Large-scale computations in chemistry: a bird's eye view of a vibrant field
AV Akimov, OV Prezhdo - Chemical reviews, 2015 - ACS Publications
1.1. The Meaning of “Large Scale” In general, the term “large scale” can have one of the
following five meanings in computational chemistry:(1) large size: power-law and …
following five meanings in computational chemistry:(1) large size: power-law and …
Density functional tight binding: values of semi-empirical methods in an ab initio era
Q Cui, M Elstner - Physical Chemistry Chemical Physics, 2014 - pubs.rsc.org
Semi-empirical (SE) methods are derived from Hartree–Fock (HF) or Density Functional
Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are …
Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are …
Acid activation mechanism of the influenza A M2 proton channel
The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel
responsible for the acidification of the influenza virus interior, an important step in the viral …
responsible for the acidification of the influenza virus interior, an important step in the viral …
Molecular simulation of water and hydration effects in different environments: Challenges and developments for DFTB based models
We discuss the description of water and hydration effects that employs an approximate
density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to …
density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to …
Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems
A Simon, M Rapacioli, E Michoulier, L Zheng… - Molecular …, 2019 - Taylor & Francis
This review is dedicated to the application of the self-consistent-charge density-functional-
based tight-binding (SCC-DFTB) approach to describe the structures, energetics …
based tight-binding (SCC-DFTB) approach to describe the structures, energetics …
Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics
Ab initio molecular dynamics (AIMD) has become one of the most popular and robust
approaches for modeling complicated chemical, liquid, and material systems. However, the …
approaches for modeling complicated chemical, liquid, and material systems. However, the …
Hydrated excess protons can create their own water wires
Grotthuss shuttling of an excess proton charge defect through hydrogen bonded water
networks has long been the focus of theoretical and experimental studies. In this work we …
networks has long been the focus of theoretical and experimental studies. In this work we …
[HTML][HTML] An analysis of hydrated proton diffusion in ab initio molecular dynamics
A detailed understanding of the inherently multiscale proton transport process raises a
number of scientifically challenging questions. For example, there remain many (partially …
number of scientifically challenging questions. For example, there remain many (partially …
Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules
Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster
than ab initio and Density Functional Theory (DFT) methods and therefore are particularly …
than ab initio and Density Functional Theory (DFT) methods and therefore are particularly …
Understanding the multifaceted mechanism of Compound I formation in unspecific peroxygenases through multiscale simulations
GJ Costa, R Liang - The Journal of Physical Chemistry B, 2023 - ACS Publications
Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated
hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen …
hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen …