Gas-phase IR Research Articles

Gas-phase infrared spectrum of the anionic GFP-chromophore

The gas-phase IR spectrum of the anionic chromophore of the green fluorescent protein (p-hydroxy-benzylidene-2,3-dimethylimidazolidinone, HBDI) is recorded in the 800–1800cm−1 frequency range using the free electron laser FELIX in combination with an electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The spectrum is substantially different from IR spectra of the anion recorded previously in solution, which were found to be difficult to interpret on the basis of electronic structure calculations involving the polarisable continuum model (PCM) method. In contrast, the IR spectrum of the isolated anion recorded here matches favourably with its DFT calculated counterpart if diffuse functions are included in the basis set. IR photo-fragmentation of the HBDI anion proceeds via loss of a methyl radical (CH3) resulting in an odd-electron product anion. The IR spectrum of this radical anion photoproduct is also recorded, which indicates that the radical site resides on the imidazolinone nitrogen atom where the methyl group is detached.

Non-Equilibrium Isomer Distribution of the Gas-Phase Photoactive Yellow Protein Chromophore.

The conjugate base of para-coumaric acid, which can be conveniently generated in the gas phase by electrospray ionization (ESI), is a commonly used model system for the chromophore of the photoactive yellow protein. Here we report its gas-phase IR spectrum, which shows that the anion easily adopts a carboxylate structure lying 60 kJ/mol higher in energy than the global minimum phenoxide structure. Generation of the biologically more relevant phenoxide isomer by ESI can be achieved using dry acetonitrile as solvent.

Activation and Coordination of Ammonia at [Cp*Ir(H)2]: NMR and Matrix Isolation Studies

(1)H NMR exchange spectroscopy of a reaction mixture of [Cp*Ir(H)(4)] (1; Cp*=1,2,3,4,5-pentamethylcyclopentadienyl) and ammonia suggests an exchange of hydrogen atoms between the hydrido ligands and ammonia. Treatment of 1 with ND(3) led to an H/D exchange between ND(3) and the hydrido ligands of 1. Subsequent studies showed that photolysis of 1 isolated in frozen argon matrices leads to the formation of the iridium compounds [Cp*Ir(H)(2)] (2) and [Cp*Ir(H)(3)] (4), as it was confirmed by IR spectroscopy. In the presence of water the aqua complex [Cp*Ir(H)(2)(OH(2))] (3) was generated simultaneously. Accordingly, photolysis of 1 in an argon matrix doped with ammonia gave rise to the ammine complex [Cp*Ir(H)(2)(NH(3))] (5). IR assignments were supported by calculations of the gas-phase IR spectra of 1-5 by DFT methods.

New Operando IR Technique to Study the Photocatalytic Activity and Selectivity of TiO2 Nanotubes in Air Purification: Influence of Temperature, UV Intensity, and VOC Concentration

The photooxidation of methanol, n-hexane, and carbon monoxide using TiO2 nanotubes (TNTs) has been investigated by a new operando IR technique. Following the photocatalytic reaction by time-resolved IR spectroscopy coupled with mass spectrometry (MS) allowed a surface study of the photocatalyst with on-line analysis of the products. Identification of the species adsorbed on the photocatalyst surface and those detected in the gas phase led to further clarification of the photooxidation mechanisms. The photocatalyst was characterized by IR, Raman, UV–visible, XRD, N2 sorption, SEM, and TEM techniques. The activity and selectivity of the photocatalyst were determined by quantitative studies using gas-phase IR spectroscopy and MS. For comparison, photooxidation reactions using TiO2 P25 as a reference were performed under the same conditions. The effects of different parameters such as temperature, VOC concentration, and UV irradiation intensity on the reactivity and selectivity of the photocatalytic reaction were investigated. The effect of temperature was observed by TPD measurements (from room temperature to 200 °C). The TNT material showed a higher reactivity and CO2 selectivity than TiO2 P25.

Explaining the Structure of the OH Stretching Band in the IR Spectra of Strongly Hydrogen-Bonded Dimers of Phosphinic Acid and Their Deuterated Analogs in the Gas Phase: A Computational Study

We present a simulation of the OH stretching band in the gas-phase IR spectra of strongly hydrogen-bonded dimers of phosphinic acid and their deuterated analogs [(R(2)POOH(D), with R = CH(2)Cl, CH(3)], which is based on a model for a centrosymmetric hydrogen-bonded dimer that treats the high-frequency OH stretches harmonically and the low-frequency intermonomer (i.e., O···O) stretches anharmonically. This model takes into account the following effects: anharmonic coupling between the OH and O···O stretching modes; Davydov coupling between the two hydrogen bonds in the dimer; promotion of symmetry-forbidden OH stretching transitions; Fermi resonances between the fundamental of the OH stretches and the overtones of the in- and out-of-plane bending modes involving the OH groups; direct relaxation of the OH stretches; and indirect relaxation of the OH stretches via the O···O stretches. Using a set of physically sound parameters as input into this model, we have captured the main features in the experimental OH(D) bands of these dimers. The effects of key parameters on the spectra are also elucidated. By increasing the number and strength of the Fermi resonances and by promoting symmetry-forbidden OH stretching transitions in our simulations, we directly see the emergence of the ABC structure, which is a characteristic feature in the spectra of very strongly hydrogen-bonded dimers. However, in the case of the deuterated dimers, which do not exhibit the ABC structure, the Fermi resonances are found to be much weaker. The results of this model therefore shed light on the origin of the ABC structure in the IR spectra of strongly hydrogen-bonded dimers, which has been a subject of debate for decades.

Infrared Multiple-Photon Dissociation Spectroscopy of Tripositive Ions: Lanthanum–Tryptophan Complexes

Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative.

ON THE ELECTRONIC STRUCTURE OF ISOLATED MONO-DEHYDROGENATED POLYAROMATIC HYDROCARBON IONS AND THEIR ASTROPHYSICAL RELEVANCE

The attribution of the unidentified infrared bands to polycyclic aromatic hydrocarbon (PAH) molecules is a key argument for their abundant occurrence in interstellar environments, which has important implications for interstellar chemistry. In contrast to terrestrial conditions, their transient forms are of importance in the low-density astrophysical environments. Here, the gas-phase IR spectra of three PAH molecules in a carbocation state (naphthyl+, C10H7+; phenanthryl+, C14H9+; and pyrenyl+, C16H9+) are investigated by action spectroscopy methods using an infrared free electron laser and an ion-trap mass spectrometer. The IR spectra of the mono-dehydrogenated PAH+ (aryl) ions in the 6–18 μm spectral range are compared to computed IR spectra for various structural isomers of the aryl ions; the comparison indicates that the most stable structures under isolated conditions have a triplet electronic configuration. Electronic structure calculations on systems as large as the mono-dehydrogenated circumcoronene cation (C54H17+) provide further evidence for the higher stability of a triplet state as compared with the singlet state. Moreover, the gas-phase IR spectra reveal that the IR signatures of a PAH cation before and after H-atom loss are very similar, in particular in the 6–9 μm region involving the skeletal CC stretching modes, so that triplet mono-dehydrogenated PAH ions are similarly compliant with the general match between PAH mid-IR features and the interstellar unidentified infrared emissions. The establishment of a triplet electronic ground state suggests that interstellar scenarios should consider the possible influence of triplet aromatic chemistry as well as the possible influence of the altered optical properties of triplet PAH species.

Chirality-Induced Conformational Preferences in Peptide−Metal Ion Binding Revealed by IR Spectroscopy

Chirality reversal of a residue in a peptide can change its mode of binding to a metal ion, as shown here experimentally by gas-phase IR spectroscopy of peptide-metal ion complexes. The binding conformations of Li(+), Na(+), and H(+) with the LL and DL stereoisomers of PhePhe were compared through IR ion spectroscopy using the FELIX free-electron laser. For the DL isomer, both Li(+) and Na(+) exclusively coordinate to the amide O atom, the carboxyl O atom, and one of the aromatic rings (the OOR conformation), while for the LL isomer, a mixture of the OOR and NOR conformations was found. The stereochemically induced change in conformation is shown to reflect the strength of an NH···π interaction remote from the metal ion site. Protonated PhePhe shows no stereochemically induced variation in binding geometry.

Characterization by mass spectrometry and IRMPD spectroscopy of the sulfoxide group in oxidized methionine and related compounds

Methionine protein residues are prone to oxidation. To unravel the controversy about the mechanism of its one-electron oxidation, we characterised the main biological product, methionine sulfoxide, using mass spectrometry and IR multiple photon dissociation spectroscopy. Gas phase IR spectra in the 800–2000 cm −1 range of protonated methionine and its sulfoxide were recorded and compared to those computed for the lowest energy structures. The signature of the S O bond was clearly identified at around 1000 cm −1. Oxidation of methionine–lysine dipeptide by OH radicals in the presence of catalase revealed the formation of methionine sulfoxide upon one-electron oxidation.

Infrared Spectra of Protonated Neurotransmitters: Serotonin

The gas-phase IR spectrum of the protonated neurotransmitter serotonin (5-hydroxytryptamine) was measured in the fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum was recorded in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. Quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set yield six low-energy isomers in the energy range up to 40 kJ/mol, all of which are protonated at the amino group. Protonation at the indole N atom or the hydroxyl group is substantially less favorable. The IRMPD spectrum is rich in structure and exhibits 22 distinguishable features in the spectral range investigated (530-1885 cm(-1)). The best agreement between the measured IRMPD spectrum and the calculated linear IR absorption spectra is observed for the conformer lowest in energy at both levels of theory, denoted g-1. In this structure, one of the three protons of the ammonium group points toward the indole subunit, thereby maximizing the intramolecular NH(+)-π interaction between the positive charge of the ammonium ion and the aromatic indole ring. This mainly electrostatic cation-π interaction is further stabilized by significant dispersion forces, as suggested by the substantial differences between the DFT and MP2 energies. The IRMPD bands are assigned to individual normal modes of the g-1 conformer, with frequency deviations of less than 29 cm(-1) (average <13 cm(-1)). The effects of protonation on the geometric and electronic structure are revealed by comparison with the corresponding structural, energetic, electronic, and spectroscopic properties of neutral serotonin.

Structure and Reactivity of the Cysteine Methyl Ester Radical Cation

The structure and reactivity of the cysteine methyl ester radical cation, CysOMe(.+) , have been examined in the gas phase using a combination of experiment and density functional theory (DFT) calculations. CysOMe(.+) undergoes rapid ion-molecule reactions with dimethyl disulfide, allyl bromide, and allyl iodide, but is unreactive towards allyl chloride. These reactions proceed by radical atom or group transfer and are consistent with CysOMe(.+) possessing structure 1, in which the radical site is located on the sulfur atom and the amino group is protonated. This contrasts with DFT calculations that predict a captodative structure 2, in which the radical site is positioned on the α carbon and the carbonyl group is protonated, and that is more stable than 1 by 13.0 kJ mol(-1) . To resolve this apparent discrepancy the gas-phase IR spectrum of CysOMe(.+) was experimentally determined and compared with the theoretically predicted IR spectra of a range of isomers. An excellent match was obtained for 1. DFT calculations highlight that although 1 is thermodynamically less stable than 2, it is kinetically stable with respect to rearrangement.

Synthesis and Characterization of Carbonyl Diazide, OC(N3)2

The previously recognized "extremely explosive" carbonyl diazide, OC(N(3))(2), was prepared as a pure compound and unambiguously characterized by gas-phase IR, matrix IR, and Raman spectroscopy and X-ray crystallography for the first time. The pure substance shows remarkable kinetic stability at room temperature in the gaseous, liquid, and solid states. A melting point of 16 °C and vapor pressure of 5.6 mbar at 0 °C were determined. Two planar conformers were found in the gas phase, and a composition of 12% anti-syn versus 88% syn-syn conformer in the gaseous equilibrium mixture at room temperature was estimated by matrix IR spectroscopy. In the crystal structure, only the more stable syn-syn conformer was observed. The preference of the syn-syn configuration was supported by DFT calculations.

ChemInform Abstract: HCN Dimers: Iminoacetonitrile and N-Cyanomethanimine.

Iminoacetonitrile (1) has been prepared by two methods: (i) thermal decomposition of the tosylhydrazone salts 13 at 200-degrees-C and (ii) Ar matrix photolysis of azidoacetonitrile (15). Ab initio calculations indicate that 1Z is of slightly lower energy than 1E, and this is confirmed by the IR spectra with use of the thermal methods. 1E/1Z undergo photochemical interconversion, giving a ca. 3:1 photostationary E:Z ratio. 1E and 1Z are fully characterized by their gas-phase, matrix, and thin-film IR spectra, which are in excellent agreement with ab initio calculations, by H-1 and C-13 NMR spectroscopy in solution, and by mass spectrometry. 1 polymerizes in solution above -40-degrees-C; pyrolysis produces HCN, and matrix photolysis produces HNC and van der Waals complexes containing HNC. N-tert-Butyliminoacetonitrile thermally fragments to tert-butyl isocyanide and HCN. N-Cyanomethanimine (3) has also been prepared by two methods: (i) pyrolysis of trimethylenetetrazole (20) at 500-800-degrees-C and (ii) pyrolysis of ditetrazolopyrazine 22 at 600-850-degrees-C. Both methods are extremely clean. 3 is fully characterized by its IR spectrum in agreement with ab initio calculations and, in conjunction with other work, by its mass and millimeter-wave spectra. 3 is thermodynamically stable in the gas phase up to ca. 800-degrees-C at low pressure and short contact times but polymerizes in the solid state above -100-degrees-C.

Cysteine radical cation: A distonic structure probed by gas phase IR spectroscopy

The interest in the radical cations of amino acids is twofold. On the one hand, these species are relevant in enzymatic catalysis and in oxidative damage of proteins. On the other hand, as constituents of peptides and proteins, they aid the mass spectrometric characterization of these biomolecules, yielding diagnostic fragmentation patterns and providing complementary information with respect to the one obtained from even electron ions. The cysteine radical cation has been obtained by S-NO bond cleavage of protonated S-nitrosocysteine and thoroughly characterized by IRMPD spectroscopy, both in the 1000-2000 cm(-1) range (the highly structurally diagnostic, so-called 'fingerprint' range) and in the 2900-3700 cm(-1) spectral range, encompassing O-H and N-H stretching vibrations. In this way the distonic structure in which the charge is on the NH(3) group and the spin is on the sulfur atom is unambiguously demonstrated. This tautomer is a local minimum on the potential energy surface, at 29.7 kJ mol(-1) with respect to the most stable tautomer, a captodative structure allowing extensive delocalization of charge and spin.

Tautomerism of cytosine probed by gas phase IR spectroscopy

The tautomerism of the gaseous protonated cytosine is studied using infrared multiple photon dissociation (IRMPD) spectroscopy of singly hydrated complexes of protonated cytosine in the 2700–3750 cm −1 wavenumber range. The hydrated complexes are formed through argon-mediated collisions between bare electrosprayed cytosine and low-pressure water vapor. In the spectra, where X–H (X C, O, and N) stretching vibrations are probed, evidence is found for the coexistence in the gas phase of hydrated complexes of two different cytosine tautomers. As the addition of a water molecule to either tautomer of protonated cytosine is energetically highly unlikely to induce interconversion, it is deduced that both C(2) O and N(3) protonated tautomers of cytosine are formed under electrospray conditions.

Gas-phase IR spectra of intact α-helical coiled coil protein complexes

Electrospray ionization (ESI) is the softest ionization method that is currently available and it is widely accepted, that ESI generated ions of proteins and protein assemblies at certain conditions retain characteristic aspects of their solution-state conformation. ESI mass spectrometry (MS) therefore evolved as a useful tool to obtain information on composition, stoichiometry, and dynamics of non-covalently associated protein complexes. While tertiary structure information of proteins can be obtained from ion mobility spectrometry (IMS), only a few techniques yield direct information on the secondary structure of gas-phase peptides and proteins. We present here the mid-IR spectroscopic secondary structural analysis of three de novo designed α-helical coiled coil model peptides and their non-covalently associated complexes in the gas-phase. The conformational stability of such coiled coil peptides in solution is primarily driven by aggregation. Isolated monomers usually remain unfolded. Two of the investigated peptides were designed to assemble into stable α-helical complexes in acidic solution, while the third one remains monomeric and unfolded at these conditions. Monomer ions of all three peptides show comparable photodissociation IR spectra and therefore suggest an unfolded conformation in the gas phase. In contrast, considerable C O stretch (amide-I) and N–H bend (amide-II) band shifts have been observed for the dimers which is consistent with an elevated H-bond content. These findings provide evidence that at least a fraction of the condensed phase α-helical structure is retained in the gas-phase coiled coil complexes.

Photochemistry of SO2/Cl2/O2Gas Mixtures: Synthesis of the New Peroxide ClSO2OOSO2Cl

Photochemically induced gas-phase reactions of Cl(2)/SO(2)/O(2) mixtures at -78 degrees C have been investigated on a preparative scale. The sulfuryl chlorides ClSO(2)(OSO(2))(n)Cl, n = 0, 1, or 2, along with SO(3) and the hitherto unknown bis(chlorosulfuryl)peroxide, ClSO(2)OOSO(2)Cl, have been obtained. The new peroxide has been purified by trap-to-trap distillation and conclusively characterized by gas-phase and matrix IR, as well as Raman, spectroscopy. At room temperature, the peroxide decomposes to form quantitatively Cl(2) and SO(3). DFT calculations suggest that ClSO(2)OOSO(2)Cl occurs at ambient temperatures in at least two different rotamers, whereas in matrix-isolation experiments in Ar at 15 K only the most stable form has been found. The mechanism of the formation of the peroxide via the ClSO(2)OO* peroxy radical and the supposed involvement of the ClSO(3)* intermediate is discussed.

Gas-phase infrared spectroscopy of the protonated dipeptides H +PheAla and H +AlaPhe compared to condensed-phase results

The influence of the physical environment on the structures of biomolecules is considered here for the dipeptide model H +AlaPhe cation, by making use of infrared multiple-photon dissociation (IRMPD) spectroscopy complemented by DFT calculations. The gas-phase structures of this peptide are also compared to the related peptide cations H +PheAla and H +AlaAla. The gas-phase IRMPD spectra of the Phe-containing cations are compared to previous studies, including the X-ray-crystallographic crystal structure for the H +AlaPheCl −·2H 2O salt, a recent IRMPD spectrum of H +AlaAla, and a recent determination of the IR absorption spectrum of the H +AlaPheCl − salt in a liquid-crystal host matrix, as well as recent cryogenic ion trap results for H +TyrAla and H +AlaTyr. Between the gas-phase H +AlaPhe ion and the H +AlaPheCl −·2H 2O crystal a conformational switch is observed, induced by hydrogen bonding with a water of crystallization, involving a 180° rotation of the COOH group. The hoped-for comparison of the gas-phase IR spectra with the liquid-crystal matrix IR spectrum was frustrated, because the literature matrix spectrum seems most likely to be that of a protonated homodimer of the dipeptide rather than the protonated monomer. The IRMPD spectra of H +AlaPhe and H +PheAla are very similar, with only minor peak shifts suggesting small differences in local interactions within a similar overall architecture. The H +AlaAla spectrum was also similar, and no significant reorganization of the structure seems to result from the presence or position of the aromatic ring. The spectra give highly satisfactory matches to the predicted IR spectra computed for the most stable conformers of the protonated dipeptides. It is suggested that the NH 3 + proton is shared through hydrogen bonding to the amide C O, giving a distinctive broadening of the associated H-bending mode.

IR photodissociation spectroscopy of O 4+, O 6+ and O 8+ cluster ions

O 4 + and larger (O 2) n + cluster ions are produced in a pulsed discharge source and studied with time-of-flight mass spectrometry and infrared laser photodissociation spectroscopy. The infrared laser photon energies used allow bracketing of the cluster dissociation energies. Sharp resonant structure is detected for each of these ions in the region of the O–O stretching vibrations and also at higher frequencies corresponding to combination bands. Although previous matrix isolation spectroscopy on O 4 + found evidence for both trans-bent and rectangular isomers of this ion, the gas phase IR spectrum only contains bands assigned to the rectangular isomer. O 6 + has a distinctive IR spectrum unlike that for O 4 +, indicating that it is not simply a solvated O 4 + species, while O 8 + has the signature of a solvated O 6 + ion.

Trifluoromethylated Compounds with SiNN and SiON Backbone, and the Crystal Structures of Trimethyl- and Trichloro(trifluoromethyl)silane

The reaction of (F3C)Cl2SiCl3 with the lithiated hydrazine LiN(Me)NMe2 gives the compound (F3C)Cl2SiN(Me)NMe2 (1) and in traces Cl3SiN(Me)NMe2 (2). The reactions with LiN(SiMe3)NMe2 and LiONMe2 give (F3C)Cl2SiN(SiMe3)NMe2 (4) and (F3C)Cl2SiONMe2 (5), respectively. The compounds were characterised by multinuclear solution NMR, gas-phase IR spectroscopy and mass spectrometry. Information about conformational preferences of 1 and 4 can be extracted by comparing experimental IR spectra with those calculated by quantum chemical methods (B3LYP/6-311G**). The former show the gas phase of the β -donor-acceptor silanes 1 and 4 to be dominated by the anti conformations, while the calculations show a preference for the gauche conformers. The crystal structure of Cl3SiN(Me)NMe2 (2) has been determined. The solid-state structures of the Ruppert reagent F3C-SiMe3 (1) and its chlorine analogue F3C-SiCl3 (2) have also been determined by X-ray diffraction of single crystals grown by in situ techniques.