ArticleJournal of chemical theory and computation2018
CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.
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 20 papers.
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20 citing papers in PubMed, 50 citations in OpenAlex.
- Molecular Dynamics-Instantaneous Frequencies of Molecules Method to Address the Performance of Classical and Rigid Water Force Fields.The journal of physical chemistry. B · 2026Article
- Insights into the Electronic and Structural Properties of Cellulose and Amylose: A Comparative Force Field Study.The journal of physical chemistry. B · 2026Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
- Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?Journal of chemical information and modeling · 2025Review
- TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations.Journal of chemical theory and computation · 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
- Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions.Journal of chemical information and modeling · 2024Article
- Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2023Article
- Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields.Physical chemistry chemical physics : PCCP · 2023Article
- Application of the 2-deoxyglucose scaffold as a new chiral probe for elucidation of the absolute configuration of secondary alcohols.Scientific reports · 2022Article
- 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
- Influence of Carbohydrate Additives on the Growth Rate of Microalgae Biomass with an Increased Carbohydrate Content.Marine drugs · 2021Article
- Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model.Methods in molecular biology (Clifton, N.J.) · 2021Article
- 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
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We present an extension of the CHARMM Drude polarizable force field to enable modeling of polysaccharides containing pyranose and furanose monosaccharides. The new force field parameters encompass 1↔2, 1→3, 1→4, and 1→6 pyranose-furanose linkages, 2→1 and 2→6 furanose-furanose linkages, 2→2, 2→3, and 2→4 furanose-pyranose, and 1↔1, 1→2, 1→3, 1→4, and 1→6 pyranose-pyranose linkages. For the glycosidic linkages, both simple model compounds and the full disaccharides with methylation at the reducing end were used for parameter optimization. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF). Target data for optimization included one- and two-dimensional potential energy scans of ω and the Φ/Ψ glycosidic dihedral angles in the model compounds and full disaccharides computed by quantum mechanical (QM) RIMP2/cc-pVQZ single point energies on MP2/6-31G(d) optimized structures. Also included in the target data are extensive sets of QM gas phase monohydrate water-saccharide interactions, dipole moments, and molecular polarizabilities for both model compounds and full disaccharides. The resulting polarizable model is shown to be in good agreement with a range of QM data, offering a significant improvement over the additive CHARMM36 carbohydrate force field, as well as experimental data including crystal structures and conformational properties of disaccharides and a trisaccharide in aqueous solution.
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