Understanding nanocellulose–water interactions: Turning a detriment into an asset

L Solhi, V Guccini, K Heise, I Solala… - Chemical …, 2023 - ACS Publications
Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and
the current trend focuses on utilizing nanocellulose in a broad range of sustainable …

Physics-inspired structural representations for molecules and materials

F Musil, A Grisafi, AP Bartók, C Ortner… - Chemical …, 2021 - ACS Publications
The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …

OPLS3: a force field providing broad coverage of drug-like small molecules and proteins

E Harder, W Damm, J Maple, C Wu… - Journal of chemical …, 2016 - ACS Publications
The parametrization and validation of the OPLS3 force field for small molecules and proteins
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …

An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications

JA Lemkul, J Huang, B Roux, AD MacKerell Jr - Chemical reviews, 2016 - ACS Publications
Molecular mechanics force fields that explicitly account for induced polarization represent
the next generation of physical models for molecular dynamics simulations. Several …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

Metal ion modeling using classical mechanics

P Li, KM Merz Jr - Chemical reviews, 2017 - ACS Publications
Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …

The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids

KG Sprenger, VW Jaeger… - The Journal of Physical …, 2015 - ACS Publications
We have applied molecular dynamics to calculate thermodynamic and transport properties
of a set of 19 room-temperature ionic liquids. Since accurately simulating the thermophysical …

Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field

D Shivakumar, J Williams, Y Wu, W Damm… - Journal of chemical …, 2010 - ACS Publications
The accurate prediction of protein− ligand binding free energies is a primary objective in
computer-aided drug design. The solvation free energy of a small molecule provides a …

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate–protein modeling

O Guvench, SS Mallajosyula, EP Raman… - Journal of chemical …, 2011 - ACS Publications
Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-
acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid …

Practical aspects of free-energy calculations: a review

N Hansen, WF Van Gunsteren - Journal of chemical theory and …, 2014 - ACS Publications
Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …