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Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association

机译:多维自由能体积提供了对反应机理,分子构象和缔合的独特见解

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摘要

Free energy is a central measure in statistical mechanics and the means by which other thermodynamic properties of a system may be accessed. Using an efficient numerical method referred to as the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method it is shown that multidimensional free energy volumes (FEVs) are computable and that they are critical to the understanding of reactions, conformational analysis and molecular association. Specifically the FEV of the hydrolysis reaction catalysed by a cellobiohydrolase I is shown to reveal molecular details of the reaction mechanism. The reaction is understood from a combination of the two dimensional reaction free energy surface, W(ξ1, ξ2) and the three dimensional glucopyranose ring pucker FEV, W(ξ1, ξ2,ξ3). These studies provide for the first time details of the evolution of the oxocarbenium ion, which is a key to characterizing transition state structures seen in carbohydrate chemistry. A long-standing challenge has been the unambiguous assignment of the relative orientation of molecular pairs in solution. Here we describe how the molecular association of the benzene dimer in water and their relative orientational attraction are found from four dimensional, FEVs W(ξ1, ξ2, ξ3, ξ4).
机译:自由能是统计力学中的一项核心指标,也是可以获取系统其他热力学性质的手段。使用一种有效的数值方法,称为“自适应反应坐标力的自由能”(FEARCF)方法,表明多维自由能体积(FEV)是可计算的,并且它们对于理解反应,构象分析和分子缔合至关重要。具体而言,显示由纤维二糖水解酶I催化的水解反应的FEV揭示了反应机理的分子细节。从二维反应自由能表面W(ξ1,ξ2)和三维吡喃葡萄糖环式折皱FEV,W(ξ1,ξ2,ξ3)的组合可以理解反应。这些研究首次提供了氧碳鎓离子演变的细节,这是表征在碳水化合物化学中发现的过渡态结构的关键。长期存在的挑战是溶液中分子对相对方向的明确分配。在这里,我们描述了如何从四维FEV W(ξ1,ξ2,ξ3,ξ4)中发现水中苯二聚体的分子缔合及其相对定向吸引力。

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