Potential functions, intermolecular

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

Intermolecular potential functions have been fitted to various experimental data, such as second virial coefficients, viscosities, and sublimation energy. The use of data from dense systems involves the additional assumption of the additivity of pair interactions. The viscosity seems to be more sensitive to the shape of the potential than the second virial coefficient hence data from that source are particularly valuable. These questions are discussed in full by Hirschfelder, Curtiss, and Bird17 whose recommended potentials based primarily on viscosity data are given in the tables of this section. 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

Gao JL, Habibollazadeh D, Shao L (1995) A polarizable intermolecular potential function for simulation of liquid alcohols. J Phys Chem 99(44) 16460-16467... 

Gao JL, Pavelites JJ, Habibollazadeh D (1996) Simulation of liquid amides using a polarizable intermolecular potential function. J Phys Chem 100(7) 2689-2697... 

Xie WS, Pu JZ, MacKerell AD, Gao JL (2007) Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput 3(6) 1878-1889... 

The simplest aromatic-aromatic system, the benzene-benzene complex, has been studied by Jorgensen and Severance41" using intermolecular potential functions in a Lennard-... 

W. L. Jorgensen, Transferable intermolecular potential functions for water, alcohols, and... 

First, we need to elaborate on the concept of the radius or diameter of the molecules involved in the binding process. Real molecules do not have well-defined boundaries as do geometrical objects such as spheres or cubes. Nevertheless, one can assign to each molecule an effective radius. This assignment depends on the form of the intermolecular potential function between any pair of real particles. 

Moraldi gives an estimate of this integral for large times t, on the basis of a dimensional argument. The integral must diverge as t for t — oo it must also be proportional to the cross section for binary interactions which is of the order of a1, the square of the zero of the intermolecular potential functions, V (a) = 0. In other words, the factor of proportionality not specified as yet has units of speed, i.e., the root mean square speed, or... 

The Lennard-Jones interaction is often used as the intermolecular potential function to estimate transport properties. The form of the Lennard-Jones interaction between molecules i and j as a function of distance is... 

Thus the reduced collision integrals can be done once and for all and tabulated as a function of T for a given intermolecular potential function... 

Shielding Surfaces for Two Interacting Molecules. In the Maryland meeting Jameson and de Dios reported the first ab initio calculations of the rare gas pair intermolecular shielding surfaces for Ar2, ArNe, Ne2, and NeHe (55). With these shielding surfaces it was possible to calculate the second virial coefficient for nuclear shielding as a function of temperature, using the well established intermolecular potential functions V(R) for the pair. 

Jefferson Tester I think a comment on ab initio calculations and the fundamental nature of the intermolecular potential function would be appropriate. Perhaps Ted Davis would respond. 

W.L. Jorgensen, Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers, application to liquid water, J. Am. Chem. Soc. 103 (1981) 335. 

Jorgensen WL (1979) An intermolecular potential function for the methanol dimer from ab-initio calculations. J Chem Phys 71 5034-5038... 

First, a complete description of the adsorbent is required this must include details of its solid structure, surface chemical structure, pore size and shape. One starts by assuming that the pores in the model adsorbent are all of the same size and shape and that they are unconnected. Secondly, the nature of the fluid-fluid and fluid-solid interactions must be precisely defined since the validity of the calculations is dependent on the accuracy of the intermolecular potential functions. 

Direct Determination of the intermolecular Potential Function for Argon... 

The most general of the equations of state is the virial equation, which is also the most fundamental since it has a direct theoretical connection to the intermolecular potential function. The virial equation of state expresses the deviation from ideality as a series expansion in density and, in terms of molar volume, can be written... 

Wee, S. S., Kim, S., Jhon, M. S., and Scheraga, H. A., Analytical intermolecular potential functions from ab initio self-consistent field-calculations for hydration of methylamine and methyl-ammonium ion, J. Phys. Chem. 94, 1656-1660 (1990). 

Campbell, E. S., and Mezei, M., Use of a non-pair-additive intermolecular potential function to fit quantum-mechanical data on water molecule interactions, J. Chem. Phys. 67, 2338-2344 (1977). 

Muenter, J. S., An intermolecular potential function model applied to acetylene dimer, carbon dioxide dimer, and carbon dioxide acetylene, J. Chem. Phys. 94, 2781-2793 (1991). 

Optimized Intermolecular Potential Functions for Liquid Hydrocarbons. 

J. Gao, D. Habibollahzadeh and L. Shao, A Polarizable Intermolecular Potential Function for Simulation of Liquid Alcohols, J. Phys. Chem. 99 (1995) 16460. 

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