Abstract: The fragmentation algorithm [M]+.n-alkanes C1-C60 and n-perfluoroalkanes C1-C20 was established by analysis of spectra from NIST libraries. The alkyl ions of [CnH2n + 1]+ n-alkanes were obtained as a result of two series that arise during primary separations from [M]+.methyl and ethyl radicals that open up a methylene chain, and subsequent emissions of neutral ethylene molecules. This fragmentation algorithm is confirmed by examples of mass spectra emulation of deuteroalkanes. A series of olefinic [CnH2n]+ and alkenyl [CnH2n-1]+ n-alkane ions are formed from [M-H]+ and [M -2H]+ at detachment of methyl and ethyl radicals and subsequent emissions of ethylene molecules.
In spectra of n-perfluoroalkanes, a series of perfluoroalkyl ions [CnF2n +1]+ occurs as a result of initial detachment of fluorine atom and subsequent emissions of difluorocarbene. The less intense series of perfluoroalkenyl ions [CnF2n-2]+ peaks are the result of three successive detachments of fluorine atom M-57 and subsequent emissions of difluorocarbene: M-107, M-157, M-207 ... The primary alkenyl fragmentation process of n-perfluoroalkanes is different from primary process of alkyl fragmentation with two additional detachments of fluorine atom, which require additional time.
By comparing the spectra of n-octane and n-perfluorooctane recorded via the magnetic mass spectrometer and the ion trap mass spectrometer (Polaris Q), it was confirmed that the ratio of peak intensities of competing alkyl and alkenyl fragmentation depends on ion residence time in the separation zone.

Keywords: mass spectrometry, n-alkanes, n-perfluoroalkanes, n-deuteroalkanes, fragmentation algorithms, spectrum emulation, fragmentation competition.


Over the past 50-60 years the mysterious and not decrypted algorithms of fragmentation due to ionisation of n-alkanes and n-perfluoroalkanes by electrons have moved from the terra incognita category to the similis est category (it’s not fashionable). To restore the lost status of this problem, a real literature review and analysis of mass spectra of n-alkanes and n-perfluoroalkanes presented in the NIST libraries were performed.

The mass spectra of n-alkanes were described, on the one hand, as a simplest mass spectra of heavy hydrocarbons [1], and on the other, as possibly the most complex hydrocarbons [2-3].

A theoretical analysis of molecular ions decay for normal hydrocarbons [4] postulated that the resulting fragment ions are a result of successive decay events in which each ion decays to produce an ion with the number of hydrocarbon atoms with at least half of the original number of atoms.

In a number of papers, the fragmentation of n-alkanes was studied using the technique of metastable peaks, notably along with primary separation of ·C2H5, ·C3H7 and ·C4H9 radicals; the emission of molecules: H2, CH4, C2H2, C2H4, C3H6 was also considered [5-7]. The base publication, which made it possible to determine the isotopic composition of formed ions and to be able to evaluate the results of emulation of deuteroalkanes spectra along one or another fragmentation path, was the paper [3]. However, none of n-alkane decay algorithms was recognized as adequate when conformance inspection between existing experimental isotopic distribution of formed ions in the spectra of labeled alkanes [3] and the distributions obtained as a result of proposed fragmentation paths [8-11,12,13].

On page 47 of review [14], summarizing the previous publications, their authors conclude: “It can be assumed with sufficient reliability that decay of normal paraffin hydrocarbon molecules during electron impact is characterized by an initial non-selective detachment of C-C bonds with subsequent stagewise decomposition of initially formed products”. Based on this conclusion, presented in Fig. 1, the mass spectra of n-alkane C60 and n-perfluoroalkane C20, illustrating methylene and difluoromethylene “glide paths”, are “mirages” that hide a complex real mechanism of decay.


Figure 1. Mass spectra of n-C60H122 and n-C20F42 (from NIST libraries).

However, such harmonious, regular, smoothly increasing spectra permits to suppose that it are based on a simple and universal fragmentation algorithm. Given the “methylene” nature of alkanes and perfluoroalkanes fragmentation, the first question has always been the possibility of methylene (as well as difluorocarbene) separation from ions formed after chain opening, when the H, F atoms, methyl or trifluoromethyl radicals are detached from the molecular cation radicals.

In monograph [15], the author concludes: «There are very weak peaks of metastable ions in mass spectra of alkanes, which correspond to process of CH2 formation. However, the contribution of such processes to fragmentation is negligible, given the high enthalpy of formation of EO CH2 equal 90 kcal/mol. The detachment of CH2 is observed only for very simple molecules with limited potential fragmentation.

100% CH2 = CH2+. +.CH2 1.8%

A much more intensive release of difluorocarbene occurs, which is 43 kcal/mol more stable than methylene (Atlas, 1970; Budzikiewicz, 1979)».

On page 146 of review [14] the authors report: «In spectra of perfluoroparaffins, between two fairly intense peaks the peaks of metastable transitions are observed, which corresponds to detachment of the CF2 group».

The relative probability of fragmentation paths for alkanes and perfluoroalkanes: with the detachment of H and F atoms, CH2 and CF2 carbenes, alkyl and perfluoroalkyl radicals, must be estimated taking into account both the standard enthalpies of formation of detached fragments (see Table 1) [15,16], and the magnitude of their masses. When choosing a participant in fragmentation processes from applicants with admissible education enthalpies, a priority remains for a fragment with a minimum mass value.

Table 1. Enthalpy of formation ΔHf0 [15*, 16P].

Enthalpy of formation ΔHf0 (g), 298K (kkal/mol)

H 52,1*

F 19,0*

СH2 90*

CF2 -43,2*

·CH3 34,8*

·CF3 -115*

·C2H5 26,5*

·C2F5 -217*

C2H4 12,5 (ref.)

C2F4 -152P

C3H6 4,88 (ref.)

C3F6 -259P

n-·C3H7 21,0*

n-·C3F7 -313*

n-·C4H9 15,4*

СH4 - 17,89 (ref.)

CF4 -218P

A most energy-consumption way of alkanes and perfluoroalkanes fragmentation (except for CH2 detachment) (see Table 1.) is the emission of H and F atoms with minimal masses, with detachment of which fragmentation of both lower and higher homologs begins.

The detachment of ·H (52.1 kcal/mol), methyl .CH3 (34.8 kcal/mol) and ethyl radicals .C2H5 (26.5 kcal/mol) are three main primary processes of decay the M·+ homologs of C4-C60 n-alkanes, which open up the methylene chain, which is further fragmented by successive detachments of ethylene molecules (12.5 kcal/mol). The presented n-alkane fragmentation algorithm was successfully confirmed by emulation of spectra of deuterosubstituted analogues [3].

In spectra of perfluoroalkanes, in addition to process of atom detachment of·F atoms (19 kcal/mol), the second really occurring process should be considered (for all possible participants in fragmentation CF2 (-43.2), ·CF3 (-115), C2F4 (-152) , ·C2F5 (-217)) only as sequential detachment of difluorocarbene with minimum weight. This perfluoroalkane fragmentation algorithm is described in detail in corresponding section of this publication.

Despite the energy utility, the synchronous detachments of neutral CH4 and CF4 molecules are unlikely in comparison with actually occurring sequential detachments of ·H and ·CH3, as well as the detachments of 2·F and CF2.

Fragmentation of n-alkanes

The fragmentation of n-alkanes, as well as of alkyl halides, depends on molecular weight [17]. As the mass of homologues of n-alkanes increase, the vibrational excitation M·+ decreases. The peaks of basic ions: m/z 16-C1, 28-C2, 29-C3, 43- (C4-C5),! 57-C6 ,! 43 (C7-C10), 57 (C11-C60) change, and the growth of weak peaks of alkyl ions [CnH2n + 1]+, the intensities of which in C60 spectrum increase to 87%+ [C5H11] m/z 71, 69%+ [C6H13 ] 85 and 34%+ [С7H15] 99 (Fig. 2).

The intensity of most intensive peak of alkenyl [CnH2n-1]+ of ion +[C3H5] m/z 41, equal to 70% in spectrum of C6, decreases to 20% in C21 and to 11% in C60, and the intensities of weak alkenyl peaks increase in spectrum of C60 to 44 % +7H13] m/z 97 and to 27% +8H15] m/z 111 (Fig. 2). The peak of +[C7H13] (m/z 97) becomes the most intense peak of alkenyl fragmentation [CnH2n-1], and ion +[C3H5] becomes its fragment ion.

In compared with increase in peak intensities of alkyl and alkenyl ions occurring with an increase in molecular weight of homologs, the peak increase of olefin ions [CnH2n]+ is minimal. Perhaps this is due to the fact that olefin ions are an “intermediate link” between alkyl and more stable alkenyl ions.

Figure 2. Dependences of Irel (in %) on its molecular weight for ion peaks of n-alkanes homologues.

In contrast to spectra of C1-C8, in which there are two zones: the zone of increase in peak intensities and the zone of its decline; the spectra of C12-C60 have the plateau, after which there is a sharp increase in intensity of fragment peaks. With increase in molecular weight of homologs, the plateau of spectrum increases. If this plateau in spectrum includes a large number of weak peaks (the intensities of which gradually increase as their mass decreases), then the sharp fragmentation section will contain no more than 4 peaks with a sharply increasing intensity. A sharp increase in intensity of alkyl peaks begins when the ratio of formed ions masses to the mass of detached ethylene will reach 71: 28 = 2,5: 1 and 85: 28 = 3,0: 1, respectively.

In spectra of C9-C60, the almost unchanged position of transition the plateau zone to the sharp fragmentation zone corresponds to ions +[C7H15] m/z 99 and +[C8H17] m/z 113, whose masses are approximately twice as large the masses of basic ions m/z 43 and m/z 57.

First two homologues of n-alkanes C1 and C2 are fragmented with alternating formation of corresponding cations and radical cations by successive detachment of four and six hydrogen atoms, respectively. The detachment of hydrogen atoms from [M]·+ is a primary process of fragmentation of all n-alkanes homologues. The base ion [C2H4]+ in ethane spectrum is formed by detachment of two hydrogen atoms, while decomposition of C2 (M/2) leads to +[CH3] ion whose peak intensity does not exceed 4.4%. C3 is fragmented by successive detachment of eight hydrogen atoms. Its base ion +[C2H5] is the result of methyl radical release. The mass ratio +[C2H5] and .CH3 during decay of C3 29: 15 = 1.93: 1 allows us to conclude that, in comparison with CH3, base ion receives almost twice as large of energy. The detachment of methyl radical is clearly visible in C2-C7 spectra, in which the molecular mass is minimal, and excitation energy (in comparison with C8-C60 homologs) is maximum. With rising in its molecular weight and decreasing in vibrational excitation of M+, the detachment of methyl radical as before is more energy-consumption (by about 8 kcal/mol) compared to detachment for ethyl radical, but its peak intensity decreases.

In spectra of C8-C60, the primary detachment of ethyl radical is visible, but the detachment of methyl radical no matter somewhat happens. However, this is not so, the primary detachment of methyl radical occurs in all homologues, except C1, only M-CH3 peak in C8-C60 spectra acquires a trace intensity. In spectra of C18, C22, C25, C26 and C35 (NIST Library), the peaks +[M-CH3] are clearly visible.

The detachments of methyl and ethyl radicals are two main primary processes of alkyl fragmentation of n-alkanes. Further fragmentation is a sequential detachment of neutral ethylene molecules, with formation of methyl and ethyl series of ions. The first ethylene release appears to occur during fragmentation of C4 homolog. In C4, the detachment of methyl radical leads to base ion +[C3H7], and the detachment of ethyl radical (decomposition M/2) to ion +[C2H5] equal to 43%. The peak +[CH3] equal to 6% in spectrum of C4 arises either as a result of detachment from M·+ radical ·C3H7 (m/z 43, enthalpy 21.0 kcal/mol), or by detachment of ethylene molecule (m/z 28, enthalpy 12,5 kcal/mol) from the base ion +[C3H7]. The release of ethylene with a mass of 28 is more likely, since it requires less energy compared to the detachment of ·C3H7 (with mass of 43).

The comparison of alkyl peaks in mass spectrum of n-octane with the mass numbers of its spectrum emulated by algorithm of parallel primary detachments of ·CH3 and ·C2H5, with subsequent sequential emissions of ethylene (see Table 2) confirms its complete coincidence.

Table 2. The alkyl [CnH2n + 1] ions in mass spectrum of n-octane C8H18.

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH[NIST Library]

15 1%

29 27%

43 100%

57 М/2 33%

71 20%

85 26%

99 0,1%

114 6% М

The mass numbers for spectrum of n-octane emulated at primary ·CHdetachment


















The mass numbers for spectrum of n-octane emulated at primary ·C2Hdetachment















The mass numbers for spectrum of n-octane emulated at primary CH3 and ·C2Hdetachment









In spectra of n-alkanes homologues with an even number of carbon atoms, there is M/2 ion, when both the detached radical and the observed formed ion have the same mass. The presented fragmentation algorithm leads to formation of alkyl ions, including M/2 ion. However, in homologues C6 and C8 direct decomposition of M/2 is also possible (with detachment of radicals larger than ethyl (Fig. 2). In spectra of C4, C6 and C8, the peak intensities +[M/2] are 43%, 81%, and 33%, respectively.

With further increase in molecular mass of a homologue, with increase in masses of formed ion and radical, the M/2 peak moves from the zone of increase in spectrum intensities to the plateau zone with minimal intensities. The maximum intensity of 81%, close to the intensity for base ion, peak M/2 has only in spectrum of C6. Since the excess energy M is divided between the ion and the radical in half, the peak of M/2 ion cannot become the base one. For this reason, it is precisely in C6 spectrum that a certain “dumping” of base ion +[C3H7]” 43: 43 = 1: 1 occurs (Fig. 2). Instead of ion +[C3H7], the base ion in C6 temporarily becomes the ion [C4H9]+ 57: 29 = 1.96: 1, which is formed upon detachment of ethyl radical, which has a mass less than the mass of ion. In C6, the formation of M/2 ion 81% is accompanied by its strong hydrogen fragmentation with detachment of H atom and formation of olefin ion with m/z 42 41%, as well as the emission of second hydrogen atoms with formation of allylic ion [C3H5]+ 70% (Fig. 2 )

In Cspectra, the intensity of M/2 ion with m/z 57 decreases to 33% and remains the same until C14, and [C3H7]+ ion, which is not formed by radical detachment ·С5H11 m/z 71 43 : 71 = 1: 1,65, but by release of methyl radical and two ethylene molecules. The final ethylene detachment leads to formation of base ion 43: 28 = 1.54: 1.

Sequential detachment of ethylene molecules is a more economical and more efficient process than detachment of the corresponding alkyl radicals with increasing masses. In case of ethylene emissions, the excitation energy is divided between the ion with a decreasing mass and ethylene with a constant mass that is more favorable for ion being formed than if it was divided between radical with an increasing mass and ion with a decreasing mass. The ion arising from detachment of ethylene receives a large fractio

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