Pairs of atom types

The force fields in HyperChem that use the above 6-12 potential allow six ways of specifying the constants Ay and B.. three by single atom type and three by pairs of atom types. Single atom type means that there are constants for individual atom types, i, that are combined by a combining rule that results in a parameters for a specific pair, ij, of atom types. Pairs of atom types means that parameter files contain explicit parameters for a pair of atom types... 

This descriptor is defined for each pair of atom types and simply encodes the occurrence numbers of the given atom type pair at different distance values. It can be normalized by using two different procedures the first one consists in dividing each ATACfc value by the total number of atom pairs at distance k independently of their types the second one consists in dividing each ATACi value by a constant, which can be equal to the total number of atoms in the molecule or, alternatively, to the total number of (u,v) atom type pairs in the molecule. 

Proposed by Clerc and Terkovics [Clerc and Terkovics, 1990], also called start-end vectors (or SE-vectors),are —> vectorial descriptors coWecting —> path counts ofdifferent lengths relative to pairs of atom types in the —> H-depleted molecular graph. 

Modified SE-vectors were proposed simply using the shortest path between any pair of atom types in place of all the existing paths. These descriptors were called SESP-Top vectors, where SP stands for shortest path [Baumann, 2002a]. Moreover, to take into account not only the topological and hybridization aspects of the molecule but also the stereochemical and con-... 

Using the geometric distance in place of the topological distance between any pair of atom types, geometric atom pair descriptors were analogously defined [Sheridan, Nilakantan et al, 1989 Sheridan, Miller et al, 1996]. Atom types are defined here by the chemical element, number of heavy-atom cormections, number of n electron pairs, number of attached hydrogens, and formal charge. 

For a particular conformation of a molecule, all geometrical distances between any pair of atom types are calculated and distributed into a number of discrete bins. For each combination of two atom types, the same number of distance bins is allocated in the final bit string. 

Distance-counting descriptors (SE vectors) are a particular implementation of topological atom pairs proposed by Clerc and Terkovics in 1990. These are holographic vectors encoding information on the occurrence frequency of any combination of two atom types and a distance relationship between them. All the paths and not only the shortest one between any pair of atom types are considered in the original proposal. Based on the shortest path, revised S E vectors were proposed by Baumann in 2002 and called SESP-Top vectors and SESP-Geo vectors. 

I 3D-VAIF descriptors (= Three-Dimensional Vector of Atomic Interaction Field descriptors) These are vectorial descriptors derived by an approach similar to that of MEDV-13 descriptor and defined in terms of nonbonding interaction energies between pairs of atom types [Zhou, Zhou et al, 2006]. Five atom types are defined on the basis of the chemical element of the most occurring atoms in organic compounds these are (1) H (2) C (3) N or P (4) O or S (5) F, Cl, Br, or I. 

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... 

The two parameters and dy in equation (1) for any pair of atom types are usually obtained by combination of atom parameters e and rf... 

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