Biochemistry and theory of proton-coupled electron transfer
Through incremental change, Nature reworks and repurposes its functional machinery. In
this way, proteins that photochemically repair DNA by moving protons and electrons have a …
this way, proteins that photochemically repair DNA by moving protons and electrons have a …
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 …
Subsystem density‐functional theory
CR Jacob, J Neugebauer - Wiley Interdisciplinary Reviews …, 2014 - Wiley Online Library
Subsystem density‐functional theory (subsystem DFT) has developed into a powerful
alternative to Kohn–Sham DFT for quantum chemical calculations of complex systems. It …
alternative to Kohn–Sham DFT for quantum chemical calculations of complex systems. It …
Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation …
SCL Kamerlin, M Haranczyk… - The journal of physical …, 2009 - ACS Publications
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …
to provide a general scheme for chemical reactions in proteins. However, such approaches …
Block-localized wavefunction (BLW) method at the density functional theory (DFT) level
The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method
incorporating the efficiency of molecular orbital (MO) theory. It can generate the …
incorporating the efficiency of molecular orbital (MO) theory. It can generate the …
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems
SCL Kamerlin, S Vicatos, A Dryga… - Annual review of …, 2011 - annualreviews.org
Recent years have witnessed an explosion in computational power, leading to attempts to
model ever more complex systems. Nevertheless, there remain cases for which the use of …
model ever more complex systems. Nevertheless, there remain cases for which the use of …
Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds
S Fux, CR Jacob, J Neugebauer, L Visscher… - The Journal of chemical …, 2010 - pubs.aip.org
The frozen-density embedding (FDE) scheme [Wesolowski and Warshel, J. Phys. Chem. 97,
8050 (1993)] relies on the use of approximations for the kinetic-energy component v T [ρ 1, ρ …
8050 (1993)] relies on the use of approximations for the kinetic-energy component v T [ρ 1, ρ …
The empirical valence bond model: theory and applications
SCL Kamerlin, A Warshel - Wiley Interdisciplinary Reviews …, 2011 - Wiley Online Library
Recent years have seen an explosion in computer power, allowing for the examination of
ever more challenging problems. For instance, a recent simulation study, which was the first …
ever more challenging problems. For instance, a recent simulation study, which was the first …
Efficient empirical valence bond simulations with GROMACS
We describe a protocol to perform empirical valence bond (EVB) simulations using
GROMACS software. EVB is a fast and reliable method that allows one to determine the …
GROMACS software. EVB is a fast and reliable method that allows one to determine the …
Chromophore-specific theoretical spectroscopy: From subsystem density functional theory to mode-specific vibrational spectroscopy
J Neugebauer - Physics reports, 2010 - Elsevier
Spectroscopy forms the bridge between theory and experiment in the analysis of structure,
properties, and reactivity of functional molecules and molecular aggregates. Our knowledge …
properties, and reactivity of functional molecules and molecular aggregates. Our knowledge …