scholarly journals Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

2018 ◽  
Vol 14 (2) ◽  
pp. 759-767 ◽  
Author(s):  
Xiu Yang ◽  
Huan Lei ◽  
Peiyuan Gao ◽  
Dennis G. Thomas ◽  
David L. Mobley ◽  
...  
Keyword(s):  
Parameter Uncertainty ◽  
Atomic Radius ◽  
Solvation Energy ◽  
Energy Calculations ◽  
Biomolecular Solvation ◽  
Charge Parameter

Investigation of Factors Affecting Conformational Preference in Complex Haloethane Derivatives by Classical Energy Calculations

1973 ◽  
Vol 51 (16) ◽  
pp. 2659-2670 ◽  
Author(s):  
William F. Reynolds ◽  
Donald J. Wood
Keyword(s):  
Solvation Energy ◽  
Coupling Constants ◽  
Conformational Preference ◽  
Factors Affecting ◽  
Energy Calculations ◽  
Vicinal Coupling Constants ◽  
Classical Energy ◽  
Dipole Interactions ◽  
Related Compounds ◽  
Good Agreement

Classical energy calculations are used in combination with Abraham's electrostatic theory of solvation energy to estimate rotamer energy differences for haloethane derivatives. The calculations are tested by comparing experimental and calculated ΔE values for several di- and tetrahaloethanes. There is good agreement for chloro and bromo derivatives but poorer agreement for fluoro and iodo derivatives. ΔE values in solution are also estimated for l4 complex chloro- and bromoethanes which we have previously investigated by n.m.r. spectroscopy. The calculations generally parallel the experimental results as reflected by vicinal coupling constants. They are particularly useful for trends in conformational preference for closely related compounds and are used in conjunction with vicinal coupling constants to identify diastereomers produced by halogenation of alkenes. Steric interactions, dipole–dipole interactions and solvation energy are all important in determining conformational preference for complex haloethanes in solution.

scholarly journals Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

2021 ◽  
Vol 22 (10) ◽  
pp. 5061
Author(s):  
Dipankar Roy ◽  
Andriy Kovalenko
Keyword(s):  
Ligand Binding ◽  
Molecular Simulation ◽  
Solvation Energy ◽  
Modeling Framework ◽  
Time Step ◽  
Interaction Site ◽  
Energy Calculations ◽  
Site Model ◽  
Reference Interaction Site ◽  
Solvation Theory

The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.

The annealed (0001) α-alumina surface and its influence on thin-film growth

1995 ◽  
Vol 53 ◽  
pp. 336-337
Author(s):  
Michael W. Bench ◽  
Paul G. Kotula ◽  
C. Barry Carter
Keyword(s):  
Electron Microscopy ◽  
Surface Energy ◽  
Film Growth ◽  
Thin Film Growth ◽  
Energy Calculations ◽  
Transmission Electron ◽  
Reflection Electron Microscopy ◽  
Low Energy Electron ◽  
Surface Nature

The growth of semiconductors, superconductors, metals, and other insulators has been investigated using alumina substrates in a variety of orientations. The surface state of the alumina (for example surface reconstruction and step nature) can be expected to affect the growth nature and quality of the epilayers. As such, the surface nature has been studied using a number of techniques including low energy electron diffraction (LEED), reflection electron microscopy (REM), transmission electron microscopy (TEM), molecular dynamics computer simulations, and also by theoretical surface energy calculations. In the (0001) orientation, the bulk alumina lattice can be thought of as a layered structure with A1-A1-O stacking. This gives three possible terminations of the bulk alumina lattice, with theoretical surface energy calculations suggesting that termination should occur between the Al layers. Thus, the lattice often has been described as being made up of layers of (Al-O-Al) unit stacking sequences. There is a 180° rotation in the surface symmetry of successive layers and a total of six layers are required to form the alumina unit cell.

CO2 and CO monolayers on MgO(100) : LEED experiments and potential energy calculations

1994 ◽  
Vol 4 (6) ◽  
pp. 905-920 ◽  
Author(s):  
V. Panella ◽  
J. Suzanne ◽  
P. N. M. Hoang ◽  
C. Girardet
Keyword(s):  
Potential Energy ◽  
Energy Calculations ◽  
Potential Energy Calculations

POTENTIAL ENERGY CALCULATIONS ON POLYACETYLENE

1983 ◽  
Vol 44 (C3) ◽  
pp. C3-447-C3-450
Author(s):  
E. Cernia ◽  
L. D'Ilario ◽  
G. Nencini
Keyword(s):  
Potential Energy ◽  
Energy Calculations ◽  
Potential Energy Calculations
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