Generating molecular formulas

In this section we recap methods described earlier in this book, adapting for HR-MS where necessary. Recall that, mathematically, a molecular formula/Scan be considered as a mapping that relates each chemical element X to its multiplicity /S(X). Moreover, we know that not every such mapping represents the molecular formula of a chemical compound. Two types of rules can be used to recognize invalid or unlikely molecular formulas mathematical and heuristic rules. 

Mathematical rules are based on the fact that (uncharged) chemical compounds correspond to (non-ionic) molecular graphs [150]. For example, CH2, C2H8, C2H7O do not correspond to a molecular graph. In order to result in a molecular graph, a molecular formula has to fulfill conditions (Grl), (Gr2) and (Con) of Theorem 1.23. 

The sum of all valencies in (Grl) must be an even number in order to ensure all bonds are complete. Inequality (Gr2) specifies that there are sufficient bonds available for the atom of maximum valency. Condition (Con) requires a molecular graph to be connected (i.e. one component). The above examples C2H7O, CH2, and C2H8 violate 

The monoisotopic mass of an element is the mass of its most abundant isotope. Thus, the monoisotopic mass of a compound with molecular formula p is defined as the sum of monoisotopic masses of its elements 

Given an instrument accuracy of S, the condition A(m) S must be fulfilled. 

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We wrote a program to remove in-house idiosyncrasies from the WLN file and to reformat it for CROSSBOW. Programs from this suite were then used to remove outdated conventions, check for what errors could be detected algorithmically and generate molecular formulae. This was achieved and the file, then of some 13,000 FPL Compounds, was subsequently maintained by CROSSBOW. 

An interesting feature in order to generate molecular formulas and to facihtate an extra confident identification is the use of different isotopic filters. These filters work based on the isotopic pattern deviation between the empirically measured and the theoretical spectrum. The presence of an abundant isotopic pattern in the analyte molecule helps to confirm the presence of that compound in the sample. Thus, the presence of atoms such as carbon, chlorine, bromine, or sulfur in the molecule gives a characteristic isotopic pattern that allows reducing the number of possible elemental compositions fora certain mass-accuracy window. The match between empirical and theoretical data is given by the isotope fit (i-FTT) or sigmaFlT values. These values are calculated, taking into account not only the isotopic distribution but also the accurate masses. The lower the value, the more plausible the elemental composition (Ojanpera et al., 2006 Ibanez et al., 2008). 

Furthermore, the prediction of and NMR spectra is of great importance in systems for automatic structure elucidation. In many such systems, aU isomers with a given molecular formula are automatically produced by a structure generator, and are then ranked according to the similarity of the spectrum predicted for each isomer to the experimental spectrum. 

In Problem 2 5 you were asked to write structural formulas for the five isomeric alkanes of molecular formula C6H14 In the next section you will see how the lUPAC rules generate a unique name for each isomer... 

Generation Surface Groups (Z) Molecular Formula MW Diameter (nm) ... 

CASRN 56-40-6 molecular formula C2H5NO2 FW 75.07 Chemical/Physical Products identified from the oxidation of glycine and OH radicals (generated from H2O2/UV) in oxygenated water were oxalic acid, formic acid, and ammonium ions. In oxygen-free water, oxalic and formic acids were not produced, i.e., glycine oxidized directly to ammonium ions. The rate constant for the reaction of OH radicals with the zwitterion ion is 1.7 X 10 /M-sec and with the anionic form is 1.9 x 10 /M-sec (Vel Leitner et al., 2002). 

The first step of the design of stress experiments should be to examine the molecular formula of the test compound. Does the structure resemble substances for which a degradation pattern is already known Does it contain easy oxidizable functional groups Do tautomers exist, that can be more sensitive to oxidants Can pH affect the sensitivity, because prototropic equilibria can generate easily oxidizable species Are potential degradation impurities available Time spent in answering these questions and in collecting literature data is never lost. 

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