摘要:

In real solutions the solvent is made up of molecules but for many purposes it can be described as a continuous medium with a dielectric constant. This allows one to make corrections for the finite size of an atomistic simulation (long range corrections). On the other hand results from simulations show that the local structure is not uniform and that the entropy of solvation is dominated by short range effects which are molecular in origin. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301520

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Lattice-sum methods for computing electrostatic interactions are becoming increasingly popular in the area of molecular simulation. Although these methods are generally considered to be significantly more accurate than cutoff-based methods, there are two intrinsic difficulties linked with their application: (i) the relatively complicated mathematical formalism and somewhat non-intuitive physical picture associated with electrostatics under periodic boundary conditions makes the development of new algorithms a difficult task; (ii) the assumption of exact periodicity in simulations of liquids and solutions is an approximation and may lead to periodicity-induced artifacts, the nature and magnitude of which are still poorly characterized. The present text addresses these two issues by (i) providing a detailed and consistent derivation of the two main lattice-sum algorithms (Ewald and particle-particle–particle-mesh), and (ii) discussing the nature of periodicity-induced artifacts in the context of a few simple systems. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301521

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

We review the treatment of electrostatic interactions in computer simulations under periodic boundary conditions, with emphasis on Ewald summation. Connections between Ewald summation and reaction field approaches will be made within a unifying picture of electrostatic potentials in Wigner lattices. The calculation of thermodynamic pressures in simulations of polar and ionic media will be discussed. Effects of finite system size on charging free energies will be analyzed. In addition, we will briefly review the problem of defining proper thermodynamic limits for single-ion properties. We find that cluster (or droplet) calculations of ionic solvation enthalpies or free energies (e.g., based on quantum mechanical methods) contain a contribution stemming from the charge ordering in the cluster-vacuum interface. This interfacial potential can lead to deviations of calculated single-ion enthalpies and free energies from the values in a properly defined thermodynamic limit at infinite ionic dilution. Finally, we will study the validity of linear response approximations for Coulomb systems. The origin of non-linearities in charging free energies will be traced to variations in the microscopic structure. We will conclude with a discussion of accurate integration methods for non-linear free energy expressions. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301522

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The PME approach to Ewald summation is based on local spline approximation of the complex exponentials appearing in the Ewald reciprocal sum. In this paper we show how the optimal influence function of Hockney and Eastwood can be easily derived using this approach. This result is used to explain why the force-interpolated PME method using least-squares spline approximation has the same accuracy as force-interpolated P3M. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301523

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Different schemes for the treatment of long-ranged electrostatic interactions will be examined for water simulations using the polarizable fluctuating charge potential. Several different methods are compared, including Ewald sums, potential shifting, spherical truncation and reaction field corrections. For liquid water, properties such as the energy, pressure, dynamics and structure are more sensitive to the treatment of the long-ranged interactions with polarizable than with non-polarizable potentials. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301524

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

This chapter discusses methods for efficiently solving Poisson and eigenvalue problems on grids in real space using multigrid techniques. The purpose of the chapter is to provide an introduction to developing useful solvers for electrostatics and electronic structure problems. High order finite difference approximations are used in the discretization, leading to structured sparse matrix representations of the equations. The fully numerical solution is then obtained iteratively on a sequence of grids of increasing resolution. Preconditioning from the coarser levels and the multigrid correction cycles on the finer scales lead to rapid convergence of the desired functions. Typically, the solution is obtained to within the truncation errors due to discretization in roughly ten relaxation sweeps on the finest level. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301525

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Long range interactions in periodic systems should be treated using the Ewald potential. For systems larger than a few hundred particles this is best calculated using the particle-particle, particle-mesh(P3M)method. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301526

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Some traditional approximation techniques are reviewed, concerning the effect of inserting a localized particle in an initially uniform fluid. They are put in a dynamical context, valid for both classical and quantum systems. The above picture, aimed at simple fluids, is generalized to include internal degrees of freedom. Both density profile and solvation free energy are treated in this fashion, in which a suitably defined frequency spectrum for the solvent plays a principal role. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301527

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent model is based upon the quasi-chemical approach, distinct from the common integral equation trunk of the theory of liquid solutions. The idea is geometrically to define molecular-scale regions attached to the solute macromolecule of interest. It is then shown that the quasi-chemical approach corresponds to calculation of a partition function for an ensemble analogous to, but not the same as, the grand canonical ensemble for the solvent in that proximal volume. The distinctions include: (a) the defined proximal volume—the volume of the system that is treated explicitly—resides on the solute; (b) the solute conformational fluctuations are prescribed by statistical thermodynamics and the proximal volume can fluctuate if the solute conformation fluctuates; and (c) the interactions of the system with more distant, extra-system solution species are treated by approximate physical theories such as dielectric continuum theories. The theory makes a definite connection to statistical thermodynamic properties of the solution and fully dictates volume fluctuations, which can be awkward in more ambitious approaches. It is argued that with the close solvent neighbors treated explicitly the thermodynamic results become less sensitive to the inevitable approximations in the implicit solvent theories of the more distant interactions. The physical content of this theory is the hypothesis that a small set of solvent molecules are decisive for these solvation problems. A detailed derivation of the quasi-chemical theory escorts the development of this proposal. The numerical application of the quasi-chemical treatment toLi+ion hydration in liquid water is used to motivate and exemplify the quasi-chemical theory. Those results underscore the fact that the quasi-chemical approach refines the path for utilization of ion-water cluster results for the statistical thermodynamics of solutions. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301528

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

We focus on prediction of structural organization of water in the vicinity of molecular ions and relating this water structure quantitatively to the ion hydration free energy. Analogous to results for clusters comprising covalently bonded nonpolar sites, we found that water structure near tetramethylammonium (TMA) ions in various charge states can be predicted sufficiently accurately by using proximity approximation. In particular, we show that a modified two-site proximity approximation that uses pair and triplet correlations with three nearest ion sites is able to capture details of water structure including asymmetry of hydration of positive and negative ions. We integrate the predicted charge densities along with a background charge applied uniformly within the integration sphere to calculate electrostatic potentials at the charge sites. The background charge density is chosen such that Stillinger-Lovett zeroth moment sum rule is satisfied within the integration sphere. Hydration free energies of TMA ion in seven different charge states(−3e,−2e,&ellip;+3e)calculated using electrostatic potentials are in excellent agreement with molecular simulation results using Ewald summation technique and reproduce accurately the favorable hydration of negative ions with respect to positive ions. ©2000 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.1301529

出版商:AIP    

年代:1999

数据来源: AIP