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 …

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 …

Semiempirical quantum–chemical methods

W Thiel - Wiley Interdisciplinary Reviews: Computational …, 2014 - Wiley Online Library
The semiempirical methods of quantum chemistry are reviewed, with emphasis on
established neglect of diatomic differential overlap‐based methods (MNDO, AM 1, PM 3) …

[图书][B] COSMO-RS: from quantum chemistry to fluid phase thermodynamics and drug design

A Klamt - 2005 - books.google.com
The COSMO-RS technique is a novel method for predicting the thermodynamic properties of
pure and mixed fluids which are important in many areas, ranging from chemical …

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 …

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 …

A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method

Q Cui, M Elstner, E Kaxiras, T Frauenheim… - The Journal of …, 2001 - ACS Publications
A quantum mechanical/molecular mechanical (QM/MM) approach based on an approximate
density functional theory, the so-called self-consistent charge density functional tight binding …

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 …

Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates

SR Billeter, AJ Turner, W Thiel - Physical Chemistry Chemical Physics, 2000 - pubs.rsc.org
An algorithm for linear scaling geometry optimisation and transition state search using
hybrid delocalised internal coordinates (HDLC) has been developed and implemented in …

A pseudobond approach to combining quantum mechanical and molecular mechanical methods

Y Zhang, TS Lee, W Yang - The Journal of chemical physics, 1999 - pubs.aip.org
A major challenge for combined quantum mechanical and molecular mechanical methods
(QM/MM) to study large molecules is how to treat the QM/MM boundary that bisects some …