Formation and reactions of clusters in the gas phase: small peptides and carboxylic acids

The cluster formation of seventeen small dipeptides with different primary structures and vanillic acid was investigated by means of a neutral laser desorption and supersonic beam expansion followed by multi photon ionization time of flight mass spectrometry. The structures of these clusters have been characterized by mass spectrometric methods as well as by DFT calculations. It is shown that the structure of the cluster from a dipeptide and vanillic acid is described by a hydrogen bond between the phenolic group of the vanillic acid and the N-terminal amino function of the dipeptide. The intensity of the cluster ion and the main fragmentation product, the protonated peptide ion, can be linked to the proton affinity of the peptide. Furthermore the fragmentation reactions of the protonated peptide are accompanied by extensive hydrogen rearrangements yielding both a and y fragments. The intensities of these fragments follow the proton affinity of the dipeptide.     

Effect of phenylalanine on the fragmentation of deprotonated peptides

The fragmentation reactions of a variety of deprotonated dipeptides and tripeptides containing phenylalanine have been studied using energy-resolved collision-induced dissociation, isotopic labeling and MS/MS/MS experiments. The benzyl a-group has a substantial effect on the fragmentation reactions observed. When the phenylalanine is in the C-terminal position of dipeptides or tripeptides a major fragmentation reaction is elimination of neutral cinnamic acid to from a deprotonated amino acid amide (c1 ion) for dipeptides and a deprotonated dipeptide amide (c2 ion) for tripeptides. Fragmentation of the [M - H]- ions of tripeptides with phenylalanine in the central position also results in substantial formation of the deprotonated amide of the N-terminal amino acid residue. When the phenylalanine residue is in the N-terminal position elimination of C7H8 from the [M - H - CO2]- ion and formation of the benzyl anion become important fragmentation pathways. Sequence ions frequently observed are the y1 ions, "b2 ions and a3-Nt ions.     

A short synthesis of bicyclic dipeptides corresponding to Xxx-L-Pro Xxx-D-Pro having constrained trans-proline amides

[formula: see text] A short synthesis that generates two isomeric bicyclic dipeptides having constrained, trans-proline amide bonds has been developed. One of these bicyclic dipeptides corresponds to an Xxx-L-Pro dipeptide (4), while the other isomer corresponds to an Xxx-D-Pro dipeptide (5). The two isomers are readily distinguished by their 1H NMR spectra.     

Characterization of electrospray ionization mass spectrometry for N-diisopropyloxyphosphoryl dipeptide methyl esters

A systematic study of the fragmentation pattern of N-diisopropyloxyphosphoryl (DIPP) dipeptide methyl esters in an electrospray ionization (ESI) tandem mass spectrometry (MS/MS) was presented. A combination of accurate mass measurement and tandem mass spectrometry had been used to characterize the major fragment ions observed in the ESI mass spectrum. It was found that the alkali metal ions acted as a fixed charge site and expelled the DIPP group after transferring a proton to the amide nitrogen. For all the N-phosphoryl dipeptide methyl esters, under the activation of a metal ion, the rearrangement product ion at m/z 163 was observed and confirmed to be the sodium adduct of phosphoric acid mono-isopropyl esters (PAIE), via a specific five-membered penta-co-ordinated phosphorus intermediate. However, no rearrangement ion was observed when a beta-amino acid was at the N-terminal. This could be used to develop a novel method for differentiating isomeric compounds when either alpha- or beta-amino acid are at the N-terminus of peptides. From the [M+Na]+ ESI-MS/MS spectra of N-phosphoryl dipeptide methyl esters (DIPP Xaa1 Xaa2 OMe), the peaks corresponding to the [M+Na Xaa1 C3H6]+ were observed and explained. The [M+Na]+ ESI-MS/MS spectra of N-phosphoryl dipeptide methyl esters with Phe located in the C-terminal, such as DIPPValPheOMe, DIPPLeuPheOMe, DIPPIlePheOMe, DIPPAlaPheOMe and DIPPPhePheOMe, had characteristic fragmentation. Two unusual gas-phase intramolecular rearrangement mechanisms were first proposed for this fragmentation. These rearrangements were not observed in dipeptide methyl ester analogs which did not contain the DIPP at the N-terminal, suggesting that this moiety was critical for the rearrangement.     

157 nm Photodissociation of Dipeptide Ions Containing N-Terminal Arginine

Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m₂ and m₂+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.

Fragmentation reactions of protonated peptides containing glutamine or glutamic acid

A variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy-resolved mass spectrometry and triple-stage mass spectrometry (MS(3)) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H-Gln-Gly-OH fragments by loss of NH(3) and loss of H(2)O in metastable ion fragmentation; under collision-induced dissociation (CID) conditions loss of H-Gly-OH + CO from the [MH - NH(3)](+) ion forms the base peak C(4)H(6)NO(+) (m/z 84). Protonated dipeptides with an alpha-linkage, H-Glu-Xxx-OH, are characterized by elimination of H(2)O and by elimination of H-Xxx-OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a gamma-linkage, H-Glu(Xxx-OH)-OH, do not show elimination of H(2)O or formation of m/z 102 but rather show elimination of NH(3), particularly in metastable ion fragmentation, and elimination of H-Xxx-OH to form m/z 130. Both the alpha- and gamma-dipeptides show formation of [H-Xxx-OH]H(+), with this reaction channel increasing in importance as the proton affinity (PA) of H-Xxx-OH increases. The characteristic loss of H(2)O and formation of m/z 102 are observed for the protonated alpha-tripeptide H-Glu-Gly-Phe-OH whereas the protonated gamma-tripeptide H-Glu(Gly-Gly-OH)-OH shows loss of NH(3) and formation of m/z 130 as observed for dipeptides with the gamma-linkage. Both tripeptides show abundant formation of the y(2)' ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H-Xxx-Glu-OH show abundant elimination of H(2)O whereas those of structure H-Xxx-Gln-OH show abundant elimination of NH(3). The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a(1) ion or the y(1)' ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH(3) from the glutamine containing dipeptide is followed by elimination of a second NH(3) while the initial loss of H(2)O from the glutamic acid dipeptide is followed by elimination of NH(3). Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H-Gly-Glu-Gly-OH]H(+) and [H-Gly-Gln-Gly-OH]H(+) fragment mainly to form b(2) and a(2) ions, the latter also shows elimination of NH(3) plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon-bonded hydrogens in the formation of protonated glycinamide.     

Development of a practical solid-phase synthesis approach to 1,3,5-triazepan-2,6-diones

1,3,5-Triazepan-2,6-diones are a class of conformationally restricted heterocycles derived from dipeptides. With the aim to develop a general and practical method useful for library production, three polymer-assisted syntheses, all based on a catch and release approach, have been evaluated and compared. The method involving a Hofmann rearrangement of N-Boc dipeptide carboxamides and subsequent trapping of the isocyanate on polymer-supported N-hydroxysuccinimide (PS-HOSu) was found to be the most reliable and versatile, allowing rapid access to the 1,3,5-triazepan-2,6-dione skeleton.     

Fragmentation of deprotonated cyclic dipeptides by electrospray ionization mass spectrometry

The fragmentation pathways of deprotonated cyclic dipeptides have been studied by electrospray ionization multi‐stage mass spectrometry (ESI‐MSⁿ) in negative mode. The results showed that the fragmentation pathways of deprotonated cyclic dipeptides depended significantly on the different substituents, the side chains of amino acid residues at the diketopiperazine ring. In the spectra of deprotonated cyclic dipeptides, the ion [M? H? substituent radical]^? was firstly observed in the ESI mode. The characteristic fragment ions [M? H? substituent radical]^? and [M? H? (substituent? H)]^? could be used as the symbols of particular cyclic dipeptides. The hydrogen/deuterium (H/D) exchange experiment, the high‐resolution mass spectrometry (Q‐TOF) and theoretical calculations were used to rationalize the proposed fragmentation pathways and to verify the differences between the fragmentation pathways. The relative Gibbs free energies (ΔG) of the product ions and possible fragmentation pathways were estimated using the B3LYP/6–31++G(d, p) model. The results have some potential applications in the structural elucidation and interpretation of the mass spectra of homologous compounds and will enrich the gas‐phase ESI‐MS ion chemistry of cyclic dipeptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Structural and mechanistic information on c<Subscript>1</Subscript> ion formation in collision-induced fragmentation of peptides

The formation of c₁ ions during collision-induced fragmentation of peptides with asparagine, ornithine, or glutamine at the N-terminal position 2 has been studied. For this purpose, the corresponding fragment ion spectra of a large set of synthetic peptides were investigated. It is demonstrated that the c₁ ion intensity depends on the nature of the second residue in the N-terminal dipeptide motif as well as on the peptide length. It is shown that the formation of c₁ ions proceeds by two competing mechanisms. One mechanism is the secondary fragmentation of the b₂ ion, the efficiency of which shows only a minor dependency on the complete peptide sequence. The other mechanism is the direct formation from the molecular ion, which is identified to be connected with sequence-specific c₁ ion intensities. A model for this latter mechanism is proposed based on the analysis of the formation and secondary fragmentation of the z_max-1 ion, which is the complementary ion to the c₁ ion. Additional evidence is obtained by investigation of peptides with ornithine in N-terminal position 2, which in general exhibit c₁ ion intensities intermediate between the asparagine- and glutamine-containing species. The data presented support the reliable assignment of N-terminal dipeptide motifs using collision-induced dissociation.     

Separation of amino alcohols using divalent dipeptides as counter ions in aqueous CE

Divalent dipeptides have been introduced as counter ions in aqueous CZE. The dipeptides form ion pairs with amino alcohols in the BGE and facilitate the separation of amino alcohols. High concentrations of dipeptide caused reversed effective mobility for the analytes. The net charge of the dipeptide can be controlled using a buffer or a strong base, and regulates the interaction between the dipeptide and the amino alcohol. A stronger interaction and higher selectivity of amino alcohols was observed when the dipeptides were used as divalent counter ions, than in monovalent or uncharged form. Association constants for ion pairs between divalent dipeptides and amino alcohols can be used to enhance selectivity for amino alcohols in CZE. No chiral separation of amino alcohols was observed when using the dipeptides as ion‐pairing chiral selectors in aqueous BGE, but addition of methanol to the BGE promoted enantioselectivity.     

DFT study on reaction mechanisms of cyclic dipeptide generation

In this work, three possible reaction pathways (Path 1, Path 2 and Path 3) for the generation process of cyclic dipeptide from amino acid have been investigated in detail using density functional theory. Path 1 and Path 2 are the intramolecular reaction processes, while Path 3 involves the intermolecular reaction process that assisted with water molecule. Our calculated results indicate that Path 3 is more energy favorable than Path 1 and Path 2. There are four steps in Path 3 proceed from the amino acid to cyclic dipeptide. The first step is two adjacent amino acids to form precursor of dipeptide, the second step is the removal of water molecule of precursor of dipeptide for the formation of the linear dipeptide, the third step is generation of precursor of cyclic dipeptide associated with other hydrogen atom transfer, and the last step is another dehydration process to generate the final product of cyclic dipeptide. Moreover, the obtained results indicate that the generation mechanisms of different cyclic dipeptides are similar, and the energy barrier of the rate-determined step influenced somewhat by the hydrophilic or hydrophobic group linked to the C_α atom. Additionally, the potential energy profiles suggest that the generation reactions of the studied nine cyclic dipeptides are exothermic processes. The detailed mechanisms should be helpful for people to understanding the title reaction at the molecular level, and the proposed novel intermolecular process might provide valuable insights on rational improve reaction condition for this type of reaction.     

Robust and straightforward chemo-enzymatic enantiopure dipeptide syntheses and diketopiperazines thereof

We have explored the scope of the synthetic route towards d-phenylglycyl diketopiperazines, involving a penicillin acylase catalysed formation of d-phenylglycyl dipeptides of l-amino acids with functional groups in the side chain. The synthesis of dipeptides from serine, threonine, glutamic acid, glutamine and methionine was successful. In contrast, aspartic acid, asparagine and cysteine only afforded trace amounts of dipeptides while no dipeptide was detected with arginine, lysine and tyrosine. Isolated dipeptide yields varied from 10% to 76%. The dipeptides were successfully converted into their corresponding enantiopure diketopiperazines by chemical esterification and cyclization under alkaline conditions, in 35–43% yield. In the case of glutamic acid, the procedure yielded the diketopiperazine with an esterified side chain. Remarkably with glutamine, the amide function in the side chain was transformed into an ester moiety, resulting in the same diketopiperazine as with glutamic acid.     

气相条件下金属离子/肽复合物电喷雾串联质谱研究

研究蛋白质与金属离子之间的相互作用的本质一直是生物学家感兴趣的课题。但蛋白结构的复杂性使得二者之间相互作用的研究难度很大,常选用氨基酸或小肽作为模型化合物进行研究^[1-4]。目前该方法的研究甩缺乏系统性。     

Enzyme-labile protecting groups in peptide synthesis: development of glucose- and galactose-derived urethanes

The development of the tetra-O-acetyl-D-glucopyranosyloxycarbonyl (AGlOC) and tetra-O-acetyl-beta-D-galactopyranosyloxycarbonyl (AGalOC) protecting groups, which are fully enzyme-labile, carbohydrate-derived urethanes, is described. The protected amino acids were easily synthesized and subsequently converted into a series of model dipeptides through classical peptide couplings. Cleavage of an alpha/beta-anomeric mixture of a model AGlOC dipeptide was achieved with a "one-pot" procedure in good yield. To gain a better understanding of the enzymatic deprotection reaction, the AGalOC group was removed through a two step biotransformation (lipase catalyzed deacetylation, followed by beta-galactosidase catalyzed glycosidic bond fragmentation). Under these very mild reaction conditions (aq. buffer pH7.0, 37 degrees C), the desired N-terminal, unprotected dipeptide conjugates were obtained. The methodology was further utilized for the synthesis of an advanced tetrapeptide model system.     

157 nm Photodissociation of a Complete Set of Dipeptide Ions Containing C-Terminal Arginine

Twenty singly-charged dipeptide ions with C-terminal arginine were photodissociated with 157 nm light and their tandem mass spectra recorded. Many of the small product ions that were observed are standard peptide fragments that have been commonly seen in VUV photodissociation studies. However, the study of a library of dipeptides containing all 20 N-terminal amino acids enabled the recognition of trends associated with the occurrence of w-, v-, and immonium ions, the observation of competition between forming N- and C-terminal fragments in dipeptide RR, and the identification of some unusual fragment ions appearing at masses of 183, 187, 196, and 197 Da. A highly accurate internal calibration of the photodissociation TOF-TOF data enabled molecular formulae for these four product ions to be derived. Their proposed structures reflect the rather high-energy nature of this fragmentation phenomenon.      

Helical pores self-assembled from homochiral dendritic dipeptides based on L-Tyr and nonpolar alpha-amino acids

The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe where X = Gly, L-Val, L-Leu, L-Ile, L-Phe, and L-Pro is reported. Their self-assembly in bulk and in solution and the structural and retrostructural analysis of their periodic assemblies were compared to those of the previously reported and currently reinvestigated dendritic dipeptides with X = L-Ala. All dendritic dipeptides containing as X nonpolar alpha-amino acids self-assemble into helical porous columns. The substituent of X programs the structure of the helical pore and the resulting periodic array, in spite of the fact that its molar mass represents only between 0.05 and 4.77% from the molar mass of the dendritic dipeptide. In addition to the various 2-D columnar lattices, the dendritic dipeptides based on L-Ala, L-Leu, and L-Phe self-organize into 3-D hexagonal columnar crystals while those based on L-Val and L-Ile into an unknown columnar crystal. The principles via which the aliphatic and aromatic substituents of X program the structure of the helical pores indicate synthetic pathways to helical pores with bioinspired functions based on artificial nonpolar alpha-amino acids.     

Extensive study on physicochemical properties of polychlorinated biphenyls in a commercial ion trap mass spectrometer,relevance in analytical and environmental chemistry

Polychlorinated biphenyls (PCBs) exist as 209 congeners, consisting of biphenyl molecules, where the number and substitution positions of halogen atoms are known to affect industrial uses, environmental transport mechanisms, distribution, fate, and toxicity. The complexity of the problem requires accurate physicochemical studies of an increasing number of congeners in order to understand the environmental and biological processes at play. This work presents a systematic study on the thermodynamic and kinetic properties of PCBs by quadrupole ion trap mass spectrometry. A clear relationship between structure and behavior of PCBs in mass spectrometry experiments has been observed. Overall data demonstrate that di‐ortho congeners show lower thermodynamic stability and higher fragmentation rate than non/mono‐ortho. Congeners follow different fragmentation mechanisms according to the number of chlorine atoms in ortho position of the biphenyl system. Experimental kinetic curves of mono/non‐ortho and di‐ortho congeners show a strong similarity with classical first‐order kinetics curves; in particular, di‐ortho congeners follow a first‐order consecutive reaction, while mono/non‐ortho follow a first‐order parallel reaction. For each studied congener, the kinetic constant of reaction (fragmentation) has been determined. Data support environmental levels and biochemical transformations described in literature. The general picture of the PCB behavior inside a quadrupole ion trap provides the basis for the development of reliable and cost‐effective analytical methods to the determination of ultra‐low level trace of PCB congeners.     

IRREVERSIBLE REDOX REARRANGEMENT OF DIOXYGEN COMPLEXES. I. SELECTIVE OXIDATION OF DIPEPTIDES COORDINATED TO COBALT(II)

Abstract

The decomposition of the cobalt dioxygen complexes of three dipeptides has been investigated by removal of the metal from the final reaction mixtures, followed by gas chromatographic and mass spectrometric analyses of the organic reaction products. The results indicate that the reaction involves the oxidation of coordinated dipeptide, and that the ligands are oxidized exclusively at the N-terminal amino acid residue.     

Negative ion electrospray mass spectrometry of aminomethylphosphonic acid and glyphosate: elucidation of fragmentation mechanisms by multistage mass spectrometry incorporating in-source deuterium labelling

Glyphosate and its main metabolite, aminomethylphosphonic acid, introduced by direct infusion in (2)H(2)O, appear in negative ion electrospray mass spectrometry (ES-MS) as triply deuteriated [M[bond]H](-) ions. Sites of deuterium residence and loss were established using the multistage (MS(n)) capabilities of an ion trap mass spectrometer to assist in the determination of fragmentation mechanisms. The study reveals specific mechanisms, common to each analyte, such as those involving a five-membered transition state between the amine and phosphonate group, as well as analyte specific transitions.     

An efficient synthesis of 5-aminolaevulinic acid (ALA)-containing peptides for use in photodynamic therapy

An efficient and cost-effective procedure has been devised for the preparation of urethane-protected 5-aminolaevulinic acid (5-ALA) dipeptide ester derivatives which avoids problems associated with the instability of 5-ALA under basic conditions. The procedure is also applicable to the direct synthesis of N-(α)-acetyl amino acid-ALA dipeptides in high enantiomeric purity as potential novel prodrugs for photodynamic therapy (PDT).