Shishkin Oleg V, Palamarchuk Gennady V, Gorb Leonid, Leszczynski Jerzy
STC Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61001, Ukraine.
J Phys Chem B. 2006 Mar 9;110(9):4413-22. doi: 10.1021/jp056902+.
The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers. These conformers as well as syn conformers of pdG are stabilized by intramolecular N-H...O hydrogen bonds. Analysis of the electron density distribution within the atoms in molecules theory reveals the presence of numerous C-H...O hydrogen bonds in the nucleotides. However, a more detailed consideration of the properties of these bonds demonstrates that many of them should be considered as strong attractive electrostatic interactions rather than true hydrogen bonds. True hydrogen bonds are represented mainly by C6/ C8-H...O5'/O-P in anti conformers and the N-H...O-P bonds in syn conformers. It is demonstrated that the values of ellipticity of the electron density at the bond critical point (BCP) and the distance between BCP and ring critical point are the most reliable indicators for determining the true intramolecular hydrogen bonds.
使用B3LYP/6 - 31++G(d,p)理论水平计算了分离的标准2'-脱氧核糖核苷酸5'-磷酸胸苷（pdT）、5'-磷酸2-脱氧胞苷（pdC）、5'-磷酸2-脱氧腺苷（pdA）和5'-磷酸2'-脱氧鸟苷（pdG）不同构象体的分子结构和相对稳定性。计算结果表明，除pdG外，所有核苷酸中碱基呈顺式取向的构象体在势能面上并非对应于最低点。在pdA和pdC的情况下，核碱基呈正交取向的构象体，即北/顺式构象体取而代之。这些构象体以及pdG的顺式构象体通过分子内N-H...O氢键得以稳定。分子中原子理论内电子密度分布的分析揭示了核苷酸中存在大量C-H...O氢键。然而，对这些键性质的更详细考量表明，其中许多应被视为强吸引性静电相互作用而非真正的氢键。真正的氢键主要由反式构象体中的C6/C8-H...O5'/O-P以及顺式构象体中的N-H...O-P键表示。结果表明，键临界点（BCP）处电子密度的椭圆率值以及BCP与环临界点之间的距离是确定真正分子内氢键的最可靠指标。
