ArticleJournal of computer-aided molecular design2017
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- 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
- Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.Journal of computer-aided molecular design · 2020Article
- Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.Journal of computational chemistry · 2020Article
- Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Article
- Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.Journal of chemical information and modeling · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.Journal of chemical theory and computation · 2018Article
- Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.Journal of chemical information and modeling · 2018Article
- Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.Carbohydrate research · 2018Article
- Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.Journal of chemical theory and computation · 2018Article
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5 authors.
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Abstract
The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.
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