ArticleJournal of chemical theory and computation2018
Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Extending the Python RESP Framework for Extra Point Charge Fitting.Journal of chemical information and modeling · 2026Article
- 6,7-Dichloro-1H-indole-2,3-dione-3-oxime functions as a superagonist for the intermediate-conductance CaMolecular pharmacology · 2025Article
- Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- An Atomic and Molecular Insight into How PFOA Reduces α-Helicity, Compromises Substrate Binding, and Creates Binding Pockets in a Model Globular Protein.Journal of the American Chemical Society · 2024Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.The Journal of chemical physics · 2020Article
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
- FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.Journal of computational chemistry · 2020Article
- Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.Journal of computational chemistry · 2020Article
- Solvation dynamics: improved reproduction of the time-dependent Stokes shift with polarizable empirical force field chromophore models.Physical chemistry chemical physics : PCCP · 2019Article
- Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.Chemical reviews · 2019Review
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.Annual review of biophysics · 2019Review
- Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.Journal of chemical information and modeling · 2019Article
- Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors.Journal of molecular modeling · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
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2 authors.
Funding
Abstract
The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.
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