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Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal–lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800–1830 cm–1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sens...

Sustainable energy generation by means of wind or from solar radiation through photovoltaics or concentrated solar power will be a significant part of the energy mix in 2025. Intermittency (due to e.g. day/night cycle) as well as regional variation of these energy sources requires means to store and transport energy on a large scale. A promising option is creating artificial solar fuels (or CO2 neutral fuels) with sustainable energy, which can easily be deployed within the present infrastructure for conventional fossil fuels.

© 2016 American Chemical Society. Gas-phase organoactinyl complexes possessing discrete An-C bonds (An = U, Np, Pu) were synthesized in a quadrupole ion trap by endothermic decarboxylation of [AnO2(O2C-R)3]-anion complexes in which a formally AnO22+actinyl core is coordinated by three carboxylate ligands, with R = CH3(methyl), CH3CC (1-propynyl), C6H5(phenyl), C6F5(pentafluorophenyl). Decarboxylation and competing ligand loss were studied computationally by density functional theory complementing experiment. Although decarboxylation was computed to be the energetically most favorable process in all cases, reduction from An(VI) to An(V) via neutral ligand loss was often prevalent, particularly for An = Np, Pu, presumably resulting from barriers associated with decarboxylation. Comparative hydrolysis rates of the An-C bonds were experimentally determined, and the chemical properties of these bonds were analyzed by the quantum theory of atoms in molecules. The measured hydrolysis rates differed by up to 3 orders of magnitude: the fastest was for [(CH3CC)UO2(O2C-CCCH3)2]-and the slowest for [(C6F5)PuO2(O2C-C6F5)2]-. There is a general correlation between hydrolysis exothermicity and hydrolysis rate. Prototypical hydrolysis reaction pathways computed for R = CH3(An = U, Np) reveal a mechanism in which an outer-sphere water becomes inner-sphere concomitant with transfer of an H atom to yield an OH ligand and CH4, with a net energy release of 170 kJ mol-1and a transition state barrier of 45 kJ mol-1for An = U. Infrared multiphoton dissociation spectra of selected complexes were acquired to confirm the predicted structures by agreement between the computed and observed vibrational frequencies. The experiment and theory results provide an evaluation of the comparative propensities for formation of the organoactinyls as a function of actinide and carboxylate and an assessment of the nature and stability toward hydrolysis of the primarily ionic An-C bonds.

The benchmark inclusion complexes formed by α-cyclodextrin (αCD) with alkali-metal cations are investigated under isolated conditions in the gas phase. The relative αCD-M(+) (M=Li(+), Na(+), K(+), Cs(+)) binding affinities and the structure of the complexes are determined from a combination of mass spectrometry, infrared action spectroscopy and quantum chemical computations. Solvent-free laser desorption measurements reveal a trend of decreasing stability of the isolated complexes with increasing size of the cation guest. The experimental infrared spectra are qualitatively similar for the complexes with the four cations investigated, and are consistent with the binding of the cation within the primary face of the cyclodextrin, as predicted by the quantum computations (B3LYP/6-31+G*). The inclusion of the quantum-chemical cation disrupts the C(6) symmetry of the free cyclodextrin to provide the optimum coordination of the cations with the -CH(2)OH groups in C(1), C(2) or C(3) symmetry arrangements that are determined by the size of the cation.

Crown ethers constitute central building blocks for the synthesis of molecular tweezers capable of trapping cationic species. In this study, isolated ternary complexes comprising two [18]crown-6 (18c6) ether molecules and one divalent cation of varying size (Cu2+, Ca2+, Ba2+) are investigated by means of laser vibrational action spectroscopy and computations. In the ternary (18c6)(2)-Cu2+ complex, one of the crown units folds tightly around the cation, while the second crown ether unit binds peripherally. Such asymmetrical binding manifests itself as a bimodal splitting of the vibrational bands measured for the complex. The size of the cation in the Ca2+ and Ba2+ complexes leads to a progressively more symmetrical coordination of the two crown ether molecules with the metal. In particular, in the spectrum of the (18c6)(2)-Ba2+ complex, the two components of the vibrational bands are merged into single-maximum envelopes. This is consistent with a C-2 arrangement predicted by the computation, in which the cation coordinates with the two crown ether units in a fully symmetrical way.

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.

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.

The gas-phase structures of singly and doubly charged complexes involving transition metal cations, Zn and Cd, bound to the amino acid histidine (His) as well as deprotonated His (His-H) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser. IRPMD spectra are measured for CdCl(+)(His), [Zn(His-H)](+), [Cd(His-H)](+), Zn(2+)(His)(2), and Cd(2+)(His)(2) in the 550-1800 cm(-1) range. These studies are complemented by quantum mechanical calculations of the predicted linear absorption spectra at the B3LYP/6-311+G(d,p) and B3LYP/Def2TZVP levels. The monomeric spectra are similar to one another and indicate that histidine coordinates to the metal in a charge-solvated (CS) tridentate form in the CdCl(+)(His) complex and has a similar tridentate configuration with a deprotonated carboxylic acid terminus in the [M(His-H)](+) complexes. The preference for these particular complexes is also found in the relative energetics calculated at the B3LYP, B3P86, and MP2(full) levels. The spectra of the dimer complexes have obvious CS characteristics, suggesting that at least one of the His ligands is charge solvated; however, there are also signatures for a salt-bridge (SB) formation in the second His ligand. The definitive assignment of a SB ligand is complicated by the presence of the CS ligand and conflicting relative energetics from the different levels of theory.

Infrared multiple photon dissociation (IRMPD) kinetics measured with tunable laser radiation from a free electron laser (FEL) are used to probe the relative populations of and interconversions between energetically competitive isomers of gas-phase ions at 298 K. On-resonance IRMPD kinetics of monoisomeric benzoate anion and anilinium (protonated aniline) are measured to determine the extent of overlap of the laser beam with the precursor ion population (similar to 93%). IRMPD kinetics indicating different photodissociation behavior for different isomers obtained at isomer-specific resonances are used to determine relative populations of salt bridge and charge-solvated isomers for ArgGly center dot Na+, Ser center dot Cs+, and Arg center dot Na+. These values and Gibbs free energy differences obtained from them for thermal precursor populations are compared to values reported using other, less direct population probes. Rapid interconversion of two charge-solvated isomers occurs for ArgGly center dot Li+ precluding population analysis for this ion. ArgGly center dot Na+ ArgGly center dot Li+, and Arg center dot Na+ exhibit IRMPD induction periods lasting many seconds for some isomers at the laser photon energies and power used, indicating that IRMPD relative spectral intensities are time-dependent for these ions and that the relative band intensities in IRMPD spectra measured with short irradiation times may not provide meaningful information about relative isomer populations. These results constitute the first direct probe of ion isomer populations using IRMPD kinetics obtained with a FEL and illustrate a number of caveats in interpreting IRMPD spectra measured with just a single irradiation time. These results also indicate that more complete overlap of the laser beam with the ions will be highly advantageous in future instrument designs for IRMPD kinetics and spectroscopy experiments.

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich. This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively. The infrared (IR) spectrum of the isolated protonated neurotransmitter dopamine was recorded in the fingerprint range (570–1880 cm−1) by means of IR multiple photon dissociation (IRMPD) spectroscopy. The spectrum was obtained in a Fourier transform ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source, which was coupled to a free electron laser (FEL). The spectroscopic studies are complemented by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. Several low-energy isomers with protonation occurring at the amino group are predicted in the energy range 0–50 kJ mol−1. Good agreement between the measured IRMPD spectrum and the calculated linear absorption spectra is observed for the two gauche conformers lowest in energy (ΔE) and free energy (ΔG) at both levels of theory, denoted g−1 and g+1. Minor contributions of higher lying gauche isomers cannot be ruled out spectroscopically but their calculated energies suggest only minor population in the sampled ion cloud. In all these gauche structures, one of the three protons of the ammonium group is pointing toward the catechol subunit, thereby maximizing the intramolecular NH–π interaction of the positive charge with the aromatic ring. In total, 16 distinct vibrational bands are observed in the IRMPD spectrum and assigned to individual normal modes of the energetically most stable g−1 conformer, with deviations of less than 24 cm−1 (average 11 cm−1) between measured and calculated frequencies. Comparison with neutral dopamine reveals the effects of protonation on the geometric and electronic structure.

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.

All eight D-aldohexoses and aldohexoses derived from the non-reducing end of disaccharides were investigated by variable-wavelength infrared multiple-photon dissociation (IRMPD) as anions in the negative-ion mode. Spectroscopic evidence supports the existence of a relatively abundant open-chain configuration of the anions in the gas phase, based on the observation of a significant carbonyl absorption band near 1710 cm(-1). The abundance of the open-chain configuration of the aldohexose anions was approximately 1000-fold or greater than that of the neutral sugars in aqueous solution. This provides an explanation as to why it has not been possible to discriminate the anomeric configuration of aldohexose anions in the gas phase when derived from the non-reducing sugar of a disaccharide. Evidence from photodissociation spectra also indicates that the different aldohexoses yield product ions with maximal abundances at different wavelengths, and that the carbonyl stretch region is useful for differentiation of sugar stereochemistries. Quantum-chemical calculations indicate relatively low energy barriers to intramolecular proton transfer between hydroxyl groups and adjacent alkoxy sites located on open-chain sugar anions, suggesting that an ensemble of alkoxy charge locations contributes to their observed photodissociation spectra. Ring opening of monosaccharide anions and interconversion among configurations is an inherent property of the ions themselves and occurs in vacuo independent of solvent participation. (C) 2011 Elsevier Ltd. All rights reserved.

The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. The competitive binding of small protonated amines constitutes a particularly key issue in the biochemistry of nonactin, which finds application in sensing and extraction technologies. In this study, isolated complexes of nonactin with ammonium and hydroxylammonium are investigated with infrared action spectroscopy and quantum chemical computations. The focus of the investigation is on the coordination achieved by the protonated guest with the oxygen atoms of either the oxolane groups or the carboxyl groups in the ester linkages of the macrocyle host and their relative contributions to the stability of the complexes. The experimental and computational data converge to a preferred coordination arrangement associated with a tight binding of the N—Hδ+ bonds with the oxolane groups. In the NH4+ complex, this results in a compact complex of S4 symmetry. In contrast, symmetry is disrupted in the NH3OH+ complex, as it incorporates a bifurcated coordination of the —OH bond with a carbonyl group and an oxolane group of the host, involving also a more stretched arrangement of the nonactin backbone. These gas-phase conformations are in agreement with the structures postulated for these complexes in condensed phases, from previous Raman and crystallographic experiments.The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. The competitive binding of small protonated amines constitutes a particularly key issue in the biochemistry of nonactin, which finds application in sensing and extraction technologies. In this study, isolated complexes of nonactin with ammonium and hydroxylammonium are investigated with infrared action spectroscopy and quantum chemical computations. The focus of the investigation is on the coordination achieved by the protonated guest with the oxygen atoms of either the oxolane groups or the carboxyl groups in the ester linkages of the macrocyle host and their relative contributions to the stability of the complexes. The experimental and computational data converge to a preferred coordination arrangement associated with a tight binding of the N—Hδ+ bonds with the oxolane groups. In the NH4+ complex, this results in a compact complex of S4 symmetry. In contr...

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.

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Astronomical IR emission spectra form the basis for the now widely accepted abundant presence of polycyclic aromatic hydrocarbons (PAHs) in inter- and circumstellar environments. A small but consistent frequency mismatch is found between the astronomically observed emission band near 6.2 μm and typical CC-stretching vibrations of PAHs measured in laboratory spectra near 6.3–6.4 μm. The shift of the band has been tentatively attributed to a variety of effects, among which the inclusion of heteroatoms, in particular nitrogen, in the PAH skeleton (PANH) as well as to metal ion binding to the PAH molecule. Here we experimentally investigate the combined effect of nitrogen-inclusion and metal ion binding on the IR spectra. In particular, infrared multiple-photon dissociation (IRMPD) spectra are recorded for coordination complexes of Cu+ with one or two quinoline, isoquinoline, and acridine ligands; complexes of the form Cu+(PANH) (MeCN), where the MeCN (acetonitrile) ligand acts as a relatively weakly bound “m...

Intramolecular hydrogen atom transfer (HAT) was examined in homocysteine (Hcy) thiyl radical/alkali metal ion complexes in the gas phase by combination of experimental techniques (ion‐molecule reactions and infrared multiple photon dissociation spectroscopy) and theoretical calculations. The experimental results unequivocally show that metal ion complexation (as opposed to protonation) of the regiospecifically generated Hcy thiyl radical promotes its rapid isomerisation into an α‐carbon radical via HAT. Theoretical calculations were employed to calculate the most probable HAT pathway and found that in alkali metal ion complexes the activation barrier is significantly lower, in full agreement with the experimental data. This is, to our knowledge, the first example of a gas‐phase thiyl radical thermal rearrangement into an α‐carbon species within the same amino acid residue and is consistent with the solution phase behaviour of Hcy radical.

A terahertz (THz) optical single-sideband modulator (OSSB) for direct conversion of free-space THz electromagnetic radiation to THz optical modulations is realized. The THz OSSB operates in the 0.3–1.0 THz range without any frequency-dependent tuning.

The influence of noncovalent interactions with a sodium cation on the gas-phase structures and N-glycosidic bond stabilities of 2'-deoxyadenosine (dAdo) and adenosine (Ado), [dAdo+Na](+) and [Ado+Na](+), are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and energy-resolved collision-induced dissociation (ER-CID) experiments. ER-CID experiments are also performed on the protonated forms of these nucleosides, [dAdo+H](+) and [Ado+H](+), for comparison purposes. Complementary electronic structure calculations are performed to determine the structures and relative stabilities of the stable low-energy conformations of the sodium cationized nucleoside complexes and to predict their IR spectra. Comparison between the measured IRMPD action spectra and calculated IR spectra enables the conformations of the sodium cationized nucleosides present in the experiments to be elucidated. The influence of sodium cationization versus protonation on the structures and IR spectra is elucidated by comparison to IRMPD and theoretical results previously reported for the protonated forms of these nucleosides. The influence of sodium cationization versus protonation on the glycosidic bond stability of the adenine nucleosides is determined by comparison of the ER-CID behavior of these systems. All structures present in the experiments are found to involve tridentate binding of Na(+) to the N3, O4', and O5' atoms forming favorable 5- and 6-membered chelation rings, which requires that adenine rotate to a syn configuration. This mode of sodium cation binding results in moderate flexibility of the sugar moiety such that the sugar puckering of the conformations present varies between C2'-endo and O4'-endo. Sodium cationization is found to be less effective toward activating the N-glycosidic bond than protonation for both dAdo and Ado. Both the IRMPD yields and ER-CID behavior indicate that the 2'-hydroxyl substituent of Ado stabilizes the N-glycosidic bond relative to that of dAdo.

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

Ion/ion reactions have in recent years seen widespread use in ion activation methods such as electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) as well as in charge manipulation of highly charged peptides/proteins and their fragments by proton transfer reaction (PTR). These techniques have, in combination, enabled top-down proteomics on limited-resolution benchtop mass spectrometry platforms such as quadrupole ion traps. Anions generated by chemical ionization of fluoranthene are often used for both ETD and PTR reactions; the radical anion of fluoranthene (m/z 202) for ETD and the closed-shell anion resulting from H atom attachment to the radical anion (m/z 203) for PTR. Here we use infrared ion spectroscopy in combination with density functional theory calculations to identify the structures of these reagent anions. We establish that the m/z 203 PTR reagent anion possesses a structure that deviates from what has been suggested previously and provides some insight into the reaction mechanism involved in PTR.

Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of 2'-deoxyguanosine-5'-monophosphate and guanosine-5'-monophosphate, [pdGuo+H](+) and [pGuo+H](+), are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Electronic structure calculations are performed to generate low-energy conformations of [pdGuo+H](+) and [pGuo+H](+) and determine their relative stabilities at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparative analyses of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers are performed to determine the most favorable site of protonation and the conformers present in the experiments. These comparisons and the computed energetics find that N7 protonation is considerably preferred over O6 and N3, and the N7 protonated ground-state conformers of [pdGuo+H](+) and [pGuo+H](+) are populated in the experiments. The 2'-hydroxyl substituent does not significantly impact the stable low-energy conformers of [pdGuo+H](+)vs. those of [pGuo+H](+). The effect of the 2'-hydroxyl substituent is primarily reflected in the relative intensities of the measured IRMPD bands, as the IRMPD profiles of [pdGuo+H](+) and [pGuo+H](+) are quite similar. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of the guanine nucleosides, [dGuo+H](+) and [Guo+H](+), and deprotonated forms of the guanine nucleotides, [pdGuo-H](-) and [pGuo-H](-), provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Protonation is found to induce base rotation of the guanine residue to an anti orientation vs. the syn orientation found for the deprotonated forms of the guanine nucleotides.

Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.

We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action Spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate, moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment.

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 similar to 55% N3 vs 45% O2 protonated conformers of [dCyd+H](+), whereas similar to 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.

Electro-optic (EO) detection of relativistic Coulomb fields offers a method for non-destructive longitudinal profile measurements of ultrashort bunches. Techniques for single-shot EO characterisation of Coulomb fields which have been developed or demonstrated at the FELIX free electron laser (FEL) facility are discussed. In addition, recent FELIX experiments have used single-shot electro-optic detection to measure the temporal profile of the far-infrared electric field pulse of coherent synchrotron radiation (CSR), initial results of which are reported here. Such time-resolved CSR measurements have the potential for a completely non-invasive bunch longitudinal profile determination, without the ambiguity in profile that is present in CSR spectral measurements.

Correction for ‘Zn2+ and Cd2+ cationized serine complexes: infrared multiple photon dissociation spectroscopy and density functional theory investigations’ by Rebecca A. Coates et al., Phys. Chem. Chem. Phys., 2016, 18, 22434–22445.

Rearranged: The attachment of gas‐phase divalent metal ions that bind as strongly as Mg2+ and transition‐metal ions to the dipeptide PhePhe results in displacement of the amide proton by the newly characterized iminol tautomerization rearrangment. More weakly coordinating ions bind in the known charge‐solvation mode. Infrared multiple‐photon dissociation spectroscopy using the free‐electron laser clearly shows the tautomeric transition.

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.

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.

The gas-phase complex UO2(TMOGA)(2)(2+) (TMOGA = tetramethyl-3-oxa-glutaramide) prepared by electrospray ionization was characterized by infrared multiphoton dissociation (IRMPD) spectroscopy. The IRMPD spectrum from 700-1800 cm(-1) was interpreted using a computational study based on density functional theory. The predicted vibrational frequencies are in good agreement with the measured values, with an average deviation of only 8 cm(-1) (

Infrared multiple-photon dissociation (IRMPD) spectroscopy has been used to examine the gas-phase conformations of a series of short protonated polyproline ions (Pro 3 –Pro 6 ), their CID/IRMPD fragmentation pathways, and the associated fragment identities. Consistent with previous findings, and in combination with density functional theory (DFT) and MM/MD methods, a series of conformers for the protonated parent ions having their first peptide bond in the cis conformation has been identified. This conformation maximizes the solvation of the protonated N-terminus and stabilizes these compact globular-type conformations. This is in contrast to the PPI and PPII polyproline-type helices reported for larger polyproline peptides in solution. As well, this conformation leads to a unique fragmentation pattern upon collisional or multiple-photon activation. We report observation of the uncommon, but thermodynamically favored, diketopiperazine-type b 2 + fragment ion. Formation of b 2 + ions along the diketopiperazine pathway is in line with a cis configuration of the first amide linkage in the protonated parent ion. Additionally, the parent ion conformations, fragmentation pathways, and proton affinities of the resulting fragments have been related to the observed proline-effect in CID mass spectra.

CO stretching frequencies of free, gaseous, fluorinated alkoxide ions shift substantially to the blue, relative to those of corresponding alcohols complexed with ammonia. Free α-fluorinated ions, pentafluoroethoxide and heptafluoroisopropoxide anions, display further blue shifts relative to cases with only β-fluorination, providing experimental evidence for fluorine negative hyperconjugation. DFT analysis with the atoms in molecules (AIM) method confirms an increase in CO bond order for the α-fluorinated ions, demonstrating an increase in carbonyl character for the free ions.

DNA nucleobases make use of hydrogen bonding, whether in associating to form the Watson–Crick double-helix or in producing alternative structures such as the G-quadruplex or the i-motif. Nucleoside proton-bound dimers provide an avenue for investigating characteristics that they possess within the i-motif and related non-Watson–Crick conformations. In addition, several nucleosides are approved antiviral and anticancer agents. The nucleosides under investigation (2′-deoxycytidine, gemcitabine, and decitabine) are capable of forming proton-bound dimers (PBDs) with their conjugate acids. Protonated monomers of 2′-deoxycytidine, gemcitabine, and decitabine and proton-bound dimers of gemcitabine and decitabine have been produced in the gas phase using electrospray ionization (ESI). This paper reports proton affinities of the neutral nucleosides as well as their infrared multiple photon dissociation (IRMPD) spectra from 2800 to 3800 cm−1 collected using an Optical Parametric Oscillator (OPO) laser. In the case of the conjugate acid of 2′-deoxycytidine, a partial deuteration experiment suppresses overtones and combination bands, leading to the inference that a single tautomer predominates in the protonated monomer. IRMPD spectra of proton-bound dimers of gemcitabine and decitabine suggest furanose sugar ring puckering to be in the South orientation, as they are in the protonated monomers.

The strong non-equilibrium conditions provided by the plasma phase offer the opportunity to beat traditional thermal process energy efficiencies via preferential excitation of molecular vibrations. Simple molecular physics considerations are presented to explain potential dissociation pathways in plasma and their effect on energy efficiency. A common microwave reactor approach is evaluated experimentally with Rayleigh scattering and Fourier transform infrared spectroscopy to assess gas temperatures (exceeding 104 K) and conversion degrees (up to 30%), respectively. The results are interpreted on a basis of estimates of the plasma dynamics obtained with electron energy distribution functions calculated with a Boltzmann solver. It indicates that the intrinsic electron energies are higher than is favorable for preferential vibrational excitation due to dissociative excitation, which causes thermodynamic equilibrium chemistry to dominate. The highest observed energy efficiencies of 45% indicate that non-equilibrium dynamics had been at play. A novel approach involving additives of low ionization potential to tailor the electron energies to the vibrational excitation regime is proposed.

To gain a better understanding of the binding mechanism and assist in the optimization of chemical probing and drug design applications, experimental and theoretical studies of a series of amino acid-linked cisplatin derivatives are being pursued. Glyplatin (glycine-linked cisplatin) was chosen for its structural simplicity and to enable backbone effects to be separated from side-chain effects on the structure and reactivity of ornithine- and lysine-linked cisplatin (Ornplatin and Lysplatin, respectively). Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on Glyplatin to characterize its structure and guide the selection of the most effective hybrid theoretical approach for determining its structure and IR spectrum. The simplicity of the Glyplatin system allows a wide variety of density functionals, treatments of the Pt center including the use of all-electron basis sets vs valence basis sets combined with an effective core potential (ECP), and basis sets for all other atoms to be evaluated at a reasonable computational cost. The results for Glyplatin provide the foundation for calculations of more complex amino acid-linked cisplatin derivatives such as Ornplatin and Lysplatin. Present results suggest that the B3LYP/mDZP/def2-TZVP hybrid method can be effectively employed for structural and IR characterization of more complex amino acid-linked cisplatin complexes and their nucleic acid derivatives.

Linear accelerators employed as drivers for X-ray free electron lasers (FELs) require relativistic electron bunch with sub-picosecond bunch length. Precise bunch length measurements are important for the tuning and operation of the FELs. Previously, we have demonstrated that electro-optic detection is a powerful technique for sub-picosecond electron bunch length measurements. In those experiments, the measured bunch length was the average of all electron bunches within a macropulse. Here, for the first time, we present the measurement of the length of individual electron bunches using a development of our previous technique. In this experiment, the longitudinal electron bunch shape is encoded electro-optically on to the frequency spectrum of a chirped laser pulse. Subsequently, the laser pulse is dispersed by a grating and the spectrum is imaged with a CCD camera. Single bunch measurements are achieved by using a nanosecond gated camera, and synchronizing the gate with both the electron bunch and the laser pulse repetition rates. The electron bunch length is determined by measuring the laser pulse spectra with and without the presence of an electron bunch. We demonstrate that this method enables a real-time diagnostic for the bunch length of single electron bunches with a time resolution of 370 femtoseconds and a high signal-noise-ratio.

Infrared multiphoton dissociation (IRMPD) spectra of mass selected isolated metal-lumichrome ionic complexes, M(q+)LCn with M(q+) = Li(+), Na(+), K(+), Rb(+), Cs(+), Ag(+) (n = 1), and Mg(2+) (n = 2), are recorded in the fingerprint range. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by density functional theory calculations at the B3LYP/cc-pVDZ level, which provide insight into the structure, binding energy, bonding mechanism, and spectral properties of the complexes. The two major binding sites identified involve metal bonding to the oxygen atoms of the two available carbonyl groups of LC (denoted O2 and O4). The more stable O4 isomer benefits from an additional interaction with the lone pair of the nearby N5 atom of LC. While M(+)LC with alkali metals are mainly stabilized by electrostatic forces, the Ag(+)LC complex reveals additional stabilization arising from partly covalent contributions. Finally, the interaction of Mg(2+) ions with LC is largely enhanced by the doubled positive charge. The frequencies of the C[double bond, length as m-dash]O stretching modes are a sensitive indicator of both the metal binding site and the metal bond strength.

Fully rotationally resolved spectra of the two lowest-frequency bands the origin (00 0 ) and the inversion (140 1) band! of the S1(n p*)AS0 transition of jet-cooled (Trot'6 K) acetaldehyde, CH3CHO, have been recorded with a resolution of '0.01 cm21 using a pulsed dye amplified continuous wave cw! laser. In modeling the spectra a nonperturbative solution of the rotational– torsional coupling problem was used, but the torsion–inversion and the rotation–inversion couplings were neglected. All the lines of the origin band were reproduced with a model using the same rotational–torsional Hamiltonian for the ground- and excited electronic state. The inversion band could not be described with this model, since the ordering of the torsional levels in the excited state is reversed. The measured spectrum was reproduced by using a rigid asymmetric rotor Hamiltonian for the two torsional levels in the excited state. Some rotational levels of 00 and 141 states were found to be shifted from their predicted energy values. These shifts were explained by an accidental resonance between the excited singlet level and some higher rovibronic triplet level. The relative intensities of the ab-type and c-type torsional subbands and the Herzberg–Teller– induced transition dipole moment direction, characterizing the ab-type subband, were determined by an intensity fit.

Orientational effects in rotationally elastic collisions of OH with Ar were studied in a crossed molecular beam setup. A static electric field was applied to orient the molecules before the collision. After the collision the orientation was measured by using a narrow-band laser system to probe the Stark-split states corresponding to different orientations. Differential and integral cross sections for reorientation of the molecular axis have been determined as a function of the initial orientation. The cross section for reorientation by one quantum is 25 A2 with a preference for O-end collisions.

$^{a}$ L. Lundsberg-Nielsen, F. Hegelund, and F.M. Nicolaisen. J. Mol. Spectrosc. 162, 230 (1993). $^{b}$ R. Engeln, G. Berden, R. Peeters, and G. Meijer, Rev. Sci. Instruct. 69, 3763 (1998).

It is experimentally demonstrated that a narrow band continuous wave (cw) light source can be used in combination with a high-finesse optically stable cavity to perform sensitive, high-resolution direct absorption and optical rotation spectroscopy in an amazingly simple experimental setup, using ideas from the field of cavity ring down spectroscopy. Light from a scanning narrow band cw laser is coupled into the cavity via accidental coincidences of the laser frequency with the frequency of one of the multitude of modes of the cavity. The absorption and polarization rotation information is extracted from a measurement of the time-integrated light intensity leaking out of the cavity as a function of laser wavelength.

The rotationally resolved ultraviolet (UV) excitation spectra of the S1(1Lb)←S0 origin bands of 3-methylindole and 5-methylindole have been measured and analyzed. As a result of an internal rotation of the methyl group, each spectrum consists of rotational lines of overlapping 0a1←0a1 and 0e←0e torsional transitions. Like indole, 3-methylindole and 5-methylindole undergo axis reorientation upon electronic excitation. The Hamiltonian used to describe all observed spectral features includes a pure rotational part, a pure torsional part, and terms describing the interaction between the internal rotation and the overall rotation. It also accounts for the axis reorientation effect. Values for the barrier heights of the methyl torsion, the angle of the methyl top axis with the inertial axes, and the rotational constants are obtained for both the S0 and the S1 state. From an analysis of the intensities of the rotational transitions, the direction of the transition moment and the axis reorientation angle are obta...