Descriptors physicochemical

There are finer details to be extracted from such Kohonen maps that directly reflect chemical information, and have chemical significance. A more extensive discussion of the chemical implications of the mapping of the entire dataset can be found in the original publication [28]. Gearly, such a map can now be used for the assignment of a reaction to a certain reaction type. Calculating the physicochemical descriptors of a reaction allows it to be input into this trained Kohonen network. If this reaction is mapped, say, in the area of Friedel-Crafts reactions, it can safely be classified as a feasible Friedel-Qafts reaction. 

HYBOT-Plus (hydrogen bonding thermodynamics, calculation of local and molecular physicochemical descriptors) http //www.timtec.net/soJiware/hybot-plus.htm... 

A proton can be (numerically) represented by a series of topological and physicochemical descriptors, which account for the influence of the neighborhood on its chemical shift. Fast empirical procedures for the calculation of physicochemical descriptors are now easily accessible [45. Geometric descriptors were added in the case of some rigid substructures, as well as for rr-systems, to account for stereochemistry and 3D effects. 

An extended set of physicochemical descriptors was used in this study, including, for example, partial atomic charge and effective polari2 ability of the protons, average of electronegativities of atoms two bonds away, or maximum, T-atomic charge of atoms two bonds away. 

A proper representation of the molecular structure is crucial for the prediction of spectra. Fragment-based methods, topological descriptors, physicochemical descriptors, and 3D descriptors have been used for this endeavor. 

Of course, class 4 is not valuable in medicinal chemistry. Such compounds have to be excluded from drug discovery processes as early as possible. At present, there are computer alert programs based on the Rule-of-5 or similar approaches that are used in preliminary screening to select and exclude compounds of class 4 [71]. Van de Waterbeemd indicated in 1998 that the four BCS classes of drugs can be determined solely by considering physicochemical descriptors such as molecular weight and PSA [72]. However, as mentioned in this chapter, those descriptors are too crude for the quantitative description of molecular size and H-bonding ability. 

Raevsky, 0. A. Physicochemical descriptors in property-based drug design. Minirev. Med. Chem. 2004, 4, 1041-1052. 

Raevsky, O. A., Schaper, K.-J. Physicochemical descriptors governing the solubility and partitioning of chemicals in water-solvent-gas systems. In Abstracts of 12th International Workshop on Quantitative Structure-Activity Relationships in Environmental Toxicology, Lyon, France, 2006, p. 23. 

E. SLIPPER-2001 - software for predicting molecular properties on the basis of physicochemical descriptors and structural similarity. /. Chem. Inf. Comput. Sci. 2002, 42, 540-549. 

Of the physicochemical descriptors, lipophilicity (as described by clogP and Topological Polar Surface Area (TPSA) gave the strongest overall correlation to incidence of adverse in vivo outcomes, whether analyzed in terms of free or total drug threshold concentrations. In the case of free drug threshold analysis, a Random Forest statistical method indicated that there was a higher chance of a compound with TPSA <70... 

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).

Lipophilicity is an important physicochemical descriptor used in correlating chemical stmcture with biological activity. It is traditionally expressed as the logarithm of the partition coefficient (i.e., log Aqw) of the solute between n-octanol and the aqueous phase, thus representing the rate of concentrations of a compound (X) in M-octanol and water, that is,... 

ADRIANA.code Global physicochemical descriptors, size and shape descriptors, atom property-weighted 2D and 3D autocorrelations and RDF, surface property-weighted autocorrelations 1,244... 

A physical model usually predisposes to physicochemical descriptors, such as p/Ca, log P or molar volume for the whole molecule, or the equivalent descriptors for substituents on a common molecular framework. But different structures can have the same or similar property values, and we are interested in designing structures. So at some stage we must choose structural descriptors (atom types, substructural fragments, connections, or indices from molecular orbital calculations) or at least relate structure to property in order to design the appropriate structure. 

Quantitative structure-activity relationships represent an attempt to correlate activities with structural descriptors of compounds. These physicochemical descriptors, which include hydrophobicity, topology, electronic properties, and steric effects, are determined empirically or, more recently, by computational methods. The success of a QSAR method depends on two factors the training dataset obtained by testing a group of chemicals and the descriptors obtained from some easily measurable or calculable property of the chemicals. 

Quantitative structure-activity relationship (QSAR) (Hansch and Klein, 1986 Hansch and Leo, 1995) represents an attempt to correlate structural descriptors of compounds with activities. The physicochemical descriptors include numerical parameters to account for electronic properties, steric effect, topology, and hydrophobicity of analogous compounds. In its simplest form, the biochemical activities are correlated to the numerical substituent descriptors of analogous compounds tested by a linear equation such as... 

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