Rearrangement Pathways of the a 4 Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling (original) (raw)
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International Journal of Mass Spectrometry, 2012
a b s t r a c t IRMPD spectroscopy in the 'fingerprint' and X H (X = C, N, O) stretching regions was used to probe the structures of the YG a 2 ions generated from protonated YGGFL and doubly protonated YGGFLR. Our experiments indicate a mixture of cyclic and rearranged 'imine-amide' structures. The cyclic isomer is generated from the initially formed protonated imine terminated linear structure by head-to-tail cyclization. Proton transfer between the secondary amine of the ring and the amide nitrogen followed by ring opening leads to the rearranged 'imine-amide' isomer. Quantum chemical calculations demonstrate that this proton transfer is catalyzed by the tyrosine side chain ring for the YG a 2 ion. Isomer specific IRMPD bands observed in the two spectral regions clearly show the presence of the cyclic and rearranged 'imine-amide' isomers, the latter being characterized by an IR signature at ∼3545 cm −1 associated with the C-terminal amide NH 2 asymmetric stretch.
Rearrangement chemistry of a ions probed by IR spectroscopy
International Journal of Mass Spectrometry, 2015
The structure and the dynamics of the isomerization of a n ions, which are observed upon low-energy collision induced dissociation of protonated peptides in tandem mass spectrometry (MS/MS), are investigated using a combination of gas phase infrared spectroscopy and theory. IR spectra in the fingerprint region are discussed, but a particular emphasis is given to the NH stretching region which turns out to be highly structurally diagnostic. Overall, theory and infrared spectroscopy provide compelling evidence that a n ions undergo cyclisation and/or rearrangement reactions. In the cases of the a 2 and a 3 ions of oligoglycine, the analysis of the NH stretching region is fully consistent with our previous conclusions based on the IR fingerprint spectra. In the case of the a 4 ions of oligoglycine, a band observed near 3550 cm À1 provides a clear-cut signature of the permuted imine-amide structure, thus allowing for a better structural assignment. The dynamics of the rearrangement chemistry of the imine-amide structure is discussed in details, and a critical discussion on the influence of the experimental CID conditions is proposed in the case of the YG a 2 ion. 2014 Elsevier B.V. All rights reserved.
IR Spectroscopy of b 4 Fragment Ions of Protonated Pentapeptides in the X–H (X = C, N, O) Region
The Journal of Physical Chemistry A, 2013
The structure of peptide fragments was studied using "action" IR spectroscopy. We report on room temperature IR spectra of b 4 fragments of protonated GGGGG, AAAAA, and YGGFL in the X−H (X = C, N, O) stretching region. Experiments were performed with a tandem mass spectrometer combined with a table top tunable laser, and the multiple photon absorption process was assisted using an auxiliary high-power CO 2 laser. These experiments provided well-resolved spectra with relatively narrow peaks in the X−H (X = C, N, O) stretching region for the b 4 fragments of protonated GGGGG, AAAAA, and YGGFL. The 3200−3700 cm −1 range of the first two of these spectra are rather similar, and the corresponding peaks can be assigned on the basis of the classical b ion structure that has a linear backbone terminated by the oxazolone ring at the C-terminus and ionizing proton residing on the oxazolone ring nitrogen. The spectrum of the b 4 of YGGFL, on the other hand, is different from the two others and is characterized by a band observed near 3238 cm −1 . Similar band positions have recently been reported for one of the four isomers of the b 4 of YGGFL studied using double resonance IR/UV technique. As proposed in this study, the IR spectrum of this ion at room temperature can also be assigned to a linear N-terminal amine protonated oxazolone structure. However, an alternative assignment could be proposed because our room temperature IR spectrum of the b 4 of YGGFL nicely matches with the predicted IR absorption spectrum of a macrocyclic structure. Because not all experimental IR features are unambiguously assigned on the basis of the available literature structures, further theoretical studies will be required to fully exploit the benefits offered by IR spectroscopy in the X−H (X = C, N, O) stretching region.
2005
Ion mobility-mass spectrometry (IM-MS) data is interpreted as evidence that gas-phase bradykinin fragment 1-5 (BK1-5, RPPGF) [M ϩ H] ϩ ions exist as three distinct structural forms, and the relative abundances of the structural forms depend on the solvent used to prepare the matrix-assisted laser desorption ionization (MALDI) samples. Samples prepared from organic rich solvents (90% methanol/10% water) yield ions having an ion mobility arrival-time distribution (ATD) that is dominated by a single peak; conversely, samples prepared using mostly aqueous solvents (10% methanol/90% water) yield an ATD composed of three distinct peaks. The BK1-5 [M ϩ H] ϩ ions were also studied by gas-phase hydrogen/deuterium (H/D) exchange ion-molecule reactions and this data supports our interpretation of the IM-MS data. Plausible structures for BK1-5 ions were generated by molecular dynamics (MD). Candidate MD-generated structures correlated to measured cross-sections suggest a compact conformer containing a -turn whereas a more extended, open form does not contain such an interaction. This study illustrates the importance of intra-molecular interactions in the stabilization of the gas-phase ions, and these results clearly illustrate that solution-phase parameters (i.e., MALDI sample preparation) greatly influence the structures of gas-phase ions.
The Journal of Physical Chemistry B, 2012
Infrared multiphoton dissociation (IRMPD) spectroscopy, using a free-electron laser, and ion mobility measurements, using both drift-cell and traveling-wave instruments, were used to investigate the structure of gas-phase peptide (AAHAL + 2H)(2+) ions produced by electrospray ionization. The experimental data from the IRMPD spectra and collisional cross section (Ω) measurements were consistent with the respective infrared spectra and Ω calculated for the lowest-energy peptide ion conformer obtained by extensive molecular dynamics searches and combined density functional theory and ab initio geometry optimizations and energy calculations. Traveling-wave ion mobility measurements were employed to obtain the Ω of charge-reduced peptide cation-radicals, (AAHAL + 2H)(+●), and the c(3), c(4), z(3), and z(4) fragments from electron-transfer dissociation (ETD) of (AAHAL + 2H)(2+). The experimental Ω for the ETD charge-reduced and fragment ions were consistent with the values calculated for fully optimized ion structures and indicated that the ions retained specific hydrogen bonding motifs from the precursor ion. In particular, the Ω for the doubly protonated ions and charge-reduced cation-radicals were nearly identical, indicating negligible unfolding and small secondary structure changes upon electron transfer. The experimental Ω for the (AAHAL + 2H)(+●) cation-radicals were compatible with both zwitterionic and histidine radical structures formed by electron attachment to different sites in the precursor ion, but did not allow their distinction. The best agreement with the experimental Ω was found for ion structures fully optimized with M06-2X/6-31+G(d,p) and using both projection approximation and trajectory methods to calculate the theoretical Ω values.
From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry
Journal of Mass Spectrometry, 2013
Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(À) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic.
Infrared Spectroscopy of Mobility-Selected H(+)-Gly-Pro-Gly-Gly (GPGG)
Journal of the American Society for Mass Spectrometry, 2015
We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational families with collisional cross-sections of 93.8 and 96.8 Å(2). After separation, each family is independently analyzed by acquiring the infrared predissociation spectrum of the H2-tagged molecules. The ion mobility and spectroscopic data combined with density functional theory (DFT) based molecular dynamics simulations confirm the presence of one major conformer per family, which arises from cis/trans isomerization about the proline residue. We induce isomerization between the two conformers by using collisional activation in the drift tube and monitor the evolution of the ion distribution with ion mobility and infrared spectroscopy. While the cis-proline species is the preferred gas-phase structure, its relative population is smaller t...
Rapid Communications in Mass Spectrometry, 2013
Ion mobility spectrometry-mass spectrometry (IMS-MS) offers an opportunity to combine measurements and/or calculations of the collision cross-sections and subsequent mass spectra with computational modelling in order to derive the threedimensional structure of ions. IMS-MS has previously been reported to separate two components for the compound norfloxacin, explained by protonation on two different protonation sites enabling the separation of protonated isomers (protomers) using ion mobility with distinguishable MS/MS data. This study reveals further insights into the specific example of norfloxacin and wider implications for ion mobility mass spectrometry. METHODS: Using a Waters Synapt G2 quadrupole-ion mobility-time of flight mass spectrometer the IMS and MS/MS spectra of norfloxacin were recorded and compared with theoretical calculations using molecular modelling (density functional theory), and subsequent collision cross section calculations using projection approximation. RESULTS: A third significant component in the ion mobilogram of norfloxacin was observed under similar experimental conditions to those previously reported. The presence of the new component is convoluted by co-elution with another previously observed component. CONCLUSIONS: This case demonstrates the potential of combined IMS-MS/MS with molecular modelling information for increased understanding of 'small-molecule' fragmentation pathways.
The proton-and the sodium ion-bound glycine homodimers are studied by a combination of infrared multiple photon dissociation (IRMPD) spectroscopy in the N-H and O-H stretching region and electronic structure calculations. For the proton-bound glycine dimer, in the region above 3100 cm -1 , the present spectrum agrees well with one recorded previously. The present work also reveals a weak, broad absorption spanning the region from 2650 to 3300 cm -1 . This feature is assigned to the strongly hydrogen-bonded and anharmonic N-H and O-H stretching modes. As well, the shared proton stretch is observed at 2440 cm -1 . The IRMPD spectra for the proton-bound glycine dimer confirms that the lowest energy structure is an ion-dipole complex between N-protonated glycine and the carboxyl group of the second glycine. This spectrum also helps to eliminate the existence of any of the higher-energy structures considered. The IRMPD spectrum for the sodium ion-bound dimer is a much simpler spectrum consisting of three bands assigned to the O-H stretch and the asymmetric and symmetric NH 2 stretching modes. The positions of these bands are very similar to those observed for the proton-bound glycine dimer. Numerous structures were considered and the experimental spectrum agrees with the B3LYP/6-31+G(d,p) predicted spectrum for the lowest energy structure, two bidentate glycine molecules bound to Na + . Though some of the structures cannot be completely ruled out by comparing the experimental and theoretical spectra, they are energetically disfavored by at least 20 kJ mol -1 .
Chemistry-a European Journal, 2005
We investigated the potential-energy surface (PES) of the phenylalanyl–glycyl–glycine tripeptide in the gas phase by means of IR/UV double-resonance spectroscopy, and quantum chemical and statistical thermodynamic calculations. Experimentally, we observed four conformational structures and we recorded their IR spectra in the spectral region of 3000–4000 cm−1. Computationally, we investigated the PES by a combination of molecular dynamics/quenching procedures with high-level correlated ab initio calculations. We found that neither empirical potentials nor various DFT functionals provide satisfactory results. On the other hand, the approximative DFT method covering the dispersion energy yields a reliable set of the most stable structures, which we subsequently investigated with an accurate, correlated ab initio treatment. The global minimum contains three moderately strong intramolecular hydrogen bonds and is mainly stabilized by London dispersion forces between the phenyl ring, the carboxylic acid group, and various peptide bonds. A proper description of the last type of interaction requires accurate correlated ab initio calculations, including the complete basis set limit of the MP2 method and CCSD(T) correction terms. Since in our beam experiments the conformations are frozen by cooling from a higher temperature, it is necessary to localize the most stable structures on the free-energy surface rather than on the PES. We used two different procedures (rigid rotor/harmonic oscillator/ideal gas approximation based on ab initio characteristics and evaluation of relative populations from the molecular dynamic simulations using the AMBER potential) and both yield four structures, the global minimum and three local minima. These four structures were among the 15 most energetically stable structures obtained from accurate ab initio optimization. The calculated IR spectra for these four structures agree well with the experimental frequencies, which validates the localization procedure.