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Determination of the crystal structure of three organic compounds by X-ray diffraction Schaffrin, Roger Michael 1970

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THE  DETERMINATION OF THE CRYSTAL STRUCTURE OF THREE ORGANIC COMPOUNDS BY X-RAY DIFFRACTION  BY  ROGER MICHAEL SCHAFFRIN M.D., U n i v e r s i t y of Saskatchewan, 1963 B.A., U n i v e r s i t y o f Saskatchewan, 1965  A THESIS SUBMITTED IN PARTIAL; FULFILMENT OF THE  REQUIREMENTS FOR THE.DEGREE OF DOCTOR OF PHILOSOPHY  i n the Department of CHEMISTRY  We accept t h i s t h e s i s as conforming required  THE  t o the  standard  UNIVERSITY OF BRITISH COLUMBIA J u l y , 1970  In p r e s e n t i n g  this  thesis  an a d v a n c e d d e g r e e a t the L i b r a r y I  further  for  agree  scholarly  by h i s of  shall  this  written  the U n i v e r s i t y  make  it  freely  that permission  thesis  for  It  financial  C  .  of  Columbia,  British for  gain  Columbia  the  requirements  reference copying o f  I agree and this  shall  that  not  copying or  for  that  study. thesis  by t h e Head o f my D e p a r t m e n t  is understood  of  OcJ-cA^,,  of  for extensive  permission.  The U n i v e r s i t y o f B r i t i s h V a n c o u v e r 8 , Canada  fulfilment  available  p u r p o s e s may be g r a n t e d  representatives.  Department  Date  in p a r t i a l  or  publication  be a l l o w e d w i t h o u t my  - i i-  ABSTRACT Supervisor:  P r o f e s s o r James T r o t t e r  The c r y s t a l s t r u c t u r e of dibenzothiophene has been determined X-ray d i f f r a c t i o n .  Mo-K  by  s c i n t i l l a t i o n counter d a t a were used f o r  a  t h i s a n a l y s i s ; the s u l f u r atom p o s i t i o n was  determined by means of a  P a t t e r s o n f u n c t i o n ; the carbon atoms were l o c a t e d from a F o u r i e r s y n t h e s i s , and the hydrogen Refinement methods.  atoms, from a d i f f e r e n c e  o f p o s i t i o n a l and thermal parameters was  synthesis. by l e a s t - s q u a r e s  The m o l e c u l e i s s l i g h t l y f o l d e d , the d i h e d r a l a n g l e s between  the five-membered  r i n g and the six-membered r i n g s b e i n g 0.4°  and  1.2°.  The bond d i s t a n c e s and v a l e n c y angles are s i m i l a r to those i n r e l a t e d o  molecules.  The C-S bond l e n g t h i s 1.740  A, and the C-S-C  angle i s  91.5°. The c r y s t a l s t r u c t u r e of D L - o r n i t h i n e hydrobromide determined by means o f v i s u a l Cu-K  data. a  was  The bromine i o n p o s i t i o n ;  found by P a t t e r s o n methods; carbon, n i t r o g e n , and oxygen atoms  were l o c a t e d on F o u r i e r summations and the hydrogen difference synthesis.  The o r n i t h i n e m o l e c u l e i s a z w i t t e r i o n ,  w i t h both n i t r o g e n s a c c e p t i n g p r o t o n s . o  1.249  ,  o  A; C-N,  atoms, on a  The p o s i t i o n a l and thermal parameters were  r e f i n e d by l e a s t - s q u a r e s .  C-0,  has been  1.469  A; C-C,  t o g e t h e r by a system o f N — H  The mean bond d i s t a n c e s are o  1.532  A.  The s t r u c t u r e i s h e l d  0 (2.84, 2.84,  2.89  A) and N—H...Br  O  (3.29, 3.36,.3.46 A) hydrogen The  bonds.  c r y s t a l and m o l e c u l a r s t r u c t u r e of h i s t a m i n e diphosphate  monohydrate has been determined w i t h s c i n t i l l a t i o n counter Mo-K J  data.  a  - iii  -  The p o s i t i o n s o f the phosphorus atoms were determined  by P a t t e r s o n  methods; t h e carbon, n i t r o g e n and oxygen atoms were l o c a t e d by means o F o u r i e r s y n t h e s e s ; t h e hydrogen atoms were found on a d i f f e r e n c e synthesis.  The thermal and p o s i t i o n a l parameters  least-squares.  were r e f i n e d by  The atoms of t h i s h i s t a m i n e c a t i o n l i e i n two almost  p e r p e n d i c u l a r p l a n e s , t h e p l a n e o f t h e i m i d a z o l e r i n g and t h a t o f the side chain.  The bond l e n g t h s and angles a r e s i m i l a r to t h e correspond  i n g v a l u e s i n h i s t i d i n e h y d r o c h l o r i d e monohydrate. o  The dimensions o f  o  the two P 0 ( O H ) ~ i o n s a r e P-0 1.51 A, P-OH 1.57 A, O-P-0 115.5°, and 2  HO-P-OH 107.0°. complex system  2  The most important  f e a t u r e o f the p a c k i n g i s a  o f 0-H...0 and N-H...0 hydrogen bonds.  - iv -  TABLE OF CONTENTS Page TITLE PAGE  i  ABSTRACT  i i  TABLE OF CONTENTS  iv  LIST OF TABLES  vi  LIST OF FIGURES  v i i  ACKNOWLEDGEMENTS  viii  GENERAL INTRODUCTION  PART I .  1  THE DETERMINATION OF THE STRUCTURE OF DIBENZOTHIOPHENE  2  A.  INTRODUCTION  ,  B.  THE STRUCTURE OF DIBENZOTHIOPHENE  3  Experimental  3  Structure Analysis  5  R e s u l t s and D i s c u s s i o n  3  12  PART I I . THE DETERMINATION OF THE STRUCTURE OF DL-ORNITHINE HYDROBROMIDE  18  A.  INTRODUCTION  19  B.  THE STRUCTURE OF DL-ORNITHINE HYDROBROMIDE  19  Experimental  19  Structure Analysis  20  R e s u l t s and D i s c u s s i o n  22  PART I I I . THE DETERMINATION OF THE STRUCTURE OF HISTAMINE DIPHOSPHATE MONOHYDRATE A.  INTRODUCTION  B.  THE STRUCTURE OF HISTAMINE DIPHOSPHATE MONOHYDRATE Experimental Structure Analysis R e s u l t s and D i s c u s s i o n  BIBLIOGRAPHY  - vi-  LIST OF TABLES Table  Page Dibenzothiophene  1.  F i n a l p o s i t i o n a l and thermal parameters  8  2.  Measured and c a l c u l a t e d s t r u c t u r e  3.  Displacements from mean p l a n e s  4.  Bond d i s t a n c e s and angles i n dibenzothiophene and  factors  10 13  r e l a t e d molecules  14  D L - O r n i t h i n e Hydrobromide 5.  Measured and c a l c u l a t e d s t r u c t u r e  6.  F i n a l p o s i t i o n a l and thermal parameters  26  7.  Bond l e n g t h s and angles  27  8.  Hydrogen atoms  28  9.  Carbon-oxygen bond l e n g t h s i n some amino a c i d s  29  10.  factors  23  C a r b o x y l a t e bond angles i n o r n i t h i n e and l y s i n e derivatives  11.  30  C a r b o n - c a r b o n - n i t r o g e n angles i n o r n i t h i n e and l y s i n e derivatives  12.  13.  30  Carbon-carbon-carbon  angles i n o r n i t h i n e and l y s i n e  derivatives  31  Hydrogen bonds  35  Histamine Diphosphate Monohydrate 14.  F i n a l p o s i t i o n a l and thermal parameters  42  15.  Measured and c a l c u l a t e d s t r u c t u r e  47  16.  Bond d i s t a n c e s and angles  50  17.  Hydrogen bonds  57  18.  Environments  o f atoms i n v o l v e d  factors  i n hydrogen  bonding...  58  - vii -  LIST OF FIGURES Figure  Page Dibenzothiophene  1. (a) (b)  P e r s p e c t i v e drawing showing atom numbering  7  Projected difference synthesis  7  2.  Projected electron density d i s t r i b u t i o n  .9  3.  P a c k i n g diagram  17  DL-Ornithine 4. (a) (b) 5.  Hydrobromide  Projected electron density d i s t r i b u t i o n  24  P e r s p e c t i v e drawing showing atom numbering  24  P a c k i n g diagram  32  Histamine Diphosphate  Monohydrate  6.  Projected difference synthesis  41  7.  Projected electron-density d i s t r i b u t i o n  44  8.  P e r s p e c t i v e drawing showing atom numbering  45  9.  P a c k i n g diagram  55  Hydrogen  56  10.  bonding scheme  - viii -  ACKNOWLEDGEMENTS  I want t o thank P r o f e s s o r James T r o t t e r f o r h i s h e l p and f o r h i s great patience.  While working under him I grew t o r e s p e c t him v e r y  much f o r h i s g e n t l e manner and s c i e n t i f i c thoroughness. I s h o u l d l i k e t o thank Dr. R.J. Zwarich f o r s u g g e s t i n g t h e a n a l y s i s o f d i b e n z o t h i o p h e n e and f o r p r o v i d i n g me w i t h a sample o f t h i s compound. For  t h e a s s i s t a n c e which I r e c e i v e d from t h e U n i v e r s i t y o f B r i t i s h  Columbia Computing Finally  Centre I am g r a t e f u l .  I w i s h t o thank the M e d i c a l Research C o u n c i l o f Canada  f o r p r o v i d i n g M e d i c a l Research F e l l o w s h i p s f o r the academic y e a r s 1965-1967.  - 1 -  GENERAL INTRODUCTION  In 1912 von Laue suggested t h a t c r y s t a l s s h o u l d d i f f r a c t X - r a y s ; t h i s was confirmed e x p e r i m e n t a l l y by F r i e d r i c h and K n i p p i n g .  Bragg  e l u c i d a t e d the mathematical i n t e r p r e t a t i o n o f X-ray d i f f r a c t i o n and determined the f i r s t  c r y s t a l s t r u c t u r e by X-ray d i f f r a c t i o n i n 1913.  S i n c e t h a t time X-ray c r y s t a l l o g r a p h y has been used to i n v e s t i g a t e the s t r u c t u r e o f matter on an atomic s c a l e .  With t h e advent o f automated  s p e c t r o g o n i o m e t e r s and d i g i t a l computers, s i z e and c o m p l e x i t y , such as hemoglobin examined by means o f X-ray  s t r u c t u r e s of r e l a t i v e l y  great  and myoglobin, have been  crystallography.  Of the v a r i o u s a n a l y t i c a l t o o l s a v a i l a b l e to the chemist, c r y s t a l l o graphy i s the o n l y one that g i v e s a complete t h r e e - d i m e n s i o n a l p i c t u r e of the m o l e c u l e .  The d e t a i l e d m o l e c u l a r s t r u c t u r e , i n t u r n , i s o f t e n  n e c e s s a r y f o r an u n d e r s t a n d i n g o f the p h y s i c a l , c h e m i c a l and b i o l o g i c a l p r o p e r t i e s of substances o c c u r r i n g i n l i v i n g organisms.  V a r i o u s amino  a c i d s , hormones, enzymes and p r o t e i n s have been s t u d i e d by means o f X-ray c r y s t a l l o g r a p h y .  I t was w i t h t h e a i d o f t h i s t o o l t h a t the Watson-  C r i c k model f o r DNA was developed.  S i n c e then,the m o l e c u l a r approach  to b i o l o g i c a l systems has gained tremendously i n f a v o r . T h i s t h e s i s concerns i t s e l f w i t h the d e t e r m i n a t i o n , by s i n g l e c r y s t a l X-ray d i f f r a c t i o n , o f the s t r u c t u r e s o f t h r e e o r g a n i c compounds. Since the methods o f g a t h e r i n g the d a t a , d e r i v i n g s t r u c t u r e  factors,;  s o l v i n g the s t r u c t u r e s by P a t t e r s o n and F o u r i e r t e c h n i q u e s as w e l l as the subsequent.refinement by l e a s t - s q u a r e s methods a r e adequately d e s c r i b e d i n many r e f e r e n c e books (1,2,3), they w i l l n o t be d e s c r i b e d i n d e t a i l i n the t h e s i s .  The compounds a n a l y s e d a r e l i s t e d  d i f f i c u l t y and m e d i c a l importance.  i n order of increasing  PART I  THE DETERMINATION OF THE STRUCTURE OF DIBENZOTHIOPHENE  -  A.  3 -  INTRODUCTION In 1955 Burns and I b a l l  (4) r e p o r t e d the c r y s t a l and m o l e c u l a r  s t r u c t u r e o f f l u o r e n e , C^H^n. determined  K u r a h a s h i e t a l (5) and L a h i r i (6,7)  the s t r u c t u r e o f c a r b a z o l e , C H N, between 1966 and 1969. 1 0  F i n a l l y , McCullough  e t a l (8) r e p o r t e d the c r y s t a l and m o l e c u l a r  s t r u c t u r e o f dibenzoselenophene,  C.„H Se, i n the w i n t e r o f 1969. I t o  i z  seemed o f i n t e r e s t  t h e r e f o r e to determine the s t r u c t u r e o f d i b e n z o t h i o -  phene C^2^gS.  B.  THE STRUCTURE OF DIBENZOTHIOPHENE Experimental When sublimed a t atmospheric p r e s s u r e i n a stream o f n i t r o g e n ,  dibenzothiophene forms t h i n , c o l o r l e s s p l a t e s which b, w i t h  are elongated along  (102) w e l l developed and s m a l l e r (100) and (001) forms.  u n i t c e l l parameters  and space group were determined  The  from v a r i o u s  p h o t o g r a p h i c and d i f f r a c t o m e t e r measurements. o  C r y s t a l data (A, Mo-K  ,  = 0.7107 A ) .  Dibenzothiophene, C . „ H S ; 0  M = 184.3; mp = 99°C. o  M o n o c l i n i c , a = 8.67 ± 0.01, b = 6.00 ± 0.01, c = 18.70 ± 0.02 A, 3 = 113.9 ± 0.1°.  °3 U = 889.5 A . :.D = 1.35, Z = 4, D = 1.38. m x F(000) = 384. A b s o r p t i o n c o e f f i c i e n t f o r X-rays, Absent  reflexions:  Space group  h0>! when £ i s odd, 0k0 when k i s odd.  is-•P2 /c (C^, ) . 1  u(Mo-K ) = 2.99 cm  The  i n t e n s i t i e s o f a l l r e f l e x i o n s w i t h 2 6 (Mo-K )< a  50° (minimum d,  o  0.84 A) were measured on a G.E. XRD 5 Spectrogoniometer, w i t h s i n g l e C r y s t a l O r i e n t e r , u s i n g a s c i n t i l l a t i o n c o u n t e r , Mo-K^ r a d i a t i o n (zirconium  f i l t e r and p u l s e h e i g h t  a n a l y s e r ) , and the m o v i n g - c r y s t a l  moving-counter t e c h n i q u e o f Furnas ( 9 ) . corrected and  A l l the i n t e n s i t i e s were  f o r background r a d i a t i o n (approximately o n l y a f u n c t i o n of 8 )  the s t r u c t u r e amplitudes were d e r i v e d  as u s u a l .  The c r y s t a l , a  square p l a t e measuring 0.58 x 0.53 x 0.20 mm was mounted w i t h b p a r a l l e l to the a x i s o f the g o n i o s t a t  so t h a t the c r o s s  t r a v e r s e d by the X-ray was 0.58 x 0.20 mm.  section  The f o l l o w i n g s o u r c e s o f  e r r o r i n the measured s t r u c t u r e f a c t o r s were c o n s i d e r e d .  Firstly,  t a k i n g the c r y s t a l as a c y l i n d e r w i t h a mean diameter o f 0.39 uR i s 0.058 and the a b s o r p t i o n constant  correction factor A  mm,  i s 1.10 and  over the range o f 6 = 0-25°; thus the maximum a b s o r p t i o n ;  e r r o r i s n e g l i g i b l e f o r the above range o f 6 .  Secondly,  absorption  e r r o r s due t o n o n - u n i f o r m i t y o f c r y s t a l dimension were e s t i m a t e d by considering lengths  the s h o r t e s t  i n the c r y s t a l .  (0.20 mm)  and the l o n g e s t  The a b s o r p t i o n  path  c o r r e c t i o n s f o r the c o r r e s p o n d -  i n g s t r u c t u r e f a c t o r s a r e exp(2.99 x 0.02/2) or 1.03 and 1.13 r e s p e c t i v e l y .  (0.8 mm)  Therefore,  and exp(2.99 x 0.08/2)  the maximum d e v i a t i o n from  the mean c o r r e c t i o n i s l e s s than 5%. Since the t o t a l maximum e r r o r i n F due t o a b s o r p t i o n i s 5% and s i n c e most o f the e r r o r s w i l l be much o • r  smaller  than t h i s v a l u e , no c o r r e c t i o n s were made f o r a b s o r p t i o n .  - 5 -  Structure The  p o s i t i o n o f t h e s u l f u r atom was determined from a t h r e e -  dimensional Patterson synthesis f a c t o r s were c a l c u l a t e d only, using s c a t t e r i n g Crystallography One  Analysis  (0.156, 0.167, 0.135) and s t r u c t u r e  f o r a l l the three-dimensional data f o r s u l f u r factors  from t h e I n t e r n a t i o n a l  1962 (10) and an i s o t r o p i c thermal parameter o f 4.0 A .  l e a s t - s q u a r e s refinement reduced R to 0.56.  Fourier  T a b l e s f o r X-ray  A three-dimensional  s e r i e s summed w i t h phases based on t h e s u l f u r atom  the  positions  o f a l l t h e carbon atoms.  the  structure  factor calculations with s c a t t e r i n g  revealed  When these were i n t r o d u c e d factors  into  from t h e  °2 International  T a b l e s and B = 4.0 A , R dropped t o 0.45.  Further,  refinement o f t h e p o s i t i o n a l and i s o t r o p i c thermal parameters w i t h an o v e r a l l s c a l e  together  f a c t o r , proceeded by t h e method o f b l o c k 2 the f u n c t i o n minimized b e i n g Z w ( j F | - | F | ) .  diagonal least-squares, Since the s t r u c t u r e  q  f a c t o r s were c o n s i d e r e d t o be l e a s t  £  accurately  measured f o r the v e r y s t r o n g r e f l e x i o n s which a r e a f f e c t e d most by , a b s o r p t i o n , and f o r the v e r y weak and unobserved r e f l e x i o n s the i n t e n s i t i e s o f which a r e c l o s e  to that  w e i g h t i n g scheme employed was  v*w~ = 1 i f | F | <F , i/w" = | F |/F  where F  was taken as 5.  o f background r a d i a t i o n , j t h e q  F o r unobserved r e f l e x i o n s  i f |F |>F  i/w was 0.70.  A f t e r f o u r t e e n i s o t r o p i c l e a s t - s q u a r e s refinement c y c l e s , R was 0.12 and s h i f t s i n p o s i t i o n a l and thermal parameters were s m a l l i n magnitude and random i n d i r e c t i o n , t h e l a r g e s t one  fourth  o f a. s t a n d a r d  s h i f t b e i n g l e s s than '  deviation.  F u r t h e r refinement commenced w i t h a n i s o t r o p i c seven a n i s o t r o p i c  refinement c y c l e s  dimensional d i f f e r e n c e  synthesis  thermal parameters;  decreased R to 0.10.  A three-  summed a t t h i s stage o f the a n a l y s i s  Q  - 6 -  r e v e a l e d a l l e i g h t hydrogen atoms ( F i g u r e 1 ) . °-3 d e n s i t i e s v a r i e d between 0.4 and 1.0 eA .  T h e i r peak e l e c t r o n  When these hydrogen atoms  were i n t r o d u c e d i n t o the s t r u c t u r e f a c t o r c a l c u l a t i o n s w i t h s c a t t e r i n g °2 f a c t o r s from the I n t e r n a t i o n a l T a b l e s During  and B = 4.0 A , R f e l l  the subsequent t h r e e l e a s t - s q u a r e s c y c l e s the s h i f t s of the  i s o t r o p i c thermal and p o s i t i v e .  parameters o f hydrogen atoms 1, 3, and 8 were l a r g e  A second d i f f e r e n c e s y n t h e s i s was prepared  determine the p r e c i s e p o s i t i o n s o f hydrogens 1, 3, and 8. of  f i v e l e a s t - s q u a r e s c y c l e s completed the r e f i n e m e n t .  c y c l e , parameter s h i f t s were s m a l l and n o n s y s t e m a t i c , shift and  to 0.09.  b e i n g one q u a r t e r of a standard  one h a l f of a s t a n d a r d The  i n o r d e r to A final  During  series  the l a s t  the l a r g e s t  d e v i a t i o n f o r the h e a v i e r atoms  d e v i a t i o n f o r the hydrogen atoms.  p o s i t i o n a l and thermal parameters o f a l l the atoms as d e r i v e d  from the f i n a l l e a s t - s q u a r e s c y c l e a r e g i v e n i n T a b l e 1, t o g e t h e r  with  t h e i r s t a n d a r d d e v i a t i o n s computed from the i n v e r s e s o f the d i a g o n a l terms o f the m a t r i x of the l e a s t - s q u a r e s normal e q u a t i o n s . numbering used i s shown i n F i g u r e 1.  The atom  The hydrogen atoms were  the numbers of the carbon atoms to which they  are bonded.  assigned  The f i n a l  three dimensional all for  e l e c t r o n d e n s i t y d i s t r i b u t i o n i s shown i n F i g u r e 2; °-3 the h e a v i e r atoms are w e l l r e s o l v e d w i t h peak d e n s i t i e s o f 10 eA °-3 carbon atoms and 30 eA The  Table  f o r the s u l f u r atom.  f i n a l measured and c a l c u l a t e d s t r u c t u r e f a c t o r s a r e l i s t e d i n  2; R i s 0.083 f o r 1176 observed  dimensional  reflexions.  A final  three-  d i f f e r e n c e s y n t h e s i s was computed and showed random f l u c t u a °_3 t i o n s i n e l e c t r o n d e n s i t y as g r e a t as ± 0.6eA  (b) T h r e e - d i m e n s i o n a l d i f f e r e n c e s y n t h e s i s p r o j e c t e d a l o n g b. The hydrogen atoms have the same number as the carbon atom t o which they a r e bonded.  - 8-  Table 1 Final positional thermal  ( f r a c t i o n a l , x 10  f o r C and S, x 10  f o r H) and  °2 2 °2 (A x 10 ; B i n A ) parameters, w i t h s t a n d a r d d e v i a t i o n s i n parentheses.  Atom C(l) C(2) C(3) C(4) C(5) C(6) C(7) C(8) S(9) C(10) C(ll) C(12) C(13)  H(l) H(2) H(3) H(4) H(5) H(6) H(7) H(8)  -1496(11) -2755(11) -2693(12) -1380(10) 1934(10) 3393(11) 4362(10) 3905(11) 1542( 3) -0163(10) -0082( 8) 1403( 9) 2416( 9)  3036(16) 4659(17) 6565(17) 6938(14) 6997(14) 6675(15) 4800(17) 3197(15) 1674( 4) 3435(14) 5383(13) 5405(13) 3499(13)  -160(22) -381(11) -346(15) -126(11) 129(11) 353(10) 531(11) 463(15)  173(32) 409(32) 782(23) 846(14) 823(14) 790(16) 454(16) 209(24)  Atom  u_ 11  u, „ 12  II. 13  c(i). C(2) C(3) C(4) C(5) C(6) C(7) C(8) C(9) C(10) C(ll) C(12) C(13)  5. 33 4. 69 4. 60 4. 21 4. 6.3 4. 40 3. 87 4. 19 5. 23 4. 62 3. 10 3. 44 3. 28  -0.49 -0.60 0.51 0.32 -0.04 -1.05 -0.91 0.43 0.75 0.03 0.04 -0.58 0.01  1. 50 0. 76 1. 59 1. 88 1. 75 1. 38 1. 34 1. 51 1. 49 1. 71 1. 56 1. 28 1. 59  22 6.03 6.39 6.02 4.24 4.56 5.15 6.74 5.19 4.49 4.67 3.95 3.88 4.08  0192(5) -0087(5) 0346(5) 1047(5) 2652(5) 3314(5) 3379(5) 2808(5) 1361(1) 0903(5) 1336(4) 2060(4) 2151(4)  -023(11) -058( 5) 011( 8) 127( 5) 254( 5) 357 ( 5) 388 ( 5) 275( 7)  9(5) 2(2) 5(3) 1(2) 1(2) 1(2) 2(2) 5(3)  U „ 23  TT 33  Mean a(U)  -0.58 0.17 0.73 0.04 -0.05 -0.83 0.49 0.78 -0.63 -0.14 0.29 -0.14 0.32  3. 49 4. 06 5. 01 4. 69 4. 01 4. 31 4. 61 4. 80 4. 84 3. 55 3. 72 3. 23 4. 26  0.38 0.40 0.40 0.33 0.33 0.36 0.38 0.37 0.09 0.32 Q.28 Q.28 0.31  10 -  -  Table 2 Measured and calculated structure factors (Unobserved r e f l e x i o n s are indicated by a negative sign i n front of | F | ) . Q  L  c 0 0 c c 0 0 0 c c c i c 0 c a c c 0 c c c  L  0 c c  c  It -It) 16 -16 16 -1" 16 - 16 - 16 -16 - 16 - 1* -16 IS - Ifl l" -11 1" -18 -IB -16 -11 -11 -1" 70 -20 - 20 -7" -nr. •JW! -m -/C -72  s0c -** -22  1 _1 1 1 1 1 1  1 1 1  11.7 l.e - 1 •( la.* 12.C rl.7 4." i.? 1.1 li."  2. 7 4.7 1.4 -IK.C - 17.5 _ o,r -3. 1 -0.1 -1.C -17.1  '.r  i  2 2 7 2 2  -l.t 8.5  *•*  ;| 1 -I I  1  -}  1  -2  1  2  I  2  3:1 ICC -1 IC; SC. 1 24.C 23.7 11.4 14.* 5.4. 2i.e 15.5 -1.0 10. r t.l n . i . 14.5 -1.5 7.1 -l.t 5,H_  1  -2  1  •2  1 1  -1  *>c'.f t4.C  ">  SC. 1  3  1  -1  1  - J  1 I  -1 J  1  -s  1  -1  1 I.  4 -4  I  -*  -2.5 -5.6 CM -CP -74.4  2 -l.t -2 5.4 7 - 1 . 1 '2 -l.t 1 2».t  14. 0 •0.7 3V. £, 7.1 »C,7 -75. 7 -4 . 1 -17.7 -6.4 -11.5  i  i  11.1  2 2 2 2 J 2 2 7  1 - 1 3 -1 1 -1 1 -1  4U.» 7.5 7 C 25.4 1.4 14.1 6.5 11.*  2  -3  7.0  7.1  2  - 1  It."  It.ft  2 2  - 1 4  - U « l.F  ' I 2 2  4 -4 1H.3 4 11.1 -4 12.\  -2.1 -C.9 16.4 -16." - 1 ».4 -12.4 -70.t  "1.1  2  -4  14.)  -d.6  j 7  -4 4  5t_i_ 14.1 -19.7  2  4  4.1  2  4  5.1  10.c 4.4  0 19.* - Hi. 1 It.4 0 - IT. 1 0 3. 5 -1.7 c . . Irt.l . Al.l 0 5. 1 4 .4 0 1C.» I 1.1 0 1C1 4.' c 11.4 -to.* -6.4 1 -15. 1 4|.£ 5C.9 -*>5. 1 1 4.0 -».H IS.9 16. 1 1 15. 1 - 14.5 _ 31. 1 - 10.1 it -70.r 11.4 -1*. t 29. T - 2 * . 1 1.5 •• 7.4 T.l  J "j  0 -1C - 17.t  -4,4 79.7" - L 5. 7 L2.« -8.1 -5.Q -2.3 -14.7 -17.6 -I .2 2.4 1 .> l.H -5.7 -17.7 -12.6  14.2 ICC 14. 1 11.4 1.4 1.1 -1.5 16.4 I 7.P -1.5 -l.t -l-l -1.1 12.5 i r.) 12. C 1.4  4.1  2 I ^ 2  4 -1.5 -4 5.4 5 3 7.J - 5 11.4  2  -5  2 ? 2 2  -4 ft.7 4 7C1 -4 24.5 4 14.4  2 -4 l_ 4 2 -4  -0. ; -10.1 -7.4 -11.1 2.0 -O.t - 4 6 . *. 24.4 -22.4 -1 7.ft 14.1 4.6 I*. 4. - 1 7. 1 O.t ICS -5.1  7.7  -lie  -5. 7 -Ml.4 74. 3 - 1 1. * -0. 1  LI. 2 -12.1 15.9 . 1 6 . 4 "**•*  -5  *:!  -«.?  7 2 Z 2 2  6 71.9 -t 11.7 6 29.4 -6 22.it 6 7.4  71.1 U . "* -74.H 21."  2 2  6 l.f -ft - 1 . 2 8 Hri -t t.fl 6 l?.t -ft 4. 1 6 3.4 -ft K . l 6 -(.4 -ft 1 0 . 1  _|t ' ~\ -7  -4H. 3 15.1 -6.9 45. »  -4*4 56.o -12. 1  2  I 2 2 2 2 2 2  -15.1 -2.1 -fl.C 2.6 5,5  8.4  2 7 i i 2 2 2 2 2 2  7 -7 7 -7 1 - 7 7 -7 T -T  z  m  ie.? 16.2 12.C 21.1 4C.1 12..1 32 .1 5.1 1.1 P.4 5.7  -1.1  -•t.t 13.4 -IC-J -2.4 11.7 10. i _ _ - 2 \j> - 19.1 -16. h -14. 1 -24.1 4 3.1 -JIV 3 l.ft  15. 1 14. 1 5.S -1.1 1.2 _1 ' » C _ l f t . l -0. 1 -1.2 11.2 11 . 1 3.2 2.6 4.4 4.C 5.B -5.1 -4.4 t.J 14 . 1 15.C -1.7 -8.1 12. . 12.2 27.H 7 6.1 47.7> 46. 1 1».4 3ft. 1 I4y,4 12 3.7 36.4 35,4 22. 1 21. t  1.2 -5.-J  r  I -t 1  4  1 I  4  !  -*  17.4 75. 3 ifl.4. 12.< 17. 1 1C1 15.1 _ W•? _  1.  "9  }  .4  1  -5  l_  -4  •M.I -75.1 - 11.1 -17.0 -10.,? 14.4 I M  -1.7 2.1 14.1 -IT.ft IH.l _-18.7 14.54.» 12. 1 It.*  12.4 43.6 12.ft 15.e _ fl.l  1 1 . 1 -12.2 24.? -71. » 22.5 - 7 1 . 1 I*-? _ - 1 2 . ? 12.1 10.0  i  i*5  -3.>4  t.t ),7 12.4  II.1 8.2  - l i v a b l e 2 (Continued)  -4  ft.I tc. I 3." 26.7  II.I  _ .6.6 „  2.5 22-* 4.2  -* 4 -* \  14.2 - 1 . ( fa.7 tea  ._  -4 -s -54 -4  L  -1.4  -»  1J. t  5.4 -l.f -1.2 1. 1 i.i 4. 7 4.1 7.1  5 I.J -4 J.C 5 _- 1C.1 -4 -1.s  _  -4 6 -6 6  -*6  -4 4  -2.4 15.5 -15.1  6 -6  -{."•  11.9 p .5 2. 1 12. f 1.* -1.5 - 1  - l.t -1.4 ). I  7.1 7_ _ - L . 1. -T ~ 2.* 7 -T ). 1 7 -1.1 -T IC. » 7 I.J l.t -T7 -7  -ft 14.3  lei  z]  21 ,.e_ -t?.C 12.) • 14.5 14.2 11.2  -I. t  4. 1  li.C  -  2. ' _ - *j . 2  JC.2  21.2 it.e 25.9  -!:«  1 -M • -P  -1. i IC. 1  -H e -p i"  4. r - i .* i.i  1.7  9.4  U.H -2.4  -23.4 -5. 1 -11.1 1.2 10.1  13. 1  5.5 l.t  -9.1 1..9 -*.2 10.7 6.7  1.6  -5. a 8.C -2.*  -4. ' - 1C.9 9. 3 -2.2 12.l.ft -1.1  1 6 2 fat 1 4 0  fa (  0 C 0 0 0 1  1  6  1 -1  j 1 )  A6  -1  2  t t  4 6 4 fa 5 6 0 t 1  6  1 fa 2 t  fcft  J3  4 fa 4 o  fa e  i 6 2 fa J b *  6  1  I -1 -2 •2  .]  .\  CI fa 2  t  -10.Ii -2.6  -- 1.1.5t 1.4  uS  2.S  13.9 4.4 2.7 4.1 4. » -l.h 7.0 -9.<:  1  - j  -1*4 4.1  3. ' -9. 1 -17.1 •1.9 -o. r  5.4  1.4  -l.c  2.2  7.9 -2.* 1 1.* C. 1 2.6 -3. 1  0.4  -0. 1  ft.9 6,1. -2.° -2. 1  4 •4  IC. 1  - *. 1  4 -4  2 ) 3  * fa fa  (.  1*9 -I.I  -4,4  l.t  .. 1 6 "J  fa fa  9. 1 - 1 .*  7..1 -7.1  - 1 - 1• ' -1.4 -I." 1 1. 1  -J  t  1 1  -1.7 - 1. * -1.6  -1.4  0 !  5  12. T -I.fa 4.t -1.7  IC. 1 -U4  fa ~ 4  4 fa 4 fa  -1.? 9.7  1  -Ll.fr -2.1  fa.4 K. 1  9  2.1  1.0 -3.ft  10.5  5.C l iit. i I  -9.5  5.4  IC. 1 1.2  «. 1  4.H  -1.  J  fc.5_ •VI  4.r  -1. ' -9. 7  -5.1  "J ft.-fa. i 1  .$  _. 5 -4  -ft  2 fa« -fa 2  •  l.\ - 1 •-1.7 - 1." t. 1 IC.l  5.*.  IC. . -1 .<.  1.4  -0.1 -10.4  - J. t I .1  - 12 -  R e s u l t s and D i s c u s s i o n The  e q u a t i o n s of the mean p l a n e o f the i n d i v i d u a l r i n g s as w e l l  as the e q u a t i o n o f the mean m o l e c u l a r p l a n e a r e g i v e n i n T a b l e 3.  The  i n d i v i d u a l f i v e - and six-membered r i n g s a r e s t r i c t l y p l a n a r , but the molecule as a whole shows a s m a l l d e v i a t i o n from exact p l a n a r i t y .  The  outer atoms of the six-membered r i n g s a r e d i s p l a c e d from the mean molecular plane  (plane 1, T a b l e 3) i n the o p p o s i t e d i r e c t i o n t o the  atoms o f the five-membered r i n g , so t h a t the m o l e c u l e slightly.  i s folded very  The d i h e d r a l a n g l e s between the five-membered r i n g and the  six-membered r i n g s a r e 0.4° and 1.2°.  S i m i l a r d e v i a t i o n s from  p l a n a r i t y were r e p o r t e d f o r dibenzoselenophene ( 8 ) . The bond l e n g t h s and v a l e n c y angles a r e l i s t e d i n T a b l e 4 t o g e t h e r w i t h the c o r r e s p o n d i n g bonds and a n g l e s o f dibenzoselenophene  (8)  and c a r b a z o l e ( 7 ) .  except,  of  The d i s t a n c e s and angles a r e v e r y s i m i l a r  c o u r s e , those i n v o l v i n g u n l i k e atoms.  There a r e s m a l l v a r i a t i o n s  i n the bond l e n g t h s i n the six-membered r i n g s , l o n g e s t , and C ( l ) - C ( 2 ) and C(3)-C(4)  C ( 1 0 ) - C ( l l ) b e i n g the  the s h o r t e s t .  These v a r i a t i o n s  agree w i t h bond o r d e r d i f f e r e n c e s c a l c u l a t e d by simple m o l e c u l a r orbital  theory  (11).  deviate s l i g h t l y to  about  The i n t e r n a l angles o f the six-membered  rings  from 120° w i t h angles a t C ( l ) and C ( l l ) b e i n g  118° w h i l e the o t h e r a n g l e s are s l i g h t l y  increased.  a n g l e s i n the five-membered r i n g s o f the t h r e e m o l e c u l e s  reduced The  show g r e a t e r  d i f f e r e n c e s as a r e s u l t o f the d i f f e r e n c e i n angle a t t h e hetero-atom, the angles being 91.5°, 86.6°, and 108.3°. f o r d i b e n z o t h i o p h e n e , selenophene,  and c a r b a z o l e r e s p e c t i v e l y . o  dibenzothiophene,  dibenzo-  The C-S bond d i s t a n c e i n o  1.740 (a = 0.008)A i s c l o s e t o the mean v a l u e o f 1.72 A  - 13 -  Table 3  o Displacements  (A) from mean p l a n e s atoms used  t o d e f i n e the p l a n e s )  1  2  +0.016 +0.001 +0.009 -0.004 -0.007 +0.028 +0.012 -0.010 +0.001 -0.003 -0.019 -0.015 -0.014  C(l) C(2) C(3) C(4) C(5) C(6) C(7) C(8) S(9) C(10) C(ll) C(12) C(13)  Equations o f p l a n e s  ( v a l u e s u n d e r l i n e d r e f e r to the  3  +0.007 -0.011 +0.005 +0.005 +0.027 +0.074 +0.058 +0.026 +0.011 0 -0.007 +0.009 +0.011  ( X , Y, ; 1  +0.015 +0.006 +0.025 +0.017 +0.022 +0.059 +0.036 +0.003 +0.001 +0.001 -0.003 +0.004 -0.003  o  -0.7534 X' - 0.4711 Y + 0.4587 Z' = 0.3631  2  -0.7504 X' - 0.4682 Y + 0.4666 Z' = 0.3751  3  -0.7551 X' - 0.4647 Y + 0.4626 Z' = 0.3791  4  -0.7567 X' - 0.4773 Y + 0.4468 Z* = 0.2862  Angles between-plane normals (degrees)  . 2 3  +0.082 +0.069 +0.063 +0.033 -0.009 +0.011 -0.001 -0.006 +0.043 +0.045 +0.014 +0.001 +0.004  i n A r e f e r r e d to a, b, c*)  1  1  4  2  3  4  0.5  0.4  0.8  0.4  1.3 1.2  !  - 14 -  Table 4  o Bond d i s t a n c e s  (A) and  angles  (degrees) i n d i b e n z o t h i o p h e n e  and  related  molecules  Dibenzothiophene  o  o(C- •S) = 0.008 A o(C- •C) = 0.011 a(C- •H) ~ 0.1  a(C-S-C) a(S-C-C) CT(C-C-C) c(C-C-H)  Dibenzothiophene X=S  = 0.4° = 0.6 = 0.7 ~ 6 g  Dibenzoselenophene X=Se  Carbazo! X=NH  C(l)-C(2) C(7)-C(8)  1.396 1.371  1.384  1.371  1.390  C(2)-C(3) C(6)-C(7)  1.390 1.380  1.385  1.377  1.398  C(3)-C(4) C(5)-C(6)  1.361 1.379  1.370  1.380  1.395  C(4)-C(ll) C(5)-C(12)  1.391 1.393  1.392  1.395  1.400  C(10)-C(ll) C(12)-C(13)  1.408 1.409  1.409  1.398  1.404  C(l)-C(10) C(8)-C(13)  1.384 1.387  1.386  1.395  1.395  C(ll)-C(12)  1.441  1.441  1.453  1.467  C(10)-X(9) C(13)-X(9)  1.734 1.746  1.740  1.899  1.414  C(l)-C(2)-C(3) C(6)-C(7)-C(8)  121.1 . 122.0  121.6  121.1  121.3  C(2)-C(3)-C(4) C ( 5 ) - C ( 6 ) - C ( 7 ) ••  121.1 119.8  120.5  120.6  120.4  C(3)-C(4)-C(ll) C(12)-C(5)-C(6)  119.5 120.4  120.0  120.3  119.5  C(4)-C(ll)-C(10) C(5)-C(12)-C(13)  119.2 118.1  118.7  118.1  118.8  - 15 -  Table 4 (Continued)  X=S  X=Se  X=NH  C(ll)-C(10)-C(l) C(8)-C(13)-C(12)  121.6 121.5  121.6  121.6  122.3  C(10)-C(l)-C(2) C(7)-C(8)-C(13)  117.4 118.1  117.8  118.7  117.7  C(ll)-C(10)-S(9) C(12)-C(13)-S(9)  112.8 111.8  112.3  112.4  108.8  C(10)-C(ll)-C(12) C(ll)-C(12)-C(13)  111.4 112.4  111.9  114.3  107.1  C(4)-C(ll)-C(12) C(ll)-C(12)-C(5)  129.3 129.4  129.4  127.6  134.1  C(l)-C(10)-X(9) C(8)-C(13)-X(9)  125.6 126.7  126.2  126.0  128.9  91.5  91.5  86.6  108.3  C(10)-X(9)-C(13)  Dibenzothiophene C(l)-H C(2)-H C(3)-H C(4)-H C(5)-H C(6)-H C(7)-H C(8)-K  1.09 1.06 0.99 0.99 0.90 0.85 0.98 0.95  '  H-C(l)-C(2,10) H-C(2)-C(l,3) H-C(3)-C(2,4) H-C(4)-C(3,ll) H-C(5)-C(6,12) H-C(6)-C(5,7) H-C(7)-C(6,8) H-C(8)-C(7,13)  114,128 112,126 120,117 117,122 126,114 104,135 118,120 126,114  - 16 -  found  for related  conjugated  h e t e r o c y c l i c molecules ( 1 2 ) .  The hydrogen atoms have been l o c a t e d w i t h l e s s p r e c i s i o n .  The  o  C-H bond l e n g t h s range between 0.85 and 1.09 (a = 0.12) A w i t h a mean o  v a l u e o f 0.97 A.  The H-C-C v a l e n c y angles v a r y from 104 t o 135 (a =  o  6)  w i t h a mean v a l u e of 120°. The  The  p a c k i n g o f molecules  i n the u n i t c e l l  i s shown i n F i g u r e 3.  s h o r t e s t heavy-atom i n t e r m o l e c u l a r d i s t a n c e i s a C(5)...C(11) o  d i s t a n c e o f 3.57 A. i s no s t e r i c  S i n c e o n l y C(5) c a r r i e s a hydrogen atom, t h e r e  interaction.  The s h o r t e s t hydrogen-hydrogen i n t e r m o l e c u l a r  o  d i s t a n c e i s 2.39 A and i n v o l v e s the hydrogens o f C(2) and C ( 7 ) . o  the van der Waal r a d i u s o f hydrogen i n 1.2 A, t h e r e i s no s t e r i c strain.  Since  F i g u r e 3.  P r o j e c t i o n of the s t r u c t u r e along  b.  PART I I  THE DETERMINATION OF THE STRUCTURE OF DL-ORNITHINE HYDROBROMIDE  -  A.  19 -  INTRODUCTION L - o r n i t h i n e H N(CH ) CH(NH )COOH i s the key amino a c i d o f the 2  Krebs-Henseleit, highly  2  3  2  o r o r n i t h i n e c y c l e i n the mammalian l i v e r .  The  t o x i c ammonia produced by the deamination o f amino a c i d s i s  c o n v e r t e d i n t o the much l e s s t o x i c urea by means o f the o r n i t h i n e cycle.  Urea, the c h i e f n i t r o g e n  eliminated  v i a the k i d n e y s .  Thus, a l t h o u g h o r n i t h i n e i s not a c o n s t i -  tuent  amino .acid o f p r o t e i n s ,  acids  i n protein  B.  end p r o d u c t i n mammals, i s then,  i t i s one o f the more important amino  metabolism.  THE STRUCTURE OF DL-ORNITHINE HYDROBROMIDE Experimental DL-ornithine  small  hydrobromide was r e c r y s t a l l i z e d  from water and a  s i n g l e c r y s t a l was c u t from a l a r g e c r y s t a l l i n e mass.  c r y s t a l appeared  to be s t a b l e a t room temperature.  Unit  The  c e l l and  space group d a t a were determined from r o t a t i o n , Weissenberg, and precession  photographs. o  o  C r y s t a l d a t a (X, Cu-K a = 1.5418 A, X, Mo-K a = 0.7107 A ) . — i DL-ornithine Monoclinic,  hydrobromide,  C ^ ^ N ^ B r ; M = 213.1; m.p.  223°.  0 a = 12.18 ± 0.02, b = 7.88 + 0.02, c = 11.61 ± 0.02 A,  6 = 133° 39' ± 20'. °3 U = 806.3 A , D =1.74 m  ( f l o a t a t i o n ) , Z = 4, D = 1.75. x  F(000) = 432. Absorption c o e f f i c i e n t f o r X-rays, 53 cm Absent  uCCu-K^) = 72 cm \  \  reflexions:  h0£ when £ i s odd, OkO when k i s odd.  u(Mo-K^) =  - 20 -  Space group i s P2^/c The Cu-K^  5 ( 2 )* C  n  i n t e n s i t i e s of the r e f l e x i o n s were e s t i m a t e d v i s u a l l y  from  e q u i - i n c l i n a t i o n Weissenberg f i l m s of the h0£-h7£ l a y e r s ;  l a y e r s were c o r r e l a t e d w i t h i n t e n s i t i e s measured from Mo-K  the  precession a  f i l m s of the hkO 0.38  x 0.50  mm  and hkh  and was  the p o s s i b l e 2171 1559  zones.  approximately  independent  were observed.  The  The  c r y s t a l used measured 0.25  x  a right-angled parallelepiped.  r e f l e x i o n s w i t h i n the copper  sphere ,  i n t e n s i t i e s were c o r r e c t e d f o r L o r e n t z  p o l a r i z a t i o n e f f e c t s , but not f o r a b s o r p t i o n .  Structure  and  amplitudes  were d e r i v e d as u s u a l .  Structure Analysis The bromide i o n was  l o c a t e d by means of a  P a t t e r s o n f u n c t i o n (0.0458, 0.1271, 0.1875).  three-dimensional S t r u c t u r e f a c t o r s were  c a l c u l a t e d f o r a l l the t h r e e - d i m e n s i o n a l d a t a f o r bromine a l o n e . The  s c a t t e r i n g f a c t o r f o r Br  was  o b t a i n e d from the curve f o r the  uncharged bromine atom from the I n t e r n a t i o n a l T a b l e s f o r X-ray Crystallography of X  and X  (10) by comparison w i t h the d i f f e r e n c e s i n the v a l u e s  (X = F, CI, I) and was  c o r r e c t e d f o r anomalous d i s p e r s i o n  a c c o r d i n g to the e x p r e s s i o n  u s i n g the v a l u e s Af' and A f " g i v e n i n the I n t e r n a t i o n a l T a b l e s . i s o t r o p i c thermal parameter, B, was f a c t o r was  0.39.  taken as 4.0  A .  The  A t h r e e - d i m e n s i o n a l F o u r i e r s e r i e s was  The  discrepancy summed w i t h  Of  -  21 -  phases based on the bromide i o n ; i n t h i s e l e c t r o n - d e n s i t y d i s t r i b u t i o n , all  the carbon, n i t r o g e n ,  were i n t r o d u c e d  and oxygen atoms were i d e n t i f i e d .  These  to the s t r u c t u r e f a c t o r c a l c u l a t i o n s w i t h s c a t t e r i n g °2  f a c t o r s from the I n t e r n a t i o n a l T a b l e s and B = 4.0 A . first  least-squares  Fourier synthesis  r e f i n e m e n t c y c l e R dropped to 0.27.  gave w e l l - r e s o l v e d  D u r i n g the A second  peaks f o r each of the t e n heavy  atoms. Further  refinement of the p o s i t i o n a l and i s o t r o p i c thermal  parameters, t o g e t h e r w i t h an o v e r a l l s c a l e f a c t o r proceeded by the block-diagonal  least-squares  method, the f u n c t i o n minimized b e i n g  2 Zw(j F |—|F |) . As the s t r u c t u r e f a c t o r s a r e l e a s t a c c u r a t e f o r the v e r y s t r o n g r e f l e x i o n s which a r e d i f f i c u l t to e s t i m a t e v i s u a l l y , the w e i g h t i n g scheme employed was I  for  I  *  '  '  = F /|F |  Q  *  |F |>F , where F  was taken as 9.  o  least-squares  = 1 f o r |F |<F' and  r e f i n e m e n t , R was 0.20.  of a few r e f l e x i o n s w i t h v e r y marked estimated v i s u a l l y .  A f t e r four cycles of i s o t r o p i c At t h i s p o i n t  the i n t e n s i t i e s  |F |-|F | d i f f e r e n c e s were r e -  A f t e r an a d d i t i o n a l s i x c y c l e s o f isotropic,,  r e f i n e m e n t , R was 0.15 and the parameter s h i f t s were s m a l l and  i n magnitude  random i n d i r e c t i o n . Subsequent a n i s o t r o p i c c y c l e s o f refinement reduced R to 0.14.  At t h a t p o i n t  the t h i r t e e n hydrogen atoms o f the m o l e c u l e were  l o c a t e d by means of a d i f f e r e n c e s y n t h e s i s .  The hydrogen atoms a r e °-3 moderately w e l l - r e s o l v e d w i t h peak d e n s i t i e s of 0.7-1.3 eA . The hydrogen atoms were i n t r o d u c e d i n t o the s t r u c t u r e f a c t o r c a l c u l a t i o n s °2 w i t h s c a t t e r i n g f a c t o r s from the I n t e r n a t i o n a l T a b l e s and B = 4.0 A . During the f i n a l  three  cycles of least-squares  r e f i n e m e n t , the thermal  parameters of the hydrogen atoms were r e f i n e d i s o t r o p i c a l l y those of the h e a v i e r atoms were r e f i n e d a n i s o t r o p i c a l l y . parameter s h i f t s were s m a l l and n o n s y s t e m a t i c ; shift  d u r i n g the l a s t  while  A l l the  the l a r g e s t parameter  c y c l e b e i n g o n e - t h i r d of a s t a n d a r d d e v i a t i o n  f o r the non-hydrogen atoms and  t h r e e q u a r t e r s of a s t a n d a r d d e v i a t i o n  f o r hydrogen atoms. The  f i n a l observed  T a b l e 5; R i s 0.13  and  c a l c u l a t e d s t r u c t u r e f a c t o r s are  f o r the 1559  observed  reflexions.  d i m e n s i o n a l F o u r i e r s y n t h e s i s i s shown i n F i g u r e 4.  The The  listed,in  f i n a l threeatoms are  °-3 w e l l r e s o l v e d w i t h peak d e n s i t i e s of 70 eA f o r the bromide i o n , ° ~* 3 °™3 °~3 16 eA f o r oxygen atoms, 12 eA f o r n i t r o g e n atoms, and 10 eA for carbon  atoms.  absorption.  These h i g h peak d e n s i t i e s may The  final  be the r e s u l t of h i g h  three-dimensional d i f f e r e n c e synthesis revealed  random f l u c t u a t i o n s i n e l e c t r o n d e n s i t y d i s t r i b u t i o n as g r e a t as 1 eA  .  1  However, i n the v i c i n i t y of the bromide i o n t h e r e i s a 3 eA ,  peak f l a n k e d on two :  remaining The  opposing  °-3 s i d e s by troughs at 2 eA °-3 s i d e s by a peak of 1 eA  f i n a l p o s i t i o n a l and  atoms are i n T a b l e 6. T a b l e 7.  The  and on each of the  thermal parameters of the non-hydrogen  The bond l e n g t h s and v a l e n c y angles are i n  p o s i t i o n a l parameters of the hydrogen atoms which have  been determined  w i t h much l e s s accuracy are l i s t e d  w i t h a summary, of the m o l e c u l a r dimensions  i n T a b l e 8,  together  i n v o l v i n g hydrogen atoms.  R e s u l t s and D i s c u s s i o n Due two  to the presence  of a c e n t r e of symmetry, the u n i t c e l l  of each of. the o p t i c a l isomers of o r n i t h i n e hydrobromide.  s t a n d a r d molecule  i n t h i s a n a l y s i s happens to be the D-isomer.  contains The The  -  23 Table 5  Measured and c a l c u l a t e d  structure factors  (Unobserved r e f l e x i o n s a r e  i n d i c a t e d by a minus s i g n i n f r o n t o f J F | ) .  •ii Ii  1  h k  i'  ; :  fi 1  0 -  iii  t V  i  i1  ii.i  -ft) |-i 1  1' "  .J  1  i i .i  iii  iiii iiii  j  r;  :i [ 1? 0  i  !:»  E  1:  |i i  Mil  I  tie  ;i; 'ii :  :  •!  ij  -j ii;  :  ;  :  I  iii  I  lw  :ii '; .*  is i l :  i  § !jii  I  -i't  1  :  Ii 1 j 1i| iii1 iii; iiii j  -j'.t  iii i i i Ii 1 i !jij |j i  :|!  iii iii  .si;  %  ;  • 1 ;i 1  Ii 1  'iiihiii ;i i iii Iii:i Hi: iiiii  \  il  1  •ii iiii 1 _Jll|_ ill* ;•  i iii |i  !;"  ;i ii  -•  .-;  11  iiii a!  •i;i s  j1  ioi!  I":  —  ;i  j'ii  i ' ; •.  TW  !  loit  *  i iii  i.i- .  -J_ _ .  L  M..  -\'.'  '!;*  ii  Ii  °  lti( " i -  i  —i»tf~  ii  -  -a.  -ill  nii  S  u!»_  11 iiii ;j -j  I:! "it  1 1  iii  i  j  jjii  3—  i  • il'i  H» '  •  'r'ii  ^ i l  i  «ij  _-t  la  iV.o  -ii.'i  ill's  |  ii  4-  !__ Ijij.. fi:!  a J,i.  "ii  :;;  i  ; i :l ->.'<  i  t'a  J!J  -lis  .',  I  -i _ _ 1  • •  II'N  til  I  i'i'  -iii 1  -!'  j jl«i  io!»  lo'.b  \ ii;i :i;i  •  j j i i |*io  -ij  iiii iiii ; :  iii' -Jii'  i ;ii iii'  iiii ;|i i  i ii ;i ':! * i:p -I.N  : .  -10  I I «I  ! iil^l: i iiii iiiii  iii iiiii ii ;i i j i;i i;i ;  i't  '''4  -10  -l.t  *  ii ii  w  :',  1  •i -il i  ii  iii iii  :*  i ii  -jjii  »ii 1 fill II.I  i  'i  iii ii iiii iii:; :| ii iii* 4-  jji*  t  III:!  J.ii  :J  Iii)  ! (til  1—a—•!:;  :| ;  •  if"!" III* -  .j  j  i  1  3  •I i  !  ; i;i .i;iil  n'.l M'.l  I  -l "rl!  j ijjj |:• n.  i & is!; ;|  L.  • I  \  L 4l!«  J».o 11.'  - J "If"ii  ill'.  i  «ii •»!  i  I;  i iiii  :  io  *'•>  1S»1_  Itij  i  ~-W.\  1  t  i iii iii \ j ti  ;!.;.:  j  :i;  !! It!'  i iii; :i! ii iiii -iii:;; ~K i i iiii a jjlt i  *:  iiii.  |1  M  •i.  i  :1  :J j  i  H; iiii  11  (»i»  'i ji'i '\'\  -t  1..4 -11.'  -Ii:' •I «: i  ii  *  Ii  iiii ii; -!  S3 "B:  "i  :  J  ;•  i £  ii 1, iii  | j| i  1  iii ;jii  i ii iii :| "J ii;! 1  ,:i; si;  ;  t  i  .J  *;  i ii: ":*  i iii iiii :jj j i ii;! |j i  >i. 77*  >.l  'iii 1  iii iii 1 \ i  .iii  'ii>  -*_ _  «:]  • \a  :  i.t  - 1— -I.  iiii i i :  1.0  [  i  :  iI  '»il_ i  ii  •ii iiii :i j iii i •mi iiit iiii J i "• ' iilii ij ;< -ii Iii ii |;i  iiii iii;! I'i I ;  ii 1  1'. •  |  si; rS  :| i iii  iii; Ii \ i ii;2ii 1 \ i 'ii i:i iii; i i iii jjii  :i  i \ iii \  ii ii ii iii !" :j if" -\t  v  :j | 'iii: 'ii:: •i i \ jp |i ii Ii if i  iiii iii i  ;•  1 •'  -11  :  4  o  Figure 4(a).  (b).  A  Sections  of the f i n a l e l e c t r o n - d e n s i t y d i s t r i b u t i o n p a r a l l e l to °-3 (010). Contours at i n t e r v a l s of 2 eA , exceDt at Br where °-3 contours are at i n t e r v a l s of 10 eA  A p e r s p e c t i v e drawing o f the m o l e c u l e as viewed a l o n g b - a x i s , showing  atom numbering used.  the  - 25 -  final  t h r e e - d i m e n s i o n a l e l e c t r o n d e n s i t y d i s t r i b u t i o n i s shown i n  F i g u r e 4 t o g e t h e r w i t h a drawing o f the m o l e c u l e numbering used  -+  i n this analysis.  +  g i v i n g t h e atom  The compound i s a z w i t t e r i o n ,  -  Br NH (CH ) CH(NH )COO , w i t h b o t h n i t r o g e n s  a c c e p t i n g protons to  form t e t r a h e d r a l C-NH  i s composed o f two  3  2  3  approximately aliphatic  3  groups.  + 3  p l a n a r groupings  The molecule  of atoms, a c a r b o x y l group and an  s i d e c h a i n t e r m i n a t i n g i n n i t r o g e n atoms.  the mean p l a n e through  The e q u a t i o n o f  0 ( 1 ) , 0 ( 2 ) , C ( l ) , C(2) i s  -0.3206 X' + 0.9459 Y - 0.0501 Z' = 1.2152 O where X', Y, Z' a r e c o o r d i n a t e s i n A w i t h r e f e r e n c e t o o r t h o g o n a l axes a, b, and c*.  0(1),  The  to  The d e v i a t i o n s o f the atoms from  o  o  o  the p l a n e a r e :  o  +0.005 A; 0 ( 2 ) , +0.005 A; C ( l ) , -0.014 A; and C ( 2 ) , +0.003 A.  o  a - n i t r o g e n atom, N ( l ) , l i e s 0.823 A out o f the p l a n e as compared  o  o  a v a l u e o f 0.436 A f o r L - g l y c i n e (13), 0.446 A f o r L - l y s i n e  o  h y d r o c h l o r i d e d i h y d r a t e (14) and 0.838 A f o r L - o r n i t h i n e h y d r o c h l o r i d e (15).  The a l i p h a t i c s i d e - c h a i n i s f u l l y  extended; i t s mean p l a n e has  the e q u a t i o n : 0.8133 X' + 0.4790 Y - 0.3302 Z' = 2.5741  o  o o  The d e v i a t i o n s from the p l a n e a r e N ( l ) , -0.074 A; C ( 2 ) , +0.086 A;  C(3),  b o o oo  +0.069 A; C ( 4 ) , -0.116 A; C ( 5 ) , -0.029 A; and N(2), +0.050 A.  mean iC71.4° (s l )77.9° v The iafsloudreas itwo ls being yp scompared liC-0 ancee d (1.249 d1+1.399 i4s)t . to a n A. ce 78.7° A. s a rThe efequal o rd o i rh newidi trh taihlnieangle n he y xd pe r between ro ic mhelnotraild the e e r(15) r otwo r ,and the planes  Table 6 Final positional  4 ( f r a c t i o n a l x 10 ) and thermal  °2 2 (A x 10 ) parameters,  w i t h s t a n d a r d d e v i a t i o n s i n parentheses Atom  X  C(l) C(2) C(3) C(4) C(5) N(l) N(2) 0(1) 0(2) Br  4628(15) 3243(12) 2284(13) 3073(14) 2141(13) 2316(13) 3032(12) 5823(11) 4434(11) 0447(1)  Atom  U-,., 11  C(l) C(2) C(3) C(4) C(5) N(l) N(2) 0(1) 0(2) Br Mean a: C,N,0 Br  z  y  2064(16) 1749(15) 1371(14) 2857(15) 2421(14) 0435(15) 3772(13) 3481(13) 0873(12) 1891(2)  3446(22) 2833(22) 4375(23) 5464(26) 7068(23) 1615(21) 8259(22) 3692(15) 3710(16) 1279(2)  12  U, ^ 13  22  2.56 2.20 '2.37 3.41 2.80 3.32 2.96 2.45 4.11 3.20  0.55 -0.16 -0.41 0.35 0.06 -0.06 -0.11 -0.25 0.09 -0.10  1.75 1.98 1.92 2.32 1.94 2.31 2.05 2.18 3.25 2.22  2.98 2.77 3.18 4.48 3.08 2.90 4.16 4.00 5.06 3.85  0.27 0.01 -0.51 -0.47 -0. 32 -0.05 -0.58 0.27 0.81 -0.09  3.33 3.72 3.23 3.36 2.90 4.31 3.36 4.37 4.19 3.66  0.35 0.05  0.44 0.04  0.23 0.04  0.85 0.14  0.44 0.05  0.35 0.06  23  33  - 27 -  Table 7 o  Bond d i s t a n c e s  (A) and angles  o  (degrees) (a = 0.02 A and 1.5°)  C(l)-C(2)  1.537  C(l)-C(2)-C(3)  108.3  C(2)-C(3)  1.525  C(2)-C(3)-C(4)  111.2  C(3)-C(4)  1.532  C(3)-C(4)-C(5)  110.1  C(4)-C(5)  1.533  Mean C-C-C  109.9  Mean C-C  1.532 C(l)-C(2)-N(l)  112.6  C(2)-N(l)  1.465  C(3)-C(2)-N(l)  109.6  C(5)-N(2)  1.473  C(4)-C(5)-N(2)  109.9  Mean C-N  1.469  Mean C-C-N  110.7  C(l)-0(1)  1.249  C(2)-C(l)-0(1)  116.8  C(l)-0(2)  1.248  C(2)-C(l)-0(2)  116.9  Mean C-0  1.249  Mean C-C-0  116.9  0(l)-C(l)-0(2)  126.2  - 28 -  Table 8 Hydrogen atoms 3 ° ( f r a c t i o n x 10 ; a ^ 0.25 A; the mean B b e i n g  P o s i t i o n a l parameters o  2  o  o  1.3 A ) , bond l e n g t h s (A, a ^ 0.25 A ) , and v a l e n c y angles  (degrees,  a ^ 15 - 20°)  Atom H(l) H(2) H(3) H(4) H(5) H(6) H(7) H(8) H(9) H(10) H(ll) H(12) H(13)  N-H C-H C-N-H H-N-H C-C-H, N-C-H H-C-H  Bonded to N(l) N(l) N(l) N(2) N(2) N(2) C(2) C(3) C(3) C(4) C(4) C(5) C(5)  0.8-1.1, 0.9-1.4, 107-130, 86-124, 78-127,  mean mean mean mean mean  0.9 1.1 117 101 108  111-120, mean 114  x  y  269 185 157 393 360 260 358 217 123 470 283 192 155  077 205 098 832 762 903 250 517 398 563 493 752 725  z 049 -055 013 411 494 369 284 031 093 381 374 152 256  - 29 -  Table 9 Carbon-oxygen bond l e n g t h s i n some amino a c i d s Amino A c i d DL-ornithine L-ornithine  C(l)-0(1)  C(l)-0(2)  hydrobromide  1.249  O 1.248 A  1.249  hydrochloride  1.257  1.245  1.251  1.250  1.246  1.248  1.247  1.256  1.253  L-lysine hydrochloride  dihydrate  L-alanine  As shown i n T a b l e  A  Mean A  9, these v a l u e s agree w e l l w i t h the c o r r e s p o n d i n g  i n t e r n u c l e a r d i s t a n c e s o f o t h e r amino a c i d s . a l s o a r e equal w i t h i n e x p e r i m e n t a l  The two C-NH^"*" bonds  e r r o r (Table 7 ) ; the average v a l u e  o  o  of 1.469 A i s s i m i l a r to t h a t o f 1.482 A f o r L - l y s i n e (14), and t h a t o  of 1.492 A f o r o r n i t h i n e h y d r o c h l o r i d e not b e i n g s i g n i f i c a n t . from each o t h e r  (15), these d i f f e r e n c e s p r o b a b l y  The C-C bond l e n g t h s do not d i f f e r  significantly  (Table 7 ) . The mean C-C d i s t a n c e o f 1.532 A agrees,  w e l l w i t h the s i n g l e bond l e n g t h o f 1.533 proposed by B a r t e l l (16) on the b a s i s o f e l e c t r o n d i f f r a c t i o n s t u d i e s o f normal hydrocarbons butane through heptane. '.'  The mean C-C d i s t a n c e i s s i m i l a r to the o  analogous v a l u e s o f 1.524 A f o r l y s i n e  ;  o  (14), 1.525 A f o r L - a l a n i n e ( 1 7 ) ,  o  and  1.530 A f o r o r n i t h i n e h y d r o c h l o r i d e  (15).  The bond angles  c a r b o x y l a t e group a r e equal w i t h i n the l i m i t s o f e x p e r i m e n t a l the analogous'angles  i n lysine  (14), and o r n i t h i n e ( 1 5 ) .  o f the e r r o r to  - 30 T a b l e 10 Carboxylate  bond angles  i n o r n i t h i n e and l y s i n e d e r i v a t i v e s  Angle O r n i t h i n e HBr  Compound O r n i t h i n e HC1  L y s i n e HC1-2H 0 2  0(l)-C(l)-0(2)  126.2°  126.6°  125.5°  C(2)-C(l)-0(1)  116.8  116.0  116.8  C(2)-C(l)-0(2)  116.9  117.0  117.7  S i m i l a r l y , the C-C -N angles of the above compounds resemble one another;  however, the agreement i s not so good as i n the case of the  c a r b o x y l a t e group a n g l e s .  T a b l e 11 Carbon-carbon-nitrogen  angles  i n o r n i t h i n e and l y s i n e d e r i v a t i v e s  Angle O r n i t h i n e HBr  Compound O r n i t h i n e HC1  L y s i n e HC1-2H 0 2  C(l)-C(2)-N(l)  112.6°  110.3°  109.7°  C(3)-C(2)-N(l) •  109.6  107.8  111.8  C(4)-C(5)-N(2).  109.9  110.4  C(5)-C(6)-N(2).  ;  110.9  The C-C-C angles o f the t h r e e amino a c i d s a r e s i m i l a r and c l o s e to the t e t r a h e d r a l v a l u e o f 109.5,  - 31 -  Table  12  Carbon-carbon-carbon angles i n o r n i t h i n e and Angle Ornithine  lysine derivatives  Compound O r n i t h i n e HC1  HBr  L y s i n e HC1-2H 0 2  C(l)-C(2)-C(3)  108.3°  110.2°  109.8°  C(2)-C(3)-C(4)  111.2  112.4  114.6  C(3)-C(4)-C(5)  110.1  109.0  110.0  C(4)-C(5)-C(6)  111.5  The v i s u a l d a t a are not s u f f i c i e n t l y a c c u r a t e to y i e l d v a l u e s f o r the hydrogen parameters.  0.89  The  average N-H  o  o  A i s c l o s e to the v a l u e of 0.94  A for lysine  f o r o r n i t h i n e h y d r o c h l o r i d e (15).  On  reliable  bond l e n g t h of o  (14), and  0.95  A  the o t h e r hand, a l l these bonds  are somewhat s h o r t e r than the s t a n d a r d N-H  bond d i s t a n c e of 1.03  o  A  o  f o r the ammonium i o n and d i f f e r e n c e s are not The mean C-H  t h a t of 1.01  A f o r ammonia.  However, these  significant. o  bond l e n g t h of 1.14  A is insignificantly  longer  o  than the analogous mean v a l u e s of 1.06 ornithine  (15)  and  1.05  A for lysine  (14)  and  respectively.  A p r o j e c t i o n of the s t r u c t u r e i s shown i n F i g u r e 5. s i g n i f i c a n t f e a t u r e of the p a c k i n g  The most  i s a system of t h r e e N-H...0 and  three N-H...Br hydrogen bonds i n v o l v i n g a l l s i x a c t i v e hydrogen atoms. The  t e r m i n a l n i t r o g e n atom, N(2), donates t h r e e p r o t o n s , one  bromide i o n of the s t a n d a r d molecule  at  0(2) of the n e a r e s t s c r e w - a x i s - g e n e r a t e d  [010], another molecule  at  to the  to the c a r b o x y l a t e  [111]  and  the  last  gure 5.  P r o j e c t i o n of the s t r u c t u r e a l o n g b; broken l i n e s are hydrogen  bonds.  - 33 -  p r o t o n to the c a r b o x y l a t e 0(1) of the a d j a c e n t generated  molecule  at  [111],  The  a l s o donates three p r o t o n s , one screw-axis-generated bromide i o n s . One  The  molecule  to the c a r b o x y l a t e 0(1)  at  [101]  and  of the  closest  the remainder to nearby  hydrogen bond d i s t a n c e s and angles are i n T a b l e  are a l l i n the range 95-109°.  The  13.  the o t h e r C-N...0,Br angles  p o s i t i o n s of the hydrogen atoms  the hydrogen bond assignments; the H...0  o  2.0  s i d e - c h a i n n i t r o g e n atom, N ( l ) ,  of the C-N...Br angles i s 155°, but  support  center-of-symmetry-  d i s t a n c e s a r e about  o  A,  the H...Br d i s t a n c e s 2.6  A,  and  i  the bonds a l l show the  u s u a l d e v i a t i o n s from exact l i n e a r i t y , the H-N...0, Br angles v a r y i n g from 7° to 25°. c o n t a c t of 2.97  There i s one o  A, but  f u r t h e r s h o r t N(2)...0(2) i n t e r n u c l e a r  the C-N...0 angle i s 166°  and  t h e r e i s no o  i n t e r v e n i n g hydrogen atom, the s h o r t e s t H...0  d i s t a n c e b e i n g 2.6  so t h a t t h i s c o n t a c t does not r e p r e s e n t a hydrogen bond. distances  (2.84, 2.84,  2.89  A) and  A,  The N-H...0  the N-H...Br d i s t a n c e s (3.29,  3.36,  o  3.46  A) are c l o s e to the v a l u e s u s u a l l y found  (18).  The  bromide i o n a c t s as an a c c e p t o r f o r t h r e e hydrogen bonds,  the N...Br ...N protons,  angles being 91,  91, and  the C-0...N angles being 124°  angle 108°. . 0(2) 118°.  The  a c c e p t s one  and  0(1)  127°, and  accepts  two  the N...0...N  the C-0...N angle i s  above system of hydrogen bonds i s complex i n t h a t the  bonds which i n v o l v e the c o r r e s p o n d i n g different  The  139°.  hydrogen bond, and  h e a v i e r atoms of the s t a n d a r d molecule  twelve  i n these types of systems  p a r t i c i p a t e i n twelve  five  hydrogen  atoms [ N ( l ) , N(2), 0 ( 1 ) , 0 ( 2 ) , Br] i n  molecules.  s t r u c t u r e of D L - o r n i t h i n e hydrobromide i s s i m i l a r to t h a t of  L-ornithine hydrochloride.  L a y e r s of L - o r n i t h i n e molecules  parallel  - 34  -  to the ab p l a n e are almost i d e n t i c a l i n the s t r u c t u r e s .  In L - o r n i t h i n e o  hydrochloride  these l a y e r s are s t a c k e d  i n DL-ornithine r e l a t e d by  along  c, g i v i n g a c - a x i s of 5  hydrobromide, the l a y e r s of L - o r n i t h i n e molecules  the c g l i d e p l a n e to l a y e r s of D-molecules  r e s u l t i n g i n a c - a x i s of about double the  length.  (Figure  5)  are  A;  - 35 -  T a b l e 13 o  Distances  (A) and a n g l e s  (degrees) i n the hydrogen  bonds, N-H...A  (A = 0 o r Br)  Bond  C-N...A  N(l)-H(l)...0(1),  2.84  105  3.46  109  N(l)-H(3)...Br, III[000]  3.36  155  N(2)-H(4)...0(2),  IV[111]  2.84  99  N(2)-H(5)...0(1),  III[111]  2.89  106  3.29  95  N(l)-H(2)...Br,  N(2)-H(6)...Br,  IV[101]  II[001]  I[010]  Equivalent p o s i t i o n s are I  x  II  x  III  -x  IV  -x  - y -y  + z -z  + y  t o g e t h e r w i t h t r a n s l a t i o n i n a, b, and c i n d i c a t e d i n square b r a c k e t s .  PART I I I  THE DETERMINATION OF THE STRUCTURE OF HISTAMINE DIPHOSPHATE MONOHYDRATE  - 37 -  A.  INTRODUCTION H i s t a m i n e , one o f the most important a u t a c o i d s i n the human body,  i s s y n t h e s i z e d i n v i v o by the enzymatic d e c a r b o x y l a t i o n o f h i s t i d i n e . Almost  a l l mammalian t i s s u e s c o n t a i n h i s t a m i n e and a r e capable o f synthes  ing i t .  The h i s t a m i n e which  i s r e l e a s e d by i n j u r e d body t i s s u e s g i v e s  r i s e to many o f the s i g n s and symptoms o f trauma and a l l e r g y .  B.  THE STRUCTURE OF HISTAMINE DIPHOSPHATE MONOHYDRATE Experimental H i s t a m i n e diphosphate was r e c r y s t a l l i z e d  c o l o r l e s s , t r a n s p a r e n t , needle-shaped appear  from water.  The r e s u l t a n t  c r y s t a l s a r e e l o n g a t e d along a and  t o be s t a b l e i n room a i r ; no r a d i a t i o n damage was observed.  The u n i t c e l l parameters r o t a t i o n , Weissenberg  and space group were determined  and p r e c e s s i o n f i l m s .  The m e l t i n g p o i n t  not be determined as the c r y s t a l began to l o s e water 88° and became c o m p l e t e l y l i q u i d  from v a r i o u s could  of h y d r a t i o n at  a t 118°C. o  C r y s t a l data (A, Mo-K  —  a  = 0.7107 A ) .  4 - ( 2 - a m i n o e t h y l ) - i m i d a z o l e diphosphate monohydrate, C<.H.j^N 0gP2; 3  M = 325.2.-; O M o n o c l i n i c , a =.7.99 + 0.01, b = 13.17 ± 0.01, c = 13.19 ± 0.01 A, 3 = 111.2 ± 0.1°. °3 ' U = 1294 A , D. = 1.669 ( f l o a t a t i o n ) , Z = 4 , m ;:  D = 1.668. x  F(000) = 680 . Absorption c o e f f i c i e n t  Absent  f o r X-rays,  u(Mo-K ) = 3.90 cm  a  \  r e f l e x i o n s : hOfc when % i s odd, OkO when k i s odd.  Space group P2^/c ( C ^ ) . The  i n t e n s i t i e s o f a l l r e f l e x i o n s w i t h 26(Mo-K ) l e s s than 46°  a  - 38 -  were measured on a G.E. XRD-5 Spectrogoniometer, w i t h S i n g l e C r y s t a l O r i e n t e r , u s i n g a s c i n t i l l a t i o n c o u n t e r , Mo-K^ filter  and p u l s e h e i g h t  counter technique  radiation  a n a l y z e r ) , and the m o v i n g - c r y s t a l  (zirconium moving-  ( 9 ) . The c o r r e s p o n d i n g minimum i n t e r p l a n a r  spacing  o  i s 0.91 A.  A l l the  i n t e n s i t i e s were c o r r e c t e d  the s t r u c t u r e amplitudes were d e r i v e d measuring 0.5  x0.5  x 2.0 mm,  p a r a l l e l to the g o n i o s t a t  tion factor A  as u s u a l .  The c r y s t a l ,  was mounted w i t h a*  axis.  P o s s i b l e e r r o r s i n the measured  s t r u c t u r e f a c t o r s were examined. of mean diameter 0.5 mm,  f o r background and  Considering  the c r y s t a l as a c y l i n d e r  uR i s 0.0975 and hence the a b s o r p t i o n  i s 1.10 and constant  the e r r o r due to a b s o r p t i o n  i n the range 9 = 0-40°;  i s negligible.  In a d d i t i o n ,  correc-  therefore,  absorption  e r r o r s due t o n o n - u n i f o r m i t y of c r y s t a l dimension were e s t i m a t e d by considering  the l o n g e s t  of the c r y s t a l .  and s h o r t e s t path l e n g t h s  The a b s o r p t i o n  i n the c r o s s - s e c t i o n  c o r r e c t i o n s f o r the c o r r e s p o n d i n g  s t r u c t u r e f a c t o r s a r e exp (3.9 x 0.07/2) and exp (3.9 x 0.05/2), t h a t i s 1.15 and 1.10 r e s p e c t i v e l y .  Thus the maximum d e v i a t i o n from the  mean c o r r e c t i o n o f 1.125 i s 0.025 o r 2.2%.  Since  the c u m u l a t i v e p o s s i b l e  maximum e r r o r i n F majority  due to a b s o r p t i o n i s l e s s than 2.3% and s i n c e the o of e r r o r s w i l l be much s m a l l e r than t h i s v a l u e , no c o r r e c t i o n  o was made f o r a b s o r p t i o n . observed; 1554  1747 r e f l e x i o n s i n the range 0 < 26 < 46 were  (89%) had i n t e n s i t i e s above background.  Structure The  Analysis  p o s i t i o n s of the two phosphorus atoms were determined from a  three-dimensional  Patterson  synthesis  ( P - l , 0.333, 0.125, 0.370; P-2,  0.740, 0.290,.0.216) and s t r u c t u r e f a c t o r s were c a l c u l a t e d f o r a l l the  39  -  t h r e e - d i m e n s i o n a l d a t a f o r phosphorus o n l y u s i n g s c a t t e r i n g from the  International  T a b l e s f o r X-ray C r y s t a l l o g r a p h y ,  factors  1962  (10)  °2 and  i s o t r o p i c thermal parameters of 4.0  was  0.57  f o r the observed r e f l e x i o n s .  synthesis  i n t o the  T a b l e s and  w i t h an o v e r a l l s c a l e  B = 4.0  A  o  1  |-|F 1  c '  2 I) .  f a c t o r , was  S i n c e the  least accurately a f f e c t e d by  i n t e n s i t i e s are  measured f o r the  where F* = 16 and  |F  | =42,  assigned  •w  G*  After  = 26.  the  Subsequent  c a r r i e d out function  by means of  the  block-  minimized b e i n g  f a c t o r s were c o n s i d e r e d  to  be  s t r o n g r e f l e x i o n s which are most  of background r a d i a t i o n , the  |F  Q  This  | = 16  f o r example, •w =  f a c t o r s from  following  1  maximum i^w = 1 f o r at  When these were i n t r o d u c e d  employed:  ••  r  revealed  as f o r the weak r e f l e x i o n s whose  s i m i l a r to that  w e i g h t i n g scheme was  Fourier  the phosphorus atoms  , R dropped to 0.32.  structure  a b s o r p t i o n as w e l l  R,  i s o t r o p i c thermal parameters t o g e t h e r  d i a g o n a l l e a s t - s q u a r e s method, the  1  discrepancy factor,  factor calculations with scattering °2  refinement of the p o s i t i o n a l and  Ew(|F  The  of a l l the non-hydrogen atoms.  structure  International  .  A three-dimensional  w i t h the phase angles based on  the p o s i t i o n s  A  and  scheme g i v e s thereafter  = 0.71.  = 0.80  for  |F  |  d e c r e a s i n g weights so  =1, that  Unobserved r e f l e x i o n s were  0.29.  seven i s o t r o p i c l e a s t - s q u a r e s refinement c y c l e s , R was 0.12;  i n p o s i t i o n a l parameters were about o n e - t h i r d  of a s t a n d a r d d e v i a t i o n  shifts while  - 40 -  thermal parameter s h i f t s were of the o r d e r of one s t a n d a r d The  deviation.  parameter s h i f t s of the water oxygen atom, however, were l a r g e r .  Therefore,  i t s p o s i t i o n was redetermined on an a d d i t i o n a l d i f f e r e n c e  synthesis. S i x a n i s o t r o p i c r e f i n e m e n t c y c l e s reduced R to 0.09. a difference synthesis  was summed and a l l 17 hydrogen atoms (with peak  °-3 v a l u e s of 0.5-0.7 eA ) were l o c a t e d were i n c l u d e d  Thereafter,  (Figure 6).  The hydrogen atoms  i n subsequent s t r u c t u r e f a c t o r c a l c u l a t i o n s w i t h °2  s c a t t e r i n g f a c t o r s from the I n t e r n a t i o n a l T a b l e s and B = 4.0 A .  After  s i x refinement c y c l e s i n which the thermal parameters of the heavy atoms were r e f i n e d a n i s o t r o p i c a l l y w h i l e those of the hydrogens were r e f i n e d i s o t r o p i c a l l y , R was 0.07.  However, as the temperature  of the water hydrogens were too h i g h  at t h i s point,  were  redetermined on a d i f f e r e n c e s y n t h e s i s .  final  s e r i e s of e i g h t  least-squares  factors  their positions  At the c o m p l e t i o n of the  r e f i n e m e n t s , the p o s i t i o n a l  parameter s h i f t s were s m a l l and n o n s y s t e m a t i c , the l a r g e s t s h i f t one-sixth  of a s t a n d a r d d e v i a t i o n f o r the heavy atoms and  being  one-third  of a s t a n d a r d d e v i a t i o n f o r the hydrogen atoms. The  p o s i t i o n a l and a n i s o t r o p i c thermal parameters of the h e a v i e r  atoms from t h e . f i n a l l e a s t - s q u a r e s with t h e i r standard d e v i a t i o n s  cycle are given  computed from the i n v e r s e s  terms of the m a t r i x of the l e a s t - s q u a r e s listed  normal e q u a t i o n s .  Figure  of the d i a g o n a l Also  i n T a b l e 14 are the hydrogen atom p o s i t i o n a l and i s o t r o p i c thermal  parameters t o g e t h e r w i t h t h e i r s t a n d a r d d e v i a t i o n s . density  i n T a b l e 14, t o g e t h e r  d i s t r i b u t i o n i s shown i n F i g u r e 8.  The f i n a l  electron-  7, the atom numbering used i n  - 42 -  T a b l e 14 F i n a l p o s i t i o n a l parameters ( f r a c t i o n a l , x 10^ f o r P, 0, N, and C; 3 2 2 2 x 10 f o r H) and thermal parameters (U.. i n A x 10 ; B i n A ) , w i t h 0  0  p t h e i r s t a n d a r d d e v i a t i o n s i n parentheses Atom P(l) P(2) 0(3) 0(4) 0(5) 0(6) 0(7) 0(8) 0(9) 0(10) N(ll) C(12) C(13) C(14) 0(15) N(16) 0(17) N(18) 0(w,19) H(20) H(21) H(22) H(23) H(24) H(25) H(26) H(27) H(28) H(29) H(30) H(31) H(32) H(33) H(34) H(35) H(36)  x 3466(4) 7489(4) 1917(11) 2743(11) 3879(11) 4989(11) 5669(11) 7098(11) 8026(12) 8852(11) 2734(14) 1971(17) 3389(19) 2775(16) .: 2361(17) 2046(14) '2231(16) 2659(14) ' 9536(15) 363(23) 187(17) 323(22) 117(18) 099(18) 424(17) 394(19) 234(13) 204(18) 196(13) 295(18) 894(25) 870(25) 084(22) , 561(22) 612(21) "• 753(24)  v 1287(2) 2879(2) 1800(7) 0259(7) 1925(7) 1139(7) 2715(7) 2715(7) 3965(7) 2118(7) 4402(9) 4447(12) 4695(12) 4695(10) 5467(10) 5058(8) 4070(10) 3819(8) 1440(13) 379(13) 433(10) 504(13) 375(11) 500(11) 407(11) 540(11) 624(8) 542(11) 355(8) 315(11) 167(15) 160(15) 192(13) 212(13) 278(13) 485(14)  2  [a(B) f o r hydrogen=3-4 A ]. z 3749(2) 2299(2) 2789(6) 4005(6) 4759(6) 3351(7) 2463(7) 1062(7) 2565(7) 2915(7) 1352(8) 2232(10) 3299(11) 4246(10) 4782(10) 5662(8) 5648(9) 4790(8) 4990(9) 166(13) 065(10) 121(13) 226(11) 208(11) 338(10) 319(11) 461(8) 628(11) 615(8) 469(11) 430(15) 540(15) 296(13) 283(13) 076(13) 151(14)  B  3.8 1.3 3.7 1.5 1.7 1.3 2.3 1.0 2.0 1.0 1.7 5.5 5.5 3.7 3.7 3.2 4.7  - 43 -  T a b l e 14  Atom  P(D P(2) 0(3) 0(4) 0(5) 0(6) 0(7) 0(8) 0(9) 0(10) N(ll) C(12) C(13) C(14) C(15) N(16) C(17) N(18) 0(19)  U  l l  2. 53(12) 2. 78(13) 3. 36(38) 4. 55(40) 3. 53(40) 3. 38(37) 4. 56(40) 3. 39(40) 6. 24(51) 3.45(40) 4. 74(53) 3. 77(62) 4. 64(64) 3. 13(56) 3. 91(58) 4. 25(51) 3. 55(57) 4. 60(54) 7. 66(60)  U  12  0.06(12) 0.64(12) 1.17(40) -1.11(39) 0.20(37) 0.39(36) 1.72(41) 0.55(38) 0.05(42) 0.62(40) -0.18(51) 0.12(62) -0.47(67) -0.15(55) -0.09(55) 0.19(47) 0.20(54) 0.02(47) 7.99(69)  (Continued)  U  13  1. 43(9) 1. 43(10) 1. 50(28) 2. 22(29) 1. 31(30) 2. 08(29) 3. 54(32) 1. 19(31) 2. 07(35) 1. 58(31) 2. 26(37) 1. 48(45) 2. 09(46) 1. 39(43) 1. 68(44) 1. 61(36) 1. 28(42) 1. 86(40) 4. 36(45)  U  22  2. 69(16) 2. 43(15) 5. 57(55) 3. 61(47) 3. 50(46) 3. 45(47) 4. 78(54) 4. 05(48) 3. 07(47) 4. 43(51) 4. 47(65) 5. 43(84) 5.63(87) 4. 03(72) 3. 34(67) 3. 62(58) 3. 62(67) 2. 78(54) 18. 55(121)  U  23  -0. 06(12) 0. 43(12) 0. 64(39) -0. 36(37) -0.91(37) 0.40(38) 2. 18(44) -0. 76(39) 0. 05(39) 1. 21(41) -0. 60(48) 0. 26(61) 0. 39(65) 0. 36(56) 0. 22(55) -0. 37(44) 1. 09(52) -0. 36(46) 6. 73(70)  U  33  2. 80(12) 3. 10(13) 2. 87(36) 3.62(37) 3. 49(38) 4. 40(40) 6. 57(47) 3. 59(40) 3. 78(41) 4. 16(41) 3. 63(47) 3. 26(57) 3. 95(60) 3. 48(57) 3. 66(57) 2. 99(45) 2. 78(51) 4. 05(51) 7. 02(58)  - 44 -  Figure 8.  Drawing of the structure viewed along a  and showing the atom numbering used.  - 46 The  f i n a l measured and c a l c u l a t e d s t r u c t u r e f a c t o r s are g i v e n  i n T a b l e 15; R i s 0.072 f o r 1554 independent  observed  reflexions.  A  f i n a l t h r e e - d i m e n s i o n a l d i f f e r e n c e s y n t h e s i s was computed and showed °-3 random f l u c t u a t i o n s as h i g h as ± 0.6 eA , The  R e s u l t s and D i s c u s s i o n  s t r u c t u r e c o n t a i n s a h i s t a m i n e c a t i o n , two H„P0, 2 4  a molecule  of water.  anions and  The i m i d a z o l e r i n g o f h i s t a m i n e appears  w i t h i n the l i m i t s of e x p e r i m e n t a l e r r o r .  to be p l a n a r  The e q u a t i o n of the mean p l a n e  is 0.8206 X' + 0.0908 Y + 0.5642 Z' = 3.659 O where X , Y, and Z' are c o o r d i n a t e s i n A r e f e r r e d to the o r t h o g o n a l axes a, f  b, and c .  The d e v i a t i o n s of the atoms from the mean p l a n e a r e :  C(14),  +0.009 A; C(15), -0.008 A; N(16), +0.004 A; C(17), +0.002 A; and N(18), 0 -0,007 A, The d e v i a t i o n s of the c o r r e s p o n d i n g hydrogen atoms from the p l a n e o f the i m i d a z o l e r i n g a r e : o  o  o  H(27), +0.02 A; H(28), +0.23 A; H(29),  o  -0.08 A; and H(30), +0.08 A.  Thus the hydrogens l i e i n the p l a n e of  the h e t e r o c y c l i c r i n g w i t h i n the l i m i t s of accuracy of the method. d e v i a t i o n s o f the s i d e c h a i n atoms from the i m i d a z o l e p l a n e a r e : o  o  -0.93 A; a l l h i g h l y  significant  The ethylamine s i d e c h a i n i s a p p r o x i m a t e l y p l a n a r ; the  e q u a t i o n of the mean p l a n e through N ( l l ) , -0.1541 X  C(13),  o  +0.12 A; C(12), -1.16 A; and N ( l l ) , displacements.  The  1  C(12), C(13), C(14) b e i n g :  + 0.9743 Y - 0.1643 Z' = 5.159 O  w i t h d e v i a t i o n s o f +0.021, -0.018, -0.024, and +0.021 A r e s p e c t i v e l y . The d i h e d r a l angle between the p l a n e o f the r i n g and the p l a n e of the side, c h a i n i s 82.5°. not b i s e c t  However, the p l a n e of the c h a i n does  the r i n g , i n s t e a d i t i s r o t a t e d toward  N(18) so t h a t  - 47 T a b l e 15 Measured  and c a l c u l a t e d  structure  factors  (Unobserved r e f l e x i o n s a r e i n d i c a t e d  by a n e g a t i v e s i g n i n f r o n t o f JF j ) . kl /FD/FC h=0 0  0 0 0 0 0 t 1 1  1 1 1 1  2 4 6 8 10 12 I 3 5 7 9 11 1) 2  2 2 2  2  4 6  8 10 2—T2 2  3 3 J  )  3  i  4 4 4 4 4  1  3 5 7 9  13 0 2 4 6 8  * 4  5 5 5  5 5  10 12 1 3 5 7 9  6  0  6  4 6 G  6 6 6  2  12  6 7  7 7 7 7  7 b «  1  9 9 •Y 9 9  10 10 10 10 10 11 11 11 11 12 12 12  12 13 13  13 14 14  8  10 1  5  7  0 2 4  fc 1 3  5 0 2  10 12  6  1  2 2  1 5  2 2 2 3  13 2  4 4 4 4 4 4 5 5  5 5 5 5 6 6  "6  6 6  6 / 7 ""/  7  9 11  -12.5  -B.4  38.2 -4.0 9.0  b.H  -7.9.  -0.9  13.2 5.2  13,4  12.6 -5.9  32.7 -42 .7 n . i  -13.6  25. 1  2 « . 6  4>>.7 - 4 4 . 6 •-2.1  9. /  -2.0 -9.2 33.B  6 . 3  9.5  -7.1 ii, J  4  15.4  -2.4  7  6 B I i  9.3  10.7  -1,6 -I.8  13.2  9 0 2  17.5 -13.7 -7.0 11 .4 105.1 -26.8 45.5 -10.7 21.1  19.9  1  5  A9.8 -92.1  11.0 -55.5 12.b - 2 b . 9 10.5 <}.li.J 10.t 28.a - 2 6 . 7 24.6 -20.8 4 8 . J -46.1 44.7 4b.7 3 B . 1 -40.8  -1.4 53.4  to. r  I 1  1 i 1  32.3  9  11 11  2 4  J  10.2 16.1  31.3 44.5  1 1  1  ,92.H 92.5 16.1 30.9 ' 5.6 rBT8 111.1 39.0 45.0 10.a 20.1  3 5 7  4  a 8  5B.2 - 5 1 , 9 6 7.6 62.lt 50.3 - 4 7 . 9 62.J 63.1 -2.0 -2.9 -2.3 -7.2 1 7 . 9 -11.7 96.2 35.8 b.l 6.0 26.5 - 2 6 . 6 45.2 -•.8.4 '16.3 17.2 -2.4 6.6  0.1 -0.3  4.4  IB.2  16.0  13.6  I 7. J 1.2  17.7  -  IS.0 13.9  -IB. v ii.L -17.1 - 6 . 9 17.5  2 I.i - 2 7 . 7 70.1 - 2 3 . 6 -7.1 SB.2 - 5 6 . 1 14.6 16.1 -2.2 -3.7 7.1  9.8  1.2  a.2 - 2 . 4  26.2  0.5 1.4  -7.5 - 6 . 2 6.8  16,1  -14.9  4 3.2  39. 1  26.8 - 2 4 . 3 11.4  ?!l 15.2 -8.5 71.7  44.5 - U 9  19.'» 11.7  H .9  7.5 15.7 -7.6  -72.h 46.1 2.2  -21.1 11.1  4  60.B 18.9 1.7 - 3 . 0  8  14,7  10 12 t 3 5 7 9  11 2 4  t a 10 12 1 1 5 7 9  11 2 4 6 II  14.9  B.l  »9.J 17.4  -14.7 15.2 -0.2  )5.i  - 1'. . 9  12.4 17.5 -2.U 1.6  -U.O  15.0 -I.I  14.7  19.1 0 . 5 7.6  40.2 -51.1 -1.9  6.4  2.4  47.1 - 4 5 . 9 10.6 a.L 70.1 19.5  71.5 14.6  2 r.H-~-"2TT43 7.7 - 39. 3 19.2 15.7 14.1 - 1 i . 9 8.4  22.2 15.6 24.2  6.B  21-0 15.9  -21.9  8 8  I 3  37.7 28.0  -38.1  It 8 8 9 9  / 9 11 2 4 6 8 10 9 1  45.4  46.5 -22.b -7.1 37.0 10.2 -24.0 -6.9  9  9 9 10 10 10 10 10 11 11 11  11 12 12  12 12 13 13 14  1  5 7 2 4 6 8 I 1  5 7 2 4 1  22.4  20.1  6.6 37.5 10.5 23.3 16.0 6.5 7.5 -J.6 10.1 1.7 31.2 - 3 1 . 1 49.2 4 5.0 -2.2 -D.4 35.4 37.0 6.7 6.3 8.7 - 9 . 1 12.5 1 0 . a 15.7 - 1 5 . 1 7.0 1.0 7.2 -i.5 6.6  5.2  6. 1  0.1 -5.9 12.0  7.4 11.1  0 3 3  0 -2  -4 4 6  a -10 3 10 D -12 3 12 -I 1 -3 J -5 1 -7 7 -9 9 -11 11 - 13 0 -2 2  65 .0 Bi . 6 .6 49 .0 70 . 9  -53.6  -77.3 90.4  54.1  69.3  15 . 0 - 1 5 . 9 .3 - 1. 1 2a ,0 - 2 9 . H 11 6 -34.0 5J.1 51 . 4 19 .1 - 1 6 . 4 -2 . 4 12.'. 54 7 49.2 12 . a -11.7 6 .6 -5.1 J? .7 -JV7T 8 -4B,4 4b . 6 -fcl.2' 19 . 6 55.1 51 . J 7 - 2 .0 It . 4 -2 2  -2.1  -10.8 -1.'7  -12.0,' 11 . 8 10.5. 12 .5 41.7. 4 1.8 19 .2 - n . r -4 19 . 9 18.94 23 . 6 2".'. 7 .5 - 2 . 6 -J6.4 6 J5 . 6 -a I J. 5 - 1 2 . f 54.5 6 1 1 .0 -10 25 .6 24.5 10 34 .1 - J 5 . 7 -12 2 7. 6 -27.2 2 12 21 . B 73.7 J - 1 10a .1 - 1 0 5 . 6 HI . 6 1 1 B6 .i - 3 70 . 9 7 1'. 4' 3 J 12 . 6 -lf.2' 1 -5 5 .9 5.7 5 25 .9 26.1 1 - 7 9 .3 &. ) t 1 9 .2 -40. r -9 20 .6 -21.1. 1 9 30 . 6 32.7. -1.5. 1 -11 5 .4 b. 73 i i a. o 11.» 1-13 14 .2 ?  .2  0  2T<T  20 . 0 - 1 7 . 4 4 -1 . 1 J.4 -4 52 . 5 -42.7 4 4U .9 - 4 ? , 5 fc - 6 10 .7 1.2' \ i, 24. ' 11.0. -8 20 .0 19.1 a 26 .5 - 2 5 . 6 -10 10 .b 3.9 10 9 .1 -9.7 -12 10 .2 - 9 . 0 12 U .0 - 1 3 . 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T 50-1 40.9 14.0 *1.9 4.4 34.7 -1.7 8.8 7.2 28.7 1 7.0  61 .4 -51 .8 43,b -1 I .6 41 .8 -4,4 -16.8 20.4 -7.9 -6.2 27. 7 12.1  33.4 47.7 21.2 30.4 12.1 21.4 -2.2 -1.8 4.3 16.0 11.7  15. 1 48.3 22.2 -29.4 12.7 - IB.4 9. J 4 ,0 -2.1 16.4  ~V779-14.0 34.4  -2.2  9.2  14.1 -2.1  30. 9 7b.0 21.0 3a. 1  11.0 19.9 21.4  -20.1 ~TB~rr 14.5  h=4 • 0 0 0 0 0 0 0 0 0 0 0 0 -14  20. 1 28. 3 20.2  -11.5 •10.2 -2.9  B.S  9  -49  12.4  IB. 7 25.6 IB.6 12.2 19.4 35. I 15. 1  -14.4  27.0 37.6 -12.5 19.7 -777B -8.5 12.2  4T4~"  16.4 25.8 22.0  -2b. * I 1.0 _-U--*  14.7  4.0 11.0 27.2  59.2 -10.2 -27.0 73.7 2.5 ~670' 12.b 1 i.u  6.1 2B. 1 43. 4 11.2 21.5  U.C  -11.5  21.2  -23.9  •17.6  39.0  -20.1  -  the d i s t a n c e between N(18)  49  and  O A whereas t h a t of  the plane i s 1.20  o  C(15)  i s o n l y 0.95 The  A.  bond d i s t a n c e s and v a l e n c y angles of the h i s t a m i n e  i o n are  g i v e n i n T a b l e 16,  t o g e t h e r w i t h the c o r r e s p o n d i n g v a l u e s o b t a i n e d  Donohue and  (19) f o r h i s t i d i n e .  Caron  a n a l y s e s are i n good agreement except  The bond l e n g t h s of the  by  two  f o r the C(12)-C(13) bond i n  h i s t i d i n e which i s s i g n i f i c a n t l y l o n g e r than the analogous bond i n histamine.  S i n c e the c a r b o x y l group i s a t t a c h e d  histidine,  to the C(12)  the i n c r e a s e i n the C(12)-C(13) bond i s not  surprising.  C o n s i d e r i n g the hydrogen bonding scheme, the p r o b a b l e of  the i m i d a z o l e r i n g  I  III  IV  V  Upon a p p l y i n g the c a r b o n - n i t r o g e n b o n d - o r d e r - l e n g t h  x  =  r  l"  where r.. = s i n g l e  (  r  tautomers  are:  II  r  of  l  "  r  )  (  3  x  )  /  (  2  x  +  equation  (20)  1 )  2  bond l e n g t h , r  X.  = double  bond l e n g t h , r  bond.character  c a r b o n - n i t r o g e n bond l e n g t h s i n the i m i d a z o l e r i n g , C(15)-N(16), C(17)-N(16), and  observed  X  Z.  bond l e n g t h , and x = p e r c e n t double  =  to the  observed  the C(14)-N(18),  C(17)-N(18) bonds were found  to have  - 50 -  T a b l e 16 o  Bond d i s t a n c e s (A) and v a l e n c y angles  (degrees)  Standard d e v i a t i o n s a(P-O) a(C-N) o(C-C) a(C-H) a(N-H) a(O-H)  0.009 0.018 0.020 0.15  a(O-P-O) a(< a t C,N)  0.5 1.0-1  a(X-Y-H) a(H-X-H)  9 12  Histamine i o n C(12) C(12) C(13) C(14) C(14) C(15) C(17) C(17)  -N(ll) -C(13) -C(14) -C(15) -N(18) -N(16) -N(16) -N(18)  Histidine 1.494 1.490 1.498 1.346 1.379 1.383 1.311 1.336  N ( l l ) -C(12) -C(13) C(12) -C(13) -C(14) C(13) -C(14) -C(15) C(i3) -C(14) -N(18) 0(15) -C(14) -N(18) C(14: -C(15) -N(16) C(15] -N(16) -C(17) C(14) -N(18) -C(17) N(16) -C(17) -N(18)  111.0 114.9 130.9 122.5 106.4 107.5 108.6 108.6 108.8  N ( l l ] -H(20) N ( I I ; -H(21) N ( l l ) -H(22) c ( i 2 : -H(23) C(12] -H(24) C(13} -H(25) C ( 1 3 : -H(26) C(15} -H(27) N(16; -H(28] -H(29) N(18] -H(30]  1.06 0.94 0.98 1.13 1.04 1.05 1.06 1.04 0.95 1.03 0.93  C(12; - N ( l l ) -H(20) c(i'2;) - N ( l l ] -H(21) c ( i 2 ;>-N(ll} -H(22) H(.2O;- N ( l l ) -H(21) H(20: ) - N ( I I ; -H(22) H(2I;) - N ( I I ; -H(22) N ( i i ; > - c ( i 2 ; -H(23) N(:ll]) - c ( i 2 : -H(24)  98 114 115 117 118 96 113 112  1.495 1.527 1.508 1.358 1.386 1.359 1.314 1.319  - 51 -  T a b l e 16  C(13) -C(12) -H(23) C(13) -C(12) -H(24) H(23) -C(12) -H(24) C(12) -C(13) -H(25) C(12) -C(13) -H(26) C(14) -C(13) -H(25) C(14) -C(13) -H(26) H(25) -C(13) -H(26) C(14) -C(15) -H(27) N(16) -C(15) -H(27) C(15) -N(16) -H(28) C(17) -N(16) -H(28) N(16) -C(17) -H(29) N(18) -C(17) -H(29) C(14) -N(18) -H(30) C(17) -N(18) -H(30)  (Continued)  113 107 100 100 106 108 113 115 128 125 126 123 127 124 131 120  Phosphate groups P ( D -0(3) P ( l ) -0(4) P ( D -0(5) P ( i ) -0(6) P(2.) -0(7) P(2) -0(8) P(2) -0(9) P(2) -0(10)  1.568 1.556 1.507 1.502 1.560 1.561 1.498 1.487  0(3) -H(33) 0(4) -H(36) 0(7) -H(34) 0(8) -H(35)  0.98 0.83 0.93 0.74  0(3 )>-P(l)-0(4) 0(3) - P ( l ) - 0 ( 5 ) 0(3) - P ( l ) - 0 ( 6 ) 0(4) - P ( l ) - 0 ( 5 ) 0(4) - P ( l ) - 0 ( 6 ) 0(5) - P ( l ) - 0 ( 6 ) 0(7) -P(2)-0(8) 0(7) -P(2)-0(9) 0(7))-P(2)-0(10) 0(8) -P(2)-0(9) 0(8) -P(2)-0(10) 0(9) -P(2)-0(10)  107.7 109.3 106.1 105.9 112.0 115.8 106.3 107.6 111.5 108.0 108.0 115.2  :  - 52 -  T a b l e 16  P(l)-0(3)-H(33) P(l)-0(4)-H(36) P(2)-0(7)-H(34) P(2)-0(8)-H(35)  (Continued)  113 114 114 109  Water molecule 0(19)-H(31) 0(19)-H(32) H(31)-0(19)-H(32)  0.91 1.02 105  - 53 -  21,  20, 54, and 39 p e r c e n t  i m p l i e s 66 p e r c e n t same time a t o t a l  double bond c h a r a c t e r , r e s p e c t i v e l y .  This  double bond c h a r a c t e r f o r C(14)-C(15) and, a t the c o n t r i b u t i o n o f tautomers I and I I o f about 60%.  preponderance o f these charge s e p a r a t i o n .  The  tautomers i s expected because they do n o t i n v o l v e  The i n t e r n a l angles  to one another w i t h i n the accuracy  o f the i m i d a z o l e  r i n g a r e equal  of the method. o  The  N ( l l ) - C ( 1 2 ) bond l e n g t h o f 1.494 A i s s l i g h t l y g r e a t e r  the s t a n d a r d  v a l u e o f 1.479 A, but agrees w e l l w i t h  amino-nitrogen bond l e n g t h s d e s c r i b e d  f o r other  than  the a-carbon-  amino a c i d s ; t h e s e  o  range  o  from 1.46 to 1.52 A, the m a j o r i t y b e i n g  c l o s e to 1.51 A i n l e n g t h .  The  carbon-carbon bond l e n g t h s o f the s i d e c h a i n have an average v a l u e o f 1.494 A which i s s i g n i f i c a n t l y  s h o r t e r than the s t a n d a r d  paraffinic  o  bond l e n g t h o f 1.541 A. The listed  bond l e n g t h s  i n Table  16.  and v a l e n c y  angles  o f the E^PO^  The mean P-0 and P-OH d i s t a n c e s o f 1.561 and  o  1.499 with  o  A (with a s t a n d a r d  e r r o r o f the mean o f 0.005 A) a r e i n agreement  those observed i n s i m i l a r compounds  are a l s o i n good agreement w i t h f o r i o n s of t h i s type lengths  ions also are  f o r E^PO^  (23).  (21-25).  The bond  those p r e d i c t e d by iT-bonding  Cruickshank  (23) p o i n t e d  lengths theories  out t h a t the bond  i n a c r y s t a l a r e c l o s e to the average of those i n  -3 PO^  and those i n P02(0R)2  from the P02(0R)2  where R = a l k y l .  Presumably the d e v i a t i o n  bond l e n g t h i s due t o hydrogen bonding o f H^PO^ _  i n the c r y s t a l .  The p r e d i c t e d v a l u e s  f o r E^PO^  o  °^ 1-50 A f o r P-0 and  o  1.59 A f o r P-OH a r e c l o s e to the observed v a l u e s . used c o r r e l a t i o n s between i . r .  Robinson  s t r e t c h i n g frequencies  and bond o  to p r e d i c t P-0 and P-OH bond l e n g t h s  (26) has lengths _  o f 1.48 and 1.58 A f o r the H P0. i o n .  The mean 0-P-0 angle o f 115.5° d i f f e r s s i g n i f i c a n t l y from t h e mean H0-P-0H angle o f 107.0°.  T h i s d e v i a t i o n from a t e t r a h e d r a l  t i o n would be expected on the b a s i s of the e l e c t r o n - p a i r theory  (27).  The v a l u e s a r e c l o s e t o those observed  i o n i n K H P 0 , namely, 115.4 and 105.5° r e s p e c t i v e l y 2  4  configura-  repulsion  f o r the H^PO^ (21).  The s m a l l  d i f f e r e n c e s among the v a r i o u s O-P-OH a n g l e s a r e p o s s i b l y due t o c r y s t a l packing. o  The mean 0-H bond l e n g t h i n t h e H^PO^ o  i o n i s 0.87 A w i t h a range  o  o  of 0.74-0.98 A (a 0.15 A ) .  The d i f f e r e n c e between 0.87 A and the  o  1.04 A o b t a i n e d f o r the same bond by means o f n e u t r o n d i f f r a c t i o n (21) is  thought  hydrogen range  t o be due t o a n u c l e a r displacement from the c e n t r e o f the  electron cloud.  The P-O-H a n g l e s w i t h a mean o f 112 - 9°  from 109 to 114°. o  o  The mean 0-H bond l e n g t h i n the water molecule i s 0.97 A (a 0.15 A) and t h e H-0-H angle 105°, both as expected.  The h i g h temperature  of the water molecule may be t h e r e s u l t o f weak hydrogen  factors  bonding o r a  s l i g h t v a r i a t i o n i n the water c o n t e n t . The  s t r u c t u r e may be thought o f as a l e a n i n g s t a c k o f h i s t a m i n e  i o n s surrounded by a c y l i n d e r o f H„P0, 2 4 shown i n F i g u r e 9. bonding  The s i g n i f i c a n t  i o n s and water m o l e c u l e s as  f e a t u r e s o f the complex  hydrogen  scheme which i n c l u d e s s i x 0-H...0 and f i v e N-H...0 bonds and  i n v o l v e s every a c t i v e hydrogen  atom, a r e o u t l i n e d i n F i g u r e 10 and  T a b l e s 17 and 18. The observed bond a n g l e s and bond l e n g t h s o f t h e hydrogen system  suggest t h a t a l l t h e hydrogen  bonding  bonds have been c o r r e c t l y a s s i g n e d .  In a d d i t i o n to those a s s i g n e d , N ( l l ) has a f u r t h e r two near oxygen  Figure 9.  P r o j e c t i o n of s t r u c t u r e along  a.  - 56 -  - 57 -  T a b l e 17 Distances  (A) and angles (degrees) i n the  hydrogen bonds X-H. . .0  (X = 0 or N) Bond  0(3)-H(33). . .O(K) ) [100] 0(4)-H(36). . . 0 ( 9 ) [ 1 0 1 ] 0(7)-H(34). . .0C6 )[000] 0(8)-H(35). . . 0 ( 5 ) [ 0 0 1 ] 0(19)-H(31) . . .0(101)[000] 0(19)-H(32) . . . 0 ( 8 ) [000] N ( l l ) - H ( 2 1 ) . . . 0 ( 1 9 ) [101] N(ll)-H(22) . ..0(6 )[111] N ( l l ) - H ( 2 0 ) .. . 0 ( 7 ) [ 0 0 0 ] N(16)-H(28) . . . 0 ( 9 ) [111] N(18)-H(30) . . .0(5!)[000] 1  I V  1  I][  i:c  n  IV  I  m  X. . .0 X-H  H. . .0 H-X. , . .0  2.55 2.58 2.54 2.57 2.74 3.00 2.77 2.86 3.18 2.69 2.68  1.59 1.75 1.62 1.84 1.90 2.01 2.02 1.96 2.13 1.74 1.76  0.98 0.83 0.93 0.74 0.91 1.02 0.94 0.98 1.06 0.95 0.93  9 2 9 10 19 10 31 19 6 2 8  Donor A c c e p t o r (X) OH OH OH OH H 0 H 0 NH3 NH + NH NH NH 2  2  +  3  +  3  0 0 0 0 0 OH H 0 0 0H 0 0 9  E q u i v a l e n t p o s i t i o n s a r e shown by s u p e r i o r Roman numerals: I II III IV  X  y  X  l/2-y  -X  -y  -X  -l/2+y  z 1/2+z z -1/2-z  t o g e t h e r w i t h t r a n s l a t i o n i n a, b, and c i n d i c a t e d i n square b r a c k e t s .  - 58 Table 18 Environments of atoms involved i n hydrogen bonding Atoms involved  Angle i n degrees  P(l)-0(3)...0(10)  121  P(l)-0(4)...0(9)  114  P(l)-0(5)...0(8) P(1)-0(5)...N(18) 0(8)...0(5)...N(18)  123 125 96  P(l)-0(6)...0(7) P(l)-0(6)...N(ll) 0(7)...0(6)...N(11)  113 128 119  P(2)-0(7)...0(6) P(2)-0(7)...N(ll) 0(6)... .0(7). . . N ( l l )  123 114 123  P(2)-0(8)...0(5) P(2)-0(8)...0(19) 0(5)...0(8)...0(19)  117 121 106  P(2)-0(9)...0(4) P(2)-0(9)...N(16) 0(4)...0(9)...N(16)  119 125 108  P(2)-0(10)...0(3) P(2)-0(10)...0(19) 0(3)...0(10)...0(19)  127 127 99  N(ll)...0(19)...0(8) N(ll)...0(19)...0(10) 0(8)...0(19)...0(10)  117 126 115  C(15)-N(16)...0(9) C(17).-N(16)...0(9) C(15)-N(16)-C(17)  128 122 109  C(14)-N(18)...0(5) C(17)-N(18)...0(5) C(14)-N(18)-C(17)  133 117 109  C(12)-N(ll)...0(6) C(12)-N(ll)...0(7) C(12)-N(ll)...0(19) 0(6)...N(ll)...0(7) 0(6)...N(ll)...0(19) 0(7)...N(ll)...0(19)  106 96 89 100 143 112  - 59 o  neighbours:  0(4) a t 3.13 A and 0(5) a t 3.11 A.  N-H...0 angles be bonded  o  S i n c e the c o r r e s p o n d i n g  a r e 156 and 148° r e s p e c t i v e l y , they  to N ( l l ) .  Mo r e o v e r ,  a r e n o t l i k e l y to  the p o s i t i o n o f H(20) f a v o r s the 0(7)  bond. As i n d i c a t e d i n F i g u r e 10, t h e water m o l e c u l e i s l i n k e d v i a two 0-H...0 hydrogen bonds t o t h e phosphate network. accepts  The water m o l e c u l e  one hydrogen from the t e r m i n a l n i t r o g e n o f h i s t a m i n e .  0-H...0 bonds between reported  The f o u r  the phosphate i o n s a r e t y p i c a l o f the d i s t a n c e s  f o r inorganic acids  ( 1 8 ) . The hydrogen bonds  formed by t h e  o  water as a donor a r e 2.74 and 3.00 A, a l s o w i t h i n t h e u s u a l range, (18). The h i s t a m i n e  i o n a c t i n g as a donor forms a t o t a l o f f i v e N-H...0 o  bonds which range from 2.66 to 3.18 A i n l e n g t h and i n v o l v e f o u r d i f f e r e n t phosphate ions and one water m o l e c u l e ( F i g u r e 1 0 ) . Except o  f o r the N(18)-H(30) . . .0(5) bond l e n g t h o f 3.18 A, t h e bonds a r e i n • • the u s u a l range (24). The geometry o f t h i s l o n g bond i s otherwise  quite  acceptable. The N ( l l ) atom i s roughly  i n a tetrahedral configuration  the 0 ( 6 ) . . . N ( l l ) . . . 0 ( 1 9 ) angle o f 143° (Table 18) does d e v i a t e from t h e t e t r a h e d r a l v a l u e .  although appreciably  The hydrogens of N ( l l ) approach a t e t r a -  h e d r a l arrangement much c l o s e r (Table 1 6 ) . Oxygens (3) and (4) take i n o n l y one hydrogen bond each. two hydrogen bonds.  A l l o t h e r oxygen atoms p a r t i c i p a t e i n  The arrangement o f c o v a l e n t and hydrogen bonds  around the oxygen atoms approximates p l a n a r i t y w i t h of three angles  part  ranging  between  344 and 360°.  the sum o f the s e t s  The hydrogen bonds show  the u s u a l d e v i a t i o n (28) from 180°, o f up t o about 30° as i n d i c a t e d i n Table 17.  - 60 -  There a r e o n l y two o t h e r s h o r t i n t e r m o l e c u l a r d i s t a n c e s i n the o  structure.  One i s an N(16)...N(16) d i s t a n c e o f 3.10 A a c r o s s  of symmetry; parallel, o  (3.0 A ) .  the c o n t a c t  and i s s l i g h t l y  the c e n t r e  i s between two m o l e c u l e s whose p l a n e s a r e longer  The second c o n t a c t  than t h e sum o f the van der Waals  radii  i s a C(17)-H(29)...0(3) i n t e r a c t i o n O  ( F i g u r e 10).  The C...0 d i s t a n c e i s 3.14 (a 0.017) A, t h e H...0 O  d i s t a n c e i s 2.22 (a 0.15) A, and t h e H-C...0 angle who has d e s c r i b e d s i m i l a r c o n t a c t s , concluded  22°.  Donohue. ( 2 8 ) ,  t h a t they d i d n o t  r e p r e s e n t hydrogen bonds i n t h e same sense as 0-H...0 o r N-H...0 bonds.  - 61 -  BIBLIOGRAPHY 1.  G.H. Stout and L.H. Jensen, "X-Ray S t r u c t u r e D e t e r m i n a t i o n . P r a c t i c a l Guide", M a c m i l l a n , New York, 1968.  2.  M.J.  3.  S.C. Nyburg, "X-Ray A n a l y s i s of Organic S t r u c t u r e s " , Academic P r e s s , New York, 1961.  4.  D.M.  5.  M. K u r a h a s h i , M. Fukuyo, A. Shimada, A. F u r u s a k i , and I. B u l l . Chem. Soc. Japan, 39, 2564, 1966.  6.  B.N.  Lahiri,  7.  B.N.  L a h i r i , A c t a C r y s t . , A25,  8.  J.D. McCullough, C. K n o b l e r , and H. Hope, American C r y s t a l l o g r a p h i c A s s o c i a t i o n , Winter Meeting, S e a t t l e , Washington, 1969, Program and A b s t r a c t s , p. 52, H4.  9.  T.C. Furnas, " S i n g l e - C r y s t a l O r i e n t e r I n s t r u c t i o n Manual", Milwaukee, G e n e r a l E l e c t r i c Company, 1957.  Buerger,  " C r y s t a l S t r u c t u r e A n a l y s i s " , W i l e y , New  Burns and J . I b a l l , P r o c . Roy.  Soc. , 227A, 200,  Z. K r i s t a l l o g r . , 127_, 456, 5127,  York,  1960.  1955. Nitta,  1968.  XIII-4,  1969.  10.  " I n t e r n a t i o n a l T a b l e s f o r X-ray Birmingham, volume I I I , 1962.  11.  " D i c t i o n a r y of i r - E l e c t r o n p. 344, 1965.  12.  Chem. Soc.  C r y s t a l l o g r a p h y " , Kynoch P r e s s ,  13.  R.E.  Marsh, A c t a C r y s t . , 11, 654,  14.  D.A.  Wright  15.  A. Chiba, T. U e k i , T. A s h i d a , Y. A c t a C r y s t . , 22., 863, 1967.  16.  L.S.  Bartell,  17.  H.J.  Simpson and R.E.  18.  G.H. Stout and L.H. Jensen, "X-ray S t r u c t u r e D e t e r m i n a t i o n . P r a c t i c a l Guide", M a c m i l l a n , New York, p. 303, 1968.  C a l c u l a t i o n s " , W.H.  S p e c i a l P u b l . , number 11, 1958  and R.E.  A  Freeman, San F r a n c i s c o ,  and number 18,  1965.  1958.  Marsh, A c t a C r y s t . , 15, 54, Sasada, and M.  J . Amer. Chem. S o c ,  81,  3497,  1962. Kakudo,  1959.  Marsh, A c t a C r y s t . , 20, 550,  1966. A  - 62 -  19.  J . Donohue and A. Caron, A c t a C r y s t . , 17_, 1178, 1964.  20.  J . Donohue, L.R. L a v i n e , and J.S. R o l l e t t , A c t a C r y s t . , 9_, 655, 1956.  21.  G.E. Bacon and R.S. Pease, P r o c . Roy. S o c , A230, 359, 1955.  22.  J.D. D u n i t z and J.S. R o l l e t t , A c t a C r y s t . , £ , 327, 1956.  23.  D.W.J. Cruickshank,  24.  G.H. McCallum, J.M. Robertson,  25.  D.E.C. C o r b r i d g e , T o p i c s i n Phosphorus Chem., _3, 57, 1966.  26.  E.A. Robinson, Canad. J . Chem., 41_, 3021, 1963.  27.  R.J. G i l l e s p i e and R.S. Nyholm, Quart.  28.  J . Donohue, i n " S t r u c t u r a l Chemistry and M o l e c u l a r B i o l o g y " , ed. A. R i c h and N.Davidson. Freeman, San F r a n c i s c o , p. 433, 1968.  J . Chem. S o c , 5486, 1961. and G.A. Sim, Nature,  184, 1863, 1959.  Rev., 11, 339, 1957.  

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