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Ab Initio Calculations
Ab initio calculations rest on solving the Schrödinger equation; the nature of the necessary approximations determines the level of the calculation....
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Reaction Mechanism of Actin ATP Hydrolysis Studied by QM/MM Calculations
Actin fibers are an important part of the cytoskeleton, providing vital support for the plasma membrane. This function is driven by its ATPase (ATP:...
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Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of...
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Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme
Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid methods have become very popular schemes to incorporate environmental effects in the calculation...
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Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling
ContextIn cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic...
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The Use of MM/QM Calculations of 13C Chemical Shifts in the Analysis of Edaravone Tautomers
The 13 C NMR chemical shifts of the three Edaravone tautomers (keto, enol, and amine) were calculated using a combined molecular mechanics (Pcmod...
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QM/MM Study of Bioluminescent Systems
BioluminescenceBioluminescence is a chemical reaction of (usually multi-steps) oxidation of a substrate (luciferinLuciferin) in the presence of an...
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QM/MM Approaches Shed Light on GFP Puzzles
The green fluorescent proteinGreen Fluorescent Protein (GFP) (GFP) is one of the most important light-responsive biological systems. We describe...
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Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids
Electric fields produce a range of effects by interacting with atoms, molecules, and complex matter modifying the activation barriers of chemical...
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Enantioselectivity in the Dihydroxylation of Alkenes by Osmium Complexes
The asymmetric dihydroxylation of olefins by osmium tetroxide is one of the most useful reactions in organic synthesis. Apart from the enormous...
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On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems
The automatic building of quantum mechanical/molecular mechanical models (QM/MM) of rhodopsinsRhodopsin Rhodopsin has been recently proposed. This is...
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Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational...
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An Outline of What Computational Chemistry Is All About
You can calculate molecular geometries, rates and equilibria, spectra, and other physical properties with the tools of computational chemistry:...
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FMO Interfaced with Molecular Dynamics Simulation
Three ways to combine FMO and MD are described: FMO-MD, FMO-QM/MM-MD, and MM-MD/FMO. FMO-MD is an ab initio MD in which force is updated on-the-fly...
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Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′
Quantum mechanical (QM) semiempirical methods (SMs), combined with molecular mechanics (MM) force fields, are extensively used in theoretical studies...
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Computational Methods
This chapter describes the different methods used in computational chemistry to determine the structure of a molecule. It starts with the...
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Approach of Electronic Structure Calculations to Crystal
Nowadays, the importance of molecular crystals and solids with regular structures is increasing in both basic chemistry and applied fields. However,...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
At the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic...
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The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study
In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energy of two biscarbene-Au(I)...
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Solvation Structure and Dynamics of Aqueous Solutions of Au+ Ions: A Molecular Dynamics Simulation Study
Although gold (Au) as an element is precious and noble, its elemental as well as ionic form is of huge scientific importance in view of its...
