Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.
Sign Up to like & getrecommendations! Published in 2021 at "Archives of biochemistry and biophysics"
DOI: 10.1016/j.abb.2021.108807
Abstract: The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with… read more here.
Keywords: biosynthesis; hybrid quantum; molecular mechanics; mechanics molecular ... See more keywords
Advanced nonlinear buckling analysis of a compressed single layer graphene sheet using the molecular mechanics method
Sign Up to like & getrecommendations! Published in 2021 at "International Journal of Mechanical Sciences"
DOI: 10.1016/j.ijmecsci.2021.106703
Abstract: Abstract The standard molecular mechanics (MM) method with the DREIDING force field (see Mayo et al. The Journal of Physical Chemistry, 1990, 94: 8897–8909) and the molecular structural mechanics (MSM) method with Bernoulli–Euler beam elements are… read more here.
Keywords: buckling; molecular mechanics; post buckling; mechanics method ... See more keywords
Molecular mechanics modelling of amorphous silicon oxycarbide clusters by bottom-up approach
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Molecular Structure"
DOI: 10.1016/j.molstruc.2020.127930
Abstract: Abstract In this work, a large data set of SiCO amorphous clusters was created from predefined primary building units (PBUs), connected statistically using custom made Python interface to GULP program and employing ReaxFF force field.… read more here.
Keywords: bottom approach; molecular mechanics; mechanics modelling; modelling amorphous ... See more keywords
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00057
Abstract: FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants… read more here.
Keywords: novel esterase; mechanics molecular; molecular mechanics; fmta ... See more keywords
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c01505
Abstract: We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK… read more here.
Keywords: mechanics molecular; molecular mechanics; quantum mechanics; graphics processing ... See more keywords
A New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.0c00247
Abstract: Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution, and is thus of great… read more here.
Keywords: molecular mechanics; chemistry; mechanics model; biology ... See more keywords
Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion–Protein Interactions
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.1c00898
Abstract: Metal ions are associated with a variety of proteins and play critical roles in a wide range of biochemical processes. There are multiple ways to study and quantify protein–metal ion interactions, including molecular dynamics simulations.… read more here.
Keywords: mechanics; lennard jones; molecular mechanics; metal ion ... See more keywords
Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00178
Abstract: RNA modulation via small molecules is a novel approach in pharmacotherapies, where the determination of the structural properties of RNA motifs is considered a promising way to develop drugs capable of targeting RNA structures to… read more here.
Keywords: molecular mechanics; thermodynamics; force; force fields ... See more keywords
Vertical Excitation Energies and Lifetimes of the Two Lowest Singlet Excited States of Cytosine, 5-Aza-cytosine, and the Triazine Family: Quantum Mechanics–Molecular Mechanics Studies
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c01262
Abstract: A swarm of semi-classical quantum mechanics/molecular mechanics molecular-dynamics simulations where OM2/MNDO is combined with the Gromacs program for consideration of explicit water is performed, solving the time-dependent Schrödinger equation in each step of the trajectories… read more here.
Keywords: mechanics molecular; molecular mechanics; triazine; quantum mechanics ... See more keywords
Structure and Dynamics of the Reactive State for the Histidine Methylation Process and Catalytic Mechanism of SETD3: Insights from Quantum Mechanics/Molecular Mechanics Investigation
Sign Up to like & getrecommendations! Published in 2020 at "ACS Catalysis"
DOI: 10.1021/acscatal.0c03390
Abstract: The SETD3 enzyme adds a methyl group to Ne2 of His73 in β-actin, and such methylation finetunes actin’s biochemical properties and cellular function. Here, quantum mechanics/molecular mechanics mol... read more here.
Keywords: methylation; molecular mechanics; mechanics molecular; setd3 ... See more keywords
Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B
Sign Up to like & getrecommendations! Published in 2017 at "ACS Catalysis"
DOI: 10.1021/acscatal.6b02310
Abstract: Classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the origin of the enantioselectivity of the Candida antarctica lipase B (CalB) catalyzed O-acetylation of (R,S)-propranolol. The reaction is… read more here.
Keywords: candida antarctica; molecular mechanics; mechanics molecular; quantum mechanics ... See more keywords