Constitutional descriptor

The meaning of the G-WHIM descriptors is that previously defined for WHIM descriptors, but now the descriptors refer to the interaction molecular field instead of the molecule. For example, the eigenvalues X,i, Xz and >,3, relate to the interaction field size the eigenvalue proportions i9i and i>2 relate to the interaction field shape the group of descriptors constituted by the inverse function of the kurtosis (k), i.e., = 1/k ... 

SVM 14% (ft = 56) CODESSA descriptors constitutional, topological, electrostatic, geometrical, and quantum mechanical (ft — 5)... 

As we have seen, molecular descriptors constitute information about steric and electronic constraints conferred by chemical structure [104, 105]. Molecular descriptors underlie both pharmacophore models [106, 107] and analyses of similarity or diversity among compound collections [108,109]. The calculation of descriptors therefore serves as a starting point in the analyses of small-molecule relationships assessed prior to compound synthesis, before selecting compounds for HTS, and in the interpretation of biological measurements of small-molecule perturbation. 

Several new 2D and 3D molecular descriptors have been invented and proposed for QSAR use [4]. However, (he relatively high uncertainty associated with molecular descriptors constitutes a difficult problem. Thus, the search for more informative 2D and/or 3D molecular descriptors has been of major concern in QSAR research. Using variable selection from a very large pool of descriptors, PLS can detect the informative molecular descriptors [5]. 

CODESSA University of Florida Program automatieally ealculates more than 500 types of descriptors (Constitutional, Topological, Geometrical, Electrostatic, Thermodynamic, Quantum-chemical) http //www.codessa-pro.com/index.htm... 

CODESSA can compute or import over 500 molecular descriptors. These can be categorized into constitutional, topological, geometric, electrostatic, quantum chemical, and thermodynamic descriptors. There are automated procedures that will omit missing or bad descriptors. Alternatively, the user can manually define any subset of structures or descriptors to be used. 

The shape of an object is a descriptor of the outline of its external surface only. Thus the shape of an object is a property that reflects the recognized pattern of relationships among all the points that constitute its external surface. The difference between the shapes of two objects arises from the differences between the patterns of relationships among these point coordinates corresponding to the two shapes. While the size of an object, for example a material particle, is an indicator of the quantity of matter contained in it, its shape is concerned with the pattern according to which this quantity of matter is assembled together. Shape is an intrinsic rather than an extrinsic characteristic in that it is not additive. 

A common feature of the various methods that we have developed for the calculation of electronic effects in organic molecules is that they start from fundamental atomic data such as atomic ionization potentials and electron affinities, or atomic polarizability parameters. These atomic data are combined according to specific physical models, to calculate molecular descriptors which take account of the network of bonds. In other words, the constitution of a molecule (the topology) determines the way the procedures (algorithms) walk through the molecule. Again, as previously mentioned, the calculations are performed on the entire molecule. 

Table 1 Calculation of some molecular-based descriptors for BOA, DIMBOA and MBOA. Physicochemical descriptor like logP (partition coefficient between octanol and water) constitutional descriptors like the number of a specified atoms or bonds (number of carbons, hydrogens, oxygens, nitrogens, single and aromatic bonds, the total number of atoms and bonds) and molecular weight quantum-mechanical descriptors like HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital).

Each of these columns of this symmetrical matrix may be seen as representing a molecule in the subspace formed by the density functions of the N molecules that constitute the set. Such a vector may also be seen as a molecular descriptor, where the infinite dimensionality of the electron density has been reduced to just N scalars that are real and positive definite. Furthermore, once chosen a certain operator in the MQSM, the descriptor is unbiased. A different way of looking at Z is to consider it as an iV-dimensional representation of the operator within a set of density functions. Every molecule then corresponds to a point in this /V-dimensional space. For the collection of all points, one can construct the so-called point clouds, which allow one to graphically represent the similarity between molecules and to investigate possible relations between molecules and their properties [23-28]. 

The permutational descriptor of the given chemical constitution is then a permutation of atom indices (or the inverse permutation of graph indices) which transforms the reference constitution into the considered constitution. 

Winkler and Burden [47] Topological, constitutional, hydrogen-bonding, and descriptors based on adjacency matrices... 

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