ArticleJournal of chemical theory and computation2010
An implicit solvent model for SCC-DFTB with Charge-Dependent Radii.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.ACS catalysis · 2020Article
- Analysis of Density Functional Tight Binding with Natural Bonding Orbitals.The journal of physical chemistry. A · 2019Article
- Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.Journal of chemical theory and computation · 2018Article
- Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.Journal of the American Chemical Society · 2016Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
- Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.The journal of physical chemistry. B · 2014Article
- Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.Journal of the American Chemical Society · 2013Article
- A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.Journal of chemical theory and computation · 2012Article
- QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily.Journal of the American Chemical Society · 2012Article
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3 authors.
Funding
Abstract
Motivated by the need of rapidly exploring the potential energy surface of chemical reactions that involve highly charged species, we have developed an implicit solvent model for the approximate density functional theory, SCC-DFTB. The solvation free energy is calculated using the popular model that employs Poisson-Boltzmann for electrostatics and a surface-area term for non-polar contributions. To balance the treatment of species with different charge distributions, we make the atomic radii that define the dielectric boundary and solute cavity depend on the solute charge distribution. Specifically, the atomic radii are assumed to be linearly dependent on the Mulliken charges and solved self-consistently together with the solute electronic structure. Benchmark calculations indicate that the model leads to solvation free energies of comparable accuracy to the SM6 model (especially for ions), which requires much more expensive DFT calculations. With analytical first derivatives and favorable computational speed, the SCC-DFTB based solvation model can be effectively used, in conjunction with high-level QM calculations, to explore the mechanism of solution reactions. This is illustrated with a brief analysis of the hydrolysis of mono-methyl mono-phosphate ester (MMP) and tri-methyl mono-phosphate ester (TMP). Possible future improvements are also briefly discussed.
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