Potentials empirical

The Ar-HCl and Ar-HF complexes became prototypes for the study of intennolecular forces. Holmgren et al [30] produced an empirical potential energy surface for Ar-HCl fitted to the microwave and radiofrequency spectra,... 

For this reason, there has been much work on empirical potentials suitable for use on a wide range of systems. These take a sensible functional form with parameters fitted to reproduce available data. Many different potentials, known as molecular mechanics (MM) potentials, have been developed for ground-state organic and biochemical systems [58-60], They have the advantages of simplicity, and are transferable between systems, but do suffer firom inaccuracies and rigidity—no reactions are possible. Schemes have been developed to correct for these deficiencies. The empirical valence bond (EVB) method of Warshel [61,62], and the molecular mechanics-valence bond (MMVB) of Bemardi et al. [63,64] try to extend MM to include excited-state effects and reactions. The MMVB Hamiltonian is parameterized against CASSCF calculations, and is thus particularly suited to photochemistry. 

Abstract. A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the amino acid labels and of the distances between the Ca atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Angstrom. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic progrmnming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7A of the PDB geometry, with one exception that has an error of S.SA. 

Keywords, protein folding, tertiary structure, potential energy surface, global optimization, empirical potential, residue potential, surface potential, parameter estimation, density estimation, cluster analysis, quadratic programming... 

An ideal empirical potential function on the residue level is a function V that assigns to each sequence-coordinates pair s,x) an energy V s,x) such that... 

Unfortunately, the approach of determining empirical potentials from equilibrium data is intrinsically limited, even if we assume complete knowledge of all equilibrium geometries and their energies. It is obvious that statistical potentials cannot define an energy scale, since multiplication of a potential by a positive, constant factor does not alter its global minimizers. But for the purpose of tertiary structure prediction by global optimization, this does not not matter. 

While this is disappointing, the nonuniqueness theorem also shows that if some empirical potential is able to predict correct protein folds then many other empirical potentials will do so, too. Thus, the construction of empirical potentials for fold prediction is much less constrained than one might think initially, and one is justified in using additional qualitative theoretical assumptions in the derivation of an appropriate empirical potential function. 

The additional penalty function that is added to the empirical potential energy function in restrained dynamics X-ray refinement has the form ... 

M Schlenkrich, J Bnckmann, AD MacKerell Jr, M Karplus. In KM Merz, B Roux, eds. Empirical Potential Energy Eunction for Phospholipids Criteria for Parameter Optimization and Applications. Boston Birkhaiiser, 1996, pp 31-81. 

According to the namre of the empirical potential energy function, described in Chapter 2, different motions can take place on different time scales, e.g., bond stretching and bond angle bending vs. dihedral angle librations and non-bond interactions. Multiple time step (MTS) methods [38-40,42] allow one to use different integration time steps in the same simulation so as to treat the time development of the slow and fast movements most effectively. 

AD MacKerell Jr, D Bashford, M Bellott, RL Dunbrack Jr, JD Evanseck, MJ Eield, S Eischer, J Gao, H Guo, S Ha, D Joseph-McCarthy, L Kuchnir, K Kuczera, ETK Lau, C Mattos, S Michmck, T Ngo, DT Nguyen, B Prodhom, WE Reiher III, B Roux, M Schlenkrich, JC Smith, R Stote, J Straub, M Watanabe, J Wiorkiewicz-Kuczera, D Ym, M Karplus. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102 3586-361 6, 1998. 

S Vajda, M Sippl, J Novotny. Empirical potentials and functions for protein folding and binding. Cuit Opm Struct Biol 7 228-228, 1997. 

Recently, many experiments have been performed on the structure and dynamics of liquids in porous glasses [175-190]. These studies are difficult to interpret because of the inhomogeneity of the sample. Simulations of water in a cylindrical cavity inside a block of hydrophilic Vycor glass have recently been performed [24,191,192] to facilitate the analysis of experimental results. Water molecules interact with Vycor atoms, using an empirical potential model which consists of (12-6) Lennard-Jones and Coulomb interactions. All atoms in the Vycor block are immobile. For details see Ref. 191. We have simulated samples at room temperature, which are filled with water to between 19 and 96 percent of the maximum possible amount. Because of the hydrophilicity of the glass, water molecules cover the surface already in nearly empty pores no molecules are found in the pore center in this case, although the density distribution is rather wide. When the amount of water increases, the center of the pore fills. Only in the case of 96 percent filling, a continuous aqueous phase without a cavity in the center of the pore is observed. 

Empirical methods are of two types those that permit potential energy surfaces to be calculated and those that only allow activation energies to be estimated. Laidler has reviewed these. A typical approach is to establish a relationship between experimental activation energies and some other quantity, such as heats of reaction, and then to use this correlation to predict additional activation energies. In Section 5.3 we will encounter a different type of empirical potential energy surface. 

In all these examples, the importance of good simulation and modeling cannot be stressed enough. A variety of methods have been used in this field to simulate the data in the cases studies described above. Blander et al. [4], for example, used a semi-empirical molecular orbital method, MNDO, to calculate the geometries of the free haloaluminate ions and used these as a basis for the modeling of the data by the RPSU model [12]. Badyal et al. [6] used reverse Monte Carlo simulations, whereas Bowron et al. [11] simulated the neutron data from [MMIM]C1 with the Empirical Potential Structure Refinement (EPSR) model [13]. 

The atomic interactions of the system are derived from a many-body empirical potential, the attractive part of which is expressed within the SMA of the TB theory ", while the repulsive term is a pair-potential of Bom-Mayer type. Accordingly, the total energy of the system is written as ... 

Langenegger, E. E. and Callaghan, B. G., Use of an Empirical Potential Shift Technique for Predicting Dezincihcation Rates of a/3-brasses in Chloride Media , Corrosion, 28, 245 (1972)... 

The discussion in the previous section indicated that Nett values would be expected to exceed substantially the actual number of outer shell electrons. Table IV amply confirms this conclusion. Since N appears to the power in the Slater-Kirkwood equation, the deviations are exaggerated. Thus, in making a very similar treatment a few years ago in which slightly different empirical potentials were used, the writer31 found substantially smaller effective N values. For the same reason a relatively crude effective... 

The empirical potentials for the molecules were obtained on the assumption of single attraction centers. This assumption is probably good for H2, fair for CH4 and N2, and very poor for Cl2. Even for molecules such as CH4 which are relatively spherical in shape, the fact that some atoms are near the outer surface rather than the center has an important effect. The closest interatomic distances are emphasized by the i 6 dependence of the potential. This point has been considered by several authors who worked out examples showing the net intermolecular potential for several models. 

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