Kumar Anil, Knapp-Mohammady Michaela, Mishra P C, Suhai Sándor
Department of Physics, Banaras Hindu University, Varanasi-221 005, India.
J Comput Chem. 2004 Jun;25(8):1047-59. doi: 10.1002/jcc.20020.
Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine-cytosine (G-C), adenine-thymine (A-T), and hypoxanthine-cytosine (HX-C) base pairs were studied using the self-consistent charge, density functional tight-binding (SCC-DFTB-D) method, augmented by the empirical London dispersion energy term. Performance of the SCC-DFTB-D method was examined by comparing the calculated results using it with those obtained from experiment as well as ab initio and other different density functional theoretical studies. An excellent agreement between the SCC-DFTB-D results and those obtained by the other calculations regarding the structural modifications, hydrogen bonding, and dissociation energies of the neutral and radical anion base pairs was found. It is shown that adiabatic electron affinity can be better predicted by considering reaction enthalpies of formation of the respective neutral and anionic base pairs from their respective molecular components instead of taking the difference between their total energies. The calculated AEAs of the base pairs were compared with those obtained by the bracketing method from Schaefer and coworkers, where a satisfactory agreement was found. It shows applicability of the SCC-DFTB-D method to study charged DNA models at a highly economical computational cost.
使用自洽电荷密度泛函紧束缚（SCC-DFTB-D）方法，并结合经验性伦敦色散能项，研究了由于向中性鸟嘌呤 - 胞嘧啶（G-C）、腺嘌呤 - 胸腺嘧啶（A-T）和次黄嘌呤 - 胞嘧啶（HX-C）碱基对中各添加一个过量电子而产生的绝热电子亲和能（AEA）和结构扰动。通过将使用该方法计算得到的结果与实验结果以及从头算和其他不同密度泛函理论研究的结果进行比较，检验了SCC-DFTB-D方法的性能。结果发现，SCC-DFTB-D结果与其他计算结果在中性和自由基阴离子碱基对的结构修饰、氢键以及解离能方面具有极好的一致性。结果表明，通过考虑各自中性和阴离子碱基对从其各自分子组分形成的反应焓，而不是取它们总能量之间的差值，可以更好地预测绝热电子亲和能。将计算得到的碱基对的AEA与Schaefer及其同事通过括号法得到的结果进行了比较，发现二者具有令人满意的一致性。这表明SCC-DFTB-D方法能够以非常经济的计算成本研究带电DNA模型。
