Mass spectrometry of trialkylsilyl and acyl derivatives of 2′-deoxynucleosides

The electron impact mass spectra of monosilyl and mixed acyl-silyl derivatives of 2′-deoxynucleosides are described in detail. (Silyl = tert-butyldimethylsilyl, cyclo-tetramethylene-isopropylsilyl, or cyclo-tetramethylene-tert-butylsilyl; acyl = acetyl or trifluoroacetyl.) The interpretation of the fragmentation pathways was aided by metastable ion decomposition studies, precise mass and deuterium labelling measurements. Mass spectrally, the acyl substituents are mostly ‘passive’ and have (with possibly one exception) little fragmentation directing capability. In contrast, the silyl groups have powerful fragmentation directing properties. Elimination of the bulky alkyl radical R^˙ (tert-butyl or isopropyl) from the molecular ion produces the siliconium ion, [M–R]⁺, which is the precursor for most of the other prominent ions in the spectra. These arise from ‘siliconium ion rearrangements’ resulting from the interaction of the positively charged siliconium ion centre with the electron dense regions (i.e. oxygens) in the molecule, to form cyclic silyloxonium ions which subsequently decompose. Since the interacting oxygen and silicon must be sterically accessible, the fragment ion types and their abundances are very dependent upon structure. Consequently, [M–R]⁺ ions formed from 3′- or 5′-O-silyl groups give rise to different sets of daughter ions which, for the most part, are not found, or have very low abundances, in the mass spectra of underivatized or trimethylsilylated nucleosides. Detailed information on sugar and base moieties and isomeric substitution is readily obtained.     

Mass spectra of sterically crowded trialkylsilyl derivatives of nucleosides

The electron impact mass spectra of tert-butyldimethylsilyl-, cyclo-tetramethylene-tert-butylsilyl and cyclo-tetramethylene-isopropylsilyl- ether derivatives of ribo- and 2′-deoxyribonucleosides are described in detail. The interpretation of fragmentation pathways of full and mixed derivatives was aided by metastable ion decomposition studies, precise mass and deuterium labelling measurements, and spectra of mixed derivatives containing the ‘passive’ (in these spectra) trimethylsilyl group. The sterically crowded silyl groups have a powerful fragmentation directing effect. Elimination of a bulky radical, R˙ (tert-butyl or isopropyl), from the molecular ion produces the siliconium ion [M? R]⁺, which is the precursor for most of the other prominent ions in the spectra. These arise from ‘siliconium ion rearrangements’ resulting from the interaction of the positively charged siliconium ion center with electron dense regions (i.e. oxygens) in the molecule, to form cyclic silyloxonium ions which subsequently decompose. Since the interacting oxygen and silicon must be sterically accessible, the fragment ion types and their abundances are very dependent upon structure. Consequently, [M? R]⁺ ions formed from 2′, 3′ or 5′-O-silyl groups give rise to different sets of daughter ions which, for the most part, are not found, or have very low abundances, in the mass spectra of underivatized or trimethylsilylated nucleosides. Detailed information on sugar and base moieties and isomeric substitution is readily obtained.     

The Remarkable Effect of the Manganese Ion with Dioxygen on the Stability of π‐Conjugated Radical Cations

In this paper, nanosecond laser flash photolysis has been used to investigate the influence of metal ions on the kinetics of radical cations of a range of carotenoids (astaxanthin (ASTA), canthaxanthin (CAN), and β‐carotene (β‐CAR)) and various electron donors (1,4‐diphenyl‐1,3‐butadiene (14DPB), 1,6‐diphenyl‐1,3,5‐hexatriene (16DPH), 4‐methoxy‐trans‐stilbene (4 MeOSt), and trans‐stilbene (trans‐St)) in benzonitrile. Radical cations have been generated by means of photosensitized electron‐transfer (ET) using 1,4‐dicyanonaphthalene (14DCN) and biphenyl (BP). The kinetic decay of CAR ^{. +} shows a strong dependence on the identity of the examined metal ion. For example, whereas NaClO₄ has a weak effect on the kinetics of CAR ^{. +}, Ni(ClO₄)₂ causes a strong retardation of the decay of CAR ^{. +}. It is also interesting to note that Mn²⁺, which is a biologically relevant metal ion, shows the strongest effect of all the investigated metal ions (e.g., in the presence of Mn²⁺ ions, the half‐life (t_1/2) of CAN ^{. +} (t_1/2>90 ms) is more than three orders of magnitude higher than in the absence of the metal ions (t_1/2≈16 μs)). Furthermore, the influence of metal‐ion and oxygen concentrations on the kinetics of CAR ^{. +} reveals their pronounced effect on the kinetic decay of CAR ^{. +}. However, these remarkable effects are greatly diminished if either oxygen or metal ions are removed from the investigated solutions. Therefore, it can be concluded that oxygen and metal ions interact cooperatively to induce the observed substantial effects on the stabilities of CAR ^{. +}. These results are the first direct observation of the major role of oxygen in the stabilization of radical cations, and they support the earlier mechanism proposed by Astruc et al. for the role of oxygen in the inhibition of cage reactions. On the basis of these results, the factors that affect the stability of radical cations are discussed and the mechanism that shows the role of oxygen and metal ions in the enhancement of radical‐cation stability is described.     

Identification of esters by collisional charge inversion of their enolate ions

The collisional charge inversion and neutralization-reionization (^?NR) mass spectra of the enolate ions of m/z 115 derived from the four butyl acetates, the two propyl propionates, ethyl butyrate, ethyl isobutyrate, methyl valerate, methyl 2-methylbutyrate and methyl 3-methylbutyrate were recorded. The major primary fragmentation reactions of the unstable carbenium ion formed by charge inversion involve elimination of an alkoxy radical to form a ketene or alkylketene molecular ion and formation of an alkyl ion consisting of the R¹ group of RCOOR¹. A minor fragmentation reaction involves elimination of an alkyl radical by cleavage of a C? C bond α to the ether oxygen. The alkylketene ions fragment by β-cleavage eliminating an alkyl radical to form an olefinic acylium ion. In most cases the charge inversion mass spectra of the enolate ions allow identification of the ester.     

Influence of Cu(II) Ions on the Mechanism of the Ring Transformation of S‐(2‐Oxotetrahydrofuran‐3‐yl)‐N‐(4‐methoxyphenyl)isothiouronium Bromide

The effect of additional Cu(II) ions on the rate of transformation of S‐(2‐oxotetrahydrofuran‐3‐yl)‐N‐(4‐methoxyphenyl)isothiouronium bromide ( 1 ) into 5‐(2‐hydroxyethyl)‐2‐[(4‐methoxyphenyl)imino]‐1,3‐thiazolidin‐4‐one ( 2 ) has been studied in aqueous buffer solutions. The reaction acceleration in acetate buffers is caused by the formation of a relatively weakly bonded complex (K_c = 600 L·mol^?1) of substrate with copper(II) acetate in which the Cu(II) ion acts as a Lewis acid coordinating the carbonyl oxygen and facilitating the intramolecular attack, leading to the formation of intermediate T^±. The formation of the complex of copper(II) acetate with free isothiourea in the fast preequilibrium (K_c) is followed by the rate‐limiting transformation (k_Cu) of this complex. At the high concentrations of the acetate anions, the reaction is retarded by the competitive reaction of these ions with copper(II) acetate to give an unreactive complex [Cu(OAc)₄]^2?_. The influence of Cu(II) ions on the stability of reaction intermediates and the leaving group ability of the alkoxide‐leaving group compared to the Cu(II)‐uncatalyzed reaction is also discussed.     

The mass spectrometry of volatile derivatives—II: N-alkyl trifluoracetamides

Under electron-impact, N-alkyl trifluoracetamides exhibit peaks due to [CF₃]⁺ and [M ? CF₃]⁺. Ions corresponding to [COCF₃]⁺ are absent. The base peak in many straight chain derivatives occurs at m/e 126 due to alkyl radical loss from the molecular ion; the mass of this ion rising to m/e 140 in the α-substituted N-sec-butyltrifluoracetamide and to m/e 154 in the tert-butyl derivative. High resolution measurements on a number of peaks indicate that they originate by loss of HF from other fragment ions.     

A mass spectrometry/mass spectrometry investigation of the nature of [C10H10]+˙, [C9H7]+ and [C10H8]+˙ gas phase ions

Additional evidence for the rearrangement of the 1- and 3-phenylcyclobutene radical cations, their corresponding ring-opened 1,3-butadiene ions and 1,2-dihydronaphthalene radical cations to methylindenetype ions has been obtained for the decomposing ions by mass analysed ion kinetic energy spectroscopy (MIKES). The nature of the [C₉H₇]⁺ and [C₁₀H₈]^+˙ daughter ions arising from the electron ionization induced fragmentation of these [C₁₀H₁₀]^+˙ precursors has been investigated by collisionally activated dissociation (CAD), collisional ionization and ion kinetic energy spectroscopy. The [C₉H₇]⁺ produced from the various C₁₀H₁₀ hydrocarbons are of identical structure or an identical mixture of interconverting structures. These ions are similar in nature to the [C₉H₇]⁺ generated from indene by low energy electron ionization. The [C₁₀H₈]^+˙ ions also possess a common structure, which is presumably that of the maphthalene radical cation.     

Substituent effects in mass spectrometry—II. The effect of substituents on the dissociation of para and meta disubstituted benzenes

The effect of substituents on the activation energy for primary dissociation processes in the molecular ions of mono- and para and meta di-substituted benzenes has been examined. Where the daughter ion retains the substituent group, variation of the energy of activation derives from a combination of the effects of substituents on the ionisation potential of the molecular ion and the appearance potential of the daughter ion. An equation relating the energy of activation for the fragmentation of the molecular ion of a mono-substituted benzene to that of related para and meta di-substituted benzenes is presented.     

Substituent effects in mass spectrometry—III: Substituent effects in the dissociation of the molecular ions of para and meta substituted benzoic acids

The effect of substituents on the electron-impact-induced fragmentation of the molecular ions of para and meta substituted benzoic acids has been examined. The substituent is observed to exert an effect on the ionisation potential of the molecular ion, on the appearance potentials of the primary daughter ions and on the amount of H/D scrambling in the molecular ion of the carboxyl-d₁ analogues prior to the loss of hydroxyl therefrom. The energy of activation for the loss of hydroxyl from the molecular ion is in general dependent upon the nature but not the position of the substituent, while the amount of H/D scrambling in the molecular ion of the carboxyl-d₁ derivative is dependent upon both the nature and the position of the substituent. No correlation of the relative ion abundances with σ⁺ constants was observed. The results are consistent with the molecular ions of each compound having a dissimilar energy distribution, which could arise either by different energy transfers from the electron beam to the molecule or by the participation of different isolated electronic excited states (or similar states but to varying extents) in the dissociation of the molecular ions.     

A mass spectral study of the acid-catalysed oxygen exchange in laevulinic acid

The sequence, i.e. site selectivity of the acid-catalysed ¹⁶O/¹⁸O exchange in laevulinic acid (1) is studied by mass spectrometry, ion kinetic energy spectroscopy and accurate mass measurements on 1 and its ¹³C(1)-labelled congener. In the fragmentation pathways all ions of interest in the spectrum of 1 originate from the molecular ion, which may exist in six tautomeric or isomeric forms (1a–1d). The mechanism of gas-phase cyclization of 1a is rationalized in terms of three different pathways. Formation of the most prominent fragment ions and the sequence of ¹⁶O/¹⁸O exchange at the carbonyl and carboxy group are discussed. The results indicate the ions of m/z 56, m/z 61 and m/z 98 to be the only three which have incorporated oxygen atoms originating from the carboxy group in 1 and could thus be used in further elucidadon of the rearrangement mechanism of 5-hydroxymethylfuran (2) or 5-hydroxymethylfuran-2-carbaldehyde (3) into laevulinic acid (1).     

From an Icosahedron to a Plane: Flattening Dodecaiodo‐dodecaborate by Successive Stripping of Iodine

It has been shown by electrospray ionization–ion‐trap mass spectrometry that B₁₂I₁₂^2? converts to an intact B₁₂ cluster as a result of successive stripping of single iodine radicals or ions. Herein, the structure and stability of all intermediate B₁₂I_n^? species (n=11 to 1) determined by means of first‐principles calculations are reported. The initial predominant loss of an iodine radical occurs most probably via the triplet state of B₁₂I₁₂^2?, and the reaction path for loss of an iodide ion from the singlet state crosses that from the triplet state. Experimentally, the boron clusters resulting from B₁₂I₁₂^2? through loss of either iodide or iodine occur at the same excitation energy in the ion trap. It is shown that the icosahedral B₁₂ unit commonly observed in dodecaborate compounds is destabilized while losing iodine. The boron framework opens to nonicosahedral structures with five to seven iodine atoms left. The temperature of the ions has a considerable influence on the relative stability near the opening of the clusters. The most stable structures with five to seven iodine atoms are neither planar nor icosahedral.     

Characterization of an exception to the ‘even‐electron rule’ upon low‐energy collision induced decomposition in negative ion electrospray tandem mass spectrometry

Electrospray‐generated precursor ions usually follow the ‘even‐electron rule’ and yield ‘closed shell’ fragment ions. We characterize an exception to the ‘even‐electron rule.’ In negative ion electrospray mass spectrometry (ES‐MS), 2‐(ethoxymethoxy)‐3‐hydroxyphenol (2‐hydroxyl protected pyrogallol) easily formed a deprotonated molecular ion (M‐H)^? at m/z 183. Upon low‐energy collision induced decomposition (CID), the m/z 183 precursor yielded a radical ion at m/z 124 as the base peak. The radical anion at m/z 124 was still the major fragment at all tested collision energies between 0 and 50 eV (E_lab). Supported by computational studies, the appearance of the radical anion at m/z 124 as the major product ion can be attributed to the combination of a low reverse activation barrier and resonance stabilization of the product ions. Furthermore, our data lead to the proposal of a novel alternative radical formation pathway in the protection group removal of pyrogallol. Copyright © 2009 John Wiley & Sons, Ltd.     

Unidirectional triple and double hydrogen rearrangement reactions in the radical cations of γ-arylalkanols

A novel fragmentation reaction accompanied by the unidirectional migration of three hydrogen atoms has been found in the radical cations of γ-arylpropanols with electron-donating substituents in the para position. This triple hydrogen (3H) rearrangement reaction is the dominant fragmentation channel of the long-lived molecular ions of trans-2-(4′-dimethylaminobenzyl)-l-indanol, 2, but it occurs also in simpler γ-arylpropanol ions. Deuterium labelling of 2 reveals that the three hydrogen atoms originate with extraordinarily high specificity from the C(l), C(2) and O positions of the alcohol moiety. Cis- and 3′-substituted isomers do not undergo this reaction. Along with the 3H rearrangement reaction a unidirectional double hydrogen (2H) rearrangement reaction takes place independently and with less specificity in the trans-2-(4′-X-benzyl)-l-indanol ions 1⁺˙ and 2⁺˙. No hydrogen exchange occurs during the 3H and 2H rearrangement reactions. Mechanistic alternatives of these unusual fragmentation reactions are discussed; the experimental evidence strongly favours pathways via several intermediate ion–neutral complexes.     

Mass spectrometry of aryl substituted di- and trisiloxanes

The mass spectra of arylpentamethyldisiloxanes, sym-diaryltetramethyldisiloxanes and 1,5-diaryl-1,1,3,3,5,5-hexamethyltrisiloxanes were examined. Isotopic labeling and peak matching were used to substantiate the proposed fragmentation mechanisms. Siliconium ions dominate the spectra. Loss of neutral fragments from the [M-15]⁺ ions is important. Phenylpentamethyldisiloxane, sym-tetramethyldiphenyldisiloxane and 1,1,3,3,5,5-hexamethyl-1,5-diphenyltrisiloxane are representative examples of the three classes of compounds discussed. The [M-15]⁺ ion of phenylpentamethyldisiloxane loses methane, dimethylsilanone [(CH₃)₂Si?O] and phenylmethylsilanone [PhCH₃Si?O] to yield daughter siliconium ions. The [M-15]⁺ ion of sym-tetramethyldiphenyldisiloxane loses benzene, methane, dimethylsilanone and phenylmethylsilanone to yield daughter siliconium ions. The [M-15]⁺ ion of 1,1,3,3,5,5-hexamethyl-1,5-diphenyltrisiloxane loses benzene, tetramethylcyclodisiloxane and phenyltrimethylcyclodisiloxane to yield daughter siliconium ions. Finally, doubly charged ions are important in the mass spectra of the three series of aryl substituted di- and trisiloxanes discussed.     

Determination of the fragmentation mechanisms of organophosphorus ions by H2O and D2O atmospheric-pressure ionization tandem mass spectrometry

Dimethylmethyl phosphonate (DMMP), dimethyl phosphite (DMPI), trimethyl phosphite (TMPI) and trimethyl phosphate (TMP) were investigated using H₂O and D₂O atmospheric-pressure ionization (API) tandem mass Spectrometry. All daughter ions could be explained by losses of one or a successive number of stable molecules as opposed to losses of radicals such as the hydride, methyl and methoxy species. Losses of neutral methanol and dimethyl ether and of protonated methanol and formaldehyde ions from all four organophosphorus pseudo-molecular ions were observed. The DMMP and DMPI MH⁺ pseudomolecular ions produced the losses of neutral C₂H₆ and water, respectively. Formaldehyde loss was not observed for the MH⁺ ions, but it was well represented in the decomposition pathways of daughter ions. The D₂O reagent gas highlighted the role of the ionizing proton/ deuteron in the various daughter ions, including m/z 95, 79, 65, 49, 33, 31 and 47. The last ion was found to be isobaric in that m/z 47 and 48 both appeared with similar abundances in the D₂O-API daughter ion mass spectra of TMPI and TMP.     

Low-energy,low-temperature mass spectra. 10—urethanes

The 12.1 eV, 75°C electron impact mass spectra of 24 urethanes, RNHCO₂C₂H₅ [R ? H, C₂H_{2n +1} (n = 1-8), CH₂?CHCH₂, Ph, PhCH₂ and PhCH₂CH₂], and seven symmetrically disubstituted urethanes R₂NCO₂C₂H₅ (R ? C_n H_{2n + 1} (n = 1?4)) are reported and discussed. All 31 spectra show appreciable molecular ion peaks. For n ?Cn H_{2n +1} NHCO₂C₂H₅, M^{+ ˙} usually is the most abundant ion in the spectrum. A peak at m/z 102 of comparable intensity also is present; this corresponds to formal cleavage of the bond connecting the α- and β-carbon atoms in the N-alkyl group, though it is unlikely that the daughter ion has the structure [CH₂?NHCO₂C₂H₅]⁺. In the RNHCO₂C₂H₅ series, branching at the α-carbon atom enhances the relative abundance of the ion arising by notional α-cleavage at the expense of that of M^{+ ˙}. Formal cleavage of the bond between β- and γ-carbon atoms occurs to some extent for [RNHCO₂C₂H₅]⁺˙ ions; this reaction provides information on the degree of branching at the β-carbon, especially if metastable molecular ions are considered. The higher n-C_nH_{2n +1}NHCO₂C₂H₅ (n = 5?8) urethanes exhibit two other significant ions in their mass spectra. First, there is a peak at [M ? C₂H₅]⁺. Secondly, a peak is present at m/z 90; the most plausible structure for this ion is [H₂N(HO)COC₂H₅]⁺, arising by double hydrogen transfer from the alkyl group and expulsion of a [C_nH_{2n ?1}]˙ radical. Ions originating from secondary decomposition of the primary ionic species are generally of only very low abundance in these spectra.     

Mass spectra of substituted Δ2-1,2,4-oxadiazolines. II

5,5-Pentamethylene-3-(phenyl or para-substituted-phenyl)-Δ²-1,2,4-oxadiazolines, 1a-e , were examined by electron-impact mass spectrometry. Defocussed metastable ion detections confirmed the formation of certain daughter fragments from the mother ions. The exact mass measurements helped to make the correct assignment of various species. We conclude that it is the spiro arrangement which caused such a dramatic change in the decomposition pattern. Several new fragmentation pathways have been found in the present studies. Out of five oxadiazolines prepared for the present work, three ( 1b,d,e ) are new.     

Characterization of cyclotetramethylenetetranitramine (HMX) thermal degradation by isotope analyses with analytical pyrolysis-atmospheric pressure ionization tandem mass spectrometry

Analytical pyrolysis-atmospberic pressure ionization (Py-API) tandem mass Spectrometry was used in the structure elucidation of the oxidalive and non-oxidative thermal decomposition products of cyclotetramethylenetetranitramine (HMX). The [¹⁵NO₂]-, [¹⁵N₈]- and [²H₈]-HMX isotope preparations provided fundamental information in the determination of the identities of the various pyrolyzate species. All RDX pyrolysis product ions that were identified by Py-API tandem mass Spectrometry, i.e. m/z 44, 60, 74, 75, 85 and 98, were present in the pyrolyzate of HMX. In both RDX and HMX investigations, these ions provided identical mass spectral daughter ion analyses. HMX, however, provided additional ions at m/z 30, 58, 69, 71, 83 and 141. Of all thirteen ions identified in the Py-APJ mass spectrum of HMX, only that at m/z 75 contained a nitrogen atom that originated from the NO₂ group. Standards analysis confirmed the identities of the ions at m/z 69, 71 and 141 as methyleneaminoacetonitrile, methylaminoacetonitrile and the caged compound hoxamethylenetetraamine, respectively. Isotopic analyses provided a high degree of confidence on the structural assignments of the ions at m/z 30 and 58 as methyleneimine and methyleneformamide; the ion at m/z 83, however, appeared to be a heterocyclic compound with daughter ion mass spectral elements similar to but not identical with that of 1-methylimidazole and 3-methylpyrazole.     

Analysis of tetrabenzyl N-giucosidic,N-mannosidic and N-galactosidic Isomers using fast atom bombardment/mass-analysed ion kinetic energy spectrometry

A series of new synthetic tetrabenzyl N-glucosidic, N-mannosidic and N-galactosidic isomers were investigated by fast atom bombardment (FAB)/mass-analysed ion kinetic energy (MIKE) spectrometry. The [M + H]⁺ ions were obtained with high abundance in the FAB spectra when using 3-nitrobenzyl alcohol as the matrix. The FAB/MIKE spectra provide characteristic daughter ions fragmented from selected molecular parent ions, allowing these isomers to be differentiated. In addition, an interesting rearrangement was found from the MIKE spectra, indicating that the benzyl (Bzl) group on the sugar ring is rearranged on to the N atom of the base (R) group to form [R + Bzl + H]⁺ and [R+ 2Bzl]⁺ ions.