Department of Physics, The Centre of Higher Technologies, Tashkent, Uzbekistan.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
J Chem Phys. 2018 Feb 21;148(7):074504. doi: 10.1063/1.5017694.
Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li, Na, K, Cs, Mg, Ca, Sr, and Ba in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups.
金属阳离子在许多重要的生命过程中都是必不可少的。为了在生物过程的全原子分子动力学模拟中捕捉不同阳离子的作用，准确的参数化是至关重要的。在这里，我们结合生物分子模拟中常用的 TIP3P 水模型，为金属阳离子 Li、Na、K、Cs、Mg、Ca、Sr 和 Ba 开发了力场参数。在推进改进的力场方面，这里提出的方法是以前工作的扩展，使我们能够同时再现水溶液的热力学和动力学性质。我们系统地推导了 12-6 Lennard-Jones 势能的参数，该参数准确地再现了实验的溶剂化自由能、活性导数以及金属阳离子第一水合壳层中水交换的特性。为了重现所有的实验性质，需要对 Mg 进行 Lorentz-Berthelot 组合规则的修正。使用一组平衡的溶液性质，优化后的力场参数旨在捕捉不同金属阳离子之间的细微差异，包括特定的离子结合亲和力和阳离子与生物重要阴离子基团结合的动力学。
