Atomic potential

Figure Bl.6.7 An angular momentum barrier ereated by the addition of the eentrifiigal potential to the eleetron-atom potential.

The pseudopotential is derived from an all-electron SIC-LDA atomic potential. The relaxation correction takes into account the relaxation of the electronic system upon the excitation of an electron [44]- The authors speculate that ... the ability of the SIRC potential to produce considerably better band structures than DFT-LDA may reflect an extra nonlocality in the SIRC pseudopotential, related to the nonlocality or orbital dependence in the SIC all-electron potential. In addition, it may mimic some of the energy and the non-local space dependence of the self-energy operator occurring in the GW approximation of the electronic many body problem [45]. 

Sellers H 1991 On modeling chemisorption processes with metal cluster systems. II. Model atomic potentials and site specificity of N atom chemisorption on Pd(111) Chem. Phys. Lett. 178 351-7... 

An extended discussion on embedded-atom potentials necessary for MD calculations can also be found (49). 

Despite their simplicity, certainly compared to the all-atom potentials used in molecular dynamics studies, these contact energy functions enable the exploration of different interaction scenarios. This diversity is achieved by changing the heterogeneity of the sequence, by altering the number N of different types of residues that are being used. The most elementary lattice model involves only two types of monomers hydrophobic... 

Fig. 55. The potential of hindered rotation of the CH3 group in nitromethane (CH3NO2) crystal, (a) calculated from INS data, Vi = 0.586 kcal/mol, V = 0.356 kcal/mol, S = 30°, and (b) calculated with the atom-atom potential method [Cavagnat and Pesquer 1986]. The barrier height is 0.768 kcal/mol.

A multidimensional PES for the reaction (6.45a) has been calculated by Wight et al. [1993] with the aid of the atom-atom potential method combined with the semiempirical London-Eyring-Polanyi-Sato method (see, e.g., Eyring et al. [1983]). Because of high exoergicity, the PES... 

Pertsin, A.J. and A.I. Kitaigorodskii, 1987, The Atom-Atom Potential Method. Application to Organic Molecular Solids (Springer, Berlin). 

The singlet-level theory has also been used to describe the structure of associating fluids near crystalline surfaces [30,31,76,77]. The surface consists explicitly of atoms which are arranged on a lattice of a given symmetry. The fluid atom-surface atom potential can also involve an associative term, i.e., the chemical-type bonding of the adsorbate particles with the surface may be included into the model. However, we restrict ourselves to the case of a nonassociative crystalline surface first. 

There is still great scope then for the design of more realistic membranes and for the development of more realistic atomic potentials... 

Dislocation core structures of (100), (110) and (111) dislocations in NiAl have been studied by molecular statics calculations using a new many-body embedded atom potential. They... 

In this work, we present calculated SFE using the LKKR-CPA method for Al-Cu and Al-Mg which are of interest from the point of view of superplasticity. We use the SFE to validate the rigid band model which allows a deeper insight into the electronic structure and its implication on the nature of inter-atomic potentials. 

Pertsin AJ, Kitaigorodsky AI (1986) The atom-atom potential method. Series in Chemical Physics. Springer, Berlin Heidelberg New York... 

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

As stated above, the most important missing piece in protein folding theory is an accurate all-atom potential. Recently there has been much effort in this direction, and much more is needed [48,55,72-77]. The existence of a potential satisfying minimal criteria such as folding and stability for a single protein was demonstrated in [73]. It is not a realistic potential by any means, but its existence validates the all-atom, implicit solvent, Monte Carlo approach as a serious candidate for theory. The method used to derive this potential was ad hoc, and has recently been compared with other standard methods in a rigorous and illuminating study [77]. 

Kussell E, Shimada J, Shakhnovich EE A structure-based method for derivation of all-atom potentials for protein folding. Proc Natl Acad Sci USA 2002 99 5343-8. 

Chen WW, Shakhnovich EE Lessons from the design of a novel atomic potential for protein folding. Protein Sci 2005 14 1741-52. 

Early experimental spectroscopic investigations on Rg- XY complexes resulted in contradictory information regarding the interactions within them and their preferred geometries. Rovibronic absorption and LIF spectra revealed T-shaped excited- and ground-state configurations, wherein the Rg atom is confined to a plane perpendicular to the X—Y bond [10, 19, 28-30]. While these results were supported by the prediction of T-shaped structures based on pairwise additive Lennard-Jones or Morse atom-atom potentials, they seemed to be at odds with results from microwave spectroscopy experiments that were consistent with linear ground-state geometries [31, 32]. Some attempts were made to justify the contradictory results of the microwave and optical spectroscopic studies, and... 

The availability of a phase space probability distribution for the steady state means that it is possible to develop a Monte Carlo algorithm for the computer simulation of nonequilibrium systems. The Monte Carlo algorithm that has been developed and applied to heat flow [5] is outlined in this section, following a brief description of the system geometry and atomic potential. 

In the PP theory, the valence electron wave function is composed of two parts. The main part is the pseudo-wave function describing a relatively smooth-varying behavior of the electron. The second part describes a spatially rapid oscillation of the valence electron near the atomic core. This atomic-electron-like behavior is due to the fact that, passing the vicinity of an atom, the valence electron recalls its native outermost atomic orbitals under a relatively stronger atomic potential near the core. Quantum mechanically the situation corresponds to the fact that the valence electronic state should be orthogonal to the inner-core electronic states. The second part describes this CO. The CO terms explicitly contain the information of atomic position and atomic core orbitals. 

The angular dependence of lateral interactions for nonpolar molecules (including quadrupole-quadrupole and Van der Waals dipole-dipole interactions as well as major terms of the power series expansion of repulsive atom-atom potentials in terms of the molecular linear dimension to intermolecular distance ratio) can be represented in a unified form 47 52... 

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