Soto-Verdugo Víctor, Metiu Horia, Gwinn Elisabeth
Department of Physics, UCSB, California 93106, USA.
J Chem Phys. 2010 May 21;132(19):195102. doi: 10.1063/1.3419930.
We study the binding of neutral silver clusters, Ag(n) (n=1-6), to the DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T) and the absorption spectra of the silver cluster-base complexes. Using density functional theory (DFT), we find that the clusters prefer to bind to the doubly bonded ring nitrogens and that binding to T is generally much weaker than to C, G, and A. Ag(3) and Ag(4) make the stronger bonds. Bader charge analysis indicates a mild electron transfer from the base to the clusters for all bases, except T. The donor bases (C, G, and A) bind to the sites on the cluster where the lowest unoccupied molecular orbital has a pronounced protrusion. The site where cluster binds to the base is controlled by the shape of the higher occupied states of the base. Time-dependent DFT calculations show that different base-cluster isomers may have very different absorption spectra. In particular, we find new excitations in base-cluster molecules, at energies well below those of the isolated components, and with strengths that depend strongly on the orientations of planar clusters with respect to the base planes. Our results suggest that geometric constraints on binding, imposed by designed DNA structures, may be a feasible route to engineering the selection of specific cluster-base assemblies.
我们研究了中性银簇Ag(n)（n = 1 - 6）与DNA碱基腺嘌呤（A）、胞嘧啶（C）、鸟嘌呤（G）和胸腺嘧啶（T）的结合以及银簇 - 碱基复合物的吸收光谱。使用密度泛函理论（DFT），我们发现这些簇倾向于与双键环氮结合，并且与T的结合通常比与C、G和A的结合弱得多。Ag(3)和Ag(4)形成更强的键。巴德电荷分析表明，除了T之外，对于所有碱基都有从碱基到簇的轻微电子转移。供体碱基（C、G和A）与簇上最低未占分子轨道有明显突出的位点结合。簇与碱基结合的位点由碱基较高占据态的形状控制。含时DFT计算表明不同的碱基 - 簇异构体可能具有非常不同的吸收光谱。特别是，我们在碱基 - 簇分子中发现了新的激发，其能量远低于孤立组分的能量，并且强度强烈依赖于平面簇相对于碱基平面的取向。我们的结果表明，由设计的DNA结构施加的结合几何约束可能是设计特定簇 - 碱基组装体选择的可行途径。
