Experimental Infrared Multiple Photon Dissociation Spectra Research Articles

Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium.

The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.

Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes.

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol−1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.

IRMPD action spectroscopy, ER-CID experiments, and theoretical approaches investigate intrinsic L-thymidine properties compared to D-thymidine: Findings support robust methodology

L-Thymidine (L-dThd) is the enantiomer of D-thymidine (dThd), a naturally-occurring pyrimidine nucleoside found within DNA nucleic acids. L-dThd, also known as Telbivudine, does not occur naturally, but in the last decade has found successful application as an antiviral medication for hepatitis B virus infection. In this work, the gas-phase conformers of the protonated and sodium cationized forms of L-dThd, [L-dThd+H]+ and [L-dThd + Na]+, are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy complemented by electronic structure calculations performed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. Comparisons between the experimental IRMPD spectra and theoretical linear IR spectra elucidate the stable low-energy conformations adopted by these L-dThd complexes generated by electrospray ionization. Minor 2,4-dihydroxy tautomers (T) and O2 protonated conformers contribute to the experimental [L-dThd+H]+ population, whereas conformers involving tridentate binding of Na+ to the O2, O4′, and O5′ atoms primarily contribute to the experimental [L-dThd + Na]+ population. Theory predicts a tautomer as the protonated ground conformer of [L-dThd+H]+ with thymine in an anti orientation and a tridentate (O2O4′O5′) sodium cationized ground conformer with a syn thymine orientation, consistent with theoretical predictions for [dThd+H]+ and [dThd + Na]+, respectively. Both protonated and sodium cationized L-dThd and dThd illustrate highly parallel IRMPD spectral features as expected. Survival yield analyses of data from energy-resolved collision-induced dissociation experiments elucidate the relative stabilities of [L-dThd+H]+ and [L-dThd + Na]+ as compared to the corresponding enantiomeric systems. Identical results are exhibited in the survival yield analyses as anticipated for enantiomeric complexes to simple cations. This work employs the same robust methodology that has provided structural characterization and energetic insight for similar systems preceding it to validate the parallel theoretical and experimental behaviors expected for enantiomers.

Impact of the 2'- and 3'-Sugar Hydroxyl Moieties on Gas-Phase Nucleoside Structure.

Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogues, those based on 2',3'-dideoxyribose sugars are quite common, particularly in anti-HIV applications. The gas-phase structures of several protonated 2',3'-dideoxyribose nucleosides are examined in this work and compared with those of the analogous protonated DNA, RNA, and arabinose nucleosides to elucidate the influence of the 2'- and combined 2',3'-hydroxyl groups on intrinsic structure. Infrared multiple photon dissociation (IRMPD) action spectra are collected for the protonated 2',3'-dideoxy forms of adenosine, guanosine, cytidine, thymidine and uridine, [ddAdo+H]+, [ddGuo+H]+, [ddCyd+H]+, [ddThd+H]+, and [ddUrd+H]+, in the IR fingerprint and hydrogen-stretching regions. Molecular mechanics conformational searching followed by electronic structure calculations generates low-energy conformers of the protonated 2',3'-dideoxynucleosides and corresponding predicted linear IR spectra to facilitate interpretation of the measured IRMPD action spectra. These experimental IRMPD spectra and theoretical calculations indicate that the absence of the 2'- and 3'-hydroxyls largely preserves the protonation preferences of the canonical forms. The spectra and calculated structures indicate a slight preference for C3'-endo sugar puckering. The presence of the 3'- and further 2'-hydroxyl increases the available intramolecular hydrogen-bonding opportunities and shifts the sugar puckering modes for all nucleosides but the guanosine analogues to a slight preference for C2'-endo over C3'-endo. Graphical Abstract.

Selective C[sbnd]H bond activation of ethane by free gold clusters

The activation and potential dissociation of ethane mediated by small cationic gold clusters Aux+ (x = 2–4) has been explored by infrared multiple photon dissociation (IR-MPD) spectroscopy and density functional theory (DFT) calculations. The calculations show that the interaction between the gold clusters and ethane is mainly governed by the mixing of the ethane CH3 bond-forming orbitals π−(CH3) with gold d-orbitals. While the CC single bond appears to be unaffected, this mixing leads to the selective activation of up to two ethane C–H bonds and a reduction of the activation barrier for C–H bond dissociation to up to 0.82 eV, making the reaction kinetically feasible at room temperature. In agreement with this, experimental IR-MPD spectra of the complexes Au2(C2H6)2+ and Au2(C2D6)2+ show strong indications for the co-existence of two isomeric structures, one representing the encounter complex and one where a single ethane C–H bond is dissociated resulting in a complex which contains an ethyl group and a bridge-bonded H atom along with a second, adsorbed C2H6 molecule. A similar C–H bond dissociation mechanism is theoretically predicted for the Au3(C2H6)y+ (y = 2,3) and Au4(C2H6)y+ (y = 2,3) complexes, albeit thermodynamically less favorable. IR-MPD spectra of Au3(C2H6)y+ (y = 2,3) and Au4(C2H6)y+ (y = 2,3) confirm the encounter product to be the dominant one, although the co-existence of isomers containing ethyl groups cannot be excluded. Various pathways for C–H bond activation are theoretically explored and the ethane activation mechanism is compared to the gold mediated activation of methane and ethylene.

Sequential activation of methane by Ir+: An IRMPD and theoretical investigation

The sequential activation of up to 4 CH4 molecules by Ir+ is investigated through a gas-phase infrared multiple photon dissociation (IRMPD) experiment and theoretical calculations. A molecular beam apparatus was used to generate Ir+ by laser ablation and expose it to controlled amounts of CH4. Product ions were irradiated with IR light from a free electron laser over the 500–1800 cm−1 spectral range and photodissociation was monitored using a time-of-flight mass spectrometer. Experimental spectra were obtained for five distinct species: [Ir,3C,8 H]+, [Ir,3C,10 H]+, [Ir,4C,10 H]+, [Ir,4C,12 H]+, and [Ir,O,3C,12 H]+. To identify these species, B3LYP/def2-TZVPPD geometry optimizations were performed on a variety of possible structures, with computed IR spectra compared to the experimental IRMPD spectra. This has led to the following assignments: [Ir,3C,8 H]+ = IrCH2(CH3)2+, [Ir,3C,10 H]+ = HIr(CH3)3+, [Ir,4C,10 H]+ = Ir(CH3)2(C2H4)+, [Ir,4C,12 H]+ = a mixture of HIr(CH3)(C2H4)+(CH4), HIr(CH3)2(C2H5)+, Ir(CH3)4+, and (H2)Ir(CH3)2(C2H4)+, and [Ir,O,3C,12 H]+ = (H2O)HIr(CH3)3+. Notably, evidence for CC coupling is observed upon reaction with a fourth methane. Mechanisms for the formation of the observed products were also explored computationally by examining the reaction coordinate pathways for the reactions of methane with HIrCH+, IrCH2+, Ir(CH3)2+, HIrCH2(CH3)+, HIr(CH3)3+, and IrCH2(CH3)2+.

Cytosine Radical Cations: A Gas-Phase Study Combining IRMPD Spectroscopy, UVPD Spectroscopy, Ion-Molecule Reactions, and Theoretical Calculations.

The radical cation of cytosine (Cyt.+ ) is generated by dissociative oxidation from a ternary CuII complex in the gas phase. The radical cation is characterized by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint region, UV/Vis photodissociation (UVPD) spectroscopy, ion-molecule reactions, and theoretical calculations (density functional theory and ab initio). The experimental IRMPD spectrum features diagnostic bands for two enol-amino and two keto-amino tautomers of Cyt.+ that are calculated to be among the lowest energy isomers, in agreement with a previous study. Although the UVPD action spectrum can also be matched to a combination of the four lowest energy tautomers, the presence of a nonclassical distonic radical cation cannot be ruled out. Its formation is, however, unlikely due to the high energy of this isomer and the respective ternary CuII complex. Gas-phase ion-molecule reactions showed that Cyt.+ undergoes hydrogen-atom abstraction from 1-propanethiol, radical recombination reactions with nitric oxide, and electron transfer from dimethyl disulfide.

N3 Protonation Induces Base Rotation of 2′-Deoxyadenosine-5′-monophosphate and Adenosine-5′-monophosphate

Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments combined with theoretical calculations are performed to investigate the stable gas-phase conformations of the protonated adenine mononucleotides, [pdAdo+H](+) and [pAdo+H](+). Conformations that are present in the experiments are elucidated via comparative analyses of the experimental IRMPD spectra and the B3LYP/6-311+G(d,p) IR spectra predicted for the conformers optimized at this level of theory. N3 protonation is preferred as it induces base rotation, which allows a strong hydrogen bond to be formed between the excess proton of adenine and the phosphate moiety. In contrast, both N1 and N7 protonation are predicted to be >35 kJ/mol less favorable than N3 protonation. Only N3 protonated conformers are present in the experiments in measurable abundance. Both the low-energy conformers computed and the experimental IRMPD spectra of [pdAdo+H](+) and [pAdo+H](+) indicate that the 2'-hydroxyl moiety does not significantly impact the structure of the most stable conformer or the IRMPD spectral profile of [pAdo+H](+) vs that of [pdAdo+H](+). However, the 2'-hydroxyl leads to a 3-fold enhancement in the IRMPD yield of [pAdo+H](+) in the fingerprint region. Comparison of present results to those reported in a previous IRMPD study of the analogous protonated adenine nucleosides allows the effects of the phosphate moiety on the gas-phase conformations to be elucidated.

Structural determination of niobium-doped silicon clusters by far-infrared spectroscopy and theory.

In this work, the structures of cationic SinNb(+) (n = 4-12) clusters are determined using the combination of infrared multiple photon dissociation (IR-MPD) and density functional theory (DFT) calculations. The experimental IR-MPD spectra of the argon complexes of SinNb(+) are assigned by comparison to the calculated IR spectra of low-energy structures of SinNb(+) that are identified using the stochastic 'random kick' algorithm in conjunction with the BP86 GGA functional. It is found that the Nb dopant tends to bind in an apex position of the Sin framework for n = 4-9 and in surface positions with high coordination numbers for n = 10-12. For the larger doped clusters, it is suggested that multiple isomers coexist and contribute to the experimental spectra. The structural evolution of SinNb(+) clusters is similar to V-doped silicon clusters (J. Am. Chem. Soc., 2010, 132, 15589-15602), except for the largest size investigated (n = 12), since V takes an endohedral position in Si12V(+). The interaction with a Nb atom, with its partially unfilled 4d orbitals leads to a significant stability enhancement of the Sin framework as reflected, e.g. by high binding energies and large HOMO-LUMO gaps.

Structures and Energetics of Protonated Clusters of Methylamine with Phenylalanine Analogs, Characterized by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations.

Gas-phase clusters of protonated methylamine and phenylalanine (Phe) derivatives have been studied using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. Experiments were performed on several Phe derivatives including 4-chloro-l-phenylalanine (4Chloro-Phe), 4-nitro-l-phenylalanine (4Nitro-Phe), 3-cyano-l-phenylalanine (3Cyano-Phe), and 3-trifluoromethyl-l-phenylalanine (3CF3-Phe). Through comparisons between experimental IRMPD spectra and stimulated spectra obtained by electronic structure calculations, charge-solvated structures were found to be prevalent in both 4Chloro-Phe and 4Nitro-Phe, whereas 3Cyano-Phe favored zwitterionic structures and 3-CF3-Phe likely have both zwitterionic and charge-solvated structures present.

Vibrational signatures of S-nitrosoglutathione as gaseous, protonated species.

Gas-phase ions of protonated l-glutathione as native species, [GSH + H](+), and S-nitroso derivative, [GSNO + H](+), have been generated by electrospray ionization and probed via infrared multiple photon dissociation (IRMPD) action spectroscopy. Insight into the conformational landscape is gained from interpretation of the IR spectra aided by high-level theoretical calculations, which enables structural assignment disclosing both the site of protonation and the intramolecular hydrogen-bond network. Calculations yield the low-energy structures of [GSNO + H](+). A admixture of the four most stable ones (SN1, AN1, SN2, and AN2) is apt to account for the experimental IRMPD spectra obtained in both the 1000-2000 and the 3100-3700 cm(-1) spectral ranges. The most stable form of [GSNO + H](+), SN1, protonated at the amino group, presents a syn conformation at the S-N (partial) double bond and all peptidic carbonyls involved in (strong) C═O···H-N hydrogen bonds, so allowing closure of a C5 (β-strand), two C7 (γ-turn), and one C9-membered rings. An appreciable barrier to rotation of 43 kJ mol(-1) about the S-N bond is found to separate SN1 from the analogous anti isomer AN1, which lies only 0.70 kJ mol(-1) higher in free energy. Conformers obtained for [GSH + H](+) are very similar to the [GSNO + H](+) counterparts, indicating that the S-nitrosation motif does not affect significantly the geometry of the peptide. The observed ν(NO) signatures at 1622 and 1690 cm(-1), merged with other absorptions, are revealed by their sensitivity to (15)NO isotope labeling and by comparison with the IRMPD spectrum of native [GSH + H](+), providing a diagnostic probe for the S-nitrosation feature in natural peptides.

Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin–water non-covalent complexes

We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.

IRMPD Spectroscopic Study of Microsolvated [Na(GlyAla)]+ and [Ca(GlyAla–H)]+ and the Blue Shifting of the Hydrogen-Bonded Amide Stretch with Each Water Addition

In this study, the structures of [Na(GlyAla)(H2O)](+) and [Ca(GlyAla-H)(H2O)n](+), (n = 1-3) solvated ion-molecule complexes (as well as the AlaGly isomers) were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and with computational methods. Calculations showed that in the calcium clusters, the lowest-energy complex is the one in which the peptide is deprotonated at the carboxylic acid end and that Ca(2+) binds to both carboxylate oxygen atoms as well as the amide carbonyl oxygen. For the microsolvated structures, all three water molecules also bind directly to Ca(2+). For the singly, doubly, and triply solvated complexes, these structures are supported by experimental IRMPD spectra. For the [Na(GlyAla)(H2O)](+) complex, both carbonyl oxygen atoms, one from the intact carboxylic acid and one from the amide group, as well as the water molecule were found to be bound to the Na(+). In all of the spectra, a strong band is observed between 3300 and 3400 cm(-1) and is assigned to the amide N-H stretch, which is red-shifted due to hydrogen bonding with the amine nitrogen. The position of the hydrogen-bonded amide N-H stretch is experimentally and theoretically found to be sensitive to the number of water molecules; it is shown to blue shift upon successive hydrations.

IRMPD spectroscopic and computational study of gas phase [M(Ura-H)(Ura)]+ and [M(Ura-H)(H2O)n]+ (M = Sr, Ba; n = 1, 2) complexes

Infrared multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance mass spectrometer is used to investigate the structures of Sr2+ or Ba2+ complexes with uracil in the gas phase. [Sr(Ura-H)(Ura)]+, [Ba(Ura-H)(Ura)]+, [Sr(Ura-H)(H2O)]+, [Ba(Ura-H)(H2O)]+, and [Sr(Ura-H)(H2O)2]+ were examined in the NH/OH stretching region from 3200 to 3900cm−1. Calculations for the corresponding structures and infrared spectra were carried out using the B3LYP density functional theory in conjunction with the 6-31+G(d,p) basis set for the non-metal atoms and with the LANL2DZ basis set with relativistic core potential on Ba and Sr. The results were in good agreement with similar studies involving Pb2+ which showed that all lowest energy monomer structures involved an N3 deprotonated uracil molecule with the metal cation bound between the N3 and O4 positions. The [Sr(Ura-H)(Ura)]+ and [Ba(Ura-H)(Ura)]+ complexes were found to have a tetracoordinate metal ion, and both singly and doubly solvated complexes proved to have the water molecules coordinated to the metal ion. For all the complexes studied, the computed spectra for the lowest energy structures agreed very well with the experimental IRMPD spectra obtained. The structures of the Sr2+- and Ba2+-centred complexes are compared with those of the Pb2+-centred complexes.

Experimental and Theoretical Investigation of the Proton-Bound Dimer of Lysine

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.

Structural Elucidation of Direct Analysis in Real Time Ionized Nerve Agent Simulants with Infrared Multiple Photon Dissociation Spectroscopy

Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds.

Structures of electrosprayed Pb(Uracil-H) + complexes by infrared multiple photon dissociation spectroscopy

The structures of three ion molecule complexes of [Pb(Ura-H)] + have been explored by infrared multiple photon dissociation (IRMPD) spectroscopy in the gas phase. A complex of [Pb(Ura-H)] + with uracil, [Pb(Ura-H)(Ura)] +, or the singly or doubly water solvated complexes, [Pb(Ura-H)(H 2O)] + and [Pb(Ura-H)(H 2O) 2] +, have been irradiated with tunable infrared radiation in the N–H/O–H stretching region (3200–4000 cm −1) to produce IRMPD spectra which were compared with IR spectra computed using B3LYP/6-31+G(d,p) for various isomers. In all cases, the computed spectra for the lowest energy structures agree very well with the experimental IRMPD spectrum. Results show that all complexes involved a [Pb(Ura-H)] + core which is deprotonated at N3 and has lead bound to either N3 and O4 or N3 and O2. Our results suggest that the [Pb(Ura-H)] + structure that is deprotonated at N1 and lead is bound to N1 and O2 is not an significant contributor to the electrosprayed complexes. [Pb(Ura-H)(Ura)] + was found to have a four-coordinate lead. The water molecules in [Pb(Ura-H)(H 2O)] + and [Pb(Ura-H)(H 2O) 2] + were determined to be directly coordinated to lead, the first also hydrogen bonded to one carbonyl oxygen.

Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine

Structural characterization of protonated gas-phase ions of cysteine and dopamine by infrared multiple photon dissociation (IRMPD) spectroscopy using a free electron laser in combination with theory based on DFT calculations reveals the presence of two types of protonated dimer ions in the electrospray mass spectra of the metabolites. In addition to the proton-bound dimer of each species, the covalently bound dimer of cysteine (bound by a disulfide linkage) has been identified. The dimer ion of m/z 241 observed in the electrospray mass spectra of cysteine has been identified as protonated cystine by comparison of the experimental IRMPD spectrum to the IR absorption spectra predicted by theory and the IRMPD spectrum of a standard. Formation of the protonated covalently bound disulfide-linked dimer ions (i.e. protonated cystine) from electrospray of cysteine solution is consistent with the redox properties of cysteine. Both the IRMPD spectra and theory indicate that in protonated cystine the covalent disulfide bond is retained and the proton is involved in intramolecular hydrogen bonding between the amine groups of the two cysteine amino acid units. For cysteine, the protonated covalently bound dimer (m/z 241) dominated the mass spectrum relative to the proton-bound dimer (m/z 243), but this was not the case for dopamine, where the protonated monomer and the proton-bound dimer were both observed as major ions. An extended conformation of the ethylammonium side chain of gas-phase protonated dopamine monomer was verified from the correlation between the predicted IR absorption spectra and the experimental IRMPD spectrum. Dopamine has the same extended ethylamine side chain conformation in the proton-bound dopamine dimer identified in the mass spectra of electrosprayed dopamine. The structure of the proton-bound dimer of dopamine is confirmed by calculations and the presence of an IR band due to the shared proton. The presence of the shared proton in the protonated cystine ion can be inferred from the IRMPD spectrum.

Structures of Alkali Metal Ion−Adenine Complexes and Hydrated Complexes by IRMPD Spectroscopy and Electronic Structure Calculations

Complexes between adenine and the alkali metal ions Li(+), Na(+), K(+), and Cs(+) have been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy between 2800 and 3900 cm(-1), as have some singly hydrated complexes. The IRMPD spectra clearly show the N-H stretching and the NH(2) symmetric and asymmetric stretching vibrations of adenine; and for the solvated ions, the O-H stretching vibrations are observed. These experimental spectra were compared with those for a variety of possible structures, including both A9 (A9 refers to the tautomer where hydrogen is on the nitrogen in position 9 of adenine, see Scheme 1) and A7 adenine tautomers, computed using B3-LYP/6-31+G(d,p). By comparing the experimental and the simulated spectra it is possible to rule out various structures and to further assign structures to the species probed in these experiments. Single-point calculations on the B3-LYP/6-31+G(d,p) geometries have been performed at MP2/6-311++G(2d, p) to obtain good estimates of the relative thermochemistries for the different structures. In all cases the computed IR spectrum for the lowest energy structure is consistent with the experimental IRMPD spectrum, but in some cases structural assignment cannot be confirmed based solely upon comparison with the experimental spectra so computed thermochemistries can be used to rule out high-energy structures. On the basis of the IRMPD spectra and the energy calculations, all adenine-M(+) and adenine-M(+)-H(2)O are concluded to be composed of the A7 tautomer of adenine, which is bound to the cations in a bidentate fashion through N3 and N9 (see Scheme 1 for numbering convention). For the hydrated ions water binds directly to the metal ion through oxygen, as would be expected since the metal contains most positive charge density. For the hydrated lithium cation-bound adenine dimer, the water molecule is concluded to be hydrogen bonded to a free basic site of one of the adenine monomers, which is also bound to the lithium cation. Experimental and theoretical results on adenine-Li(+)-H(2)O suggest that the electrosprayed adenine-Li(+) resembles the lowest-energy solution phase ion rather than the lowest-energy gas-phase ion, which is the imine form.

IRMPD spectroscopy of protonated S-nitrosocaptopril, a biologically active, synthetic amino acid

S-Nitrosocaptopril, a biologically active S-nitrosothiol, is generated as protonated species and isolated in the gas phase by electrospray ionization coupled to Fourier Transform Ion Cyclotron Resonance (FT-ICR) or ion-trap mass spectrometry. The structural and IR spectroscopic characterization of protonated S-nitrosocaptopril (SNOcapH(+)) is aided by the comparative study of the parent species lacking the NO feature, namely protonated captopril. The study is accomplished by methodologies based on tandem mass spectrometry, namely by energy resolved collision-induced dissociation and infrared multiple-photon dissociation (IRMPD) spectroscopy, backed by density functional theory calculations. IRMPD spectra have been obtained both in the 1000-1900 cm(-1) fingerprint range, using a beamline of the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO), and in the O-H and N-H stretching region (2900-3700 cm(-1)) using the tunable IR radiation of a tabletop parametric oscillator/amplifier (OPO/OPA) laser source. The structural features of the ion have been ascertained by comparison of the experimental IRMPD spectra with the IR transitions calculated for the lowest energy isomers. Evidence is obtained that protonation occurs at the amide carbonyl oxygen which is found to be the thermodynamically most basic site. However, SNOcapH(+) is present as a thermally equilibrated mixture of low-energy structures, with a major contribution of the most stable isomer characterized by a trans relationship of the positively charged OH group with respect to the carboxylic acid functionality on the adjacent proline ring and by an anti conformation at the S-N (partial) double bond, though the energy difference with the analogous trans-syn isomer is less than 1 kJ mol(-1). The highly diagnostic N-O stretching mode has been unambiguously identified, which may be regarded as an informative probe for S-nitrosation features in more complex, biologically active molecules.