Leng Yongsheng, Krstić Predrag S, Wells Jack C, Cummings Peter T, Dean David J
Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA.
J Chem Phys. 2005 Jun 22;122(24):244721. doi: 10.1063/1.1942468.
We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.
我们基于从头算密度泛函理论（DFT）计算构建了一组经典势，以描述苯二硫醇盐（BDT）分子与金原子之间的化学键合，包括分子与金簇界面处涉及的键伸缩、键角弯曲和二面角扭转。已采用三种DFT泛函，即局域密度近似（LDA）、PBE0和X3LYP，来计算BDT - 1,2 Au配合物大量分子构型的单点能（SPE）。这三种DFT方法产生相似的键合曲线。已详细研究了分子/金属配合物中穆利肯布居分析得到的原子电荷随不同分子构型的变化。我们发现，除了BDT - 1,2 Au配合物中的成键原子外，BDT中其他原子的穆利肯部分电荷相当稳定，这显著降低了经典分子模拟中部分电荷选择的不确定性。进行了分子动力学（MD）模拟，以研究BDT自组装单分子层（SAM）的结构以及S吸附原子在Au（111）表面的吸附几何结构。我们发现键伸缩势是化学键合中最主要的部分。虽然BDT分子构型的局部键合几何结构可能取决于所使用的DFT泛函，但BDT SAM的整体堆积结构与DFT泛函相当独立，即使化学键合的一些力场参数的不确定性可能高达约100%。这表明分子间相互作用在决定BDT SAM的整体堆积结构中起主导作用。
