Molecular modelling local minimum energy value

In this equation, r is the distance between two non-bonded atoms and e and <7 are parameters that determine the shape of the potential. This potential has a minimum at the distance r = 21/6cr and a well depth of e. Different values of a and s may be chosen for different pairs of atom types. Some potential energy functions for side chains may also include a hydrogen bond term. Depending on the potential parameters, these potentials may not accurately model the relative energies of rotamers for each side-chain type that are determined from local interactions within each side chain and between the side chain and the local backbone. For instance, in molecular... 

Murray, Politzer, and their co-workers have developed several descriptors based on features of the molecular electrostatic potential surface (EPS) that can be used to characterize a variety of chemical and physical properties, including pK s [26,199,231]. In studies of the acidities of substituted azoles and anilines they showed that values of the most negative surface potentials (Vrma) and the minimum local ionization energy on the molecular surface (Is,min) showed strong correlations (r 0.97) with the pK s of these compounds. Later, Ma et al. [27] found that Is,jjn and several other EPS descriptors provided good models of the pK variations in substituted phenols and benzoic acids. Sakai and co-workers [232] have shown that Vmin yields an excellent fit (r = 0.996) for the aqueous pK s of a set of 22 amines. These studies demonstrate that features of the molecular electrostatic potential surfaces of acids can offer useful guides for pK, estimatioa... 

Model systems can be, on the one hand, subjected to a static structure optimization. There, the fact is considered that the potential energy of a relaxed atomistic system (cf. Equation 1.1) should show a minimum value. Static optimization then means that by suited numeric procedures the geometry of the simulated system is changed as long as the potential energy reaches the next minimum value [16]. In the context of amorphous packing models, the main application for this kind of procedure is the reduction of unrealistic local tensions in a model as a prerequisite for later molecular dynamic (MD) simulations. 

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