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” …
From NWChem to NWChemEx: Evolving with the computational chemistry landscape
Since the advent of the first computers, chemists have been at the forefront of using
computers to understand and solve complex chemical problems. As the hardware and …
computers to understand and solve complex chemical problems. As the hardware and …
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
The latest release of NWChem delivers an open-source computational chemistry package
with extensive capabilities for large scale simulations of chemical and biological systems …
with extensive capabilities for large scale simulations of chemical and biological systems …
NWChem: Past, present, and future
Specialized computational chemistry packages have permanently reshaped the landscape
of chemical and materials science by providing tools to support and guide experimental …
of chemical and materials science by providing tools to support and guide experimental …
Distinct roles of catalytic cysteine and histidine in the protease and ligase mechanisms of human legumain as revealed by DFT-based QM/MM simulations
B Elsässer, FB Zauner, J Messner, WT Soh… - ACS …, 2017 - ACS Publications
The cysteine protease enzyme legumain hydrolyzes peptide bonds with high specificity after
asparagine and under more acidic conditions after aspartic acid [Baker, ENJ Mol. Biol. 1980 …
asparagine and under more acidic conditions after aspartic acid [Baker, ENJ Mol. Biol. 1980 …
Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations
We present results of a theoretical analysis of the phosphorylation reaction in cAMP-
dependent protein kinase using a combined quantum mechanical and molecular mechanics …
dependent protein kinase using a combined quantum mechanical and molecular mechanics …
Recent developments in QM/MM methods towards open-boundary multi-scale simulations
Combined quantum mechanics/molecular mechanics (QM/MM) methods have been widely
used in multi-scale modelling and simulations of physical, chemical and biological …
used in multi-scale modelling and simulations of physical, chemical and biological …
Carbon and chlorine isotope fractionation patterns associated with different engineered chloroform transformation reactions
C Torrento, J Palau… - … science & technology, 2017 - ACS Publications
To use compound-specific isotope analysis for confidently assessing organic contaminant
attenuation in the environment, isotope fractionation patterns associated with different …
attenuation in the environment, isotope fractionation patterns associated with different …
Vertical ionization potentials of nucleobases in a fully solvated DNA environment
Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA
fragment (12-mer B-DNA fragment+ 22 sodium counterions+ 5760 water molecules …
fragment (12-mer B-DNA fragment+ 22 sodium counterions+ 5760 water molecules …
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
We demonstrate that Jarzynski's equation can be used to reliably compute free energy
differences between low and high level representations of systems. The need for such a …
differences between low and high level representations of systems. The need for such a …