Robust and efficient implicit solvation model for fast semiempirical methods
… For hydration free energies of small molecules, GFN1-xTB(… explicitly solvated approaches,
with a mean absolute … with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) …
with a mean absolute … with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) …
[HTML][HTML] Accurate determination of solvation free energies of neutral organic compounds from first principles
L Pereyaslavets, G Kamath, O Butin, A Illarionov… - Nature …, 2022 - nature.com
… We compute the free energies of solvation for a diverse set of … absolute errors (MAE) of
hydration, cyclohexane solvation, … 6, and Supplementary methods (Comparison to Implicit solvent …
hydration, cyclohexane solvation, … 6, and Supplementary methods (Comparison to Implicit solvent …
Efficient quantum chemical calculation of structure ensembles and free energies for nonrigid molecules
… correction from energy to free energy at absolute temperature … benchmarks comprised
of smaller molecules. Of particular … be combined with available implicit solvation models (see …
of smaller molecules. Of particular … be combined with available implicit solvation models (see …
Prediction of solvation free energies of ionic solutes in neutral solvents
… not modeled explicitly, but it may be fitted implicitly into the … results for the calculation of
solvation free energies of ions … Nonetheless, the more important absolute deviations in this …
solvation free energies of ions … Nonetheless, the more important absolute deviations in this …
Hydration free energies of polypeptides from popular implicit solvent models versus all-atom simulation results based on molecular quasichemical theory
RS Adhikari, AV Parambathu… - The Journal of …, 2022 - ACS Publications
… molecular quasi-chemical theory (QCT)─an approach that enables calculation of the hydration
free energy of … same resolution as is possible for small molecular solutes. The theory also …
free energy of … same resolution as is possible for small molecular solutes. The theory also …
[HTML][HTML] Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model
A Alibakhshi, B Hartke - Nature Communications, 2021 - nature.com
… solvation free energy can be generally divided into two main categories, namely explicit solvent
and implicit … for the same dataset and solvation free energy computations at B3LYP/6–31 …
and implicit … for the same dataset and solvation free energy computations at B3LYP/6–31 …
Advances in the calculation of binding free energies
A de Ruiter, C Oostenbrink - Current opinion in structural biology, 2020 - Elsevier
… showed a direct comparison of absolute binding free energy calculations and MM/PBSA …
Implicit Ligand Theory (ILT) uses an MD-generated ensemble of snapshots of the protein for …
Implicit Ligand Theory (ILT) uses an MD-generated ensemble of snapshots of the protein for …
Meta-analysis reveals that absolute binding free-energy calculations approach chemical accuracy
H Fu, Y Zhou, X Jing, X Shao, W Cai - Journal of Medicinal …, 2022 - ACS Publications
… calculate absolute protein–ligand binding free energies remains … We also reveal the
importance of always using the latest … to an implicit solvent model in absolute binding free-energy …
importance of always using the latest … to an implicit solvent model in absolute binding free-energy …
Ion solvation free energy calculation based on Ab initio molecular dynamics using a hybrid solvent model
… Free energy calculation of small molecules or ion species in … can use an implicit solvent
model to calculate the free energy … at single-ion absolute hydration free energies since real bulk …
model to calculate the free energy … at single-ion absolute hydration free energies since real bulk …
Efficient quantum-chemical calculations of acid dissociation constants from free-energy relationships
… T (S) is the implicit solvation free energy for the solvent S, including … The thermal populations
p i at absolute temperature T are … deprotonation sites, using a set of 171 small molecules. A …
p i at absolute temperature T are … deprotonation sites, using a set of 171 small molecules. A …