Kelly R E A, Lee Y J, Kantorovich L N
Department of Physics, School of Physical Sciences and Engineering, King's College London, The Strand, London, WC2R 2LS, United Kingdom.
J Phys Chem B. 2005 Nov 24;109(46):22045-52. doi: 10.1021/jp055207z.
All the planar homopairings of cytosine and guanine are reported for the first time in this study. The idea of binding sites suggested for the simple case of adenine homopairs (J. Phys. Chem. B 2005, 109, 11933) is shown to be applicable to more complicated molecules binding to each other via multiple hydrogen bonds and can be considered as a general method for constructing hydrogen bonding structures. As an example we consider homopairs formed by DNA bases cytosine and guanine, suggesting that there may be 13 cytosine and 17 guanine homopairs. However, only 11 cytosine and 15 guanine homopairs remain after atomic relaxation performed using ab initio density functional theory. Most of the homopairs obtained have not been studied before. The homopairs have significant binding energies, varying from -0.19 to -1.12 eV, that are explained by multiple hydrogen bonds formed between monomers in the pairs, up to four hydrogen bonds in most energetically favorable cases. The detailed information on all guanine and cytosine planar homopairs contained in this work can be used to construct various cytosine and guanine superstructures observed on different surfaces.
本研究首次报道了胞嘧啶和鸟嘌呤的所有平面同配体。对于腺嘌呤同配体的简单情况所提出的结合位点概念（《物理化学杂志B》2005年，第109卷，第11933页）被证明适用于通过多个氢键相互结合的更复杂分子，并且可被视为构建氢键结构的通用方法。作为示例，我们考虑由DNA碱基胞嘧啶和鸟嘌呤形成的同配体，表明可能存在13种胞嘧啶同配体和17种鸟嘌呤同配体。然而，使用从头算密度泛函理论进行原子弛豫后，仅剩下11种胞嘧啶同配体和15种鸟嘌呤同配体。所获得的大多数同配体此前尚未被研究过。这些同配体具有显著的结合能，范围从-0.19到-1.12电子伏特，这是由同配体中单体之间形成的多个氢键所解释的，在能量最有利的情况下多达四个氢键。这项工作中包含的所有鸟嘌呤和胞嘧啶平面同配体的详细信息可用于构建在不同表面上观察到的各种胞嘧啶和鸟嘌呤超结构。
