In this paper, we present a theoretical method to describe molecular structures in terms of hierarchically related substructures. The approach is based on the location of local maxima (peaks) in promolecular electron density distributions (EDD) established at continuously varying resolution levels. For each of the so-calculated EDD, the local maxima are determined by using a hierarchical clustering algorithm wherein peaks obtained at a given resolution are used as starting points for discovering peaks at the next lower resolution level through gradient trajectories of the EDD. The use of such an approach allows assignment of molecular fragments or chemical groups to peaks, at any resolution level. Results, obtained for a set of four benzodiazepine-related molecules and three thrombin inhibitors, are presented in terms of dendrograms wherein each node corresponds to a well-defined molecular substructure.

Structural Identification of Local Maxima in Low-Resolution Promolecular Electron Density Distributions

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbo, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes.

Similarity measures based on Gaussian‐type promolecular electron density models: Alignment of small rigid molecules

The performance of CNDO/2D and SCC-MO methods in estimating NQCCs of 14 N atom in planar compounds is tested against the ab initio DZ results and experimental data. A salient feature of the procedure is a rigorous calculation of electric field gradient matrix elements. The semiempirical values are in good qualitative accordance with results of more sophisticated methods. Quantitative discrepancies may serve as a useful guide in determining satisfactory basis sets for semiempirical schemes. The electric field gradients (EFG) provide useful information on screening constants of 2p orbitals and their relative populations. It is suggested that EFGs should be synergetically used with other observables such as ESCA shifts in finding optimal parametrization for semiempirical methods.

Semiempirical vs. Ab initio calculations of molecular properties: Part 4. Nuclear quadrupole coupling constants of 14N in some medium sized heterocyclic molecules

Magnetic anisotropy data of CHO 2 Cl

Magnetic anisotropy data of C 4 H 2 S 2 Se 2

Diamagnetic susceptibilities in some linear van der Waals complexes using the promolecule model

The promolecule model has been shown to give reasonable estimates of the second moments and diamagnetic susceptibilities of small Van der Waals complexes. The model is here extended to larger Van der Waals complexes. Results for medium-size complexes are found to be in good agreement with experimental data and for ab initio values.

Božidar Vidić

Papers

Diamagnetic susceptibilities in some linear van der Waals complexes using the promolecule model

Second moments and diamagnetic susceptibilities in van der waals complexes by the promolecule model