New molecular descriptors for 2D and 3D structures. Theory

Abstract

SUMMARYNew theoretical molecular indices are defined. They contain information about the whole molecular structure in terms of size, shape, symmetry and atom distribution. These indices are calculated from the ( x , y , I) co-ordinates of a molecule within different weighting schemes in a straightforward manner and represent a very general approach to describe molecules, molecular fragments, macromolecules and molecular conformations in a unitary conceptual framework. Their interpretability is quite evident and is defined by the same mathematical properties as the algorithm used for their calculation. Examples on the total surface area, toxicity of PCDD and PCDF and reaction rate of catalysed reactions show a high modelling power of these indices.

Experimental and modelling studies on antifungal compounds

“…407 molecular descriptors from Dragon software (Milano Chemometerics, Italy) that included constitutional, topological, charge, geometrical and empirical, aromaticity indices, and constitutive properties; 19 descriptors from Hyperchem software that included quantum mechanics and thermodynamics; and 48 descriptors from Cerius 2 software (Acceryls Inc, USA) were evaluated. Several literature reports give a very detailed description of these descriptors [10][11][12][13][14]. Statistical techniques such as Cluster Analysis, Principal Component Analysis and Non linear regression analysis were performed on the data set using SYSTAT (SPSS Inc., USA) and Ky Plot (ver 2, Beta, free Application, USA) software.…”

Quantitative Structure-cytotoxicity Relationship of 3-Benzylidenechromanones

“…The mean pCC 50 values for normal cells and tumor cell lines were defined as N and T, respectively (24). (26); (b) Vsurf_IW6 (Hydrophilic interaction-energy moment 6), Vsurf_ID7 (Hydrophobic interaction-energy moment 7), Vsurf_ID1 (Hydrophobic interaction-energy moment 1) and Vsurf_HB7 (Hbond donor capacity 7) that are similar to the VolSurf descriptors (27) and depend on the structure connectivity and conformation; (c) Mor03v (signal 03/weighted by van der Waals volume), Mor03m (signal 03/weighted by mass), Mor09m (signal 09/weighted by mass), Mor03p (signal 03/weighted by polarizability) and Mor25v (signal 25/weighted by van der Waals volume) that are 3D-MoRSE (3D-Molecule Representation of Structures based on Electron diffraction) descriptors (28); (d) G1u (1st component symmetry directional WHIM index/unweighted encoding molecular symmetry that extracts the global symmetry information) (29); (e) R3m+ (R maximal autocorrelation of lag 3/weighted by mass) that reflects three-dimensional structure and molecular volume (30); and (f) SpMAD_AEA(dm) (Spectral mean absolute deviation from augmented edge adjacency matrix weighted by dipole moment edge adjacency indices) (31). …”

A knowledge‐based approach for screening chemical structures withinde novomolecular evolution

“…The QSAR literature contains a large number of possible choices. Examples of "cheap" descriptors that may be used are Fingal [6], where the different inter-atomic distances in a molecule are coded into a hash-key fingerprint, the Weighted Holistic Invariant Molecular (WHIM) descriptors [7,8], which are based on statistical indices calculated on the projections of the atoms along principal axes, and the GEometry, Topology and Atom-Weights AssemblY (GETAWAY) descriptors [9,10], which are computed on the basis of the Molecular Influence Matrix (MIM). There are also 3D-Molecule Representation of Structures based on electron diffraction (3D-MoRSE) [11], which are based on theoretical scattering curves calculated from the same transforms as used in electron diffraction studies.…”