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We present an analytical model, suitable for molecular dynamics applications, of a five-dimensional potential energy surface, based on the expansion in spherical harmonics, for non-linear-triatomic molecule (C2v) – heteronuclear-diatomic molecule systems, with both molecules having a rigid structure. The method consists in the exact transformation of quantum chemical input data related to a minimal number of significant configurations. This approach is applied to the case study of H2O–HF at various levels of theory. The interaction potential has been analyzed and compared with state-of-art theoretical models. Pros and cons of the method are presented and discussed.

Large sets of data need to be compacted for classification and extraction of information regarding structural changes of aminoacid units in specific sequences of proteins. The screen is constructed by opposite sides of the virtual tetrahedron built by the six distances between four centers and provides coordinates for a two-dimensional square plot. As alternative e.g. to Ramachandran diagrams based on angles, it may offer greater accuracy and sensitivity. The screen was initially employed to peroxides and persulfides, to monitor the distances relevant to chirality changing processes and successively to show some electric and kinetic properties. The smallest chiral aminoacid, alanine, was therefore chosen for the basic illustration presented here. A virtual tetrahedron is built by the six distances between four centers of the aminoacid skeleton: they do not necessarily coincide with bonds, so a computer program permits their calculation from tabulations of experimental and theoretical data. Here, the screen is applied to treat significant geometrical features of alanine as affected by adjacent aminoacids in peptide chains, as available on protein databases. In this exemplary presentation applications of screen plots are limited to biochemistry: elsewhere have been shown useful in other areas, such as spin networks and the kinematics of a four-bar mechanism.

For the prototypical diatomic-molecule - diatomic molecule interactions H2-HX and H2-X2, where X = F, Cl, Br, quantum-chemical ab initio calculations are carried out on grids of the configuration space, which permit a spherical-harmonics representation of the potential energy surfaces (PESs). Dimer geometries are considered for sets of representative leading configurations, and the PESs are analyzed in terms of isotropic and anisotropic contributions. The leading configurations are individuated by selecting a minimal set of mutual orientations of molecules needed to build the spherical-harmonic expansion on geometrical and symmetry grounds. The terms of the PESs corresponding to repulsive and bonding dimer geometries and the averaged isotropic term, for each pair of interacting molecules, are compared with representations in terms of a potential function proposed by Pirani et al. (see Chem. Phys. Lett. 2004, 394, 37-44 and references therein). Connections of the involved parameters with molecular properties provide insight into the nature of the interactions., 27 pages, 8 figures, 4 tables

A great variety of data on molecular structure and changes, accumulated both experimentally and theoretically, need be compacted and classified to extract the information arguably relevant to understand the basic mechanisms of chemical transformations. Here a screen for displaying four-center processes is developed and as an illustration applied to conformations involving torsions around O – O and S – S bonds, extending the structural properties previously calculated in this laboratory. The construction of the screen follows from connections recently established between the classical kinematic mechanism – the four-bar linkage – and the basic ingredient of quantum angular momentum theory – the 6j symbol.