2024 |
Dupont, J., Hartwig, B., Le Barbu-Debus, K., Lepere, V., Guillot, R., Suhm, M. A., & Zehnacker, A. (2024). Homochiral vs. heterochiral preference in chiral self-recognition of cyclic diols. PCCP, 2622(1411), 1061011–1062111.
Résumé: The structure and clustering propensity of a chiral derivative of cis-1,2-cyclohexanediol, namely, 1-phenyl-cis-1,2-cyclohexanediol (cis-PCD), has been studied under supersonic expansion conditions by combining laser spectroscopy with quantum chemistry calculations. The presence of the phenyl substituent induces conformational locking relative to cis-1,2-cyclohexanediol (cis-CD), and only one conformer of the bare molecule is observed by both Raman and IR-UV double resonance spectroscopy. The homochiral preference inferred for the dimer formation at low enough temperature is in line with the formation of a conglomerate in the solid state. The change in clustering propensity in cis-PCD relative to trans-1,2-cyclohexanediol (trans-CD), which shows heterochiral preference, is explained by the presence of the phenyl substituent rather than the effect of cis-trans isomerism. Indeed the transiently chiral cis-CD also forms preferentially heterodimers, whose structure is very close to that of the corresponding trans-CD dimer.
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2023 |
Gutiérrez-Quintanilla, A., Chevalier, M., Platakyte, R., Ceponkus, J., & Crépin, C. (2023). Revisiting Photoisomerization in Fluorinated Analogues of Acetylacetone Trapped in Cryogenic Matrices. EPJD, 77, 158.
Résumé: UV-induced processes are commonly studied in acetylacetone analogues. In this contribution,
we revisit the existing work on the photoisomerization process in some of the fluorinated analogues of
acetylacetone, i.e., trifluoroacetylacetone (F3-acac) and hexafluoroacetylacetone (F6-acac). We performed
selective UV laser excitation of these molecules trapped in soft cryogenic matrices, namely neon and parahydrogen,
and probed by vibrational spectroscopy. Clear spectroscopy of 3 isomers of F6-acac and 6 isomers
of F3-acac is obtained, including the first characterization of a second open enol isomer of hexafluoroacetylacetone.
In addition, we present the electronic absorption spectra of both molecules in cryogenic matrices
before and after specific UV irradiations, giving new data on the electronic transitions of photoproducts.
Vibrational and electronic experimental results are analyzed and discussed within comparisons with DFT
and TD-DFT calculations. Our findings contribute to a deeper understanding of the photoisomerization
process in these molecules after electronic excitation in gas and condensed phase.
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Imani, Z., Mundlapati, V. R., Brenner, V., Gloaguen, E., Le Barbu-Debus, K., Zehnacker, A., Robin, S., Aitken, D. J., & Mons, M. (2023). Non-covalent interactions reveal the protein chain δ conformation in a flexible single-residue model. ChemComm, 59, 1161–1164.
Résumé: The δ conformation is a local secondary structural feature in proteins that implicates a πamide N-H···N interaction between a backbone N atom and the NH of the following residue. Small molecule probes of this conformation have been limited so far to rigid proline-type models that may over-emphasize the significance of the interaction. We show here that, in thiacyclic amino acid derivatives with a sulphur atom in the γ-position, specific side-chain/backbone N-H···S interactions stabilize the δ conformation sufficiently to allow it to compete with classical C5 and C7 H-bonding conformers. With support from quantum chemistry, the δ-folded conformers have been characterized by IR spectroscopy in the gas phase. In solution, the IR absorption of the πamide N-H appears at 3450 cm-1, notably less red-shifted than in proline-type models, in a frequency range often considered as implicating a free NH motif and suggestive of very weak hydrogen bonding at best.
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Nejad, A., Mellor, A. P. F., Lange, M., Alata, I., Zehnacker, A., & Suhm, M. A. (2023). Subtle hydrogen bond preference and dual Franck-Condon activity – the interesting pairing of 2-naphthol with anisole. PCCP, 25(15), 10427–10439.
Résumé: The hydrogen-bonded complexes between 2-naphthol (or beta-naphthol) and anisole are explored by detecting their IR absorption in the OH stretching range as well as their UV absorption by means of laser-induced fluorescence and resonance-enhanced two-photon UV ionisation. For the more stable cis and the metastable trans conformations of the OH group in 2-naphthol, hydrogen bonding to the oxygen atom of anisole is consistently detected in different supersonic jet expansions. Alternative hydrogen bonding to the aromatic ring of anisole remains elusive, although the majority of state-of-the-art hybrid DFT functionals with London dispersion correction and – less surprisingly – MP2 wavefunction theory predict it to be slightly more stable at zero-point level, unless three-body dispersion correction is added to the B3LYP-D3(BJ) approach. This changes at the CCSD(T) level, which forecasts an energy advantage of 1-3 kJ mol(-1) for the classical hydrogen bond arrangement even after including (DFT) zero-point energy contributions. The UV and IR spectra of the cis complex exhibit clear evidence for intensity redistribution of the primary OH stretch oscillator to combination states with the same low-frequency intermolecular bending mode by Franck-Condon-type vertical excitation mechanisms. This rare case of dual (vibronic and vibrational) Franck-Condon activity of a low-frequency mode invites future studies of homologues where aromatic ring docking of the OH group may be further stabilised, e.g. through anisole ring methylation.
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Pollet, R., & Chin, W. (2023). In silico Investigation of the Thermochemistry and Photoactivity of Pyruvic Acid in an Aqueous Solution of NaCl. Chem. Eur. J., 2922(5555).
Résumé: Abstract The photochemistry of oxocarboxylic acids contributes significantly to the complex chemistry occurring in the atmosphere. In this regard, pyruvic acid undergoes photoreactions that lead to many diverse products. The presence of sodium cation near pyruvic acid in an aqueous solution, or its conjugate base in non-acidic conditions, influences the hydration equilibrium and the photosensitivity to UV-visible light of the oxocarboxylic acid. We performed an ab?initio metadynamics simulation which serves two purposes: first, it unveils the mechanisms of the reversible hydration reaction between the keto and the diol forms, with a free-energy difference of only 2?kJ/mol at 300?K, which shows the influence of sodium on the keto/diol ratio; second, it provides solvent-shared ion pairing (SSIP) and contact ion pairing (CIP) structures, including Na+ coordinated to carbonyl, for the calculations of the electronic transition energies to an antibonding π* orbital, which sheds light on the photoactivity of these two forms in the actinic region.
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Rouquet, E., Roy Chowdhury, M., Garcia, G. A., Nahon, L., Dupont, J., Lepere, V., Le Barbu-Debus, K., & Zehnacker, A. (2023). Induced photoelectron circular dichroism onto an achiral chromophore. Nat Commun, 1411(1), 629066.
Résumé: An achiral chromophore can acquire a chiral spectroscopic signature when interacting with a chiral environment. This so-called induced chirality is documented in electronic or vibrational circular dichroism, which arises from the coupling between electric and magnetic transition dipoles. Here, we demonstrate that a chiroptical response is also induced within the electric dipole approximation by observing the asymmetric scattering of a photoelectron ejected from an achiral chromophore in interaction with a chiral host. In a phenol-methyloxirane complex, removing an electron from an achiral aromatic pi orbital localised on the phenol moiety results in an intense and opposite photoelectron circular dichroism (PECD) for the two enantiomeric complexes with (R) and (S) methyloxirane, evidencing the long-range effect (~5 A) of the scattering chiral potential. This induced chirality has important structural and analytical implications, discussed here in the context of growing interest in laser-based PECD, for in situ, real time enantiomer determination.
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2022 |
Dupont, J., Guillot, R., Lepère, V., & Zehnacker, A. (2022). Jet-cooled laser spectroscopy and solid-state vibrational circular dichroism of the cyclo-(Tyr-Phe) diketopiperazine dipeptide. Journal of Molecular Structure, 24, 19783–19791.
Résumé: The structures of the diastereomer diketopiperazine dipeptides cyclo(LTyr-LPhe) and cyclo-(DTyr-LPhe) are studied in the gas phase using resonance-enhanced two-photon ionization, IR/UV double resonance spectroscopy and quantum chemical calculation. Both diastereomers exhibit two conformations, with the tyrosine ring folded over the DKP ring and the phenylalanine ring extended outwards, or vice versa. The two diastereomers differ only slightly by the nature of weak CH···π and NH···π interactions. The crystal structure of cyclo(LTyr-LPhe) is determined by X-ray crystallography and is composed of monomers with folded tyrosine ring. The vibrational circular dichroism spectrum is interpreted by the existence of dimers in the solid state. Quantum chemical calculation shed light on the structural modifications between the gas phase and the solid state.
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Fischer, T. L., Bödecker, M., Zehnacker-Rentien, A., Mata, R. A., & Suhm, M. A. (2022). Setting up the HyDRA blind challenge for the microhydration of organic molecules. PCCP, 24, 11442–11454.
Résumé: The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates with experimentally known and published water donor vibrations is presented and a test set of 10 monohydrates with unknown or unpublished water donor vibrational wavenumbers is described together with relevant background literature. The rules for data submissions from computational chemistry groups are outlined and the planned publication procedure after the end of the blind challenge is discussed.
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Jähnigen, S., Le Barbu-Debus, K., Guillot, R., Vuilleumier, R., & Zehnacker, A. (2022). How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State. Angew. Chem. Int. Ed., 62(e20221559).
Résumé: Abstract Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P21 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.
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Laurent, J., Bozek, J., Briant, M., Carcabal, P., Cubaynes, D., Milosavljevic, A., Puttner, R., Shafizadeh, N., Simon, M., Soep, B., & Goldsztejn, G. (2022). Consistent characterization of the electronic ground state of iron(II) phthalocyanine from valence and core-shell electron spectroscopy. Phys Chem Chem Phys, 4(24), 2656–2663.
Résumé: We studied the iron(II) phthalocyanine molecule in the gas-phase. It is a complex transition organometallic compound, for which, the characterization of its electronic ground state is still debated more than 50 years after the first published study. Here, we show that to determine its electronic ground state, one needs a large corpus of data sets and a consistent theoretical methodology to simulate them. By simulating valence and core-shell electron spectra, we determined that the ground state is a (3)E(g) and that the ligand-to-metal charge transfer has a large influence on the spectra.
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Le Barbu-Debus, K., Pérez-Mellor, A., Lepère, V., & Zehnacker, A. (2022). How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. PCCP, 24, 19783–19791.
Résumé: The protonated dimers of the diketopiperazine dipeptide cyclo (lPhe-lHis) and cyclo (lPhe-dHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (lPhe-dHis), that of cyclo (lPhe-lHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Lietard A, Piani G, Pollet R, Soep B, Mestdagh JM, & Poisson L. (2022). Excited state dynamics of normal dithienylethene molecules either isolated or deposited on an argon cluster. Phys Chem Chem Phys, 24, 10588–10598.
Résumé: Real-time dynamics of the electronically excited open-ring isomer of 1,2-bis(2-methylbenzo[b]thiophen-3-yl)perfluorocyclopentene (BTF6) and 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (PTF6) molecules was investigated using a set-up that associates a molecular beam, femtosecond lasers and velocity map imaging. The molecules were either free in the gas phase or bound to an argon cluster. DFT and TDDFT calculations were performed on BTF6. The calculated vertical excitation energies indicate an excitation by the pump laser towards a superposition of S5 and S6 states. The free molecule dynamics was found to follow a three wavepacket model. One describes the parallel conformer (P) of these molecules. It is unreactive with respect to the ring closure reaction which is responsible for the photochromic property of these molecules. It has no observable decay at the experiment time scale (up to 350 ps). The other two wavepackets describe the reactive antiparallel conformer (AP). They are formed by an early splitting of the wavepacket that was launched initially by the pump laser. They can be considered as generated by excitation of different, essentially uncoupled, deformation modes. They subsequently evolve along independent pathways. One is directed ballistically towards a conical intersection (CI) and decays through the CI to a potential energy surface where it can no longer be detected. The other fraction of the wavepacket decays also towards undetected states but in this case the driving mechanism is a non-adiabatic electronic relaxation within a potential well of the energy surfaces where it was launched. When BTF6 and PTF6 molecules are bound to an argon cluster, the same three wavepacket model applies. The vibronic relaxation timespan is enhanced by a factor 5 and a larger fraction of AP conformers follows this pathway. In contrast, the time constant associated with the ballistic movement is enhanced by only a factor of 2.
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Perez-Mellor, A. F., Spezia, R., & Zehnacker, A. (2022). How Symmetry Influences the Dissociation of Protonated Cyclic Peptides. Symmetry, 14(4), 679.
Résumé: Protonated cyclic dipeptides undergo collision-induced dissociation, and this reaction mechanism strongly depends on the symmetry and the nature of the residues. We review the main dissociation mechanism for a series of cyclic dipeptides, obtained through chemical dynamics simulations. The systems range from the symmetrical cyclo-(glycyl-glycyl), with two possible symmetrical protonation sites located on the peptide ring, to cyclo-(tyrosyl-prolyl), where the symmetry of protonation sites on the peptide ring is broken by the dissimilar nature of the different residues. Finally, cyclo-(phenylalanyl-histidyl) shows a completely asymmetric situation, with the proton located on one of the dipeptide side chains, which explains the peculiar fragmentation mechanism induced by shuttling the proton, whose efficiency is strongly dependent on the relative chirality of the residues.
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Raphaël Thon, Wutharath Chin, Didier Chamma, Mindaugas Jonusas, Jean-Pierre Galaup, & Claudine Crépin. (2022). Vibrational dynamics of iron pentacarbonyl in cryogenic matrices. J Chem Phys, 156(2), 024301-12.
Résumé: Iron pentacarbonyl is a textbook example of fluxionality. We trap the molecule in cryogenic matrices to study the vibrational dynamics of
CO stretching modes involved in the fluxional rearrangement. The infrared spectrum in Ar and N2 is composed of about ten narrow bands
in the spectral range of interest, indicating the population of various lattice sites and a lowering of the molecular symmetry in the trapping
sites. The vibrational dynamics is explored by means of infrared stimulated photon echoes at the femtosecond scale. Vibrational dephasing
and population relaxation times are obtained. The non-linear signals exhibit strong oscillations useful to disentangle the site composition
of the absorption spectrum. The population relaxation involves at least two characteristic times. An evolution of the photon echo signals
with the waiting time is observed. The behavior of all the signals can be reproduced within a simple model that describes the population
relaxation occurring in two steps: relaxation of v = 1 (population time T1 < 100 ps) and return to v = 0 (recovery time > 1 ns). These two steps
explain the evolution of the oscillations with the waiting time in the photon echo signals. These results discard fluxional rearrangement on
the time scale of hundreds of ps in our samples. Dephasing times are of the same order of magnitude as T1: dephasing processes due to the
matrix environment are rather inefficient. The photon echo experiments also reveal that intermolecular resonant vibrational energy transfers
between guest molecules occur at the hundreds of ps time scale in concentrated samples (guest/host > 104).
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Szczepaniak, U., Kolos, R., Guillemin, J. - C., & Crépin, C. (2022). Phosphorescence of C5N– in rare gas solids. Photochem, 2, 263–271.
Résumé: Phosphorescence of C5N– was discovered following the ArF-laser (193 nm) photolysis of cy-anodiacetylene (HC5N) isolated in cryogenic argon, krypton and xenon matrices. This visible emission, with the origin around 460 nm, is vibrationally resolved, permitting the measurement of frequencies for eight ground-state fundamental vibrational modes, including the three known from previous IR absorption studies. Phosphorescence lifetime amounts to tens or even hun-dreds of ms depending on the matrix host; it is 5 times longer than in the case of HC5N.
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2021 |
Awali, S., Mestdagh, J. - M., Gaveau, M. - A., Briant, M., Soep, B., Mazet, V., & Poisson, L. (2021). Time-Resolved Observation of the Solvation Dynamics of a Rydberg Excited Molecule Deposited on an Argon Cluster. II. DABCO* at Long Time Delays. J Phys Chem A, 125(20), 4341–4351.
Résumé: The real-time dynamics of DABCO-argon clusters is investigated in a femtosecond pump-probe experiment where the pump excites DABCO to the S1 state within the argon cluster. The probe operates by photoionization and documents the energy and angular distributions of the resulting photoelectrons. The present work complements a previous work from our group [Awali Phys. Chem. Chem. Phys., 2014, 16, 516-526] where this dynamics was probed at short time, up to 4 ps after the pump pulse. Here, the dynamics is followed up to 500 ps. A multiscale dynamics is observed. It includes a jump between two solvation sites (time scale 0.27 ps) followed by the relaxation of the solvation cage excess vibrational energy (time scale 14 ps) and then by that of DABCO (time scale >150 ps). Polarization anisotropy, double polarization, and angular anisotropy effects are reported also. They are interpreted (quantitatively for the former effect) in terms of decoherence of rotational alignment, driven by the overall rotation of the DABCO-argon clusters. A tomographic view of the DABCO excited orbital, provided by the double anisotropy effect, is discussed on a qualitative basis.
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Gutiérrez-Quintanilla, A., Platakyte, R., Chevalier, M., Crépin, C., & Ceponkus J. (2021). Hidden Isomer of Trifluoroacetylacetone Revealed by Matrix Isolation Infrared and Raman Spectroscopy. J Phys Chem A, 125, 2249–2266.
Résumé: Enol forms of trifluoroacetylacetone (TFacac) isolated in molecular and rare gas matrices were studied using infrared (IR) and Raman spectroscopy. Additionally, calculations using DFT B3LYP and M06-2X as well as MP2 methods were performed in order to investigate the possibility of coexistence of more than one stable enol form isomer of TFacac. Calculations predict that both stable enol isomers of TFacac, 1,1,1-trifluoro-4-hydroxy-3-penten-2-one (1) and 5,5,5-trifluoro-4-hydroxy-3-penten-2-one (2), could coexist, especially in matrices where the room temperature population is frozen, 1 being the most stable one. Raman and IR spectra of TFacac isolated in nitrogen (N2) and carbon monoxide (CO) matrices exhibit clear absorption bands, which cannot be attributed to this single isomer. Their relative band positions and intensity profiles match well with the theoretical calculations of 2. This allows us to confirm that in N2 and CO matrices both isomers exist in similar amounts. Careful examination of the spectra of TFacac in argon, xenon, neon, normal, and para-hydrogen (Ar, Xe, Ne, nH2, and pH2 respectively) matrices revealed that both isomers coexist in all the explored matrices, whereas 2 was not considered in the previous spectroscopic works. The amount of the second isomer (2) in the as-deposited samples depends on the host. The analysis of TFacac spectra in the different hosts and under various experimental conditions allows the vibrational characterization of both chelated isomers. The comparison with theoretical predictions is also investigated.
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Jahnigen, S., Zehnacker, A., & Vuilleumier, R. (2021). Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge. J. Phys. Chem, 12(30), 7213–7220.
Résumé: We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S)-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.
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Le Barbu-Debus, K., & Zehnacker, A. (2021). Competition between inter and intramolecular hydrogen bond evidenced by vibrational circular dichroism spectroscopy: The case of (1S,2R)-(−)-cis-1-amino-2-indanol. Chirality, 33(12), 858–874.
Résumé: Abstract The infrared (IR) absorption and vibrational circular dichroism (VCD) spectra of an intramolecularly hydrogen-bonded chiral amino-alcohol, (1S,2R)-(−)-cis-1-amino-2-indanol, are studied in DMSO-d6. The spectra are simulated at the density functional theory (DFT) level within the frame of the cluster-in-the-liquid model. Both IR and VCD spectra show a clear signature of the formation of intermolecular hydrogen bonds at the detriment of the intramolecular OH … N interaction present in the isolated molecule. Two solvent molecules are necessary to reproduce the experimental spectra. Whereas the first DMSO molecule captures the main spectral modifications due to hydrogen bond formation between the solute and the solvent, the second DMSO molecule is necessary for a good description of the Boltzmann contribution of the different complexes, based on their Gibbs free energy.
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Mundlapati, V. R., Imani, Z., Goldsztejn, G., Gloaguen, E., Brenner, V., Le Barbu-Debus, K., Zehnacker-Rentien, A., Baltaze, J. - P., Robin, S., Mons, M., & Aitken, D. J. (2021). A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids, 53(4), 621–633.
Résumé: S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-l-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5–C6γ conformation which combines an intra-residue N–H···O=C backbone interaction (C5) and an inter-residue N–H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).
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Pérez-Mellor, A., Alata, I., Lepere, V., Spezia, R., & Zehnacker-Rentien, A. (2021). Stereospecific collision-induced dissociation and vibrational spectroscopy of protonated cyclo (Tyr-Pro). International Journal of Mass Spectrometry, 465, 116590.
Résumé: The protonated cyclo (LTyr-LPro) and cyclo (LTyr-DPro) dipeptides based on a diketopiperazine (DKP) ring are studied by tandem mass spectrometry in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Collision-induced dissociation (CID) and infrared multiple-photon dissociation (IRMPD) spectroscopy results are interpreted with the aid of quantum chemical calculations and chemical dynamics simulations. All the conformers identified for each diastereomer, denoted c-LLH+ and c-LDH+, respectively, are protonated on the carbonyl group of the tyrosine. The most stable form has an extended structure with the aromatic ring oriented outside the DKP ring; it is stabilized by an OH+…π interaction. Distinct IR signatures are obtained for the extended conformers of c-LLH+ and c-LDH+, which differ by the strength of the OH+…π interaction, much stronger in c-LLH+. Less stable species with the aromatic ring folded over the DKP ring are kinetically trapped in our experimental conditions, but their IR spectrum is identical for c-LLH+ and c-LDH+. The main collision-induced dissociation products of the protonated dipeptides are analyzed using chemical dynamics simulations. More efficient CID is observed for c-LDH+, in particular for the formation of the iminium ion of tyrosine. In contrast to the monomers, the protonated dimers of c-LLH+ and c-LDH+ show identical IR spectra. This is explained in terms of a structure involving a single strong OH+…O interaction between subunits not sensitive to the absolute configuration of the residues, i.e., from a folded protonated monomer to an extended neutral monomer.
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Perez-Mellor, A., Le Barbu-Debus, K., Lepere, V., Alata, I., Spezia, R., & Zehnacker, A. (2021). Structure and collision-induced dissociation of the protonated cyclo His-Phe dipeptide: mechanistic studies and stereochemical effects. EUROPEAN PHYSICAL JOURNAL D, 75(6), 1–7.
Résumé: The role of stereochemical factors on the structure and the fragmentation paths of the protonated cyclic dipeptide cyclo histidine-phenylalanine is studied under ion traps conditions by combining tandem mass spectrometry, laser spectroscopy, quantum chemical calculations and chemical dynamics simulations. Vibrational spectroscopy obtained by Infrared Multiple Photon Dissociation (IRMPD) reveals a small difference between the two diastereomers, c-LLH+ and c-LDH+, arising mainly from ancillary CH center dot center dot center dot pi interactions. In contrast, there is a strong influence of the residues chirality on the collision-induced dissociation (CID) processes. Chemical dynamics simulations rationalize this effect and evidence that proton mobility takes place, allowing isomerization to intermediate cyclic structures that are different for c-LLH+ and c-LDH+, resulting in different barriers to proton mobility. This effect is related to the protonation of the imidazole ring. It contrasts with the minute stereochemical effects observed for other cyclic dipeptides in which the proton is borne by an amide CO.
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Pollet R, & Chin, W. (2021). Reversible Hydration of alpha-Dicarbonyl Compounds from Ab Initio Metadynamics Simulations: Comparison between Pyruvic and Glyoxylic Acids in Aqueous Solutions. J Phys Chem B, 125(11), 2942.
Résumé: Glyoxylic and pyruvic oxoacids are widely available in the atmosphere as gas-phase clusters and particles or in wet aerosols. In aqueous conditions, they undergo interconversion between the unhydrated oxo and gem-diol forms, where two hydroxyl groups replace the carbonyl group. We here examine the hydration equilibrium of glyoxylic and pyruvic acids with first-principles simulations in water at ambient conditions using ab initio metadynamics to reconstruct the corresponding free-energy landscapes. The main results are as follows: (i) our simulations reveal the high conformational diversity of these species in aqueous solutions. (ii) We show that gem-diol is strongly favored in water compared to its oxo counterpart by 29 and 16 kJ/mol for glyoxylic and pyruvic acids, respectively. (iii) From our atomic-scale simulations, we present new insights into the reaction mechanisms with a special focus on hydrogen-bond arrangements and the electronic structure of the transition state.
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2020 |
Gutierrez-Quintanilla, A., Chevalier M, Platakyte, R., Ceponkus J, & Crepin, C. (2020). Intramolecular hydrogen tunneling in 2-chloromalonaldehyde trapped in solid para-hydrogen. Phys Chem Chem Phys, 20, 28658–28666.
Résumé: The internal dynamics of a 2-chloromalonaldehyde (2-ClMA) molecule, possessing a strong internal hydrogen bond (IHB), was examined by means of matrix isolation spectroscopy in a soft host: para-hydrogen (pH2). 2-ClMA is a chlorinated derivative of malonaldehyde (MA), a model molecule in hydrogen transfer studies, better suited to low temperature experiments than its parent molecule. The infrared absorption spectra of 2-ClMA isolated in pH2 exhibit temperature dependent structures which are explained as transitions occurring from split vibrational levels induced by hydrogen tunneling. The doublet components associated with higher and lower energy levels are changing reversibly with the increase/decrease of the matrix temperature. The ground state splitting is measured to be 7.9 +/- 0.1 cm(-1). The presence of oH2 impurities in the pH2 matrix close to the neighborhood of the 2-ClMA molecule is found to quench the H tunneling. The data provide a powerful insight into the dynamical picture of intramolecular hydrogen tunneling in a molecule embedded in a very weakly perturbing environment.
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Hartwig, B., Lange, M., Poblotzki, A., Medel, R., Zehnacker, A., & Suhm, M. A. (2020). The reduced cohesion of homoconfigurational 1,2-diols. PCCP, 22(3), 1122–1136.
Résumé: By a combination of linear FTIR and Raman jet spectroscopy, racemic trans-1,2-cyclohexanediol is shown to form an energetically unrivalled S4-symmetric heterochiral dimer in close analogy to 1,2-ethanediol. Analogous experiments with enantiopure trans-1,2-cyclohexanediol reveal the spectral signature of at least three unsymmetric homochiral dimers. A comparison to signal-enhanced spectra of 1,2-ethanediol and to calculations uncovers at least three transiently homochiral dimer contributions as well. In few of these dimer structures, the intramolecular OH⋯O contact present in monomeric 1,2-diols survives, despite the kinetic control in supersonic jet expansions. This provides further insights into the dimerisation mechanism of conformationally semi-flexible molecules in supersonic jets. Racemisation upon dimerisation is shown to be largely quenched under jet cooling conditions, whereas it should be strongly energy-driven at higher temperatures. The pronounced energetic preference for heterochiral aggregation of vicinal diols is also discussed in the context of chirality-induced spin selectivity.
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Hirata, K., Mori, Y., Ishiuchi, S. -ichi, Fujii, M., & Zehnacker, A. (2020). Chiral discrimination between tyrosine and β-cyclodextrin revealed by cryogenic ion trap infrared spectroscopy. PCCP, 22(43), 24887–24894.
Résumé: Complexes of permethylated β-cyclodextrin (β-MCD) with the two enantiomers of protonated tyrosine (l- and d-TyrH+) are studied by cryogenic ion trap infrared photo-dissociation spectroscopy. The vibrational spectra in the OH/NH stretch and fingerprint regions are assigned based on density functional theory calculations. The spectrum of both l- and d-TyrH+ complexes contains features characteristic of a first structure with ammonium and acid groups of the amino acid simultaneously interacting with the β-MCD, the phenolic OH remaining free. A second structure involving additional interaction between the phenolic OH and the β-MCD is observed only for the complex with d-TyrH+. The larger abundance of the d-TyrH+ complex in the mass spectrum is tentatively explained in terms of (1) better insertion of d-TyrH+ within the cavity with the hydrophobic aromatic moiety less exposed to hydrophilic solvent molecules and (2) a stiff structure involving three interaction points, namely the ammonium, the phenolic OH and the carboxylic acid OH, which is not possible for the complex with l-TyrH+. The recognition process does not occur through size effects that induce complementarity to the host molecule but specific interactions. These results provide a comprehensive understanding of how the cyclodextrin recognises a chiral biomolecule.
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Imani, Z., Mundlapati, V. R., Goldsztejn, G., Brenner, V., Gloaguen, E., Guillot, R., Baltaze, J. P., Le Barbu-Debus, K., Robin, S., Zehnacker, A., Mons, M., & Aitken, D. J. (2020). Conformation control through concurrent N–H⋯S and N–H⋯O=C hydrogen bonding and hyperconjugation effects. CHEMICAL SCIENCE, 11(34), 9191–9197.
Résumé: In addition to the classical N-HMIDLINE HORIZONTAL ELLIPSISO-C non-covalent interaction, less conventional types of hydrogen bonding, such as N-HMIDLINE HORIZONTAL ELLIPSISS, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane alpha-amino acid. 6-Membered ring inter-residue N-HMIDLINE HORIZONTAL ELLIPSISS interactions (C6(gamma)), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-HMIDLINE HORIZONTAL ELLIPSISO-C interactions (C5) to provide a C5-C6(gamma)feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6(gamma)features in the planar dimer implicate an unprecedented three-centre H-bond of the type C-OMIDLINE HORIZONTAL ELLIPSISH(N)MIDLINE HORIZONTAL ELLIPSISSR2, while the trimer adopts two C5-C6(gamma)features separated by a Ramachandran alpha-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.
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Le Barbu-Debus, K., Bowles, J., Jähnigen, S., Clavaguéra, C., Calvo, F., Vuilleumier, R., & Zehnacker, A. (2020). Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches. PCCP, 22, 26047–26068.
Résumé: Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra. Several approaches have been proposed to include them into computational models for calculating VCD signals, in particular those resting on the “cluster-in-a-liquid” model. Here we examine the capabilities of this ansatz on the example of flexible (1S,2S)-trans-1-amino-2-indanol solvated in dimethyl sulfoxide (DMSO). We compare cluster sets obtained from static calculations with results from explicit molecular dynamics (MD) trajectories based on either force field (FF) or first-principles (FP) methods. While the FFMD approach provides a broader sampling of configurational space, FPMD and time-correlation functions of dipole moments account for anharmonicity and entropy effects in the VCD calculation. They provide a means to evaluate the immediate effect of the solvent on the spectrum. This survey singles out several challenges associated with the use of clusters to describe solvation effects in systems showing shallow potential energy surfaces and non-covalent interactions. Static structures of clusters involving a limited number of solvent molecules satisfactorily capture the main effects of solvation in the bulk limit on the VCD spectra, if these structures are correctly weighted. The importance of taking into consideration their fluxionality, i.e. different solvent conformations sharing a same hydrogen bond pattern, and the limitations of small clusters for describing the solvent dynamics are discussed.
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Le Barbu-Debus, K., Scuderi, D., Lepère, V., & Zehnacker, A. (2020). Homochiral vs. heterochiral sodium core dimers of tartaric acid esters: A mass spectrometry and vibrational spectroscopy study. Journal of Molecular Structure, 1205, 127583.
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Pérez-Mellor, A., Le Barbu-Debus, K., & Zehnacker, A. (2020). Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits. Chirality, 32(5), 693–703.
Résumé: Abstract The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.
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Strom, A. I., Gutierrez-Quintanilla A, Chevalier, M., Ceponkus J, Crepin, C., & Anderson DT. (2020). Matrix Isolation Spectroscopy and Nuclear Spin Conversion of Propyne Suspended in Solid Parahydrogen. J Phys Chem A, 124(22), 4471–4483.
Résumé: Parahydrogen (pH2) quantum solids are excellent matrix isolation hosts for studying the rovibrational dynamics and nuclear spin conversion (NSC) kinetics of molecules containing indistinguishable nuclei with nonzero spin. The relatively slow NSC kinetics of propyne (CH3CCH) isolated in solid pH2 is employed as a tool to assign the rovibrational spectrum of propyne in the 600-7000 cm(-1) region. Detailed analyses of a variety of parallel (DeltaK = 0) and perpendicular (DeltaK=+/-1) bands of propyne indicate that the end-over-end rotation of propyne is quenched, but K rotation of the methyl group around the C3 symmetry axis still persists. However, this single-axis K rotation is significantly hindered for propyne trapped in solid pH2 such that the energies of the K rotational states do not obey simple energy-level expressions. The NSC kinetics of propyne follows first-order reversible kinetics with a 287(7) min effective time constant at 1.7 K. Intensity-intensity correlation plots are used to determine the relative line strengths of individual ortho- and para-propyne rovibrational transitions, enabling an independent estimation of the ground vibrational state effective A'' constant of propyne.
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Szczepaniak, U., Gutiérrez-Quintanilla, A., Crépin, C., Guillemin, J. - C., Turowski, M., Custer, T., & Kołos, R. (2020). Spectroscopy of methylcyanodiacetylene revisited. Solid parahydrogen and solid neon matrix studies. Journal of Molecular Structure, 1218, 128437.
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Szczepaniak, U., Ozaki, K., Tanaka, K., Ohnishi, Y., Wada, Y., Guillemin, J. - C., Crépin, C., Kołos, R., Morisawa, Y., Suzuki, H., & Wakabayashi, T. (2020). Phosphorescence excitation mapping and vibrational spectroscopy of HC9N and HC11N cyanopolyynes in organic solvents. Journal of Molecular Structure, 1214, 128201.
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2019 |
Ben Nasr, F., Alata, I., Scuderi, D., Lepere, V., Brenner, V., Jaidane, N. E., & Zehnacker, A. (2019). Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase. Physical Chemistry Chemical Physics, 21(28), 15439–15451.
Résumé: The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the nu(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.
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Crépin-Gilbert, C., & Savchenko, E. (2019). Nanostructures and impurity centers in cryogenic environment. Low Temperature Physics, 45(6), 581–582.
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de Pujo, P., Ryan, M., Crépin, C., Mestdagh, J. M., & McCaffrey, J. G. (2019). The role of spin-orbit coupling in the optical spectroscopy of atomic sodium isolated in solid xenon. Low Temperature Physics, 45(7), 715–720.
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Declerck, V., Perez-Mellor, A., Guillot, R., Aitken, D. J., Mons, M., & Zehnacker, A. (2019). Vibrational circular dichroism as a probe of solid-state organisation of derivatives of cyclic beta-amino acids: Cis- and trans-2-aminocyclobutane-1-carboxylic acid. Chirality, 31(8), 547–560.
Résumé: Peptide models built from cis- and trans-2-aminocyclobutane-1-carboxylic acids (ACBCs) are studied in the solid phase by combining Fourier-transform infrared spectroscopy (FTIR) absorption spectroscopy, vibrational circular dichroism (VCD), and quantum chemical calculations using density functional theory (DFT). The studied systems are N-tert-butyloxycarbonyl (Boc) derivatives of 2-aminocyclobutanecarboxylic acid (ACBC) benzylamides, namely Boc-(cis-ACBC)-NH-Bn and Boc-(trans-ACBC)-NH-Bn. These two diastereomers show very different VCD signatures and intensities, which of the trans-ACBC derivative being one order of magnitude larger in the region of the nu (CO) stretch. The spectral signature of the cis-ACBC derivative is satisfactorily reproduced by that of the monomer extracted from the solid-state geometry of related ACBC derivatives, which shows that no long-range effects are implicated for this system. In terms of hydrogen bonds, the geometry of this monomer is intermediate between the C6 and C8 structures (exhibiting a 6- or 8-membered cyclic NHMIDLINE HORIZONTAL ELLIPSISO hydrogen bond) previously evidenced in the gas phase. The benzyl group must be in an extended geometry to reproduce satisfactorily the shape of the VCD spectrum in the nu (CO) range, which qualifies VCD as a potential probe of dispersion interaction. In contrast, reproducing the IR and VCD spectrum of the trans-ACBC derivative requires clusters larger than four units, exhibiting strong intermolecular H-bonding patterns. A qualitative agreement is obtained for a tetramer, although the intensity enhancement is not reproduced. These results underline the sensitivity of VCD to the long-range organisation in the crystal.
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Gutiérrez-Quintanilla A., Chevalier M., Platakyte R., Ceponkus J., & Crépin C. (2019). Selective photoisomerisation of 2- chloromalonaldehyde. J Chem Phys, 150, 034305.
Résumé: Isomerization of 2-chloromalonaldehyde (2-ClMA) is explored giving access to new experimental data on this derivative of malonaldehyde,
not yet studied much. Experiments were performed isolating 2-ClMA in argon, neon, and para-hydrogen matrices.
UV irradiation of the matrix samples induced isomerization to three open enolic forms including two previously observed along
with the closed enolic form after deposition. IR spectra of these specific conformers were recorded, and a clear assignment
of the observed bands was obtained with the assistance of theoretical calculations. UV spectra of the samples were measured,
showing a blue shift of the absorption with the opening of the internal hydrogen bond of the most stable
enol form. Specific sequences of UV irradiation at different wavelengths allowed us to obtain samples containing only one
enol conformer. The formation of conformers is discussed. The observed selectivity of the process among the enol forms is
analyzed.
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Gutiérrez-Quintanilla,, Briant,, Mengesha,, Gaveau, M. - A., Mestdagh,, Soep,, & Poisson,. (2019). Propyne-water complexes hosted in helium droplets. Low Temperature Physics, 45(6), 634–638.
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Pérez-Mellor A. Zehnacker A. (2019). Chirality Effects in Jet-Cooled Cyclic Dipeptides. In Ebata T. Fujii M. (Ed.), Physical Chemistry of Cold Gas-Phase Functional Molecules and Clusters (pp. 63–87). Singapore: Springer.
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Perez-Mellor, A., Alata, I., Lepere, V., & Zehnacker, A. (2019). Conformational Study of the Jet-Cooled Diketopiperazine Peptide Cyclo Tyrosyl-Prolyl. Journal Of Physical Chemistry B, 123(28).
Résumé: The conformational landscape of the diketopiperazine (DKP) dipeptide built on tyrosine and proline, namely, cyclo Tyr-Pro, is studied by combining resonance-enhanced multiphoton ionization, double resonance infrared ultraviolet (IR-UV) spectroscopy, and quantum chemical calculations. Despite the geometrical constraints due the two aliphatic rings, DKP and proline, cyclo Tyr-Pro is a flexible molecule. For both diastereoisomers, cyclo LTyr-LPro and cyclo LTyr-DPro, two structural families coexist under supersonic jet conditions. In the most stable conformation, the aromatic tyrosine substituent is folded over the DKP ring (g(+) geometry of the aromatic ring) as it is in the solid state. The other structure is completely extended (g(-) geometry of the aromatic ring) and resembles that proposed for the vapor phase. IR-UV results are not sufficient for unambiguous assignment of the observed spectra to either folded or extended conformations and the simulation of the vibronic pattern of the S-0-S-1 transition is necessary. Still, the comparison between IR-UV results and anharmonic calculations allows explanation of the minor structural differences between cyclo LTyr-LPro and cyclo LTyr-DPro in terms of different NH center dot center dot center dot pi and CH center dot center dot center dot pi interactions.
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Platakyte, R., Gutiérrez-Quintanilla, A., Sablinskas, V., & Ceponkus, J. (2019). Influence of environment and association with water, to internal structure of trifluoroacetylacetone. Matrix isolation FTIR study. Low Temperature Physics, 45(6), 615–626.
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Rojas-Lorenzo,, Lara-Moreno,, Gutierrez-Quintanilla,, Chevalier,, & Crépin,. (2019). Theoretical study of “trapping sites” in cryogenic rare gas solids doped with β-dicarbonyl molecules. Low Temperature Physics, 45, 363–370.
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Tamura, M., Sekiguchi, T., Ishiuchi, S., Zehnacker-Rentien, A., & Fujii, M. (2019). Can the Partial Peptide SIVSF of the beta(2)-Adrenergic Receptor Recognize Chirality of the Epinephrine Neurotransmitter? Journal Of Physical Chemistry Letters, 10(10), 2470–2474.
Résumé: Chirality plays an essential role in biological molecular recognition, such as neurotransmission. Here, we applied electrospray-cold ion trap spectroscopy to complexes of a partial binding motif SIVSF of a beta(2)-adrenergic receptor pocket with L- and D-epinephrine AdH(+). The ultraviolet spectrum of the SIVSF-AdH(+) complex changed drastically when L-AdH(+) was replaced by its enantiomer. The isomer-selected infrared spectra revealed that D-AdH(+) was bound to SIVSF by its protonated amino-group or a single catechol OH and induced nonhelical secondary structures of SIVSF. This is in sharp contrast to the helical SIVSF complex with L-AdH(+), which is close to the natural binding structure with two catechol OHs binding in the receptor. This shows that a short pentapeptide SIVSF can distinguish the chirality of the ligand AdH(+) as well as the receptor. This stereoselectivity is suggested to arise from an additional interaction involving the hydroxyl group on the chiral carbon.
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2018 |
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Babikov, D., Benoit, D., Bowman, J., Burd, T., Clary, D., Donovan, R., Fischer, I., Gianturco, F., Hochlaf, M., Kar, S., Kirrander, A., Leone, S., Malcomson, T., Manthe, U., McCoy, A. B., Petersen, J., Richardson, J., Slavicek, P., Stoecklin, T., Szalewicz, K., van der Avoird, A., Wester, R., Worth, G., & Zehnacker-Rentien, A. (2018). Quantum dynamics of isolated molecules: general discussion. Faraday Discussions, 212, 281–306.
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Bacic, Z., Benoit, D., Besemer, M., Bowman, J., Bradforth, S., Clary, D., Donovan, R., Fischer, I., Gianturco, F., Hochlaf, M., Houston, P., Knowles, P., Leone, S., Linguerri, R., Manthe, U., McCoy, A. B., Petersen, J., Richardson, J., Shan, X., Slavicek, P., Stoecklin, T., Szalewicz, K., van der Avoird, A., Wester, R., Worth, G., & Zehnacker-Rentien, A. (2018). Precise characterisation of isolated molecules: general discussion. Faraday Discussions, 212, 137–155.
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Bacic, Z., Benoit, D., Biczysko, M., Bowman, J., Bradforth, S., Burd, T., Chambaud, G., Clary, D., Crepin, C., Dracinsky, M., Felker, P., Fischer, I., Gianturco, F., Hochlaf, M., Kouril, K., Kratochvilova, I., Liu, C. M., McCoy, A., Miyazaki, J., Mouhib, H., Richardson, J., Slavicek, P., Stoecklin, T., Szalewicz, K., van der Avoird, A., & Zehnacker-Rentien, A. (2018). Molecules in confinement in clusters, quantum solvents and matrices: general discussion. Faraday Discussions, 212, 569–601.
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Ban, L., Bowman, J., Bradforth, S., Chambaud, G., Dracinsky, M., Fischer, I., Gora, R., Hochlaf, M., Janicki, M., Kirrander, A., McCoy, A. B., Petersen, J., Richardson, J., Slavicek, P., Szalewicz, K., & Zehnacker-Rentien, A. (2018). Molecules in confinement in liquid solvents: general discussion. Faraday Discussions, 212, 383–397.
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BenNasr, F., Perez-Mellor, A., Alata, I., Lepere, V., Jaidane, N. E., & Zehnacker, A. (2018). Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discussions, 212, 399–419.
Résumé: Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NH and CH interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Bouchet, A., Klyne, J., Ishiuchi, S. - I., Dopfer, O., Fujii, M., & Zehnacker, A. (2018). Stereochemistry-dependent structure of hydrogen-bonded protonated dimers: the case of 1-amino-2-indanol. Phys Chem Chem Phys, 20, 12430–12443.
Résumé: To understand the role of chirality in shaping biological supramolecular systems it is instructive to visualize the subtle effects of stereochemistry on the structure of model aggregates at the molecular level. Here, we apply conformer-specific IR-UV double-resonance laser spectroscopy in a cold ion trap to derive a detailed description of the protonated homodimers of (1R,2S)-cis- and (1R,2R)-trans-1-amino-2-indanol (c-AI2H+, t-AI2H+). Although the protonated monomers (c-AIH+, t-AIH+) only differ by the chirality of one carbon atom, their conformations are clearly distinct. c-AIH+ has an intramolecular NH+O hydrogen bond (H-bond), while t-AIH+ lacks such an interaction. This has crucial consequences on the geometry and stability of the corresponding c-AI2H+ and t-AI2H+ dimers. While there is a competition between intra- and intermolecular H-bonds in c-AI2H+, the formation of t-AI2H+ does not require deformation of the monomers. This difference results in higher binding energies of t-AI2H+ compared to c-AI2H+. To optimize the H-bond network, the two dimers do not necessarily involve the corresponding most stable monomers. c-AI2H+ and t-AI2H+ differ in their UV photodissociation mass spectra and in their electronic spectra, which suggests different geometries also in the excited state.
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Gutierrez-Quintanilla, A., Briant M, Mengesha, E., Gaveau MA, Mestdagh, J. - M., Soep B, Crepin, C., & Poisson L. (2018). A HElium NanoDroplet Isolation (HENDI) investigation of the weak hydrogen bonding in the propyne dimer (CH3CCH)2. Phys Chem Chem Phys, 20, 28658.
Résumé: A HElium Nanodroplet Isolation (HENDI) experiment was performed to explore the absorption spectra of the propyne monomer (CH3CCH), dimer and (CH3CCH)>/=3 multimers in the vicinity of the CH stretch region nu1 of the monomer. Ab initio calculations were performed at the MP2 level to document the potential energy surface of the dimer. This provided the necessary parameters to simulate the absorption spectrum of the dimer and thus facilitate the interpretation of the experiment. The central result was to observe three isomers of the dimer, hence reflecting the complexity of the weak CHpi H-bonding when several H-donors are at play.
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Gutierrez-Quintanilla, A., Chevalier M, Ceponkus, J., Lozada-Garcia RR, Mestdagh, J. - M., & Crepin C. (2018). Large amplitude motions within molecules trapped in solid parahydrogen. Faraday Discuss, 212, 499–515.
Résumé: Molecules of the beta-diketone and beta-dialdehyde families were trapped in solid parahydrogen (pH2) to investigate the vibrational behavior of systems containing an intramolecular hydrogen bond (IHB). In the simplest beta-diketone, acetylacetone (AcAc), H transfer related to the IHB is coupled with methyl torsions. In pH2, the study of nuclear spin conversion (NSC) in methyl groups allows the characterisation of the influence of these large amplitude motions on the vibrational modes. The deuteration of the OH group involved in the IHB has important consequences on the vibrational spectrum of the molecule and evidence of NSC in methyl groups is difficult to obtain. In the chlorine derivative (3-chloroacetylacetone), the H-transfer is no longer coupled with methyl torsion, and NSC has undetectable effects on the IR spectrum. A search of H tunnelling splitting in the IR spectra of beta-dialdehydes trapped in pH2 was performed. A few modes of 2-chloromalonaldehyde appear as doublets and were assigned to tunnelling levels. The spectroscopic results related to large amplitude motions are detailed and discussed, highlighting puzzling effects.
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Gutierrez-Quintanilla, A., Chevalier M, Platakyte, R., Ceponkus J, Rojas-Lorenzo, G. A., & Crepin C. (2018). 2-Chloromalonaldehyde, a model system of resonance-assisted hydrogen bonding: vibrational investigation. Phys Chem Chem Phys, 20, 12888.
Résumé: The chelated enol isomer of 2-chloromalonaldehyde (2-ClMA) is experimentally characterized for the first time by IR and Raman spectroscopies. The spectra are obtained by trapping the molecule in cryogenic matrices and analyzed with the assistance of theoretical calculations. Experiments were performed in argon, neon and para-hydrogen matrices. The results highlight puzzling matrix effects, beyond site effects, which are interpreted as due to a tunneling splitting of the vibrational levels related to the proton transfer along the internal hydrogen bond (IHB). 2-ClMA is thus one of the very few molecules in which the H tunneling has been observed in cryogenic matrices. The comparison with its parent molecule (malonaldehyde) shows experimentally and theoretically the weakening of the IHB upon chlorination, with a reduced cooperative effect in the resonance assisted hydrogen bond. In addition, the Cl substitution induces an important stabilization of two open enol conformers. These two open forms appear in the spectra of as-deposited samples, meaning that, in contrast with other well-studied molecules of the same family (beta-dialdehydes and beta-diketones), they are present in the gas phase at room temperature.
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Le Barbu-Debus, K., Scherrer, A., Bouchet, A., Sebastiani, D., Vuilleumier, R., & Zehnacker, A. (2018). Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: the case of (S)-1-indanol. Phys Chem Chem Phys, 20(21), 14635–14646.
Résumé: The influence of flexibility and hydrogen bond formation on the IR absorption and vibrational circular dichroism (VCD) spectrum of a floppy protic molecule, namely, (S)-1-indanol, is studied in both non-polar CCl4 and polar DMSO solvents. The experimental IR absorption and VCD spectra obtained by Fourier transform spectroscopy are interpreted using both static density functional theory (DFT) calculations and first principles molecular dynamics (FPMD) within DFT, using the nuclear velocity perturbation theory (NVPT). Simulation of the spectra based on static optimised geometries is not sufficient in CCl4 and going beyond static calculations is mandatory for satisfactorily reproducing the VCD spectra. The FPMD results obtained in DMSO indicate that (S)-1-indanol is hydrogen-bonded to one DMSO molecule. As a result, static “cluster-in-the-bulk” DFT calculations in which the solute-solvent interaction is modeled as the most stable (S)-1-indanol:DMSO complexes in a DMSO continuum yield satisfactory agreement with the experiment. Correspondence between experimental and simulated spectra is slightly improved when the VCD spectrum is calculated as the summed contributions of snapshots extracted from FPMD trajectories, due to better sampling of the potential-energy surface. Finally, NVPT calculations further improve the description of experimental spectra by taking into account higher-energy structures, which are not necessary local minima.
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Nieuwjaer, N., Desfrancois, C., Lecomte, F., Manil, B., Soorkia, S., Broquier, M., & Gregoire, G. (2018). Photodissociation Spectroscopy of Cold Protonated Synephrine: Surprising Differences between IR-UV Hole-Burning and IR Photodissociation Spectroscopy of the O-H and N-H Modes. J Phys Chem A, .
Résumé: We report the UV and IR photofragmentation spectroscopies of protonated synephrine in a cryogenically cooled Paul trap. Single (UV or IR) and double (UV-UV and IR-UV) resonance spectroscopies have been performed and compared to quantum chemistry calculations, allowing the assignment of the lowest-energy conformer with two rotamers depending on the orientation of the phenol hydroxyl (OH) group. The IR-UV hole burning spectrum exhibits the four expected vibrational modes in the 3 mum region, i.e., the phenol OH, Cbeta-OH, and two NH2(+) stretches. The striking difference is that, among these modes, only the free phenol OH mode is active through IRPD. The protonated amino group acts as a proton donor in the internal hydrogen bond and displays large frequency shifts upon isomerization expected during the multiphoton absorption process, leading to the so-called IRMPD transparency. More interestingly, while the Cbeta-OH is a proton acceptor group with moderate frequency shift for the different conformations, this mode is still inactive through IRPD.
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Noble, J. A., Broquier, M., Gregoire, G., Soorkia, S., Pino, G. A., Marceca, E., Dedonder-Lardeux, C., & Jouvet, C. (2018). Tautomerism and electronic spectroscopy of protonated 1- and 2-aminonaphthalene. Phys. Chem. Chem. Phys., 20, 6134–6145.
Résumé: Experimental and theoretical investigations of the excited states of protonated 1- and 2-aminonaphthalene are presented. The electronic spectra are obtained by laser induced photofragmentation of the ions captured in a cold ion trap. Using ab initio calculations, the electronic spectra can be assigned to different tautomers which have the proton on the amino group or on the naphthalene moiety. It is shown that the tautomer distribution can be varied by changing the electrospray source conditions, favoring either the most stable form in solution (amino protonation) or that in the gas phase (aromatic ring protonation). Calculations for larger amino-polyaromatics predict that these systems should behave as “proton sponges” i.e. have a proton affinity larger than 11 eV.
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Pérez-Mellor, A., Alata, I., Lepere, V., & Zehnacker, A. (2018). Chirality effects in the structures of jet-cooled bichromophoric dipeptides. Journal of Molecular Spectroscopy, 349, 71–84.
Résumé: Diastereomer cyclic dipeptides built on a diketopiperazine (DKP) ring and phenylalanine residues of either identical or opposite chirality have been studied in jet-cooled conditions by combining conformer-specific IR-UV laser spectroscopy. Comparison between the IR-UV double resonance experiments and anharmonic calculations shows the presence of only one conformer of cyclo Phe-Phe, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. This allows weak NH…π and CH…π interactions to take place, which are slightly different in cyclo SPhe-SPhe and cyclo SPhe-RPhe. In both diastereomers, comparison between the S0 and S1 spectra of the all 12C species and that containing one 13C indicates that the electronic excitation is localized on one aromatic ring. This study has been extended to linear SPhe-SPhe and linear SPhe-RPhe, already studied by Abo-Riziq (2005).
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Peukert, S., Kijak, M., Ostapko, J., Sepiol, J., Le Bris, C., Zehnacker-Rentien, A., Gil, M., & Waluk, J. (2018). Supersonic jet spectroscopy of parent hemiporphycene: Structural assignment and vibrational analysis for S-0 and S-1 electronic states. Journal Of Chemical Physics, 149(13), 134307.
Résumé: Hemiporphycene (HPc), a constitutional isomer of porphyrin, is studied under supersonic expansion conditions by means of laser-induced fluorescence, visible-visible hole-burning experiments, single vibronic level fluorescence techniques, and quantum chemical calculations. Only one trans form of jet-cooled HPc is observed, in contrast to solution studies that evidence a mixture of two trans tautomeric forms separated in energy by similar to 1 kcal/mol. Reliable structural assignment is provided by simulating absorption and emission patterns at the density functional theory and time-dependent density functional theory levels of theory. The vibronic spectra are nicely reproduced for both electronic ground and lowest excited singlet states for the most stable trans form. In contrast to another porphyrin isomer, porphycene (Pc), no tunneling or photo-induced hydrogen transfer is detected. The lower symmetry of HPc compared with Pc and the concomitant non-equivalent positions of the inner-cavity nitrogen atoms result in a non-symmetric double minimum potential for tautomerization, larger energy barrier, and a longer tunneling distance, with the average intramolecular hydrogen bond length larger in HPc than in Pc. HPc readily forms hydrates that show red-shifted absorption relative to the bare molecule. Published by AIP Publishing.
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Sekiguchi, T., Tamura, M., Oba, H., Carcarbal, P., Lozada-Garcia, R. R., Zehnacker-Rentien, A., Gregoire, G., Ishiuchi, S. - I., & Fujii, M. (2018). Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom-Up Approach. Angew Chem Int Ed Engl, 57, 5626–5629.
Résumé: Receptor-neurotransmitter molecular recognition is key for neurotransmission. Although crystal structures of the receptors are known, the mechanism for recognition is not clear. Reported here is the ultraviolet (UV) and infrared (IR) spectra of complexes between a partial peptide (SIVSF), mimicking the binding motif of a catechol ring in the adrenergic receptor, and various ligands. The UV spectra show that two isomers coexist in the complex of SIVSF with properly recognized ligands, such as protonated adrenaline (adrenalineH(+) ). From IR spectra, they are assigned to catechol- and amino-bound structures. The catechol-bound structure is not observed when the ligand is replaced by nonproper molecules, such as noradrenalineH(+) . The results suggest that SIVSF not only recognizes the catechol ring but can distinguish differences in the amine side chain. The method provides a new possibility for screening molecules as potential therapeutics for activating the receptor.
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Shafizadeh, N., Boyé-Péronne, S., Soorkia, S., Chen, S., de la Lande, A., Cunha de Miranda, B., Garcia, G. A., Nahon, L., Poisson, L., & Soep, B. (2018). The surprisingly high ligation energy of CO to Ruthenium porphyrins. Phys. Chem. Chem. Phys., 20, 11730–11739.
Résumé: A combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenylporphyrin [RuII TPP], in the RuII oxidation degree. Measurements performed with VUV ionization using the DESIRS beamline at Synchrotron SOLEIL led to adiabatic ionization energies of [RuII TPP] and its complex with CO, [RuII TPP–CO], of 6.48
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Szczepaniak, U., Kolos R, Gronowski, M., Chevalier M, Guillemin, J. - C., & Crepin C. (2018). Synthesis and Electronic Phosphorescence of Dicyanooctatetrayne (NC10N) in Cryogenic Matrixes. J Phys Chem A, 122(25), 5580–5588.
Résumé: The rodlike 1,8-dicyano-octa-1,3,5,7-tetrayne (NC10N) molecule was synthesized with UV-assisted coupling of rare-gas matrix-isolated cyanobutadiyne (HC5N) molecules. Detection of NC10N molecule was possible due to its strong orange-red (origin at 618 nm) electronic luminescence. Excitation spectra of this emission (a (3)Sigmau(+)-X (1)Sigmag(+) phosphorescence) gave access to studying the fully allowed H (1)Sigmau(+)-X (1)Sigmag(+) UV system of NC10N. The identification of observed spectral features was assisted with quantum chemical computations. Certain regularities shaping the electronic spectroscopy of NC2 nN molecules have been discussed.
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Szczepaniak, U., Kołos, R., Gronowski, M., Guillemin, J. - C., & Crépin, C. (2018). Low Temperature Synthesis and Phosphorescence of Methylcyanotriacetylene. The Journal of Physical Chemistry A, 122(1), 89–99.
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Usabiaga, I., Camiruaga, A., Insausti, A., Carcabal, P., Cocinero, E. J., Leon, I., & Fernandez, J. A. (2018). Phenyl-beta-D-glucopyranoside and Phenyl-beta-D-galactopyranoside Dimers: Small Structural Differences but Very Different Interactions. Frontiers In Physics, 6, à venir.
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2017 |
Alata, I., Perez-Mellor, A., Ben Nasr, F., Scuderi, D., Steinmetz, V., Gobert, F., Jaidane, N. E., & Zehnacker-Rentien, A. (2017). Does the Residues Chirality Modify the Conformation of a Cyclo-Dipeptide? Vibrational Spectroscopy of Protonated Cyclo-diphenylalanine in the Gas Phase. J. Phys. Chem. A, 121(38), 7130–7138.
Résumé: The structure of a protonated diketopiperazine dipeptide, cyclo-diphenylalanine, is studied by means of infrared multiple photon dissociation spectroscopy combined with quantum chemical calculations. Protonation exclusively occurs on the oxygen site and, in the most stable conformer, results to an intramolecular OH center dot center dot center dot pi interaction, accompanied by a CH-pi interaction. Higher energy conformers with free OH and NH center dot center dot center dot pi interactions are observed as well, due to kinetic trapping. Optimization of the intramolecular interactions involving the aromatic ring dictates the geometry of the benzyl substituents. Changing the chirality of one of the residues has consequences on the CH center dot center dot center dot pi interaction, which is of C alpha H center dot center dot center dot pi nature for LD, while LL shows a C beta H center dot center dot center dot pi interaction. Higher-energy conformers also display some differences in the nature of the intramolecular interactions.
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Bourguignon, B., Béroff, K., Bréchignac, P., Dujardin, G., Leach, S., & and Zehnacker-Rentien, A. (2017). In the wake of Physical Chemistry under irradiation: onward to the Institute of Molecular Sciences at Orsay. Histoire de la Recherche Contemporaine, 6, 16–27.
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Broquier, M., Soorkia, S., Pino, G., Dedonder-Lardeux, C., Jouvet, C., & Gregoire, G. (2017). Excited State Dynamics of Cold Protonated Cytosine Tautomers: Characterization of Charge Transfer, Intersystem Crossing, and Internal Conversion Processes. J. Phys. Chem. A, 121(34), 6429–6439.
Résumé: Charge transfer reactions are ubiquitous in chemical reactivity and often viewed as ultrafast processes. For DNA, femtochemistry has undeniably revealed the primary stage of the deactivation dynamics of the locally excited state following electronic excitation. We here demonstrate that the full time scale excited state dynamics can be followed up to milliseconds through an original pump-probe photodissociation scheme applied to cryogenic ion spectroscopy. Protonated cytosine is chosen as a benchmark system in which the locally excited (1)pipi* state decays in the femtosecond range toward long-lived charge transfer and triplet states with lifetimes ranging from microseconds to milliseconds, respectively. A three-step mechanism ((1)pipi* --> (1)CT --> (3)pipi*) is proposed where internal conversion from each state can occur leading ultimately to fragmentation in the ground electronic state.
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Garcia, R. L., Nieuwjaer, N., Desfrancois, C., Lecomte, F., Leite, S. D., Manil, B., Broquier, M., & Gregoire, G. (2017). Vibronic spectra of protonated hydroxypyridines: contributions of prefulvenic and planar structures. Phys. Chem. Chem. Phys., 19(12), 8258–8268.
Résumé: Various hydroxypyridine derivatives are endogenous or synthetic photosensitizers which could contribute to solar radiation damage. The study of their excited states could lead to a better understanding of their action mechanisms. We present here the ultraviolet (UV) spectra of the protonated 2-, 3- and 4-hydroxypyridine. These spectra were obtained with an experimental device coupling an electrospray ion source with a cold quadrupole ion trap and a time of flight mass spectrometer. They display well resolved vibrational structures, with a clear influence of the position of the OH group. These results are interpreted with excited states calculations at the coupled cluster CC2 level.
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Perez-Mellor, A., & Zehnacker, A. (2017). Vibrational circular dichroism of a 2,5-diketopiperazine (DKP) peptide: Evidence for dimer formation in cyclo LL or LD diphenylalanine in the solid state. Chirality, 29(2), 89–96.
Résumé: The diastereomer diketopiperazine (DKP) peptides built on phenylalanine, namely, cyclo diphenylalanine LPhe-LPhe and LPhe-DPhe, were studied in the solid phase by vibrational circular dichroism (VCD) coupled to quantum chemical calculations. The unit structure of cyclo LPhe-LPhe in KBr pellets is a dimer bridged by two strong NH center dot center dot center dot O hydrogen bonds. The intense bisignate signature in the CO stretch region is interpreted in terms of two contributions arising from the free COs of the dimer and the antisymmetrical combination of the bound COs. In contrast, cyclo LPhe-DPhe shows no VCD signal in relation to its symmetric nature.
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Shafizadeh, N., Soorkia, S., Gregoire, G., Broquier, M., Crestoni, M. E., & Soep, B. (2017). Dioxygen Binding to Protonated Heme in the Gas Phase, an Intermediate Between Ferric and Ferrous Heme. Chem.-Eur. J., 23(54), 13493–13500.
Résumé: With a view to characterizing the influence of the electronic structure of the Fe atom on the nature of its bond with dioxygen (O-2) in heme compounds, a study of the UV/Vis action spectra and binding energies of heme-O-2 molecules has been undertaken in the gas phase. The binding reaction of protonated ferrous heme [Fe-II-hemeH](+) with O-2 has been studied in the gas phase by determining the equilibrium of complexed [Fe-II-hemeH(O-2)](+) with uncomplexed protonated heme in an ion trap at controlled temperatures. The binding energy of O-2 to the Fe atom of protonated ferrous heme was obtained from a van't Hoff plot. Surprisingly, this energy (1540 +/- 170 cm(-1), 18.4 +/- 2 kJmol(-1)) is intermediate between those of ferric heme and ferrous heme. This result is interpreted in terms of a delocalization of the positive charge over the porphyrin cycle, such that the Fe atom bears a fractional positive charge. The resulting electron distribution on the Fe atom differs notably from that of a purely low-spin ferrous heme [Fe-II-heme(O-2)] complex, as deduced from its absorption spectrum. It also differs from that of ferric heme [Fe-III-heme(O-2)](+), as evidenced by the absorption spectra. Protonated heme creates a specific bond that cannot accommodate strong sigma donation.
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Szczepaniak, U., Kolos, R., Gronowski, M., Chevalier, M., Guillemin JC., Turowski M., Custer, T., & Crépin, C. (2017). Cryogenic Photochemical Synthesis and Electronic Spectroscopy of Cyanotetracetylene. JOURNAL OF PHYSICAL CHEMISTRY A, 121(39), 7374–7384.
Résumé: HC9N is a molecule of astrochemical interest. In this study, it was produced in cryogenic Ar and Kr matrices from UV-photolyzed diacetylene/cyanodiacetylene mixtures. Its strong phosphorescence was discovered and served for the identification of the compound. Vibrationally resolved phosphorescence excitation spectra gave insight into excited singlet electronic states. Two electronic systems were observed around 26 00034 000 cm(-1) and 35 000-50 000 cm(-1). Energies of the second excited singlet and the lowest triplet state were derived from analysis of these systems. Vibrational and electronic spectroscopic features were assigned with the assistance of density functional theory calculations. Some trends concerning the electronic spectroscopy of HC2+1N family molecules are presented.
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Thon, R., Chin, W., Chamma, D., Gutiérrez-Quintanilla, A., Chevalier, M., Galaup, J. - P., & Crépin, C. (2017). W(CO) 6 in cryogenic solids: A comparative study of vibrational properties. Journal of Luminescence, 191, 78–86.
Résumé: A comparative study of the vibrational properties of W(CO)6 has been performed in different solids at cryogenic temperatures focusing on the IR absorption and the vibrational dynamics of the CO stretching mode of the organometallic compound. Guest-host interactions are investigated in doped solids through the linear IR spectroscopy and four-wave mixing techniques at different temperatures. We show how the host nature, the trapping site, the crystallographic ordering affect the properties of the guest molecule and in particular its vibrational dynamics.
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Uriarte, I., Ecija, P., Lozada-Garcia, R., Carcabal, P., & Cocinero, E. J. (2017). Investigating the Conformation of the Bridged Monosaccharide Levoglucosan. Chemphyschem, , 01242.
Résumé: Levoglucosan is one of the main products of the thermal degradation of glucose and cellulose and is commonly used as a tracer for biomass burning. Herein we report a conformational analysis of levoglucosan under isolation conditions, by means of microwave spectroscopy coupled with ultrafast laser vaporization in supersonic expansions. We observed three different conformations of levoglucosan in the gas phase. They all share a common heavy atom rigid bicyclic structure. The difference between the three of them lies in the network of intramolecular hydrogen bonds that arises from the OH groups at positions 2, 3 and 4. The different combinations of H-bonds give richness to the conformational landscape of levoglucosan. The gas phase conformers obtained in this work are compared to the crystal structure of levoglucosan previously reported. Although the heavy atom frame remains unchanged, there are significant differences in the positions of the H-atoms. In addition, the levoglucosan structure can be compared to the related glucose, for which gas phase conformational studies exist in the literature. In this case, in going from glucose to levoglucosan, there is an inversion in the chair conformation of the pyranose ring. This forces the OH groups to adopt axial positions (instead of the more favorable equatorial positions in glucose) and completely changes the pattern of intramolecular H-bonds.
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2016 |
Asselin, P., Madebene, B., Soulard, P., Georges, R., Goubet, M., Huet, T. R., Pirali, O., & Zehnacker-Rentien, A. (2016). Competition between inter- and intra-molecular hydrogen bonding: An infrared spectroscopic study of jet-cooled amino-ethanol and its dimer. Journal Of Chemical Physics, 145(22), 224313.
Résumé: The Fourier transform IR vibrational spectra of amino-ethanol (AE) and its dimer have been recorded at room temperature and under jet-cooled conditions over the far and mid infrared ranges (50-4000 cm(-1)) using the White-type cell and the supersonic jet of the Jet-AILES apparatus at the synchrotron facility SOLEIL. Assignment of the monomer experimental frequencies has been derived from anharmonic frequencies calculated at a hybrid CCSD(T)-F12/MP2 level. Various thermodynamical effects in the supersonic expansion conditions including molar dilution of AE and nature of carrier gas have been used to promote or not the formation of dimers. Four vibrational modes of the observed dimer have been unambiguously assigned using mode-specific scaling factors deduced from the ratio between experimental and computed frequencies for the monomer. The most stable g 'Gg' monomer undergoes strong deformation upon dimerization, leading to a homochiral head to head dimer involving two strong hydrogen bonds. Published by AIP Publishing.
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Broquier, M., Soorkia, S., Dedonder-Lardeux, C., Jouvet, C., Theule, P., & Gregoire, G. (2016). Twisted Intramolecular Charge Transfer in Protonated Amino Pyridine. J. Phys. Chem. A, 120(21), 3797–3809.
Résumé: The excited state properties of protonated ortho (2-), meta (3-), and para (4-) aminopyridine molecules have been investigated through UV photofragmentation spectroscopy and excited state coupled-cluster CC2 calculations. Cryogenic ion spectroscopy allows recording well-resolved vibronic spectroscopy that can be reproduced through Franck-Condon simulations of the pipi* local minimum of the excited state potential energy surface. The excited state lifetimes have also been measured through a pump-probe excitation scheme and compared to the estimated radiative lifetimes. Although protonated aminopyridines are rather simple aromatic molecules, their deactivation mechanisms are indeed quite complex with unexpected results. In protonated 3- and 4-aminopyridine, the fragmentation yield is negligible around the band origin, which implies the absence of internal conversion to the ground state. Besides, a twisted intramolecular charge transfer reaction is evidenced in protonated 4-aminopyridine around the band origin, while excited state proton transfer from the pyridinic nitrogen to the adjacent carbon atom opens with roughly 500 cm-1 of excess energy.
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Capello, M. C., Hernandez, F. J., Broquier, M., Dedonder-Lardeux, C., Jouvet, C., & Pino, G. A. (2016). Hydrogen bonds vs. pi-stacking interactions in the p-aminophenol ... p-cresol dimer: an experimental and theoretical study. Physical Chemistry Chemical Physics, 18(45), 31260–31267.
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Carcabal, P., Descamps, D., Petit, S., Mairesse, Y., Blanchet, V., & Cireasa, R. (2016). Using high harmonic radiation to reveal the ultrafast dynamics of radiosensitiser molecules. Faraday Discussions, 194, 407–425.
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De la Lande, A., Ha-Thi, M. H., Chen, S. F., Soep, B., & Shafizadeh, N. (2016). Structure of cobalt protoporphyrin chloride and its dimer, observation and DFT modeling. Phys. Chem. Chem. Phys., 18(25), 16700–16708.
Résumé: In this article we present a joint study by time-of-flight mass spectroscopy and density functional theory of cobalt protoporphyrin dimer complexes. The main novelty of the experimental part is to reveal the formation of porphyrin dimers that eventually include a chlorine atom. Density functional theory calculations have been performed to shed light on the structural and electronic properties of monomers and dimers that may be formed experimentally. Various geometries of the monomers are analyzed in the two lowest spin states. The electronic structures are examined by means of population analysis relying on the iterative Hirshfeld scheme and the topological analyses of the electron localization function. It is shown that the cobalt ligand bond is purely ionic in the triplet states but shows a noticeable covalent character in the singlet state. Ionization potential of Co-protoporphyrin and binding energies of the chlorine ligand are also reported. Concerning the dimers, several association patterns are investigated for the chlorinated and non-chlorinated complexes. It is found that the structures of the most stable complexes involve four hydrogen bonds between the carboxylic acid moieties of the protoporphyrins. However other association modes are likely to be possible in the experiments.
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Gans, B., Lamarre, N., Broquier, M., Liévin, J., & Boyé-Péronne, S. (2016). Experimental and ab initio characterisation of HC3N+ vibronic structure: II- High-resolution VUV PFI-ZEKE spectroscopy. JOURNAL OF CHEMICAL PHYSICS, 145, 234309.
Résumé: VUV pulsed-field-ionization zero-kinetic-energy photoelectron spectra of X+ 2Π ←X 1Σ+ and B+ 2Π ← X 1Σ+ transitions of the HC14N and HC15N isotopologues of cyanoacetylene have been recorded. The resolution of the photoelectron spectra allowed to resolve the vibrational structures and the spin-orbit splittings in the
cation. Accurate values of the adiabatic ionization potentials of the two isotopologues (E /hc(HC14N) = 93909(2) cm−1 and E /hc(HC15N) = 93912(2) cm−1), the vibrational frequencies of the ν2, ν6, and ν7 vibrational modes, and the spin-orbit coupling constant (ASO = −44(2) cm−1) of the X+ 2Π cationic ground state have been derived from the measurements. Using ab initio calculations, the unexpected structure of the B+ 2Π ← X 1Σ+ transition is tentatively attributed to a conical intersection between the A+ and B+ electronic states of the cation.
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Gutierrez-Quintanilla, A., Chevalier, M., & Crepin, C. (2016). Double deuterated acetylacetone in neon matrices: infrared spectroscopy, photoreactivity and the tunneling process. Phys Chem Chem Phys, 18(30), 20713–20725.
Résumé: The effect of deuteration of acetylacetone (C5O2H8) is explored by means of IR spectroscopy of its single and double deuterated isotopologues trapped in neon matrices. The whole vibrational spectra of chelated enols are very sensitive to the H-D exchange of the hydrogen atom involved in the internal hydrogen bond. UV excitation of double deuterated acetylacetone isolated in neon matrices induces the formation of four open enol isomers which can be divided into two groups of two conformers, depending on their formation kinetics. Within each group, one conformer is more stable than the other: slow conformer interconversion due to a tunneling process is observed in the dark at low temperature. Moreover, IR laser irradiation at the OD stretching overtone frequency is used to induce interconversion either from the most stable to the less stable conformer or the opposite, depending on the excitation wavelength. The interconversion process is of great help to assign conformers which are definitively identified by comparison between experimental and calculated IR spectra. Kinetic constants of the tunneling process at play are theoretically estimated and agree perfectly with experiments, including previous experiments with the totally hydrogenated acetylacetone.
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Kumar, S., Lucas, B., Fayeton, J., Scuderi, D., Alata, I., Broquier, M., Le Barbu-Debus, K., Lepere, V., & Zehnacker, A. (2016). Photofragmentation mechanisms in protonated chiral cinchona alkaloids. Phys. Chem. Chem. Phys., 18(32), 22668–22677.
Résumé: The photo-stability of protonated cinchona alkaloids is studied in the gas phase by a multi-technique approach. A multi-coincidence technique is used to demonstrate that the dissociation is a direct process. Two dissociation channels are observed. They result from the C-8-C-9 cleavage, accompanied or not by hydrogen migration. The branching ratio between the two photo-fragments is different for the two pseudo-enantiomers quinine and quinidine. Mass spectrometry experiments coupling UV photo-dissociation of the reactants and structural characterization of the ionic photo-products by Infra-Red Multiple Photo-Dissociation (IRMPD) spectroscopy provide unambiguous information on their structure. In addition, quantum chemical calculations allow proposing a reactive scheme and discussing it in terms of the ground-state geometry of the reactant.
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Lamarre, N., Gans, B., Vieira Mendes L.A., Gronowski, M., Guillemin, J. - C., de Oliveira N., Douin, S., Chevalier, M., Crépin, C., Kolos, R., & Boyé-Péronne, S. (2016). Excited electronic structure of methylcyanoacetylene probed by VUV Fourier-transform absorption spectroscopy. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER, 182, 286–295.
Résumé: High resolution photoabsorption spectrum of gas-phase methylcyanoacetylene (CH3C N) has been recorded from 44 500 to 130 000 cm-1 at room temperature with a vacuum ultraviolet Fourier-transform spectrometer on the DESIRS synchrotron beamline (SOLEIL). The absolute photoabsorption cross section in this range is reported for the first time. Valence shell transitions and Rydberg series converging to the ground state X+ 2E of the cation as well as series converging to electronically excited states (A+ 2 A1 and C+) are observed and assigned. Time-dependent density-functional-theory calculations have been performed to support the assignment of the experimental spectrum in the low energy range. A tentative scaling of the previously measured CH3C3N ion yield by Lamarre et al. [17] is proposed, based on the comparison of the absorption data above the first ionization potential with the observed autoionization structures.
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Lepere, V., Le Barbu-Debus, K., Clavaguera, C., Scuderi, D., Piani, G., Simon, A. L., Chirot, F., MacAleese, L., Dugourd, P., & Zehnacker, A. (2016). Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies. Phys. Chem. Chem. Phys., 18(3), 1807–1817.
Résumé: Ion mobility experiments are combined with Infra-Red Multiple Photon Dissociation (IRMPD) spectroscopy and quantum chemical calculations for assessing the role of chirality in the structure of protonated and sodiated di- or tetra-peptides. Sodiated systems show a strong chirality dependence of the competition between Na+...O and Na+...pi interactions. Chirality effects are more subtle in protonated systems and manifest themselves by differences in the secondary interactions such hydrogen bonds between neutral groups or those involving the aromatic rings.
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Lozada-Garcia, R., Mu, D., Plazanet, M., & Carcabal, P. (2016). Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy. Physical Chemistry Chemical Physics, 18(32), 22100–22107.
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Pino, G. A., Feraud, G., Broquier, M., Gregoire, G., Soorkia, S., Dedonder, C., & Jouvet, C. (2016). Non-radiative processes in protonated diazines, pyrimidine bases and an aromatic azine. Phys. Chem. Chem. Phys., 18(30), 20126–20134.
Résumé: The excited state lifetimes of DNA bases are often very short due to very efficient non-radiative processes assigned to the pipi*-npi* coupling. A set of protonated aromatic diazine molecules (pyridazine, pyrimidine and pyrazine C4H5N2+) and protonated pyrimidine DNA bases (cytosine, uracil and thymine), as well as the protonated pyridine (C5H6N+), have been investigated. For all these molecules except one tautomer of protonated uracil (enol-keto), electronic spectroscopy exhibits vibrational line broadening. Excited state geometry optimization at the CC2 level has been conducted to find out whether the excited state lifetimes measured from line broadening can be correlated to the calculated ordering of the pipi* and npi* states and the pipi*-npi* energy gap. The short lifetimes, observed when one nitrogen atom of the ring is not protonated, can be rationalized by relaxation of the pipi* state to the npi* state or directly to the electronic ground state through ring puckering.
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Soorkia, S., Broquier, M., & Gregoire, G. (2016). Multiscale excited state lifetimes of protonated dimethyl aminopyridines. Phys. Chem. Chem. Phys., 18(34), 23785–23794.
Résumé: The excited state dynamics of protonated ortho (2-) and para (4-) dimethyl aminopyridine molecules (DMAPH(+)) has been studied through pump-probe photofragmentation spectroscopy and excited state coupled-cluster CC2 calculations. Multiscale temporal dynamics has been recorded over 9 orders of magnitude from subpicosecond to millisecond. The initially locally excited pipi* state rapidly decays within about 100 fs into a charge transfer state following 90 degrees twist motion of the dimethyl amino group. While this twisted intramolecular charge transfer (TICT) state does not trigger any fragmentation, it selectively leads to specific two-color photofragments through absorption of the probe photon at 355 nm. Besides, the optically dark TICT state provides an efficient deactivation path with high intersystem probability to non-dissociative long-lived triplet states. Such a multiscale pump-probe photodissociation scheme paves the way to systematic studies of charge transfer reactions in the excited state of cold ionic systems stored in a cryogenic cooled ion trap and probed continuously up to the millisecond time scale.
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Thon, R., Chin, W., Chamma, D., Galaup, J. - P., Ouvrard, A., Bourguignon, B., & Crépin, C. (2016). Vibrational spectroscopy and dynamics of W(CO)6in solid methane as a probe of lattice properties. J. Chem. Phys., 145(21), 214306.
Résumé: Methane solids present more than one accessible crystalline phase at low temperature at zero pressure. We trap W(CO)6 in CH4 and CD4 matrices between 8 and 35 K to probe the interaction between an impurity and its surrounding molecular solid under various physical conditions. Linear and nonlinear vibrational spectroscopies of W(CO)6 highlight different kinds of interaction and reveal new and remarkable signatures of the phase transition of methane. The structures in the absorption band of the antisymmetric CO stretching mode exhibit a clear modification at the transition between phase II and phase I in CH4 and motional narrowing is observed upon temperature increase. The vibrational dynamics of this mode is probed in stimulated photon echo experiments performed with a femtosecond IR laser. A short component around 10 ps is detected in the population relaxation lifetime in the high temperature phase of solid CH4 (phase I) and disappears at lower temperatures (phase II) where the vibrational lifetime is in the hundreds of ps. The analysis of the nonlinear time-resolved results suggests that the short component comes from a fast energy transfer between the vibrational excitation of the guest and the lattice in specific families of sites. Such fast transfers are observed in the case of W(CO)6 trapped in CD4 because of an energy overlap of the excitation of W(CO)6 and a lattice vibron. In solid CH4, even when these V-V transfers are not efficient, pure dephasing processes due to the molecular nature of the host occur: they are temperature dependent without a clear modification at the phase transition.
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2015 |
Alata, I., Scuderi, D., Lepere, V., Steinmetz, V., Gobert, F., Thiao-Layel, L., Le Barbu-Debus, K., & Zehnacker-Rentien, A. (2015). Exotic Protonated Species Produced by UV-Induced Photofragmentation of a Protonated Dimer: Metastable Protonated Cinchonidine. Journal Of Physical Chemistry A, 119(39), 10007–10015.
Résumé: A metastable protonated cinchona alkaloid was produced in the gas phase by UV-induced photodissociation (UVPD) of its protonated dimer in a Paul ion trap. The infrared multiple photon dissociation (IRMPD) spectrum of the molecular ion formed by UVPD was obtained and compared to DFT calculations to characterize its structure. The protonation site obtained thereby is not accessible by classical protonation ways. The protonated monomer directly formed in the ESI source or by collision-induced dissociation (CID) of the dimer undergoes protonation at the most basic alkaloid nitrogen. In contrast, protonation occurs at the quinoline aromatic ring nitrogen in the UVPD-formed monomer.
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Alauddin, M., Gloaguen, E., Brenner, V., Tardivel, B., Mons, M., Zehnacker-Rentien, A., Declerck, V., & Aitken, D. J. (2015). Intrinsic Folding Proclivities in Cyclic β-Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer-Selective Spectroscopy and Quantum Chemistry. Chem. Eur. J., 21(46), 16479–16493.
Résumé: This work describes the use of conformer-selective laser spectroscopy following supersonic expansion to probe the local folding proclivities of four-membered ring cyclic β-amino acid building blocks. Emphasis is placed on stereochemical effects as well as on the structural changes induced by the replacement of a carbon atom of the cycle by a nitrogen atom. The amide A IR spectra are obtained and interpreted with the help of quantum chemistry structure calculations. Results provide evidence that the building block with a trans-substituted cyclobutane ring has a predilection to form strong C8 hydrogen bonds. Nitrogen-atom substitution in the ring induces the formation of the hydrazino turn, with a related but distinct hydrogen-bonding network: the structure is best viewed as a bifurcated C8/C5 bond with the N heteroatom lone electron pair playing a significant acceptor role, which supports recent observations on the hydrazino turn structure in solution. Surprisingly, this study shows that the cis-substituted cyclobutane ring derivative also gives rise predominantly to a C8 hydrogen bond, although weaker than in the two former cases, a feature that is not often encountered for this building block.
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Arabei, S., McCaffrey, J. G., Galaup, J. - P., Shafizadeh, N., & Crepin, C. (2015). Stimulated emission in cryogenic samples doped with free-base tetraazaporphine. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(22), 14931–42.
Résumé: Thin cryogenic samples of inert gas solids doped with free-base tetraazaporphine (H2TAP) were irradiated with a tunable pulsed laser. Under resonant electronic excitation of the guest, specific vibronic transitions of the fluorescence spectra were found to be strongly enhanced with only a moderate increase of the laser power. This enhancement is due to stimulated emission (SE). The characteristics of SE bands are described in the three hosts (Ar, N2, and Ne) explored, as well as their excitation spectra. SE is observed in transitions involving different vibrational modes of the guest, depending on the host and the electronic excitation. The results are discussed in comparison with previous works on other tetrapyrrolic molecules trapped in inert gas matrices. From this comparison the key features required to observe SE are deduced to be: (1) SE can be obtained with various tetrapyrrolic molecules; (2) free-base molecules are preferable to their metallo-counterparts; (3) the results highlight a specific molecular vibrational mode involved in the process; and (4) cryogenic crystal structures are also of importance in the detection of SE.
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Bouchet, A., Klyne, J., Piani, G., Dopfer, O., & Zehnacker, A. (2015). Diastereo-specific conformational properties of neutral, protonated and radical cation forms of (1R,2S)-cis- and (1R,2R)-trans-amino-indanol by gas phase spectroscopy. Physical Chemistry Chemical Physics, 17(39), 25809–25821.
Résumé: Chirality effects on the intramolecular interactions strongly depend on the charge and protonation states. Here, the influence of chirality on the structure of the neutral, protonated, and radical cation forms of (1R,2S)-cis- and (1R,2R)-trans-1-amino-2-indanol diastereomers, prototypical molecules with two chiral centers, is investigated in a molecular beam by laser spectroscopy coupled with quantum chemical calculations. The neutral systems are structurally characterised by double resonance IR-UV spectroscopy, while IR-induced dissociation spectroscopy is employed for the charged molecules. The sterical constraints due to the cyclic nature of the molecule emphasise the chirality effects, which manifest themselves by the formation of an intramolecular hydrogen bond in neutral or protonated (1R,2S)-cis-amino-indanol. In contrast, this interaction is not possible in (1R,2R)-trans-amino-indanol. In the protonated species, chirality also influences the spectroscopic probes in the NH/OH stretch range by fine-tuning subtle effects such as the hyperconjugation between the sigma(OH) orbital and sigma* orbitals localised on the alicyclic ring. The radical cation undergoes opening of the alicyclic ring, which results in an ionisation-induced loss of the chirality effects.
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Briant, M., Poisson, L., Shafizadeh, N., & Soep, B. (2015). Tribute to Jean-Michel Mestdagh (Vol. 119). American Chemical Society.
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Broquier, M., Soorkia, S., & Gregoire, G. (2015). A comprehensive study of cold protonated tyramine: UV photodissociation experiments and ab initio calculations. Phys Chem Chem Phys, 17, 25854–25862.
Résumé: We present a comprehensive experimental study of protonated tyramine ions in a cold 3D quadrupole ion trap coupled to a time-of-flight mass spectrometer. Multiple UV photodissociation techniques have been developed, including single and double resonance spectroscopy along with time-resolved excited state lifetime measurements through a picosecond pump-probe scheme. An original UV-UV hole burning method is presented which can be used without modification of the quadrupole ion trap. The electronic spectrum of the cold protonated tyramine exhibits well-defined vibronic transitions, allowing the firm assignment of its two low-lying energy conformations by comparison with CC2 ab initio excited state calculations.
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Cocinero, E. J., & Carcabal, P. (2015). Carbohydrates. In Gas-Phase Ir Spectroscopy And Structure Of Biological Molecules (Vol. 364, pp. 299–333).
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Douin, S., Gronowski, M., Lamarre, N., Phung, V. - T., Boyé-Péronne, S., Crépin, C., & and Kołos, R. (2015). Cavity Ring Down Spectroscopy Measurements for High-Overtone Vibrational Bands of HC3N. Journal of Physical Chemistry A, 119(36), 9494–9505.
Résumé: Overtone (5ν1 and 6ν1) and combination (4ν1+ν3 and 4ν1+ν2) vibrational bands of gaseous HC3N, located in the visible range (14 600-15 800 cm-1 and 17 400-18 600 cm-1), were investigated by cavity ring-down absorption spectroscopy. The 5ν1+ν3 and 5ν1+ν2 combinations as well as the 6ν1+ν5-ν5 hot overtone band have also been identified, based on previous overtone assignments. Absolute integrated intensity values and the ensuing oscillator strengths have been measured here for the first time; f –values are typically confined between 4×10-12 and 7×10-11. For the even weaker 5ν1+ν2 combination band, the oscillator strength was estimated as 9×10-13.
The values concerning CH-stretch overtones (nν1) are similar to those found in the literature for HCN and C2H2, the molecules with sp-hybridized carbon atoms. Data presented here may prove useful for studying the photochemistry triggered with visible or near-IR radiation within the atmospheres of certain Solar System bodies, including Titan.
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Feraud, G., Broquier, M., Dedonder, C., Jouvet, C., Gregoire, G., & Soorkia, S. (2015). Excited State Dynamics of Protonated Phenylalanine and Tyrosine: Photo-Induced Reactions Following Electronic Excitation. J Phys Chem A, 119(23), 5914–5924.
Résumé: The electronic spectroscopy and the electronic excited state properties of cold protonated phenylalanine and protonated tyrosine have been revisited on a large spectral domain and interpreted by comparison with ab initio calculations. The protonated species are stored in a cryogenically cooled Paul trap, maintained at approximately 10 K, and the parent and all the photofragment ions are mass-analyzed in a time-of-flight mass spectrometer, which allows detecting the ionic species with an improved mass resolution compared to what is routinely achieved with a quadrupole mass spectrometer. These new results emphasize the competition around the band origin between two proton transfer reactions from the ammonium group toward either the aromatic chromophore or the carboxylic acid group. These reactions are initiated by the coupling of the locally excited pipi* state with higher charge transfer states, the positions and coupling of which depend on the conformation of the protonated molecules. Each of these reaction processes gives rise to specific fragmentation channels that supports the conformer selectivity observed in the photofragmentation spectra of protonated tyrosine and phenylalanine.
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Ferrand, L., Soorkia, S., Gregoire, G., Broquier, M., Soep, B., & Shafizadeh, N. (2015). Bonding of heme FeIIIwith dioxygen: Observation and characterization of an incipient bond. Phys. Chem. Chem. Phys., 17, 25693–25699.
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Hernandez, F. J., Capello, M. C., Naito, A., Manita, S., Tsukada, K., Miyazaki, M., Fujii, M., Broquier, M., Gregoire, G., Dedonder-Lardeux, C., Jouvet, C., & Pino, G. A. (2015). Trapped Hydronium Radical Produced by Ultraviolet Excitation of Substituted Aromatic Molecule. J Phys Chem A, 119(51), 12730–12735.
Résumé: The gas phase structure and excited state dynamics of o-aminophenol-H2O complex have been investigated using REMPI, IR-UV hole-burning spectroscopy, and pump-probe experiments with picoseconds laser pulses. The IR-UV spectroscopy indicates that the isomer responsible for the excitation spectrum corresponds to an orientation of the OH bond away from the NH2 group. The water molecule acts as H-bond acceptor of the OH group of the chromophore. The complexation of o-aminophenol with one water molecule induced an enhancement in the excited state lifetime on the band origin. The variation of the excited state lifetime of the complex with the excess energy from 1.4 +/- 0.1 ns for the 0-0 band to 0.24 +/- 0.3 ns for the band at 0-0 + 120 cm(-1) is very similar to the variation observed in the phenol-NH3 system. This experimental result suggests that the excited state hydrogen transfer reaction is the dominant channel for the non radiative pathway. Indeed, excited state ab initio calculations demonstrate that H transfer leading to the formation of the H3O(*) radical within the complex is the main reactive pathway.
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Lamarre, N., Gans, B., Alcaraz, C., Cunha de Miranda, B., Guillemin, J. - C., Broquier, M., Liévin, J., & Boyé-Péronne, S. (2015). Vibronic structure of the 2Πu ground electronic state of dicyanoacetylene cation revisited by PFI-ZEKE photoelectron spectroscopy and ab initio calculations. Molecular Physics, 113(24), 3946–3954.
Résumé: The X+ 2Piu ← X 1Sigma+ g transition of dicyanoacetylene has been recorded for the first time using Pulsed-Field-Ionization ZEro-Kinetic Energy (PFI-ZEKE) photoelectron spectroscopy.
The analysis of the photoelectron spectrum allowed an accurate determination of the adiabatic ionization potential of C4N2 (Ei, ad./hc = 95479±2 cm−1) and a description of the vibrational structure of the electronic ground state of the cation which is affected by Renner-Teller effect and spin-orbit interaction. The spin-orbit coupling constant was measured as −52 ± 2 cm−1.
These results are supported by ab initio calculations performed at the Complete Active Space Self Consistent Field and Second order Perturbation Theory (CASSCF and CASPT2) levels of theory, with extrapolation to the complete basis set limit.
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Lozada-Garcia, R., Rojas-Lorenzo, G., Crepin, C., Ryan, M., & McCaffrey, J. G. (2015). Hg-Xe Exciplex Formation in Mixed Xe/Ar Matrices: Molecular Dynamics and Luminescence Study. Journal Of Physical Chemistry A, 119(11), 2307–2317.
Résumé: Luminescence of Hg(P-3(1)) atoms trapped in mixed Ar/Xe matrices containing a small amount of Xe is reported. Broad emission bands, strongly red-shifted from absorption are recorded which are assigned to strong complexes formed between the excited mercury Hg* and xenon atoms. Molecular dynamics calculations are performed on simulated Xe/Ar samples doped with Hg to follow the behavior of Hg* in the mixed rare gas matrices leading to exciplex formation. The role of Xe atoms in the first solvation shell (SS1) around Hg was investigated in detail, revealing the formation of two kinds of triatomic exciplexes; namely, Xe-Hg*-Xe and Ar-Hg*-Xe. The first species exists only when two xenon atoms are present in SS1 with specific geometries allowing the formation of a linear or quasi-linear exciplex. In the other geometries, or in the presence of only one Xe in SS1, a linear Ar-Hg*-Xe exciplex is formed. The two kinds of exciplexes have different emission bands, the most red-shifted being that involving two Xe atoms, whose emission is very close to that observed in pure Xe matrices. Simulations give a direct access to the analysis of the experimental absorption, emission, and excitation spectra, together with the dynamics of exciplexes formation.
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Mengesha, E. T., Zehnacker-Rentien, A., Sepiol, J., Kijak, M., & Waluk, J. (2015). Spectroscopic Study of Jet-Cooled Deuterated Porphycenes: Unusual Isotopic Effects on Proton Tunneling. J. Phys. Chem. B, 119(6), 2193–2203.
Résumé: Porphycene (Pc) is a well-known model for studying double hydrogen transfer, which shows vibrational-mode-specific tunneling splitting when isolated in supersonic jets or helium nanodroplets. The effect of deuteration on tunneling splitting is reported for jet-cooled heterogeneous, deuterated Pc samples (Pc-d(mix)) with the prevailing contribution of Pc-d(12) isotopologue. The sample introduced into the gas phase using laser desorption is studied by means of laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) measurements, in combination with quantum chemical calculations. The influence of molecular symmetry is studied by comparing Pc, Pc-d(12), and Pc-d(11). The spectra of Pc-d(12) show strong similarity to those of the parent undeuterated porphycene (Pc). Comparable tunneling splitting is observed in the two isotopologues, both for the 00 transition and the most efficient promoting 2A(g) mode. In contrast, an unusual isotopic effect is observed for the totally symmetrical 4A(g) mode. While this vibration behaves as a neutral mode in Pc, neither enhancing nor decreasing the tunneling efficiency, it strongly promotes hydrogen transfer in Pc-d(12). This observation is explained in terms of modification of the displacement vectors of the 4A(g) mode upon deuteration. It demonstrates that isotope substitution affects hydrogen transfer even when the weak structural modifications are far from the reaction center, emphasizing the strongly multidimensional nature of the tunneling process.
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Soorkia, S., Dehon, C., S, S. K., Perot-Taillandier, M., Lucas, B., Jouvet, C., Barat, M., & Fayeton, J. A. (2015). Ion-Induced Dipole Interactions and Fragmentation Times: Calpha-Cbeta Chromophore Bond Dissociation Channel. J Phys Chem Lett, 6(11), 2070–2074.
Résumé: The fragmentation times corresponding to the loss of the chromophore (Calpha-Cbeta bond dissociation channel) after photoexcitation at 263 nm have been investigated for several small peptides containing tryptophan or tyrosine. For tryptophan-containing peptides, the aromatic chromophore is lost as an ionic fragment (m/z 130), and the fragmentation time increases with the mass of the neutral fragment. In contrast, for tyrosine-containing peptides the aromatic chromophore is always lost as a neutral fragment (mass = 107 amu) and the fragmentation time is found to be fast (<20 ns). These different behaviors are explained by the role of the postfragmentation interaction in the complex formed after the Calpha-Cbeta bond cleavage.
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Spagnoli, S., Morfin, I., Gonzalez, M. A., Carcabal, P., & Plazanet, M. (2015). Solvent Contribution to the Stability of a Physical Gel Characterized by Quasi-Elastic Neutron Scattering. Langmuir, 31(8), 2554–2560.
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Turowski, M., Crepin, C., Douin, S., & Kolos, R. (2015). Formation and Spectroscopy of Dicyanotriacetylene (NC8N) in Solid Kr. Journal Of Physical Chemistry A, 119(11), 2701–2708.
Résumé: Thermally induced creation of dicyanotriacetylene (NC8N) was observed in solid krypton. Samples were obtained by cryogenic trapping of gaseous cyanoacetylene/Kr mixtures subjected to electric discharges. Strong a (3)Sigma(+)(u) -> X (1)Sigma(+)(g) phosphorescence of NC8N is reported here for the first time; its vibronic structure permitted the measurement of several ground-state vibrational frequencies. Other chemical species, mostly smaller than the precursor molecule, have also been formed, among them the dicarbon molecule (C-2), and these may serve as indispensable building blocks in the NC8N synthesis. Processes leading to the elongation of cyanoacetylenic chains are of potential importance for the chemistry of icy grains present in the interstellar gas clouds.
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Zehnacker, A. (2015). Optical spectroscopy coupled with mass spectrometry methods. Physical Chemistry Chemical Physics, 17(39), 25672–25675.
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2014 |
Bouchet, A., Altnoder, J., Broquier, M., & Zehnacker, A. (2014). IR-UV spectroscopy of jet-cooled 1-indanol: Restriction of the conformational space by hydration. JOURNAL OF MOLECULAR STRUCTURE, 1076, 344–351.
Résumé: The effect of hydration on a flexible amphiphilic molecule has been studied on the example of 1-hydroxyindan (1-indanol). Studies in jet-cooled conditions by means of resonance-enhanced two-photon ionization and IR-UV double resonance experiments show that the mono-hydrate 1-indanol(H2O) is formed in a dominant isomer, as well as the di-hydrate 1-indanol(H2O)(2). 1-Indanol(H2O) favors a cooperative hydrogen bond pattern with -OH center dot center dot center dot O(H)-H center dot center dot center dot pi it topology, while 1-indanol(H2O)(2) forms a cyclic hydrogen bond network with three OH center dot center dot center dot O interactions. The single conformation observed for the hydrates contrasts with the bare molecule which shows two dominant conformations, with the hydroxyl in axial or in equatorial position, respectively. Hydration therefore results in a restriction of the conformational space and conformational locking. (C) 2014 Elsevier B.V. All rights reserved.
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Capello, M. C., Broquier, M., Ishiuchi, S. I., Sohn, W. Y., Fujii, M., Dedonder-Lardeux, C., Jouvet, C., & Pino, G. A. (2014). Fast Nonradiative Decay in o-Aminophenol. Journal of Physical Chemistry A, 118, 2056–2062.
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Chaudret, R., de Courcy, B., Contreras-Garcia, J., Gloaguen, E., Zehnacker-Rentien, A., Mons, M., & Piquemal, J. P. (2014). Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16(21), 9876–9891.
Résumé: The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
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Chin, W., Chevalier, M., Thon, R., Pollet, R., Ceponkus, J., & Crepin, C. (2014). Photochemistry of glycolaldehyde in cryogenic matrices. JOURNAL OF CHEMICAL PHYSICS, 140(22), 224319.
Résumé: The photochemistry of glycolaldehyde (GA) upon irradiation at 266 nm is investigated in argon, nitrogen, neon, and para-hydrogen matrices by IR spectroscopy. Isomerization and fragmentation processes are found to compete. The hydrogen-bonded Cis-Cis form of GA is transformed mainly to the open Trans-Trans conformer and to CO and CH3OH fragments and their mixed complexes. Different photo-induced behaviours appear depending on the matrix. In nitrogen, small amounts of Trans-Gauche and Trans-Trans conformers are detected after deposition and grow together upon irradiation. The Trans-Gauche conformer is characterized for the first time. In para-hydrogen due to a weaker cage effect additional H2CO and HCO fragments are seen. Calculations of the potential energy surfaces of S-0, S-1, and T-1 states – to analyse the torsional deformations which are involved in the isomerization process – and a kinetic analysis are presented to investigate the different relaxation pathways of GA. Fragmentation of GA under UV irradiation through the CO+CH3OH molecular channel is a minor process, as in the gas phase. (C) 2014 AIP Publishing LLC.
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Couturier-Tamburelli, I., Pietri, N., Crepin, C., Turowski, M., Guillemin, J. - C., & Kolos, R. (2014). Synthesis and spectroscopy of cyanotriacetylene (HC7N) in solid argon. Journal Of Chemical Physics, 140(4), 044329.
Résumé: UV laser irradiations of cryogenic solid argon matrices doped with a mixture of acetylene and cyanodiacetylene (HC5N) resulted in the formation of a longer carbon-nitrogen chain, cyanotriacetylene (HC7N). The identification of this species was accomplished based on IR vibrational spectroscopy (including the study of isotopically labeled compounds), on electronic luminescence spectroscopy, and on theoretical predictions. Additionally, IR absorption bands recognized as due to HC7N were detected in photolysed Ar matrices doped with a cyanoacetylene/diacetylene mixture; this assignment was confirmed with the mass spectrometry of gases released upon the warm-up of the sample. (C) 2014 AIP Publishing LLC.
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Dopfer, O., Patzer, A., Chakraborty, S., Alata, I., Omidyan, R., Broquier, M., Dedonder, C., & Jouvet, C. (2014). Electronic and vibrational spectra of protonated benzaldehyde-water clusters, BZ-(H2O)(n <= 5) H+: Evidence for ground-state proton transfer to solvent for n >= 3. Journal of Chemical Physics, 140(12), 124314.
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Feraud, G., Broquier, M., Dedonder-Lardeux, C., Gregoire, G., Soorkia, S., & Jouvet, C. (2014). Photofragmentation spectroscopy of cold protonated aromatic amines in the gas phase. Phys Chem Chem Phys, 16(11), 5250–5259.
Résumé: The electronic spectra of cold protonated aromatic amines: anilineH(+) C6H5-NH3(+), benzylamineH(+) C6H5-CH2-NH3(+) and phenylethylamineH(+) C6H5-(CH2)2-NH3(+) have been investigated experimentally in a large spectral domain and are compared to those of their hydroxyl homologues. In the low energy region, the electronic spectra are similar to their neutral analogues, which reveals the pipi* character of their first excited state. A second transition is observed from 0.4 to 1 eV above the origin band, which is assigned to the excitation of the pisigma* state. In these protonated amine molecules, there is a competition between different fragmentation channels, some being specific to UV excitation i.e., not observed in low-energy collision induced dissociation experiments. Besides, for one amine a drastic change in the fragmentation branching ratio is observed within a very short energy range that reveals the complex excited state dynamics and fragmentation processes. The experimental observations can be rationalized using a simple qualitative model, the pipi*-pisigma* model [A. L. Sobolewski, W. Domcke, C. Dedonder-Lardeux and C. Jouvet, Phys. Chem. Chem. Phys., 2002, 4, 1093-1100], which predicts that the excited state dynamics is controlled by the crossing between the pipi* excited state and a pisigma* state repulsive along the XH (X being O or N) coordinate.
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Feraud, G., Dedonder-Lardeux, C., Soorkia, S., & Jouvet, C. (2014). Photo-fragmentation spectroscopy of benzylium and 1-phenylethyl cations. J Chem Phys, 140(2), 024302.
Résumé: The electronic spectra of cold benzylium (C6H5-CH2 (+)) and 1-phenylethyl (C6H5-CH-CH3 (+)) cations have been recorded via photofragment spectroscopy. Benzylium and 1-phenylethyl cations produced from electrosprayed benzylamine and phenylethylamine solutions, respectively, were stored in a cryogenically cooled quadrupole ion trap and photodissociated by an OPO laser, scanned in parts of the UV and visible regions (600-225 nm). The electronic states and active vibrational modes of the benzylium and 1-phenylethyl cations as well as those of their tropylium or methyl tropylium isomers have been calculated with ab initio methods for comparison with the spectra observed. Sharp vibrational progressions are observed in the visible region while the absorption features are much broader in the UV. The visible spectrum of the benzylium cation is similar to that obtained in an argon tagging experiment [V. Dryza, N. Chalyavi, J. A. Sanelli, and E. J. Bieske, J. Chem. Phys. 137, 204304 (2012)], with an additional splitting assigned to Fermi resonances. The visible spectrum of the 1-phenylethyl cation also shows vibrational progressions. For both cations, the second electronic transition is observed in the UV, around 33,000 cm(-1) (4.1 eV) and shows a broadened vibrational progression. In both cases the S2 optimized geometry is non-planar. The third electronic transition observed around 40,000 cm(-1) (5.0 eV) is even broader with no apparent vibrational structures, which is indicative of either a fast non-radiative process or a very large change in geometry between the excited and the ground states. The oscillator strengths calculated for tropylium and methyl tropylium are weak. Therefore, these isomeric structures are most likely not responsible for these absorption features. Finally, the fragmentation pattern changes in the second and third electronic states: C2H2 loss becomes predominant at higher excitation energies, for both cations.
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Gloaguen, E., Brenner, V., Alauddin, M., Tardivel, B., Mons, M., Zehnacker-Rentien, A., Declerck, V., & Aitken, D. J. (2014). Direct Spectroscopic Evidence of Hyperconjugation Unveils the Conformational Landscape of Hydrazides. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 53(50), 13756–13759.
Résumé: The stereochemistry of hydrazides makes them especially interesting as building blocks for molecular design. An exhaustive conformational analysis of three model hydrazides was conducted in a conformer-selective approach by using a combination of high-level quantum chemistry calculations and vibrational spectroscopy in the gas phase and in solution. The NH stretch frequency was found to be highly sensitive to hyperconjugation, thus making it an efficient probe of the conformation of the neighboring nitrogen atom. This property greatly assisted the identification of the isomers observed experimentally in the conformer pool. A rationalization of the hydrazide conformational landscape is proposed, therefore paving the way for a better characterization of secondary structures in larger systems.
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Henchy, C., McCaffrey, J. G., Arabei, S., Pavich, T., Galaup, J. - P., Shafizadeh, N., & Crepin, C. (2014). Free base tetraazaporphine isolated in inert gas hosts: Matrix influence on its spectroscopic and photochemical properties. JOURNAL OF CHEMICAL PHYSICS, 141(12), 124303.
Résumé: The absorption, fluorescence, and excitation spectra of free base tetraazaporphine (H(2)TAP) trapped in Ne, N-2, and Ar matrices have been recorded at cryogenic temperatures. Normal Raman spectra of H(2)TAP were recorded in KBr discs and predicted with density functional theory (DFT) using large basis sets calculations. The vibrational frequencies observed in the Raman Spectrum exhibit reasonable agreement with those deduced from the emission spectra, as well as with frequencies predicted from large basis set DFT computations. The upper state vibrational frequencies, obtained from highly resolved, site selected excitation spectra, are consistently lower than the ground state frequencies. This contrasts with the situation in free base phthalocyanine, where the upper state shows little changes in vibrational frequencies and geometry when compared with the ground state. Investigations of the photochemical properties of H(2)TAP isolated in the three matrices have been performed using the method of persistent spectral hole-burning (PSHB). This technique has been used to reveal sites corresponding to distinct N-H tautomers which were not evident in the absorption spectra. An analysis of the holes and antiholes produced with PSHB in the Q(x) (0-0) absorption band made it possible to identify inter-conversion of distinct host sites.
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Scuderi, D., Lepere, V., Piani, G., Bouchet, A., & Zehnacker-Rentien, A. (2014). Structural Characterization of the UV-Induced Fragmentation Products in an Ion Trap by Infrared Multiple Photon Dissociation Spectroscopy. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5(1), 56–61.
Résumé: Protonated cinchona alkaloids and their dimers undergo photochemical reaction in the gas phase, leading to UV-specific photofragments, not observed by collision-induced dissociation. Simultaneous coupling of UV and IR lasers with a Paul ion trap has been achieved for obtaining the vibrational spectrum of the fragments arising from the photodissociation. The structure of the photoproduced radical has been fully characterized by comparing the experimental spectrum to that simulated by DFT calculations.
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Shafizadeh, N., Ha-Thi, M. - H., Poisson, L., Soep, B., & Maillard, P. (2014). Observation in the gas phase of the ligation of 1-Methylimidazole to hemoprotein mimics. JOURNAL OF CHEMICAL PHYSICS, 141(17), 174310.
Résumé: Hemoprotein mimics, cobalt picket fence porphyrins have been prepared in the gas phase as neutral molecules for the first time. Their ligation properties have been studied with 1-methylimidazole and compared with those of other cobalt porphyrins, tetraphenyl porphyrin, and cobalt protoporphyrin IX chloride, in view of studying the sterical properties of the ligation. It is shown that the cobalt picket fence porphyrin can only accept one 1-methylimidazole ligand in contrast to less sterically crowded porphyrins like cobalt tetraphenylporphyrin that present two accessible ligation sites. The femtosecond dynamics of these ligated systems have been studied after excitation at 400 nm, in comparison with the unligated ones. The observed transients are formed in much shorter times, 30 fs for the ligated species, as compared to free species (100 fs), supporting the porphyrin to metal charge transfer nature of these transients. The similar decays of the ligated transients <1 ps reveal the absence of photodissociation of the cobalt-1-methylimidazole bond at this step of evolution.
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Sohn, W. Y., Ishiuchi, S., Carcabal, P., Oba, H., & Fujii, M. (2014). UV-UV hole burning and IR dip spectroscopy of homophenylalanine by laser desorption supersonic jet technique. Chemical Physics, 445, 21–30.
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Soorkia, S., Broquier, M., & Grégoire, G. (2014). Conformer- and Mode-Specific Excited State Lifetimes of Cold Protonated Tyrosine Ions. J. Phys. Chem. Lett., 5(24), 4349–4355.
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Soorkia, S., Dehon, C., Kumar, S. S., Pedrazzani, M., Frantzen, E., Lucas, B., Barat, M., Fayeton, J. A., & Jouvet, C. (2014). UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture. J Phys Chem Lett, 5(7), 1110–1116.
Résumé: Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a sigma-sigma* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.
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Zehnacker, A. (2014). Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies. INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY, 33(2), 151–207.
Résumé: This review focuses on chirality effects in spectroscopy and photophysics of chiral molecules or protonated ions, and their weakly bound complexes, isolated in the gas phase. Low-temperature studies in jet-cooled conditions allow disentangling the different interactions at play and shed light on the ancillary interactions responsible for chiral recognition, like OH...pi or CH...pi, which would be blurred at room temperature. The consequences of these interactions on chiral recognition in condensed phase are described, as well as the influence of higher energy conformers, which can be accessed in room-temperature experiments. The role of kinetic effects and solvation in jet-cooled experiments is discussed. Last, examples of dramatic chirality effects in photo-induced dissociation are given.
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Alata, I., Bert, J., Broquier, M., Dedonder, C., Feraud, G., Gregoire, G., Soorkia, S., Marceca, E., & Jouvet, C. (2013). Electronic Spectra of the Protonated Indole Chromophore in the Gas Phase. J. Phys. Chem. A, 117, 4420–4427.
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Altnöder J., B. A., Lee J.J., Otto K.E., Suhm M.A., Zehnacker-Rentien A. (2013). Chirality-dependent balance between hydrogen bonding and London dispersion in isolated (±)-1-indanol clusters. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15, 10167–10180.
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Barry, C. S., Cocinero, E. J., Carcabal, P., Gamblin, D. P., Stanca-Kaposta, E. C., Remmert, S. M., Fernandez-Alonso, M. C., Rudic, S., Simons, J. P., & Davis, B. G. (2013). 'Naked' and Hydrated Conformers of the Conserved Core Pentasaccharide of N-linked Glycoproteins and Its Building Blocks. Journal Of The American Chemical Society, 135(45), 16895–16903.
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Capello, M. C., Broquier, M., Dedonder-Lardeux, C., Jouvet, C., & Pino, G. A. (2013). Fast excited state dynamics in the isolated 7-azaindole-phenol H-bonded complex. J Chem Phys, 138(5), 054304.
Résumé: The excited state dynamics of the H-bonded 7-azaindole-phenol complex (7AI-PhOH) has been studied by combination of picosecond pump and probe experiments, LIF measurements on the nanosecond time scale and ab initio calculations. A very short S(1) excited state lifetime (30 ps) has been measured for the complex upon excitation of the 0(0)(0) transition and the lifetime remains unchanged when the nu(6) vibrational mode (0(0)(0) + 127 cm(-1)) is excited. In addition, no UV-visible fluorescence was observed by exciting the complex with nanosecond pulses. Two possible deactivation channels have been investigated by ab initio calculations: first an excited state tautomerization assisted by a concerted double proton transfer (CDPT) and second an excited state concerted proton electron transfer (CPET) that leads to the formation of a radical pair (hydrogenated 7AIH() radical and phenoxy PhO() radical). Both channels, CDPT and CPET, seem to be opened according to the ab initio calculations. However, the analysis of the ensemble of experimental and theoretical evidence indicates that the excited state tautomerization assisted by CDPT is quite unlikely to be responsible for the fast S(1) state deactivation. In contrast, the CPET mechanism is suggested to be the non-radiative process deactivating the S(1) state of the complex. In this mechanism, the lengthening of the OH distance of the PhOH molecule induces an electron transfer from PhOH to 7AI that is followed by a proton transfer in the same kinetic step. This process leads to the formation of the radical pair (7AIH()...PhO()) in the electronically excited state through a very low barrier or to the ion pair (7AIH(+)...PhO(-)) in the ground state. Moreover, it should be noted that, according to the calculations the pisigma* state, which is responsible for the H loss in the free PhOH molecule, does not seem to be involved at all in the quenching process of the 7AI-PhOH complex.
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Carcabal, P., Cocinero, E. J., & Simons, J. P. (2013). Binding energies of micro-hydrated carbohydrates: measurements and interpretation. CHEMICAL SCIENCE, 4(4), 1830–1836.
Résumé: The strength of the interaction between three monosaccharides (O-phenyl-beta-D-gluco-, beta-D-galacto-and alpha-D-mannopyranoside) and a single water molecule has been investigated experimentally in the gas phase by means of 2-colour UV-UV ionisation and dissociation threshold measurements. Their binding energies have also been calculated using dispersion corrected DFT methods and the resolution of identity approximation. The calculated and experimental relative binding energies are in good correspondence at all considered levels of theory, and the RI-B97D+ disp/ TZVPP level of theory in particular, provides very good agreement with a considerable reduction in computational time. Although these systems experience some conformational changes upon photo-ionisation, the experimental measurements lead to reliable estimates of the binding energies of the different conformers of the monosaccharide-water complexes and their relative values reflect their structural differences.
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