Treatment of electrostatic interactions in computer simulations and calculation of thermodynamic properties such as free energies and pressures

1999 ◽  
Author(s):  
Gerhard Hummer ◽  
Lawrence R. Pratt ◽  
Angel E. Garcı́a ◽  
Martin Neumann
Keyword(s):  
Thermodynamic Properties ◽  
Computer Simulations ◽  
Electrostatic Interactions ◽  
Free Energies

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

scholarly journals Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhan Chen
Keyword(s):  
Differential Geometry ◽  
Electrostatic Interactions ◽  
Polar Component ◽  
Great Success ◽  
Free Energies ◽  
Dispersion Interactions ◽  
Solvation Models ◽  
Nonpolar Solvation ◽  
Solvation Analysis

AbstractDifferential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications. Recently, a series of efforts have been made to improve the parameterization of these new implicit solvent models. In thiswork, we aim at studying the role of dispersion attraction in the parameterization of our DG based solvation models. To this end, we first investigate the necessity of van derWaals (vdW) dispersion interactions in the model and then carry out systematic parameterization for the model in the absence of electrostatic interactions. In particular, we explore how the changes in Lennard-Jones (L-J) potential expression, its decomposition scheme, and choices of some fixed parameter values affect the optimal values of other parameters as well as the overall modeling error. Our study on nonpolar solvation analysis offers insights into the parameterization of nonpolar components for the full DG based models by eliminating uncertainties from the electrostatic polar component. Therefore, it can be regarded as a step towards better parameterization for the full DG based model.

scholarly journals Effect of truncating electrostatic interactions on predicting thermodynamic properties of water–methanol systems

2018 ◽  
Vol 45 (4-5) ◽  
pp. 336-350 ◽  
Author(s):  
A. Rahbari ◽  
R. Hens ◽  
S. H. Jamali ◽  
M. Ramdin ◽  
D. Dubbeldam ◽  
...  
Keyword(s):  
Thermodynamic Properties ◽  
Electrostatic Interactions

Thermodynamic properties of the binary molten salt systems, PbBr2-KBr, PbBr2-RbBr and PbBr2-CsBr, by measurement of the electromotive forces of galvanic cells

1981 ◽  
Vol 34 (3) ◽  
pp. 479 ◽  
Author(s):  
H Bloom ◽  
MS White
Keyword(s):  
Thermodynamic Properties ◽  
Molten Salt ◽  
Activity Coefficients ◽  
Molten Salts ◽  
Free Energies ◽  
Complex Ions ◽  
Galvanic Cells ◽  
Salt Systems

The electromotive forces of galvanic cells for the formation of PbBr2 in the molten binary salt systems, PbBr2-KBr, PbBr2,-RbBr and PbBr2-CsBr, have been measured. Activities, activity coefficients and partial molar free energies have been calculated for each component of the three systems. Integral free energies of mixing have also been calculated. Various models of mixing of molten salts have been applied to the results. The systems contain complex ions, probably mixtures of PbBr42-, PbBr64- with some PbBr3-.

REMC computer simulations of the thermodynamic properties of argon and air plasmas

2002 ◽  
Vol 100 (15) ◽  
pp. 2487-2497 ◽  
Author(s):  
MARTIN LÍSAL ◽  
WILLIAM R. SMITH ◽  
MICHAL BUREŠ ◽  
VÁCLAV VACEK ◽  
JIŘÍ NAVRÁTIL
Keyword(s):  
Thermodynamic Properties ◽  
Computer Simulations ◽  
Air Plasmas

Calculation on the Free Energy of Mixing of some Silane Systems

2011 ◽  
Vol 391-392 ◽  
pp. 1017-1021
Author(s):  
Ru Zhang ◽  
Yan Fen Wu ◽  
Ping Hu
Keyword(s):  
Free Energy ◽  
Thermodynamic Properties ◽  
Activity Coefficients ◽  
Influence Factors ◽  
Critical Parameters ◽  
Model Parameters ◽  
Free Energies ◽  
Wilson Model ◽  
Energy Of Mixing ◽  
Free Energy Of Mixing

Six binary silane systems were chosen to calculate the activity coefficients (γ) and free energies of mixing (ΔGm). These systems included: methyldichlorosilane + methyltrichlorosilane, methyldichlorosilane + methylvinyldichlorosilane, methyldichlorosilane + toluene, methyltrichlorosilane + methylvinyldichlorosilane, methyltrichlorosilane + toluene, methylvinyldichlorosilane + toluene. Based on the Antoine constants, critical parameters of the pure components and Wilson model parameters, γ and ΔGmwere calculated. The influence factors of these thermodynamic properties were also discussed.

Redox Systems

1993 ◽  
Author(s):  
Greg M. Anderson ◽  
David A. Crerar
Keyword(s):  
Thermodynamic Properties ◽  
Oxidation State ◽  
Point Of View ◽  
Single Variable ◽  
Free Energies ◽  
Chemical Behavior ◽  
Redox Systems ◽  
Sufficient Detail ◽  
Electron Distributions ◽  
Nuclear Processes

Up until this point we have dealt with familiar intensive variables such as temperature, pressure, density, and molar thermodynamic properties (molar entropies, free energies, and so on). There exists another, equally important intensive variable that we have used implicitly, but have not yet discussed in sufficient detail—the oxidation state of a system. This involves concepts and applications so useful to Earth scientists that we devote a complete chapter to this single variable. Except for nuclear processes, most chemical behavior is determined by electron distributions and interactions. From this point of view, the oxidation state of an atom is among the most fundamental of all its properties. Most elements can exist in multiple valences with each state usually displaying quite different behavior from the others. As an example, consider the element sulfur.

Methods to extract interfacial free energies of flat and curved interfaces from computer simulations

2009 ◽  
Vol 177 (1) ◽  
pp. 103-127 ◽  
Author(s):  
M. Schrader ◽  
P. Virnau ◽  
D. Winter ◽  
T. Zykova-Timan ◽  
K. Binder
Keyword(s):  
Computer Simulations ◽  
Free Energies ◽  
Interfacial Free Energies

Interactions between cations and sugars. III. Free energies, enthalpies, and entropies of association of Ca2+, Sr2+, Ba2+, La3+, Gd3+ with D-ribose in water at 25 °C

1987 ◽  
Vol 65 (11) ◽  
pp. 2656-2660 ◽  
Author(s):  
Alfredo Maestre Alvarez ◽  
Nicole Morel-Desrosiers ◽  
Jean-Pierre Morel
Keyword(s):  
Thermodynamic Properties ◽  
Aqueous Solutions ◽  
Equilibrium Constant ◽  
The Other ◽  
Free Energies ◽  
Mean Values ◽  
Enthalpies Of Transfer ◽  
Other Hand ◽  
Solutions Of Electrolytes

The standard enthalpies of transfer of ribose and arabinose from water to aqueous solutions of electrolytes (CaCl2, SrCl2, BaCl2, LaCl3, and GdCl3) have been measured at 25 °C. A method is described to calculate from these data the equilibrium constant and the enthalpy for the association between the cations and the complexing isomers of ribose. Mean values relative to these isomers are given: the constants vary from 2.0 to 4.3 and the enthalpies from −5.9 to −17.9 kJ mol−1 for the different cations studied. The thermodynamic properties of association are not related to the size nor to the charge of the complexed cation in a simple way. On the other hand, the enthalpies of reaction are linearly correlated to the entropies of reaction.

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