Theoretical study of the main fragmentation pathways for protonated glycylglycine

Quantum chemical and RRKM calculations were carried out on protonated glycylglycine in order to determine the atomic details of the main fragmentation pathways leading to formation of a1 and y1 ions. Two possible mechanisms were considered. The first path results in elimination of aziridinone as a neutral counterpart of the y1 ion formed. Our calculations show that this pathway has a relatively high threshold energy (48.6 kcal/mol) and the corresponding unimolecular rate constants are quite small even at large internal energy. An alternative pathway (a1-y1) proposed in the present paper seems, however, to be favored against the above 'aziridinone' one from the points of view of both energetics and kinetics. The 'a1-y1' pathway leads to simultaneous formation of a1 and y1 ions, the ratio of which depends on the energy distribution of the fragmenting species for a particular dipeptide. However, even if y1 ions are formed via the 'a1-y1' pathway, the corresponding neutrals eliminated do not have a strained cyclic aziridinone structure. Instead, in a two-step process, CO and NHCH2 are formed leading to neutral products energetically more favored than aziridinone. The available experimental data reevaluated in the present paper lend support to the 'a1-y1' pathway.     

Experimental and theoretical investigation of the main fragmentation pathways of protonated H-Gly-Gly-Sar-OH and H-Gly-Sar-Sar-OH

The fragmentation pathways of protonated H-Gly-Gly-Sar-OH and H-Gly-Sar-Sar-OH are investigated by using both computational and experimental techniques. The main goal of these studies is to further investigate which factors determine the branching ratio of the b₂-y₁ (Paizs, B.; Suhai, S. Rapid Commun. Mass Spectrom. 2002, 16, 375.) and “diketopiperazine” (Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. Anal. Chem. 1993, 65, 1594.) pathways of protonated tripeptides. Protonated H-Gly-Sar-Sar-OH represents a sensitive test for the branching ratio of the b₂-y₁ and “diketopiperazine” pathways since this ion cannot produce y₁ ions on the b₂-y₁ channel but only b₂ ions. Protonated H-Gly-Gly-Sar-OH and H-Gly-Sar-Sar-OH exhibit very different fragmentation behavior under the investigated experimental conditions. The former fragments forming mainly y₁ ions (maximum abundance of the b₂ and y₂ ions is 15%), while the latter produces mainly b₂ ions while at larger internal energies the a₂, y₂, and y₁ ions become also moderately abundant. Theoretical modeling and analysis of the main fragmentation pathways indicate that the majority of the b₂ and y₁ ions of protonated H-Gly-Gly-Sar-OH and the b₂ ions of H-Gly-Sar-Sar-OH are formed on the b₂-y₁ pathway.     

The fragmentation pathways of protonated glycine: A computational study

Numerous studies have demonstrated that protonated aliphatic amino acids, [H2NCHRCO2H + H]+, fragment in the gas phase to form iminium ions, H2N=CHR+. Unfortunately none of these studies have probed the structure of the neutral(s) lost as well as the mechanism of fragmentation. Three main mechanisms have been previously proposed: (1) loss of the combined elements of H2O and CO; (2) loss of dihydroxycarbene (HO)2C: and (3) loss of formic acid, HC(=O)OH. Herein, ab initio and density functional theory calculations have been used to calculate the key reactants, transition states, and products of these and several other competing reaction channels in the fragmentation of protonated glycine. The loss of the combined elements of H2O and CO is thermodynamically and kinetically favored over the alternative formic acid or (HO)2C fragmentation processes.     

Proton mobility in protonated peptides: a joint molecular orbital and RRKM study

The mobile proton model was critically evaluated by using purely theoretical models which include quantum mechanical calculations to determine stationary points on the potential energy surface (PES) of a model compound, and Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to determine the rate constants of various processes (conformational changes, proton transfer reactions) which occur during mass analysis of protonated peptides. Extensive mapping of the PES of protonated N-formylglycinamide resulted in various minima which were stabilized by one or more of the following types of interaction: internal hydrogen bond, charge transfer interaction, charge delocalization, and ring formation. The relative energies of most of the investigated minima are less then 20 kcal mol(-1) compared with the most stable species. More importantly, the relative energies of the transition structures connecting these minima are fairly low, allowing facile transitions among the energetically low-lying species. It is demonstrated that a path can be found leading from the energetically most stable species, protonated on an amide oxygen, to the structure from which the energetically most favorable fragmentation occurs. It is also shown that the added proton can sample all protonation sites prior to fragmentation. The RRKM calculations applied the results of ab initio computations (structures, energetics, vibrational frequencies) to the reactions (internal rotations, proton transfers) occurring in protonated N-formylglycinamide, and clearly lend additional evidence to the mobile proton model. Based on the results of the PES search on protonated N-formylglycinamide, we also comment on the mechanism proposed by Arnot et al. (Arnot D, Kottmeier D, Yates N, Shabanowitz J, Hunt D F. 42(nd) ASMS Conference on Mass Spectrometry, 1994; 470) and Reid et al. (Reid G E, Simpson R J, O'Hair R A J. J. Am. Soc. Mass Spectrom. 1998; 9:945) for the formation of b(2)(+) ions. According to the high level ab initio results, the mechanism relying on amide oxygen protonated species seems to be less feasible than the one which involves N-protonated species.     

Competing gas-phase fragmentation pathways of asparagine-, glutamine-, and lysine-containing protonated dipeptides

The fragmentation chemistry of protonated H–Val–Asn–OH, H–Val–Gln–OH and H–Val–Lys–OH is investigated in this work by means of modeling and density functional theory calculations. Former experimental studies indicate that the ratio of a ₁ and y ₁ ions cannot be explained by considering the proton affinities of the corresponding dissociating species on the a ₁–y ₁ pathway, while the fragmentation of other dipeptides can be understood in this way. We demonstrate that considering the correct PA value for H–Asn–OH eliminates the deviation observed for H–Val–Asn–OH. The larger than expected a ₁/y ₁ ratio of H–Val–Gln–OH is explained by considering the dissociation kinetics of the proton-bound dimers formed on the a ₁–y ₁ pathway and competition of the deamidation and a ₁–y ₁ channels. For H–Val–Lys–OH, it is proposed that a ₁ ions are indeed formed from one of the primary products, protonated H–Val–Cap–OH.     

Energy-dependent kinetic method: application to the multicompetitive fragmentation pathways of protonated peptides

A variation of the kinetic method for the analysis of fragmentation patterns in mass spectra is proposed. The procedure presents three notable features: no evaluation of the effective temperature of the parent ion is required; the ratio of the activation energies for all competitive channels at play are provided; and the measurement is not biased by the mass discrimination of the instrument. The method is based on the analysis of mass spectra recorded as a function of both the excitation energy and the excitation time. Collision-activated dissociation of protonated Leu-enkephalin achieved in a quadrupolar ion trap and analyzed with this method is presented.     

Gas-phase fragmentation of protonated benzodiazepines

Protonated 1,4-benzodiazepines dissociate in the gas phase by the common pathway of CO elimination and by unique pathways dictated by the substituents; the latter typically differentiate one benzodiazepine from another. Protonated 3-dihydro-5-phenyl-1,4-benzodiazepin-2-one, the base diazepam devoid of substituents, dissociates by eliminating CO, HNCO, benzene, and benzonitrile. Mechanisms of these reactions are proposed with ionic products being resonance stabilized. The abundant [MH-CO]+ ion dissociates to secondary products via elimination of benzene, benzonitrile, the NH2 radical, and ammonia, yielding again ionic products that are stabilized by resonance.     

Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study

Theoretical model calculations were performed to investigate the degree of validity of the mobile proton model of protonated peptides. The structures and energies of the most important minima corresponding to different structural isomers of protonated diglycine and their conformers, as well as the barriers separating them, were determined by DFT calculations. The rate coefficients of the proton transfer reactions between the isomers were calculated using the RRKM method in order to obtain a quantitative measure of the time scale of these processes. The proton transfer reactions were found to be very fast already at and above the threshold to the lowest energy decomposition pathway. Two possible mechanisms of b2+-ion formation via water loss from the dipeptide are also discussed. The rate-determining step of the proton migration along a peptide chain is also investigated using the model compound N-formylglycylglycinamide. The investigations revealed that this process very possibly occurs via the protonation of the carbonyl oxygens of the amide bonds, and its rate-determining step is an internal rotation-type transition of the protonated C=O-H group between two adjacent C=O-HellipsisO=C bridges.     

Unimolecular and collision-induced fragmentation of protonated nitroarenes

The unimolecular fragmentation reactions of 28 protonated nitroarenes, occurring on the metastable ion time-scale, are reported. In addition, the collision-induced fragmentation of the same species have been studied at 10 eV and at 50 eV collision energy. When an OH, COOH or NH₂ substituent is ortho to the nitro function, the dominant fragmentation involves loss of H₂O, for both unimolecular and collision-induced reactions. When there is an electron-releasing substituent ortho or para to the litro group, loss of OH is the dominant fragmentation reaction both on the metastable ion time-scale and for ions activated by collision. When the electron-releasing substituent is meta to the nitro group, loss of NO₂ is the dominant low-energy unimolecular fragmentation reaction while loss of HNO₂ is the most important fragmentation for ions activated by 50 eV collisions. Elimination of NO from [MH]⁺ occurs to a significant extent in the unimolecular fragmentation of protonated nitrobenzene and those protenated nitrobenzenes containing electron- attracting substituents. In the collision-induced dissociation of these species loss of HNO₂ occurs at the expense of loss of NO. The results are consistent with protonation predominantly at the nitro group. The results are discussed in terms of the use of neutral loss scans in tandem mass spectrometry to monitor complex mixtures for nitroarenes.     

Proton migration and tautomerism in protonated triglycine.

Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.     

Unimolecular fragmentation reactions of protonated and methyl-cationated n-octanones and N-nonanones. Sequential fragmentation reactions

Protonated and methyl-cationated n-octanonts and n-nonanones have been prepared by chemical ionization methods and the unimolecular fragmentation reactions occurring on the metastable ion time-scale have been exam ined. The [R₁R₂COR₃]⁺ (R₃ = H or CH₃) species fragment by elimination of R₃OH and by elimination of neutral alkenes. The elimination of (R₁ — H), where R₁ is the larger alkyl group of the original ketone, is particularly important. In addition, alkenyl ions are observed corresponding, nominally, to elimination of C₃H₇OR₃ from the ionized octanones and to elimination of C₃H₇OR₃ and C₄H₉OR₃ from the nonanones. These ions are shown to arise largely, if not completely, by sequential elimination of R₃OH plus an olefin (C₃H₆ or C₄H₈) from [R₁R₂COR₃]⁺. A comparison is made of the unimolecular fragmentation reactions occurring in the second field-free region and in the radio-frequency-only quadrupole of a hybrid BEQQ mass spectrometer.     

The mobility and ion structure of protonated aminoazoles

The reduced mobility of protonated pyrazole derivatives was measured by ion mobility spectrometry (IMS) in air, nitrogen, and carbon dioxide, at temperatures between 150 and 250°C. It was found that the mobility of protonated 5-amino-1-phenylpyrazole was higher than that of its 3- and 4-isomers. This was attributed to the fact that in the 5-isomer the preferred site of protonation is on the endocyclic nitrogen, which leads to delocalization of the ionic charge, and thus to a diminished interaction with the drift gas molecules. On the other hand, protonated 5-amino-1-methylpyrazole has a slightly lower mobility than its isomers, which is indicative of a different protonation mechanism.     

Reaction competition in the fragmentation of protonated dipeptides

A major low-energy fragmentation reaction of many protonated dipeptides involves cleavage of the amide bond resulting in formation of either the y(1)" ion or the a(1) ion. For a series of protonated dipeptides H-Val-Xxx-OH it is observed that log(y(1)"/a(1)) is a linear function of the proton affinity of the variable C-terminal amino acid. For the series of protonated dipeptides H-Xxx-Phe-OH log(a(1)/y(1)") gives a poor correlation with the proton affinity or gas-phase basicity of H-Xxx-OH. However, a good limited correlation of log(a(1)/y(1)") with the Taft-Topsom sigma(alpha) for the alkyl group is observed when Xxx is an aliphatic amino acid. It is proposed that fragmentation occurs by initial formation of a proton-bound complex of an aziridinone and an amino acid which may fragment to form either a protonated amino acid (y(1)") or an N-protonated aziridinone with the corresponding neutrals being an aziridinone and an amino acid. Ab initio calculations show that the N-protonated aziridinone is unstable and fragments by loss of CO to form the a(1) immonium ion. However, the proton-bound complex of an aziridinone and an amine base is a stable species which exists in a potential well. Copyright 2000 John Wiley & Sons, Ltd.     

Gas-phase proton-transfer pathways in protonated histidylglycine

Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Proton mobility in water clusters

Proton mobility in water occurs quickly according to the so-called Grotthuss mechanism. This process and its elementary reaction steps can be studied in great detail by applying suitable mass spectrometric methods to ionic water clusters. Careful choice of suitable core ions in combination with analysis of cluster size trends in hydrogen/deuterium isotope exchange rates allows for detailed insights into fascinating dynamical systems. Analysis of the experiments has been promoted by extensive and systematic quantum chemical model calculations. Detailed low-energy mechanistic pathways for efficient water rearrangement and proton transfer steps, in particular cases along short preformed "wires" of hydrogen bonds, have been identified in consistency with experimental findings.     

Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b(2), y(1), and y(2) ions

Quantum chemical and RRKM calculations were performed on protonated GGG in order to determine the atomic details of the main fragmentation pathways leading to formation of b(2),y(1), and y(2) ions. Formation of y(1) ions on the "diketopiperazine" pathway is initiated from relatively high-energy C-terminal amide nitrogen protonated species for which the N-terminal amide bond is in the cis isomerization state. The reaction goes through a transition structure which is only slightly less favored than the reactive configuration itself. RRKM calculations indicate that this reaction is extremely fast as soon as the fragmenting species have more internal energy than the reaction threshold. The calculated energetics suggests that y(1) ions are formed on the "diketopiperazine" pathway with a non-negligible (6-10 kcal/mol) reverse activation barrier. Investigation of species occurring during the formation of b(2) ions having an oxazolone structure indicates that y(1) ions can be formed also from intermediates previously thought to result in only b(2) ions. As the first step of the "b(x)-y(z)" pathway proposed here the extra proton must reach the nitrogen of the C-terminal amide bond. Attack of the N-terminal amide oxygen on the carbon center of the C-terminal amide bond results in formation of the oxazolone ring while the detaching G leaves the precursor ion. Under low-energy collision conditions the complex of protonated 2-aminomethyl-5-oxazolone and G can rearrange to form a proton-bonded dimer of these species. In such circumstances the extra proton is shared by the two monomers and dissociation of the dimer will be determined by the thermochemistry involved. Based on the "b(x)-y(z)" pathway one can easily explain the linear relationship between the logarithm of the y(1)/b(2) ion abundance ratio and the proton affinity of the C-terminal amino acid substituent for the series of H-Gly-Gly-Xxx-OH tripeptides where Xxx was varied (Morgan DG, Bursey MM. Org. Mass. Spectrom. 1994; 29: 354). The calculated energetics indicates that both y(1) and b(2) ions are formed with no reverse activation barrier on the "b(x)-y(z)" pathway.     

Functional group interaction in the fragmentation of protonated 2,7-octanedione

The fragmentation of 2,7-octanedione, induced by chemical ionization with methane as a reagent gas (CI (CH₄)), is shown to be extensively governed by the interaction of the two carbonyl groups. Tandem mass spectrometry reveals that a sequential loss of H₂O and C₂H₄O from the [M + H]⁺ ion competes with sequential loss of H₂O and C₆H₁₀, and that both processes occur via the same [MH - H₂O]⁺ intermediate. This intermediate is likely to be formed via intramolecular gas-phase aldol condensation and subsequent dehydration. The resulting C(1) protonated 1-acetyl-2-methylcyclopentene structure readily accounts for the observed further decomposition to CH₃C?O⁺ and 1-methylcyclopentene (C₆H₁₀) or, alternatively, to [C₆H₉]⁺ (e. g. 1-methylcyclopentenylium) ions and acetaldehyde (C₂H₄O). Support for this mechanistic rationale is derived from deuterium isotope labelling and low-energy collision-induced dissociation (CID) of the [MH - H₂O]⁺ ion. The common intermediate shows a CID behaviour indistinguishable by these techniques from that of reference ions, which are produced by gas-phase protonation of the authentic cyclic aldol or by gas-phase addition of an acetyl cation to 1-methylcyclopentene in a CI (CH₃COOCH₃) experiment.