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Liquid chromatography-mass spectrometry (LC-MS) is, due to its high sensitivity and selectivity, currently the method of choice in (bio)analytical studies involving the (comprehensive) profiling of metabolites in body fluids. However, as closely related isomers are often hard to distinguish on the basis of LC-MS(MS) and identification is often dependent on the availability of reference standards, the identification of the chemical structures of detected mass spectral features remains the primary limitation. Infrared ion spectroscopy (IRIS) aids identification of MS-detected ions by providing an infrared (IR) spectrum containing structural information for a detected MS-feature. Moreover, IR spectra can be routinely and reliably predicted for many types of molecular structures using quantum-chemical calculations, potentially avoiding the need for reference standards. In this work, we demonstrate a workflow for reference-free metabolite identification that combines experiments based on high-pressure liquid chromatography (HPLC), MS and IRIS with quantum-chemical calculations that efficiently generate IR spectra and give the potential to enable reference-standard free metabolite identification. Additionally, a scoring procedure is employed which shows the potential for automated structure assignment of unknowns. Via a simple, illustrative example where we identify lysine in the plasma of a hyperlysinemia patient, we show that this approach allows the efficient assignment of a database-derived molecular structure to an unknown.

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.

Infrared multiple photon dissociation (IRMPD) spectroscopy shows the [GPGG + H – H2O]+ ion to have an imidazolone structure. Collision-induced dissociation of this [b4]+ ion results in the loss of HN CH2 from the first residue; the IRMPD spectrum of this MS3 product ion is very similar to that of the [b4]+ ion itself, strongly indicating that the [b4 – HN CH2]+ ion also has an imidazolone structure. Losses of CO and glycine are the dominant dissociation pathways for the [b4 – HN CH2]+ ion. The latter loss requires tautomerism of the keto-form of the imidazolone ring to become the lower-energy enol-form, prior to dissociation. Isotopic labelling showed that loss of CO occurs from the ring of the keto-form. Density functional theory calculations were performed at both the B3LYP/6–311++G (d,p) and M06–2X/6–311++G (d,p) levels and the results are in good agreement.

Synthesis and spectra of isocytosino-8-trifluoromethylquinolone (1), as well as the gas phase InfraRed Multiple Photon Dissociation (IRMPD) spectra in the fingerprint region of the corresponding deprotonated anion (3), its d3 analogue, the monodeprotonated homodimer (2), and its d7 analogue are reported here. The anions represent nucleobase analogues having the hydrogen bonding pattern ADAAD (where A stands for acceptor and D stands for donor), in which the site of negative charge is unambiguous (as opposed to guanine, which has more than one acidic nitrogen). The match between experimental vibrational spectra and calculation is good, except for the out-of-plane HNH bends of the undeuterated and deuterated monomer anions between 400 and 600 cm−1. The anionic homodimers form in a parallel orientation.

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with metal cations. In order to determine the effects of sodium cationization on the structures of 2′-deoxycytidine and cytidine, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides, [dCyd+Na]+ and [Cyd+Na]+, are measured using the FELIX free electron laser and an OPO/OPA laser system. Energy-resolved collision-induced dissociation (ER-CID) experiments for the protonated and sodium cationized forms of the cytosine nucleosides are performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (QIT MS) to evaluate the relative propensities of protons and sodium cations for activating the glycosidic bonds of the cytosine nucleosides. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of [dCyd + Na]+ and [Cyd + Na]+. For both cytosine nucleosides, theory suggests that tridentate binding of Na+ to the O2, O4′ and O5′ atoms of the cytosine nucleobase and sugar moiety is the most stable binding mode. However, comparison of the measured IRMPD action spectrum and computed linear IR spectra suggests that anti oriented bidentate conformers of [Cyd + Na]+ are predominantly populated in the experiments. The 2′-hydroxyl substituent of Cyd stabilizes the anti oriented bidentate conformers of [Cyd + Na]+, and enables formation of a 2′OH⋯3′OH hydrogen-bonding interaction. The 2′-hydroxyl substituent is found to stabilize the glycosidic bond of Cyd vs. that of dCyd for both the protonated and sodium cationized cytosine nucleosides. Compared to protonation, sodium cationization activates the N-glycosidic bond less effectively.

The role of specific amino acid side-chains in the fragmentation chemistry of gaseous protonated peptides resulting from collisional activation remains incompletely understood. For small peptides containing asparagine and glutamine, a dominant fragmentation channel induced by collisional activations is, in addition to deamidation, the loss of neutral water. Identifying the product ion structures from H2O-loss from four protonated dipeptides containing Asn or Gln using infrared ion spectroscopy, mechanistic details of the dissociation reactions are revealed. Several sequential dissociation reactions have also been investigated and provide additional insights into the fragmentation chemistry. While water loss can in principle occur from the C-terminus, the side chain or the amide bond carbonyl oxygen, in most cases the C-terminus was found to detach H2O, leading to a b2-sequence ion with an oxazolone structure for AlaGln, and bifurcating mechanisms leading to both oxazolone and diketopiperazine species for AlaAsn and AsnAla. In contrast, GlnAla expels water from the amide side chain leading to an imino-substituted prolinyl structure.

Complexes of divalent metal ions (Cu2+ and Ni2+) with histidine tripeptide complexes (HAA, AHA and AAH) are interesting gas-phase models for some of the most widely observed patterns of metal ion binding to peptides and proteins. Gas-phase structures were characterized using infrared multiple photon dissociation (IRMPD) spectroscopy in ion-trapping mass spectrometers, along with density functional theory (DFT) computations. Ground states are square-planar with two deprotonated amide nitrogens bound to the metal ion via a double iminol rearrangement (IM binding mode), but contrary to expectations based on solution behavior, the histidine imidazole group is not bound to the metal, but instead is hydrogen bonded remote from the metal ion. The alternative “charge-solvated” (CS) binding mode (amide carbonyl oxygens binding the metal ion) lies higher in energy, but in many cases was observed to be present as conformationally unrelaxed ions with an abundance (relative to the IM conformation) that was dependent on instrument configuration and source and trap conditions. Taking advantage of the ability to form and trap both IM and CS conformations for a few of the complexes, the infrared spectroscopy of both conformations was explored in the fingerprint (1000–1800 cm−1) and hydrogen-stretching (3200–3800 cm−1) regions. For the fingerprint region, agreement is very good between the observed IRMPD spectra and the spectra predicted by DFT calculations at the B3LYP/6–311 + +g(d,p) level. Agreement in the H-stretching region is not perfect, but the characteristic IM and CS spectral patterns are evident.

In a previous study [Int. J. Mass Spectrom. 2010; 297: 67–75], the asymmetric O=U=O stretch (ν3) was measured for anionic uranyl complexes with composition [UO2(X)3]-, X = Cl-, Br- and I-. Within this group of complexes, the ν3 frequency red-shifts following the trend I > Br > Cl, suggesting concomitant weakening of the U=O bonds. However, a value for [UO2(F)3]- was not measured, which prevented a comprehensive comparison of measured ν3 positions to computed frequencies from density functional theory (DFT) calculations. Because the shift in ν3 is predicted to be most dramatic when X = F, we revisited these species using infrared multiple-photon photodissociation spectroscopy. As in our earlier study, a modest red-shift to the ν3 vibration of ∼ 6 cm-1 was observed for X = I-, Br-, and Cl-, and the position of the frequency follows the trend I- > Br- > Cl-. The value measured for [UO2(F)3]- is ∼43 cm-1 lower than the one measured for [UO2(Cl)3]-. Overall, the trend with respect to ν3 position is reproduced well by computed frequencies from DFT.

The gas-phase InfraRed Multiple Photon Dissociation (IRMPD) spectra in the fingerprint region of the anion (m/z 163) and mono-deprotonated homodimer of 9-methyl-guanine (2, m/z 329) and its d5 analogue (2-d5) are reported here. The anionic dimer is reverse Watson-Crick paired with the hydrogen bonding pattern ADD/DAA (where A stands for acceptor and D stands for donor), in which the site of negative charge is unambiguously found to be N1. The match between experimental vibrational spectra and DFT-computed spectra is good with the exception of the region between 2000 and 2900 cm-1 that contains symmetrical and antisymmetrical N-H stretches of the adjacent hydrogen-bond donor-donor pair.

In this study, peptides were derivatized by reaction with salicylaldehyde to create N-terminal imines (Schiff bases). Collision-induced dissociation of the imine-modified peptides produces a complete series of b and a ions (which reveal sequence). However, an unusual pathway is also observed, one that leads to elimination of the residue mass of the N-terminal amino acid despite the chemical modification to create the imine. This pathway was investigated further using infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory with alanine-glycine-glycine (AGG) as the test peptide. The IRMPD spectrum for the product generated by loss of 71 from modified AGG (Sal-AGG) matches one predicted for protonated Sal-GG, as well as the IRMPD spectrum of glycine-glycine derivatized independently to produce a Schiff base. We conclude that the residue mass of the N-terminal amino acid is likely eliminated through a pathway that involves nucleophilic attack by an amide N atom and possible formation of an imidazole-4-one intermediate.

The structures of Gly3·X−, Ala3·X− and Leu3·X− (X = Cl, Br and I) are investigated with computational chemistry and infrared multiple-photon dissociation (IRMPD) spectroscopy. Low-energy structures calculated at the B3LYP/6-31+G** level of theory (or with the CRENBL basis set and effective core potential implemented for Br and I) for these complexes have similar structural motifs in which the halide anion binds to the peptide via hydrogen bonds at amide, amine, and/or carboxylic acid H atoms. The IRMPD spectra do not depend significantly on anion identity. Comparisons between measured spectra and those calculated for low-energy structures of each of the chloridated complexes indicate that all three complexes have similar binding motifs. These results suggest that the size of the alkyl side chain does not significantly influence how halide anions bind to these peptides. The coordination geometries of Gly3·X− and Ala3·X− are “inverted” compared to those for the Na+ cationized peptides, where the peptides coordinate to Na+ via lone pair electrons of O and N atoms. The “inversion” in structures between Ala3·Na+ and Ala3·X− results in greater steric hindrance for some geometries of the latter. There is a subtle blue shift in the C-terminal C O stretch frequency with increasing halide anion size for each peptide, consistent with contributions from Stark and charge transfer effects. In contrast, the N H bends red shift with increasing halide anion size, which can only be attributed to the charge transfer effect. This is the first report of IR spectra of peptides complexed with anions, and these results provide insights into anion-peptide binding interactions.

The gas-phase structures of sodium cationized complexes of 5- and 6-halo-substituted uracils are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The halouracils examined in this investigation include: 5-flourouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, and 6-chlorouracil. Experimental IRMPD action spectra of the sodium cationized halouracil complexes are measured using a 4.7 T Fourier transform ion cyclotron resonance mass spectrometer coupled to the FELIX free electron laser (FEL). Irradiation of the mass selected sodium cationized halouracil complexes by the FEL was carried out over the range of frequencies extending from 950 to 1900 cm −1 . Theoretical linear IR spectra predicted for the stable low-energy conformations of the sodium cationized halouracils, calculated at B3LYP/6-31G(d) level of theory, are compared with the measured IRMPD action spectra to identify the structures accessed in the experiments. Relative stabilities of the low-energy conformations are determined from single-point energy calculations performed at the B3LYP/6-311+G(2d,2p) level of theory. The evolution of IRMPD spectral features as a function of the size (F, Cl, Br, and I) and position (5 versus 6) of the halogen substituent are examined to elucidate the effects of the halogen substituent and noncovalent interactions with sodium cations on the structure of the nucleobase. Present results are compared with results from energy-resolved collision-induced dissociation and IRMPD action spectroscopy studies previously reported for the protonated and sodium cationized forms of uracil, and halo-, methyl-, and thioketo-substituted uracils. The present results suggest that only a single conformer is accessed for all of the 5-halouracil complexes, whereas multiple conformers are accessed for the Na + (6ClU) complex. In all cases, the experimental IRMPD action spectra confirm that the sodium cation binds to the O4 carbonyl oxygen atom of the canonical diketo tautomer in the ground-state conformers, and gains additional stabilization via chelation interactions with the halogen substituent in the complexes to the 5-halouracils as predicted by theory.

The fragmentation chemistry of protonated sulfoserine was probed using a combination of collision-induced dissociation (CID) mass spectrometry, infrared multiple photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations. The IRMPD spectra of the dominant fragment ions at m/z 106 and 88 (i.e., loss of SO3 and H2SO4) were obtained and used to determine the corresponding structures. By comparison to a synthetic standard and calculations, it was determined that the m/z 106 ion is structurally identical to protonated serine. The m/z 88 fragment ion was assigned an aziridine structure based on a comparison to theory, analogous to the structure previously proposed by others for phosphoric acid loss from phosphoserine. This work provides the first spectroscopic insights into the dissociation pathways of a sulfated amino acid, laying the groundwork for future studies on related amino acids and peptides with this important, labile post-translational modification.

Binding to proteins and peptides in condensed phases, it is normal for alkali and alkaline earth metal ions to interact preferentially with Lewis-basic oxygen, nitrogen and similar open chelation points, while late transition metals like cobalt, nickel and copper characteristically deprotonate and bind to amide nitrogens along the peptide chain. Parallel to these contrasting condensed-phase binding-mode alternatives, metal ions in the gas phase can form complexes with small peptides in several complexation modes, among them the charge-solvated (CS) and the Iminol patterns. Reported here is a computational study of the factors determining the choice between these patterns in the gas phase for model ligands, dialanine and trialanine, also including illustrative experimental spectroscopic results for Ag + (Ala) 3 using the infrared multiple photon dissociation (IRMPD) technique (which has also provided previous experimental results for many of the ions studied here). Across a survey of 29 metal ions in normal oxidation states (+1, +2 and +3), unexpectedly strong correlations are found (for each charge state) between the preference for CS versus Iminol binding and the overall binding energies of the ions. Ions of +1 charge invariably prefer CS binding, while those with higher charge exhibit variable preferences. Within a given charge state, Iminol binding is more favorable, and overall binding is stronger, for light metal ions and for metal ions (“transition metals”) late in the periodic table. The tendency to go from CS to Iminol in the gas phase is generally parallel to the tendency to bind deprotonated amide nitrogens in condensed-phase, but with possible divergence between the differing environments at the point where the tendencies cross over near Mg(II). Hard/soft character of the metal ions correlates to some extent with the binding preferences, but this correlation shows numerous discrepancies. For “main-group” metal ions, electrostatic character of the binding is suggested by excellent scaling of binding energies with a scaling parameter q / R , while a contribution of enhanced binding in addition to the electrostatic binding energy is indicated for “transition” metals.

The gas-phase structures of alkali metal cationized complexes of cyclen (1,4,7,10-tetraazacyclododecane) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure theory calculations. The measured IRMPD action spectra of four M+(cyclen) complexes are compared to IR spectra predicted for the stable low-lying conformers of these complexes calculated at the B3LYP/def2-TZVPPD level of theory to identify the structures accessed in the experiments. The IRMPD yields of the M+(cyclen) complexes investigated increase as the size of the alkali metal cation increases, in accordance with the decrease in the strength of alkali metal cation binding. The IRMPD spectrum of the Na+(cyclen) complex is relatively simple, and the features observed are retained for all of the other alkali metal cation–cyclen complexes. New spectral features begin to appear for K+(cyclen) and become very obvious for the Rb+(cyclen) and Cs+(cyclen) complexes. The IRMPD action spectra for the complexes of cyclen to K+, Rb+, and Cs+ are well reproduced by the calculated spectra predicted for the most stable conformations computed. Overall comparisons suggest that only the ground-state conformations of the M+(cyclen) complexes were accessed in the experiments for the complexes to Na+ and K+, whereas evidence for a very small population of the first excited conformers is observed for the complexes to Rb+ and Cs+.

Collision-induced dissociation (CID) of the peptide alanine-4-aminomethylbenzoic acid-glycine, A(AMBz)G generates a prominent b(2) ion despite a previous report [ER. Talaty, T.J. Cooper, S.M. Osburn, M.J. Van Stipdonk, Collision-induced dissociation of protonated tetrapeptides containing beta-alanine, gamma-aminobutyric acid, e-aminocaproic acid or 4-aminomethylbenzoic acid residues, Rapid Commun. Mass Spectrom. 20 (2006) 3443-3455] which showed that incorporation of the aromatic amino acid into a peptide sequence inhibits generation of b(n) ions formed by cleavage to the immediate C-terminal side of the residue. Infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations suggest that the b(2) ion generated from A(AMBz)G has an acylium structure. The b2 ion generated from (AMBz)AG, in which the aromatic residue is situated at the amino-terminus, is instead a conventional oxazolone. (c) 2012 Elsevier B.V. All rights reserved.

Laser infrared multiple photon dissociation (IRMPD) spectroscopy has been employed to probe the C-O and C-C stretching vibrational modes of 18-crown-6 ether (18c6) complexes with alkaline-earth metals (Mg(2+), Ca(2+). Sr(2+) and Ba(2+)) stored in the cell of a Fourier Transform Ion Cyclotron Resonance mass spectrometer. Computations at the B3LYP/6-311++G(2d,2p) and B3LYP/aug-cc-pVDZ levels of theory agree well with the most salient features of the experimental spectra and allow to characterize the lower energy conformers for each type of complex. A pronounced shift of the C-O stretching band, but not of the C-C band, is found in comparison to the similar IRMPD spectra reported previously for the 18c6 complexes with alkali metals. This is attributed to the tighter coordination and stronger binding of the divalent alkaline-earth cations to the oxygen sites, and to the degree of folding of the crown ether backbone. Nevertheless, the conformational landscape and symmetry constraints of the complexes follow a pattern similar to that found for the alkali metal cations. The most stable conformers evolve from compact D(2) geometries for the smaller cations, Mg(2+) and Ca(2+), to more open C(2) configurations for Sr(2+) and to a planar D(3d) structure for Ba(2+). (C) 2011 Elsevier B.V. All rights reserved.

Interactions of halide anions (Cl-, Br-, and I-) with glutamic acid (Glu), histidine (His), and arginine (Arg) and their effects on stabilizing the zwitterionic form of these amino acids were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy between 850 and 1900 cm(-1) and hybrid density functional theory. The IRMPD spectra of Glu.X- and His.X- each have a diagnostic carbonyl stretching band at 1750 cm(-1) from a carboxylic acid group, indicating that the nonzwitterionic form of these amino acids is most stable. In contrast, a broad band at similar to 1625 cm(-1) for Arg.X- consisting of the antisymmetric stretch of a carboxylate group and hydrogen bonded NH bends, clearly shows that Arg is zwitterionic in these complexes. There are many similarities between these spectra and those of cationized amino acids, which aid in spectral interpretation. Cl- and Cs+ are of comparable size, and attachment of either ion to these amino acids has little effect on the frequencies of these diagnostic carbonyl stretches. The coordination of cations to these amino acids is different from that of anions, resulting in a favorable alignment of the dipole moment of the carbonyl group with the electric field of ions of either polarity, which causes a redshift in this band, i.e., a Stark effect. There is a slight redshift (similar to 10 cm(-1)) in the carbonyl stretch band at similar to 1750 cm(-1) for Glu.X- and His.X- with decreasing anion size, consistent with both a Stark effect and with greater carboxylate character for the carboxylic acid group in complexes with the less acidic halide ions. The anion size has little effect on the structures and relative zwitterion stabilities for most of these complexes, which can be attributed to the large size of the halide anions investigated compared to that of the alkali metal cations where size effects are more pronounced. The spectra calculated for the lowest energy structures are generally consistent with the experimental spectra, although no single structure accounts for the many distinct bands in the IRMPD spectra of His.X-. (C) 2010 Elsevier B.V. All rights reserved.