Debora Scuderi

Infrared Spectroscopy of Fragments of Protonated Peptides: Direct Evidence for Macrocyclic Structures of b5 Ions

b ions are of fundamental importance in peptide sequencing using tandem mass spectrometry. These ions have generally been assumed to exist as protonated oxazolone derivatives. Recent work indicates that medium-sized b ions can rearrange by head-to-tail cyclization of the oxazolone structures generating macrocyclic protonated peptides as intermediates. Here, we show using infrared spectroscopy and density functional theory calculations that the b(5) ion of protonated G(5)R exists in the mass spectrometer as an amide oxygen protonated cyclic peptide rather than fleetingly as a transient intermediate. This assignment is supported by our DFT calculations which show this macrocyclic isomer to be energetically preferred over the open oxazolone form despite the entropic constraints the cyclic form introduces.

Vibrational signatures of protonated, phosphorylated amino acids in the gas phase.

Structural characterization of protonated phosphorylated serine, threonine, and tyrosine was performed using mid-infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The ions were generated and analyzed by an external electrospray source coupled to a Paul ion-trap type mass spectrometer. Their fragmentation was induced by the resonant absorption of multiple photons from a tunable free electron laser (FEL) beam. IRMPD spectra were recorded in the 900-1850 cm(-1) energy range and compared to the corresponding computed IR spectra. On the basis of the frequency and intensity of two independent bands in the 900-1400 cm(-1) energy range, it is possible to identify the phosphorylated residue. IRMPD spectra for a 12-residue fragment of stathmin in its phosphorylated and nonphosphorylated forms were also recorded in the 800-1400 cm(-1) energy range. The lack of spectral congestion in the 900-1300 cm(-1) region makes their distinction facile. Our results show that IRMPD spectroscopy may became a valuable tool for structural characterization of small phosphorylated peptides.

Interaction of a laser-produced plume with a second time delayed femtosecond pulse

Time resolved emission spectroscopy coupled with a secondary time-delayed femtosecond pulse technique has been used to study laser–matter interaction that occurs within ablation processes from a solid target, in the 1012–1014W∕cm2 energy range. It allows an examination of the emitted optical signals that characterize the species escaping from the target, namely ions, neutrals, and nanoparticles. Size distributions of nanoparticles are deduced from an analysis of the deposition substrate. The newest result concerns the huge drop of emission signal from the nanoparticles, which occurs at a delay (0.8

Interaction of cisplatin with adenine and guanine: a combined IRMPD, MS/MS, and theoretical study.

Infrared multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH(3))(2)(G)Cl](+) and cis-[Pt(NH(3))(2)(A)Cl](+) ions (where A is adenine and G is guanine) has been performed in two spectral regions, 950-1900 and 2900-3700 cm(-1). Quantum chemical calculations at the B3LYP/LACV3P/6-311G** level yield the optimized geometries and IR spectra for the conceivable isomers of cis-[Pt(NH(3))(2)(G)Cl](+) and cis-[Pt(NH(3))(2)(A)Cl](+), whereby the cisplatin residue is attached to the N7, N3, or carbonyl oxygen atom, (O6), of guanine and to the N7, N3, or N1 position of adenine, respectively. In addition to the conventional binding sites of native adenine, complexes with N7-H tautomers have also been considered. In agreement with computational results, the IR characterization of cis-[Pt(NH(3))(2)(G)Cl](+) points to a covalent structure where Pt is bound to the N7 atom of guanine. The characterized conformer has a hydrogen-bonding interaction between a hydrogen atom of one NH(3) ligand and the carbonyl group of guanine. The experimental C═O stretching feature of cis-[Pt(NH(3))(2)(G)Cl](+) at 1718 cm(-1), remarkably red-shifted with respect to an unperturbed C═O stretching mode, is indicative of a lengthened CO bond in guanine, a signature that this group is involved in hydrogen bonding. The IRMPD spectra of cis-[Pt(NH(3))(2)(A)Cl](+) are consistent with the presence of two major isomers, PtAN3 and PtAN1, where Pt is bound to the N3 and N1 positions of native adenine, respectively.

Molecular complexes of simple anions with electron-deficient arenes: spectroscopic evidence for two types of structural motifs for anion-arene interactions.

Anion-pi interactions between a pi-acidic aromatic system and an anion are gaining increasing recognition in chemistry and biology. Herein, the binding features of an electron-deficient aromatic system (1,3,5-trinitrobenzene (TNB)) and selected anions (OH-, Br-, and I-) are examined in the gas phase by using the combined information derived from collision-induced dissociation experiments at variable energy, infrared multiple-photon dissociation spectroscopy, and quantum chemical calculations. We provide spectroscopic evidence for two different structural motifs of anion-arene complexes depending on the nature of the anion. The TNB-OR- complexes (R=H, or alkyl groups which were studied earlier) adopt an anionic sigma-complex structure whereby RO- attacks the aromatic ring with covalent bond formation, and develops a tetrahedral ring carbon bound to H and OR. The halide complexes rather conform to a structure in which the TNB moiety is hardly altered, and the halogen is placed on an unsubstituted carbon atom over the periphery of the ring at a C-X distance that is appreciably longer than a typical covalent bond length. The ensuing structural motif, previously characterized in the solid state and named weak sigma interaction, is now confirmed by an IR spectroscopic assay in the gas phase, in which the sampled species are unperturbed by crystal packing or solvation effects.

Naked Five-Coordinate FeIII(NO) Porphyrin Complexes: Vibrational and Reactivity Features

Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the dianion of 5,10,15,20-tetrakis-phenyl-porphyrin and TPFPP is the dianion of 5,10,15,20-tetrakis-pentafluorophenyl-porphyrin, have been obtained as isolated species by the gas phase reaction of NO with [Fe(III)(TPP)](+) and [Fe(III) (TPFPP)](+) ions delivered in the gas phase by electrospray ionization, respectively. The so-formed nitrosyl complexes have been characterized by vibrational spectroscopy also exploiting (15)N-isotope substitution in the NO ligand. The characteristic NO stretching frequency is observed at 1825 and 1859 cm(-1) for [Fe(III)(TPP)(NO)](+) and [Fe(III)(TPFPP)(NO)](+) ions, respectively, providing reference values for genuine five-coordinate Fe(III)(NO) porphyrin complexes differing only for the presence of either phenyl or pentafluorophenyl substituents on the meso positions of the porphyrin ligand. The vibrational assignment is aided by hybrid density functional theory (DFT) calculations of geometry and electronic structure and frequency analysis which clearly support a singlet spin electronic state for both [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+) complexes. Both TD-DFT and CASSCF calculations suggest that the singlet ground state is best described as Fe(II)(NO(+)) and that the open-shell AFC bonding scheme contribute for a high-energy excited state. The kinetics of the NO addition reaction in the gas phase are faster for [Fe(III)(TPFPP)](+) ions by a relatively small factor, though highly reliable because of a direct comparative evaluation. The study was aimed at gaining vibrational and reactivity data on five-coordinate Fe(III)(NO) porphyrin complexes, typically transient species in solution, ultimately to provide insights into the nature of the Fe(NO) interaction in heme proteins.

Structural Characterization by IRMPD Spectroscopy and DFT Calculations of Deprotonated Phosphorylated Amino Acids in the Gas Phase

Gas-phase infrared spectra of deprotonated phosphorylated amino acids ([pAA-H](-))-phosphoserine ([pSer-H](-)), phosphothreonine ([pThr-H](-)), and phosphotyrosine ([pTyr-H](-))-and of the dihydrogen phosphate anion H(2)PO(4)(-) have been recorded in the mid-IR region (650-2000 cm(-1)) under tandem mass spectrometry conditions. The experimental setup involved a Paul ion trap equipped with an electrospray ionization source coupled with a tunable free electron laser (FEL). Spectral assignment of the observed IRMPD bands and identification of the vibrational signatures of the phosphorylation have been performed by comparison with DFT calculations. The H(2)PO(4)(-) anion has been used as a simple model of a free deprotonated phosphate group, helping the identification of the IR signatures of phosphorylation. Our results show that deprotonation occurs on the phosphate group for the three amino acids. A comparison between the deprotonated and protonated phosphorylated amino acids is reported for the most important vibrational features.

Chiral recognition in cinchona alkaloid protonated dimers: mass spectrometry and UV photodissociation studies.

Chiral recognition in protonated cinchona alkaloid dimers has been studied in mass spectrometry experiments. The experimental setups involved a modified 7T FT-ICR (Fourier transform-ion cyclotron resonance) mass spectrometer (MS) and a modified Paul ion trap both equipped with an electrospray ionization source (ESI). The Paul ion trap has been coupled to a frequency-doubled dye laser. The fragmentation of protonated dimers made from cinchonidine (Cd) and the two pseudoenantiomers of quinine, namely, quinine (Qn) and quinidine (Qd), has been assessed by means of collision-induced dissociation (CID) as well as UV photodissociation (UVPD). Whereas CID fragmentation of the dimers only leads to the evaporation of the monomers, UVPD results in the additional loss of a neutral radical fragment corresponding to the quinuclidinyl radical. The effect of the excitation wavelength and of complexation with H(2)SO(4) has been studied to cast light on the reaction mechanism. Complexation with H(2)SO(4) modifies the photoreactivity of the dimers; only evaporation of the monomeric fragments, quinine, and cinchonidine is observed. Comparison between the mass spectra of the cinchona alkaloid (CdQnH(+)) or (CdQdH(+)) dimers resulting from the UVPD of (CdQnH(2)SO(4)H(+)) and that of bare (CdQnH(+)) helps propose a fragmentation mechanism, which is thought to involve fast proton transfer from the quinuclidine part of a molecular subunit to the quinoline ring. CID and UV fragmentation experiments show that the homochiral dimer is more strongly bound than the heterochiral adduct.

Conformational Analysis of Quinine and Its Pseudo Enantiomer Quinidine: A Combined Jet-Cooled Spectroscopy and Vibrational Circular Dichroism Study

Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.

IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide†

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.