流体的自由能密度及其在溶剂化和结合中的作用。
Free Energy Density of a Fluid and Its Role in Solvation and Binding.
作者信息
Gilson Michael K, Kurtzman Tom
机构信息
Skaggs School of Pharmacy and Pharmaceutical Sciences and Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, United States.
PhD Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, New York 10016, United States.
出版信息
J Chem Theory Comput. 2024 Apr 9;20(7):2871-2887. doi: 10.1021/acs.jctc.3c01173. Epub 2024 Mar 27.
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. , we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, (), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, , near a solute but should asymptotically approach with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential. , we use statistical thermodynamics to formulate a definition of the free energy density that satisfies these desiderata. , we show how any free energy density satisfying the desiderata may be used to analyze molecular processes in solution. In particular, because the spatial integral of () equals the free energy of the system, it can be used to compute free energy changes that result from the rearrangement of solutes as well as the forces exerted on the solutes by the solvent. This enables the use of a thermodynamic analysis of water in protein binding sites to inform ligand design. Finally, we discuss related literature and address published concerns regarding the thermodynamic plausibility of a position-dependent free energy density. The theory presented here has applications in theoretical and computational chemistry and may be further generalizable beyond fluids, such as to solids and macromolecules.
流体具有位置相关的自由能密度这一概念已出现在文献中,但尚未得到充分发展或被广泛接受。我们通过以下策略将这一概念置于明确的理论基础之上。首先,我们提出了四个要求,对于仅由流体和刚性溶质组成的系统中位置相关的自由能密度()的任何定义都应满足这些要求:其体积积分加上溶质的固定内能应等于系统自由能;它在溶质附近偏离其体相值,但随着与溶质距离的增加应渐近趋近于;在溶剂密度为零的地方它应趋近于零;并且在由具有任意相互作用势的柔性分子组成的流体的最一般情况下它应是明确定义的。其次,我们使用统计热力学来制定满足这些要求的自由能密度的定义。然后,我们展示了任何满足这些要求的自由能密度如何可用于分析溶液中的分子过程。特别是,由于()的空间积分等于系统的自由能,它可用于计算溶质重排导致的自由能变化以及溶剂对溶质施加的力。这使得能够利用对蛋白质结合位点中水分子的热力学分析来指导配体设计。最后,我们讨论相关文献并回应关于位置相关自由能密度的热力学合理性的已发表的担忧。这里提出的理论在理论化学和计算化学中有应用,并且可能进一步推广到流体之外,例如固体和大分子。