Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles
Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles
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基于近端分布函数与热力循环耦合的自由能计算
DOI：
10.1021/acs.jctc.8b01157
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发表时间：
2019
影响因子：
5.5
通讯作者：
Pettitt, B. Montgomery
中科院分区：
文献类型：
--
作者：
Ou, Shu-Ching;Pettitt, B. Montgomery
计算系统自由能变化的技术在生物物理和生化性质的研究中是非常有用的。在实践中，自由能的变化可以用热力学循环来描述，并且可以通过对相应构型进行充分采样来计算单个过程的自由能变化。然而，这仍然是耗时的，特别是对于大型生物分子系统。在此之前，我们已经证明，通过使用预先计算的溶质-溶剂相关性，即所谓的近端分布函数（pDF），我们能够重建溶质原子附近的溶剂环境，从而估计溶质-溶剂相互作用和分子的溶剂化自由能。在这篇贡献中，我们应用pdf重建技术来计算化学势，并在热力学循环中使用该信息。这说明了如何快速估计水溶液系统中重要化学过程的自由能变化。
Techniques to calculate the free energy changes of a system are very useful in the study of biophysical and biochemical properties. In practice, free energy changes can be described with thermodynamic cycles, and the free energy change of an individual process can be computed by sufficiently sampling the corresponding configurations. However, this is still time-consuming especially for large biomolecular systems. Previously, we have shown that by utilizing precomputed solute–solvent correlations, so-called proximal distribution functions (pDF), we are capable of reconstructing the solvent environment near solute atoms, thus estimating the solute–solvent interactions and solvation free energies of molecules. In this contribution, we apply the technique of pDF-reconstructions to calculate chemical potentials and use this information in thermodynamic cycles. This illustrates how free energy changes of nontrivial chemical processes in aqueous solution systems can be rapidly estimated.