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We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni 2+ . The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial ( fac ) versus a meridional ( mer ) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol -1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d 8 Ni 2+ -ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.

The syntheses of cationic nickel complexes using N,N'-dimethyl piperazine 2,3-dithione (Me2Dt(0)) and N,N'-diisopropyl piperazine 2,3-dithione ((i)Pr2Dt(0)) ligands are reported. These ligands were used in synthesizing bis and tris(dithione)Ni(II) complexes as tetrafluoroborate or hexafluorophosphate salts, i.e., [Ni((i)Pr2Dt(0))2][BF4]2 ([1a][BF4]2), [Ni((i)Pr2Dt(0))2][PF6]2 ([1a][PF6]2), [Ni(Me2Dt(0))2][BF4]2 ([1b][BF4]2), [Ni((i)Pr2Dt(0))3][BF4]2 ([2a][BF4]2), and [Ni((i)Pr2Dt(0))3][PF6]2 ([2a][PF6]2), respectively. Complex [2a][PF6]2 was isolated from a methanolic solution of [1a][PF6]2. Compound [1a][BF4]2 crystallizes in a trigonal crystal system (space group, P31/c) and exhibits unique packing features, whereas [2a][BF4]2 crystallizes in a monoclinic (P21/n) space group. Cyclic voltammograms of [1a][BF4]2 and [1b][BF4]2 are indicative of four reduction processes associated with stepwise single-electron reduction of the ligands. Spectroelectrochemical experiments on [1a][BF4]2 exhibit an intervalence charge transfer (IVCT) transition as a spectroscopic signature of the mixed-valence [Ni((i)Pr2Dt(0))((i)Pr2Dt(1-))](-) species. Analysis of this IVCT band suggests that this ligand based mixed valence complex, [Ni((i)Pr2Dt(0))((i)Pr2Dt(1-))](-), behaves more like a traditional class II/III metal based mixed-valence complex. The density functional theory (DFT) and time dependent DFT calculations provide a theoretical framework for understanding the electronic structures and the nature of excited states of the target compounds that are consistent with their spectroscopic and redox properties. Vibrational spectra of [1a](2+) and [2a](2+) were investigated as discrete species in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy.

Infrared multiple photon dissociation action spectra of the protonated forms of the cytidyl nucleosides, 2'-deoxycytidine, [dCyd+H](+), and cytidine, [Cyd+H](+), are acquired over the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level to determine the stable low-energy tautomeric conformations of these species generated upon electrospray ionization (ESI) and to generate the linear IR absorption spectra of these protonated nucleosides. Comparison between the experimental and theoretical spectra allows the tautomeric conformations of [dCyd+H](+) and [Cyd+H](+) populated by ESI to be determined. B3LYP predicts N3 as the preferred protonation site for both [dCyd+H](+) and [Cyd+H](+), whereas MP2 suggests that protonation at O2 is more favorable. The 2'-hydroxyl substituent does not significantly alter the structures of the B3LYP N3 and MP2 O2 protonated ground tautomeric conformations of [dCyd+H](+) vs [Cyd+H](+). [dCyd+H](+) and [Cyd+H](+) exhibit very similar spectral signatures in both regions. Nonetheless, the 2'-hydroxyl does affect the relative intensities of the IRMPD bands of [dCyd+H](+) vs [Cyd+H](+). The spectral features observed in the hydrogen-stretching region complement those of the fingerprint region and allow the N3 and O2 protonated tautomeric conformations to be readily distinguished. Comparison between the measured and computed spectra indicates that both N3 and O2 protonated tautomeric conformations coexist in the experiments, and the populations are dominated by the most stable N3 and O2 protonated tautomeric conformations. Least-squares fitting of the IRMPD spectra to the IR spectra for these most stable conformers suggests relative populations of ∼55% N3 vs 45% O2 protonated conformers of [dCyd+H](+), whereas ∼47% N3 vs 53% O2 protonated conformers of [Cyd+H](+). This change in the preferred site of protonation indicates that the 2'-hydroxyl substituent plays an important role in controlling the reactivity of the cytidyl nucleosides.

The gas-phase conformations of protonated 2'-deoxyadenosine, [dAdo+H](+), and its RNA analogue protonated adenosine, [Ado+H](+), generated upon electrospray ionization are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques and supported by complementary theoretical electronic structure calculations. IRMPD action spectra are measured over the IR fingerprint region using the FELIX free-electron laser and the hydrogen-stretching region using an optical parametric oscillator/amplifier laser system. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of [dAdo+H](+) and [Ado+H](+) computed at the B3LYP/6-311+G(d,p) level of theory to determine the preferred site of protonation and to identify the structures populated in the experiments. N3 is found to be the most favorable site of protonation for both [dAdo+H](+) and [Ado+H](+), whereas conformers protonated at the N1 and N7 positions are much less stable by >25 kJ/mol. The 2'-hydroxyl substituent of Ado does not lead to a significant change in the structure of the ground-state conformer of [Ado+H](+) as compared to that of [dAdo+H](+), except that it provides additional stabilization via the formation of an O2'H···O3' hydrogen bond. Therefore, [dAdo+H](+) and [Ado+H](+) exhibit highly parallel IRMPD spectral features in both the fingerprint and hydrogen-stretching regions. However, the additional 2'-hydroxyl substituent markedly affects the IRMPD yield of the measured IR bands. The spectral signatures in the hydrogen-stretching region provide complementary information to that of the fingerprint region and enable facile differentiation of the conformers that arise from different protonation sites. In spite of the relative gas-phase stabilities of the N3 and N1 protonated conformers, present results suggest that both are accessed in the experiments and contribute to the measured IRMPD spectrum, indicating that the relative stabilities in solution also influence the populations generated by electrospray ionization.

The combination of mass spectrometry, infrared action spectroscopy and quantum-chemical calculations provides a variety of approaches to the study of the structure of biologically relevant molecules in vacuo. This chapter reviews some of the experimental methods that are currently in use, which can roughly be divided into two main categories: (1) low-temperature neutral molecules in a molecular beam environment, which can be investigated in a conformationally selective manner by the application of double-resonance laser spectroscopy and (2) ionized species which can conveniently be manipulated and selected by mass spectrometric methods and which can be investigated spectroscopically by wavelength-dependent photo-dissociation. Both approaches rely on the application of infrared tunable laser spectroscopy and the laser sources most commonly used in current studies are briefly reviewed in Sect. 3. Along with quantum-chemical calculations, reviewed in Chapter 3 of this book (Gaigeot and Spezia, Top Curr Chem doi:10.1007/128_2014_620), the experimental IR spectra reveal a wealth of information on the structural properties of the biological species.

Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500 cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5'-monophosphate (A5'p), guanosine-5'-monophosphate (G5'p), cytidine-5'-monophosphate (C5'p), and uridine-5'-monophosphate (U5'p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570-1900 cm(-1), that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G(d,p) level of theory finds that the most stable conformations of the deprotonated forms of A5'p, C5'p, and U5'p are accessed in the experiments, and these conformers adopt the C3' endo conformation of the ribose moiety and the anti conformation of the nucleobase. In the case of deprotonated G5'p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the syn rather than anti conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2'-hydroxyl group on their structure, stability, and fragmentation behavior.

The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in combination with density functional theory (DFT) calculations, provide insight into the occurrence of intramolecular proton transfer and detailed information on the conformational preferences of the peptides Z-Glu-Alan-Arg-NHMe (n = 0,1,3). Low-energy structures are obtained using molecular dynamics simulations via the simulated annealing approach, resulting in three types of SC-SC interactions, in particular two types of pair-wise interactions and one bifurcated interaction. These low-energy structures are optimized and frequency calculations are performed using the B3LYP functional, for structural analysis, and the M05-2x functional, for relative energies, employing the 6-311+G(d,p) basis set. Comparison of experimental and computed spectra suggests that only a single conformation was present for each of the three peptides. Despite the increasing spacing between the Glu and Arg residues, the peptides have several types of interactions in common, in particular specific SC-SC and dispersion interactions between the Arg side chain and the phenyl ring of the Z-cap. Comparison with previous experiments on Ac-Glu-Ala-Phe-Ala-Arg-NHMe as well as molecular dynamics simulations further suggest that the pairwise interaction observed here is indeed energetically most favorable for short peptide sequences.

A series of aluminium complex ions with trifluoromethyl-heteroarylalkenolato (TMHA) ligands are studied by gas-phase infrared multiphoton-dissociation (IRMPD) spectroscopy and computational modelling. The selected series of aluminium TMHA complex ions are promising species for the initial study of intrinsic binding characteristics of Al(III) cations in the gas phase as corresponding molecular ions. They are readily available for examination by (+) and (-) electrospray ionization mass spectrometry (ESI-MS) by spraying of [Al(3+)⋅(L(-))(3)] solutions. The complex ions under investigation contain trivalent Al(3+) cations with two chelating anionic enolate ligands, [Al(3+)⋅(L(-))(2)](+), providing insights in the nature of the heteroatom-Al bonds. Additionally, the structure of a deprotonated benzimidazole ligand, L(-,) and an anionic complex ion of Al(III) with two doubly deprotonated benzimidazole ligands, [Al(3+)⋅(L(2-))(2)](-), are examined by (-)ESI-IRMPD spectroscopy. Experimental and computational results are highly consistent and allow a reliable identification of the ion structures. In all complex ions examined the planar TMHA ligands are oriented perpendicular to each other around the metal ion, leading to a tetrahedral coordination sphere in which aluminium interacts with the enolate oxygen and heteroaryl nitrogen atoms available in each of the bidentate ligands., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In an effort to understand the chemical factors that stabilize dianions, experimental and theoretical studies on the stability of the tartrate dianion were performed. Quantum chemical calculations at the coupled cluster level reveal only a metastable state with a possible decomposition pathway (O(2)C-CH(OH)-CH(OH)-CO(2))(2-) → (O(2)C-CH(OH)-CH(OH))(•-) + CO(2) + e(-) explaining the observed gas-phase instability of this dianion. Further theoretical data were collected for the bare dianion, this molecule complexed to water, sodium, and a proton, in both the meso and l forms as well as for the uncomplexed radical anion and neutral diradical. The calculations suggest that the l-tartrate dianion is more thermodynamically stable than the dianion of the meso stereoisomer and that either dianion can be further stabilized by association with a separate species that can help to balance the charge of the molecular complex. Mass spectrometry was then used to measure the energy needed to initiate collisionally induced dissociation of the racemic tartrate dianion and for the proton and sodium adducts of both the racemic and meso form of this molecule. Infrared action spectra of the dianion stereoisomers complexed with sodium were also acquired to determine the influence of the metal ion on the vibrations of the dianions and validate the computationally predicted structures. These experimental data support the theoretical conclusions and highlight the instability of the bare tartrate dianion. From the experimental work, it could also be concluded that the pathway leading to dissociation is under kinetic control because the sodium adduct of the racemic stereoisomer dissociated at lower collisional energy, although it was calculated to be more stable, and that decomposition proceeded via C-C bond dissociation as computationally predicted. Taken together, these data provide insight into the gas-phase stability of the tartrate dianion and highlight the role of adducts in stabilizing this species.

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.

The infrared (IR) spectrum of protonated histamine (histamineH(+)) was recorded in the 575-1900 cm(-1) fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum of mass-selected histamineH(+) ions was obtained in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. A variety of isomers were identified and characterized by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. The low-energy isomers are derived from various favourable protonation sites--all of which are N atoms--and different orientations of the ethylamine side chain with respect to the heterocyclic imidazole ring. The measured IRMPD spectrum was monitored in the NH(3) loss channel and exhibits 14 bands in the investigated spectral range, which were assigned to vibrational transitions of the most stable isomer, denoted A. This imidazolium-type isomer A with protonation at the imidazole ring and gauche conformation of the ethylamine side chain is significantly stabilized by an intramolecular ionic Nπ-H(+)···Nα hydrogen bond to the ethylamino group. The slightly less stable ammonium-type isomer B with protonation at the ethylamino group is only a few kJ mol(-1) higher in energy and may also provide a minor contribution to the observed IRMPD spectrum. Isomer B is derived from A by simple proton transfer from imidazole to the ethylamino group along the intramolecular Nπ-H(+)···Nα hydrogen bond via a low barrier, which is calculated to be of the order of 5-15 kJ mol(-1). Significantly, the most stable structure of isolated histamineH(+) differs from that in the condensed phase by both the protonation site and the conformation of the side chain, emphasizing the important effects of solvation on the structure and function of this neurotransmitter. The effects of protonation on the geometric and electronic structure of histamine are evaluated by comparing the calculated properties of isomer A with those of the most stable structure of neutral histamine A(n)., (This journal is © the Owner Societies 2011)

The capability of infrared multiple photon dissociation (IRMPD) spectroscopy to gain structural information on surfactant-based supramolecular aggregates has been exploited to elucidate intermolecular interactions and local organization of positively charged sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) aggregates in the gas phase. A detailed analysis of the stretching modes of the AOTNa CO and SO(3)(-) head groups allows one to directly probe their interactions with sodium counterions and to gain insight in their organization within the aggregate. Similarities and differences of the IRMPD spectra as compared to the infrared absorption spectrum of micellized AOTNa in CCl(4) have been analyzed. They strongly suggest a reverse micelle-like organization of AOTNa charged aggregates in the gas phase. Apart from low-abundance fragmentation channels of the AOTNa (molecule) itself, the main dissociation pathway of singly charged surfactant aggregates is the loss of neutral surfactant molecules, while doubly charged aggregates dissociate preferentially by charge separation forming singly charged species. In both cases, decomposition leads to the formation of the most energetically stable charged fragments., (© 2011 American Chemical Society)

In the condensed phase, the peptide gramicidin S is often considered as a model system for a beta-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C=O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm(-1). To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm(-1). A comparison to calculations shows that for this complexed ion, four C=O groups are in an antiparallel beta-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these beta-sheet C=O groups give rise to the vibrations near 1680 cm(-1). This is in sharp contrast to expectations based on values for the condensed phase, where resonances of beta-sheet sections are thought to occur near 1630 cm(-1). The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for beta-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species.

Infrared multiple photon dissociation spectroscopy of gas-phase doubly charged alkaline earth complexes of histidine reveals a transition from dominance of the zwitterion (salt bridge, SB) conformation with Ba2+ to substantial presence of the canonical (charge-solvated, CS) conformation with Ca2+. This result is a clear illustration of the importance of metal-ion size in governing the delicate balance between these two modes of complexation of gas-phase amino acids. The two conformational motifs are clearly distinguished by characteristic spectral features, confirmed by density functional theory simulated IR spectra of the low-energy conformers. As a further illustration of histidine complexation possibilities, the spectrum of the Na+His complex shows purely CS character and emphasizes the greater tendency toward SB character induced by the higher charge in the alkaline earth complexes. Calculation of the complete series of alkaline earth/histidine complexes confirms the increasing stability of the SB conformations relative to CS with increasing metal ion size, as well as showing that among SB conformations the most highly chelated conformation (SB3) is favored for small metals, whereas the most extended conformation (SB1) is favored for large metals. A decomposition of the binding thermochemistry shows that these thermochemical trends versus metal-ion size are due to differences in electrostatic binding energies, with relatively little contribution from the deformation and rearrangement energy costs of distorting the ligand framework.

Gas-phase structures of cationized asparagine (Asn) including complexes with Li(+), Na(+), K(+), Rb(+), Cs(+), and Ba(2+), as well as protonated Asn, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser. Experimental spectra for the alkali metal cation complexes exhibit systematic trends, whereas spectra for Ba(2+)(Asn) and H(+)(Asn) are more distinct. To identify the structures formed experimentally, measured IRMPD spectra are compared to spectra calculated at a B3LYP/6-311+G(d,p) level with several effective core potentials and basis sets evaluated for the heavy metal systems. The dominant conformation ascertained for complexes with the smaller metal cations, Li(+)(Asn) and Na(+)(Asn), is a charge-solvated, tridentate [N,CO,CO] structure that binds the metal cation with the amine group of the amino acid backbone and to the carbonyl oxygen atoms of the backbone and amino acid side chain. For the larger alkali metal cation complexes, K(+)(Asn), Rb(+)(Asn), and Cs(+)(Asn), an additional charge-solvated, tridentate [COOH,CO] structure that binds the metal cation with the two oxygen atoms of the backbone carboxylic acid group and the carbonyl oxygen atom of the Asn side chain may also be present. The Ba(2+)(Asn) spectrum is characteristic of a single charge-solvated [N,CO,CO] conformation, in contrast to Gly, Trp, Arg, Gln, Pro, Ser, Val, and Glu, which all take on a zwitterionic structure when complexed to Ba(2+). In no case do the cationized Asn complexes show definitive evidence of forming a zwitterionic structure in the complexes studied here. For H(+)(Asn), a mixture of two [N,CO] structures, which differ only in the orientation the side chain and are calculated to be nearly identical in energy, explains the experimental spectrum well.

The gas-phase structures of alkali metal cationized lysine (Lys), alpha-N-methyllysine (NMeLys), and epsilon-N,N-dimethyllysine (Lys(Me)(2)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser and ab initio calculations. The proton affinities of the compounds span a range of approximately 20 kJ/mol. For NMeLys x M(+), experiment and theory indicate that NMeLys is nonzwitterionic for M = Li and zwitterionic for M = Na and K. For Lys(Me)(2) x M(+), experiment and theory indicate that Lys(Me)(2) is zwitterionic for M = Li, Na, and K. This is the first spectroscopic observation of the zwitterionic form of an amino acid complexed with Li(+). The results are compared with IRMPD spectra reported previously for Lys and -N-methyllysine (Lys(Me)) complexed with Li, Na, and K, and new calculations performed at higher levels of theory for those ions. The combined experimental and theoretical results indicate that protonation in the zwitterionic forms of the these amino acids is favored at the more basic methylated amine site, but that any relationship between the proton affinity of the amino acid and the relative zwitterion stability of the alkali metal cationized amino acid is only indirect. These results provide additional evidence that proton affinities are not a reliable indicator of zwitterion stability for cationized amino acids because side chains can have very different effects on the stability of different conformers in the neutral, protonated, and metal cationized forms.

Although solution-phase amino acids normally exist as zwitterions, this is not the case under gas-phase conditions, where the canonical structure is favored. Complexation to a metal ion can increase the relative zwitterion stability, but even then, the zwitterion (salt bridge, SB) form is not the most stable form of such singly charged complexes except for basic amino acids. Computation suggests enhanced SB stability for doubly charged complexes of weakly binding metal ions, but this has not hitherto been verified experimentally. Using infrared-spectroscopic characterization of the ion structure by multiple-photon infrared dissociation by the FELIX free electron laser, the Ba2+ complex of Trp has been shown to have the SB structure, and the presence of the nonzwitterionic (charge-solvated) form has been ruled out. The principal spectroscopic signatures of the SB structure are the appearance of the antisymmetric CO stretch of the carboxylate group at 1600 cm-1 and the umbrella mode of NH3 at 1400 cm-1.

The structures of cationized arginine complexes [Arg + M]+, (M = H, Li, Na, K, Rb, Cs, and Ag) and protonated arginine methyl ester [ArgOMe + H]+ have been investigated in the gas phase using calculations and infrared multiple-photon dissociation spectroscopy between 800 and 1900 cm-1 in a Fourier transform ion cyclotron resonance mass spectrometer. The structure of arginine in these complexes depends on the identity of the cation, adopting either a zwitterionic form (in salt-bridge complexes) or a non-zwitterionic form (in charge-solvated complexes). A diagnostic band above 1700 cm-1, assigned to the carbonyl stretch, is observed for [ArgOMe + H]+ and [Arg + M]+, (M = H, Li, and Ag), clearly indicating that Arg in these complexes is non-zwitterionic. In contrast, for the larger alkali-metal cations (K+, Rb+, and Cs+) the measured IR-action spectra indicate that arginine is a zwitterion in these complexes. The measured spectrum for [Arg + Na]+ indicates that it exists predominantly as a salt bridge with zwitterionic Arg; however, a small contribution from a second conformer (most likely a charge-solvated conformer) is also observed. While the silver cation lies between Li+ and Na+ in metal-ligand bond distance, it binds as strongly or even more strongly to oxygen-containing and nitrogen-containing ligands than the smaller Li+. The measured IR-action spectrum of [Arg + Ag]+ clearly indicates only the existence of non-zwitterionic Arg, demonstrating the importance of binding energy in conformational selection. The conformational landscapes of the Arg-cation species have been extensively investigated using a combination of conformational searching and electronic structure theory calculations [MP2/6-311++G(2d,2p)//B3LYP/6-31+G(d,p)]. Computed conformations indicate that Ag+ is di-coordinated to Arg, with the Ag+ chelated by both the N-terminal nitrogen and Neta of the side chain but lacks the strong M+-carbonyl oxygen interaction that is present in the tri-coordinate Li+ and Na+ charge-solvation complexes. Experiment and theory show good agreement; for each ion species investigated, the global-minimum conformer provides a very good match to the measured IR-action spectrum.

The gas-phase structures of protonated and alkali-metal-cationized lysine (Lys) and epsilon-N-methyllysine (Lys(Me)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. IRMPD spectra of Lys.Li(+) and Lys.Na(+) are similar, but the spectrum for Lys.K(+) is different, indicating that the structure of lysine in these complexes depends on the metal ion size. The carbonyl stretch of a carboxylic acid group is clearly observed in each of these spectra, indicating that lysine is nonzwitterionic in these complexes. A detailed comparison of these spectra to those calculated for candidate low-energy structures indicates that the bonding motif for the metal ion changes from tricoordinated for Li and Na to dicoordinated for K, clearly revealing the increased importance of hydrogen-bonding relative to metal ion solvation with increasing metal ion size. Spectra for Lys(Me).M(+) show that Lys(Me), an analogue of lysine whose side chain contains a secondary amine, is nonzwitterionic with Li and zwitterionic with K and both forms are present for Na. The proton affinity of Lys(Me) is 16 kJ/mol higher than that of Lys; the higher proton affinity of a secondary amine can result in its preferential protonation and stabilization of the zwitterionic form.

Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of limited use when sample quantities are low. Mass spectrometry (MS) on the other hand has been very successful in analyzing biological molecules down to atto-mole quantities and has hence begun to challenge XRD and NMR as the key technology in the life sciences. This trend has been further assisted by the development of MS techniques that yield structural information on biomolecules. Of these techniques, collision-induced dissociation (CID) and hydrogen/deuterium exchange (HDX) are among the most popular. Despite advances in applying these techniques, little direct experimental evidence had been available until recently to verify their proposed underlying reaction mechanisms. The possibility to record infrared spectra of mass-selected molecular ions has opened up a novel avenue in the structural characterization of ions and their reaction products. On account of its high pulse energies and wide wavelength tunability, the free electron laser for infrared experiments (FELIX) at FOM Rijnhuizen has been shown to be ideally suited to study trapped molecular ions with infrared photo-dissociation spectroscopy. In this paper, we review recent experiments in our laboratory on the infrared spectroscopic characterization of reaction products from CID and HDX, thereby corroborating some of the reaction mechanisms that have been proposed. In particular, it is shown that CID gives rise to linear fragment ion structures which have been proposed for some time, but also yields fully cyclical ring structures. These latter structures present a possible challenge for using tandem MS in the sequencing of peptides/proteins, as they can lead to a scrambling of the amino acid sequence information. In gas-phase HDX of an amino acid it is shown that the structure can be changed from a charge solvated to a zwitterionic structure, thereby demonstrating that HDX can be an invasive technique, in fact changing the structure of the analyte. These results emphasize that more fundamental work is required in order to understand the underlying mechanisms in two of the most important structural techniques in MS.

Infrared spectra of a 104 amino-acid protein in the gas phase as a function of its charge state are presented. The spectra contain clearly resolvable bands in the amide I and II spectral regions, as well as a band at 1483 cm(-1), which is not observed in solution phase spectroscopy and is especially prominent for the higher charge states. Compared to solution, the amide I band is blue-shifted and the amide II band red-shifted, as expected for species in an environment with reduced hydrogen bonding. The band positions are suggestive of a mostly alpha-helical structure of the protein and their widths are comparable to those in solution, suggesting a similar conformational distribution.