Molecular Dynamics on a Water Model with Polarizability and Hyperpolarizability

1994 ◽  
pp. 73-76
Author(s):  
G. Ruocco ◽  
M. Sampoli
Keyword(s):  
Molecular Dynamics ◽  
Water Model

scholarly journals Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
S. Tolosa ◽  
A. Hidalgo ◽  
J. A. Sansón
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Infinite Dilution ◽  
Theoretical Study ◽  
Water Model ◽  
Dynamics Simulations ◽  
Hydrolysis Of

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

Molecular Dynamics Study of an Aqueous LiF Solution

1991 ◽  
Vol 46 (3) ◽  
pp. 221-228 ◽  
Author(s):  
Sheng-Bai Zhu ◽  
G. Wilse Robinson
Keyword(s):  
Molecular Dynamics ◽  
Close Contact ◽  
Water Structure ◽  
Water Model ◽  
Pure Liquid ◽  
Surrounding Water ◽  
Hydration Shells ◽  
Complete Breakdown ◽  
Solvent Molecules ◽  
Dynamics Simulations

AbstractThe structure and properties of a 1.791 molal aqueous LiF solution is investigated by performing molecular dynamics simulations using a water model with both bond flexibility and instantaneously responsive polarization. On average, each cation is in close contact with about one anion. This causes a strong overlap of the hydration shells and an almost complete breakdown of the surrounding water structure. While the lone pairs of the hydration waters in the first Li+ shell occupy preferentially tetrahedral positions, the orientational distribution of the solvent molecules around F--is quite uniform. By comparing various autocorrelation functions of water molecules in the solution and in the pure liquid, the influence of solvated ions on the translational, rotational and vibrational motions of hydration water can be studied

A Molecular Dynamics Study of the Structure of an Aqueous CsF Solution

1983 ◽  
Vol 38 (2) ◽  
pp. 214-224 ◽  
Author(s):  
Gy. I. Szász ◽  
K. Heinzinger
Keyword(s):  
Molecular Dynamics ◽  
Hydration Shell ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Water Model ◽  
Water Molecules ◽  
Heat Of Solution ◽  
Average Temperature ◽  
Experimental Density ◽  
First Hydration Shell

Abstract A molecular dynamics simulation of a 2.2 molal aqueous CsF solution has been performed employing the ST2 water model. The basic periodic cube with a sidelength of 18.50 Å contained 200 water molecules, and 8 ions of each kind, corresponding to an experimental density of 1.26 g/cm3. The simulation extended over 6.5 ps with an average temperature of 307 K. The structure of the solution is discussed by means of radial distribution functions and the orientation of the water molecules. The computed hydration numbers in the first shell of Cs+ and F- are 7.9 and 6.8, respectively; the corresponding first hydration shell radii are 3.22 A and 2.64 A, respectively. Values for the hydration shell energies and the heat of solution have been calculated.

scholarly journals Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

2019 ◽  
Author(s):  
Joao Victor de Souza Cunha ◽  
Francesc Sabanes Zariquiey ◽  
Agnieszka K. Bronowska
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Water Model ◽  
High Plasticity ◽  
Solvation Model ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental and computational structural studies. To provide detailed atomic insight in IDPs dynamics governing its functional mechanisms, all-atom molecular dynamics (MD) simulations are widely employed. However, the current generalist force fields and solvent models are unable to generate satisfactory ensembles for IDPs when compared to existing experimental data. In this work, we present a new solvation model, denoted as Charge-Augmented 3 Point Water model for Intrinsically-disordered Proteins (CAIPi3P). CAIPi3P has been generated by performing a systematic scanning of atomic partial charges assigned to the widely popular molecular scaffold of the three-point TIP3P water model. We found that explicit solvent MD simulations employing CAIPi3P solvation considerably improved the SAXS scattering profiles for three different IDPs. Not surprisingly, this improvement was further enhanced by using CAIPi3P water in combination with the protein force field parametrized for IDPs. We have also demonstrated applicability of CAIPi3P to molecular systems containing structured as well as intrinsically disordered regions/domains. Our results highlight the crucial importance of solvent effects for generating molecular ensembles of IDPs which reproduce the experimental data available. Hence, we conclude that our newly developed CAIPi3P solvation model is a valuable tool assisting molecular simulations of intrinsically disordered proteins and assessing their molecular dynamics.

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