ISSN:
0006-3525
Keywords:
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
The first experimentally derived set of partial charges for a nucleotide has been determined. A high-resolution x-ray data set (5122 independent observed reflections to sin(θ)/λ = 0.995 Å-1) has been collected at T = -150°C for 2′-deoxycytidine-5′-monophosphate monohydrate in the zwitterionic form. Radial refinement was carried out on the data, a refinement method that allows variation of atomic valence sphere radii and populations and hence directly yields the partial charges of atoms in a structure [Coppens, P., Guru Row, T. N., Leung, P., Stevens, E. D., Becker, P. J. & Yang, Y. W. (1979) Acta Crystallogr., Sect. A 35, 63-72]. The atomic partial charges thus determined are in general qualitative agreement with theoretical values, but significant differences exist, indicating a reassessment of the applicability of the theoretical sets currently in use is necessary. The ab initio charges determined by Nuss and Kollman [(1979) J. Med. Chem. 22, 1517-1524] are closest to experiment in the sugar and base regions, while the Del Re charges of Renugopalakrishnan et al. [(1971) Biopolymers 10, 1159-1167] match best in the phosphate region. The presence of an additional hydrogen on N3 appears to have a small effect on the charge densities of all base atoms, rather than a large localized effect on adjacent atoms. Inspection of deformation density maps for the hydrogen bonds in this crystal suggests possible differences between those bonds that include a nitrogen atom as part of the bond and those that do not.
Additional Material:
8 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/bip.360240204
Permalink
