Peer-reviewed Publications |
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known and published water donor vibrations is presented and a test set of 10 monohydrates with unknown or unpublished water donor vibrational wavenumbers is described together with relevant background literature.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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