Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent
D Roy, A Kovalenko - Journal of Computer-Aided Molecular Design, 2019 - Springer
… solvent model depends not only on the theoretical backbone but also on the diversity of the
benchmark sets used for validation. The three-dimensional reference interaction site model (…
benchmark sets used for validation. The three-dimensional reference interaction site model (…
[HTML][HTML] Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution
S Abou-Hatab, V Carnevale, S Matsika - The Journal of Chemical …, 2021 - pubs.aip.org
… solvation models, such as molecular dynamics coupled with non-polarizable and polarizable
force fields, as well as Car–Parrinello molecular dynamics, to model … results, validating our …
force fields, as well as Car–Parrinello molecular dynamics, to model … results, validating our …
Explainable solvation free energy prediction combining graph neural networks with chemical intuition
K Low, ML Coote, EI Izgorodina - … Information and Modeling, 2022 - ACS Publications
… data set for the sake of comparison with existing models in the literature, given the limited
size of FreeSolv and the use of a random train/validation/test splitting scheme, we believe that …
size of FreeSolv and the use of a random train/validation/test splitting scheme, we believe that …
Generalized Born implicit solvent models for biomolecules
AV Onufriev, DA Case - Annual review of biophysics, 2019 - annualreviews.org
… We have reviewed the overall physical foundations and specific implementations of one of
the most widely used fast implicit solvation models—the GB approximation. Implementations …
the most widely used fast implicit solvation models—the GB approximation. Implementations …
Evaluating classical force fields against experimental cross-solvation free energies
S Kashefolgheta, MP Oliveira, SR Rieder… - … of chemical theory …, 2020 - ACS Publications
… solvation free energies are nowadays commonly included as target properties in the validation
… fashion, by considering available solvation free energies involving an arbitrary collection …
… fashion, by considering available solvation free energies involving an arbitrary collection …
Advances and challenges in modeling solvated reaction mechanisms for renewable fuels and chemicals
Y Basdogan, AM Maldonado… - Wiley Interdisciplinary …, 2020 - Wiley Online Library
… First they used DFT calculations with implicit solvation and then validated their results with
BOMD simulations with an explicit aqueous environment. These simulations demonstrated …
BOMD simulations with an explicit aqueous environment. These simulations demonstrated …
[HTML][HTML] Dependency of solvation effects on metal identity in surface reactions
… computed using the periodic electrostatic embedded cluster method (PEECM) in TURBOMOLE
under the fixed-charge approximation (fixed-charge approximation has been validated …
under the fixed-charge approximation (fixed-charge approximation has been validated …
A joint venture of ab initio molecular dynamics, coupled cluster electronic structure methods, and liquid-state theory to compute accurate isotropic hyperfine constants …
… HMI structures in order to delineate the performance of implicit and RISM-based solvation
models to account for the solvation effect on EPR parameters in comparison with explicitly …
models to account for the solvation effect on EPR parameters in comparison with explicitly …
Predicting Octanol–Water Partition Coefficients: Are Quantum Mechanical Implicit Solvent Models Better than Empirical Fragment-Based Methods?
… the use of CM5 charges with the SM12 model for the calculation of solvation free energies. …
generality of our findings may need to be validated against a more diverse set of molecules. …
generality of our findings may need to be validated against a more diverse set of molecules. …
Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike …
D Vassetti, M Pagliai, P Procacci - Journal of chemical theory and …, 2019 - ACS Publications
… Extensive and accurate simulations, including all possible combinations of organic molecule,
solvent, and solvent model, are allowed to assess the accuracy with regard to solvation …
solvent, and solvent model, are allowed to assess the accuracy with regard to solvation …