Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …
QM/MM free energy simulations: recent progress and challenges
Due to the higher computational cost relative to pure molecular mechanical (MM)
simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy …
simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy …
Water is an active matrix of life for cell and molecular biology
P Ball - Proceedings of the National Academy of Sciences, 2017 - National Acad Sciences
Szent-Győrgi called water the “matrix of life” and claimed that there was no life without it.
This statement is true, as far as we know, on our planet, but it is not clear whether it must …
This statement is true, as far as we know, on our planet, but it is not clear whether it must …
Biomolecular QM/MM simulations: What are some of the “burning issues”?
QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …
investigations. Considering the tremendous degree of success, including recognition by a …
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 …
Transient water wires mediate selective proton transport in designed channel proteins
Selective proton transport through proteins is essential for forming and using proton
gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules …
gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules …
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 …
A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces
Water-assisted proton transport through confined spaces influences many phenomena in
biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in …
biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in …
Electric fields control water-gated proton transfer in cytochrome c oxidase
P Saura, D Riepl, DM Frey… - Proceedings of the …, 2022 - National Acad Sciences
Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons
to oxygen and protons across a biological membrane. Cytochrome c oxidase (C c O) …
to oxygen and protons across a biological membrane. Cytochrome c oxidase (C c O) …
Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase
Cytochrome c oxidase (C c O) reduces oxygen to water and uses the released free energy to
pump protons across the membrane. We have used multiscale reactive molecular dynamics …
pump protons across the membrane. We have used multiscale reactive molecular dynamics …