ArticleThe journal of physical chemistry. B2014
Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Efficient Multistate Free-Energy Calculations with QM/MM Accuracy Using Replica-Exchange Enveloping Distribution Sampling.The journal of physical chemistry. B · 2025Article
- Sustainable Photocatalysis with Phenyl-Modified g-CPolymers · 2025Article
- Multi-proton dynamics near membrane-water interface.Nature communications · 2025Article
- Tight Binding Simulation of the MgO and Mg(OH)Journal of chemical theory and computation · 2025Article
- Structure, Properties, and Applications of Silica Nanoparticles: Recent Theoretical Modeling Advances, Challenges, and Future Directions.Small (Weinheim an der Bergstrasse, Germany) · 2024Review
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
- Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure HJournal of chemical theory and computation · 2024Article
- Beyond the Status Quo: Density Functional Tight Binding and Neural Network Potentials as a Versatile Simulation Strategy to Characterize Host-Guest Interactions in Metal- and Covalent Organic Frameworks.The journal of physical chemistry letters · 2023Review
- Detection of nitrofurazone with metal-organic frameworks and reduced graphene oxide composites: insights from molecular dynamics simulations.Mikrochimica acta · 2023Article
- Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA.Journal of the American Chemical Society · 2023Article
- Quantum chemical investigation of the effect of alkali metal ions on the dynamic structure of water in aqueous solutions.RSC advances · 2022Article
- A quantum chemical molecular dynamics repository of solvated ions.Scientific data · 2022Article
- Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.Chemical physics letters · 2022Article
- Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.Journal of chemical theory and computation · 2022Article
- Assessing the Structure of Protic Ionic Liquids Based on Triethylammonium and Organic Acid Anions.The journal of physical chemistry. B · 2021Article
- The electrochemical interface in first-principles calculations.Surface science reports · 2020Article
- Structural Features of Triethylammonium Acetate through Molecular Dynamics.Molecules (Basel, Switzerland) · 2020Article
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8 authors.
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Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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