Chen Hsing-Yin, Yang Po-Yu, Chen Hui-Fen, Kao Chai-Lin, Liao Li-Wenm
Department of Medicinal and Applied Chemistry, Kaohsiung Medical University , Kaohsiung 807, Taiwan.
J Phys Chem B. 2014 Sep 25;118(38):11137-44. doi: 10.1021/jp506679b. Epub 2014 Sep 15.
The benchmark study of DFT methods on the activation energies of phosphodiester C3'-O and C5'-O bond ruptures and glycosidic C1'-N bond ruptures induced by electron attachment was performed. While conventional pure and hybrid functionals provide a relatively reasonable description for the C1'-N bond rupture, they significantly underestimate the energy barriers of the C-O bond ruptures. This is because the transition states of the later reactions, which are characterized by an electron distribution delocalized from the nucleobase to sugar-phosphate backbone, suffer from a severe self-interaction error in common DFT methods. CAM-B3LYP, M06-2X, and ωB97XD are the top three methods that emerged from the benchmark study; the mean absolute errors relative to the CCSD(T) values are 1.7, 1.9, and 2.2 kcal/mol, respectively. The C-O bond cleavages of 3'- and 5'-dXMP(•-), where X represents four nucleobases, were then recalculated at the M06-2X/6-31++G**//M06-2X/6-31+G* level, and it turned out that the C-O bond cleavages do not proceed as easily as previously predicted by the B3LYP calculations. Our calculations revealed that the C-O bonds of purine nucleotides are more susceptible than pyrimidine nucleotides to the electron attachment. The energies of electron attachment to nucleotides were calculated and discussed as well.
开展了关于电子附着诱导的磷酸二酯C3'-O和C5'-O键断裂以及糖苷C1'-N键断裂活化能的密度泛函理论（DFT）方法的基准研究。虽然传统的纯泛函和杂化泛函对C1'-N键断裂提供了相对合理的描述，但它们显著低估了C-O键断裂的能垒。这是因为后一种反应的过渡态，其特征是电子分布从核碱基离域到糖磷酸主链，在常见的DFT方法中存在严重的自相互作用误差。CAM-B3LYP、M06-2X和ωB97XD是基准研究中脱颖而出的前三种方法；相对于CCSD(T)值的平均绝对误差分别为1.7、1.9和2.2 kcal/mol。然后在M06-2X/6-31++G**//M06-2X/6-31+G*水平上重新计算了3'-和5'-dXMP(•-)（其中X代表四种核碱基）的C-O键裂解，结果表明C-O键裂解不像之前B3LYP计算所预测的那样容易进行。我们的计算表明，嘌呤核苷酸的C-O键比嘧啶核苷酸更容易受到电子附着的影响。还计算并讨论了核苷酸的电子附着能。
