Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein–Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase

2014 ◽  
Vol 119 (3) ◽  
pp. 997-1001 ◽  
Author(s):  
Christopher J. Woods ◽  
Katherine E. Shaw ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Water Molecules ◽  
Free Energies

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

2008 ◽  
Vol 128 (1) ◽  
pp. 014109 ◽  
Author(s):  
Christopher J. Woods ◽  
Frederick R. Manby ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Efficient Method ◽  
Free Energies

Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data

BIOPHYSICS ◽  
2013 ◽  
Vol 58 (5) ◽  
pp. 583-591 ◽  
Author(s):  
E. González ◽  
J. Lino ◽  
A. Deriabina ◽  
J. N. F. Herrera ◽  
V. I. Poltev
Keyword(s):  
Experimental Data ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Dna Bases ◽  
Water Molecules

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

2005 ◽  
Vol 109 (20) ◽  
pp. 10474-10483 ◽  
Author(s):  
Frauke Gräter ◽  
Sonja M. Schwarzl ◽  
Annick Dejaegere ◽  
Stefan Fischer ◽  
Jeremy C. Smith
Keyword(s):  
Quantum Mechanics ◽  
Ligand Binding ◽  
Molecular Mechanics ◽  
Free Energies ◽  
Binding Free Energies

An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins’ first spectral absorption band maxima

2020 ◽  
Vol 22 (32) ◽  
pp. 18114-18123
Author(s):  
Dmitrii M. Nikolaev ◽  
Andrey A. Shtyrov ◽  
Andrey S. Mereshchenko ◽  
Maxim S. Panov ◽  
Yuri S. Tveryanovich ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Absorption Band ◽  
Molecular Mechanics ◽  
Accurate Prediction ◽  
Water Molecules ◽  
Spectral Absorption ◽  
High Quality ◽  
Placement Algorithms

Accurate prediction of water molecules in protein cavities is an important factor for obtaining high-quality rhodopsin QM/MM models.

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Molecular orientation of liquid aliphatic hydrocarbons on the surface and at the interface with water

1989 ◽  
Vol 54 (12) ◽  
pp. 3171-3186 ◽  
Author(s):  
Jan Kloubek
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Molecular Orientation ◽  
Phase Changes ◽  
Aliphatic Hydrocarbons ◽  
Water Molecules ◽  
Free Energies ◽  
Dispersion Component ◽  
System Water ◽  
Orientation Of Molecules

The validity of the Fowkes theory for the interaction of dispersion forces at interfaces was inspected for the system water-aliphatic hydrocarbons with 5 to 16 C atoms. The obtained results lead to the conclusion that the hydrocarbon molecules cannot lie in a parallel position or be randomly arranged on the surface but that orientation of molecules increases there the ration of CH3 to CH2 groups with respect to that in the bulk. This ratio is changed at the interface with water so that the surface free energy of the hydrocarbon, γH, rises to a higher value, γ’H, which is effective in the interaction with water molecules. Not only the orientation of molecules depends on the adjoining phase and on the temperature but also the density of hydrocarbons on the surface of the liquid phase changes. It is lower than in the bulk and at the interface with water. Moreover, the volume occupied by the CH3 group increases on the surface more than that of the CH2 group. The dispersion component of the surface free energy of water, γdW = 19.09 mJ/m2, the non-dispersion component, γnW = 53.66 mJ/m2, and the surface free energies of the CH2 and CH3 groups, γ(CH2) = 32.94 mJ/m2 and γ(CH3) = 15.87 mJ/m2, were determined at 20 °C. The dependence of these values on the temperature in the range 15-40 °C was also evaluated.

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