TITLE

Molecular dynamics free energy simulations: Influence of the truncation of long-range nonbonded electrostatic interactions on free energy calculations of polar molecules

AUTHOR(S)
Chipot, Christophe; Millot, Claude; Maigret, Bernard; Kollman, Peter A.
PUB. DATE
November 1994
SOURCE
Journal of Chemical Physics;11/1/1994, Vol. 101 Issue 9, p7953
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
The introduction of a reaction field dipolar contribution in free energy calculations is considered. The method is applied to a series of polar compounds, namely TIP3P water, methanol, and acetamide. The hydration free energies computed with both spherical cutoff and reaction field geometries are critically compared. Although the estimated quantities appear to be very similar, the use of a reaction field correction offers a better representation of the liquid structure. In the case of methanol, different potential derived point charge models of increasing complexity are investigated. It is found that the sophisticated models, involving either lone pairs or bond center charges, do not lead to any significant improvement over the simple atomic charge distribution. This trend is correlated to the variable strength of the modeled hydrogen bonds in solution.
ACCESSION #
7619814

 

Related Articles

  • A new definition of cavities for the computation of solvation free energies by the polarizable... Barone, Vincenzo; Cossi, Maurizio; Tomasi, Jacopo // Journal of Chemical Physics;8/22/1997, Vol. 107 Issue 8, p3210 

    Presents a set of rules for determining the atomic radii of spheres used to build molecular cavities in continuum solvation models. Computation of hydration free energy for various molecules, allowing the study of relatively large systems; Optimized radii's reduction of the mean error with...

  • Molecular-dynamics study of adiabatic proton-transfer reactions in solution. Laria, Daniel; Ciccotti, Giovanni; Ferrario, Mauro; Kapral, Raymond // Journal of Chemical Physics;7/1/1992, Vol. 97 Issue 1, p378 

    A molecular-dynamics study of adiabatic proton transfer between two ions in a polar solvent is presented. The proton is treated as a quantum particle in three dimensions and the polar solvent is composed of classical rigid, dipolar molecules. The coupled Schrödinger and Newton’s...

  • Molecular dynamics simulation of free anergy and conformational transition rates of calix[4]arene... den Otter, W.K.; Briels, W.J. // Journal of Chemical Physics;10/1/1997, Vol. 107 Issue 13, p4868 

    Calculates free-energy distribution for the isomerization of calix[4]arene in vacuo and chloroform using umbrella sampling. One umbrella covering the entire range of the reacting coordinate; Normal-mode analysis at various points along the reaction path; Use of the reactive flux method; Rate...

  • Free energy of cavity formation in solvent: Computational, methodological, and physical aspects. Beutler, Thomas C.; Béguelin, Daniel R.; van Gunsteren, Wilfred F. // Journal of Chemical Physics;3/1/1995, Vol. 102 Issue 9, p3787 

    With molecular dynamics simulation techniques, the free energy of cavity formation in water is investigated and determined at 300 K and 1 atm. Different methods are compared: Widom particle insertion, thermodynamic integration, and perturbation. It is shown that the most efficient way to get...

  • Pair dynamics in hard sphere fluids: Recollisional time correlation functions. Vesely, Franz J.; Evans, Glenn T. // Journal of Chemical Physics;1/15/1990, Vol. 92 Issue 2, p1275 

    Molecular dynamics calculations are reported on dense hard sphere fluids at three packing fractions (η=0.30,0.40,0.48). Attention is directed to the analysis of correlated recollisions of pairs of particles. The short time dynamics [t[bar_over_tilde:_approx._equal_to]0(τc) where...

  • The influence of temperature on pairwise hydrophobic interactions of methane-like particles: A molecular dynamics study of free energy. Lüdemann, Susanna; Schreiber, Hellfried; Abseher, Roger; Steinhauser, Othmar // Journal of Chemical Physics;1/1/1996, Vol. 104 Issue 1, p286 

    The association of a pair of hydrophobic solutes in water has been investigated by free energy molecular dynamics simulations of a system containing 516 water molecules. Convergence of the calculations is guaranteed by the comparison of data obtained with two independent free energy sampling...

  • Free energy of the Lennard-Jones solid. van der Hoef, Martin A. // Journal of Chemical Physics;11/8/2000, Vol. 113 Issue 18 

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around...

  • Effects of the Ewald sum on the free energy of the extended simple point charge model for water. Arbuckle, Brendan W.; Clancy, Paulette // Journal of Chemical Physics;3/22/2002, Vol. 116 Issue 12, p5090 

    The effects of including the Ewald sum on several key system properties for the extended simple point charge (SPC/E) model of water, in the temperature range of 140-300 K have been investigated using molecular dynamics simulations. The original SPC/E parameters are used without alteration since...

  • Correlation energy generating potentials for molecular hydrogen. Sharma, B. S.; Thakkar, Ajit J. // Journal of Chemical Physics;10/1/1985, Vol. 83 Issue 7, p3577 

    A variety of local correlation energy functionals are currently in use. All of them depend, to some extent, on modeling the correlation energy of a homogeneous electron fluid. Since atomic and molecular charge densities are neither uniform nor slowly varying, it is important to attempt to use...

  • Determination of solvation free energy using molecular dynamics with solute Cartesian mapping: An application to the solvation of 18-crown-6. Sun, Yaxiong; Kollman, Peter A. // Journal of Chemical Physics;10/1/1992, Vol. 97 Issue 7, p5108 

    The determination of relative stabilities of conformations of a molecule in solution has received much interest due to its relevance to chemical and biological properties in solution. Free energy perturbation (FEP) methodologies using molecular dynamics simulations have been used for the...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics