Gas-Phase Structure of a π-Allyl−Palladium Complex:  Efficient Infrared Spectroscopy in a 7 T Fourier Transform Mass Spectrometer

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Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b 2 ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800-3800 cm -1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO 2 laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm -1 , corresponding to the asymmetric N-H stretch of the (nonprotonated) N-terminal NH 2 group, is a distinct vibrational signature of the ring-protonated oxazolone structure.

Section: Resultssupporting

confidence: 72%

Section: Mass Spectrometry and Irmpd Spectroscopymentioning

confidence: 99%

Diagnosing the Protonation Site of b₂ Peptide Fragment Ions using IRMPD in the X–H (X = O, N, and C) Stretching Region

Sinha

Erlekam

Bythell

et al. 2011

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“…As discussed previously [39], this is likely to be due to the much better ion confinement with the quadrupole ion trap than in the ICR trap. It should also be noted that when the laser beam is parallel to the magnetic field, shorter irradiation time period can be used [53] than when the IR beam is perpendicular to the magnetic field, as in the configuration of the FT-ICR at FELIX.…”

Section: Yggf Versus Ggfy Sequencesmentioning

confidence: 99%

Rearrangement Pathways of the a₄ Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

Paizs

Bythell

Maı̂tre

2012

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The structure of the a 4 ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by 'action' infrared spectroscopy in the 1000-2000 cm -1 ('fingerprint') range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a 4 ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N-terminus and an amide group -CO-NH 2 at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008Chem. A , 112, 1286. Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer's work.

“…The instrument in Orsay currently is mated to both a free electron laser and a Laser Vision OPO/OPA laser. Details of IRMPD experiments with both lasers have been published previously [25]. The IRMPD spectrum reported here was recorded using the OPO/OPA laser operating in the 2500 -4000 cm Ϫ1 region covering the N-H and O-H stretching vibrations.…”

Section: Methodsmentioning

confidence: 99%

Solvation of electrosprayed ions in the accumulation/collision hexapole of a hybrid Q-FTMS

Rajabi

Easterling

Fridgen

2009

In an effort to spectroscopically determine the structures of solvated ions composed of nucleic acid bases and amino acids, methods for their gas-phase synthesis have been studied. Ions were electrosprayed and solvated in the accumulation cell of a hybrid Q-FTICR filled with methanol or water vapor at ϳ10 Ϫ2 bar. There were subsequently transferred to the FTICR cell at 10 Ϫ10 mbar. Following their isolation in the FTICR, they can be investigated by studying their unimolecular blackbody infrared radiative dissociation (BIRD) or infrared multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectra for (Ade) 2 Li ϩ and (Ade) 2 Li(H 2 O) ϩ are reported and compared as well as BIRD rate constants for multiply solvated and metalated adenine ions. . The structural properties are typically deduced from fundamental studies of their thermochemistries, reactivities, and more recently, the vibrational spectroscopy of gaseous ions [2]. The ultimate purpose and challenge for studying the physical properties of sequentially solvated ions is to extrapolate to, or contrast these properties with, those in the solution phase especially for biologically interesting ions. Mass spectrometry has become a powerful technique for investigating biomolecules following the development of electrospray ionization (ESI) [3] and matrix-assisted laser desorption/ionization (MALDI) [4 -6]. Noncovalently bound biological complexes can be transferred from aqueous solutions to the gas phase by ESI for further study of the completely desolvated complex. In some instances a small amount of solvated ions have been reported from electrospray allowing the structure, reactivity and thermochemistry of the hydrated ions to be studied [7]. Lee et al.[8] studied extensively hydrated peptides from an electrospray source by operating the capillary at room-temperature, with no nebulizer or drying gas, and optimizing the potentials in the electrospray source. These ions were found to be cooled to between 130 and 150 K by evaporation of water without drying gas, effectively freezing the biomolecules. RodriguezCruz et al. [9] studied doubly protonated gramicidin S ions with up to 50 water molecules attached in a modified instrument with a home-built electrospray source equipped with a heated capillary inlet. They formed the ions under "gentle" electrospray conditions and later described two possible mechanisms for formation of hydrated ions by ESI [10], condensation of solvent onto ions due to expansion inside the ESI interface, and/or solvent evaporation of more extensively hydrated ions or electrospray droplets. The extent of hydration of gas-phase gramicidin S (M ϩ 2H) 2ϩ ions was observed to decrease with an increase in the temperature of the capillary.Rodriguez-Cruz and Williams [11] also studied solvent exchange reactions of hydrated divalent alkaline earth metals with benzene by ESI Fourier-Transform mass spectrometry (FTMS) at room temperature. Aqueous solutions of metal chloride salts were introduced to the mass spectrometer by nanoelectrospray. Me...