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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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Zheng S, Tang Q, He J, Du S, Xu S, Wang C, Xu Y, Lin F. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems. J Chem Inf Model 2016; 56:811-8. [PMID: 26998926 DOI: 10.1021/acs.jcim.5b00687] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Qing Tang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Jian He
- Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Shahekou, Dalian, Liaoning 116023, P. R. China
| | - Shiyu Du
- Engineering Laboratory of Specialty Fibers and Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , 519 Zhuangshi Avenue, Zhenhai, Ningbo, Zhejiang 315201, P. R. China
| | - Shaofang Xu
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Chaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, P. R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
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