A Quantum Molecular Dynamics Simulation Study of the Initial Hydrolysis Step in Sol−Gel Process

Abstract

The dynamic behavior of the hydrolysis reaction of Si(OCH3)4 under neutral, basic, and acidic conditions was investigated, for the first time, at the atomic level with short time intervals using a novel tight-binding quantum chemical molecular dynamics program “Colors”. The initial parameters required for the computation were determined completely on the basis of the first principles density functional calculations using Amsterdam density functional program. The simulation results of this study clearly indicate that a flank-side attack mechanism is favored, in all the three cases, for the hydrolysis process, and pentacoordinate silicon intermediates are easy pathways for the displacement of −OCH3 by −OH on silicon. Moreover, the presence of the acid or the base as catalyst promotes the hydrolysis by rapid formation of Si−OH bond in comparison to the hydrolysis under neutral condition. Furthermore, in the case of the latter condition, it was observed that the proton oscillates between −OH and −OCH3 before it migrates to the latter group.

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

“…Quantum chemical calculations were carried out using the Colors program, which is based on our original tight-binding approximation (Kubo et al, 2004;Elanany et al, 2003;Luo et al, 2003;Jung et al, 2003). In the Colors program, high computational efficiency is realized by adopting parameters in the Hamiltonian.…”

“…In our program, the parameters are determined on the basis of DFT calculation results. This can realize both high calculation speed and high accuracy (Elanany et al, 2002(Elanany et al, , 2003Sasata et al, 2003;Jung et al, 2003). The crystal lattice size used for Colors calculations on truncated MTX-Asp27 complex and MTX-Thr113 complex was 20 Å 9 20 Å 9 20 Å and that on binding site containing MTX, Thr113, and Asp27 was 30 Å 9 30 Å 9 30 Å .…”

An Elucidation of the Interaction Between Pt Particles and CeO2 Surfaces Using Tight-Binding Quantum Chemistry Method

“…The TBQC calculations were performed using our originally [12][13][14]. In this simulator, an electronic structure calculation is performed by solving the Schrödinger equation (HC = eSC; H, C, e, and S refers to the Hamiltonian matrix, eigenvectors, eigenvalues, and overlap integral matrix, respectively) with the diagonalization condition (C T SC = I; I refers to the unit matrix).…”

Restoration of p53–DNA interaction loss upon R273H mutation by CP-31398: an ultra accelerated quantum chemical molecular dynamics approach

“…Quantum chemical calculations were carried out using Colors program, which is based on our original tightbinding approximation (Kubo et al, 2004;Elanany et al, 2003;Luo et al, 2003;Jung et al, 2003). In the ''Colors'' program, high efficiency of computation is realized by adopting parameters in the Hamiltonian.…”

“…In our program, the parameters are determined on the basis of DFT calculation results. This can realize both high calculation speed and high accuracy (Elanany et al, 2002(Elanany et al, , 2003Sasata et al, 2003, Jung et al, 2003.…”