Journal of chemical theory and computation
Jun 2, 2022
Modeling of diffusion of adsorbates through porous materials with atomistic molecular dynamics (MD) can be a challenging task if the flexibility of the adsorbent needs to be included. This is because potentials need to be developed that accurately ac...
Journal of chemical theory and computation
May 25, 2022
Discovering meaningful collective variables for enhancing sampling, via applied biasing potentials or tailored MC move sets, remains a major challenge within molecular simulation. While recent studies identifying collective variables with variational...
Journal of chemical theory and computation
Apr 28, 2022
The theoretical prediction of molecular electronic spectra by means of quantum mechanical (QM) computations is fundamental to gain a deep insight into many photophysical and photochemical processes. A computational strategy that is attracting signifi...
Journal of chemical theory and computation
Apr 11, 2022
Transition state searches are the basis for computationally characterizing reaction mechanisms, making them a pivotal tool in myriad chemical applications. Nevertheless, common search algorithms are sensitive to reaction conformations, and the confor...
Journal of chemical theory and computation
Apr 6, 2022
An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. In this work, we focus on the recently develop...
Journal of chemical theory and computation
Apr 1, 2022
The outcomes of computational chemistry and biology research, including drug design, are significantly influenced by the underlying force field (FF) used in molecular simulations. While improved FF accuracy may be achieved via inclusion of explicit t...
Journal of chemical theory and computation
Mar 15, 2022
Transferable high dimensional neural network potentials (HDNNPs) have shown great promise as an avenue to increase the accuracy and domain of applicability of existing atomistic force fields for organic systems relevant to life science. We have previ...
Journal of chemical theory and computation
Mar 15, 2022
Protonation states of ionizable protein residues modulate many essential biological processes. For correct modeling and understanding of these processes, it is crucial to accurately determine their p values. Here, we present four tree-based machine l...
Journal of chemical theory and computation
Mar 11, 2022
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to ...
Journal of chemical theory and computation
Mar 2, 2022
Machine learning (ML) has recently gained attention as a means to develop more accurate exchange-correlation (XC) functionals for density functional theory, but functionals developed thus far need to be improved on several metrics, including accuracy...