Interatomic distances Molecular geometry

Most of the compounds represented by the molecular skeletons 16-22 either had little or no antifilarial activity except for 18, which was found to be half as active as DEC. The lack of desired antifilarial activity in 16-22 was explained on the basis of their molecular geometry. None of the above non-piperazine analogues represented the exact interatomic distances and molecular geometry as shown by DEC. This indicated that the interatomic distances between the nitrogen atoms and the spatial disposition of the functional groups in DEC are of importance in governing antifilarial activity. 

The chemist s knowledge of molecular geometry extends beyond typical values of bond distances. He will also be able to predict many bond angles fairly accurately. This is equivalent to specifying a 1-3 nonbonded interatomic distance. The chemist s sketch portrays cis and trans isomerization, syn and anti, and gauche conformations which specify either torsion angles, or indirectly, a 1-4 nonbonded distance. 

Distance Geometry Changes Distances to Cartesian Coordinates. Most esperimental measures of molecular geometry provide quantities which may be most directly interpreted as defining interatomic distances. 

It was mentioned earlier that a number of special purpose routines, which do not appear in the VPLIB index, have been developed for use in structural chemistry. The most frequent requirements encountered in this area are those concerned with molecular geometry and, more specifically, with the calculation of interatomic distances, angles and torsion angles. These geometric quantities are best evaluated by vector algebra and this will always involve the calculation of vector components, lengths, direction cosines, vector cross products and vector dot products. Attention should therefore be directed at the best possible way of implementing the calculations described in the latter list on the MVP-9500. 

Autocorrelation descriptors calculated for 3D-spatial molecular geometry are based on interatomic distances collected in the -> geometry matrix and the property function is defined by the set of atomic properties. 

Other simple geometrical descriptors are interatomic distances between pairs of atoms s and t. Interatomic distances are devided into intramolecular interatomic distances, i.e. distances between any pair of atoms (s, t) within the molecule, and intermo-lecular interatomic distances, i.e. distances between atoms of a molecule and atoms of a receptor structure, a reference compound or another molecule. While classical computational chemistry describes molecular geometry in terms of three-dimensional Cartesian coordinates or internal coordinates, the -> distance geometry (DG) method takes the interatomic distances as the fundamental coordinates of molecules, exploiting their close relationship to experimental quantities and molecular energies. 

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