Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
Fragmentation methods: A route to accurate calculations on large systems
MS Gordon, DG Fedorov, SR Pruitt… - Chemical …, 2012 - ACS Publications
Theoretical chemists have always strived to perform quantum mechanics (QM) calculations
on larger and larger molecules and molecular systems, as well as condensed phase …
on larger and larger molecules and molecular systems, as well as condensed phase …
QM/MM methods for biomolecular systems
HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives
S Dapprich, I Komáromi, KS Byun, K Morokuma… - Journal of Molecular …, 1999 - Elsevier
The IMOMM, IMOMO, and ONIOM methods have been proven to be powerful tools for the
theoretical treatment of large molecular systems where different levels of theory are applied …
theoretical treatment of large molecular systems where different levels of theory are applied …
Frozen-density embedding strategy for multilevel simulations of electronic structure
Modeling properties of chemical species and chemical reactions requires usually the
quantum-mechanical level of description. Approximated methods to solve the electronic …
quantum-mechanical level of description. Approximated methods to solve the electronic …
QM/MM: what have we learned, where are we, and where do we go from here?
H Lin, DG Truhlar - Theoretical Chemistry Accounts, 2007 - Springer
This paper briefly reviews the current status of the most popular methods for combined
quantum mechanical/molecular mechanical (QM/MM) calculations, including their …
quantum mechanical/molecular mechanical (QM/MM) calculations, including their …
Dye chemistry with time-dependent density functional theory
AD Laurent, C Adamo, D Jacquemin - Physical Chemistry Chemical …, 2014 - pubs.rsc.org
In this perspective, we present an overview of the determination of excited-state properties of
“real-life” dyes, and notably of their optical absorption and emission spectra, performed …
“real-life” dyes, and notably of their optical absorption and emission spectra, performed …
Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy
DW Zhang, JZH Zhang - The Journal of chemical physics, 2003 - pubs.aip.org
A scheme to calculate fully quantum mechanical (ab initio) interaction energy involving a
macromolecule like protein is presented. In this scheme, the protein is decomposed into …
macromolecule like protein is presented. In this scheme, the protein is decomposed into …
Quantum mechanical methods for enzyme kinetics
J Gao, DG Truhlar - Annual Review of Physical Chemistry, 2002 - annualreviews.org
▪ Abstract This review discusses methods for the incorporation of quantum mechanical
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry
MS Gordon, MA Freitag… - The Journal of …, 2001 - ACS Publications
The effective fragment potential (EFP) method is described and its capabilities illustrated
using several applications. The original method, EFP1, was primarily developed to describe …
using several applications. The original method, EFP1, was primarily developed to describe …