{"title":"使用直接极化近似的简单、可极化、刚性三点水模型。","authors":"Liangyue W Drew, Michael K Gilson","doi":"10.1021/acs.jctc.5c00603","DOIUrl":null,"url":null,"abstract":"<p><p>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<sup>3</sup>, 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<sup>-5</sup> cm<sup>2</sup> s<sup>-1</sup>) 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.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6964-6978"},"PeriodicalIF":5.7000,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A Simple, Polarizable, Rigid, 3-Point Water Model Using the Direct Polarization Approximation.\",\"authors\":\"Liangyue W Drew, Michael K Gilson\",\"doi\":\"10.1021/acs.jctc.5c00603\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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<sup>3</sup>, 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<sup>-5</sup> cm<sup>2</sup> s<sup>-1</sup>) 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.</p>\",\"PeriodicalId\":45,\"journal\":{\"name\":\"Journal of Chemical Theory and Computation\",\"volume\":\" \",\"pages\":\"6964-6978\"},\"PeriodicalIF\":5.7000,\"publicationDate\":\"2025-07-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Theory and Computation\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jctc.5c00603\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/7/7 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jctc.5c00603","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/7 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
A Simple, Polarizable, Rigid, 3-Point Water Model Using the Direct Polarization Approximation.
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 Å3, 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 (2.3×10-5 cm2 s-1) 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.
期刊介绍:
The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.