Systematic derivation of implicit solvent models for the study of polymer collapse
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24754
Abstract: The conformational states adopted by a polymer chain in water are a result of a delicate balance between intra‐molecular and water‐mediated interactions. Using an explicit representation of the solvent is, however, computationally expensive and it… read more here.
Keywords: water; solvent; systematic derivation; derivation implicit ... See more keywords
`Martinizing' the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins
Sign Up to like & getrecommendations! Published in 2018 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2017.11.1922
Abstract: Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed… read more here.
Keywords: solvation; solvent method; variational implicit; method vism ... See more keywords
Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.
Sign Up to like & getrecommendations! Published in 2017 at "European journal of medicinal chemistry"
DOI: 10.1016/j.ejmech.2016.12.023
Abstract: We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned… read more here.
Keywords: treatment; active site; site; site waters ... See more keywords
Structure and ion-ion interactions in trifluoroacetate-based ionic liquids: Quantum chemical and molecular dynamics simulation studies
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Molecular Liquids"
DOI: 10.1016/j.molliq.2021.115449
Abstract: Abstract Ionic liquids (ILs) raise quite interesting but complicated questions for computational study due to the fact that different interactions, e.g., electrostatic interactions, charge-transfer interactions, steric repulsion, dispersion and hydrogen bonding that determine structural organization… read more here.
Keywords: implicit solvent; ion; trifluoroacetate based; molecular dynamics ... See more keywords
Understanding Adsorption of Organics on Pt(111) in the Aqueous Phase: Insights from DFT Based Implicit Solvent and Statistical Thermodynamics Models.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c00894
Abstract: Adsorption of organics in the aqueous phase is an area which is experimentally difficult to measure, while computational techniques require extensive configurational sampling of the solvent and adsorbate. This is exceedingly computationally demanding, which excludes… read more here.
Keywords: adsorption organics; adsorption; aqueous phase; thermodynamics ... See more keywords
How Well Can Implicit Solvent Simulations Explore Folding Pathways? A Quantitative Analysis of α-Helix Bundle Proteins.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.7b00726
Abstract: Protein folding has been posing challenges for molecular simulation for decades. Implicit solvent models are sought as routes to increase the capability of simulation, with trade-offs between computational speed and accuracy. Here, we systematically investigate… read more here.
Keywords: folding pathways; bundle proteins; solvent simulations; helix bundle ... See more keywords
Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2023 at "RSC Advances"
DOI: 10.1039/d2ra08180f
Abstract: Inspired by the recent work from Noé and coworkers on the development of machine learning based implicit solvent model for the simulation of solvated peptides [Chen et al., J. Chem. Phys., 2021, 155, 084101], here… read more here.
Keywords: solvent model; based implicit; implicit solvent; machine learning ... See more keywords