Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

Collision-induced dissociation studies of protonated ether--(H2O)n (n = 1-3) clusters

We have studied the protonated ether-(H2O)n (n = 1-3) complexes containing tetrahydrofuran, dimethyl, diethyl, dibutyl, and butylmethyl ethers using a flowing afterglow triple-quadrupole mass spectrometer. Collision-induced dissociation, CID, of all clusters with n = 1, 2 shows sequential water loss. The n = 3 cluster of dimethyl ether shows sequential water loss, while all other ether clusters display selective product formation. The CID spectra are interpreted based on known energetics, and theoretical studies of the dimethyl and diethyl ether systems.     

The structure and energetics of (GaAs)n, (GaAs)n(-), and (GaAs)n+ (n=2-15)

Electronic and geometrical structures of neutral, negatively, and positively charged (GaAs)n clusters are computed using density functional theory with generalized gradient approximation. All-electron computations are performed on (GaAs)2-(GaAs)9 while effective core potentials (ECPs) are used for (GaAs)9-(GaAs)15. Calibration calculations on GaAs and (GaAs)9 species support the use of the ECP for the larger clusters. The ground-state geometries of (GaAs)n(-) and/or (GaAs)n+ are different from the corresponding neutral ground-state geometry, except for n=7, 9, 12, 14, and 15, where the neutral and ions have similar structures. Beginning with n=6, all atoms are three coordinate, except for (GaAs)10+ and (GaAs)13+. For the larger species, there is a competition between fullerenes built from hexagons and rhombi and geometrical configurations where Ga-Ga and As-As bonds are formed, which results in the formation of pentagons. As expected, the static polarizability varies in the order of anion>neutral>cation, but the values are rather similar for all three charge states. The thermodynamic stability for the loss of GaAs is reported.     

Doubly charged protonated a ions derived from small peptides

Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.     

Fragmentation of Na(NH3) n + cluster ions

Photoionization and -fragmentation of Na(NH₃)_n clusters by 170 fs and 8 ns laser pulses are studied with photon energies of 2.98 eV to 3.46 eV. In the reflectron timeof- flight mass spectra a strong metastable loss of NH₃ is observed independent of the laser pulse length. From the fragmentation rate constants the internal energy of the cluster ions prior to the fragmentation process is determined by an RRK approach.     

Parity alternation of ground-state P(n)(-) and P(n)(+) (n = 3-15) phosphorus clusters

The ground-state structures of neutral, cationic, and anionic phosphorus clusters P(n), P(n)(+), and P(n)(-) (n = 3-15) have been calculated using the B3LYP/6-311+G* density functional method. The P(n)(+) and P(n)(-) (n = 3-15) clusters with odd n were found to be more stable than those with even n, and we provide a satisfactory explanation for such trends based on concepts of energy difference, ionization potential, electron affinity, and incremental binding energy. The result of odd/even alternations is in good accord with the relative intensities of cationic and anionic phosphorus clusters observed in mass spectrometric studies.     

Computational investigation of TiSin (n=2-15) clusters by the density-functional theory

The geometries, stabilities, and electronic properties of TiSin (n=2-15) clusters with different spin configurations have been systematically investigated by using density-functional theory approach at B3LYP/LanL2DZ level. According to the optimum TiSin clusters, the equilibrium site of Ti atom gradually moves from convex to surface, and to a concave site as the number of Si atom increases from 2 to 15. When n=12, the Ti atom in TiSi12 completely falls into the center of the Si outer frame, forming metal-encapsulated Si cages, which can be explained by using 16-electron rule. On the basis of the optimized geometries, various energetic properties are calculated for the most stable isomers of TiSin clusters, including the average binding energy, the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gap, fragmentation energy, and the second-order difference of energy. It is found that at size n=6,8,12 the clusters are more stable than neighboring ones. According to the Mulliken charge population analysis, charges always transfer from Si atoms to Ti atom. Furthermore, the HOMO-LUMO gaps of the most stable TiSin clusters are usually smaller than those of Sin clusters.     

Morphology of protonated methanol clusters: an infrared spectroscopic study of hydrogen bond networks of H+(CH3OH)n (n = 4-15)

Infrared spectroscopy of large-sized protonated methanol clusters, H(+)(MeOH)(n) (n = 4-15), was carried out in the OH stretch region to characterize the development of the hydrogen bond network with the cluster size, n. The band intensity of the free OH stretching mode decreased with n, and the band finally disappeared at n = 7. On the other hand, the broad absorption band due to hydrogen-bonded OH stretches exhibited a remarkable shift with the cluster size, and it finally converged on 3300 cm(-1) for n >/= approximately 10. The size dependence of the infrared spectra was morphologically interpreted in terms of the formation of the bicyclic hydrogen-bonded structure of the clusters.     

Optical properties of (GaAs)n clusters (n = 2-16)

The electronic and geometrical structures of the lowest triplet states of (GaAs) n clusters ( n = 2-16) are studied using density functional theory with generalized gradient approximation (DFT-GGA). It is found that the triplet-state geometries are different from the corresponding singlet-state geometries; for n = 2-8, 10, and 11, the triplets and singlets have different topologies, while the (GaAs) 9, (GaAs) 12, (GaAs) 15, and (GaAs) 16 triplets possess a reduced symmetry, due to Jahn-Teller distortions. Except for GaAs, the singlet states are the ground states. Excitation energies and oscillator strengths are computed for excitations from the ground state to ten singlet states of all (GaAs) n clusters using time-dependent density functional theory. The adiabatic singlet-triplet gap is compared to the vertical gap, and the difference in the eigenvalues of the highest-occupied and lowest-unoccupied molecular orbitals (the HOMO-LUMO gap). While these three values show large oscillations for small n, they approach each other as the cluster size grows. Thus, the HOMO-LUMO gap computed using the DFT-GGA approach presents a rather reliable estimate of the adiabatic singlet-triplet gap.     

Stable Tin (n = 2-15) clusters and their geometries: DFT calculations

We present a detailed structural analysis for small Tin (n = 2-15) clusters based on ab initio quantum mechanical calculations of their binding energies, frontier orbital gaps, and second energy derivatives. Local density approximation calculations revealed that while the smaller clusters (n < or = 8) prefer hexagonal atomic arrays with bulklike crystal symmetry, the bigger clusters prefer pentagonal atomic arrays. From the stability criteria of the magic number clusters we could identify three magic number clusters Ti7, Ti13, and Ti15. While the most stable configuration of Ti7 is a decahedral bipyramid induced by tetrahedral atomic arrays, the most stable configuration of Ti13 is an icosahedron. The other stable cluster Ti15 takes a closed-shell icosahedron-like configuration with both pentagonal and hexagonal symmetries. The stability of the Tin clusters strongly depends on their geometries and charge states. The HOMO-LUMO gap of the Tin clusters approaches its bulk value for n > 8. While there is not much difference between the HOMO and LUMO isosurface charge distributions for the Ti7 and Ti13 clusters in their most stable configurations, they are very different in the case of Ti15. Such a distinct charge distribution in Ti15 indicates its singular chemical selectivity over the other two magic number clusters.     

Fragmentation of protonated ions of peptides containing cysteine,cysteine sulfinic acid,and cysteine sulfonic acid

The oxidation of the sulfhydryl group in cysteine to sulfenic acid, sulfinic acid, and sulfonic acid in proteins is important in a number of enzymatic processes. In this study we examined the fragmentation of four peptides containing cysteine, cysteine sulfinic acid (Cys-SO(2)H), and cysteine sulfonic acid (Cys-SO(3)H) in an ion-trap mass spectrometer. Our results show that the presence of a Cys-SO(2)H in a peptide leads to preferential cleavage of the amide bond at the C-terminal side of the oxidized cysteine residue. The results are important for the determination of the site of the cysteine oxidation and might be useful for the sequencing of cysteine-containing peptides.     

Fragmentation dynamics of ionized neon clusters (Ne(n), n=3-14) embedded in helium nanodroplets

We report a theoretical study of the nonadiabatic fragmentation dynamics of ionized neon clusters embedded in helium nanodroplets for cluster sizes up to n=14 atoms. The dynamics of the neon atoms is modeled using the molecular dynamics with quantum transitions method of Tully [J. Chem. Phys. 93, 1061 (1990)] with the nuclei treated classically and transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole interactions are added. The effect of the spin-orbit interaction is also discussed. The helium environment is modeled by a friction force acting on charged atoms whose speed exceeds the critical Landau velocity. The dependence of the fragment size distribution on the friction strength and on the initial nanodroplet size is investigated. By comparing with the available experimental data obtained for Ne3+ and Ne4+, a reasonable value for the friction coefficient, the only parameter of the model, is deduced. This value is then used to predict the effect of the helium environment on the dissociation dynamics of larger neon clusters, n=5-14. The results show stabilization of larger fragments than in the gas phase, but fragmentation is not completely caged. In addition, two types of dynamics are characterized for Ne4+: fast and explosive, therefore leaving no time for friction to cool down the process when dynamics starts on one of the highest electronic states, and slower, therefore leading to some stabilization by helium when it starts on one of the lowest electronic states.     

Structure evolution of gold cluster anions between the planar and cage structures by isoelectronic substitution: Au(n)- (n = 13-15) and MAu(n)- (n = 12-14; M = Ag, Cu)

The structural and electronic effects of isoelectronic substitution by Ag and Cu atoms on gold cluster anions in the size range between 13 and 15 atoms are studied using a combination of photoelectron spectroscopy and first-principles density functional calculations. The most stable structures of the doped clusters are compared with those of the undoped Au clusters in the same size range. The joint experimental and theoretical study reveals a new C(3v) symmetric isomer for Au(13)(-), which is present in the experiment, but has hitherto not been recognized. The global minima of Au(14)(-) and Au(15)(-) are resolved on the basis of comparison between experiment and newly computed photoelectron spectra that include spin-orbit effects. The coexistence of two isomers for Au(15)(-) is firmly established with convincing experimental evidence and theoretical calculations. The overall effect of the isoelectronic substitution is minor on the structures relative to those of the undoped clusters, except that the dopant atoms tend to lower the symmetries of the doped clusters.     

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.     

Flat-structural Motives in Small Alumino-Carbon Clusters C(n)Al(m) (n = 2-3, m = 2-8)

Small clusters consisting of a carbon diatom or triatom and several aluminum atoms are investigated ab initio, at an MP2 level of theory. The mainly ionic character of C-Al bonding predominantly leads to structures different from corresponding hydrocarbons (also if starting from analogous initial geometries), while still producing closed-shell ground states. It is found that in many cases stable geometries correspond to flat CAl(3) units. These include unique metal-framed dicarbon and tricarbon all-flat species with unusual planar tetra-coordination. Another frequent feature is a hyper-coordination of carbon atoms, supported by their high negative charges and critically examined via atom-in-molecule calculations. Also characterized are anionic states, electronic excitation and ionization, electron attachment and detachment, and charge distributions.     

Infrared photodissociation spectroscopy of protonated ammonia cluster ions, NH4+(NH3)n (n=5-8), by using infrared free electron laser

Infrared photodissociation action spectra of protonated ammonia cluster ions, NH(4) (+)(NH(3))(n) (n=5-8), were measured in the range of 1020-1210 cm(-1) by using a tunable infrared free electron laser. Analyses by the density functional theory (DFT) show that the spectral features observed can be assigned to the nu(2) vibrational mode of the NH(3) molecules in NH(4) (+)(NH(3))(n). Size dependence of the spectra supports structural models obtained by the DFT calculations, in which the NH(4) (+) ion is solvated by the four nearest-neighbor NH(3) molecules. For NH(4) (+)(NH(3))(5), the spectrum between 1000 and 1700 cm(-1) was measured. The nu(4) bands of the NH(3) molecules and the NH(4) (+) ion were found in the range of 1420-1700 cm(-1).     

Anion photoelectron spectroscopy of germanium and tin clusters containing a transition- or lanthanide-metal atom; MGe(n)- (n = 8-20) and MSn(n)- (n = 15-17) (M = Sc-V, Y-Nb, and Lu-Ta)

The electronic properties of germanium and tin clusters containing a transition- or lanthanide-metal atom from group 3, 4, or 5, MGe(n) (M = Sc, Ti, V, Y, Zr, Nb, Lu, Hf, and Ta) and MSn(n) (M = Sc, Ti, Y. Zr, and Hf), were investigated by anion photoelectron spectroscopy at 213 nm. In the case of the group 3 elements Sc, Y, and Lu, the threshold energy of electron detachment of MGe(n)(-) exhibits local maxima at n = 10 and 16, while in the case of the group 4 elements Ti, Zr, and Hf, it exhibits a local minimum only at n = 16, associated with the presence of a small bump in the spectrum. A similar behavior is observed for MSn(n)(-) around n = 16, and these electronic characteristics of MGe(n) and MSn(n) are closely related to those of MSi(n). Compared to MSi(n), however, the larger cavity size of a Ge(n) cage allows metal atom encapsulation at a smaller size n. A cooperative effect between the electronic and geometric structures of clusters with a large cavity of Ge(16) or Sn(16) is discussed together with the results of experiments that probe their geometric stability via their reactivity to H(2)O adsorption.     

Global optimization of ionic Mg(n)F(2n) (n=1-30) clusters

The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of Mg(n)F(2n) (n=1-30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5 x 10(4) BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0 bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.     

Theoretical study of Al(n) and Al(n)O (n = 2-10) clusters

The stable structures, energies, and electronic properties of neutral, cationic, and anionic clusters of Al(n) (n = 2-10) are studied systematically at the B3LYP/6-311G(2d) level. We find that our optimized structures of Al5(+), Al9(+), Al9(-), Al10, Al10(+), and Al10(-) clusters are more stable than the corresponding ones proposed in previous literature reports. For the studied neutral aluminum clusters, our results show that the stability has an odd/even alternation phenomenon. We also find that the Al3, Al7, Al7(+), and Al7(-) structures are more stable than their neighbors according to their binding energies. For Al7(+) with a special stability, the nucleus-independent chemical shifts and resonance energies are calculated to evaluate its aromaticity. In addition, we present results on hardness, ionization potential, and electron detachment energy. On the basis of the stable structures of the neutral Al(n) (n = 2-10) clusters, the Al(n)O (n = 2-10) clusters are further investigated at the B3LYP/6-311G(2d), and the lowest-energy structures are searched. The structures show that oxygen tends to either be absorbed at the surface of the aluminum clusters or be inserted between Al atoms to form an Al(n-1)OAl motif, of which the Al(n-1) part retains the stable structure of pure aluminum clusters.