Volume descriptor

Calculated Changes of the Volume Descriptor AEr for the Water Exchange... 

In 1993, Fuhr et al. (159) correlated electrostatic and volume descriptors for a series of quinolone antibacterials with their percentage of inhibition effect of caffeine 3-demethylation in CYP1A2. The descriptors were derived with the SYBYL (207) and ALCHEMY II (208) software packages. It was shown that... 

Once a Feature Tree can be created from a molecule, the question arises of how to compare two Feature Trees. Using Eq. (1), we are able to compare two individual Feature Tree nodes. Owing to the additivity of the features stored at a node, we can also compare two sets of Feature Tree nodes. This is done by adding the features over all nodes within a set and applying Eq. (1) again. Obviously, we can also compare two complete Feature Trees in this way we just add all features in the two trees and apply Eq. (1). We call such a comparison level-0, because no division of the tree into pieces has been performed. Level-0 comparisons closely resemble the way linear descriptors work. If we assume for a moment that all components of a linear descriptor are additive and can be computed for each building block individually (such as the volume descriptor), adding the feature values over all Feature Tree nodes will create the linear descriptor. 

Analyzing the same data set, van de Waterbeemd and Kansy [64] derived a significant correlation when using log PCyCiohex. and a calculated volume descriptor VM (cm3) (r= 0.934, s = 0.29) ... 

The molecular volume descriptor, V, can be recognized as an important descriptor once one realizes that the free energy of solution is related in part to the size of the cavity that must be carved out of the solvent bath by the solute molecule during the solvation process. The surface area, A, of a molecule or a fragment of a molecule may be construed as a measure of the region available for interaction with another molecule. For computing V and A, one could use a particular electron density contour or a non-QM-derived measure of atomic size such as the van der Waals radii available from standard tables in physical chemistry textbooks. 

The symbol V is often associated with the electrical potential in the literature, but U is employed here so as not to conflict with the volume descriptor. Another aspect of chemical reactivity involves the molecular electrostatic potential (MEP). The MEP is the interaction energy between a unit point charge and the molecular charge distribution produced by the electrons and nuclei. The electrostatic potential, U r), at a point, r, is defined by Eq. [13]. 

Corey-Pauling-Koltun volume -> volume descriptors... 

Examples of geometrical descriptors are the - quantum-chemical descriptors, -> moment of inertia, - length-to-breadth ratio, -> surface areas, - volume descriptors, - CPSA descriptors, -> EVA descriptors, -> WHIM descriptors, 3D-MoRSE descriptors, -> interaction energy values, spectrum-like descriptors. 

There are several methods developed for the calculation of logP from molecular structure, based on -> substituent constants, - fragmental constants, - electronic descriptors, -> steric descriptors, - connectivity indices, surface areas, - volume descriptors, and -> chromatographic descriptors [Leo, 1990 Hansch et al., 1995b Carrupt et al., 1997 Reinhard and Drefahl, 1999]. 

Theoretical descriptors derived from physical and physico-chemical theories show some natural overlap with experimental measurements. Several quantum-chemical descriptors, surface areas and -> volume descriptors are examples of such descriptors also having an experimental counterpart. 

Different physical properties and molecular models have been used to define the molecular surface the most common are reported below together with the descriptors proposed as measures of surface areas and molecular volume (- volume descriptors). Molecular surface area and volume are parameters of molecules that are very important in understanding their structure and chemical behaviour such as their ability to bind ligands and other molecules. An analysis of molecular surface shape is also an important tool in QSAR and - drug design-, in particular, both - molecular shape analysis and - Mezey 3D shape analysis were developed to search for similarities among molecules, based on their molecular shape. 

Molecular descriptors related to the dimensions of the molecule and often calculated from the - molecular geometry. Combined with molecular shape information, they are closely related to - steric descriptors. The simplest size descriptors are atom count, -> bond count, -> molecular weight, and some among the -> volume descriptors such as van der Waals volume. Other size descriptors are - Sterimol parameters and - WHIM size descriptors. 

The most common steric descriptors are - molar refractivity, -> surface areas and several - volume descriptors such as molecular volume. Other steric descriptors are -> steric interaction fields, MTD descriptors, -> common overlap steric volume, and several topological descriptors accounting for both size and - molecular branching. Other popular molecular steric descriptors are listed below. 

VLOGP model Gombar hydrophobic model -> lipophilicity descriptors volume descriptors (V)... 

Steric descriptors and/or -> size descriptors representing the volume of a molecule. The volume of a molecule can be derived from experimental observation such as the volume of the unit cell in crystals or the molar volume of a solution or from theoretical calculations. In fact, analytical and numerical approaches have been proposed for the calculation of molecular volume where the measure depends directly on the definition of - molecular surface-, -> van der Waals volume and -> solvent-excluded volume are two volume descriptors based on van der Waals surface and solvent-accessible surface, respectively. 

A list of other common volume descriptors is given below. 

Bondi volume volume descriptors ( van der Waals volume)... 

Examples ofgeometrical descriptors (Figure Gl) are the quantum-chemical descriptors, moments of inertia, length-to-breadth ratio, surface areas, volume descriptors, CPSA... 

The cavity term is a measure of the endoergic cavity-forming process, that is, the free energy necessary to separate the solvent molecules, overcoming solvent-solvent cohesive interactions, and provide a suitably size cavity for the solute. The magnitude of the cavity term depends on the —> Hildebrand solubility parameter 5na.nd volume descriptors ofthe solute. The solute volume... 

---