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 …
Energy-based molecular fragmentation methods
MA Collins, RPA Bettens - Chemical reviews, 2015 - ACS Publications
1.1 Objectives A major objective of theoretical and computational chemistry is the calculation
of the energy and properties of molecules, so that chemical reactivity and material properties …
of the energy and properties of molecules, so that chemical reactivity and material properties …
QM/MM: what have we learned, where are we, and where do we go from here?
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 …
Extending the power of quantum chemistry to large systems with the fragment molecular orbital method
DG Fedorov, K Kitaura - The Journal of Physical Chemistry A, 2007 - ACS Publications
Following the brief review of the modern fragment-based methods and other approaches to
perform quantum-mechanical calculations of large systems, the theoretical development of …
perform quantum-mechanical calculations of large systems, the theoretical development of …
The effective fragment potential: a general method for predicting intermolecular interactions
Publisher Summary The interactions between molecules and molecular systems play key
roles in many important phenomena in chemistry, biological sciences, materials science and …
roles in many important phenomena in chemistry, biological sciences, materials science and …
Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin
MHM Olsson, G Hong, A Warshel - Journal of the American …, 2003 - ACS Publications
The evaluation of reduction potentials of proteins by ab initio approaches presents a major
challenge for computational chemistry. This is addressed in the present investigation by …
challenge for computational chemistry. This is addressed in the present investigation by …
A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme
We propose a parallelized integral-direct algorithm of the second-order Møller–Plesset
perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a …
perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a …
Extension of the effective fragment potential method to macromolecules
The effective fragment potential (EFP) approach, which can be described as a nonempirical
polarizable force field, affords an accurate first-principles treatment of noncovalent …
polarizable force field, affords an accurate first-principles treatment of noncovalent …
Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model
Y Meng, AE Roitberg - Journal of chemical theory and …, 2010 - ACS Publications
A constant pH replica exchange molecular dynamics (REMD) method is proposed and
implemented to improve coupled protonation and conformational state sampling. By mixing …
implemented to improve coupled protonation and conformational state sampling. By mixing …
Prediction and Rationalization of Protein pKa Values Using QM and QM/MM Methods
We describe the development and application of a computational method for the prediction
and rationalization of p K a values of ionizable residues in proteins, based on ab initio …
and rationalization of p K a values of ionizable residues in proteins, based on ab initio …