Atomic interaction energies

F Melo, E Feytmans. Assessing protein structures with a non-local atomic interaction energy. JMol Biol 277 1141-1152, 1998. 

The investigation of the colored form of spiropyrans by theoretical calculations started at the dawn of studies on photochromic compounds. The pioneering studies of a benzothiazolinic spiropyran were published by Guglielmetti and coworkers, who investigated the different planar forms of the open-form stereoisomers by calculations of the atomic interaction energies,31 the extended Hiickel method,3133 the PPP method,32 and theCNDO/2 method.34 The results of molecular mechanical (MM) calculations on spiropyrans and spirooxazines were compared with the X-ray structures and used to explain H NMR data.35... 

The basic assumptions underlying the use of most atom-atom potential calculations are that only central forces operate between pairs of atoms and that the total interaction energy is the sum of the interactions between all pairs of atoms—the additivity assumption. The individual atom-atom interaction energies include a repulsive term with a steep rise in the energy at small interatomic distances, an attractive term designed to allow for London-type dispersion attractions and, sometimes, an additional coulombic interaction as well. With an exponential function as the repulsive term, the interaction energy between a pair of atoms can be written as... 

Topological atoms are defined solely by using the gradient of the electron density, g. As a result they are independent of how g is obtained. For example, they can be derived from Gaussian, Slater or plane wave basis fimctions. Since they are not formulated in Hilbert space, the inclusion of electron correlation does not lead to conceptual difficulties. We adhere to this philosophy and extend it to the use of (spinless) reduced density matrices in the formulation of atomic interaction energy. So far our work has only focused on the Coulomb part but the exchange-correlation part can also be treated in a similar but generalised framework, as I show now. 

Cc) The stereoselectivity of an asymmetric reaction yields information about the difference in non-bonied atom interaction energies in the two diastereomeric transition states. We have recently used this approach to study the effect of various additives to water on the magnitude of these non- bonded interaction energies. This program should be expanded to a study of the stereoselectivity of adsorption on and catalysis by chiral resins. 

The ordering kinetics depends crucially on the order of transition, i.e., the stability of the system against configurational fluctuation, as demonstrated in Figs.3, S, 7 and 8. On the other hand, it is shown that the microstructural feature is mainly determined by the number of ordered variants rather than the stabilily of a system. It is noted that both the stability of a system and the number of the ordered variants originate from the atomistic nature of a given alloy such as atomic interaction energy, atomic correlation and the crystal symmetry. One realizes that the present result obtained by the hybridized calculation of the CVM and PPM explicitly reflects the atomistic nature of the system. 

The calibration of the parameters in an atom-atom interaction energy curve is better carried out in terms of the position of the minimum, 7 °, the well depth, s, and the curvature parameter, X [47]. An atom-atom potential can be written as ... 

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