Calculation of binding affinities for linear alcohols to α-cyclodextrin by twin-system enveloping distribution sampling simulations

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• 作者：Julia Gebhardt ; Niels Hansen ; ^{hansen@itt.uni-stuttgart.de" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Molecular dynamics ; Free energy ; Cyclodextrin ; Force field
• 刊名：Fluid Phase Equilibria
• 出版年：2016
• 出版时间：25 August 2016
• 年：2016
• 卷：422
• 期：Complete
• 页码：1-17
• 全文大小：4124 K

文摘

Comparison of three variants of the GROMOS force field for carbohydrates, 53A6_GLYC, 56A6_{CARBO_R} and a small modification of the latter, referred to as 56A6_{CARBO_R+}, has been conducted by examining the standard binding free enthalpy of linear alcohols from 1-butanol to 1-dodecanol to α-cyclodextrin in aqueous solution. The double decoupling approach was employed to calculate the standard binding free enthalpy of 1-hexanol, while for all other compounds relative binding free enthalpies for pairs of alcohols differing by two carbon atoms were calculated from twin-system enveloping distribution sampling simulations. While all three force fields slightly overestimate the magnitude of the standard binding free enthalpy of 1-hexanol the 53A6_GLYC and 56A6_{CARBO_R+} parameter sets are a little closer to the experimental data than 56A6_{CARBO_R}. For relative binding free enthalpies no significant difference between the force fields was observed. All three force fields support those experimental measurements that found a distinct increase in the binding affinity with increasing number of carbon atoms even for longer chain lengths up to 1-dodecanol.