Peer-reviewed Publications |
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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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