Mass spectrum prediction

Fewer fragmentation steps resulted in lower match values on average, but also lower RRPs (i.e. a better ranking of the correct candidate with respect to the other structures)  

The fragmentation prediction settings with the highest match values ACD, MetFrag Tree Depth 3) had the worst ranking of candidates, with RRPs 0.5 (i.e. on par with randomly-generated match values for all candidates)  

The average RRP was worse for spectra with few possible structures  

Including library spectra for Mass Frontier improved the match values, but had a slight adverse effect on the RRP, while the calculation time increased dramatically (e.g. from minutes to hours)  

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Explain why neopentane shows no molecular ion in its mass spectrum. Predict the structure and mlz for the base ion in its mass spectrum. 

The second step, the so called generation, created only those structures which complied with the given constraints, and imposed additional restrictions on the compounds such as the number of rings or double bonds. The third and final phase, the tester phase, examined each proposed solution for each proposed compound a mass spectrum was predicted which was then compared with the actual data of the compound. The possible solutions were then ranked depending on the deviation between the observed and the predicted mass spectra. 

Compare the Predicted Mass Spectra of the Postulated Structures with the Unknown Mass Spectrum... 

More complex detective work is required to analyze large biomolecules and drugs. However, fragmentation generally follows predictable patterns, and one compound can be identified by comparing its mass spectrum with those of other known compounds with similar structures. In Fig. 2, we see the spectrum of a sample of blood from a newborn infant. The blood is being analyzed to determine whether the child has phenylketonuria. The presence of the compound phenylalanine is a positive indication of the condition. Some... 

According to most theoretical analyses of the present neutrino experiment results, next-generation DBD experiments with mass sensitivities of the order of lOmeV may find the Majorana neutrino with a non-zero effective electron neutrino mass, if the neutrino is self-conjugate and the neutrino mass spectrum is of the quasi-degenerate type or it has inverted hierarchy [83], Majorana massive neutrinos are common predictions in most theoretical models, and the value of a few 10 2cV predicted for its effective mass, if reached experimentally, will test its Majorana nature. 

C-NMR analysis revealed signals at 6= 142.5 and 135.7 ppm due to C7a and C3a respectively, and molecular ion m/z = 386 was observed as the base peak in the mass spectrum. Although formation of oxadiazolines is possible in principle by the [3+2] cycloaddition of azoxides and alkenes, they are predicted to be unstable with the likely mode of decomposition being the retro 1,3-dipolar addition to the azoxide and alkene (Section 5.03.2). 

A similar reaction takes place with sulfuric acid. It takes 2 to 3 months to achieve thermodynamic equilibrium between 5- and 6-membered heterocycles. However, the ratio of the products may be easily predicted in several minutes measuring the ratio of intensities of peaks of [M — CH3]+ and [M — C2H4]+ ions in an El mass spectrum of the initial substituted arylcyclopropane [23]. 

Proteins and peptides are most often seen in the mass spectra as pseudomolecular ions, that is, molecules with attached charge-carrying protons (in the negative-ion mode, proteins and peptides lose protons and thus acquire a negative net charge). This additional proton has to be taken into consideration in order to predict correctly the m/z value at which the peptide of interest will be seen in a mass spectrum. For example, a peptide whose molecular weight (MW) (or molar mass) is equal to 2000 Da, when singly ionized, will be detected at 2001 m/z (for simplification, we assume the mass of proton as equal to 1) ... 

When working with non-radiolabeled drugs the major challenge is to find metabolites in the biological matrices. Because the enzymes responsible for metabolism are quite well characterized metabolic changes can partially be predicted. For example hydroxylation of the parent drug is in many cases the principal metabolic pathway. From a mass spectrometric point of view it results in an increase of 16 units in the mass spectrum. In the full-scan mode an extracted ion current profile can be used to screen for potential metabolites. In a second step a product ion spectrum is recorded for structural interpretation. Ideally, one would like to obtain relative molecular mass information and the corresponding product ion spectrum in the same LC-MS run. This information can be obtained by data dependant acquisition (DDA), as illustrated in Fig. 1.39. 

Problem 16.91 Predict the base (most prominent) peak in the mass spectrum of the compound in Problem 16.90. -4... 

I 3 Isotope patterns. (Caution This problem could lead to serious brain injury.) For an element with three isotopes with abundances a, b, and c, the distribution of isotopes in a molecule with n atoms is based on the expansion of (a + b + c)". Predict what the mass spectrum of Si2 will look like. 

Isomer 60 was calculated to be 27.5 kcalmol-1 and 20.9 kcalmol-1 more stable than 61 and 62, respectively. The relative abundances of fragment ions in the CA mass spectra reflected the predicted energetics for the dissociation processes. While CA mass spectrometry does not allow for a distinction of cyclic versus noncyclic isomers, the fact that the CA mass spectrum contained an Si2+ and Si02+ ion leads to the exclusion of isomers 61 and 62. On the neutral [Si2, 02] surface215 only two energetically low-lying... 

In neutralization-reionization mass spectrometric experiments on CH2Si+ formed by electron-impact dissociative ionization of ClCH2SiH3, Srinivas, Stilzle and Schwarz found evidence for the formation of a viable neutral molecule whose fragmentation pattern and collisional activation mass spectrum were in accord with a H2C=Si structure422. These authors suggested that their experiments supported electron-capture by CH2Si+" as a mechanism for the formation of H2C=Si in interstellar space. Various models have predicted that H2C=Si is one of the most abundant forms of silicon in dense interstellar clouds423. 

Suggest a feasible structure on the basis of the mass spectral and any other evidence. Predict the mass spectrum of the postulated compound and compare with the unknown spectrum. Make any modification to the proposed structure which appears necessary. Check the mass spectral behaviour of compounds of similar structures by consulting appropriate reference collections. 

The following table lists the most common substituents encountered in benzene rings and the neutral particles lost and observed on the mass spectrum.1 Complex rearrangements are often encountered and enhanced by the presence of one or more heteroatomic substituent(s) in the aromatic compound. All neutral particles that are not the product of rearrangement appear in parentheses and are produced alongside the species that are formed via rearrangement. Prediction of the more abundant moiety is not easy, as it is seriously affected by factors that dictate the nature of the compound. These include the nature and the position of any other substituents, as well as the stability of any intermediate(s) formed. Correlations of the data with the corresponding Hammett a constants have been neither consistent nor conclusive. 

The crystal structure of cyclopentadienylberyllium chloride has been determined by X-ray diffraction (280). As portrayed in CIII, the molecule has the same structure in the solid state as in the gas phase. These results rule out the possibility suggested by the mass spectrum (281) that H5C5BeCl is associated. Although not precisely located, the hydrogen atoms of the cyclopentadienyl ring show a slight tendency to bend toward the beryllium atom, in agreement with theoretical predictions (63). 

The structures deduced from the mass spectra must account for the observed equivalent chain length (ECL) or Kovats indices (KI) (Carlson et al., 1998 Katritzky and Chen, 2000 Zarei and Atabati, 2005). The values for monomethylalkanes (Mold et al., 1966 Szafranek et al., 1982) can be used to estimate the expected ECL or KI for a di-, tri- or tetramethyl-alkane structure proposed from a mass spectrum. For example, a dimethylalkane, such as 3,11 -dimethylnonacosane, with 31 carbons, would have its elution time decreased by about 0.3 carbons for the 3-methyl group and about 0.7 carbons for the 11-methyl group. Thus, the predicted ECL is approximately 30 and this is the ECL observed. 

The intramolecular isotope effect on the loss of a hydrogen atom as manifested in the El mass spectrum of trideuteroethylene has been observed to rise from 1.53 at an electron energy of 20 eV to 3.0 close to threshold [331]. Isotope effects in the El mass spectra of all the deuterated ethylenes have recently been re-examined [865]. The effects were found to be in accord with the predictions of QET and the calculated mass spectra agreed well with the experimental. 

A secondary hydrogen isotope effect has been observed in the loss of methyl radical from the -butylbenzene ion. In the El mass spectrum, the isotope effect IchJIct>3 was 1.1 and for metastable ions the isotope effect ranged from 1.5 to 1.9 [642], The isotope effect in the mass spectrum is equal to the ratio of the stretching frequencies of the dissociating bonds. The isotope effect on the metastable ions has been discussed in terms of an excited electronic state and specific radiationless transitions. The isotope effect is, however, explicable within QET. If the critical energy for CHj loss is 3.4 kJ mole-1 less than that for CDj loss, an isotope effect of about 2 is predicted by QET for metastable ions [853]. 

Mass spectral fragmentation patterns in the spectra of these compounds are in accord with the formation of alkynes. The first step in the fragmentation of 1,2,3-selenadiazoles is the loss of N2 followed by extrusion of selenium and formation of the corresponding alkyne. The abundance of the alkynic ion in the mass spectrum appears to be dependent on the nature of the substituent group present in the selenadiazole. When the alkynic ion cannot be stabilized by the formation of a cation on the adjacent carbon atoms, the abundance of the alkynic ion decreases (10% in the parent compound and zero for 4-f-butyl-l,2,3-selenadiazole). On the basis of the mass spectral pattern it is possible to predict the yield of the alkynic compound formed through pyrolysis or photolysis of a given... 

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