Predicting hydrophobic solvation by molecular simulation: 1. Testing united‐atom alkane models
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24690
Abstract: We present a systematic test of the performance of three popular united‐atom force fields—OPLS‐UA, GROMOS and TraPPE—at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation… read more here.
Keywords: predicting hydrophobic; united atom; solvation; hydrophobic solvation ... See more keywords
A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25072
Abstract: What factors favor protein folding? This is a textbook question. Parsing the experimental free energies of folding/unfolding into diverse enthalpic and entropic components of solute and solvent favoring or disfavoring folding is not an easy… read more here.
Keywords: methodology; thermodynamics; free energies; consensus view ... See more keywords
Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm
Sign Up to like & getrecommendations! Published in 2022 at "Journal of computational chemistry"
DOI: 10.1002/jcc.27054
Abstract: The prediction of (un)binding rates and free energies is of great significance to the drug design process. Although many enhanced sampling algorithms and approaches have been developed, there is not yet a reliable workflow to… read more here.
Keywords: weighted ensemble; high probability; quantity sampling; free energies ... See more keywords
Errors in DFT integration grids and their potential impact on chemical shift calculations
Sign Up to like & getrecommendations! Published in 2019 at "Magnetic Resonance in Chemistry"
DOI: 10.1002/mrc.4940
Abstract: Quantum chemical methods are often employed to estimate the shielding tensors and magnetic susceptibilities of nuclei in a system, chief among these techniques being density functional theory (DFT). In the estimation of chemical shift and… read more here.
Keywords: integration; free energies; integration grids; chemical shift ... See more keywords
From little string free energies towards modular graph functions
Sign Up to like & getrecommendations! Published in 2020 at "Journal of High Energy Physics"
DOI: 10.1007/jhep03(2020)077
Abstract: We study the structure of the non-perturbative free energy of a one-parameter class of little string theories (LSTs) of A-type in the so-called unrefined limit. These theories are engineered by N M5-branes probing a transverse… read more here.
Keywords: little string; graph functions; free energies; string free ... See more keywords
Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-018-0158-2
Abstract: We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim… read more here.
Keywords: challenge; free energies; binding free; host guest ... See more keywords
Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-020-00280-7
Abstract: The pKa is the standard measure used to describe the aqueous proton affinity of a compound, indicating the proton concentration (pH) at which two protonation states (e.g. A− and AH) have equal free energy. However,… read more here.
Keywords: molecule; free energies; tautomeric states; protonation ... See more keywords
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-021-00385-7
Abstract: In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The… read more here.
Keywords: usepackage; free energies; binding free; host ... See more keywords
Activation free energies for formation and dissociation of N–N, C–C, and C–H bonds in a Na–Ga melt
Sign Up to like & getrecommendations! Published in 2021 at "Computational Materials Science"
DOI: 10.1016/j.commatsci.2021.110366
Abstract: Abstract Bonding energies of N–N, C–C, and C–H in Na–Ga melts and C–H in Ga melts were investigated using first-principles calculations. Activation free energies for formation and dissociation of the above bonds were estimated via… read more here.
Keywords: formation dissociation; dissociation bonds; energies formation; free energies ... See more keywords
Predictions of solvation Gibbs free energies with COSMO-SAC approaches
Sign Up to like & getrecommendations! Published in 2020 at "Fluid Phase Equilibria"
DOI: 10.1016/j.fluid.2020.112614
Abstract: Abstract The modelling of a detailed kinetics mechanism in the liquid phase is still not well understood, and the description of solvent effect on reaction rates remains a challenge. Green and co-workers proposed an approach… read more here.
Keywords: solvation; predictions solvation; free energies; gibbs free ... See more keywords
Advances in the calculation of binding free energies.
Sign Up to like & getrecommendations! Published in 2020 at "Current opinion in structural biology"
DOI: 10.1016/j.sbi.2020.01.016
Abstract: In recent years, calculations of binding affinities from molecular simulations seem to have matured significantly. While the number of applications of such methods in drug design and biotechnology increases, the number of truly new methodological… read more here.
Keywords: free energies; calculation binding; calculation; binding free ... See more keywords