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
Some Challenges of Diffused Interfaces in Implicit‐Solvent Models
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.70036
Abstract: The standard Poisson‐Boltzmann (PB) model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute‐solvent interface. The discontinuous field parameters are not only difficult numerically, but also are not… read more here.
Keywords: solvent models; diffused interfaces; challenges diffused; interfaces 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
Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.
Sign Up to like & getrecommendations! Published in 2024 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c01366
Abstract: In this paper, we present differentiable solvent-accessible surface area (dSASA), an exact geometric method to calculate SASA analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to tetrahedra in… read more here.
Keywords: solvent; solvent accessible; surface area; solvent molecular ... See more keywords
Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.4c00833
Abstract: The ion atmosphere surrounding highly charged biomolecules, such as nucleic acids, is crucial for their dynamics, structure, and interactions. Here, we develop an approach for the explicit treatment of ions within an implicit solvent framework… read more here.
Keywords: solvent explicit; explicit ions; model; dna ... See more keywords
Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.5c00728
Abstract: The conformational ensemble of a molecule is strongly influenced by the surrounding environment. Correctly modeling the effect of any given environment is, hence, of pivotal importance in computational studies. Machine learning (ML) has been shown… read more here.
Keywords: graph neural; transferring knowledge; solvent model; model ... 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
Influence of the Dielectric Constant on the Ionic Current Rectification of Bipolar Nanopores.
Sign Up to like & getrecommendations! Published in 2024 at "ACS nano"
DOI: 10.1021/acsnano.4c03546
Abstract: In this paper, we investigate how the dielectric constant, ϵ, of an electrolyte solvent influences the current rectification characteristics of bipolar nanopores. It is well recognized that bipolar nanopores with two oppositely charged regions rectify… read more here.
Keywords: dielectric constant; bipolar nanopores; water; current rectification ... See more keywords