Fragment molecular formula

As mentioned earlier, fragmentation in a mass spectrometer generally follows known reaction schemes. We will use this knowledge during calculation of a match value for structure candidate M with respect to experimental mass spectrum I. The calculation is similar to that for molecular formula candidates. However, in the case of structural formulas we can considerably restrict the set of possible fragment molecular formulas jSj. We will consider only such molecular formulas for which fragments exist that are derived from M by successive ionization and fragmentation reactions. To simulate these we go back to the previous work in Section 2.3. 

The next step in calculation of match values is the determination of fragment molecular formulas. Table 8.8 Usts all such molecular formulas where there is a peak in the spectrum corresponding to the mass of highest intensity, f(m ) > 0. The solution Xj of the optimization problem is given in the last column. We obtain a match value... 

Separation of families by merely increasing the resolution evidently can not be used when the two chemical families have the same molecular formula. This is particularly true for naphthenes and olefins of the formula, C H2 , which also happen to have very similar fragmentation patterns. Resolution of these two molecular types is one of the problems not yet solved by mass spectrometry, despite the efforts of numerous laboratories motivated by the refiner s major interest in being able to make the distinction. Olefins are in fact abundantly present in the products from conversion processes. 

By being able to obtain an unequivocal relative molecular mass, or even a molecular formula derived from that mass, the hybrid mass spectrometer becomes a powerful tool for investigating single substances or mixtures of substances. With an APCI inlet, fragmentation can be induced to obtain structural information (see Chapter 9). 

Accurate mass measurement on a molecular ion of any substance gives directly the molecular formula for fragment ions, similar measurement gives their elemental compositions. 

A double-focusing mass spectrometer can mea.sure mass accurately to several decimal places, thus enabling the determination of molecular formulae and elemental compositions of fragment ions. 

The long-range coupling of 2.2 Hz which appears in A and B, two quaternary C atoms in the NMR spectrum with appropriate shifts (5c = 76.6 and 83.0) and the two double-bond equivalents (molecular formula C TZ/oO) suggest that a CC triple bond links the two structural fragments. Hence the compound is identified as hex-3-yn-l-ol (C) in accordance with the coupling patterns. 

Ocimene is a pleasant-smelling hydrocarbon found in the leaves of certain herbs. It has the molecular formula C10Hi6 and a UV absorption maximum at 232 nm. On hydrogenation with a palladium catalyst, 2,6-dimethyloctane is obtained. Ozonolysis of /3-ocimene, followed by treatment with zinc and acetic acid, produces the following four fragments ... 

This method can sometimes be used for determining the probable elemental composition of fragment ions. However, it is not as generally applicable and does not replace accurate mass measurement for determining molecular formulae and elemental compositions. 

The unknown gave a molecular ion at m/z 193 with fragment ions at m/zs 174, 148, and 42. From the abundance of the molecular ion, it is probably aromatic, and according to the Nitrogen Rule, contains at least one nitrogen atom. From accurate mass measurement data and an examination of the isotopic abundances in the molecular ion region, the molecular formula was found to be CnH15N02. 

The mass spectrum of the unknown compound showed a molecular ion at m/z 246 with an isotope pattern indicating that one chlorine atom and possibly a sulfur atom are present. The fragment ion at m/z 218 also showed the presence of chlorine and sulfur. The accurate mass measurement showed the molecular formula to be C]3FI7OSCl R + DB = 10. 

Compilations of Reference Spectra There are several compilations of reference mass spectra available of which the oldest is the American Petroleum Institute (Ref 82) collection of spectra obtained mostiy on the older type instruments. Recent collections index spectra variously, eg, under reference number (Ref 19). molecular weight (Refs 12 19), molecular formula (Ref 19), fragment ion values (Ref 19), and base peak (Refs 12 19). A quarterly journal, Archives of Mass Spectral Data ... 

It is not necessary to build stmctures to use the Registry File. Compounds can also be searched for by using names, combinations of name fragments. Registry Numbers, molecular formulas, and in other ways. The display methods are the same. 

If you are lucky, the ion with the highest mass to charge value will be the molecular ion. However, this is often not the case, as textbooks on mass spectrometry make clear. If it is possible to carry out high resolution mass spectrometry on the molecules in question, and the molecular ion is indeed observed, the exact mass can be used in combination with tables to obtain the molecular formula directly. Alternatively, you can use the internet (http //www.sisweb. com/cgi-bin/masslO.pl) to calculate and plot mass distributions for any molecular fragment you think may be present. 

Q5. From Spectra 15.1-15.5, construct a plausible structure for the unknown compound which has a molecular formula C11H14NO3. (It is known to be an indole and to contain the following fragments -OCH3 and -CH2-COOH.)... 

Currently, LC-MS is widely used for the analysis of polar compounds, such as medicinal metabolites and bioactive peptides, since the interface has been improved and several new ionization methods have been developed. The sensitivity and reproducibility are sufficient for a daily quantitative analysis. The usefulness of the LC-MS has been demonstrated for studies on Type II pheromones using a time-of-flight MS with electrospray ionization (ESI) [180]. Each epoxydiene derived from the (Z3,Z6,Z9)-triene shows three ion series of [M+NHJ+, [M+H]+, and [M-OH]+ with high resolution and good sensitivity, indicating its molecular formula. In addition to these, characteristic fragment... 

The mass spectra of compounds 1-14 have been discussed in CHEC-II(1996) <1996CHEC-II(8)733>. The mass spectra of all the new reported compounds displayed the corresponding molecular ions consistent with their respective molecular formulas. The mass spectra of the derivatives 17a (R1 = Ph, R2 = H) and 17b (R1=Ph, Rz = OMe) showed fragment peaks due to loss of (M-NO-CO), characteristic of sydnone-containing molecules, at m/z = 346 and 376, respectively <2002IJH287>. The other significant peaks were observed at m/z =187 and 217 due to the formation of 3-aryM-cyanosydnone. Similarly, in the mass spectrum of 25 <2002IJH287>, the peak at 324 was due to the loss of C02 from molecular ion and the peak at mlz = 171 was due to the formation of 3-cyanocoumarin. The molecular ion peak of the compound 24 (R1 =/-Bu, R2 = H) was observed at m/z = 368. 

The majority of marine isonitriles are sesquiterpenes with the molecular formula, C16H25N. Often cyclic, these are alkanes or alkenes possessing only a single isocyano-related functional group. In the mass spectrum, they exhibit a molecular ion at w/z 231, or an intense fragment ion at m/z 204, indicative of M+-HCN. Some are crystalline (see Table 2). With few exceptions most of the isothiocyano and formamido analogs are minor noncrystalline metabolites (see Table 3). 

The molecular peak of the spiro[adamantine-2,2 -(l,3,4)-thiadiazolidine]-3, 4 -dicarboxylate 29 appears with 99% intensity and shows four distinct fragmentations <1999T12783>. The molecular formulas of the fragments were confirmed by the intensities of 13C and (34S+13C2) isotope peaks. The two major fragmentations involve cleavage of the weak C-S bonds and afford the base peak at mjz 208 (100%) corresponding to and a peak at m/z 239... 

The molecular ion peak directly provides valuable information on the analyte. Provided the peak being of sufficient intensity, in addition to mere molecular mass, the accurate mass can reveal the molecular formula of the analyte, and the isotopic pattern may be used to derive limits of elemental composition (Chaps. 3.2 and 3.3). Unfortunately, the peak of highest m/z in a mass spectrum must not necessarily represent the molecular ion of the analyte. This is often the case with El spectra either as a result of rapidly fragmenting molecular ions or due to thermal decomposition of the sample (Chaps. 6.9 and 6.10.3)... 

Pseudovinblastinediol (21) (formerly named pseudovincaleukoblas-tinediol) has been isolated from C. rose us as a minor constituent (44). The high-resolution mass spectrum of 21 established a molecular formula of C44H5ftN40g. The characteristic vindoline fragments of miz 469 and 282 were shifted 58 mass units to miz 411 and 224, respectively, indicating the... 

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