On Achieving Experimental Accuracy from Molecular Dynamics Simulations of Flexible Molecules: Aqueous Glycerol

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• 作者：Austin B. Yongye ; B. Lachele Foley ; Robert J. Woods
• 刊名：Journal of Physical Chemistry A
• 出版年：2008
• 出版时间：March 27, 2008
• 年：2008
• 卷：112
• 期：12
• 页码：2634 - 2639
• 全文大小：111K
• 年卷期：v.112,no.12(March 27, 2008)
• ISSN：1520-5215

文摘

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueousphase via a 1 s conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replicaexchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. TheMD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment ofsolvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar ³J_HHcoupling constants that were comparable to those from the much longer traditional MD simulation. The ³J_HHcoupling constants computed from the MD methods were in excellent agreement with those observedexperimentally. Despite the agreement between the computed and the experimental J-values, there werevariations between the rotamer populations computed directly from the MD data and those derived from theexperimental NMR data. The experimentally derived populations were determined utilizing limiting J-valuesfrom an analysis of NMR data from substituted ethane molecules and may not be completely appropriate forapplication in more complex molecules, such as glycerol. Here, new limiting J-values have been derived viaa combined MD and quantum mechanical approach and were used to decompose the experimental ³J_HH couplingconstants into population distributions for the glycerol RIS.