Infrared Multiple Photon Dissociation Spectra of Proton- and Sodium Ion-Bound Glycine Dimers in the N−H and O−H Stretching Region

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M⁺, where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ as well as the protonated complex, (9eG:1mC)H⁺, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H⁺, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H⁺, forming much more (1mC)H⁺ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M⁺; M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li⁺, the lowest energy structure is one in which Li⁺ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na⁺, K⁺, and Rb⁺, similar binding of the metal cation to 1mC is calculated but, unlike Li⁺, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs⁺ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

Strong intramolecular hydrogen bonding in protonated β-methylaminoalanine: A vibrational spectroscopic and computational study

The gas-phase structure of protonated β-methylaminoalanine was investigated using infrared multiple photon dissociation spectroscopy in the C-H, N-H, O-H stretching region (2700-3800 cm^-1) and the fingerprint region (1000-1900 cm^-1). Calculations using density functional theory methods show that the lowest energy structures prefer protonation of the secondary amine. Formation of hydrogen bonds between the primary and secondary amine, and the secondary amine and carboxylic oxygen further stabilize the lowest energy structure. The infrared spectrum of the lowest energy structure originating with harmonic density functional theory has features that generally match the positions of the experimental spectra; however, the overall agreement with the experimental spectrum is poor. Molecular dynamics calculations were used to generate a gas-phase infrared spectrum. With these calculations a reasonable match with the experimental spectrum, especially in the high-energy region, was obtained. The results of the molecular dynamics simulation support the density functional theory calculations, with protonation of the secondary amine and the formation of a hydrogen bond between the protonated secondary amine and the primary amine. This work shows the importance of accounting for anharmonic effects in systems with very strong intramolecular hydrogen bonding.

Protonated glycine supramolecular systems: the need for quantum dynamics

Quantum mechanical simulations unequivocally explain experimental IR spectra of protonated supramolecular systems.

IR spectroscopy is one of the most commonly employed techniques to study molecular vibrations and interactions. However, characterization of experimental IR spectra is not always straightforward. This is the case of protonated glycine supramolecular systems like Gly₂H⁺ and (GlyH + nH₂), whose IR spectra raise questions which have still to find definitive answers even after theoretical spectroscopy investigations. Specifically, the assignment of the conformer responsible for the spectrum of the protonated glycine dimer (Gly₂H⁺) has led to much controversy and it is still debated, while structural hypotheses formulated to explain the main experimental spectral features of (GlyH + nH₂) systems have not been theoretically confirmed. We demonstrate that simulations must account for quantum dynamical effects in order to resolve these open issues. This is achieved by means of our divide-and-conquer semiclassical initial value representation technique, which approximates the quantum dynamics of high dimensional systems with remarkable accuracy and outperforms not only the commonly employed but unfit scaled-harmonic approaches, but also pure classical dynamics simulations. Besides the specific insights concerning the two particular cases presented here, the general conclusion is that, due to the widespread presence of protonated systems in chemistry, quantum dynamics may play a prominent role and should not be totally overlooked even when dealing with large systems including biological structures.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.

Hydrogen bond mediated stabilization of the salt bridge structure for the glycine dimer anion

The formation of a salt bridge in deprotonated glycine dimer anions in a solvent-free environment is investigated using both infrared multiple photon dissociation spectroscopy between 600 and 1800 cm(-1) and theory. The zwitterionic and nonzwitterionic forms of glycine in this complex are computed to be nearly iso-energetic, yet predominantly the zwitterionic form is observed experimentally. The zwitterion stability is attributed to both the Coulombic attraction and the high stabilization from intramolecular hydrogen bonding that drives the energetic cost of proton transfer in a solvent free environment. These results show that there is a fine balance between the stabilities of these two forms of the anion. Elucidating the role of intrinsic factors, such as hydrogen bonding, can lead to a better understanding of the stabilities of salt bridges in the interiors of large proteins or at protein interfaces.

Structures and unimolecular chemistry of M(Pro2-H)+(M = Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Cu, Zn) by IRMPD spectroscopy, SORI-CID, and theoretical studies

M(Pro₂-H)⁺complexes were electrosprayed and isolated in an FTICR cell where their unimolecular chemistries and structures were explored using SORI-CID and IRMPD spectroscopy.

The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods

IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).

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.

Nonlinear effects in infrared action spectroscopy of silicon and vanadium oxide clusters: experiment and kinetic modeling

Nonlinear effects in infrared action spectroscopy are experimentally quantified and successfully modeled for different inorganic clusters.

Structural melting of an amino acid dimer upon intersystem crossing

We present a spectroscopic investigation of the excited-state dynamics of the phenylalanine (Phe)/serine (Ser) protonated dimer in the gas phase. Using an ultraviolet (UV) laser pulse, we promote individual isomers to the S1 state and probe their fate with an infrared (IR) pulse. We find that the S1 state has a lifetime of ~70 ns and undergoes intersystem crossing (ISC) to the T1 state. Time-resolved IR spectra allow us to follow the structural evolution of the dimer. In the S1 state, the different isomers retain the hydrogen-bonding pattern of the ground state. Intersystem crossing triggers a sudden increase of the vibrational energy, so that the dimers can overcome isomerization barriers and explore large parts of the potential energy surface (PES). Their broad IR spectra largely resemble one another and indicate that the dimers adopt a molten structure.

The unimolecular chemistry of [Zn(amino acid)2-H]+ in the gas phase: H2 elimination when the amino acid is a secondary amine

The unimolecular chemistry of the [Zn(Pro-H)(Pro)](+) complex following collisional or infrared multiple photon activation was studied, and interestingly was found to lose H2 as one of the main dissociation pathways. Furthermore a second dehydrogenation step, forming [Zn(Pro-H)(Pro)-2H2](+), was also observed. When proline was substituted for sarcosine, also a secondary amine, a single dehydrogenation was observed. In contrast, [Zn(Gly-H)(Gly)](+) and [Zn(Ala-H)(Ala)](+) were found to lose H2O as their primary fragmentation route with no dehydrogenation observed. Tandem mass spectrometry, deuterium substitution, and infrared spectroscopy were used to determine the origin of the H atoms in the losses of H2, as well as for other fragmentation routes, including the loss of H2O. The hydrogen atoms for H2 loss from [Zn(Pro-H)(Pro)](+) was found to originate on the amine group and primarily from C5 on the non-deprotonated proline, with a smaller contribution from the C2 hydrogen. Both hydrogens for H2O loss were determined to be from labile hydrogens. Potential energy surfaces were computed for the H2 loss and H2O loss routes for both [Zn(Pro-H)(Pro)](+) and [Zn(Gly-H)(Gly)](+) and were compared. For [Zn(Pro-H)(Pro)](+), H2 loss was found to be the pathway with the lower energy requirement than for H2O loss, and the opposite was found for [Zn(Gly-H)(Gly)](+). The greater basicities of proline and sarcosine are most likely responsible for stabilizing the 3 coordinate Zn(2+) transition states en route to H2 loss, compared to those complexes formed with the much less basic glycine or alanine.

Assessing the impact of anion–π effects on phenylalanine ion structures using IRMPD spectroscopy

The gas-phase structures of two halide-bound phenylalanine anions (PheX⁻, X = Cl⁻ or Br⁻) and five fluorinated derivatives have been identified using infrared multiple photon dissociation (IRMPD) spectroscopy.

Infrared spectroscopic characterization of hydrogen-bonded propylene oxide − ethanol and propylene oxide − 2-fluoroethanol complexes isolated in solid neon matrices

The infrared absorption spectra of hydrogen-bonded complexes of propylene oxide with either ethanol or 2-fluoroethanol have been recorded in neon matrices. Mixtures of propylene oxide and ethanol or propylene oxide and 2-fluoroethanol vapors were mixed with an excess of neon gas and deposited onto a KBr substrate at 4.2 K. The results indicate that hydrogen-bonded complexes were formed with propylene oxide as the hydrogen bond acceptor and either ethanol or 2-fluoroethanol as the hydrogen bond donors. The features assigned to the O−H stretch were red-shifted by 175 and 193 cm−1 for the ethanol- and 2-fluoroethanol-containing complexes, respectively. The difference in red shifts can be accounted for due to the greater acidity of 2-fluroethanol. Deuterium isotope experiments were conducted to help confirm the assignment of the O–H stretch for the complexes. As well, structures and infrared spectra were calculated using B3LYP/6-311++G(2d,2p) calculations and were used to compare with the experimental spectra. A “scaling equation” rather than a scaling factor was used and is shown to greatly increase the utility of the calculations when comparing with experimental spectra. An examination of the O–H stretching red shifts for many hydrogen-bound complexes reveals a relationship between the shift and the difference between the acidity of the hydrogen bond donor and the basicity of the hydrogen bond acceptor (the enthalpy of proton transfer). Both hydrogen-bonded complexes and proton-bound complexes appear to have a maximum in the reduced frequency value that corresponds to complexes where the hydrogen/proton are equally shared between the two bases.

Spectroscopic and theoretical investigations of adenosine 5'-diphosphate and adenosine 5'-triphosphate dianions in the gas phase

Doubly deprotonated adenosine 5'-diphosphate ([ADP-2H](2-)) and adenosine 5'-triphosphate ([ATP-2H](2-)) dianions were investigated using infrared multiple photon dissociation (IR-MPD) and photoelectron spectroscopy. Vibrational spectra acquired in the X-H stretch region (X = C, N, O) and augmented by isotope-labelling were compared to density functional theory (DFT) calculations at the B3LYP/TZVPP level. This suggests that in [ATP-2H](2-) the two phosphate groups adjacent to the ribose ring are preferentially deprotonated. Photoelectron spectra recorded at 4.66 and 6.42 eV photon energies revealed adiabatic detachment energies of 1.35 eV for [ADP-2H](2-) and 3.35 eV for [ATP-2H](2-). Repulsive Coulomb barriers were estimated at ~2.2 eV for [ADP-2H](2-) and ~1.9 eV for [ATP-2H](2-). Time-dependent DFT calculations have been used to simulate the photoelectron spectra. Photodetachment occurs primarily from lone pair orbitals on oxygen atoms within the phosphate chain.

Locating protonated amines in clathrates

The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.

Accurate modeling of infrared multiple photon dissociation spectra: the dynamical role of anharmonicities

The dynamical response of a molecular system to a macropulse typically produced by a free-electron laser is theoretically modeled over experimentally long times, within a realistic kinetic Monte Carlo framework that incorporates absorption, stimulated emission, spontaneous emission, and dissociation events. The simulation relies on an anharmonic potential energy surface obtained from quantum chemistry calculations. Application to cationic naphthalene yields a better agreement with measurements than the anharmonic linear absorption spectrum, thus emphasizing the importance of specific dynamical effects on the spectral properties.

Infrared multiple photon dissociation spectroscopy and computational studies of O-glycosylated peptides

The infrared multiple photon dissociation (IRMPD) spectra of O-glycosylated peptides in the gas phase were studied in the IR scanning range of 5.7-9.5 μm. Fragmentation of protonated and sodiated O-glycopeptides was investigated using electrospray ionization (ESI) Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry (MS) with a free electron laser (FEL). FEL is used in the IRMPD technique as a tunable IR light source. In the IRMPD spectroscopic analysis of the protonated O-glycopeptide, fragment ions of the b/y and B/Y types were observed in the range of 5.7-9.5 μm, corresponding to the cleavage of the backbone in the parent amino acid sequence and glycosyl bonds, whereas the spectra of the sodiated glycopeptide showed major peaks of photoproducts of the B/Y type in the range of 8.4-9.5 μm. The IRMPD spectra of the O-glycopeptides were compared with simulated IR spectra for the structures obtained from the molecular dynamics.

Structures and physical properties of gaseous metal cationized biological ions

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Structures of bare and hydrated [Pb(aminoacid-H)]+ complexes using infrared multiple photon dissociation spectroscopy

Infrared multiple-photon dissociation (IRMPD) spectroscopy was used to determine the gas-phase structures of deprotonated Pb(2+)/amino acid (Aa) complexes with and without a solvent molecule present. Five amino acid complexes with side chains containing only carbon and hydrogen (Ala, Val, Leu, Ile, Pro) and one with a basic side chain (Lys) were compared. These experiments demonstrated that all [Pb(Aa-H)](+) complexes have Pb(2+) covalently bound between the amine nitrogen and carbonyl oxygen. The nonhydrated complexes containing Ala, Val, Leu, Ile, and Pro are amine-deprotonated, whereas the one containing Lys is deprotonated at its carboxylic acid. The difference is attributed to the polar and basic side chain of lysine, which helps stabilize Pb(2+). IRMPD spectroscopy was also performed on the monohydrated analogues of the [Pb(Aa-H)](+) complexes. The [Pb(Aa-H)H(2)O](+) complexes, where Aa = Ala, Val, Leu, and Ile, exhibited two N-H stretches as well as a carboxylic acid O-H and a PbO-H stretch. Hence, their structures are monohydrated versions of the amine-deprotonated [Pb(Aa-H)](+) complexes where a proton transfer has occurred from the lead-bound water to the deprotonated amine. The IRMPD spectrum and calculations suggest that [Pb(Pro-H)H(2)O](+) has a hydrated carboxylate salt structure. The structure of [Pb(Lys-H)H(2)O](+) was also carboxyl-deprotonated, but Pb(2+) is bound to the carbonyl oxygen and the amine nitrogen, with one of the protons belonging to the water transferred to the basic side chain. This results in an intramolecular hydrogen bond that does not absorb in the region of the spectrum probed in these experiments. The IRMPD spectra and structural characterizations were confirmed and aided by infrared spectra calculated at the B3LYP/6-31+G(d,p) level of theory and 298 K enthalpies and Gibbs energies using the MP2(full)/6-311++G(2d,2p) method on the B3LYP geometries.

Hybrid quadrupole mass filter∕quadrupole ion trap∕time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions

We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator∕amplifier (OPO∕A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure (∼10(-5) Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH(+), as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.

Hydration isomers of protonated phenylalanine and derivatives: relative stabilities from infrared photodissociation

The binding sites of water molecules to protonated Phe and its derivatives are investigated using infrared photodissociation (IRPD) spectroscopy and kinetics as well as by computational chemistry. Calculated relative energies for hydration of PheH(+) at various sites on the N- and C-termini depend on the type of theory and basis set used, and no one hydration site was consistently calculated to be most favorable. Infrared photodissociation (IRPD) spectra between approximately 2650 and 3850 cm(-1) are reported for PheH(+)(H(2)O)(1-4) at 133 K and compared to calculated absorption spectra of low-energy hydration isomers, which do not resemble the IRPD spectra closely enough to unambiguously assign spectral bands. The IRPD spectra of PheH(+)(H(2)O)(1-4) are instead compared to those of N,N-Me(2)PheH(+)(H(2)O)(1,2), N-MePheH(+)(H(2)O)(1-3), and PheOMeH(+)(H(2)O)(1-3) at 133 K, which makes possible systematic band assignments. A unique band associated with a binding site not previously reported for PheH(+)(H(2)O), in which the water molecule accepts a hydrogen bond from the N-terminus of PheH(+) and donates a weak hydrogen bond to the pi-system of the side chain, is identified in the IRPD spectra. IRPD kinetics at laser frequencies resonant with specific hydration isomers are found to be biexponential for N,N-Me(2)PheH(+)(H(2)O), N-MePheH(+)(H(2)O), and PheH(+)(H(2)O). Relative populations of ions with water molecules attached at various binding sites are determined from fitting these kinetic data, and relative energies for hydration of these competitive binding sites at 133 K are obtained from these experimental values.

Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes

In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long-awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry.