scholarly journals On differentiability of the membrane-mediated mechanical interaction energy of discrete–continuum membrane–particle models

2021 ◽  
Vol 23 (4) ◽  
pp. 459-484
Author(s):  
Carsten Gräser ◽  
Tobias Kies
Keyword(s):  
Interaction Energy ◽  
Mechanical Interaction ◽  
Membrane Particle

RANK-ORDERING THE BINDING AFFINITY FOR FKBP12 AND H1N1 NEURAMINIDASE INHIBITORS IN THE COMBINATION OF A PROTEIN MODEL WITH DENSITY FUNCTIONAL THEORY

2011 ◽  
Vol 10 (04) ◽  
pp. 541-565 ◽  
Author(s):  
GANG HE ◽  
JUYING SHI ◽  
YANTAO CHEN ◽  
YI CHEN ◽  
QIANLING ZHANG ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Interaction Energy ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Mechanical Interaction ◽  
Functional Theory ◽  
Protein Model ◽  
Autodock 4.0 ◽  
Binding Free Energies

The quantum mechanical interaction energies between FKBP12 as well as H1N1 neuraminidase and their inhibitors were directly calculated with an efficient density functional theory by mimicking the whole protein with a protein model composed of the amino acids surrounding the ligands. It was found that the calculated quantum mechanical interaction energies correlate well with the experimental binding free energies with the correlation coefficients of 0.88, 0.86, and the standard deviation of 0.93 and 1.00 kcal/mol, respectively. To compare with force field approach, the binding free energies with the correlation coefficient R = 0.80 and 0.47 were estimated by AutoDock 4.0 programs. It was indicated that the quantum interaction energy shows a better performance in rank-ordering the binding affinity between FKBP12 and H1N1 neuraminidase inhibitors than those of AutoDock 4.0 program. In combination protein model with density functional theory, the estimated quantum interaction energy could be a good predictor or scoring function in structure-based computer-aided drug design. Finally, five new FKBP12 inhibitors were designed based on calculated quantum mechanical interaction energy. In particular, the theoretical K i value of one compound is as low as 0.05 nM, nearly 8-fold more active than FK506.

The Markov Model for Alteration of Rough Surfaces during Their Mechanical Interaction

Vestnik MEI ◽  
2017 ◽  
pp. 101-110
Author(s):  
Yuri A. Goritskiy ◽  
◽  
Konstantin V. Gavrilov ◽  
Yulia S. Ismailova ◽  
Olga V. Shevchenko ◽  
...  
Keyword(s):  
Markov Model ◽  
Rough Surfaces ◽  
Mechanical Interaction

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

Interaction energy between two identical atoms chemisorbed on a normal metal

1978 ◽  
Vol 72 (1) ◽  
pp. 125-139 ◽  
Author(s):  
J.C. Le Bosse ◽  
J. Lopez ◽  
J. Rousseau-Violet
Keyword(s):  
Interaction Energy ◽  
Normal Metal

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

Structure and ligand-based drug discovery of IL-4 inhibitors via interaction-energy-based learning approaches

2021 ◽  
pp. 1-19
Author(s):  
Sehrish Naz ◽  
Sajda Ashraf ◽  
Mohammad K. Parvez ◽  
Mohammed S. Al-Dosari ◽  
Zaheer Ul-Haq
Keyword(s):  
Drug Discovery ◽  
Interaction Energy ◽  
Learning Approaches
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