Molecular fragment indicators

Several relationships aid in deducing the empirical formula of the parent ion (and also molecular fragments). From the empirical formula hypothetical molecular structures can be proposed, using the entries in the formula indices of Beilstein and Chemical Abstracts. 

The molecular ion intensity decreases with increased branching, therefore the molecular ion peak may be nonexistent. The loss of 15 Daltons from the molecular ion indicates a methyl side chain. The mass spectra of branched alkanes are dominated by the tendency for fragmentation at the branch points, and hence are difficult to interpret. 

Various methods by which the Kow of PAHs could be calculated are based on their molecular structures, i. e., a quantitative structure-property relationship (QSPR) approach [ 1,199,200]. One of the most famous techniques involves summation of hydrophobic fragmental constants (or f-values) for all groups in a molecule of a specific compound. On the other hand, Aboul-Kassim [1] and Aboul-Kassim et al. [202, 203] introduced a modeling technique based on the molecular connectivity indices of various PAHs, ranging from low- to high-molecular weight compounds. More details are given in Chap. 4 of this volume. 

Indices of order greater than two which can be computed as either path, cluster, path/cluster, or chain depending upon the configuration of the molecular fragments (Eqs. 41-47). 

A wide variety of features have been used in bit vectors, including molecular fragments, 3-D potential pharmacophores, atom pairs, 2-D pharmacophores, topological torsions, and variety of topological indices. 

On the assumption that methylation of the degraded arabic acid was complete, the location of hydroxyl groups in the various cleavage fragments indicates the positions through which the monosaccharide units are involved in union with the other residues. Thus the isolation of three molecular proportions of 2,3,4-trimethyl-D-glucuronic acid (VIII) and one molecular proportion of 2,3,4,6-tetramethyl-D-galactose (XI)... 

Fig. 12 (a) The molecular fragment (thick lines), comprising half the TDMM molecule, used in the direct-space genetic algorithm stmcture solution calculation from powder XRD data. The arrows indicate the variable torsion angles. The central carbon atom is located on a twofold rotation axis (as indicated), and the other half of the molecule (faint lines) is generated by this symmetry operation, (b) The final refined crystal structure of TDMM, with hydrogen atoms omitted for clarity... 

Characterization of the neutral processes is far more difficult, and little information is available at present. However, studies on some simple molecules (see Section V) have indicated that the ionization efficiency approaches unity quite rapidly as the energy loss increases above threshold, suggesting that, except where transitions to Rydberg states just below a new ionization threshold are significant, the dominant mode of energy loss in the far UV is by ionization often accompanied by molecular fragmentation. 

We shall explore how the orbital symmetries and energies of these small molecular fragments contribute to the observed properties of these compounds by using semiempirical electronic structure calculations. Our tools for analysis include an arsenal of computational indices, e.g. overlap populations and Mulliken populations.4 The remainder of this introduction... 

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