Quantitative Structure-Acidity Methods

We have seen in Chapters 2 and 3 that the modern power of quantum hemistry and the ingenuity of researchers who have developed methods for simulating solvation have allowed for highly accurate relative and abso-ute pK calculations for small molecules. In Chapters 4-9 we have seen low quantitative structure-acidity methods can successfully be used to stimate pKj,s on a large number of systems spanning a range of molecular rtructures and solvents. 

Shen, M., Letiran, A., Xiao, Y., Golbraikh, A., Kohn, H., Tropsha, A. Quantitative structure-activity relationship analysis of functionalized amino acid anticonvulsant agents using k nearest neighbor and simulated annealing PLS methods./. Med. Chem. 2002, 45, 2811-2823. 

Statistical and computational methods have been used to quantify structure-activi relationships leading to quantitative structure-activity relationships (QSAR). The concqpt of QSAR can be dated back to the work of Crum, Brown and Fraser from 1868 to 1869, and Richardson, also in 1869. Many notable papers were published in the period leading up to the twentieth century by men such as Berthelot and Jungfleisch in 1872, Nemst in 1891, Ov ton in 1897 and Meyer in 1899 (7). Professor Corwin Hansch is now regarded by many as the father of QSAR, because of his work in the development of new and innovative techniques for QSAR. He and his co-woikers produced a paper that was to be known as the birtii of QSAR, and was oititled "Correlation of biological activity of phenoxyacetic acids with Hammett substituent constants and partition coefficients" (2). 

Miigge, I., Podlogary, B.L. 3D Quantitative Structure-Activity Relationships of Biphenyl Carboxylic Acid MMP-3 Inhibitors Exploring Automated Docking as Alignment Method. Quant. Struct.-Act. Relat. 2001, 20, 215-223. 

In keeping with this method, several approaches have been developed to document methods and dose-response relationships for irritation in humans. This work suggests that, at least for nonreactive compounds such esters, aldehydes, ketones, alcohols, carboxylic acids, aromatic hydrocarbons, and pyridine, the percentage of vapor pressure saturation of a compound is a reasonable predictor of its irritant potency. Specific physical properties of molecules predict overall irritation potential. This work is based on the identification of irritant thresholds for homologous series of specific agents. Quantitative structure-activity relationships derived from such work suggests a reasonable model to explain mucosal irritation. 

Methods other than thermodynamic cycles are often used to calculate acid dissociation constants. Previous publications implement the theoretical relationship between pKa and structural property [6], bond valence methods and bond lengths [33], pKa correlations with highest occupied molecular orbital (HOMO) energies and frontier molecular orbitals [34], and artificial neural networks [35] to predict pKa values. In addition much work has been done using physical properties as quantitative structure-activity relationship (QSAR) descriptors, and regression equations with such descriptors to yield accurate pKa values for specific classes of molecules [36-47]. The correlation of pKas to various molecular properties, however, is often restricted to specific classes of compounds, and it is... 

The molecular weight of polymyxin B was shown by the method of partial substitution to be 1,150 d 10 per cent. Quantitative amino acid analysis yielded the amino acids a,y-diaminobutyric acid, L-threonine, D-phenylalanine and L-leucine in the molar proportions 6 2 1 1. Because no free a-carboxyl- and no free a-amino groups could be detected, polymyxin Bi had to be of a cyclic nature . Neither pepsin nor trypsin was found to attack the molecule and therefore partial hydrolysis and separation of the fragments was used for the elucidation of the structure. Of the 14 fragments isolated and identified, seven key peptides were necessary for proposing four tentative structures for polymyxin Two were formulated with a ring... 

Molecular Similarity and QSAR. - In a first contribution on the design of a practical, fast and reliable molecular similarity index Popelier107 proposed a measure operating in an abstract space spanned by properties evaluated at BCPs, called BCP space. Molecules are believed to be represented compactly and reliably in BCP space, as this space extracts the relevant information from the molecular ab initio wave functions. Typical problems of continuous quantum similarity measures are hereby avoided. The practical use of this novel method is adequately illustrated via the Hammett equation for para- and me/a-substituted benzoic acids. On the basis of the author s definition of distances between molecules in BCP space, the experimental sequence of acidities determined by the well-known a constant of a set of substituted congeners is reproduced. Moreover, the approach points out where the common reactive centre of the molecules is. The generality and feasibility of this method will enable predictions in medically related Quantitative Structure Activity Relationships (QSAR). This contribution combines the historically disparate fields of molecular similarity and QSAR. 

The study of structure-reactivity relationships by the organic chemist Hammett showed that there is often a quantitative relationship between the two-dimensional structure of organic molecules and their chemical reactivity. Specifically, he correlated the changes in chemical properties of a molecule that result from a small change in its chemical structure that is, the quantitative linear relationship between electron density at a certain part of a molecule and its tendency to undergo reactions of various types at that site. For example, there is a linear relationship between the effea of remote substituents on the equilibrium constant for the ionization of an acid with the effect of these substituents on the rate or equilibrium constant for many other types of chemical reaction. The relative value of Hammett substituent constants describes the similarity of molecules in terms of electronic properties. Taft expanded the method to include the steric hindrance of access of reagents to the reaction site by nearby substituents, a quantitation of three-dimensional similarity. In addition, Charton, Verloop, Austel, and others extended and refined these ideas. Finally, Hansch and Fujita showed that biological activity frequently is also quantitatively correlated with the hydrophobic character of the substituents. They coined the term QSAR, Quantitative Structure-Activity Relationships, for this type of analysis. 

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