) 17( 6) -3( 8) C(5) ' 40( 6) 69( 8) 60( 7) 5( 6) 1 2( 5) -20( 7) C(6) 81 ( 9) 59( 9) 1 23( 12) -1 7( 7) -1 0( 8) -2( 9) C(7) 47( 7) 64( 7) 67( 8) -1 ( 5) 18( 5) 2( 6) C(8) 51 ( 8) 50( 7) 72( 9) 1 1 ( 6) 1 ( 6) 0( 6) C(9) 66( 8) 161 ( 15) 97( 10) 20( 8) 0( 7) 39( 10) C( 10) 53( 8) 68( 9) 72( 8) -10( 8) 1 1 ( 7) -9( 7) C( 1 1 ) 84( 9) 54( 9) 48( 7) -8( 8) -5( 7) 0( 7) C( 1 2) 93( 9) 85( 10) 64( 9) -8( 9) 1 1 ( 7) 10( 8) C( 1 3) 1 85 ( 17) 59( 1 1 ) 65( 10) -2( 1 1 ) -20( 10) -7( 9) C( 1 4) 1 72( 18) 94 ( 14) 5-9 •( 10), 59-C 1*5) -&(< 1 1 ) - & ( 10) C( 1 5) 1 1 6( 13) 1 22 ( 14) 81 ( 12) 1 1 ( 1 1 ) 19( 9) -1 2( 1 1 ) C( 1 6) 90( 10) 89( 10) 64( 8) 19( 8) 8( 7) -1 1 ( 8) C( 17) 52( 7) 1 17( 10) 56( 7) -15( 8) -4( 6) 2( 8) C( 18) 77( 10) 83( 1 1 ) 49( 8) 7( 9) 1 ( 7) -2( 8) C( 19) 56( 8) 81 ( 1 1 ) 49( 7) 0( 8) -7 ( 6) -21 ( 7) C(20) 73( 9) 76( 9) 72( 8) 1 6( 8) 2( 7) 4( 7) C(21 ) 80( 9) 1 06( 12) 88( 10) 6( 10) 1 6( 7) 23( 9) C(22) 79( 10) 84( 1 1 ) 72( 9) -1 1 ( 9) -1 0( 7) 9( 8) C(23) 77 ( 10) 71 ( 10) 1 47( 14) 8( 9) -7( 9) -22( 10) C(24) 75( 9) 74( 10) 1 10( 1 1 ) -5( 9) 20( 8) -1 7( 9) 135 displacement of 0.558 A. Discussion A stereoview of the pyranoside molecule with i t s atomic l a b e l l i n g scheme i s shown in Figure 19. The sugar has the s i x - membered pyranose ring in a s l i g h t l y flattened chair conformation. Intraannular torsion angles for the six-membered ring are l i s t e d in Table XLIX. The two bulky p-chlorobenzoyl side chains both have equatorial orientations with the shorter -O-Me and C-COOMe side chains in a x i a l positions. Bond lengths and angles appear in Tables L, LI, LII, and LIII, and are normal. A packing diagram is shown in Figure 20. There are no strong intermolecular att r a c t i o n s ; the c r y s t a l i s held together by van der Waals forces. The four p-chlorobenzoyl groups in the unit c e l l do not l i e - i n . but are-very el-ose- to the ( 1 0 3) planes (see Figure 21), which is consistent with the strength of the 1 0 3 r e f l e c t i o n , as expected by Dr. Hughes. 136 Figure 19. The pyranoside molecule 1 37 TABLE XLIX. INTRAANNULAR TORSION ANGLES FOR THE SUGAR RING Atoms Value(deg) C ( 5 ) - 0 ( 1 ) - C O ) - C ( 2 ) - 5 8 . 0 ( 1 1 ) C ( 1 ) - 0 ( 1 ) - C ( 5 ) - C ( 4 ) 60 . 8 ( 1 0 ) 0 ( 1 ) - c ( D - C ( 2 ) - C ( 3 ) 51 . 6 0 2 ) C ( 1 ) - C ( 2 ) - C ( 3 ) - C ( 4 ) - 4 8 . 6 ( 1 1 ) C ( 2 ) - C ( 3 ) - C ( 4 ) - C ( 5 ) 53 . 2 ( 1 0 ) C ( 3 ) - C ( 4 ) - C ( 5 ) - 0 ( 1 ) - 5 8 . 8 ( 1 0 ) 1 38 TABLE L. NON-HYDROGEN BOND LENGTHS OF THE PYRANOSIDE Bond Length( A ) Bond Length( A ) Cl(1)-C(14) 1 .725(15) C(3)-C(7) 1 .536(14) Cl(2)-C(22) 1 .751(13) C'(4)-C(5) 1 .517(14) 0(1)-C( 1 ) 1 .407(13) C(5)-C(17) 1 .495(13) 0( 1 )-C(5) 1 .427(11 ) C(7)-C(8) 1 . 509(13) 0(2)-C(1) 1 .395(11 ) C(10)-C(11) 1 .450(15) 0(2)-C(6) 1 .419(13) C(11 )-C(12) 1 .39(2) 0(3)-C(8) 1 .181(11) C( 1 1 )-C(16) 1 .377(15) 0(4)-C(8) 1 .326(10) C(12)-C(13) ' 1 .40(2) 0(4)-C(9) 1 .427(13) C(13)-C(14) 1 .35(2) 0(5)-C(4) 1 .457(12) C(14)-C(15) 1 .34(2) 0(5)-C(10) 1 .326(12) C(15)-C(16) 1 .36(2) 0(6)-C(10) 1 .203(11) C(18)-C(19) 1 .48(2) 0(7)-C(17) 1 .433(14) C(19)-C(20) 1 .393(15) 0(7)-C(18) 1 .320(14) C(19)-C(24) 1 .35(2) 0(8)-C(18) 1 .197(14) C(20)-C(21) 1 .37(2) C(1)-C(2) 1 .52(2) C(21)-C(22) 1 .35(2) C(2)-C(3) 1 .512(15) C(22)-C(23) 1 .36(2) C(3)-C(4) 1 .508(14) C(23)-C(24) 1 .37(2) 1 3 9 TABLE LI. NON-HYDROGEN BOND ANGLES OF THE PYRANOSIDE Bonds Angle(deg) Bonds Angle(deg) C O ) - 0 ( 1 ) - C ( 5 ) 1 1 3 . 4 ( 8 ) C O O ) - c ( 11) - C ( 1 2 ) 1 1 9 . 0 ( 1 2 ) C O ) - 0 ( 2 ) - C ( 6 ) 1 1 3 . 9 ( 9 ) C O . O ) - c ( 11) - C ( 1 6 ) 1 2 1 . 8 ( 1 1 ) C ( 8 ) - 0 ( 4 ) - C ( 9 ) 1 1 5 . 5 ( 8 ) C ( 1 2 ) - c ( 11) - C ( 1 6 ) 1 1 9 . 2 ( 1 2 ) C ( 4 ) - 0 ( 5 ) - C O O ) 1 2 0 . 1 ( 7 ) C O D - c ( 1 2 ) - C O 3 ) 1 1 9 . 5 ( 1 2 ) C O . / ' ) - 0 ( 7 ) - C O 8 ) 1 1 7 . 7 ( 1 0 ) C O 2 ) - c ( 1 3 ) - C O 4 ) 1 1 9 . 4 ( 14.) 0 ( 1 ) - C O ) - 0 ( 2 ) 1 1 1 . 2 ( 8 ) C I O ) - c ( 1 4 ) - C ( 1 3 ) 1 1 9 ( 2 ) 0 ( 1 ) - C O ) - C ( 2 ) 1 1 1 . 9 ( 1 0 ) C I O ) - c ( 1 4 ) - C ( 1 5 ) 1 2 0 ( 2 ) 0 ( 2 ) - C O ) - C ( 2 ) 1 0 9 . 4 ( 9 ) C O 3 ) - c ( 1 4 ) - C O 5 ) 1 2 0 . 9 ( 1 5 ) C O ) - C ( 2 ) - C ( 3 ) 1 1 2 . 7 ( 8 ) C ( 1 4 ) - c ( 1 5 ) - C ( 1 6 ) 121 . 4( 1 5 ) C ( 2 ) - C ( 3 ) - C ( 4 ) 1 0 8 . 4 ( 9 ) C O D - c ( 1 6 ) - C ( 1 5 ) 1 1 9 . 6( 1 3 ) C ( 2 ) - C ( 3 ) - C ( 7 ) 1 1 2 . 8 ( 9 ) 0 ( 7 ) - C O 7 ) - C ( 5 ) 1 1 0 . 8 ( 9 ) C ( 4 ) - C ( 3 ) - C ( 7 ) 1 1 3 . 4 ( 8 ) 0 ( 7 ) - CO 8 ) - 0 ( 8 ) 1 2 3 . 1 ( 1 3 ) 0 ( 5 ) - C ( 4 ) - C ( 3 ) 1 1 0 . 8 ( 8 ) 0 ( 7 ) - e d 8 ) - C ( 1 9 ) 1 1 2 . 4( 1 2 ) 0 ( 5 ) - C ( 4 ) - C ( 5 ) 1 0 5 . 7 ( 7 ) 0 ( 8 ) - C O 8 ) - C ( 1 9 ) 1 2 4 . 5( 1 2 ) C ( 3 ) - C ( 4 ) - C ( 5 ) 1 1 2 . 7 ( 8 ) C ( 1 8 ) - c < 1 9 ) - C ( 2 0 ) 1 1 8 . 4< 1 3 ) 0 ( 1 ) - C ( 5 ) - C ( 4 ) 1 0 8 . 4 ( 7 ) C ( 1 8 ) - c < 1 9 ) - C ( 2 4 ) 1 2 3 . 3( 1 2 ) 0 ( 1 ) - C ( 5 ) - C O 7 ) 1 0 6 . 9 ( 9 ) C ( 2 0 ) - c , 1 9 ) - C ( 2 4 ) 1 1 8 . 3( 1 2 ) C ( 4 ) - C ( 5 1 - C ( 1 7 ) . 1 1 2 . 9 ( 9 ) C ( 1 9 ) - c 2 0 ) - C ( 2 1 ) 1 2 0 . 0( 1 1 ) C ( 3 ) - C ( 7 - C ( 8 ) 1 1 1 . 7 ( 8 ) C ( 2 0 ) - c ( 2 1 ) - C ( 2 2 ) 1 1 9 . 61 1 2 ) 0 ( 3 ' - C ( 8 1 - 0 ( 4 ) 1 2 2 . 5 ( 9 ) C l ( 2 ) - c ( 2 2 ) - C ( 2 1 ) 1 1 7 . 5 1 3 ) 0 ( 3 ' - C ( 8 l - C ( 7 ) 1 2 7 . 9 ( 9 ) C l ( 2 ) - c ( 2 2 ) - C ( 2 3 ) 1 2 0 . 4 ( 1 3 ) 0 ( 4 > - C ( 8 | - C ( 7 ) 1 0 9 . 6 ( 9 ) C ( 2 1 ) - c ( 2 2 ) - C ( 2 3 ) 1 2 2 . 1 ( 1 3 ) 0 ( 5 ) - C O O ) - 0 ( 6 ) 1 2 2 . 8 ( 1 1 ) C ( 2 2 ) - e (.2.3.). - C ' ( 2 4 ) 1 1 7 . 9 0 2 ) 0 ( 5 >-C0 0 ) - C ( 1 1 ) 1 1 0 . 8 ( 1 0 ) C ( 1 9 ) - c ( 2 4 ) - C ( 2 3 ) 1 2 2 . 1 ( 1 2 ) 0 ( 6 ) - C ( 1 0 ) - C ( 1 1 ) 1 2 6 . 4 ( 1 2 ) 1 40 TABLE LI I ., BOND. LENGTHS, OF THE. HYDROGEN ATOMS OF THE PYRANOSIDE Bond Length( A ) Bond Length( A ) C(1)"H(011 ) 1.01 C(9)-H(092) 0.95 C(2)-H(021 ) 0.9'6 C(9)'-H(0'93) 0.99 C(2)-H(022) 0.95 C( 12)-H( 1.21 ) 1 .03 . C(3)-H(031 ) 0.97 C(13)-H(131) 1 .04 C(4)-H(041 ) 1 .00 C(15)-H(151) 1 .04 C(5)-H(051) 0.98 C(16)-H(161) 0.95 C(6)-H(061) 0.99 C(17)-H(171) 0.97 C(6)-H(062) 0.93 C(17)-H(172) 0.97 C(6)-H(063) 0.96 C(20)-H(201) 1.01 C(7)-H(071) 0.96 C(21)-H(2l1) 0.99 C(7)-H(072) 1.01 C(23)-H(231) 1.01 C(9)-H(091) 0.98 C(24)-H(241) 0.95 141 TABLE LIII. BOND ANGLES INVOLVING HYDROGEN ATOMS IN THE PYRANOSIDE Bonds Angle(deg) Bonds Angle(deg) 0(1 ) - c (1) -H(011) 109 0( 4)-C(9)-H(09l) 1 1 4 0(2)-C(1) -H(011 ) 1 1 2 0( 4)-C(9)-H(092) 1 1 4 C(2)-C(1) -H(011 ) 1 04 0( 4)-C(9)-H(093) 109 C( 1 )-C(2) -H(021) 1 12 H( 091)-C(9)-H(092) 108 C(1)-C(2) -H(022) 1 10 H( 091)-C(9)-H(093) 1 04 C(3)-C(2) -H(021) 1 07 H( 092)-C(9)-H(093) 1 07 C(3)-C(2) -H(022) 107 C( 11)-C(12)-H( 1 21 ) 121 H(021)-C( 2)-H(022) 1 08 C( 1 3)-C(12)-H(121 ) 1 19 C(2)-C(3) -H(031) 1 06 C< 12)-C(13)-H(131) 1 18 C(4)-C(3) -H(031) 109 C< 14)-C(13)-H(131) 1 22 C(7)-C(3) -H(031) 1 07 C< 14)-C(15)-H(151) 1 1 5 0(5)-C(4) -H(041) 108 C 16)-C(15)-H(151) 1 24 C(3)-C(4) -H(041) 1 10 C k11)-C(16)-H(161) 1 1 7 C(5)-C(4) -H(041 ) 1 09 C [15)-C(16)-H(161) 1 24 0(1)-C(5) -H(051) 1 1 2 O k7)-C(17)-H(171) 1 1 0 C(4)-C(5] -H(051 ) 1 09 O ,7)-C(17)-H(172) 1 10 C(17)-C(5)-H(05l) 108 C [5)-C(17)-H(l7l) 1 09 0(2)-C(6] -H(061) 109 C (5)-C(17)-H(172) 1 1 2 0(2)-C(6• -H(062) 1 1 4 H (171)-C(17)-H(172) 1 06 0(2)-C(6 -H(063) 1 1 1 C (19)-C(20)-H(201) 121 H(061)-C [6)-H(062) 108 C (21)-C(20)-H(20l) 1 19 H(061)-C [6)-H(063) 1 05 c (20)-C(21)-H(211) 1 19 H(062)-C (6)-H(063) 1 10 c (22)-C(21)-H(211) 121 C(3)-C(7 >-H(071) 11 1 G ;22)-C(-23)-W(231 ) 1-1-7 C(3)-C(7 )-H(072) 1 08 C (24)-C(23)-H(231) 1 25 C(8)-C(7 )~H(071) 1 1 3 C (19)-C(24)-H(241) 1 18 C(8)-C(7 )-H(072) 1 09 C (23)-C(24)-H(241) 1 19 H(071)-C (7)-H(072) 1 04 142 F i g u r e 20. Stereo packing diagram f o r the pyranoside 143 F i g u r e 21. The u n i t c e l l viewed down b, showing t h e p r o x i m i t y of the p - c h l o r o b e n z e n e groups t o the 103 p l a n e s (dashed) 1 44 PART TWO CHAPTER 5 SPONTANEOUS RESOLUTION IN BINAPHTHYL SYSTEMS 146 Introduction 1,1'-binaphthyl may convert into i t s enantiomer by a rotation along the 1,1' bond. Two c r y s t a l l i n e forms of 1,1'-binaphthyl are known: a low melting form (m.p. = 145°C) which has been shown by x-ray crystallography to be the racemate 3 7 with two R and two S molecules per unit c e l l , and an o p t i c a l l y active high-melting form (m.p. = 158°C). Upon heating from room temperature to just below the melting point, racemic 1,1'-binaphthyl undergoes spontaneous resolution to o p t i c a l l y , active b i n a p h t h y l 3 8 " * 1. This effect i s not observed in the 4,4'-dimethyl or 4,4'-diamino d e r i v a t i v e s " 2 . O p t i c a l l y active forms of either derivative may be obtained by seeding the racemic melt with o p t i c a l l y active naphthidine" 3. In an attempt to understand these observations, the x-ray c r y s t a l structures of racemic and o p t i c a l l y active 4,4'-dimethyl-1,1'-binaphthyl were determined"""" 5. As a continuation of this project, x-ray analyses of o p t i c a l l y active 4,4'-diamino-1,1'-binaphthyl (naphthidine) and- o p t i c a l l y active- 1,1'-binaphthyl (both, prepared by Dr. R.E. Pincock) were undertaken. Hopefully t h i s would present a clear ove r a l l view of any s o l i d state properties that might give r i s e to the above differences in behaviour. Exper imental A. O p t i c a l l y active' 4 , 4" -diamino-1 , 1''^binaphthyl Preliminary photography showed the c r y s t a l to be tetragonal 147 and of one of the enantiomeric space groups P4,2,2 or P432,2 as the 001 r e f l e c t i o n s were only present for 1 = 4n. (indicating, presence of a fourfold screw axis) and the hOO (or OkO, as the system i s tetragonal) r e f l e c t i o n s were only present for h=2n (indicating a twofold screw a x i s ) . The c r y s t a l s were well-formed brown tetragonal bipyramids, but they were weakly d i f f r a c t i n g and had a tendency to decompose (become opaque, often with l i q u i f i e d surfaces) after some time. It has been reported" 3 that naphthidine slowly loses o p t i c a l a c t i v i t y over a period of months. I n i t i a l data c o l l e c t i o n was attempted using MoKo radiation, but only 226 out of 869 r e f l e c t i o n s (26.0%) in the range 0 < 6 < 25° had > 3.0 and were considered observed. Accurate c e l l parameters were obtained with t h i s radiation by least-squares refinement of sin6/X values of 25 r e f l e c t i o n s in the range 7.5 < 6 < 12°, and they are l i s t e d together with other c r y s t a l data in Table LIV. ************************************** TABLE LIV. CRYSTAL DATA FOR OPTICALLY ACTIVE NAPHTHIDINE C 2 0H 1 6N 2 Tetragonal space group = P4,2,2 or P432,2 f.w. = 254.4 Z = 4 a = 7.945(1 ) . c = 24.265(5) A V = 1532 A 3 M = 5.3 cm - 1 F ( 0 0 0 ) = 600 X = 1.5418 A Dc = 1.23 gem - 1 **************************************************************** 148 In order to obtain greater i n t e n s i t i e s and more observed r e f l e c t i o n s , the data were recollected using.CuRc. radiation and this time 316 out of 430 r e f l e c t i o n s (73.5%) in the range 0 < 8 < 45° had l / * ( l ) > 3.0. The data c o l l e c t i o n used an u- (4/3)6 scan technique with an u-scan angle of (0.60 + 0.35 tan 8)°, and the aperture was (2.50 + tan 6)mm wide and 4 mm high. The i n t e n s i t i e s of three standard re f l e c t i o n s (2 2 7 , 1 1 8, and 3 0 6) were measured every one hour and were used to scale the data. The same three r e f l e c t i o n s were used for orientation control; reorientation occurred^ i f the difference between observed and calculated scattering vectors was greater than 0.065°. The stucture was solved by d i r e c t methods. The 350 highest E's, obtained by use of the minimum p r o f i l e of a R-curve, were input into the MULTAN programme. The o r i g i n and enantiomorph were fixed by assigning phase tr/2 to the 3 3 17 r e f l e c t i o n and phase IT/4 to the 5 2 4 r e f l e c t i o n respectively, and using three symbols, 40 sets of phases were generated, one of which stood out as being correct. The E-map from t h i s set of phases revealed the positions of a l l non-hydrogen atoms. After six isotropic and three anisotropic least-squares refinement cycles including only the non-hydrogen atoms, a difference map f a i l e d to locate a l l the hydrogens. When the hydrogen atoms were inserted in calculated positions there were some d i f f i c u l t i e s with the refinement, and so the data were recollected once again in an attempt to improve data quantity and q u a l i t y . This time an o-(2/3)8 scan was used with an o-scan angle of (0.70 + 0.14 tan 6)° (CuRc radiation) and 548 out of 834 149 re f l e c t i o n s (65.7%) in the range 0 < 6 < 65° were considered observed ( i . e . , had I./cr (I) > 3.0). Three r e f l e c t i o n s (1 1 -1, 1 2 - 1 , and 1 2 4) were used for intensity control and data scaling, but no orientation control was used. The scale factor was refined to f i t the new data, but attempts to locate and refine the hydrogen atoms were s t i l l unsuccessful. A l l except the amino hydrogens (as their geometry is not uniquely defined) were placed in calculated positions and assigned an arbit r a r y isotropic temperature factors of 4.5 A 2. After six least-squares cycles (unit weights, non-hydrogen atoms anisotropic, hydrogen atoms not refined), a difference map was calculated to try and locate the two amino hydrogens. The map yielded no outstanding peaks, but after c a l c u l a t i n g bond distances and angles of the highest six peaks in the v i c i n i t y of the nitrogen, only two were chemically reasonable, and these two positions were used for the amino hydrogens. With a l l hydrogens fixed, six cycles of least-squares refinement with Hughes' weighting scheme ((w) 1/ 2 = 1.0 for | Fo | < F* and (wW 2 = F*/|Fo| for | Fo | > F*; F* = 20.0) led to convergence with R = 0.087 and Rw = 0.095 for 548 r e f l e c t i o n s . At this stage, the hydrogen temperature factors were allowed to refine (F* now equal to 19.0), and after six cycles R and Rw had dropped to their f i n a l values of 0.068 and 0.075 respectively (0.113 and 0.075 including the unobserved r e f l e c t i o n s ) . F i n a l p o s i t i o n a l and thermal parameters are shown in Tables LV and LVI . .150 TABLE LV. POSITIONAL AND ISOTROPIC THERMAL PARAMETERS OF OPTICALLY ACTIVE NAPHTHIDINE (fr a c t i o n a l x 10", H x 10 3, U x. 1 0 3 A 2 ) Atom X 1 z Ueq/Uiso CO ) 1070( 6) 193( 7) 2412(2) 68 C(2) 2654( 8) 250(10) 2640(2) 95 C(3) 3852( 8) 1496(12) 2452(3) 1 1 3 CU) 3430(10) 2615( 9) 2053(3) 108 C(5) 1381(12) 3705( 9) 1369(4) 1 1 6 C(6) -133(13) 3595(12) 1125(4) 1 36 C(7) -1340(12) 2458(11) 1312(3) 1 1 7 C(8) -954( 8) 1363( 8) 1734(2) 80 C(9) 653( 7) 1385( 7) 1992(2) 68 COO) 1846( 8) 2616( 8) 1803(3) 87 N 4680( 9) 3775(11) 1878(3) 1 66 H(2) 300 -64 295 87(17) H(3) 509 1 50 264 108(19) H(5) 228 461 1 23 217(37) H(6) -37 436 77 198(38) H(7) -255 246 1 1 4 247(52) H(8) -189 50 188 169(31) H(N1 ) 601 342 202 220(42) H(N2) 442 501 196 281(60) 151 TABLE LVI . ANISOTROPIC THERMAL PARAMETERS. FOR. OPTICALLY ACTIVE NAPHTHIDINE (Uij X 103 A 2) Atom U i 1 u 2 2 U 3 3 U12 U , 3 u 2 3 C( 1 ) 62(3) 74(4) 68(3) -20(3.) 5(3.) -3(3) C(2) 69(4) 1 38(6) 79(4) -12(4) -5(3) -11(4) C(3) 66(4) 177(8) 95(4) -41(5) 8(4) -38(5) C(4) 116(7) 105(6) 102(5) -39(5) 39(5) -20(5) C(5) 134(7) 71(4) 142(6) -2(5) 51 (6) 33(5) C(6) 144(8) 129(7) 135(7) 30(8) 40(7) 51 (6) C(7) 122(7) 124(6) 104(5) 17(5) 17(5) 40(5) C(8) 89(5) 70(4) 82(3) -3(4) 5(4) 12(3) C(9) 72(4) 59(3) 72(3) -12(3) 18(3) -7(3) C( 10) 79(4) 81(4) 100(4) -1 3(4) 28( 4). - 14(4) N 125(6) 142(7) 232(8) -80(5) 75(6) -20(6) 1 52 B. O p t i c a l l y active 1,1'-binaphthyl From x-ray photography, the c r y s t a l s were shown to give r i s e to the same systematic absences, and hence could be assigned the same space groups, as naphthidine. The c e l l parameters were refined from.the sin6 / X values of 21 r e f l e c t i o n s in the range 11 < 6 < 22° and appear with other c r y s t a l data in Table LVII. The intensity data were coll e c t e d with use of an o-6 ************** * * * **************************** * * ** ***** * * * * ** * * * * TABLE LVII. CRYSTAL DATA FOR OPTICALLY ACTIVE 1,1'-BINAPHTHYL C 2 0 H 1 U f.w. = 254.4 Tetragonal Z = 4 space group = P4,2,2 or P432,2 f — 0.6 cm"1 a = 7.164(2) F(000) = 536 c = 27.70(1) A X = 0.71073 A V = 1422 A 3 Dc = 1.19 gem"1 *********** ******,**.** *;**.**,* * i * * * * * ****** * * ****.*** ********* * * * * * * * scan technique and graphite-monochromatized MoKc radiation. The o-scan angle was (1.00 + 0.35 tan 6)°, and the aperture was (2.75 + tan 6)mm wide and 4 mm high. The i n t e n s i t i e s of three check r e f l e c t i o n s (0 -4 0, -1 0 -17, and 0 -1 -17) were measured every one hour and were used to scale the data. The same three r e f l e c t i o n s were used for orientation control; reorientation occurred 1 i f the difference' between observed and calculated" scattering vectors was greater than 0.050°. Of the 812 unique r e f l e c t i o n s c o l l e c t e d in the range 1 < 6 < 25°, 562 (69.2%) had 153 l/<r(l) > 3 . 0 and were considered observed. The structure was solved by direct methods... 30,5 E's greater than 1 . 2 0 were obtained from a K-curve and input into the MULTAN programme. Seven r e f l e c t i o n s had known phases determined from I,-relationships (8 0 0 , 0 0 1 6 , and 6 2 0 phase 0 ; 2 2 3 0 , 6 0 0 , 4 2 0 , and 5 1 0 phase ir) and the o r i g i n was fixed by assigning phase 3 i r/4 to the strongest E, 7 0 5 . Three symbols, one of which had r e s t r i c t e d values to determine the enantiomorph, were used to generate 12 sets of phases, and an E- map off the correct set enabled the location of a l l ten carbons in the asymmetric unit. After three isotropic and three anisotropic full-matrix least-squares refinement cycles, a difference map showed a l l the hydrogen atoms. After several more least-squares cycles with a polynomial weighting scheme with c o e f f i c i e n t s that were updated after every cycle, the refinement converged to a f i n a l R of 0 . 0 3 0 and Rw of 0 . 0 3 7 ( 0 . 0 6 0 and 0 . 0 3 7 including the unobserved r e f l e c t i o n s ) . In the last cycle, the c o e f f i c i e n t s of the polynomial weighting scheme were A = - 0 . 0 2 0 1 , B = 0 . 0 3 7 2 2 , C = - 0 . 0 0 4 2 1 1 , and D = 0 . 0 0 0 1 6 9 . F i n a l p o s i t i o n a l and thermal parameters are l i s t e d in Tables LVI11 and LIX. Results For each structure the asymmetric unit i s one half the molecule; the other half is generated by rotation about a twofold axis intersecting the C(1)-C(1') bond. Molecular views 1 54 TABLE LVIII. POSITIONAL AND ISOTROPIC THERMAL PARAMETERS OF OPTICALLY ACTIVE 1,1'-BINAPHTHYL (fractional- x 10", H x 10 3, U x 103 A 2) Atom X z Ueq/Uiso c ( i ) 4852(3) 3743(3) 2582(1) 45 C(2) 4660(4) 2074(3) 2347(1) 60 C(3) 3353(4) 740(4) 2493(1 ) 69 C(4) 2253(4) 1070(3) 2878(1 ) 63 C(5) 1299(4) 3116(4) 3556(1 ) ' 64 C(6) 1483(4) 4729(4) 3807 (1 ) 71 C(7) 2744(4) 6096(4) 3652(1 ) 65 C(8) 3831(3) 5813(3) 3254(1) 50 C(9) 3702(3) 4117(3) 2989(1 ) 42 COO) 2397(3) 2755(3) 3141(1) 49 H(2) 551(3) 186(3) 207(1) 66(6) H(3) 327(4) -51(4) 231 (1 ) 91 (8) H(4) 138(3) 20(4) 300(1) 71 (7) H(5) 33(4) 208(4) 364(1) 95(9) H(6) 69(4) 497(4) 409(1) 83(8) H(7) 290(4) 725(4) 383(1) 79(8) H(8) 466(3) 678(3) 314(1 ) 51 (6) 1 55 TABLE LIX. ANISOTROPIC: THERMAL PARAMETERS. OF OPTICALLY ACTIVE 1,1' -BINAPHTHYL ( U i j X 103 A 2) Atom U i 1 U 2 2 U 3 3 U 1 2 U , 3 u 2 3 C(1 ) 50(1 ) 46( 1 ) 40(1) 0(1) -5(1 ) 1(1) C(2) 73(2) 56 ( 1 ) 52(1) -3(1 ) 3(1) . -10(1) C(3) 88(2) 49(1 ) 70(1) -12(1 ) -8(2) -12(1) C(4). 67(2) 50(1 ) 72(1) -20(1 ) -7(1 ) 6(1 ) C(5) 59(1 ) 68(2) 67(1) -4(1 ) 10(1) 11(1) C(6) 67(2) 79(2) 67 ( 1 ) 4(2) 22(1) -1(1) C(7) 71 (2) 62(2) 62(1) 4(2) 9(1 ) -13(1) C(8) 53(1 ) 44(1) 52(1) K D 1(1) -2(1 ) C(9) 40(1) 44(1) 42(1) K D -6(1 ) 5(1 ) C( 10) 47(1 ) 47(1 ) 52(1) -2(1 ) -3(1 ) 10(1) 1 56 showing the l a b e l l i n g scheme and 50% thermal e l l i p s o i d s of both molecules are shown in Figure 22. The naphthalene residues are approximately at right angles to each other in both cases, although in the naphthidine the arrangement i s s l i g h t l y c i s (dihedral angle of 87°) while in binaphthyl i t i s s l i g h t l y trans (101.5°). Bond lengths and angles are shown in Tables LX and LXI . There are four types of bonds in the naphthalene unit: the C(2)-C(3) type (a), the C(1)-C(2) type (b), the C(1)-C(9) type (c) and the C(9)-C(10) type (d). For each structure the bond lengths have been averaged within each bond type and the results are compared to other structures containing the naphthalene unit in Table LXII. The structure of the naphthalene unit i s reasonably invariant in these compounds. Bond angles are a l l very close to the expected sp 2 angle of 120°. Mean plane calculations (Tables LXI11 and LXIV) show a s l i g h t bend in the asymmetric unit along the C(9)-C(10) bond of 2.54° for naphthidine and 1.6° for 1,1'-binaphthyl. The amino hydrogens are not coplanar with the rest of the asymmetric unit; rather the NH2 plane (plane 4, Table LXI11) is about 60° away from the naphthalene plane. The position of the amino hydrogens, however, should not be given too much weight considering the d i f f i c u l t y in locating them. In both structures the molecules s p i r a l around the fourfold axis in the c-direction and the c r y s t a l s are held together by van der Waals forces. Figure's 23 and 24 display packing diagrams of these two structures. In naphthidine the closest intermolecular N...N distance i s 3.48(2) A, which i s 157 F i g u r e 22. M o l e c u l a r views of o p t i c a l l y a c t i v e n aphthidine (above) and 1,1'-binaphthyl (below) 158 TABLE LX. BOND LENGTHS AND ANGLES IN OPTICALLY ACTIVE NAPHTHIDINE bond length( A ) bond length( A ) C(1)-C(2) 1.375(7) C(5)-C(6) 1.344(11) C(1)-C(9) 1 .430(7) C(5)-C(10) 1.411(9) C(1)-C(1 ) ' 1.481(9) C(6)-C(7) 1.394(11) C(2)-C(3) 1.447(9) C(7)-C(8) 1.378(9) C(3)-C(4) 1.357(10) C(8)-C(9) 1.423(7) C(4)-C(10) 1.396(9) C(9)-C(10) 1.438(8) C(4)-N 1.420(8) C(2)-H(2) 1.078(7) C(7)-H(7) 1.049(10) C(3)-H(3) 1 .084(7) C(8)-H(8) 1.072(6) C(5)-H(5) 1.075(8) N-H(N1) 1.147(9) C(6)-H(6) 1.063(9) N-H(N2) 1.028(9) bonds angle(deg) bonds angle(deg) C(2 ) - c ( D - C(9) 1 18 .4(5) C(5) -C(6)-C(7) 1 20. 9(8) C(2 ) - c d )-C(1 )' 121 .8(5) C(6) -C(7)-C(8) 119. 9(9) C(9 ) - c d )-C(1)' 1 1 9 .7(4) C(7) -C(8)-C(9) 121. 3(7) C(1 )-C(2)-C(3) 1 19 .9(6) C(1 ) -C(9)-C(8) 1 20. 9(5) C(2 )-C(3)-C(4) 1 20 .7(7) C(1 ) -C(9)-C(10) 121 . 7(5) C(3 )-C(4)-C( 10) 1 22 .2(7) C(8) -C(9)-C(10) 117. 3(6) C(3 )-C(4)-N 1 1 7 . (9) C(4] -C(10)-C(5) 1 24. 1(7) C( 10)-C(4) -N 1 20 .0(8)- C (4-: - e ( IO-)-G(9) 1 17. 0(6) C(6 )-C(5)-C( 10) 121 .6(7) C(51 -C(10)-C(9) 118. 9(7) C(1 )-C(2)-H(2) 1 19 .5(6) C(6 )-C(7)-H(7) 119. 6(8) C(3 )-C(2)-H(2) 1 20 .6(6) C(8 )-C(7)-H(7) 1 20. 5(8) C(2 )-C(3)-H(3) 1 18 . 1(8) C(7 )-C(8)-H(8) 1 20. 2(7) C(4 )-C(3)-H(3) 121 .2(8) C(9 >-C(8)-H(8) 118. 5(5) C(6 )-C(5)-H(5) 1 19 .9(9) C(4 )-N-H(N1) 113. 3(8) C(1 0)-C(5) -H(5) 1 18 .5(9) C(4 )-N-H(N2) 114. 9(7) C(5 )-C(6)-•H(6) - 1 18 .3(10) H(N 1)-N-H(N2) 111. 4(6) C(7 )-C(6)-•H(6) 1 20 .7(10) 159 TABLE LXI. BOND LENGTHS AND ANGLES IN OPTICALLY ACTIVE 1,1'-BINAPHTHYL bond length( A ) bond length( A ) C(1)-C(2) C(1)-C(9) C(1)-c(1)' C(2)-C(3) C(3)-C(4) C(4)-C(10) 1 .369(3) 1.421(3) 1.494(4) 1.398(4) 1.347(3) 1.415(3) C(5)-C(6) C(5)-C(10) C(6)-C(7) C(7)-C(8) C(8)-C(9) C(9)-C(10) 1 .354(4) 1.417(3) 1 .400(4) 1.364(3) 1 .424(3) 1 .416(3) C(2)-H(2) C(3)-H(3) C(4)-H(4) C(5)-H(5) 0.99(2) 1.02(3) 0.94(2) 1.04(3) C(6)-H(6) C(7)-H(7) C(8)-H(8) 0.98(2) 0 .96 ( 3 ) 0.97(2) bonds angle(deg) C(2) -C(1 ) -C(9) 1 19 .0(2) C(2) -C(1 ) -CO ) ' 1 20 .7(2) C(9) -CO ) -CO )' 1 20 .4(2) C(1 ) -C(2) -C(3) 121 .8(2) C(2) -C(3) -C(4) 1 20 . 1(2) C(3) -C(4) -COO) 121 .0(2) C(6) -C(5) -COO) 121 .2(3) C(5) -C(6) -C(7)- 1 20 .2X2). C(1 ) -C(2) -H(2) 1 1 6 .2(14) C(3) -C(2) -H(2) 1 22 .0(14) C(2) -C(3) -H(3) 1 1 9 .9(15) C(4) -C(3) -H(3) 120 .0(15) C(3) -C(4) -H(4) 1 23 .7(15) C(10)-C(4)-H(4) 1 1 5 .205) C(6) -C(5) -H(5) 1 23 .6(13) bonds angle(deg) C(6) -C(7)-C(8) 120 .8(2) C(7) -C(8)-C(9) 120 .5(2) CO ) -C(9)-C(8) 1 22 .2(2) CO ) -C(9)-COO) 1 19 .3(2) C(8) -C(9)-COO) 1 18 .5(2) C(4) -CO0) -C(5) 1 22 .3(2) C(4) -COO) -C(9) 1 18 .8(2) C(5) -COO) -C(90- 118 .9(2) C(10)-C(5) -H(5) 1 15 .203) C(5) -C(6)~ H(6) 1 20 .0(15) C(7) -C(6)- H(6) 120(2) C(6) -C(7)- H(7) 121 .605) C(8) -C(7)- H(7) 1 17 .705) C(7) -C(8)-•H(8) 1 20 .6(11) C(9) -C(8)-•H(8) 1 18 .9(11) 160 TABLE LXII. NAPHTHALENE UNIT BOND LENGTH COMPARISON ( A ) bond type s t r u c t u r e a b c d o p t . a c t i v e n a p h t h i d i n e 1.421(27) 1.364(13) 1 .415(13) 1.438(8) o p t . a c t i v e 1 , 1 ' - b i n a p h t h y l 1.399(4) 1.395(9) 1.419(4) 1 .416(3) racemic 1,1'- b i n a p h t h y l 1.404(3) 1.357(4) 1.418(4) 1.416(3) o p t . a c t i v e 4 , 4 ' - d i m e t h y l - 1 , 1 ' - b i n a p h t h y l 1.401(22) 1.368(4) 1.416(6) 1 .436(6) racemic 4,4'- d i m e t h y l - 1 , 1 ' - b i n a p h t h y l 1.410(3) 1.369(2) 1.426(3) 1.426(3) n a p h t h a l e n e 1.416(6) 1.357(4) 1.420(3) 1.405(3) ( e r r o r s a r e the maximum of the rms d e v i a t i o n from the mean and t h e rms s t a n d a r d d e v i a t i o n s of the bond l e n g h t h s ) TABLE LXIII. MEAN PLANES IN OPTICALLY ACTIVE NAPHTHIDINE Equations of planes (!X+mY+nZ=p) >lane 1 m n p 1 0.3352 -0 .6499 -0 .6821 -3 .81 57 2 0.3284 -0 .6382 -0 .6963 -3 .8953 3 0.3461 -0 .6628 -0 .6641 -3 .7679 4 0.3607 0 .2622 -0 .8951 -1 .9504 at ions from planes ( A ) atom 1 2 3 4 C(1 ) 0 .008(5)* 0. 000(5)* 0. 073(5) -2. 94 C(2) 0 .025(7)* 0. 002(7)* 0. 113(7) -2. 97 C(3) 0 .012(8)* -0. 001(8)* 0. 089(8) -1 . 95 C(4) -0 .018(8)* -o . 004(8)* 0. 027(8) -o . 98 C(5) 0 .005(8)* 0. 064(8) -0. 009(8)* 0. 1 4 C(6) 0 .063(10)* 0. 138(10) 0. 026(10)* 0. 21 C(7) 0 .017(8)* 0. 083(8) -0. 008(8)* -o . 77 C(8) -0 .012(6)* 0. 026(6) -0. 006(6)* -1. 80 C(9) -0 .023(5)* -0. 003(5)* 0. 008(5)* -1. 90 C(10) -0 .027(6)* 0. 005(6)* . 0. 007(6)* -o . 89 N 0 .005(8)* 0. 030(8) 0. 041(8) 0. 00* H(N1 ) 0 .309 0. 319 0. 367 0. 00* H(N2) -0 .844 -0. 810 -0. 819 0. 00* *atoms included in plane calculations Angles between normals to the planes planes (1) and (2) planes (1) and (3) planes (1) and (4) 1.13° 1.41° 55.9° planes planes planes (2) (2) (3) and (3) and (4) and (4) 2.54 55.0 57.0 TABLE LXIV. MEAN PLANES IN OPTICALLY ACTIVE 1,1'-BINAPHTHYL Equat ions of planes (!X+mY+nZ=p) plane 1 2 3 -0.6879 -0.7050 -0.6960 0, 0 0 m 4111 4143 4121 n -0.5981 -0.5762 -0.5880 -5.5682 -5.4144 -5.5119 Deviations from planes ( A ) atom 1 2 3 C(1 ) 0 .000(2)* -o. 050(2) -0. 009(2)* C(2) -0 .006(2)* -o. 071(3) -0. 022(3)* C(3) 0 .003(3)* -o. 039(3) -0. 002(3)* C(4) 0 .005(3)* 0. 000(3) 0. 017(3)* C(5) -o .047(3) 0. 004(3)* -0. 009(3)* C(6) -0 .076(3) -0. 011(3)* -0. 033(3)* C(7) -0 .040(3) 0. 004(3)* -0. 006(3)* C(8) 0 .000(2) 0. 006(2)* 0. 016(2)* C(9) 0 .004(2)* -0. 007(2)* 0. 013(2)* C( 10) -0 .007(2)* 0. 005(2)* 0. 013(2)* H(2) -0 .03(2) -0. 13(2) -0. 06(2) H(3) -0 .02.(3) -0. 08(3) -0. 04(3) H(4) -0 .02(2) -0. 01 (2) -0. 00(2) H(5) -0 .02(3) 0. 05(3) 0. 03(3) H(6) -0 .08.(2) 0-. 01( 2:) -0. 0.3(2) H(7) -0 .07(3) -0. 01 (3) -0. 03(3) H(8) 0 .06(2) 0. 06(2) 0. 07(2) *atoms included in plane calculations Angles between normals to the planes planes (1) and (2) planes (1) and (3) planes (2) and (3) 1 .60° 0.74° 0.85° 163 F i g u r e 23. Packing diagram f o r o p t i c a l l y a c t i v e naphthidine 164 F i g u r e 24. Packing diagram f o r o p t i c a l l y a c t i v e 1,1'-binaphthyl 165 considerably greater than the N...N range of 2.88 to 3.38 A normally associated with N-H...N type hydrogen bonding" 6. Discussion Table LXV compares the two structures described in this chapter to some other related compounds with known c r y s t a l structure. We are looking for some unique aspect of the c r y s t a l structures of the racemic/optically active 1,1'-binaphthyl pair that might help explain why only racemic 1,1'-binaphthyl undergoes spontaneous resolution whereas the substituted binaphthyls do not. There are five structures in question: those of racemic 3 7 and o p t i c a l l y active 1,1'-binaphthyl, racemic and o p t i c a l l y active 4,4'-dimethyl-1,1'-binaphthyl, and o p t i c a l l y active naphthidine. Of these, the two racemic structures c r y s t a l l i z e in the monoclinic space group C2/c, and the three o p t i c a l l y active structures c r y s t a l l i z e in the tetragonal, space: group-P4, 2 ,2 (or P4 32,2). This already seems more than mere coincidence, although i t may not appear immediately s i g n i f i c a n t . The dihedral angles between the naphthalene residues of the racemic structures are v i r t u a l l y i d e n t i c a l (68.4 and 68.6°), whereas those of the o p t i c a l l y active structures vary between 80 and 101°. This agrees with the calculated densities - because of the smaller dihedral angle, the racemic molecules are more compact and hence pack more densely (1.28 vs 1.19 gem - 3 for binaphthyl and 1.25 vs 1.15 gem - 3 for dimethylbinaphthyl). The 166 TABLE LXV. COMPARISON OF BINAPHTHYL-TYPE STRUCTURES structure space group c e l l param. ( A,deg.) V ( A 3) Dc (g/cc) p,q* (deg.) racemic 1,1'- binaphthyl C2/c a=21.126 b= 6.342 C=10.218 *=105.19 1 302 1 .279 p=68.6 q=1 .0 o p t i c a l l y active 1,1'- binaphthyl P4,2,2 a= 7.164 c=27.70 1 422 1.19 P=101.5 q=1 .6 racemic 4,4'- dimethyl-1,1'- binaphthyl C2/c a=13.225 b=l0.768 c=11.572 0=114.04 1505 1 .246 p=68.4 q=3.0 opt. active 4,4'-dimethyl- 1,1'-binaphthyl P4,2 , 2 a=8.3031 c=23.706 1 634 1 . 148 p=80 q=2.7 opt. active naphthidine P4 12 l2 a= 7.945 c=24.264 1 532 1 .23 p=87 q=2.5 *p = the dihedral angle between molecular halves q = the bending angle along C(9)-C(10) 1 67 racemates, because they are packed s l i g h t l y more e f f i c i e n t l y , w i l l have a s l i g h t l y higher l a t t i c e energy and thus, are. s l i g h t l y more stable, at least at room temperature. Unfortunately as t h i s i s true for both 1,1'-binaphthyl and the dimethyl derivative, room-temperature l a t t i c e energies offer no explanation for the observed differences in behaviour. The unit c e l l volume is somewhat greater for dimethyl- binaphthyl and naphthidine than for binaphthyl in both racemic and o p t i c a l l y active cases, as could be expected from the extra bulk due to the 4,4' substituents. It has been suggested 3 7 that the 'bending angle' between the two rings of the naphthalene residue i s a function of intramolecular close contacts, which in turn depend on the dihedral angle between the molecular halves, but the figures shown in Table LXV do not support t h i s suggestion. If anything, the bending angles seem to depend on the substituent: 1.0 and 1.6° for binaphthyl, 2.5° for naphthidine, and 2.7 and 3.0° for dimethylbinaphthyl; however a l l these bendings are small and the differences between them are probably i n s i g n i f i c a n t . The shapes of the unit c e l l s are worth some discussion: the o p t i c a l l y active structures a l l have unit c e l l s of similar dimensions, approximately an 8 A base and elongated along the fourfold axis (c-direction) to about 24 A. This could be the reason why o p t i c a l l y active naphthidine so readily acts as a seed" 3 in the resolution of dimethylbinaphthyl. It i s interesting to note that the binaphthyl racemate, which does undergo spontaneous resolution to the o p t i c a l l y active form, also has an elongated unit c e l l of similar dimensions 168 (21 x 6 x 10 A 3, fi = 105°), whereas the dimethylbinaphthyl racemate, which does not undergo spontaneous resolution, has a unit c e l l of quite a d i f f e r e n t shape (13 x 11 x 12 A 3, fi = 114°). I n t u i t i v e l y one might expect that the s o l i d state conversion from the racemate to the o p t i c a l l y active form would proceed more eas i l y i f the unit c e l l s were of similar shape than i f they were very d i f f e r e n t . Although i t would not be conclusive, i t would s t i l l be of great interest to see i f t h i s also holds true for naphthidine, i . e . , to see i f the racemic naphthidine unit c e l l shape i s also very di f f e r e n t to that of the o p t i c a l l y active naphthidine. Recently, I.C. Paul and co-workers" 7 have studied the spontaneous resolution process v i s u a l l y under a microscope and have observed the nucleation and subsequent migration of an opaque front through the c r y s t a l s , and also the growth of o p t i c a l l y active c r y s t a l s on the racemic c r y s t a l surfaces. They suggest that, at least at their experimental conditions, the conversion from racemic to o p t i c a l l y active 1,1'-binaphthyl involves a sublimation process rather than a s o l i d - s o l i d transformation. If t h i s is the case, room temperature investigations into the s o l i d state properties of the materials involved may not present immediate r e s u l t s . Perhaps the systems should be studied at elevated temperatures to determine the temperature effects on the r e l a t i v e energies of racemic and o p t i c a l l y active 1,1'-binaphthyl. These effects might then be able to explain why o p t i c a l l y active binaphthyl becomes' more stable at higher temperature. 169 Half-normal probability plots The probability of two (or more) simultaneous .(or nearly simultaneous) independent determinations of a given c r y s t a l structure has greatly increased since automated d i f f T a c t o m e t e r s and more powerful techniques have become widely available^ In such cases i t i s of interest to perform a s t a t i s t i c a l comparison of the derived parameters, thereby either increasing or decreasing confidence in the r e s u l t s . The o p t i c a l l y active 1,1'-binaphthyl structure presented in this chapter has recently been independently determined by I.C. Paul et a l " 7 in Urbana, I l l i n o i s (a = 7.181(2), c = 27.68(1) A, R = 0.043 for 978 r e f l e c t i o n s with l/«r(l) > 2.0), and by S.F. Mason et a l " 8 in London, U.K. (a = 7.2126(9), c = 27.510(5), R = 0.045 for 731 r e f l e c t i o n s with I/«r(I) > 3.0). These sets of results (set L from London, set U from Urbana, set V from Vancouver) may be compared using normal probability p l o t s " 9 . The ranked deviates are plotted against those- expected' for a. p a r t i c u l a r ddstri-but ion-, and i f . the- assumed d i s t r i b u t i o n i s correct, the plot should be linear with unit slope and pass through the o r i g i n . Deviations from l i n e a r i t y indicate that the assumed d i s t r i b u t i o n may not be t o t a l l y correct; deviations from unit slope indicate that the standard deviations have been overestimated ( i f slope < 1 ) or underestimated ( i f slope > 1); and deviation from zero intercept indicates either systematic error or some scaling problem. In the following plots, the magnitudes used are the posi t i o n a l parameters of the ten carbons, and their deviates are 170 plotted against those expected for a normal d i s t r i b u t i o n . The p o s i t i o n a l parameters of the hydrogen atoms could not be included in the U-V comparison as they were not refined in set U but they were in set V. For the sake of conformity they were also excluded in the L-V comparison. For p o s i t i o n a l parameters the signs of the deviates are redundant (as i t is equally v a l i d to use transformed sets of coordinates where the signs of the deviates would be d i f f e r e n t ) and a half-normal probability plot is used. The coordinates for set L are related to those of sets U and V by the symmetry operation (1/2-y, 1/2-x , 1'/2-z) . The deviates 6(Pi) of the i ' t h p o s i t i o n a l parameter are calculated as 6(Pi)=|Pi(U)-Pi(V) | / U 2 [ P i ( U ) W 2 [ P i ( V ) ] } 1 / 2 and 6(Pi)=|Pi(L)-Pi(V)| / { c 2 [ P i ( L ) ] + * 2 [ P i ( V ) ] } 1 / 2 and ranked according to magnitude. The expected ranked deviates are readily available from Table 4.3.2.D of International Tables for X-ray Crystallography 6, Vol. IV, and the resulting plots appear in Figure 25. The apparent departures from l i n e a r i t y are without significance; the l i n e a r i t y of the plot compares reasonably well to previous half-normal p l o t s " 9 . The intercepts are s u f f i c i e n t l y close to zero to indicate no systematic errors of importance. For the U-V comparison, the slope i s s l i g h t l y less than unity (0.7) indicating that the pooled standard deviations are only s l i g h t l y overestimated (by about 30%). For the L-V comparison, the slope i s around 1.5, indicating that the pooled standard deviati'oTrs'* are' underestimated by about 50%. In other words, the results of I. Paul add confidence to the results obtained in t h i s chapter, whereas the results of 3.0 H L vs. V X x « 2.0 A x x x xx l.o H U vs.V xx X X ° XX 0.0 1.0 2.0 expected 6ipL) Figure 25. A half-normal p r o b a b i l i t y plot 172 S.F. Mason are s l i g h t l y d i f f e r e n t . To account for this difference, the pooled standard deviations between sets L and V should be s l i g h t l y increased. From the R values and standard deviations of the three structure determinations, i t might be inferred that the work in set L i s the least accurate of the three, and perhaps i t is the standard deviations in set L that should be s l i g h t l y increased. It must be pointed out, however, that although the analysis in this chapter does have the lowest R value, i t i s based on the least amount of observed data. One might argue that i t is easier to create a model to f i t 562 r e f l e c t i o n s well than one to f i t 731 or 978 r e f l e c t i o n s , and that the R value might well be lower for fewer r e f l e c t i o n s . Nevertheless, the standard deviations in the analysis in t h i s chapter are lower than in the other two sets, and these have also t r a d i t i o n a l l y been taken as a measure of accurate determination. The results of the U-V comparison suggest that these standard deviations may even be s l i g h t l y reduced. In conclusion, i t may be said that the p o s i t i o n a l parameters from sets U and V are indeed representative of the true structure of 1,1'-binaphthyl, and that the p o s i t i o n a l parameters from set L would l i k e l y be more representative of the structure were their standard deviations increased by roughly 50%. 1 73 SUMMARY This thesis has presented the successful structure determinations of eight organic compounds in a variety of applications. In chapter two, the concern was the i d e n t i f i c a t i o n of two separated isomers that would have been d i f f i c u l t to characterize by other means. Some chemical evidence inspired additional analyses to investigate the p o s s i b i l i t y of one of the isomers having a highly strained trans-fused four and five membered ring system. The existence Of th i s strained ring system was disproved, leading, with true s c i e n t i f i c s p i r i t , to further organic mechanistic research. Chapter three contains a more t y p i c a l project: confirmation of a postulated structure by x-ray analysis. A strained intermediate had been proposed! for a-hydrogen' exchange reaction, a compound had been isolated with spectral properties suggesting t h i s intermediate, and the structure was confirmed by x-ray crystallography. Chapter four contains two analyses that should dispel the myth that x-ray structure determinations have become routine. These analyses required far more e f f o r t than i s obvious from their descriptions, and their ultimate solution was s u f f i c i e n t reward. Raucubaine, the f i r s t of these two structures, is an indole a l k a l o i d which could not be completely characterized by 174 other means, i . e . , i t s structure was previously unknown and hence the elucidation was more s i g n i f i c a n t . The second analysis was meant to confirm the N.M.R. structural assignments of a sugar, but was undertaken here more as a challenge than out of chemical interest (because i t was s t i l l there...). Chapter fiv e shows that x-ray analyses may be used to lend insight into problems that are not purely of a structural nature. In th i s case, packing e f f e c t s are inspected in order to try and account for differences in s t a b i l i t y between two enantiomeric forms of 1,1'-binaphthyl. It seems now, however, that this investigation would probably be more meaningful were i t c arried out at elevated temperatures. It i s hoped that the u t i l i t y of x-ray crystallography in chemical research is demonstrated. 175 REFERENCES G. H. Stout and L.H. Jensen. X-ray Structure Determination: A P r a c t i c a l Guide. The MacMillan Company, London. 1968. M.J. Buerger. Crystal Structure Analysis. J. Wiley and Sons, Inc., New York. 1959. M.J. Buerger. Vector Space. J . 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MULTAN-80, A System of Computer Programs for the Automatic Solution of Crystal Structures from X-ray D i f f r a c t i o n Data. University of York, England. 1980. 35. W.C. Hamilton. Acta Crystallogr., J_8, 502 (1965) 179 36. N.L. Paddock and S.J. Rettig, to be published. 37. K.A. Kerr and J.M. Robertson. J. Chem. Soc. B, 1146 (1969). 38. R.E. Pincock and K.R. Wilson. J . Chem. Ed., 50, 455 (1973). 39. R.E. Pincock, R.P. Bradshaw, and R.R. Perkins. J. Mol. Evol. , 4, 67 (1974). 40. R.E. Pincock and K.R. Wilson. J . Am. Chem. S o c , 9_7, 1474 (1975). 41. R.E. Pincock and K.R. Wilson. Can. J. Chem., 5_5, 889 (1977) . 42. F.N. Fung and R.E. Pincock, unpublished work, 1975. 43. M.D.-M. Lu and R.E. Pincock. J. Org. Chem., 4_3, 601 (1978) . 44. R.A. Pauptit. M.Sc. Thesis, University of B r i t i s h Columbia, Vancouver, B.C., Canada. 1978. 45. R.A. Pauptit and'J. Trotter. Can. J . Chem., 5_9, N7, 1149 (1981). 180 46. W.C. Hamilton and J.A. Ibers. Hydrogen Bonding in Solids. W.A. Benjamin Inc., New York.. 19.6.8.. 47. R.B. Kress, E.N. Duester, M.C. Etter, I.C. Paul, and D.Y. Curtin. J. Am. Chem. S o c , 102, 7709 (1980). 48. R. Kuroda and S.F. Mason. J. Chem soc. Perkin II, 167 (1981). 49. S.C. Abrahams. Acta Crystallogr., A25, 165 (1969). APPENDIX: STRUCTURE FACTOR TABLES STRUCTURE FACTOR TABLES FOR j-CYCLOBUTYL TRICYCLIC ENONE 183 * 77??????77?r7r77777?7???77777777777777777 0 0 0 c , 0 0 0 0° 07-77777 1 r??7?r77777777??T7777777::?7777777777TT7T?£?77777?7?:2'r?7'f'r * 77777777777777777777rT77???rr??777?T???2::::277??7?7'f7??*77 1 7777??7T7?7?7777777??77777?7??777777?77777777777777'vT?777? - " " " : : ; ; ;88eese °82822282S288e82888S988SS2°282SS2S*^ r •f7777"T7T 77777 T?'f7'r?77r,rif77'f'r77777?7?7,r77777'r'f^'f?7-?'r77'''"' ; . . , . , , , . » ; B . . : . ; , S . J : : . S O ; ; ; ; . J ; ; ; . ; . . . : . . . 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S 5 5 S B 5 8 S S - « B ^ . 85588 -855888883885; :^ ' SBCkSSSS-S-"""""* " o - - - - f . . - . ? - f 8 S ? . - - - - - o - - - - " " - - " S 8 » " ----»----»»»«"•>«•--" ~ M N ~ « « « . . . . W W * * * 1 0 * .o--.----^»»»«SS58S88-E:8S_S8S"oo---.<^«. - " • - 2 » K ; 2 8 . - - S - 8 « - - 8 8 - ^ u s : 5 i o . « l ! < ! » » ' ' . . ; » „ _ - _ « • . - n - - - - - - - » 5 R ; S 8 S 8 - - - - - - . 0 - - - - — 8 8 - - 8"S«"8- „ . - - . » . - g S S S _ S S 8 S - ? S S -•^o.o8SS33S8So588588X8 = S8MS^^^ o o o p _ O O O O O - * " " " " " * - * " " - i i i ( - t - - 0 9 l B ' ' * 1 1 1 * 1 i -r r> «_ »-* •> °- - - - O u> -» ' . . - - - - . S 5 S ; » 8 E 8 - - . S 8 - - - 5 £ " ' . " . 8 : ; S S » ip - o o ~ r-_ . „ " - o - - . S S s . 8 S 3 8 S S S 8 5 S S 5 : 5 - K - - £ S > 8 ? 5 ^ ° - • - . - - " I S R S S 0 ' - - " 0 " ~ ' *" - . . l - . . 3 - . 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U 91 O a fc fc fcO * (0 0» w » u fc 1 0 y u« - - cn at o »'.'»ojji'b__j";s;»5S£5-:"«!: . O O O O O O O O O O - - M ^ _ _ k , _ < J ! l » » " ~ - - , J " - - J " " " ' _oooooooo D _) 01 O 10 fc 0 __ - "•™«____K_UCDCaiO-JfcU 1U«OI3> i ~ i _ i M U M _ j O a j fc ui cf u> oi u i j i a i u i i n u ' U i u ' f c * * . « , u » _ u - - 0 " » U ' » - " - * " u * * " O O O O O O O O U M M U » O K __>O>fcW-»01Ol-_ T • O O O O O - - " . - - - - - O O O O O - (jCBOJeaWCBCnuMM -J _̂ j f c U C o f c w w O K J C O c j O w _ 1 - J f c f c i f - 5 * ' - J 7 J < n fcfcWW-JUiO^<0fc0i«o<Ji«i cn ca in t_ as - J a > fc — on fc u — ; S 3 8 S 3 a « S . . 8 S 8 8 . a - i s i : : 8 S _ e 8 8 3 ! S 8 8 3 8 8 - - . - - - - . o - - o . kCntoQOBtOMCfi'- - O *• ) - U - u * j w x i f c f c i o O u * j - - o o o O « a i o t o i o » c o c D O s c f l » c D fc cn u fc oi of - o o o o o - - — *• . oooo *" 9 t o i c n 9 i c n c n o i u « u > tf,ufcU.oi(j-«*«»'«~iUUtf,a*,ow^ « n * „ L B - - f c M M U ~ » ' « a > 0 3SS_si-==S8I28825=8oS3352S2SS3SSS»..-«. fc<ftMfcfc*U~ 0 1 f c 0 1 U i * U ' J f f | * u ^ *u co io fc w -< "» o> y> w o O U M M M — CnCD'Jffl J.M. Haigh, L.R. Nassimbeni, R . A . Pauptit. A . L . Rodgers and G.M. Sheldrick, "The Structure of A l i p h a t i c Amine Adducts of Uranyl Acetylacetonate. I. Dioxobis(2,4-pentane- dionato)mono(2-N-methyl-aminopentan-4-one)- uranium(VI)" Acta C r y s t a l l o g r . , B32, 1398 (1976) . M.R. Caira, L.R. Nassimbeni, E. Oeser, R . A . Pauptit and G.M. Sheldrick, "The Cr y s t a l and Molecular Structure of Cholest-4-en-3-one.", Acta C r y s t a l l o g r . , B32, 1984 (1978). J.M. Haigh, L.R. Nassimbeni, A.G. Orpen, R.A. Pauptit and A.L. Rodgers, "The Structure of Al i p h a t i c Amine Adducts of Uranyl Acetylacetonate. I I . Dioxobis(2,4-pentane- dionato)mono(2-N,N-dimethyl-aminopentan-4- one)uranium(VI)" Acta C r y s t a l l o g r . , B33, 959 (1977) . ~~ J.M. Haigh, L.R. Nassimbeni, A.G. Orpen, R.A. Pauptit and A.L. Rodgers, "The Structure of Al i p h a t i c Amine Adducts of Uranyl Acetylacetonate. IV. Dioxobis(2,4-pentane- dionato)mono(2-aminopentan-4-one)uranium(VI)" Acta C r y s t a l l o g r . , B33, 3110 (1977). M.Sc. Thesis, 'X-ray Crystallographic studies of Racemic and O p t i c a l l y Active 4,4'-Dimethyl- 1,1'-binaphthyl", University of B r i t i s h Columbia, November 1978. R.A. Pauptit and J . Trotter, "Crystal Strucure of Camphor-1,4-homoenol p-Bromobenzoate", Can. J . Chem., 58, N24, 2805 (1980). J.P. Kutney, R.A. Pauptit, P. S i e r r a , J . Trotter and B.R. Worth, "Raucubaine; a new type of indole a l k a l o i d from Rauwolfia s a l i c i f o l i a griseb.", Heterocycles, 14, 1309 (1980). — R . A . Pauptit and J . Trot t e r , "Crystal Structure of a Stemodin Intermediate", Can. J . Chem., 59, N3, 524 (1981). R . A . Pauptit and J . Trot t e r , "Crystal Structure of Raucubaine", Can. J . Chem., 59, N6, 1007, (1981). R . A . Pauptit and J . Tr o t t e r , "Crystal Structure of Racemic and O p t i c a l l y Active 4,4'-Dimethyl-1,1'-binaphthyl". Can. J . Chem., 59 N7, 1149 (1981).

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