Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na+/Cl鈭?/sup>, Methane/Benzene, and K+/18-Crown-6 Ether

详细信息    查看全文

• 作者：Matthew C. Zwier ; Joseph W. Kaus ; Lillian T. Chong
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2011
• 出版时间：April 12, 2011
• 年：2011
• 卷：7
• 期：4
• 页码：1189-1197
• 全文大小：871K
• 年卷期：v.7,no.4(April 12, 2011)
• ISSN：1549-9626

文摘

Atomically detailed views of molecular recognition events are of great interest to a variety of research areas in biology and chemistry. Here, we apply the weighted ensemble path sampling approach to improve the efficiency of explicit solvent molecular dynamics (MD) simulations in sampling molecular association events between two methane molecules, Na⁺ and Cl^{鈭?/sup> ions, methane and benzene, and the K+ ion and 18-crown-6 ether. Relative to brute force simulation, we obtain efficiency gains of at least 300 and 1100-fold for the most challenging system, K+/18-crown-6 ether, in terms of sampling the association rate constant k and distribution of times required to traverse transition paths, respectively. Our results indicate that weighted ensemble sampling is likely to allow for even greater efficiencies for more complex systems with higher barriers to molecular association.}