Matsubara Toshiaki, Ito Tomoyoshi
Department of Chemistry, Faculty of Science, Kanagawa University , 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan.
J Phys Chem A. 2016 May 5;120(17):2636-46. doi: 10.1021/acs.jpca.6b02308. Epub 2016 Apr 21.
The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans.
通过量子力学（QM）和分子动力学（MD）方法研究了硅原子上的亲核取代反应机制：SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-)。该反应分两步进行，构型会发生反转或保持，过程中会经过一个具有三角双锥（TBP）结构的中间体，而传统的碳原子上的SN2反应则是一步进行，构型反转会经过一个具有TBP结构的过渡态。我们通过QM计算跟踪了取代反应的所有可能路径，这些路径会经过由Cl(-)的正面和背面攻击产生的具有顺式和反式形式的TBP中间体。结果发现，高概率产生的TBPcis1很容易转化为能量上更稳定的TBPtrans。MD模拟也表明了这一事实。为了获得更多关于Cl(-)从TBPtrans解离轨迹的信息，这是我们基于QM方法确定的能量分布无法阐明的，我们进行了有无水溶剂的MD模拟并进行了详细分析。无水溶剂的QM-MD模拟表明，Cl(-)从TBPtrans的解离不经过TBPcis1'。有水溶剂的ONIOM-MD模拟进一步表明，水溶剂的热波动会显著影响底物动能和势能的振荡，从而促进TBP中间体从顺式异构体化为反式异构体以及随后Cl(-)从TBPtrans的解离。
