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一种使用直接极化近似的简单、可极化、刚性三点水模型。

A Simple, Polarizable, Rigid, 3-Point Water Model Using the Direct Polarization Approximation.

作者信息

Drew Liangyue W, Gilson Michael K

机构信息

Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States.

出版信息

J Chem Theory Comput. 2025 Jul 22;21(14):6964-6978. doi: 10.1021/acs.jctc.5c00603. Epub 2025 Jul 7.

Abstract

We present dPol, a 3-point, rigid, polarizable water model that uses the direct approximation of polarization. We show that, with a moderate computational cost (∼3× slower than TIP3P), dPol achieves additional accuracy over widely used nonpolarizable 3-point rigid water models. Unlike most polarizable force fields, dPol allows the use of a 2 fs time-step with a conventional molecular dynamics integrator. The partial charges and polarizabilities used in dPol are derived from quantum chemistry calculations, while the Lennard-Jones parameters and geometry are adjusted to reproduce liquid properties under ambient conditions. The final dPol water model reproduces key room-temperature physical properties used in training, with a heat of vaporization of 10.43 kcal/mol, a dielectric constant of 80.7, a high-frequency dielectric constant of 1.60, a molecular polarizability of 1.41 Å, a gas-phase dipole moment of 1.89 D, and a mean liquid-phase dipole moment of 2.55 D. Importantly, dPol also closely reproduces properties outside the training set, including the oxygen-oxygen radial distribution function of liquid water, as well as the self-diffusion coefficient (2.3×10 cm s) and shear viscosity (0.87 mPa s). Predicted temperature-dependent properties are also largely reproduced; although dPol does not correctly place the density maximum, this is not expected to impede successful application of the model to biomolecular systems near room temperature. The dPol water model is, by design, compatible with our AM1-BCC-dPol polarizable electrostatic model for small organic molecules [J. Chem. Theory Comput., 2024, 20, 1293-1305]. These models in combination establish a foundation for the integration of electronic polarizability into efficient force fields for heterogeneous systems of biological and pharmaceutical interest.

摘要

我们展示了dPol,一种采用极化直接近似的三点刚性可极化水模型。我们表明,以适度的计算成本(比TIP3P慢约3倍),dPol比广泛使用的非可极化三点刚性水模型具有更高的精度。与大多数可极化力场不同,dPol允许使用传统分子动力学积分器采用2飞秒的时间步长。dPol中使用的部分电荷和极化率源自量子化学计算,而 Lennard-Jones 参数和几何结构则进行了调整,以重现环境条件下的液体性质。最终的dPol水模型重现了训练中使用的关键室温物理性质,汽化热为10.43千卡/摩尔,介电常数为80.7,高频介电常数为1.60,分子极化率为1.41 Å,气相偶极矩为1.89 D,平均液相偶极矩为2.55 D。重要的是,dPol还能紧密重现训练集之外的性质,包括液态水的氧-氧径向分布函数,以及自扩散系数(2.3×10⁻⁵ cm²/s)和剪切粘度(0.87 mPa·s)。预测的温度相关性质也在很大程度上得到了重现;尽管dPol没有正确地确定密度最大值的位置,但预计这不会妨碍该模型在室温附近的生物分子系统中的成功应用。dPol水模型在设计上与我们用于小有机分子的AM1-BCC-dPol可极化静电模型[《化学理论与计算杂志》,2024年,20卷,1293 - 1305页]兼容。这些模型相结合为将电子极化率整合到针对具有生物学和药学意义的异质系统的高效力场奠定了基础。

本文引用的文献

4
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.一种用于分子动力学的快速、便捷、可极化静电模型。
J Chem Theory Comput. 2024 Feb 13;20(3):1293-1305. doi: 10.1021/acs.jctc.3c01171. Epub 2024 Jan 19.
8
Fast Polarizable Water Model for Atomistic Simulations.快速极化水分子模型用于原子模拟。
J Chem Theory Comput. 2022 Oct 11;18(10):6324-6333. doi: 10.1021/acs.jctc.2c00378. Epub 2022 Oct 3.

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