Efficient Basin-Hopping Sampling of Reaction Intermediates through Molecular Fragmentation and Graph Theory

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• 作者：Yeonjoon Kim ; Sunghwan Choi ; Woo Youn Kim
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2014
• 出版时间：June 10, 2014
• 年：2014
• 卷：10
• 期：6
• 页码：2419-2426
• 全文大小：387K
• 年卷期：v.10,no.6(June 10, 2014)
• ISSN：1549-9626

文摘

Basin-hopping sampling has been widely used for searching local minima on a potential energy surface. Reaction intermediates including reactants and products are also local minima composed of a reaction path, but their brute-force sampling is too demanding because of large degrees of freedom. We developed an efficient Monte Carlo basin-hopping method to sample reaction intermediates through the fragmentation of molecules and a postanalysis scheme using the graph theory with a matrix representation of molecular structures. The former greatly reduces the dimension of a given potential energy surface, while the latter offers not only the effective screening of resulting local minima toward desirable intermediates but also their automatic ordering along a reaction path. We combined it with the density functional tight binding method for rapid calculations and tested its performance for organic reactions.