Kelly R E A, Lee Y J, Kantorovich L N
Department of Physics, School of Physical Sciences and Engineering, King's College London, Strand, London WC2R 2LS, United Kingdom.
J Phys Chem B. 2005 Jun 23;109(24):11933-9. doi: 10.1021/jp050962y.
Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.
通过基于从头算密度泛函理论的计算，我们首次报告了所有可能的平面DNA碱基腺嘌呤同二聚体。使用了两种密度泛函以及局域基组和平面波基组，并将结果与之前针对少数几对的量子化学和半经验计算进行了比较。我们发现有21种可能的平面腺嘌呤对，其结合能在-0.03至-0.86电子伏特之间变化。更稳定的对与单体之间形成的两个强氢键相关，而最不稳定的对则以两个或一个相对较弱的键为特征。我们发现，稳定的氢键可以通过差分电荷密度来表征，该差分电荷密度显示出电子电荷交替过剩和耗尽的发达区域，类似于“烤肉串”结构。所呈现的关于所有平面腺嘌呤对的详细信息可用于，例如，考虑在各种表面上看到的可能的腺嘌呤单层。
