Thole-style mutual induction models for molecular polarization have been adopted by several popular polarizable force fields (FFs) for their simplicity and transferability. The atomic polarizability parameters of these models are typically derived by fitting to or/and experimental molecular polarizabilities. In this work, we improve upon Thole polarizability parameters by employing both high-level quantum mechanics molecular polarizabilities and electrostatic potential (ESP) responses on three-dimensional grids. Our results indicate that the two approaches to derive atomic polarizability parameters are both effective, while the ESP approaches can also capture the polarization for the atoms with lone pair electrons. The resulting polarizability parameters have been validated on a set of over 7200 molecules covering the most common elements found in organic molecules (C, H, O, N, P, S, F, Cl, Br, and I). These parameters have also been tested on the experimentally measured molecular polarizabilities of 422 molecules. The final set of parameters derived in this work show notable improvement over the current AMOEBA set. The result is a highly transferable, expanded set of atomic polarizabilities defined by the local chemical environment in the form of SMARTS patterns. These parameters can be used directly in molecular mechanics polarizable potential energy functions such as AMOEBA, AMOEBA+, and other Thole-style models.
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http://dx.doi.org/10.1021/acs.jcim.1c01307 | DOI Listing |
Naunyn Schmiedebergs Arch Pharmacol
January 2025
Hormones Department, Medical Research and Clinical Studies Institute, National Research Centre, Giza, 12622, Egypt.
The main goal of the current study is to estimate the in vivo anti-inflammatory/antioxidant ability of four selected pharmaceutical compounds: bisoprolol (Biso), piracetam (Pirc), clopidogrel (Clop), and cinnarizine (Cinna). Indomethacin (Indo) was used as a reference drug to perform a realistic comparison between the four compounds and the Indo in vivo through tracking PI3K/AKT signaling and computational chemistry via density functional theory (DFT) modeling to analyze the electrostatic potential across the molecule and provide insight into the regions for receptor binding of the studied compounds. To achieve the safe dose of these compounds, cytotoxicity was performed against isolated adipose tissue-derived mesenchymal stem cells (ADMSCs) using MTT assay.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
Rigid, non-polarizable water models are very efficient from a computational point of view, and some of them have a great ability in predicting experimental properties. There is, however, little room for improvement in simulating water with this strategy, whose main shortcoming is that water molecules do not change their interaction parameters in response to the local molecular landscape. In this work, we propose a novel modeling strategy that involves using two rigid non-polarizable models as states that water molecules can adopt depending on their molecular environment.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands.
The dielectric constant, although a simplified concept when considering atomic scales, enters many mean-field, electrochemical interface models and constant potential models as an important parameter. Here, we use ab initio and machine-learned molecular dynamics to scrutinize the behavior of the electronic contribution to ɛr(z) as a function of distance z from a Pt(111) surface. We show that the resulting dielectric profile can largely be explained as a sum of the metallic response and the density-scaled water response at the interface.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Chemical and Materials Physics Graduate Program, Departments 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.
Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both the employed force field and sampling. Polarizable force fields, which incorporate atomic polarization effects, represent a significant advancement in simulation technology. The polarizable Gaussian multipole (pGM) model has been noted for its accurate reproduction of ab initio electrostatic interactions.
View Article and Find Full Text PDFLangmuir
January 2025
College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
The recovery of valuable materials from spent lithium-ion batteries (LIBs) has experienced increasing demand in recent years. Current recycling technologies are typically energy-intensive and are often plagued by high operation costs, low processing efficiency, and environmental pollution concerns. In this study, an efficient and environmentally friendly dielectrophoresis (DEP)-based approach is proposed to separate the main components of "black mass" mixtures from LIBs, specifically lithium iron phosphate (LFP) and graphite, based on their polarizability differences.
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