Electrostatic properties of β-cytidine and cytosine monohydrate from Bragg diffraction

Abstract

1081electrostatic potential in the expected N lone-pair position as XN is increased incrementally from 0 to 48.5 ° . These calculations are consistent with the crystallographic evidence that all N...H contacts within the sum of van der Waals radii (2.75 A) that have XN > 35° and PH > 130° may be classified as hydrogen bonds. These N...H contacts are closely aligned with the assumed N lone-pair vector and such evidence is normally taken to infer an interaction between H(8+) and the lone-pair density. However, by analogy with the perpendicular approach of truly 'non-bonded' H to planar Nsp 2 systems (XIV), the lone-pair direction is also the approach direction of minimal steric hindrance to sp 3 hybridized N atoms (XV). Despite this analogy, we feel that the crystallographic results presented here provide tentative evidence that the incoming donor H atom tracks the changing direction of the N lone-pair vector as XN increases from 35 ° to --,60 ° during the latter phases of the Nsp2--+ Nsp 3 transition.We are indebted to Professor G. Gilli AbstractThe charge-density distribution in the crystal structure of the nucleoside fl-cytidine at 123 K has been determined * Author for correspondence.© 1995 International Union of Crystallography Printed in Great Britain -all rights reserved from X-ray diffraction data (Ag Kot, 2 = 0.5608 J~) using all 7233 reflections with sin0/2 < 1.14,~ -1. Maps of electrostatic potential for the cytosine base in cytidine are similar to those derived from previous charge-density studies of cytosine monohydrate and 1-fl-D-arabinosylcytosine, after taking chemical differences into account.

Dipole Moment Enhancement in Molecular Crystals from X‐ray Diffraction Data

“…1) a theoretical calculation on an isolated gas-phase molecule, using either the crystal geometry or an optimized geometry; 2052 www.chemphyschem.org [72] 8.0(14), [45] 11.1(4) [25,26] [10] 16.1(11), 12.4(10) [11] 99 (11) [82,83] 18(11) C 6 H 6 N 2 S 2 FANJOT01 2,2-bis(methylthio)-1,1-ethylenedicarbonitrile P2 1 /n 7.77 6(2) [23] À23(26) C 6 H 7 N 5 MEADEN02 9-methyladenine P2 1 /c 2.55 1.8(10) [56,84] À29 (39) [a] For the ab initio calculations, molecular structures were taken from crystal structures in the Cambridge Structural Database; REFCODES for these are given, and they do not necessarily coincide with the structure reported in the charge density analysis, as those are not always deposited.…”

Some diffractometer test crystals: a summary

“…Furberg (1950) grew crystals by letting a solution of cytidine in an alcohol-water mixture evaporate slowly, and a similar method using evaporation of a 90% alcohol solution has been reported (Chen & Craven, 1995). In our hands, on a small scale, these methods did give needle crystals but not of a suitable quality; however, layering ethanol (5 vol.)…”

AP,O,P′-tridentate mixed-donor scorpionate ligand: 6-[4,6-bis(diphenylphosphino)-10H-phenoxazin-10-yl]hexan-1-ol

“…For scorpionate ligands, see : Pettinari, (2004); Trofimenko (1993); Leung, (2007); Mayer et al (1994). For hydrogen bonding, see: Chen & Craven (1995); Monge et al (1978). For details of the synthesis, see: Reymond et al (1996); Van der Veen et al (2000).…”

“…The funtionalized N-hexanol group was found to be disordered and was refined over two positions with final occupancies of 0.68 and 0.32. If the nixantphos moiety is considered as the 'head′ of the compound (I) and the hexanol chain as its 'tail′, then the packing in (I) can be described as stacked in a 'head′ to 'tail′ Although these are unusually long for classical hydrogen bonding (Chen and Craven, 1995;Monge et al, 1978), the interactions are significant in maintaining the integrity of the disordered crystal structure. The bond angles involving the P atoms range from 100.21 (7) ° to 104.89 (7) °.…”