Electrostatic, defined

The electrochemical potential is defined as the total work of bringing a species i from vacuum into a phase a and is thus experimentally defined. It.may be divided into a chemical work p , the chemical potential, and the electrostatic work ZiC0 ... 

The work fiinction (di) is defined as the minimum work that has to be done to remove an electron from tlie bulk of the material to a sufficient distance outside the surface such that it no longer experiences an interaction with the surface electrostatic field [43, 44 and 45]. In other words, it is the minimum energy required to remove an electron from the... 

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

Bonaccorsi ct al. [204 defined for the first time the molecular electrostatic potential (MEP), wdicli is dearly tfie most important and most used property (Figure 2-125c. The clcctro.static potential helps to identify molecular regions that arc significant for the reactivity of compounds. Furthermore, the MEP is decisive for the formation of protein-ligand complexes. Detailed information is given in Ref [205]. 

It is often the case that the solvent acts as a bulk medium, which affects the solute mainly by its dielectric properties. Therefore, as in the case of electrostatic shielding presented above, explicitly defined solvent molecules do not have to be present. In fact, the bulk can be considered as perturbing the molecule in the gas phase , leading to so-called continuum solvent models [14, 15]. To represent the electrostatic contribution to the free energy of solvation, the generalized Bom (GB) method is widely used. Wilhin the GB equation, AG equals the difference between and the vacuum Coulomb energy (Eq. (38)) ... 

MM+ calculations do not usually have an electrostatic charge-charge interaction nor define a set of atomic charges for atoms. 

In stead, the electrostatic con tribn tion conies from definin g a set of bond dipole moments associated woth polar bonds. These bond moments are defined in the m m psir.LxL(dbf) file along with the bond stretching parameters and are given in units of Debyes. The cen ter of th e dipole Is defined to be th e m Idpoint of the bond an d two dipoles p. and pj. separated by Rjj. as shown beltnv ... 

The electrostatic potential at a point r, 0(r), is defined as the work done to bring unit positive charge from infinity to the point. The electrostatic interaction energy between a point charge q located at r and the molecule equals The electrostatic potential has contributions from both the nuclei and from the electrons, unlike the electron density, which only reflects the electronic distribution. The electrostatic potential due to the M nuclei is ... 

Non-covalent interactions between molecules often occur at separations where the van der Waals radii of the atoms are just touching and so it is often most useful to examine the electrostatic potential in this region. For this reason, the electrostatic potential is often calculated at the molecular surface (defined in Section 1.5) or the equivalent isodensity surface as shown in Figure 2.18 (colour plate section). Such pictorial representations... 

In some force fields the interaction sites are not all situated on the atomic nuclei. For example, in the MM2, MM3 and MM4 programs, the van der Waals centres of hydrogen atoms bonded to carbon are placed not at the nuclei but are approximately 10% along the bond towards the attached atom. The rationale for this is that the electron distribution about small atoms such as oxygen, fluorine and particularly hydrogen is distinctly non-spherical. The single electron from the hydrogen is involved in the bond to the adjacent atom and there are no other electrons that can contribute to the van der Waals interactions. Some force fields also require lone pairs to be defined on particular atoms these have their own van der Waals and electrostatic parameters. 

How should a molecule be divided into groups In some cases there may appecir to be a chemically obvious way to define the groups, especially when the molecule is a polymer that is constructed from distinct chemical residues. A particularly desirable feature is that each group should, if possible, be of zero charge. The reason for this can be understood if we recall how the different electrostatic interactions vary with distance from Section 4.9.1 ... 

A. rather complex procedure is used to determine the Born radii a values of which. calculated for each atom in the molecule that carries a charge or a partial charge. T Born radius of an afom (more correctly considered to be an effective Born radii corresponds to the radius that would return the electrostatic energy of the system accordi to the Bom equation if all other atoms in the molecule were uncharged (i.e. if the other ato only acted to define the dielectric boundary between the solute and the solvent). In Sti force field implementation, atomic radii from the OPLS force field are assigned to ec... 

CODESSA can compute or import over 500 molecular descriptors. These can be categorized into constitutional, topological, geometric, electrostatic, quantum chemical, and thermodynamic descriptors. There are automated procedures that will omit missing or bad descriptors. Alternatively, the user can manually define any subset of structures or descriptors to be used. 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

Energy, geometry, dipole moment, and the electrostatic potential all have a clear relation to experimental values. Calculated atomic charges are a different matter. There are various ways to define atomic charges. HyperChem uses Mulliken atomic charges, which are commonly used in Molecular Orbital theory. These quantities have only an approximate relation to experiment their values are sensitive to the basis set and to the method of calculation. 

Coulomb s law. This relationship poses no particular difficulties as a qualitative statement the problem arises when we attempt to calculate something with it, since the proportionality constant depends on the choice of units. In the cgs system of units, the electrostatic unit of charge is defined to produce a force of 1 dyne when two such charges are separated by a distance of 1 cm. In the cgs system the proportionality factor in Coulomb s law is unity and is dimensionless. For charges under vacuum we write... 

The vector L is so strongly coupled to the electrostatic field and the consequent frequency of precession about the intemuclear axis is so high that the magnitude of L is not defined in other words L is not a good quantum number. Only the component H of the orbital angular momentum along the intemuclear axis is defined, where the quantum number A can take the values... 

A very simple version of this approach was used in early applications. An alchemical charging calculation was done using a distance-based cutoff for electrostatic interactions, either with a finite or a periodic model. Then a cut-off correction equal to the Born free energy, Eq. (38), was added, with the spherical radius taken to be = R. This is a convenient but ill-defined approximation, because the system with a cutoff is not equivalent to a spherical charge of radius R. A more rigorous cutoff correction was derived recently that is applicable to sufficiently homogeneous systems [54] but appears to be impractical for macromolecules in solution. 

A variety of methodologies have been implemented for the reaction field. The basic equation for the dielectric continuum model is the Poisson-Laplace equation, by which the electrostatic field in a cavity with an arbitrary shape and size is calculated, although some methods do not satisfy the equation. Because the solute s electronic strucmre and the reaction field depend on each other, a nonlinear equation (modified Schrddinger equation) has to be solved in an iterative manner. In practice this is achieved by modifying the electronic Hamiltonian or Fock operator, which is defined through the shape and size of the cavity and the description of the solute s electronic distribution. If one takes a dipole moment approximation for the solute s electronic distribution and a spherical cavity (Onsager s reaction field), the interaction can be derived rather easily and an analytical expression of theFock operator is obtained. However, such an expression is not feasible for an arbitrary electronic distribution in an arbitrary cavity fitted to the molecular shape. In this case the Fock operator is very complicated and has to be prepared by a numerical procedure. 

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