Theoretical analysis of deoxycytidine‐5′‐phosphate protonation

Abstract

The electron density distribution in deoxycytidine-5'-monophosphate (5'-dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X-ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy-cytidine-5'-monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum-chemical CNDO/2 technique is applicable to the mononucleotide studies.

Three‐dimensional Hartree–Fock crystal‐orbital calculation on crystalline diprotonated deoxycytidine‐5′‐monophosphate monohydrate: Toward rationalizing nucleic acid semiconductivity

“…'l However, the correlation for all the hydrogens is poor, unlike in Ref. 21. This is obviously the result of our basis set choice.…”

“…Table VIII) . According to the data2' and assuming the 5'-dCMP * 2H * 1H20 conditional partition scheme, 21 there is a significant charge transfer from deoxyribose ( +0.327) predominantly to the phosphate (-0.294) and somewhat to the cytosine ( -0.032), whereas the water molecule remains electroneutral (cf . Table VIII) .…”

“…Like in Ref. 21, the atomic partial charges calculated by the CRYSTAL92 for the whole crystal have been compared with those published in Ref. 20, and thus the chosen basis set has been checked to be applicable to the system under study.…”

On the electronic subsystem of nucleic acid crystallohydrates

“…It has been demonstrated earlier [9], that using this semiempirical quantum-chemical scheme one can obtain reliable qualitative information concerning the distribution of the mononucleotide electron density. To this end, the present work does not use more elaborate semiempirical or ab initio techniques, since it accentuates a qualitative aspect of the problem.…”

“…That the latter bonds are intrinsically labile is supported by X-ray data on maximum thermal fluctuations in the regions of glycoside and C5'-05' bonds (as compared to other regions of these molecules) within nucleoside and nucleotide crystals [8] and by quantum-chemical calculations on the bond orders of the corresponding bonds [9]. Thus, to know whether nucleotides are rigidly intact within crystallohydrates of their complexes with alkali metal ions is also of importance for molecular biology.…”