An electrostatic approach for the interaction between molecules (original) (raw)
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The role of electrostatics in solute-solvent interactions with the continuum
Journal of Molecular Structure: THEOCHEM, 1992
of the role of electrostatic contributions in solute-solvent interactions as described by the continuous model of the solvent is systematically performed on a few solutes with rotational degrees of freedom whose preferential stabilization upon solvation has already been considered with various methods, ranging from free energy perturbation methods to the continuous solvent at several levels of approximation.
Molecular mechanics and electrostatic effects
Biophysical Chemistry, 1994
Continuum solvent models predict a quadratic charge dependence (linear response) of the free energy of a system of charged solutes. The relation between this prediction and the structure of the salvation shell around the solutes is discussed. Studies of the derivative of the free energy with respect to the charges for different reference states are shown to be a convenient way of testing the linear response assumption without resorting to the standard free energy perturbation method. We illustrate this with a system of two oppositely charged ions in aqueous solution, where nonlinearities are observed before the full charging process is completed. Since molecular mechanics (MM) simulations preserve the full nonlinearity of the problem, they are well suited to the investigation of the conditions under which linear response accurately reflects the behavior of the system. The error when using linear response theory to calculate the free energies of charging is estimated to be as large as lo-20%.
Soft Materials, 2012
ABSTRACT For predictive applications, equation of state (EOS) models have to describe all relevant physical interactions accurately. In this contribution, the vapor–liquid equilibria of various dipolar two-center Lennard-Jones model molecules are determined by molecular simulation, as function of molecular elongation and deflection angle of the dipole. It is shown that present PC-SAFT-based EOS models require additional adjustable parameters in order to describe the orientational effects of the dipole-moment. We present extensions of the model to avoid the additional parameters and apply the extended equations to model systems and real molecules.
The Journal of Chemical Physics, 2009
In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.
Calculations of the Electric Fields in Liquid Solutions
The Journal of Physical Chemistry B, 2013
The electric field created by a condensed-phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution-phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and to identify for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins.
New Computational Models for Electrostatics of Macromolecules in Solvents
IEEE Transactions on Magnetics, 2000
Electrostatic fields of macromolecules (e.g., protein molecules) in solvents are often described by the Poisson-Boltzmann equation. This paper introduces two substantial amendments to the electrostatic model: first, the effective dielectric permittivity of the aqueous solvent layer on the molecular surface is drastically different from its bulk value of 80 and, second, the recently developed flexible local approximation methods produce different schemes with much higher accuracy than the classical ones.
Electrostatic free energy calculations using the generalized solvent boundary potential method
Free energy perturbation ͑FEP͒ calculations using all-atom molecular dynamics simulations with a large number of explicit solvent molecules are a powerful approach to study ligand-macromolecule association processes at the atomic level. One strategy to carry out FEP calculations efficiently and reduce computational time is to consider the explicit dynamics of only a small number of atoms in a localized region around the ligand. Such an approximation is motivated by the observation that the factors governing binding specificity are dominated by interactions in the vicinity of the ligand. However, a straightforward truncation of the system may yield inaccurate results as the influence exerted by the remote regions of the macromolecule and the surrounding solvent through long-range electrostatic effects may be significant. To obtain meaningful results, it is important to incorporate the influence of the remote regions of the ligand-macromolecule complex implicitly using some effective potential. The generalized solvent boundary potential ͑GSBP͒ that was developed recently ͓W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 ͑2001͔͒ is an efficient computational method to represent the long-range electrostatic interactions arising from remote ͑outer͒ regions in simulations of a localized ͑inner͒ region with a small number of explicit atoms. In the present work, FEP calculations combined with GSBP are used to illustrate the importance of these long-range electrostatic factors in estimation of the charging free energy of an aspartate ligand bound to the aspartyl-tRNA synthetase. Calculations with explicit spherical simulation inner regions of different radii are used to test the accuracy of the GSBP method and also illustrate the importance of explicit protein and solvent dynamics in the free energy estimation. The influence of the represented outer region is tested using separate simulations in which the reaction field and/or the protein static field are excluded. Both components are shown to be essential to obtain quantitatively meaningful results. The ability of implicitly treating the influence of protein fluctuations in the outer region using a protein dielectric constant is examined. It is shown that accurate charging free energy calculations can be performed for this system with a spherical region of 15 to 20 Å radius, which roughly corresponds to 1500-3500 moving atoms. The results indicate that GSBP in combination with FEP calculations is a precise and efficient approach to include long-range electrostatic effects in the study of ligand binding to large macromolecules.
The electric potential of a macromolecule in a solvent: A fundamental approach
Journal of Computational Physics, 1991
A general numerical method is presented to compute the electric potential for a macromolecule of arbitrary shape in a solvent with nonzero ionic strength. The model is based on a continuum description of the dielectric and screening properties of the system, which consists of a bounded internal region with discrete charges and an infinite external region. The potential obeys the Poisson equation in the internal region and the linearized Poisson Boltzmann equation in the external region, coupled through appropriate boundary conditions. It is shown how this three-dimensional problem can be presented as a pair of coupled integral equations for the potential and the normal component of the electric field at the dielectric interface. These equations can be solved by a straightforward application of boundary element techniques. The solution involves the decomposition of a matrix that depends only on the geometry of the surface and not on the positions of the charges. With this approach the number of unknowns is reduced by an order of magnitude with respect to the usual finite difference methods. Special attention is given to the numerical inaccuracies resulting from charges which are located close to the interface; an adapted formulation is given for that case. The method is tested both for a spherical geometry, for which an exact solution is available, and for a realistic problem, for which a finite difference solution and experimental verification is available. The latter concerns the shift in acid strength (pK-values) of histidines in the copper-containing protein azurin on oxidation of the copper, for various values of the ionic strength. A general method is given to triangulate a macromolecular surface. The possibility is discussed to use the method presented here for a correct treatment of long-range electrostatic interactions in simulations of solvated macromolecules, which form an essential part of correct potentials of mean force. t7,
Free energy of solvation from molecular dynamics simulations for low dielectric solvents
Journal of computational …, 2003
Using molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl 4 , CHCl 3 , benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie-Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene.