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” …
Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr - Journal of computational chemistry, 2004 - Wiley Online Library
Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
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 …
Charge model 5: An extension of Hirshfeld population analysis for the accurate description of molecular interactions in gaseous and condensed phases
We propose a novel approach to deriving partial atomic charges from population analysis.
The new model, called Charge Model 5 (CM5), yields class IV partial atomic charges by …
The new model, called Charge Model 5 (CM5), yields class IV partial atomic charges by …
Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
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 …
QM/MM methods for biological systems
HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
Electrostatic potential derived atomic charges for periodic systems using a modified error functional
A method to generate electrostatic potential (ESP) derived atomic charges in crystalline
solids from periodic quantum mechanical calculations, termed the REPEAT method, is …
solids from periodic quantum mechanical calculations, termed the REPEAT method, is …
Comparison of computational methods for atomic charges
T Lu, FW CHEN - Acta Physico-Chimica Sinica, 2012 - ingentaconnect.com
Atomic charge is one of the simplest and the most intuitive description of charge distribution
in chemical systems. It has great significance in theory and in practical applications. In this …
in chemical systems. It has great significance in theory and in practical applications. In this …
Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome
Cleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large
cellular machineries composed of both protein and RNA. Long thought to rely on a two …
cellular machineries composed of both protein and RNA. Long thought to rely on a two …
Trajectory‐based nonadiabatic dynamics with time‐dependent density functional theory
Understanding the fate of an electronically excited molecule constitutes an important task for
theoretical chemistry, and practical implications range from the interpretation of atto‐and …
theoretical chemistry, and practical implications range from the interpretation of atto‐and …