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High-performance liquid chromatography was used in combination with infrared ion spectroscopy for the identification of positional isomers of hydroxy-atorvastatins, the primary metabolites of the drug atorvastatin. The results demonstrate the direct applicability of infrared ion spectroscopy in the field of drug metabolism and, more generally, its promising role in state-of-the-art analytical laboratories for the identification of small molecules buried in complex mixtures. In combination with chromatographic separation, infrared spectroscopy of mass-selected ions provides a promising new route for the identification of the molecular structures of unknown m/z peaks in a mass spectrum. We demonstrate that currently existing experimental protocols allow the measurement of an IR spectrum from less than 10 ng of sample obtained in a collected HPLC fraction.

© The Royal Society of Chemistry 2016. Understanding of the nature and extent of chemical bonding in uranyl coordination complexes is crucial for the design of new ligands for nuclear waste separation, uranium extraction from seawater, and other applications. We report here the synthesis, infrared spectroscopic characterization, and quantum chemical studies of a molecular uranyl-di-15-crown-5 complex. The structure and bonding of this unique complex featuring a distinctive 6-fold coplanar coordination staggered sandwich structure and an unusual non-perpendicular orientation of the uranyl moiety are evaluated using density functional theory and chemical bonding analyses. The results provide fundamental understanding of the coordination interaction of uranyl with oxygen-donor ligands.

The observed variety of metal-ion complexation sites offered by peptides reflects a basic tension between charge solvation of the ion by Lewis-basic chelating groups versus amide nitrogen deprotonation and formation of metal–nitrogen bonds. Gas-phase models of metal-ion coordination can illuminate the factors governing this choice in condensed-phase proteins and enzymes. Here, structures of gas-phase complexes of Ni(II) and Cu(II) with tri- and tetra-peptide ligands are mapped out using a combination of Infrared Multiple Photon Dissociation (IRMPD) spectroscopy and density functional theory (DFT) computations. The two binding modes give distinctive IRMPD signatures, particularly in the diagnostic region 1500–1550 cm−1. Previous observations have suggested that Ni(II) complexes preferentially show the iminol rearrangement pattern (Im) giving low-spin square-planar geometries with metal-ion bonds to deprotonated amide nitrogens. In contrast, alkaline earth metal ion complexes prefer amide carbonyl oxygens chelating the metal ion with pyramidal geometry (charge-solvation, CS). Surprisingly, it is shown here that the Gly4 complexes are CS bound, in contrast with the expectation of Im binding. It is suggested that CS binding is actually a normal Ni(II) and Cu(II) binding mode to simple peptides lacking participating side chains. Three factors are suggested to influence the choice between CS and Im binding patterns: (1) presence of an accessible side-chain Lewis-basic proton interaction site (FGGF, FGG and HAA complexes); (2) short chain length of the peptide leading to a shortage of accessible carbonyl oxygen sites for CS binding, (AAA, FGG and HAA complexes); (3) outright deprotonation of the ligand giving net negatively charged Im[Ni2+(Gly4–3H+)]− and Im[Ni2+(Ala3–3H+)]− complexes, which have a triply-deprotonated ligand. IRMPD spectra of [Cu2+Gly4]2+ and [Cu2+(Gly4–3H+)]− complexes suggest that their structures are similar to their Ni2+ analogs.

The spontaneous deamidation of asparagine residues plays a significant role in various biological functions and degenerative, aging diseases. Here, we present a full description of the deamidation reaction (as well as other key dissociation processes) of protonated asparaginyl-threonine, [AsnThr + H]+, via complementary infrared multiple photon dissociation (IRMPD) ion spectroscopy, threshold collision-induced dissociation (TCID), and theoretical studies. IRMPD spectra allow for the clear identification of precursor and product ion structural conformations when compared to theoretically calculated spectra for likely structures. Analysis of kinetic energy dependent cross sections measured via TCID with xenon using a guided ion beam tandem mass spectrometer allows for characterization of the energies involved in the decomposition processes of interest. Threshold energies are compared to relative single point energies of major reaction species calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels of theory, thereby determining important rate-limiting steps involved in [AsnThr + H]+ decomposition. Our studies confirm the formation of a succinimide intermediate via deamidation of [AsnThr + H]+, an observation consistent with condensed-phase deamidation analyses. Interestingly, our spectroscopic results suggest deamidation does not produce furanone isomers even though theoretical results indicate this pathway (exhibited in gas-phase analyses of similar dipeptide systems) should be competitive. Dehydration of [AsnThr + H]+ is also observed, where theory suggests that oxazolone and oxazoline formation are competitive at threshold energies, but IRMPD analyses conclusively confirm the formation of the oxazoline structure. The comprehensive results presented (in addition to complementary studies discussed herein) allow for a valuable analysis of C-terminal residue side-chain effects on the deamidation process.

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

Infrared ion spectroscopy (IRIS) requires reproducibility and standard protocols in order to be fully appreciated as an analytical tool. An important parameter in IRIS measurements is the infrared laser power (energy per pulse), which is often difficult to control precisely on a day-to-day basis. We have developed an automatic variable attenuator to keep the laser power at a well-defined value, independent of IR frequency and time, while maintaining full overlap of the laser beam with the ion cloud in our quadrupole ion trap mass spectrometer. The device has been used to record IR spectra of the metabolite prostaglandin D2 at different laser pulse energies, allowing us to assess the effects on the IRMPD spectra of excessive ion depletion, a threshold pulse energy below which dissociation is not observed, and unobserved fragments due to electron detachment or fragmentation to below the low mass cut-off of the trap.

Gas-phase infrared multiple-photon dissociation (IRMPD) spectra are recorded for the protonated dye molecules indigo and isoindigo by using a quadrupole ion trap (QIT) mass spectrometer coupled to the free electron laser for infrared experiments (FELIX). From their fingerprint IR spectra (600—1800 cm–1) and comparison with quantum-chemical calculations at the density functional level of theory (B3LYP/6-31++G(d,p)), we derive their structures. We focus particularly on the question of whether trans-to-cis isomerization occurs upon protonation and transfer to the gas phase. The trans-configuration is energetically favored in the neutral forms of the dyes in solution and in the gas phase. Instead, the cis-isomer is lower in energy for the protonated forms of both species, but indigo is also notorious for not undergoing double-bond trans-to-cis isomerization, in contrast to many other conjugated systems. The IR spectra suggest that protoisomerization from trans to cis indeed occurs for both dyes. To estimate the extent of isomerization, on-resonance kinetics are measured on diagnostic and common vibrational frequencies to determine the ratio of cis-to-trans isomers. We find ratios of 65–70% cis and 30–35% trans for indigo versus 75–80% cis and 20–25% trans for isoindigo. Transition-state calculations for the isomerization reactions have been carried out, which indeed suggest a lower barrier for protonated isoindigo, qualitatively explaining the more efficient isomerization.

A charge-tagged phenyl pyruvic acid derivative was investigated by tandem-MS, infrared (IR) ion spectroscopy and theory. The tailor-made precursor ions efficiently lose CO2 in collision induced dissociation (CID) experiments, offering access to study the secondary decay reactions of the product ions. IR ion spectroscopy provides evidence for the formation of an enol acid precursor ion structure in the gas phase and indicates the presence of enol products formed after CO2 loss. Extensive DFT computations however, suggest intermediate generation of hydroxycarbene products, which in turn rearrange in a secondary process to the enol ions detected by IR ion spectroscopy. Quantum mechanical tunneling of the hydroxycarbene can be excluded since no evidence for aldehyde product ion formation could be found. This finding is in contrast to the behavior of methylhydroxycarbene, which cleanly penetrates the energy barrier to form exclusively acetaldehyde at cryogenic temperatures in an argon matrix via quantum mechanical hydrogen tunneling. The results presented here are attributed to the highly excited energy levels of the product ions formed by CID in combination with different barrier heights of the competing reaction channels, which allow exclusive access over one energy barrier leading to the formation of the enol tautomer ions observed.

Dissociation chemistry of the diproline anion [Pro

RATIONALE: Deamidation of Asn and Gln residues is a primary route for spontaneous post-translational protein modification. Several structures have been proposed for the deamidation products of the protonated amino acids. Here we verify these structures by ion spectroscopy, as well as the structures of parallel and sequential fragmentation products. METHODS: Infrared ion spectroscopy using the free electron laser FELIX has been applied to the reaction products from deamidation of protonated glutamine and asparagine in a tandem mass spectrometer. IR spectra were recorded over the 800-1900 cm(-1) spectral range by infrared multiple-photon dissociation (IRMPD) spectroscopy. Molecular structures of the fragment ions are derived from comparison of the experimental spectra with spectra predicted for different candidate structures by density functional theory (DFT) calculations. RESULTS: [AsnH(+) - NH3](+) is found to possess a 3-aminosuccinic anhydride structure protonated on the amino group. The dissociation reaction involving loss of H2O and CO forms a linear immonium ion. For [GlnH(+)-NH3](+), the N-terminal nitrogen acts as the nucleophile leading to an oxo-proline product ion structure. For [GlnH(+)-NH3](+), a sequential loss of [CO + H2O] is found, leading to a pyrolidone-like structure. We also confirm by IR spectroscopy that dehydration of protonated aspartic acid (AspH(+)) and glutamic acid (GluH(+)) leads to identical structures as to those found for the loss of NH3 from AsnH(+) and GlnH(+). CONCLUSIONS: The structure determined for AsnH+ is in agreement with the suggested structure derived from measured and computed activation energies. IR ion spectra for the NH3-loss product from GlnH(+) establish that a different reaction mechanism occurs for this species as compared to AsnH(+). For both amino acids, loss of NH3 occurs from the side chain.

We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

To make functional surface effects on plastic components usable on an industrial scale, new processes have to be developed. The in-mould graining (IMG) process is a variant of the thermoforming enabling the manufacture of micro-structures. One advantage of the IMG process is that the surface structure is formed to the final shape of the part. Recent investigations show that the forming accuracy of a flat mould can be extended by applying a variothermal mould heating in the IMG process. As high mould temperatures lead to high forming accuracies but also increase the cycle time of the process, a conflict of interests follows. In this paper, it is investigated to what extent high moulding accuracies can be achieved to form three-dimensional parts by using the IMG process extended by a variothermal mould heating. The results show that forming accuracies of micro-scaled structures of >90% can be reached on the bottom and the side walls of a cup-shaped mould. To address the conflict of interests between high moulding accuracy and long cycle times, the influence of the mould temperature is investigated in detail. To analyse the micro-forming behaviour of the processed material, analyses of the rheological behaviour with a rotational rheometer are carried out.

The inflation pressure loss rate (IPLR) of a tire has been a standard test method for several decades and is used to determine the rate at which a tire will lose pressure. Following these procedures, the rate of pressure loss is obtained and expressed numerically as the percentage of loss per month. This is an investigation of two experimental variables: (1) the frequency at which the inflation pressure is measured on a daily basis, and (2) the duration of the entire test. The measurement frequency means how many data points are recorded during a 24-hour period. For example, one study may collect data as infrequently as once per day by manually reading a pressure gauge every 24 hours. Alternatively, another study may collect data electronically with pressure transducers capable of transmitting large numbers of data points over short preset periods, then numerically averaging those data into a single 24-hour daily measurement. After a 21-day period to equilibrate the newly inflated tire, the test duration can range from 90 to 180 days but is allowed to be shortened when using electronic-pressure monitoring. This is a study of data-collection frequency and duration in a newly commissioned tire IPLR laboratory at Akron Rubber Development Laboratory, Inc (ARDL). It was constructed to have excellent temperature control and was equipped with 24 pressure-sensitive transducers with data being directly transmitted into a dedicated computer where the ASTM F1112 equations were applied. The present study includes data measurements from 56 radial medium truck tires manufactured by different companies. Results were obtained by averaging data collected four times per hour over a test duration of 90 days but were then recalculated using 60, 45, or 30 days of data to establish the feasibility of using a shorter testing time.

Functional surface effects on plastic components are a matter of current research activities. To make these surface effects usable on an industrial scale, new processes have to be developed. Forming processes such as injection moulding are currently used to produce functional surfaces, but machine and tool costs are considerably high. Therefore, it is of high importance to analyse to what extent the thermoforming process can be applied to manufacture micro-structures.The so called In-Mould-Graining (IMG) process is a promising variant of the thermoforming enabling the manufacture of micro-structures. The advantage of the IMG process is, that the structure is formed to the final shape of the part. If the structure on the film surface is set before the forming, the conversion may cause a deformation of the structure. However, the forming accuracy of the IMG process is limited by the rapid cooling of the film at the cold mould surface. A significant time interval between the heating and the forming leads to a cooling of the film, especially at its surface and thereby reduces the forming accuracy in the area of the grains.In this paper it is investigated to what extent the moulding accuracy of the IMG can be increased by the use of a variothermal mould heating. To achieve the required forming accuracy, only the surface layer of the micro-structured region of the cavity is heated by induction before the contact between film and cavity occurs. At the same time, the entire mould is cooled with a conventional water cooling system. The analysis of the process and formed parts shows, that especially the mould temperature during the forming process has a significant impact on the forming accuracy. A forming accuracy of a 50 µm high micro-structure of more than 95 % can be achieved. Furthermore, the contact of angle of a water droplet on a micro structured thermoformed surface can be increased up to + 145°.

Glycosyl cations are crucial intermediates formed during enzymatic and chemical glycosylation. The intrinsic high reactivity and short lifetime of these reaction intermediates make them very challenging to characterize using spectroscopic techniques. Herein, we report the use of collision induced dissociation tandem mass spectrometry to generate glycosyl cations in the gas phase followed by infrared ion spectroscopy using the FELIX infrared free electron laser. The experimentally observed IR spectra were compared to DFT calculated spectra enabling the detailed structural elucidation of elusive glycosyl oxocarbenium and dioxolenium ions.

In mass spectrometry‐based peptide sequencing, electron transfer dissociation (ETD) and electron capture dissociation (ECD) have become well‐established fragmentation methods complementary to collision‐induced dissociation. The dominant fragmentation pathways during ETD and ECD primarily involve the formation of c‐ and z•‐type ions by cleavage of the peptide backbone at the N─Cα bond, although neutral losses from amino acid side chains have also been observed. Residue‐specific neutral side chain losses provide useful information when conducting database searching and de novo sequencing. Here, we use a combination of infrared ion spectroscopy and quantum‐chemical calculations to assign the structures of two ETD‐generated w‐type fragment ions. These ions are spontaneously formed from ETD‐generated z•‐type fragments by neutral loss of 33 Da in peptides containing a cysteine residue. Analysis of the infrared ion spectra confirms that these z•‐ions expel a thiol radical (SH•) and that a vinyl C═C group is formed at the cleavage site. z•‐type fragments containing a Cys residue but not at the cleavage site do not spontaneously expel a thiol radical, but only upon additional collisional activation after ETD.

Chelation complexes of the histidine-containing tripeptides HisAlaAla, AlaHisAla, and AlaAlaHis with Ni(II) and Cu(II) having a -1 net charge are characterized in the gas phase by infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. We address the question of whether the gas-phase complexes carry over characteristics from the corresponding condensed-phase species. We focus particularly on three aspects of their structure: (i) square-planar chelation by the deprotonated amide nitrogens around the metal ion (low-spin for the Ni case), (ii) metal-ion coordination of the imidazole side chain nitrogen, and (iii) the exceptional preference for metal-ion chelation by peptides with His in the third position from the N-terminus, as in the amino terminal Cu and Ni (ATCUN) motif. We find that square-planar binding around the metal ion, involving bonds to both deprotonated backbone nitrogens, one of the carboxylate oxygens and the N-terminal nitrogen, is the dominant binding motif for all three isomers. In contrast to the condensed-phase behavior, the dominant mode of binding for all three isomers does not involve the imidazole side chain, which is instead placed outside the coordination zone. Only for the AlaAlaHis isomer, the imidazole-bound structure is also detected as a minority population, as identified from a distinctive short-wavelength IR absorption. The observation that this conformation exists only for AlaAlaHis correlates with condensed-phase behavior at neutral-to-basic pH, in the sense that the isomer with His in the third position is exceptionally disposed to metal ion chelation by four nitrogen atoms (4N) when compared with the other isomers. These results also emphasize the divergence between the conformational stabilities in the gas phase and in solution or crystalline environments: in the gas phase, direct metal binding of the imidazole is overall less favorable than the alternative of a remote imidazole that can act as an intramolecular H-bond donor enhancing the gas-phase stability.

In uranyl coordination complexes, UO2(L)n2+, uranium in the formally dipositive [O=U=O]2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν3. This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of the enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν3 red-shift. Here, ν3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν3 frequency From computed ν3 frequencies for bare UO2 cations and neutrals, it is inferred that the effective charge of uranyl in UO2(L)n2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination.

Collision-induced dissociation of isotopically labelled protonated pentaglycine produced two abundant [b5]+ ions, the products of the loss of water from the first and second amide groups, labelled [b5]+I and [b5]+II. IRMPD spectroscopy and DFT calculations show that these two [b5]+ ions feature N1-protonated 3,5-dihydro-4H-imidazol-4-one structures. 15N-Labelling established that some interconversion occurs between these two ions but dissociations are preferred. For both ions, DFT calculations show that the barrier to interconversion is slightly higher than those to dissociation. Dehydration of protonated hexaglycine produced three imidazolone ions. Ions [b6]+I and [b6]+II exhibit analogous CID spectra to those from [b5]+I and [b5]+II; however, the spectrum of the [b6]+III ion was dramatically different, showing losses predominantly of a further water molecule or cleavage of the second amide bond to give the glycyloxazolone (a deprotonated [b2]+ ion, labelled GlyGlyox (114 Da)) from the N-terminus. Protonated polyglycines [Glyn + H]+, where n = 7-9, all readily lose at least one water molecule. The corresponding [bn]+ ions lose either a further water molecule, an oxazolone from the N-terminus or a truncated peptide from the C-terminus. The number of amino acid residues in the latter two eliminated neutral molecules provides insight into the location of the imidazolone in the peptide chain and which oxygen was lost in the initial dehydration reaction. From this analysis, it appears that water loss from the longer protonated polyglycines is predominantly from the central residues.

Infrared multiple photon dissociation (IRMPD) experiments and electronic structure computations have been used to explore the structures and energetics of binding in gas phase sodium cyclopentadienyl complexes of the general form NanCpn–1+. Computational work for the analogous anionic NanCpn+1– complexes reveals nearly identical energetics for the loss of neutral NaCp units from both cationic and anionic species leading to the conclusion that the binding in the gas phase species is largely electrostatic, arising primarily from ion–ion and ion–dipole interactions. This is supported by an examination of the molecular orbitals of these species, which show no orbital overlap between the Na and Cp moieties. Observation of peaks in the IRMPD spectra, which do not correspond to any of the computed linear absorption frequencies, strongly suggest the contribution of overtone and combination bands.

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2 + fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2 + ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2 + ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPGprecursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation.

The synthesis, reactivity, structures, and bonding in gas-phase binary and complex oxide anion molecules of protactinium and uranium have been studied by experiment and theory. The oxalate ions, An

Proton transfer in the conjugate acid cation of a symmetric diether, 1,5-dimethoxy-3,3-dimethylpentane (1), is explored both theoretically and experimentally via IRMPD spectroscopy. The optimized geometry of the cation has one oxygen pyramidalized (sum of the three angles Σ = 345°), while the other oxygen has a virtually planar geometry (if one includes the strongly hydrogen bonded O⋯H, the three bond angles sum to Σ′ = 357°). Assuming that this geometry is not preserved upon intramolecular proton transfer from one oxygen to the other, two alternatives remain: either the two oxygens trade geometries (Σ and Σ′ change places via a transition state that has a mirror plane of symmetry) or else both oxygens become pyramidalized. Because the asymmetric stretch couples with other vibrational modes of the cation, special attention is paid to the classical turning points at the zero point level corresponding to the lowest frequency vibration that shows a deuterium isotope effect, which occurs experimentally around 895 cm−1. This stretching vibration has a lower frequency than the bands assigned to O⋯H O bends, and it shifts to still lower frequency in the deuteronated ion. Because a normal modes calculation matches this vibration, we conclude that the potential energy surface matches a single-well and does not correspond to a double-well minimum.

While hydrogen tunneling at elevated temperatures has, for instance, often been postulated in biochemical processes, spectroscopic proof is thus far limited to cryogenic conditions, under which thermal reactivity is negligible. We report spectroscopic evidence for H-tunneling in the gas phase at temperatures around 320-350K observed in the isomerization reaction of a hydroxycarbene into an aldehyde. The charge-tagged carbene was generated in situ in a tandem mass spectrometer by decarboxylation of oxo[4-(trimethylammonio)phenyl]acetic acid upon collision induced dissociation. All ion structures involved are characterized by infrared ion spectroscopy and quantum chemical calcula-tions. The charge-tagged phenylhydroxycarbene undergoes 1,2-H-shift to the corresponding aldehyde with an half-life of about 10 s, evidenced by isomer-selective two-color (IR-IR) spectroscopy. In contrast, the deuterated (OD) carbene analogue showed much reduced 1,2-D-shift reactivity with an estimated half-life of at least 200 seconds under the experimental conditions, and provides clear evidence for hydrogen atom tunneling in the H-isotopologue. This is the first spectroscopic confirmation of hydrogen atom tunneling governing 1,2-H-shift reactions at non-cryogenic temperatures, which is of broad significance for a range of (bio)chemical processes, including enzymatic transformations and organocatalysis.

Contains fulltext : 174068.pdf (Publisher’s version ) (Open Access) Small molecule identification is a continually expanding field of research and represents the core challenge in various areas of (bio)analytical science, including metabolomics. Here, we unequivocally differentiate enantiomeric N-acetylhexosamines in body fluids using infrared ion spectroscopy, providing orthogonal identification of molecular structure unavailable by standard liquid chromatography/high-resolution tandem mass spectrometry. These results illustrate the potential of infrared ion spectroscopy for the identification of small molecules from complex mixtures.

Gas-phase ion chemistry methods that capture and characterize the degree of activation of small molecules in the active sites of homogeneous catalysts form a powerful new tool to unravel how ligand environments affect reactivity. A key roadblock in this development, however, is the ability to generate the fragile metal oxidation states that are essential for catalytic activity. Here we demonstrate the preparation of the key Ni(I) center in the widely used cyclam scaffold using ion–ion recombination as a gas-phase alternative to electrochemical reduction. The singly charged Ni+(cyclam) coordination complex is generated by electron transfer from fluoranthene and azobenzene anions to doubly charged Ni2+(cyclam), using the electron-transfer dissociation protocol in a commercial quadrupole ion trap instrument and in a custom-built octopole RF ion trap. The successful preparation of the Ni+(cyclam) cation is verified through analysis of its vibrational spectrum obtained using the infrared free electron laser FELIX.

© 2017 American Chemical Society. Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U6+chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidenced by CID, using deuterium and18O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy. Density functional theory (DFT) computations predict that the overall reaction requires only 132 kJ/mol, with the first oxygen activation entailing about 107 kJ/mol. Combined with analysis of similar, but unreactive ligands, these results shed light on the chelation-driven mechanism of uranyl oxo bond cleavage, demonstrating its dependence on the presence of ligand hydroxyl protons available for direct interactions with the uranyl oxygens.

© 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 vibration–rotation dynamics of acetylene are computed from a spectroscopic Hamiltonian with 468 parameters fit to 19,582 vibration–rotation transitions up to 13,000 cm−1 of vibrational energy. In this energy range, both the bending and the CH stretching vibrations can reach large amplitudes, but the maximum energy remains below the threshold for isomerization to vinylidene. In contrast to the behavior at energies below 5000 cm−1 [Mol. Phys. 108, 1115 (2010)], excitation of single bright states leads, in almost all cases, to computed intramolecular vibrational redistribution (IVR) that is irreversible on the timescales investigated. Hierarchies of IVR processes on timescales ranging from 20 fs to 20 ps result when different bright states are excited. Different parts of the vibrational quantum number space are explored as a result of the four different classes of coupling terms: vibrational l-type resonance, anharmonic resonances, the rotational l-type resonance, and Coriolis couplings. The initial IVR ...

Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy has been used to generate gas phase vibrational spectra for six protonated tetracycline derivatives: chlortetracycline, meclocycline, minocycline, doxycycline, tetracycline, and metacycline. The IRMPD spectrum for protonated chlortetracycline is compared here to theoretical gas phase vibrational spectra obtained from geometry optimization and frequency electronic structure calculations using the B3LYP hybrid density functional method with the 6-311 + G(d,p) basis set. The most energetically favorable protonation sites, tautomer structures, and hydrogen bond orientations were determined. Protonation at the dimethyl amine functional group and an extensive hydrogen bonding network lead to the most energetically favourable structures. Calculated spectra directly resembled the IRMPD spectrum, supporting the conclusion that the probable gas phase structure of protonated chlortetracycline has been determined.

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.

International audience; In this work we have studied the collision induced dissociation (CID) of C-terminally amidated, protonated di- and tri-glycine by means of chemical dynamics simulations from on-the-fly electronic structure calculations using a semi-empirical Hamiltonian. The simulations represent a collision event between the peptide and an Ar-atom addressing the reactivity at “short” time-scales, i.e. up to 5 ps. Simulations were performed for different protonation sites, greatly influencing the reactivity in agreement with what is known from the “mobile proton” model of peptide dissociation. Results are then combined with ESI-MS/MS experiments to determine the fragmentation patterns. Additionally, we used IRMPD spectra to elucidate the structure of these peptides before collisional activation and the structures of some of the CID products. Results are also compared with threshold CID experiments reported in the literature for the non-amidated peptides.Chemical dynamics simulations can provide details on the fragmentation pathways observed. We also show that it is possible to identify the protonation state(s) that are populated in the different steps involved in the fragmentation process. Finally, the chemical dynamics approach is shown to be complementary to the more typical theoretical study of the potential energy surface that becomes more problematic (and sometimes impossible) for systems of increasing complexity.

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.

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.

The enthalpy and entropy changes for the formation of the 1:1 complexes of methanol with various gaseous protonated amino acids have been measured using pulsed-ionization high-pressure mass spectrometry. The enthalpy changes for formation of the clusters Gly(MeOH)H(+), Ala(MeOH)H(+), Val(MeOH)H(+), Leu(MeOH)H(+), Ile(MeOH)H(+), and Pro(MeOH)H(+) have been determined to be -92.0, -83.3, -82.4, -79.5, -78.7, and -73.6 kJ mol(-1), respectively. These values agree very well with the energetic values computed at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory for the lowest energy adducts in each system. Both experimental observations and computational determinations of the potential energy surface for the glycine system suggest that a mixture of low-lying isomers may be present for each of the cluster systems examined. The primary structural motif for these clusters is the coordination of the methanol molecule to the ammonium group of the protonated amino acid via a strong ionic hydrogen bond. For the amino acids studied here, computational results reveal that one methanol molecule does not sufficiently stabilize any zwitterionic structure such that no appreciable extent of proton transfer from the amino acid to methanol was observed.

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

We report on modifications made to a Paul-type quadrupole ion trap mass spectrometer and discuss its application in infrared ion spectroscopy experiments. Main modifications involve optical access to the trapped ions and hardware and software coupling to a variety of infrared laser sources at the FELIX infrared free electron laser laboratory. In comparison to previously described infrared ion spectroscopy experiments at the FELIX laboratory, we find significant improvements in efficiency and sensitivity. Effects of the trapping conditions of the ions on the IR multiple photon dissociation spectra are explored. Enhanced photo-dissociation is found at lower pressures in the ion trap. Spectra obtained under reduced pressure conditions are found to more closely mimic those obtained in the high-vacuum conditions of an Fourier transform ion cyclotron resonance mass spectrometer. A gas-mixing system is described enabling the controlled addition of a secondary gas into helium buffer gas flowing into the trap and allows for ion/molecule reactions in the trap. The electron transfer dissociation (ETD) option of the mass spectrometer allows for IR structure characterization of ETD-generated peptide dissociation products.

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm(-1). The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

The structures of sodiated polyalanine peptides containing 8−12 residues are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and classical and quantum modeling. Calculations indicate that the α-helical structure is the most stable conformation for the peptides whatever their size. The IRMPD spectra provide evidence for the coexistence of helical and globular shapes for Ala8Na + , and possibly for Ala9Na + . The turning point from globule to helix is thus found at Ala8−9Na + . The N−H and O− H stretching region allows identifying a new spectroscopic pattern typical for α-helical structures of polyalanines. SECTION: Biophysical Chemistry and Biomolecules

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

International audience; Tandem mass spectrometry is a powerful analytical technique for distinguishing phosphorylated from non-phosphorylated peptides, and also to locate the phosphorylated site. It is however desirable to further extend the tandem MS capacities via the development of structure specific activation techniques. This work is part of an ongoing project which aims at characterizing the environment of the phosphate group using tunable IRMPD. The effect of microsolvation of protonated phospho-tyrosine on the phosphate environment has been investigated using a combination of tandem MS experiments and quantum chemical calculations. Infrared spectra have been recorded in the 900-1900 cm(-1) and 2500-3750 cm(-1) regions using a free electron laser and a tabletop laser, respectively. Water is found to form a hydrogen bonded bridge between the otherwise nearly isolated phosphate and ammonium groups. Theoretical and experimental results also provide consistent evidences for two weaker hydrogen bonds between the two other NH bonds with the pi-aromatic ring and the carboxylic CO. The MP2 calculated IR absorption spectrum of the lowest energy structure allows for a clear band assignment. As compared to intramolecular direct interaction between the phosphate and the ammonium, the two hydrogen bonds associated with the water bridge between these groups are found to have a larger impact on their IR structure-specific probes. This is reflected by the red-shift of the P=O stretch, and also the blue shift of the umbrella mode of the ammonium. Special attention is paid to the 2500-3750 cm(-1) spectral range. While the phosphate OH stretching modes are not affected by the addition of water, the red shifts of the three ammonium NH stretches are found to be significant and quite different for their three types of non-covalent interactions. (C) 2011 Elsevier B.V. All rights reserved.

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

Parmi les techniques de purification ultime de metaux a hauts points de fusion, le procede de refusion par bombardement electronique associe une puissance thermique garantissant la fusion du metal, et une refusion sous vide permettant l'elimination d'impuretes par distillation. Ce papier presente la technique et le potentiel d'elimination par distillation.

Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and the two protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using infrared multiphoton dissociation (IRMPD) spectroscopy and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. The proton-bound dimer (PBD) of caffeine and ammonia exhibits a low binding energy and was found to be elusive under the experimental conditions due, most probably, to collision-induced dissociation of the complex with helium buffer gas before IRMPD irradiation. The IRMPD spectrum of a PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also been obtained. The spectrum of protonated caffeine showed dominant protonation at the N(9) site, whereas the spectrum of protonated theophylline showed a mixture of two isomers. The first protonated isomer of theophylline exhibits protonation at the N(9) site and the second isomer demonstrated protonation at the C(6) carbonyl oxygen. The protonated carbonyl isomer of theophylline cannot be produced as a result of direct protonation and is thus suggested to be a consequence of proton-transport catalysis (PTC) initiated by the electrostatic interaction between water and N(9) protonated theophylline. Calculated anharmonic spectra have been simulated at the B3LYP/6-311+G(d,p) level of theory. It is shown that calculated anharmonic frequencies significantly outperform calculated harmonic frequencies in providing simulated IRMPD spectra in all cases.