TOF‐SIMS: Chemistry and the Formation of Positive Secondary Ions - mikee9265/SIMS-Wiki GitHub Wiki

The positive ion spectra one obtains with a TOF-SIMS instrument are similar in many ways to CID spectra (Pachuta and Cooks 1987), and have similarities to and differences from EI-MS (Spool 2004).

The spectra sport a variety of molecular and fragment ions. The molecular ions include the ions most often produced by EI, M^+., and in addition to this, the [M+1]⁺ protonated ion, the [M−1]⁺ de-protonated ion and sometimes even the [M−2]^+.. radical cation. There are many fragments detected with masses below that of the molecular ion, but the dominant ones have chemical significance. That is, they tend to be products of fragmentation that make chemical sense. They make sense from the point of view of kinetics, the ease with which the transformation that leads to the fragment occurs. They also make sense from the point of view of thermodynamics, the stability of the resulting fragments (both neutral and ionic). Many of the mechanisms established in the study of EI-MS (McLafferty 1993) explain the fragments found in TOF-SIMS spectra.

Sometimes, there are also ions present in the spectra at masses significantly greater than a compound’s molecular weight. Many of these are combinations of molecular ions (dimers, trimers, etc.), but there are also interesting additional products, the result of the combination of several molecules and the subsequent fragmentation of that larger molecule. The possibility of such reactions obviously depends on the amount of a compound on the sample. Bulk material will produce these larger fragments, where submonolayer levels clearly cannot. Thus chemical concentrations produce another matrix effect.

The figure below shows the TOF-SIMS spectrum for bulk stearic acid taken with an IonTof instrument using a 30 KeV Bi₃⁺ primary ion source. The molecular ions around the mass of stearic acid at the nominal mass of 284 amu are prominent. While the [M+1]⁺ ion is the largest of these at nominal mass 285 amu, the other possible molecular ions that are present in the spectrum include the [M−1]⁺ ion and the M^+. radical cation. The peaks at masses higher than the [M+1]⁺ ions are the [M+1]⁺ ions that contain ¹³C isotopes. The prominent [M+1]⁺ ion may be the result of heterogeneous bond cleavage in dimers and trimers or due to protonation, but the prominence of other odd electron species in the spectra also suggests the H atom extraction reaction shown in Equation [1]. Note that the highest occupied molecular orbital (HOMO) in a simple carboxylic acid containing molecule is the nonbonded electron pair on the carbonyl oxygen atom.

Because this is a bulk sample, interaction between stearic acid molecules at the surface is probable. In fact, most of the molecules in the sample are present as multimers, primarily dimers, bonded together via hydrogen bonds. This then is an ideal sample for which protonation could occur. It is thus a bit surprising that the [M+1]⁺ molecular ion is not more dominant within the molecular ion cluster of peaks.

The presence of the lower mass molecular ions M^+. and [M−1]⁺ could be due to an excess of vibrational energy in the sputtered protonated molecular ion leading to fragmentation and the loss of one or two H atoms. This hypothesis, however, is not supported by observations of relative ion intensities using different primary ions. The preservation of more molecular ions and those of larger molecules in the cluster induced spectra are believed to be partly due to the ability of these primary ions to produce cooler ions less likely to fragment due to excess internal energy. The energy of collision of cluster ions with the surface produces more cooperative motion, which gives leaving molecular ions more translational energy and presumably less internal or vibrational energy when compared with what is seen from atomic ion impacts. However, a comparison of the spectra from monoatomic and cluster ion-induced spectra show the M^+. and [M−1]⁺ keeping pace with the [M+1]⁺ ion intensity. In fact, the M^+. ion is relatively more intense in the cluster-induced spectra, as shown below. This observation supports the idea that these ions are the result of other ionization processes such as electron transfer and electron impact. The mechanism for the formation of the [M+1]⁺ is likely to be due to hydrogen extraction during collision of a M^+. with a neighboring molecule (Equation [1].

While it is true that the EI-MS stearic acid spectrum below has a much larger M^+. peak than its [M+1]⁺ peak, a result that is not surprising given the relative infrequency of molecule–molecule collisions in the gas phase, it is actually more striking that the [M−1]⁺ peak is completely absent from the EI spectrum. The much higher probability of collisions must be partly responsible for the presence of this species in the SIMS spectrum. This ion is in some sense the opposite of the M+1 ion. Where the M+1 ion may be the result of a radical cation snatching a H atom from a neighboring molecule, the M−1 ion is the result of a radical species snatching a H atom from the leaving radical cation.

Another peak that is intense in the SIMS spectrum but weak in the EI-MS spectrum is the [M−OH]⁺ peak at 267 amu (Equation [2]). The most propitious mechanism for the formation of this ion requires starting with the dimer. The 1,3 H transfer that would be needed in an isolated molecule is forbidden. Interestingly, in di-carboxylic acid molecules where the acids can hydrogen bond, the [M−H₂O]⁺ ion is intensely observed in EI-MS spectra. Thus the mechanism may be common with that seen in EI-MS, except that as noted above, bulk samples in the SIMS consist of multimers of the acid.

Equation [3] illustrates the McLafferty rearrangement (McLafferty 1993). Starting with the radical cation at the carbonyl, a H atom transfers from the chain to the carbonyl O via a six-membered ring transition state (the lowest energy configuration possible). The scission of the C-C bond closest to the carbonyl results in the loss of the fatty acid chain and the formation of a radical cation that is stabilized by conjugation with the carboxylic acid’s π system. The peak at 60 amu (the peak labeled (3)) is prominent in both EI mass spectra and in TOF-SIMS spectra taken with Bi₃⁺. The peak is present, but far less prominent in TOF-SIMS spectra taken with monoatomic projectiles (Spool 2004). In fact, the 60 amu fragment nearly keeps pace with the enhancement of the molecular ion in the small cluster-induced spectra. This is another indication, if needed, that this fragment is a direct descendant of the whole molecular ion.

Once the radical transfers to the chain, it can break a bond in the other direction, leaving a double bond on the ion while losing a neutral radical, as shown in Equation [4]. The resulting series of fragments start with the peak at mass 73 amu and proceed up in mass in 14 amu (CH₂) increments as shown in the figure. In the EI spectrum there are four major peaks in this series at 73, 129, 185, and 241 amu. This is a result of the McLafferty rearrangement moving the radical down the chain in even six-atom ring transition states, moving the radical four carbons down the chain each time. In the SIMS, the leaving ion has a lot more internal energy, and transition states with five or seven atoms are easily achieved, leading to more randomization in this fragmentation pattern as the radical is passed up and down the chain.

Just as the [M+1]⁺ molecular ion can lose H₂O (18 amu) to form the ion shown in Equation [2], the fragments that result from Equation [4] can lose H₂O to form the fragment series shown in Equation [5]. Again, this will be a unique series possible due to the hydrogen bonding taking place in the bulk acid surface. This series begins at 55 amu and proceeds at 14 amu intervals to shadow series [4].

Equation [6] shows one possible route to a curious set of three peaks found in the stearic acid spectrum and those of other fatty acid derivatives. The most intense of the three at 98 amu is 14 amu higher than the lowest mass peak in the series at 84 amu and 14 amu lower than the higher mass peak in the spectrum at 112 amu. The peaks are also found in the EI mass spectra. They are remarkable in the SIMS because they are odd electron ions. This in itself implies that the radical is stabilized in some fashion, and that means it must be conjugated with the carbonyl π system. The trio of peaks suggests ring structures, where the most intense ion has the most stable six-membered ring, and the other ions the less stable five and seven membered rings. The series is particularly prominent in the EI-MS spectrum of the dimethyl dicarboxylic ester shown below (“Mass Spectra of Derivatives of Dicarboxylic Acids” 2015).

The acylium ions (with an R-CO⁺ cationic end group), shown in Equations [2] and [5], can readily lose CO to form carbenium ions (R⁺), a reaction that is prominent in EI-MS (Gross 2004). From there both the shrinking of the resulting chain via loss of alkenes or dehydrogenation are both common fragmentation pathways, again common with EI-MS. The result is the series of peaks, mostly at low mass, previously dubbed the “hydrocarbon envelope”.

The esters of simple carboxylic acids produce in the TOF-SIMS ions that are both analogous to those found in the carboxylic acid spectra and the new one. The figure below shows TOF-SIMS spectra for four different straight chain carboxylic acid esters (the high mass region has been aligned to remove differences in position induced by differences in the long fatty acid chain length). The similarities and differences between these spectra and the spectra of the carboxylic acids on which these compounds are based are pretty much what might be expected based on what is seen in the EI-MS.

Source: Adapted from Spool (2004).

For all of these compounds, the molecular ion clusters are remarkably similar to each other and to those of the parent carboxylic acid. Again, the [M+1]⁺ ion is the most intense in each cluster, but the [M−1]⁺ and M⁺. are present in relative amounts similar to what was seen for the carboxylic acid. Upon reflection, this is a remarkable observation. Heterolytic cleavage leading to protonation should surely be more likely in a bulk carboxylic acid’s spectrum than in an ester spectrum. This is further evidence that at least in the TOF-SIMS spectra produced from monoatomic and small cluster primary ions, the protonation process does not dominate ion formation, even for molecular ions. The intensity of the molecular ion cluster relative to the rest of the spectrum decreases with increasing ester chain length, consistent with what is seen in EI-MS.

The odd electron ions resulting from the McLafferty rearrangement with the main chain and leading directly to olefin formation as shown in Equation [3] above are similarly present in the ester spectra, bearing the added weight of the ester chains. Similarly, the ion series, originating in the processes shown in Equations [4] and [5] in the same figure but bearing the added weight of intact ester chains, are also present in the ester spectra.

Molecules with ester chains with two or more carbons can undergo a McLafferty rearrangement that places the radical onto the ester chain. Equation [7] shows how this can lead to ions in the molecular ion cluster for the parent carboxylic acid. The rearrangement is much less likely and cannot lead to the same result for the methyl ester. Equation [8] shows a mechanism for directly producing the even electron ion without the need for further H atom extraction. For molecules with ester chains three or more carbons long, Equations [7] and [8] become major pathways for ester ion fragmentation. Esters with very long chains attached to the carbonyl and the oxygen atom of the ester group may produce characteristic peaks for the parent carboxylic acid but no molecular ion. Again, this behavior is similar to what is seen in EI-MS.

In the absence of hydrogen bonding to facilitate fragmentation leading to formation of the acylium ion, the ion is much less likely to be produced by the mechanism shown above in Equation [2]. For the methyl ester, the process is almost completely inhibited. The mechanism shown in Equation [9] provides a path to the acylium ion. The absence of hydrogen bonding, though, leaves the acylium ion a less common fragment in the ester spectra.

The carbenium ion representing the chain attached to the oxygen is prominent in the ester spectra shown below. The length of the chain is easily seen upon examination of the lower mass regions of these spectra. Within the series of esters, a comparison of the spectra shows that this peak is more intense for longer chain lengths. Equation [10] shows how this ion can form. Unexpectedly, the use of Bi₃⁺ as the primary ion instead of Ga⁺ decreases the relative intensities of these ions relative to the hydrocarbon envelope (see figure below)). There is still enhancement of the intensity of the carbenium ion associated with the ester chain, but the peak is no longer quite so obvious.

With the addition of N to a molecule, the mix of peaks in the TOF-SIMS spectrum with odd and even nominal mass no longer have the same meaning to the analyst, as discussed previously. Ions with an odd number of N atoms that have even mass are even electron ions. Ions with an odd number of N atoms, but an odd nominal mass, are actually odd electron ions. Simple amides have a single N atom, so any peaks with the amide piece of the molecule now obey these reversed rules. On the other hand, the hydrocarbon envelope, sourced from the portion of the molecule from which the amide portion of the molecule has been removed by fragmentation, looks much the same as it always has.

An amide is, of course, much like a carboxylic acid except with an NH₂ where the OH used to be. In contrast to the carboxylic acid, however, the amide does not readily lose its NH₂ to form the acylium ion, even when the molecule is hydrogen bonded to its neighbors. In other ways, however, there is a good deal of similarity to the spectra. Again, most of the ionization is expected to begin at the amide functional group where the highest occupied molecular orbital (HOMO) can be found (the molecular orbital from which it will be easiest to lose an electron).

The main molecular ion is the [M+1]⁺, now an even electron ion with an even nominal mass at 284 amu (above), but there are others present in the cluster as well. The odd electron ion M^+. of stearamide is relatively weak.

The McLafferty rearrangement is just as important to the formation of the stearamide spectrum. The parallel fragmentation process to that, shown in Equation [3] above for stearic acid, produces the prominent odd electron ion at 59 amu. Here in particular, the ion could be mistaken for an even electron ion fragment, but exact mass determination shows it to contain a single N atom and to have the formula C₂H₅NO. The series that is comparable to that produced by the process shown in Equation [4] above dominates the middle portion of the stearamide spectrum. The series is also more closely akin to that found in EI-MS with the most intense peaks in the spectrum progressing down the chain in the six-membered ring transition states producing the most intense ions in the series at 72, 128, 184, and 240 amu. Again, because formation of the acylium ion is not favorable for the amide group, the series of ions comparable to that produced in Equation [5] for stearic acid is absent from the stearamide spectrum.

There is one other ion in the spectrum that requires explanation, and its presence highlights one of the pitfalls in the interpretation of the TOF-SIMS spectra. The peak labeled [9] in the stearamide spectrum at 256 amu has an exact mass that indicates that it has two carbon atoms and four hydrogen atoms (C₂H₄) less than the molecular ion [M+1]⁺ at 284 amu. It is not a fragment, but rather a homologue. It is the molecular ion for palmitamide, the fatty amide with a two carbon shorter chain. One would not find such a feature in an EI-MS spectrum, because the GC column would separate it from stearamide, and the spectrum obtained is pretty well guaranteed to be that of a pure compound. In other samples, impurities that tend to surface segregate can come to dominate spectra even at very low concentrations. The SIMS analyst must proceed with caution.

Ketones are at once a simpler carbonyl containing functionality, but with their own individual quirks in a mass spectrometer. The carbonyl group itself has no significant acidity or basicity, but it is reactive under the right circumstances, and can be readily ionized by electron loss. With two pendant alkyl groups, the ketone radical cation can react with either side, and then the radical can cross from one alkyl group to the other.

The TOF-SIMS spectrum of bulk stearone shown above is that of a symmetric long chain ketone with 17 carbons on each side of the carbonyl. The molecular ion cluster ratios for stearone show more relative intensity for the M^+. radical cation than in stearamide, but otherwise at the low end of the range shown in that figure. It is worth noting that the H extraction available to stearone in the TOF-SIMS likely stabilizes the molecular ion, leaving an intense peak. Here the TOF-SIMS has the advantage over EI-MS in which the molecular ion for stearone is quite weak. Comparable to what is found in the EI-MS (not shown), there is a strong peak for the acylium ion that results from loss of one of the pendant alkyl groups. A possible mechanism for such an ion’s formation is shown below. The neutral alkyl radical that forms is more stable and, therefore, more likely to form than a hydroxyl, oxy, or an amine radical, so this process can take place in a unimolecular fragmentation pathway that leaves an ion containing an alkyl group, a process that in acids, esters, or amides can only result in loss of the alkyl group.

Other reactions can proceed much as has been described previously. The even electron ion that is formed in a process comparable to that shown for a carboxylic acid in Equation [3] occurs for the ketone as well, but now that ion contains one of the long alkyl chains and, therefore, still remains with a fairly high mass (species 3 in the stearone spectrum). Olefin formation after the McLafferty rearrangement and randomization of the radical up and down the chain leads to the series of ions labeled (4). Note that the radical can potentially hop from one alkyl chain across the carbonyl to the other via a McLafferty rearrangement, but olefin loss will still produce ions with the same mass as in series (4).

If a carboxylic acid should be remarkable for its ability to donate a proton relative to many other molecules, an amine’s basicity makes it an optimum acceptor. If protonation is a major path for ionization of anything, it should be so for simple amines. Indeed the [M+1]⁺ ion does very much dominate the high mass range of the TOF-SIMS spectrum of the primary n-tetradecyl amine as shown below. The secondary amine spectrum shown in below that has a similarly intense [M+1]⁺ molecular ion.

The HOMO of a simple amine is the nonbonding electron pair on N. If any of the ionization occurring for amines, it is via electron loss, and the nonbonding orbital is the one most likely to lose an electron. It turns out that it is easy to rationalize the major features of the SIMS spectrum by proposing mechanisms beginning with the odd electron radical cation molecular ion. Without a π system, however, there is no way to stabilize a radical, and so no prominent odd electron ions are present in amine molecule spectra. Nonetheless, the chemical specificity of the fragmentation found in the simple amines’ spectra is again compelling evidence for a significant role being played by electron loss in the ionization of these molecules.

The McLafferty rearrangement followed by radical movement up and down the chains ending in radical loss and olefin formation comparable to the process shown in Equation [2] below likely produces many of the fragment ions that dominate the amine spectra. The simple elimination reaction shown in Equation [1] leads to the ions labeled (10) in the amine spectra. For the primary amine, the mass and the intensity of the ion are quite low, but for the secondary amine, the higher mass and intensity make it a prominent ion in the spectrum. The McLafferty rearrangement shown in Equation [2] below can lead to the olefins already discussed earlier, but can also lead to a second McLafferty across the alkyl chains in the secondary amine, leading to ions (11) and the shortening of both alkyl chains. Presumably if the elimination occurs in the other direction leading again to a radical cation fragment, the unstabilized radical either further rearranges to fragment further, or manages, by a collision, to extract an H atom and become an even electron cation.

The figure below shows the TOF-SIMS spectrum of bulk tri-benzyl amine. This tertiary amine has its N separated from the aromatic rings by saturated carbons, so that the compound is still a strong base. Nonetheless, the [M+1]⁺ ion is not the most intense peak within the molecular ion cluster. Instead, that distinction goes to the even electron [M−1]⁺ ion, which is particularly stable because in that ion the N lone pair ends up being conjugated with one of the rings’ π systems. Whether a H radical can dissociate from the molecule in a unimolecular reaction, or if a collision is required to extract the H atom is unclear. Within the molecular ion cluster, the M^+. radical cation is more intense than the [M+1]⁺ ion, likely because ionization can also occur via loss of an electron from one of the rings. The peak at 210 amu (M-77) likely forms by a mechanism akin to that shown in Equation [1] above, which in this case will eject a neutral C₆H₅^. radical.

A saturated hydrocarbon is a hard molecule to ionize. There is no place to park an added proton, so the M^+. molecular ion is the easiest to produce with loss of an electron from a C-H or C-C bond. Whichever one it is, that bond will now be substantially weakened. This is unlikely to be a stable ion, able to survive collisions with the surface or with fellow travelers to the vacuum.

Instead of M^+. or even [M−1]⁺, the figure below shows that in the TOF-SIMS spectrum of n-nonadecane, taken with a cold stage, it is the [M−2]^+. radical cation that is the most intense of the molecular ions. This is a more stable ion. As noted above, with only one electron gone, there will be a weak one electron bond in the ion. With an electron and a hydrogen atom gone, one carbon can reorganize itself into an sp² configuration, placing the lone electron into a p orbital. With two hydrogen atoms gone along with the single electron, the lone electron is somewhat stabilized by living in a π bond. The intensity of the peak is weak. The mechanism for the formation of the ion is unclear (although a unimolecular dissociation from an initially strongly vibrationally excited molecular ion is a strong possibility), and whether a collision is required is also uncertain.

The rest of the n-nonadecane spectrum is unremarkable, with the hydrocarbon envelope in evidence but little else. As has been noted previously, branching and molecular weight will affect the relative intensities of the peaks in the hydrocarbon envelope in ways that can be rationalized (Galuska 1997). In these respects, the TOF-SIMS spectra are similar to what is found in EI-MS spectra of saturated hydrocarbons.

The introduction of unsaturation into the hydrocarbon makes ionization easier and stabilization of the odd electron possible. The figure below shows a TOF-SIMS spectrum of n-decyl benzene taken using a cold stage, which has, as its primary molecular ion, the M^+. radical cation. Also present at lower intensities is the even electron [M+1]⁺ molecular ion and the ion seen in the saturated hydrocarbon spectrum, the [M−2]^+. radical cation.

Peaks at 91 and 105 amu are the result of scission of the chain close to the phenyl group. The figure below shows a possible mechanism for the formation of the 91 amu peak. The resulting ion can rearrange itself into the aromatic tropylium ion. Studies of alkyl benzenes in the EI-MS with labeled samples suggest, however, that the mechanism for tropylium ion formation, and also for formation of the 105 amu ion with one more carbon are more complicated than the equation below implies. In any case, the processes at work in the bombardment of this sample are similarly at work in other cases of molecules with phenyl groups, for example, the tribenzyl amine whose spectrum was discussed previously.

One other odd feature in the spectrum shown above is the presence of the [M+CH]⁺ ion. This observation is not an isolated one. Spectra of many bulk aromatic materials produce this peak. The ion is likely a tropylium ion with an attached decyl chain. The ion must be the result of the reaction of a molecular radical cation with neighboring phenyl group molecules in which first the dimer is formed, and then splits unevenly.

At the other extreme of the range of hydrocarbons are completely unsaturated molecules. An example of spectra of such a molecule is shown below. The tetra-phenyl butadiene molecule naturally produces a relatively stable M^+. radical cation. In fact, the entire TOF-SIMS spectrum quite closely resembles the EI-MS spectrum, an indication that most of the processes involved in fragmentation of this molecule are primarily unimolecular.

The TOF-SIMS positive ion spectrum for glyceryl mono-stearate, chosen as an example of the multifunctional molecule, is shown below, as taken at −150°C using a cold stage. This compound is an example of an important series of compounds studied by TOF-SIMS that are lipid-based. It turns out that the molecular ion cluster dominated by the [M+1]⁺ is very weak at room temperature and higher temperatures, but cooled, the bulk material begins to produce a substantial molecular ion signal. The fragment signals are not suppressed at low temperatures, so it does not appear that the molecule is less likely to fragment when cold. Instead, it appears that neutralization of the molecular ion is reduced at lower temperatures.

The more dominant high mass ion is a result of a McLafferty rearrangement followed by loss of OH (possibly assisted by H bonding in the bulk solid). The process is shown below. Triglycerides, molecules with fatty acids attached to all three of the glycerol’s hydroxyl groups, similarly produce TOF-SIMS spectra that lack the molecular ion at room temperature, and are dominated by the olefin with one ester removed.

Without a library spectrum, running the analysis at room temperature, and not knowing that this compound was present at the sample surface, would an analyst be likely to definitively identify it? Neither the extensive library nor the interpretative tools available to other mass spectroscopists are at this time available to the TOF-SIMS analyst. Without a molecular ion to interrogate, even MS/MS would fail the analyst. The state of the art is still developing.