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.     

Proton mobility and main fragmentation pathways of protonated lysylglycine

Theoretical model calculations were performed to validate the 'mobile proton' model for protonated lysylglycine (KG). Detailed scans carried out at various quantum chemical levels of the potential energy surface (PES) of protonated KG resulted in a large number of minima belonging to various protonation sites and conformers. Transition structures corresponding to proton transfer reactions between different protonation sites were determined, to obtain some energetic and structural insight into the atomic details of these processes. The rate coefficients of the proton transfer reactions between the isomers were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) method in order to obtain a quantitative measure of the time-scale of these processes. Our results clearly indicate that the added proton is less mobile for protonated KG than for peptides lacking a basic amino acid residue. However, the energy needed to reach the energetically less favorable but-from the point of view of backbone fragmentation-critical amide nitrogen protonation sites is available in tandem mass spectrometers operated under low-energy collision conditions. Using the results of our scan of the PES of protonated KG, the dissociation pathways corresponding to the main fragmentation channels for protonated KG were also determined. Such pathways include loss of ammonia and formation of a protonated alpha-amino-epsilon-caprolactam. The results of our theoretical modeling, which revealed all the atomic details of these processes, are in agreement with the available experimental results.     

The structure and dissociation pathways of protonated methanol: An ab initio molecular orbital study

Ab initio molecular orbital calculations with moderately large polarization basis sets and including valence-electron correlation have been used to examine the structure and dissociation mechanisms of protonated methanol [CH₃OH₂]⁺. Stable isomers and transition structures have been characterized using gradient techniques. Protonated methanol is found to be the only stable isomer in the [CH₅O]⁺ potential surface. There is no evidence for a tightly-bound complex, [HOCH₂]⁺…?H₂, analogous to the preferred structure [CH₃]⁺…?H₂ of [CH₅]⁺. Protonated methanol is found to possess a pyramidal arrangement of bonds at the oxygen atom with a barrier to inversion of 8kJ mol^?1. The lowest energy fragmentation pathways are dissociation into methyl cation and water (predicted to require 284 kJ mol^?1 with zero reverse activation energy) and loss of molecular hydrogen (endothermic by 138 kJ mol^?1 but with a reverse activation barrier of 149 kJ mol^?1). The results offer a possible explanation as to why production of [CH₂OH]⁺ from the reaction of methyl cation with water is not observed. Other dissociation processes examined include loss of a hydrogen atom to yield the methylenoxonium radical cation or methanol radical cation (requiring 441 and 490 kJ mol^?1, respectively) and loss of a proton to yield neutral methanol (requiring 784 kJ mol^?1).     

Fragmentation mechanisms of protonated benzylamines. Electrospray ionisation-tandem mass spectrometry study and ab initio molecular orbital calculations

Our research into neurotransmitters in a biological fluid presented an opportunity to investigate the fragmentations under low collision energy characterising benzyl-amines protonated under electrospray ionisation (ESI) conditions in a triple quadrupole mass spectrometer. In this work we present the breakdown graphs of protonated 3,4-dihydroxybenzylamine, DHBAH(+), and 3-methoxy, 4-hydroxybenzylamine, HMBAH(+), at various source temperatures and various pressures in the collision cell, the collision energy varying from 0 to 46 eV in the laboratory frame. Both parent ions eliminate first NH(3) at very low collision energy. The fragmentations of [MH - NH(3)](+) occur at high collision energy and are quite different for DHBAH(+) and HMBAH(+): formation of [MH - NH(3) - H(2)O - CO](+) for the former; formation of the radical cation [MH - NH(3) - CH(3)](+.) for the latter. These fragmentations are interpreted by means of ab initio calculations up to the B3LYP/6-311+G(2d,2p) level of theory. The successive losses of H(2)O and CO involve first the rearrangement in two steps of benzylic ions formed by loss of NH(3) into tropylium ions. The transition states associated with this rearrangement are very high in energy (about 400 kJ mol(-1) above MH(+)) explaining (i). the absence of an ion corresponding to [DHBAH - NH(3) - H(2)O](+). The determining steps associated with the losses of H(2)O and with H(2)O + CO are located lower in energy than the transition states associated with the isomerisation of benzylic ions into tropylium ions; explaining (ii). the formation of the radical cation [MH - NH(3) - CH(3)](+.). The homolytic cleavage of CH(3)-O requires less energy than does the rearrangement.     

The rotational barrier in ethane: a molecular orbital study

The energy change on each Occupied Molecular Orbital as a function of rotation about the C-C bond in ethane was studied using the B3LYP, mPWB95 functional and MP2 methods with different basis sets. Also, the effect of the ZPE on rotational barrier was analyzed. We have found that σ and π energies contribution stabilize a staggered conformation. The σ(s) molecular orbital stabilizes the staggered conformation while the stabilizes the eclipsed conformation and destabilize the staggered conformation. The π(z) and molecular orbitals stabilize both the eclipsed and staggered conformations, which are destabilized by the π(v) and molecular orbitals. The results show that the method of calculation has the effect of changing the behavior of the energy change in each Occupied Molecular Orbital energy as a function of the angle of rotation about the C-C bond in ethane. Finally, we found that if the molecular orbital energy contribution is deleted from the rotational energy, an inversion in conformational preference occurs.     

Fragmentation mechanisms of oxidized peptides elucidated by SID, RRKM modeling, and molecular dynamics

The gas-phase fragmentation reactions of singly charged angiotensin II (AngII, DR⁺VYIHPF) and the ozonolysis products AngII+O (DR⁺VY*IHPF), AngII+3O (DR⁺VYIH*PF), and AngII+4O (DR⁺VY*IH*PF) were studied using SID FT-ICR mass spectrometry, RRKM modeling, and molecular dynamics. Oxidation of Tyr (AngII+O) leads to a low-energy charge-remote selective fragmentation channel resulting in the b ₄ +O fragment ion. Modification of His (AngII+3O and AngII+4O) leads to a series of new selective dissociation channels. For AngII+3O and AngII+4O, the formation of [MH+3O] ⁺ −45 and [MH+3O] ⁺ −71 are driven by charge-remote processes while it is suggested that b ₅ and [MH+3O] ⁺ −88 fragments are a result of charge-directed reactions. Energy-resolved SID experiments and RRKM modeling provide threshold energies and activation entropies for the lowest energy fragmentation channel for each of the parent ions. Fragmentation of the ozonolysis products was found to be controlled by entropic effects. Mechanisms are proposed for each of the new dissociation pathways based on the energies and entropies of activation and parent ion conformations sampled using molecular dynamics.     

Gas-phase chemistry of ionized and protonated GeF4: a joint experimental and theoretical study

The gas-phase ion chemistry of GeF(4) and of its mixtures with water, ammonia and hydrocarbons was investigated by ion trap mass spectrometry (ITMS) and ab initio calculations. Under ITMS conditions, the only fragment detected from ionized GeF(4) is GeF(3)(+). This cation is a strong Lewis acid, able to react with H(2)O, NH(3) and the unsaturated C(2)H(2), C(2)H(4) and C(6)H(6) by addition-HF elimination reactions to form F(2)Ge(XH)(+), FGe(XH)(2)(+), Ge(XH)(3)(+) (X = OH or NH(2)), F(2)GeC(2)H(+), F(2)GeC(2)H(3)(+) and F(2)GeC(6)H(5)(+). The structure, stability and thermochemistry of these products and the mechanistic aspects of the exemplary reactions of GeF(3)(+) with H(2)O, NH(3) and C(6)H(6) were investigated by MP2 and coupled cluster calculations. The experimental proton affinity (PA) and gas basicity (GB) of GeF(4) were estimated as 121.5 ± 6.0 and 117.1 ± 6.0 kcal mol(-1), respectively, and GeF(4)H(+) was theoretically characterized as an ion-dipole complex between GeF(3)(+) and HF. Consistently, it reacts with simple inorganic and organic molecules to form GeF(3)(+)-L complexes (L = H(2)O, NH(3), C(2)H(2), C(2)H(4), C(6)H(6), CO(2), SO(2) and GeF(4)). The theoretical investigation of the stability of these ions with respect to GeF(3)(+) and L disclosed nearly linear correlations between their dissociation enthalpies and free energies and the PA and GB of L. Comparing the behavior of GeF(3)(+) with the previously investigated CF(3)(+) and SiF(3)(+) revealed a periodically reversed order of reactivity CF(3)(+) < GeF(3)(+) < SiF(3)(+). This parallels the order of the Lewis acidities of the three cations.     

Proton mobility in thin ice films: a revisit

We have examined proton transport through an ice film in the temperature range 73-140 K by initially adding hydronium ions into the interior of the film and then monitoring the build-up of hydronium ion population at the film surface. The result confirms that the proton exhibits limited mobility in the ice film at low temperature, but it becomes highly mobile at temperature above 130 K. Based on this result we suggest an explanation of the anomalous experimental observations in the literature for the proton mobility in ice films.     

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.     

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.     

A mass spectrometric and molecular orbital study of H2O loss from protonated tryptophan and oxidized tryptophan derivatives

Protonated N-acetyltryptophan, oxindolylalanine (a mono-oxidized derivative of tryptophan), and N-acetyloxindolylalanine, as well as several di- and tripeptide derivatives containing oxindolylalanine, undergo a range of fragmentation reactions in the gas phase, including the loss of water. In order to elucidate the sites of water loss within these ions, and to determine the mechanisms associated with these processes, we have conducted a series of experiments employing multistage tandem mass spectrometry (MS/MS and MS(3)) in a quadrupole ion trap mass spectrometer, regiospecific structural labeling, and independent solution-phase syntheses of proposed product ion structures, coupled with the use of molecular orbital calculations at the B3LYP/6-31G* level of theory. We demonstrate that the loss of H(2)O from the amide carbonyl group of protonated N-acetyltryptophan O-methyl ester occurs via a "side-chain-backbone" neighboring group reaction to yield a protonated carboline derivative. In contrast, the loss of water from the O-methyl ester of protonated oxindolylalanine results in the formation of a tricyclic structure by "backbone-side-chain" nucleophilic attack from the amino nitrogen to the C2 position of the indole ring. The O-methyl ester of protonated N-acetyloxindolylalanine was found to dissociate via the loss of water from both possible sites, i.e. from the side-chain indolyl oxygen and the backbone amide carbonyl group. An estimate of the relative preference for water loss from each site was obtained from the abundances of product ions formed from MS(3) analysis of regiospecifically labeled derivatives of N-acetyloxindolylalanine, and from the results of molecular orbital calculations. These studies indicate the absence of a characteristic 'signature' ion or neutral loss for peptides containing oxindolylalanine residues under low-energy ion trap CID conditions.     

Ab initio molecular orbital and RRKM calculations of the thermal decomposition of CH2BrO radical

A theoretical study of the thermal decomposition and isomerization channels of bromomethoxy radical is carried out using ab initio molecular orbital methods and RRKM theory. Three kinds of reaction pathways are examined, bond scission, intramolecular three-center HBr elimination and isomerization. Energy-specific rate coefficients k(E) and thermal rate constants k(T,P) are evaluated using the ab initio data and RRKM theory. Relevance to existing experimental evidence is discussed.     

Gas-phase hydrogen/deuterium exchange as a molecular probe for the interaction of methanol and protonated peptides

The gas-phase hydrogen/deuterium (HID) exchange kinetics of several protonated amino acids and dipeptides under a background pressure of CH₃OD were determined in an external source Fourier transform mass spectrometer. H/D exchange reactions occur even when the gas-phase basicity of the compound is significantly larger (> 20 kcal/mol) than methanol. In addition; greater deuterium incorporation is observed for compounds that have multiple sites of similar basicities. A mechanism is proposed that involves a structurally specific intermediate with extensive interaction between the protonated compound and methanol.     

Proton hopping in phosphoric acid solvated nafion membrane: a molecular simulation study

Molecular simulation studies of the microstructure and of the proton transport properties of phosphoric acid solvated Nafion membrane are carried out. The ab initio calculations show that the phosphoric acid is a good solvent to promote the proton ionization of the sulfonic acid group, and only two phosphoric acid molecules are necessary for the dissociation of one sulfonic acid group. A mechanism of proton hopping between phosphoric acid and protonated phosphoric acid cation in the hydrophilic subphase is also elucidated by ab initio calculations. The molecular dynamics simulations, conducted at a phosphoric acid concentration of 25.4% (wt) which is slightly lower than that of phosphoric acid swollen Nafion, show that the phosphoric acid exists in subphases and that it cannot develop into a continuous subphase. Thus, proton-hopping pathways are interrupted, and the conductivity is expected to be lower than that for pure phosphoric acid. The molecular dynamics simulations, conducted at a phosphoric acid concentration of 45.1% (wt) which corresponds to an unstable state, show that the hydrophobic poly(tetrafluoroethylene) backbones trend to gather together forming hydrophobic clusters and that the phosphoric acid forms a continuous subphase with the sulfonic acid groups located at the hydrophobic/hydrophilic interface. Thus, proton-hopping pathways can develop uninterruptedly like the pure phosphoric acid, and high conductivity is expected. The molecular dynamics study also shows that the hydrogen-bonding characteristics of phosphoric acid and sulfonate anion are similar regardless of the factor that the former can move freely while the latter is attached to Nafion backbone.     

Proton affinities of the N- and C-terminal segments arising upon the dissociation of the amide bond in protonated peptides

Dissociation of the amide bonds in a protonated peptide leads to N-terminal sequence fragments with cyclic structures and C-terminal sequence fragments with linear structures. The ionic fragments containing the N-terminus (b _n ) have been shown to be protonated oxazolones, whereas those containing the C-terminus (y _n ) are protonated linear peptides. The coproduced neutral fragments are cyclic peptides from the N-terminus and linear peptides from the C-terminus. A likely determinant of these structural choices is the proton affinity (PA) of the described peptide segments. This study determines the PA values of such segments (Pep), i.e., cyclic and linear dipeptides and a relevant oxazolone, based on the dissociations of proton-bound dimers [Pep + B _i ]H⁺ in which B _i is a reference base of known PA value (Cooks kinetic method). The dissociations are assessed at different internal energies to thereby obtain both proton affinities as well as entropies of protonation. For species with comparable amino acid composition, the proton affinity (and gas phase basicity) follows the order cyclic peptide ≪ oxazolone ≈ linear peptide. This ranking is consistent with dissociation of the protonated peptide via interconverting proton-bound complexes involving N-terminal oxazolone (O) or cyclopeptide (C) segments and C-terminal linear peptide segments (L), viz. O ⋯ H⁺ ⋯ L ⇄ C ⋯ H⁺ ⋯ L. N-terminal sequence ions (b _n ) are formed with oxazolone structures which can efficiently compete for the proton with the linear segments. On the other hand, N-terminal neutral fragments detach as cyclic peptides, with H⁺ now being retained by the more basic linear segment from the C-terminus to yield y _n .     

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.     

Gln-Gly cleavage: a dominant dissociation site in the fragmentation of protonated peptides

An understanding of the gas-phase dissociation of protonated peptides within the mass spectrometer is essential for automated high-throughput protein identification. In this communication we describe a facile cleavage of the Gln-Gly peptide bond under low-collisional energy conditions. A variety of synthetic peptides have been analysed where key amino acids have been substituted within the sequence PQGPPQQGGR, which is a consensus repeat present in the tryptic peptides of acidic proline-rich protein 1 (PRP-1). The collision-induced dissociation spectra obtained from the PRP-1 tryptic peptides and the synthetic peptides indicate that facile Gln-Gly cleavage occurs when an X-Gln-Gly-Y sequence is present in a peptide, where X is any amino acid and Y any amino acid other than Gly.