Determinations of atomic partial charges for nucleic acid constituents from x‐ray diffraction data. I. 2′‐Deoxycytidine‐5′‐monophosphate

Abstract

AbstractThe 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.