Electrostatic terms

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

Fig. 10. Differences in potential energy components for the blocked alanine model (for bond length, bond angle, dihedral angle, van der Waals, and electrostatic terms, shown top to bottom) before and after the residual corrections in LIN trajectories at timesteps of 2 fs (yellow), 5 fs (red), and 10 fs (blue).

Electrostatic terms other than the simple charge interactions above are commonly included in molecular mechanics calculations. particularly dipole-dipole interactions. More recently, second-order electrostatic interactions like those describing polarizability have been added to some force fields. 

Fhe van der Waals and electrostatic interactions between atoms separated by three bonds (i.c. the 1,4 atoms) are often treated differently from other non-bonded interactions. The interaction between such atoms contributes to the rotational barrier about the central bond, in conjunction with the torsional potential. These 1,4 non-bonded interactions are often scaled down by an empirical factor for example, a factor of 2.0 is suggested for both the electrostatic and van der Waals terms in the 1984 AMBER force field (a scale factor of 1/1.2 is used for the electrostatic terms in the 1995 AMBER force field). There are several reasons why one would wish to scale the 1,4 interactions. The error associated wilh the use of an repulsion term (which is too steep compared with the more correct exponential term) would be most significant for 1,4 atoms. In addition, when two 1,4... 

In the Huckel theory of simple hydrocarbons, one assumes that the election density on a carbon atom and the order of bonds connected to it (which is an election density between atoms) are uninfluenced by election densities and bond orders elsewhere in the molecule. In PPP-SCF theory, exchange and electrostatic repulsion among electrons are specifically built into the method by including exchange and electrostatic terms in the elements of the F matrix. A simple example is the 1,3 element of the matrix for the allyl anion, which is zero in the Huckel method but is 1.44 eV due to election repulsion between the 1 and 3 carbon atoms in one implementation of the PPP-SCF method. 

The consistent force field (CFF) was developed to yield consistent accuracy of results for conformations, vibrational spectra, strain energy, and vibrational enthalpy of proteins. There are several variations on this, such as the Ure-Bradley version (UBCFF), a valence version (CVFF), and Lynghy CFF. The quantum mechanically parameterized force field (QMFF) was parameterized from ah initio results. CFF93 is a rescaling of QMFF to reproduce experimental results. These force fields use five to six valence terms, one of which is an electrostatic term, and four to six cross terms. 

DREIDING is an all-purpose organic or bio-organic molecule force field. It has been most widely used for large biomolecular systems. It uses five valence terms, one of which is an electrostatic term. The use of DREIDING has been dwindling with the introduction of improved methods. 

Empirical conformational energy program for peptides (ECEPP) is the name of both a computer program and the force field implemented in that program. This is one of the earlier peptide force fields that has seen less use with the introduction of improved methods. It uses three valence terms that are fixed, a van der Waals term, and an electrostatic term. 

Empirical force field (EFF) is a force field designed just for modeling hydrocarbons. It uses three valence terms, no electrostatic term and five cross terms. 

MMl, MM2, MM3, and MM4 are general-purpose organic force fields. There have been many variants of the original methods, particularly MM2. MMl is seldom used since the newer versions show measurable improvements. The MM3 method is probably one of the most accurate ways of modeling hydrocarbons. At the time of this book s publication, the MM4 method was still too new to allow any broad generalization about the results. However, the initial published results are encouraging. These are some of the most widely used force fields due to the accuracy of representation of organic molecules. MMX and MM+ are variations on MM2. These force fields use five to six valence terms, one of which is an electrostatic term and one to nine cross terms. 

MOMEC is a force field for describing transition metal coordination compounds. It was originally parameterized to use four valence terms, but not an electrostatic term. The metal-ligand interactions consist of a bond-stretch term only. The coordination sphere is maintained by nonbond interactions between ligands. MOMEC generally works reasonably well for octahedrally coordinated compounds. 

UFF stands for universal force held. Although there have been a number of universal force helds, meaning that they include all elements, there has only been one actually given this name. This is the most promising full periodic table force held available at this time. UFF is most widely used for systems containing inorganic elements. It was designed to use four valence terms, but not an electrostatic term. 

UFF was originally designed to be used without an electrostatic term. The literature accompanying one piece of software recommends using charges obtained with the Q-equilibrate method. Independent studies have found the accuracy of results to be signihcantly better without charges. 

In connection with electronic strucmre metlrods (i.e. a quantal description of M), the term SCRF is quite generic, and it does not by itself indicate a specific model. Typically, however, the term is used for models where the cavity is either spherical or ellipsoidal, the charge distribution is represented as a multipole expansion, often terminated at quite low orders (for example only including the charge and dipole terms), and the cavity/ dispersion contributions are neglected. Such a treatment can only be used for a qualitative estimate of the solvent effect, although relative values may be reasonably accurate if the molecules are fairly polar (dominance of the dipole electrostatic term) and sufficiently similar in size and shape (cancellation of the cavity/dispersion terms). 

Consider the electrostatic terms. These are hard to evaluate because the output charge density is a complicated non spherical function in space. In traditional LMTO calculations the charge density is first spheridised before Ees is calculated. In this method p(r) is reduced to a sum of spherically symmetric balls of charge inside each ASA sphere [2]. 

The satisfactory result shown in Table 12 suggests that one might give a more detailed and quantitative discussion of the variation with temperature. If we are to do this, we need some standard of comparison with which to compare the experimental results. Just as wq compare an imperfect gas with a perfect gas, and compare a non-ideal solution with an ideal solution, so we need a simple standard behavior with which to compare the observed behavior. We obtain this standard behavior if, supposing that. /e is almost entirely electrostatic in origin, we take J,np to vary with temperature as demanded by the macroscopic dielectric constant t of the medium 1 that is to say, we assume that Jen, as a function of temperature is inversely proportional to . For this standard electrostatic term we may use the notation, instead of... 

For large systems, the computation of the energy can require 98% or more of the total computational effort, and within the energy computation, the pair interaction energy (van der Waals and electrostatic terms) can represent more than 90% of the total effort. For this reason, the aspects of the program that deal with the generation of the nonbond list and the computation of the nonbond energy are of critical importance. 

The modification by method 2 is more acceptable. Although several types of modifications have been reported, Abraham and Liszi [15] proposed one of the simplest and well-known modifications. Figure 2(b) shows the proposed one-layer model. In this model, an ion of radius r and charge ze is surrounded by a local solvent layer of thickness b — r) and dielectric constant ej, immersed in the bulk solvent of dielectric constant ),. The thickness (b — r) of the solvent layer is taken as the solvent radius, and its dielectric constant ej is supposed to become considerably lower than that of the bulk solvent owing to dielectric saturation. The electrostatic term of the ion solvation energy is then given by... 

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