Accounting for nonuniformity of bulk‐solvent: A mosaic model
Sign Up to like & getrecommendations! Published in 2024 at "Protein Science"
DOI: 10.1002/pro.4909
Abstract: A flat mask‐based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model… read more here.
Keywords: mosaic; solvent model; model; bulk solvent ... See more keywords
Theoretical insight into the conversion of glucose to 5-hydroxymethylfurfural in subcritical water
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Fuel Chemistry and Technology"
DOI: 10.1016/s1872-5813(21)60124-x
Abstract: Abstract The reaction mechanism of the isomerization of glucose to fructose and further dehydration of fructose to 5-hydroxymethylfurfural (5-HMF) in subcritical water was investigated by the dispersion-corrected density functional theory (DFT-D) method with Dmol3 package… read more here.
Keywords: solvent model; water; kcal mol; conversion ... See more keywords
Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.2c01472
Abstract: In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules.… read more here.
Keywords: model benchmark; molecular dynamics; solvent models; solvent model ... 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
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