The reaction field method is used in molecular simulations to simulate the effect of long range dipole-dipole interactions for simulations with periodic boundary conditions. Around each molecule there is a 'cavity' or sphere within which the Coulomb interactions are treated explicitly. Outside of this cavity the medium is assumed to have a uniform dielectric constant. The molecule induces polarization in this media which in turn creates a reaction field, sometimes called the Onsager reaction field. Although Onsager's name is often attached to the technique, because he considered such a geometry in his theory of the dielectric constant, [1] the method was first introduced by Barker and Watts in 1973. [2] [3]
The effective pairwise potential becomes:
where is the cut-off radius.
The reaction field in the center of the cavity is given by :
where is the total dipole moment of all the molecules in the cavity. The contribution to the potential energy of the molecule at the center of the cavity is and the torque on molecule is simply .
When a molecule enters or leaves the sphere defined by the cut-off radius, there is a discontinuous jump in energy. [4] When all of these jumps in energy are summed, they do not exactly cancel, leading to poor energy conservation, a deficiency found whenever a spherical cut-off is used. The situation can be improved by tapering the potential energy function to zero near the cut-off radius. Beyond a certain radius the potential is multiplied by a tapering function . A simple choice is linear tapering with , although better results may be found with more sophisticated tapering functions.
Another potential difficulty of the reaction field method is that the dielectric constant must be known a priori. However, it turns out that in most cases dynamical properties are fairly insensitive to the choice of . It can be put in by hand, or calculated approximately using any of a number of well-known relations between the dipole fluctuations inside the simulation box and the macroscopic dielectric constant. [4]
Another possible modification is to take into account the finite time required for the reaction field to respond to changes in the cavity. This "delayed reaction field method" was investigated by van Gunsteren, Berendsen and Rullmann in 1978. [5] It was found to give better results—this makes sense, as without taking into account the delay, the reaction field is overestimated. However, the delayed method has additional difficulties with energy conservation and thus is not suitable for simulating an NVE ensemble.
The reaction field method is an alternative to the popular technique of Ewald summation. Today, Ewald summation is the usual technique of choice, but for many quantities of interest both techniques yield equivalent results. For example, in Monte Carlo simulations of liquid crystals, (using both the hard spherocylinder [6] and Gay-Berne models [7] ) the results from the reaction field method and Ewald summation are consistent. However, the reaction field presents a considerable reduction in the computer time required. The reaction field should be applied carefully, and becomes complicated or impossible to implement for non-isotropic systems, such as systems dominated by large biomolecules or systems with liquid-vapour or liquid-solid coexistence. [8]
In section 5.5.5 of his book, Allen [4] compares the reaction field with other methods, focusing on the simulation of the Stockmayer system (the simplest model for a dipolar fluid, such as water). The work of Adams, et al. (1979) showed that the reaction field produces results with thermodynamic quantities (volume, pressure and temperature) which are in good agreement with other methods, although pressure was slightly higher with the reaction field method compared to the Ewald-Kornfeld method (1.69 vs 1.52). The results show that macroscopic thermodynamic properties do not depend heavily on how long-range forces are treated. Similarly, single particle correlation functions do not depend heavily on the method employed. Several other results also show that the dielectric constant can be well estimated with either the reaction field or a lattice summation technique. [4]
An intermolecular force (IMF) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules. Both sets of forces are essential parts of force fields frequently used in molecular mechanics.
In electromagnetism, a dielectric is an electrical insulator that can be polarised by an applied electric field. When a dielectric material is placed in an electric field, electric charges do not flow through the material as they do in an electrical conductor, because they have no loosely bound, or free, electrons that may drift through the material, but instead they shift, only slightly, from their average equilibrium positions, causing dielectric polarisation. Because of dielectric polarisation, positive charges are displaced in the direction of the field and negative charges shift in the direction opposite to the field. This creates an internal electric field that reduces the overall field within the dielectric itself. If a dielectric is composed of weakly bonded molecules, those molecules not only become polarised, but also reorient so that their symmetry axes align to the field.
In electromagnetism, the absolute permittivity, often simply called permittivity and denoted by the Greek letter ε (epsilon), is a measure of the electric polarizability of a dielectric material. A material with high permittivity polarizes more in response to an applied electric field than a material with low permittivity, thereby storing more energy in the material. In electrostatics, the permittivity plays an important role in determining the capacitance of a capacitor.
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
In computational chemistry, molecular physics, and physical chemistry, the Lennard-Jones potential is an intermolecular pair potential. Out of all the intermolecular potentials, the Lennard-Jones potential is probably the one that has been the most extensively studied. It is considered an archetype model for simple yet realistic intermolecular interactions. The Lennard-Jones potential is often used as a building block in molecular models for more complex substances. Many studies of the idealized "Lennard-Jones substance" use the potential to understand the physical nature of matter.
In electricity (electromagnetism), the electric susceptibility is a dimensionless proportionality constant that indicates the degree of polarization of a dielectric material in response to an applied electric field. The greater the electric susceptibility, the greater the ability of a material to polarize in response to the field, and thereby reduce the total electric field inside the material. It is in this way that the electric susceptibility influences the electric permittivity of the material and thus influences many other phenomena in that medium, from the capacitance of capacitors to the speed of light.
In electromagnetism, the Clausius–Mossotti relation, named for O. F. Mossotti and Rudolf Clausius, expresses the dielectric constant of a material in terms of the atomic polarizability, α, of the material's constituent atoms and/or molecules, or a homogeneous mixture thereof. It is equivalent to the Lorentz–Lorenz equation, which relates the refractive index of a substance to its polarizability. It may be expressed as:
Polarizability usually refers to the tendency of matter, when subjected to an electric field, to acquire an electric dipole moment in proportion to that applied field. It is a property of particles with an electric charge. When subject to an electric field, the negatively charged electrons and positively charged atomic nuclei are subject to opposite forces and undergo charge separation. Polarizability is responsible for a material's dielectric constant and, at high (optical) frequencies, its refractive index.
Dielectrophoresis (DEP) is a phenomenon in which a force is exerted on a dielectric particle when it is subjected to a non-uniform electric field. This force does not require the particle to be charged. All particles exhibit dielectrophoretic activity in the presence of electric fields. However, the strength of the force depends strongly on the medium and particles' electrical properties, on the particles' shape and size, as well as on the frequency of the electric field. Consequently, fields of a particular frequency can manipulate particles with great selectivity. This has allowed, for example, the separation of cells or the orientation and manipulation of nanoparticles and nanowires. Furthermore, a study of the change in DEP force as a function of frequency can allow the electrical properties of the particle to be elucidated.
Dielectric heating, also known as electronic heating, radio frequency heating, and high-frequency heating, is the process in which a radio frequency (RF) alternating electric field, or radio wave or microwave electromagnetic radiation heats a dielectric material. At higher frequencies, this heating is caused by molecular dipole rotation within the dielectric.
Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions in periodic systems. It was first developed as the method for calculating the electrostatic energies of ionic crystals, and is now commonly used for calculating long-range interactions in computational chemistry. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an equivalent summation in Fourier space. In this method, the long-range interaction is divided into two parts: a short-range contribution, and a long-range contribution which does not have a singularity. The short-range contribution is calculated in real space, whereas the long-range contribution is calculated using a Fourier transform. The advantage of this method is the rapid convergence of the energy compared with that of a direct summation. This means that the method has high accuracy and reasonable speed when computing long-range interactions, and it is thus the de facto standard method for calculating long-range interactions in periodic systems. The method requires charge neutrality of the molecular system to accurately calculate the total Coulombic interaction. A study of the truncation errors introduced in the energy and force calculations of disordered point-charge systems is provided by Kolafa and Perram.
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
COSMO is a calculation method for determining the electrostatic interaction of a molecule with a solvent. COSMO is a dielectric continuum model. These models can be used in computational chemistry to model solvation effects. COSMO has become a popular method of these solvation models in recent years. The COSMO formalism is similar to the method proposed earlier by Hoshi et al. The COSMO approach is based - as many other dielectric continuum models - on the surface segmentation of a molecule surface.
The Stockmayer potential is a mathematical model for representing the interactions between pairs of atoms or molecules. It is defined as a Lennard-Jones potential with a point electric dipole moment.
Biology Monte Carlo methods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte environment through ion channels or nano-pores embedded in membranes. It is a 3-D particle-based Monte Carlo simulator for analyzing and studying the ion transport problem in ion channel systems or similar nanopores in wet/biological environments. The system simulated consists of a protein forming an ion channel (or an artificial nanopores like a Carbon Nano Tube, CNT), with a membrane (i.e. lipid bilayer) that separates two ion baths on either side. BioMOCA is based on two methodologies, namely the Boltzmann transport Monte Carlo (BTMC) and particle-particle-particle-mesh (P3M). The first one uses Monte Carlo method to solve the Boltzmann equation, while the later splits the electrostatic forces into short-range and long-range components.
The electric dipole moment is a measure of the separation of positive and negative electrical charges within a system: that is, a measure of the system's overall polarity. The SI unit for electric dipole moment is the coulomb-meter (C⋅m). The debye (D) is another unit of measurement used in atomic physics and chemistry.
Brendan Kevin Patrick Scaife FTCD, MRIA, Boyle Laureate, is an Irish academic engineer and physicist who carried out pioneering work on the theory of dielectrics. Scaife founded the Dielectrics Group in Trinity College Dublin where he is Fellow Emeritus and formerly Professor of Electromagnetism, and previously to that a professor of engineering science.
In computational chemistry, a solvent model is a computational method that accounts for the behavior of solvated condensed phases. Solvent models enable simulations and thermodynamic calculations applicable to reactions and processes which take place in solution. These include biological, chemical and environmental processes. Such calculations can lead to new predictions about the physical processes occurring by improved understanding.
The net electrostatic force acting on a charged particle with index contained within a collection of particles is given as:
In condensed matter physics and physical chemistry, the Lifshitz theory of van der Waals forces, sometimes called the macroscopic theory of van der Waals forces, is a method proposed by Evgeny Mikhailovich Lifshitz in 1954 for treating van der Waals forces between bodies which does not assume pairwise additivity of the individual intermolecular forces; that is to say, the theory takes into account the influence of neighboring molecules on the interaction between every pair of molecules located in the two bodies, rather than treating each pair independently.
{{cite book}}
: CS1 maint: multiple names: authors list (link)