ArticleCarbohydrate research2018
Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.
Article in Carbohydrate research, 2018. 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.
- Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?Journal of chemical information and modeling · 2025Review
- Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations.Macromolecules · 2025Article
- 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
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.Journal of chemical theory and computation · 2020Article
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- 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
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Authors and funding
3 authors.
Funding
Abstract
Motivated by underestimation of the diffusion constant of glucose in aqueous solution at high glucose concentrations we performed additional optimization of the Drude polarizable hexopyranose monosaccharide force field. This indicated aggregation of the glucose at higher concentrations, which is a concern for studies of complex glycan systems such as the HIV Envelope where high effective concentrations of sugars are present. High-level quantum mechanical calculations were undertaken on water monohydrate-glucose interactions, on water cluster-glucose interactions and on glucose-glucose dimers in stacked (parallel) and perpendicular orientations. Optimization of the nonbond and dihedral parameters targeting these data yielded a revised model that showed improved agreement with experimental aqueous diffusion data. However, limitations in the diffusion constants were still present. These were due to the SWM4-NDP inherently overestimating the diffusion constant of water, a problem that was validated by calculation of the aqueous diffusion constants using the SWM6-NDP water model. In addition, results show the water diffusion constant to be significantly overestimated at high glucose concentrations though the glucose diffusion is in satisfactory agreement with experiment. These results indicate the subtle balance of water-sugar, water-water and sugar-sugar interactions that needs to be properly modeled to account for the full range of aqueous behavior of sugars in aqueous solution.
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