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Streamlining and Optimizing Strategies of Electrostatic Parameterization.
Zhu, Qiang; Wu, Yongxian; Zhao, Shiji; Cieplak, Piotr; Duan, Yong; Luo, Ray.
Afiliação
  • Zhu Q; Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
  • Wu Y; Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
  • Zhao S; Nurix Therapeutics, Inc., 1700 Owens St, Suite 205, San Francisco, California 94158, United States.
  • Cieplak P; SBP Medical Discovery Institute, La Jolla, California 92037, United States.
  • Duan Y; UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States.
  • Luo R; Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
J Chem Theory Comput ; 19(18): 6353-6365, 2023 Sep 26.
Article em En | MEDLINE | ID: mdl-37676646
Accurate characterization of electrostatic interactions is crucial in molecular simulation. Various methods and programs have been developed to obtain electrostatic parameters for additive or polarizable models to replicate electrostatic properties obtained from experimental measurements or theoretical calculations. Electrostatic potentials (ESPs), a set of physically well-defined observables from quantum mechanical (QM) calculations, are well suited for optimization efforts due to the ease of collecting a large amount of conformation-dependent data. However, a reliable set of QM ESP computed at an appropriate level of theory and atomic basis set is necessary. In addition, despite the recent development of the PyRESP program for electrostatic parameterizations of induced dipole-polarizable models, the time-consuming and error-prone input file preparation process has limited the widespread use of these protocols. This work aims to comprehensively evaluate the quality of QM ESPs derived by eight methods, including wave function methods such as Hartree-Fock (HF), second-order Møller-Plesset (MP2), and coupled cluster-singles and doubles (CCSD), as well as five hybrid density functional theory (DFT) methods, used in conjunction with 13 different basis sets. The highest theory levels CCSD/aug-cc-pV5Z (a5z) and MP2/aug-cc-pV5Z (a5z) were selected as benchmark data over two homemade data sets. The results show that the hybrid DFT method, ωB97X-D, combined with the aug-cc-pVTZ (a3z) basis set, performs well in reproducing ESPs while taking both accuracy and efficiency into consideration. Moreover, a flexible and user-friendly program called PyRESP_GEN was developed to streamline input file preparation. The restraining strengths, along with strategies for polarizable Gaussian multipole (pGM) model parameterizations, were also optimized. These findings and the program presented in this work facilitate the development and application of induced dipole-polarizable models, such as pGM models, for molecular simulations of both chemical and biological significance.

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies Idioma: En Revista: J Chem Theory Comput Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies Idioma: En Revista: J Chem Theory Comput Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos
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