Peer-reviewed Publications |
Basire, M., Parneix, P., & Calvo, F. (2010). Finite-Temperature IR Spectroscopy of Polyatomic Molecules: A Theoretical Assessment of Scaling Factors. JOURNAL OF PHYSICAL CHEMISTRY A, 114(9), 3139–3146.
Résumé: With I recently developed simulation method (Basire, M; et al. J. Phys. Chem A 2009, 113, 6947), the infrared vibrational spectra of several polyatomic molecules are calculated over I broad range of temperature, taking into account quantum, anharmonic, and couplings effects. Anharmonic force fields, generated from static first-principle calculations, are Sampled in the microcanonical ensemble to provide energy-resolved absorption intensities and their finite temperature analogues after Laplace transformation Effective anharmonic frequencies ire characterized as a continuous function of temperature for vinyl fluoride, the N-acetyl-Phe-NH(2) peptide. and protonated naphthalene. These frequencies generally deviate increasingly from the harmonic value with increasing temperature although the overestimation due to the harmonic approximation is particularly Salient for high-frequency Modes Anharmonicities may also be sufficient 10 alter structural assignment of experimental spectra experimental spectra with respect to empirically scaled harmonic bands. These results, emphasize some possible limatations and inaccuractes, Inherent to such static Scaling factors for correcting harmonic IR Spectra.
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Bernhardt, B., Ozawa, A., Jacquet, P., Jacquey, M., Kobayashi, Y., Udem, T., Holzwarth, R., Guelachvili, G., Haensch, T. W., & Picque, N. (2010). Cavity-enhanced dual-comb spectroscopy. NATURE PHOTONICS, 4(1), 55–57.
Résumé: The sensitivity of molecular fingerprinting is dramatically improved when the absorbing sample is placed in a high-finesse optical cavity, because the effective path length is increased. When the equidistant lines from a laser frequency comb are simultaneously injected into the cavity over a large spectral range, multiple trace gases may be identified(1) within a few milliseconds. However, efficient analysis of the light transmitted through the cavity remains challenging. Here, a novel approach-cavity-enhanced, frequency-comb, Fourier-transform spectroscopy-fully overcomes this difficulty and enables measurement of ultrasensitive, broad-bandwidth, high-resolution spectra within a few tens of microseconds without any need for detector arrays, potentially from the terahertz to ultraviolet regions. Within a period of just 18 μs, we recorded the spectra of the ammonia 1.0 μm overtone bands comprising 1,500 spectral elements and spanning 20 nm, with a resolution of 4.5 GHz and a noise equivalent absorption at 1 s averaging of 1 x 10(-10) cm(-1) Hz(-1/2), thus opening a route to time-resolved spectroscopy of rapidly evolving single events.
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Bernhardt, B., Sorokin, E., Jacquet, P., Thon, R., Becker, T., Sorokina, I. T., Picque, N., & Haensch, T. W. (2010). Mid-infrared dual-comb spectroscopy with 2.4 μm Cr2+:ZnSe femtosecond lasers. APPLIED PHYSICS B-LASERS AND OPTICS, 100(1), 3–8.
Résumé: The mid-infrared part of the electromagnetic spectrum is the so-called molecular fingerprint region because gases have tell-tale absorption features associated with molecular rovibrations. This region can be for instance exploited to detect small traces of environmental and toxic vapors in atmospheric and industrial applications. Novel Fourier-transform spectroscopy without moving parts, based on time-domain interferences between two comb sources, can in particular benefit optical diagnostics and precision spectroscopy. To date, high-resolution and -sensitivity proof-of-principle experiments have only been reported in the near-infrared region where frequency-comb oscillators are conveniently available. However, as most of the molecular transitions in this region are due to weak overtone bands, this spectral domain is not ideal for sensitive and rapid detection. Here we present a proof-of-principle experiment of frequency-comb Fourier-transform spectroscopy with two Cr2+:ZnSe femtosecond oscillators directly emitting in the 2.4 μm mid-infrared region. The acetylene absorption spectrum in the region of the nu(1)+nu 1/5 band, extending from 2370 to 2525 nm, could be recorded within a 10 μs acquisition time without averaging with 12 GHz resolution.
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Boudon, V., Pirali, O., Roy, P., Brubach, J. B., Manceron, L., & Auwera, J. V. (2010). The high-resolution far-infrared spectrum of methane at the SOLEIL synchrotron. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER, 111(9), 1117–1129.
Résumé: As a tetrahedral molecule, methane has no permanent dipole moment. Its spectrum, however, displays faint absorption lines in the THz region, due to centrifugal distorsion effects. This is important for planetary applications since this region is used to measure methane concentration in some planetary atmospheres, in particular on Titan. Up to now, all measurements relied either on some old low resolution infrared absorption spectra, or on high resolution Stark measurements for low J values only. Even if these results have been reexamined recently [Wishnow EH, Orton GS, Ozier I. Gush HP. The distorsion dipole rotational spectrum of CH(4): a low temperature far-infrared study.J Quant Spectrosc Radiat Transfer 2007:103:102-17], it seemed highly desirable to obtain much more precise laboratory data. The high-intensity synchrotron radiation, combined with a 151.75 +/- 0.1 m optical path in a White cell and a Bruker IFS 125 HR FTIR spectrometer at the AILES beamline of SOLEIL, enabled us to record this very weak spectrum at high resolution for the first time. Spectra were obtained in the 50-500 cm(-1) wavenumber range at 296K and 9.91, 20, 50 and 100 mbar with a resolution of 0.00074, 0.00134, 0.0034 and 0.0067 cm(-1) (FWHM of the sinc function), respectively. The rotational clusters are fully resolved and the good signal-to-noise ratio has enabled precise measurements of transition intensities (92 cold band lines and 96 Dyad-Dyad hot band lines, with normal abundance intensities in the range 2 x 10(-26)-1 x 10(-24) cm(-1) /(mol cm(-2))), yielding an accurate determination of the dipole moment derivatives. Such results should allow a better determination of CH(4) concentration in planetary objects. (C) 2010 Elsevier Ltd. All rights reserved.
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Calvo, F., Basire, M., & Parneix, P. (2010). Efficiency of Monte Carlo methods for densities and sums of rovibrational states. CHEMICAL PHYSICS LETTERS, 496(1-3), 196–200.
Résumé: Absolute quantum densities of rovibrational states of fully coupled Hamiltonians are computed using Wang-Landau, virtual-move parallel tempering (VMPT), and the Bortz-Kalos-Lebowitz (or kMC) Monte Carlo methods. The validity of the methods is checked by comparing to exact counting in the case of the H(2)SiO molecule, but applications are also presented for vinyl fluoride and neutral naphthalene. The numerical efficiencies obtained by measuring the statistical deviation to the converged value under finite sampling times suggest that the Wang-Landau and kMC methods are generally superior to VMPT for this class of problem. A simple application to isomerization in protonated pyrene is presented. (C) 2010 Elsevier B.V. All rights reserved.
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Calvo, F., Parneix, P., & Van-Oanh, N. - T. (2010). Finite temperature infrared spectroscopy of polycyclic aromatic hydrocarbon molecules: Path-integral molecular dynamics. JOURNAL OF CHEMICAL PHYSICS, 132(12), 124308.
Résumé: The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm(-1) infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.
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Calvo, F., Parneix, P., & Van-Oanh, N. - T. (2010). Finite-temperature infrared spectroscopy of polycyclic aromatic hydrocarbon molecules. II. Principal mode analysis and self-consistent phonons. JOURNAL OF CHEMICAL PHYSICS, 133(7), 074303.
Résumé: Following previous work [F. Calvo et al. J. Chem. Phys. 132, 124308 (2010)], infrared spectra of several polycyclic aromatic hydrocarbon molecules are simulated with classical and quantum molecular dynamics trajectories. The interactions are modeled using a tight-binding potential energy surface and quantum delocalization is accounted for using the partially adiabatic centroid and ring-polymer molecular dynamics frameworks, both built upon the path-integral representation. The spectra obtained directly by Fourier transformation of the dipole moment autocorrelation function are here compared with several quasiharmonic approximations that provide additional information about the vibrational modes. A principal mode analysis (PMA) is carried out from the covariance matrix of atomic displacements in classical and quantum trajectories. The method systematically overestimates the line shifts due to anharmonicities, except in the power spectra of atomic displacements, and is not robust in predicting IR intensities for such large molecules. Alternatively, effective normal modes have also been determined by adapting the self-consistent phonon (SCP) theory of condensed matter physics to the present tight-binding model, in both classical and quantum mechanical descriptions. The SCP approximation turns out as semiquantitative in estimating the redshift of tight stretching modes, and performs better for classical systems. More problematic, it predicts that many low-or medium-frequency modes should be blueshifted, in contradiction with the molecular dynamics results. The sets of anharmonic normal modes extracted from the PMA and SCP approaches reveal important mixings within the tightest C-H and C-C stretching modes, which are also manifested on the corresponding power spectra. (C) 2010 American Institute of Physics. [doi:10.1063/1.3465554]
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Chabot, M., Mezdari, F., Beroff, K., Martinet, G., & Hervieux, P. - A. (2010). Scaling Law for the Partitioning of Energy in Fragmenting Multicharged Carbon Clusters. PHYSICAL REVIEW LETTERS, 104(4), 043401.
Résumé: The complete fragmentation of highly excited and multicharged C(n)(q+) clusters (n = 5-10; q = 2-4), produced in high velocity collisions of C(n)(+) with atoms, has been measured. Multiplicity distributions are presented and used to deduce, within a statistical framework, the partitioning of energy between the fragments' production and fragments' kinetic energy. This partitioning is found to scale as the charge over mass ratio of the cluster.
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Chabot, M., Tuna, T., Beroff, K., Pino, T., Le Padellec, A., Desesquelles, P., Martinet, G., Nguyen-Thi, V. O., Carpentier, Y., Le Petit, F., Roueff, E., & Wakelam, V. (2010). Statistical universal branching ratios for cosmic ray dissociation, photodissociation, and dissociative recombination of the Cn=2-10, Cn=2-4H and C3H2 neutral and cationic species. ASTRONOMY & ASTROPHYSICS, 524, A39.
Résumé: Context. Fragmentation-branching ratios of electronically excited molecular species are of first importance for the modeling of gas phase interstellar chemistry. Despite experimental and theoretical efforts that have been done during the last two decades there is still a strong lack of detailed information on those quantities for many molecules such as C-n, CnH or C3H2. Aims. Our aim is to provide astrochemical databases with more realistic branching ratios for C-n (n = 2 to 10), CnH (n = 2 to 4), and C3H2 molecules that are electronically excited either by dissociative recombination, photodissociation, or cosmic ray processes, when no detailed calculations or measurements exist in literature. Methods. High velocity collision in an inverse kinematics scheme was used to measure the complete fragmentation pattern of electronically excited C-n (n = 2 to 10), CnH (n = 2 to 4), and C3H2 molecules. Branching ratios of dissociation where deduced from those experiments. The full set of branching ratios was used as a new input in chemical models and branching ratio modification effects observed in astrochemical networks that describe the dense cold Taurus Molecular Cloud-1 and the photon dominated Horse Head region. Results. The comparison between the branching ratios obtained in this work and other types of experiments showed a good agreement. It was interpreted as the signature of a statistical behavior of the fragmentation. The branching ratios we obtained lead to an increase of the C-3 production together with a larger dispersion of the daughter fragments. The introduction of these new values in the photon dominated region model of the Horse Head nebula increases the abundance of C-3 and C3H, but reduces the abundances of the larger C-n and hydrocarbons at a visual extinction AV smaller than 4. Conclusions. We recommend astrochemists to use these new branching ratios. The data published here have been added to the online database KIDA (KInetic Database for Astrochemistry, http://kida.obs.u-bordeaux1.fr).
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Crepin C., S. N., Chin W., Galaup J.P., M. C. J. G., & Arabei S.M. (2010). Emission stimulée par des molécules de tétrabenzoporphine en matrice de gaz rares à basse température. PROCEEDINGS of the VIII International Conference on “Quantum Electronics”, (Minsk, Belarus), 57.
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Crepin, C., Shafizadeh, N., Chin, W., Galaup, J. - P., McCaffrey, J. G., & Arabei, S. M. (2010). Unveiled optical properties of tetrapyrollic pigments in cryogenic environments. LOW TEMPERATURE PHYSICS, 36(5), 451–457.
Résumé: An unexpected phenomenon was revealed in the laser induced fluorescence spectra of free-base (H(2)Pc) and zinc (ZnPc) phthalocyanines trapped in rare gas and nitrogen matrices under a moderate increase in the laser intensity. In all matrices the intensity of an emission band near 755 nm increased drastically when pumping the S(1)<- S(0) transition. This observation was assigned to stimulated emission in a four-level scheme involving a vibronic transition from the lowest electronic state to a vibrational level of the ground state. In the present work, we expose new similar results obtained with porphyrin molecules, i.e. tetra-benzoporphin (TBP). With free-base H(2)TBP, stimulated emission was observed in Ar or N(2) matrices, but not in Xe matrices. A possible reason could be a fast inter-system crossing rate due to the heavy atom effect induced by Xe. We also report the observation of persistent burnt spectral holes, although the low efficiency of this process is not competitive with stimulated emission and no decrease of the stimulated emission with time was observed. With ZnTBP no stimulated emission could be recorded but the appearance of rather strong phosphorescence was noticed. Similar studies focusing on the stimulated emission phenomenon is that they should allow new insights into site effects and site selectivity. (C) 2010 American Institute of Physics.
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Cuisset, A., Nanobashvili, L., Smirnova, I., Bocquet, R., Hindle, F., Mouret, G., Pirali, O., Roy, P., & Sadovskii, D. A. (2010). Far-infrared high resolution synchrotron FTIR spectroscopy of the nu(11) bending vibrational fundamental transition of dimethylsulfoxyde. CHEMICAL PHYSICS LETTERS, 492(1-3), 30–34.
Résumé: We report the first successful high resolution gas phase study of the 'parallel' band of DMSO at 380 cm(-1) associated with the nu(11) bending vibrational mode. The spectrum was recorded with a resolution of 0.0015 cm(-1) using the AILES beamline of the SOLEIL synchrotron source, the IFS 125 FTIR spectrometer and a multipass cell providing an optical path of 150 m. The rotational constants and centrifugal corrections obtained from the analysis of the resolved rotational transitions reproduce the spectrum to the experimental accuracy. (C) 2010 Elsevier B.V. All rights reserved.
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de Miranda, B. K. C., Alcaraz, C., Elhanine, M., Noller, B., Hemberger, P., Fischer, I., Garcia, G. A., Soldi-Lose, H., Gans, B., Mendes, L. A. V., Boye-Peronne, S., Douin, S., Zabka, J., & Botschwina, P. (2010). Threshold Photoelectron Spectroscopy of the Methyl Radical Isotopomers, CH3, CH2D, CHD2 and CD3: Synergy between VUV Synchrotron Radiation Experiments and Explicitly Correlated Coupled Cluster Calculations. JOURNAL OF PHYSICAL CHEMISTRY A, 114(14), 4818–4830.
Résumé: Threshold photoelectron spectra (TPES) of the isotopomers of the methyl radical (CH3, CH2D, CHD2, and CD3) have been recorded in the 9.5-10.5 eV VUV photon energy range using third generation synchrotron radiation to investigate the vibrational spectroscopy of the corresponding cations at a 7-11 meV resolution. A threshold photoelectron-photoion coincidence (TPEPICO) spectrometer based on velocity map imaging and Wiley-McLaren time-of-flight has been used to simultaneously record the TPES of several radical species produced in a Ar-seeded beam by dc flash-pyrolysis of nitromethane (CHxDyNO2, x + y = 3). Vibrational bands belonging to the symmetric stretching and out-of-plane bending modes have been observed and P, Q, and R branches have been identified in the analysis of the rotational profiles. Vibrational configuration interaction (VCI), in conjunction with near-equilibrium potential energy surfaces calculated by the explicitly correlated coupled cluster method CCSD(T*)-F12a, is used to calculate vibrational frequencies for the four radical isotopomers and the corresponding cations. Agreement with data from high-resolution IR spectroscopy is very good and a large number of predictions is made. In particular, the calculated wavenumbers for the out-of-plane bending vibrations, v(2)(CH3+) = 1404 cm(-1), v(4)(CH2D+) = 1308 cm(-1), v(4)(CHD2+) = 1205 cm(-1), and v(2)(CD3+) = 1090 cm(-1), should be accurate to ca. 2 cm(-1). Additionally, computed Franck-Condon factors are used to estimate the importance of autoionization relative to direct ionization. The chosen models globally account for the observed transitions, but in contrast to PBS spectroscopy, evidence for rotational and vibrational autoionization is found. It is shown that state-selected methyl cations can be produced by TPEPICO spectroscopy for ion-molecule reaction studies, which are very important for the understanding of the planetary ionosphere chemistry.
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Galue, H. A., Pirali, O., & Oomens, J. (2010). Gas-phase infrared spectra of cationized nitrogen-substituted polycyclic aromatic hydrocarbons. ASTRONOMY & ASTROPHYSICS, 517, A10.
Résumé: Gas-phase infrared spectra of several ionized nitrogen substituted polycyclic aromatic hydrocarbons (PANHs) have been recorded in the 600-1600 cm(-1) region via IR multiple-photon dissociation (IRMPD) spectroscopy. The UV photoionized PANH ions are trapped and isolated in a quadrupole ion trap where they are irradiated with an IR free electron laser. The PANHs were studied in their radical cation (PANH(+)) and protonated (H(+) PANH) forms, and include quinoline, isoquinoline, phenanthridine, benzo[h] quinoline, acridine, and dibenzo[f,h] quinoline. Experimental IRMPD spectra were interpreted with the aid of density functional theory methods. The PANH(+) IR spectra are found to resemble those of their respective non-nitrogenated PAH cations. The IR spectra of H(+) PANHs are significantly different owing to the NH inplane bending vibration, which generally couples very well with the aromatic CH bending and CC stretching modes. Implications of the NPAH (+, H(+)) laboratory spectra are discussed for the astrophysical IR emissions and, in particular, for the band at 6.2 μm.
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Gans, B., Mendes, L. A. V., Boye-Peronne, S., Douin, S., Garcia, G., Soldi-Lose, H., de Miranda, B. K. C., Alcaraz, C., Carrasco, N., Pernot, P., & Gauyacq, D. (2010). Determination of the Absolute Photoionization Cross Sections of CH3 and I Produced from a Pyrolysis Source, by Combined Synchrotron and Vacuum Ultraviolet Laser Studies. JOURNAL OF PHYSICAL CHEMISTRY A, 114(9), 3237–3246.
Résumé: A pyrolysis source coupled to a supersonic expansion has been used to produce the CH3 radical from two precursors, iodomethane CH3I and nitromethane CH3NO2. The relative ionization yield of CH3 has been recorded at the SOLEIL Synchrotron Radiation source in the range 9.0-11.6 eV, and its ionization threshold has been modeled by taking into account the vibrational and rotational temperature of the radical in the molecular beam. The relative photoionization yield has been normalized to an absolute cross section scale at a fixed wavelength (118.2 nm, sigma(CH3)(i) = 6.7(-1.8)(+2.4) Mb, 95% confidence interval) in an independent laboratory experiment using the same pyrolysis source, a vacuum ultraviolet (VUV) laser, and a carefully calibrated detection chain. The resulting absolute cross section curve is in good agreement with the recently published measurements by Taatjes et al.,((1)) although with an improved signal-to-noise ratio. The absolute photoionization cross section of CH3I at 118.2 nm has also been measured to be sigma(CH3I)(i) = (48.2 +/- 7.9) Mb, in good agreement with previous electron impact measurements. Finally, the photoionization yield of the iodine atom in its ground state P-2(3/2) has been recorded using the synchrotron source and calibrated for the first time on an absolute cross section scale from our fixed 118.2 nm laser measurement, sigma(I2P3/2)(i) = 74(-23)(+33) Mb (95% confidence interval). The ionization curve of atomic iodine is in good agreement, although with slight variations, with the earlier relative ionization yield measured by Berkowitz et al.((2)) and is also compared to an earlier calculation of the iodine cross section by Robicheaux and Greene.((3)) It is demonstrated that, in the range of pyrolysis temperature used in this work, all the ionization cross sections are temperature-independent. Systematic care has been taken to include all uncertainty sources contributing to the final confidence intervals for the reported results.
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Ha-Thi, M. - H., Shafizadeh, N., Poisson, L., & Soep, B. (2010). First observation in the gas phase of the ultrafast electronic relaxation pathways of the S-2 states of heme and hemin. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12(45), 14985–14993.
Résumé: The time evolution of electronically excited heme (iron II protoporphyrin IX, [Fe-II PP]) and its associated salt hemin (iron III protoporphyrin IX chloride, [Fe-III PP-Cl]), has been investigated for the first time in the gas phase by femtosecond pump-probe spectroscopy. The porphyrins were excited at 400 nm in the S-2 state (Soret band) and their relaxation dynamics was probed by multiphoton ionization at 800 nm. This time evolution was compared with that of the excited state of zinc protoporphyrin IX [Zn PP] whose S2 excited state likely decays to the long lived S-1 state through a conical intersection, in less than 100 fs. Instead, for [Fe-II PP] and [Fe-III PP-Cl], the key relaxation step from S-2 is interpreted as an ultrafast charge transfer from the porphyrin excited orbital pi* to a vacant d orbital on the iron atom (ligand to metal charge transfer, LMCT). This intermediate LMCT state then relaxes to the ground state within 250 fs. Through this work a new, serendipitous, preparation step was found for Fe II porphyrins, in the gas phase.
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Hartmann, J. - M., Boulet, C., Tran, H., & Nguyen, M. T. (2010). Molecular dynamics simulations for CO2 absorption spectra. I. Line broadening and the far wing of the nu(3) infrared band. JOURNAL OF CHEMICAL PHYSICS, 133(14), 144313.
Résumé: Classical molecular dynamics simulations (CMDS) have been carried out for gaseous CO2 starting from the intermolecular potential energy surface. Through calculations for a large number of molecules treated as rigid rotors, various autocorrelation functions (ACFs) are obtained together with probabilities of rotational changes. Those used in the present paper are the ACFs of the center of mass velocity and of the molecular orientation, and the conditional probability of a change of the angular speed. They enable calculations, respectively, of the mass diffusion coefficient, of the infrared (dipolar) band shape including the wings, and of individual line-broadening coefficients. It is shown that these calculations, free of any adjustable parameter, lead to good agreement with measured values. This is expected from previous studies for the mass diffusion coefficient and line-broadening coefficients, but it is, to our knowledge, the first demonstration of the interest of CMDS for the prediction of band wings. The present results thus open promising perspectives for the theoretical treatment of the difficult problem of far wings profiles. (C) 2010 American Institute of Physics. [doi:10.1063/1.3489349]
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Jacquemart, D., Gomez, L., Lacome, N., Mandin, J. Y., Pirali, O., & Roy, P. (2010). Measurement of absolute line intensities in the nu(5)-nu(4) band of (C2H2)-C-12 using SOLEIL synchrotron far infrared AILES beamline. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER, 111(9), 1223–1233.
Résumé: Absolute intensities of about 120 lines of the (C2H2)-C-12 molecule are reported for the nu(4)-nu(5) band between 65 and 192 cm(-1), with an average accuracy of 5%. Vibrational transition dipole moment squared values and empirical Herman-Wallis coefficients are obtained allowing modelling the rotational dependence of the transition dipole moment squared. Special care is taken to accurately determine an apparatus function for the Bruker IFS 125-HR coupled to the synchrotron SOLEIL far infrared AILES beamline in order to minimize its effects on the line parameter retrieval. (C) 2010 Elsevier Ltd. All rights reserved.
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Jiang, J., Abramavicius, D., Falvo, C., Bulheller, B. M., Hirst, J. D., & Mukamel, S. (2010). Simulation of Two-Dimensional Ultraviolet Spectroscopy of Amyloid Fibrils. JOURNAL OF PHYSICAL CHEMISTRY B, 114(37), 12150–12156.
Résumé: Revealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two-dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources are extending multidimensional spectroscopy into the ultraviolet (UV) region, and this opens up new opportunities for probing fibrils. In a simulation study, we show that 2DUV spectra of the backbone of a 32-residue beta-amyloid (A beta(9-40)) fibril associated with Alzheimer's disease and two intermediate prefibrillar structures carry characteristic signatures of fibril size and geometry that could be used to monitor its formation kinetics. The dependence of these signals on the fibril size and geometry is explored. We demonstrate that the dominant features of the beta-amyloid fibril spectra are determined by intrainolecular interactions within a single A beta(9-40), and intermolecular interactions at the “external interface” have clear signatures in the fine details of these signals.
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Murray, C., Dozova, N., McCaffrey, J. G., FitzGerald, S., Shafizadeh, N., & Crepin, C. (2010). Infra-red and Raman spectroscopy of free-base and zinc phthalocyanines isolated in matrices. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12(35), 10406–10422.
Résumé: The infrared absorption spectra of matrix-isolated zinc phthalocyanine (ZnPc) and free-base phthalocyanine (H(2)Pc) have been recorded in the region from 400 to 4000 cm(-1) in solid N(2), Ar, Kr and Xe. Raman spectra have been recorded in doped KBr pellets. The isotopomers HDPc and D(2)Pc have been synthesised in an attempt to resolve the conflicting assignments that currently exist in the literature for the N-H bending modes in H2Pc spectra. A complete correlation between the vibrational modes of the three free-base isotopomers and ZnPc has been achieved. Comparison of the IR and Raman spectroscopic results, obtained with isotopic substitution and with predictions from large basis set ab initio calculations, allows identification of the in-plane (IP) and out-of-plane (OP) N-H bending modes. The largest IP isotope shift is observed in the IR at 1046 cm(-1) and at 1026 cm(-1) in Raman spectra while the largest effect in the OP bending modes is at 764 cm(-1). OP bending modes are too weak to be observed in the experimental Raman data. The antisymmetric N-H stretching mode is observed at similar to 3310 cm(-1) in low temperature solids slightly blue shifted from, but entirely consistent with the literature KBr data. With the exception of the N-H stretches, the recorded H/D isotope shifts in all the N-H vibrations are complex, with the IP bending modes exhibiting small nu H/nu D ratios (the largest value is 1.089) while one of the observed OP modes has a ratio < 1. DFT results reveal that the small ratios arise in particular from strong coupling of the N-H IP bending modes with IP stretching modes of C-N bonds. The unexpected finding of a nu H/nu D ratio smaller than one was analysed theoretically by examining the evolution of the frequencies of the free base by increasing the mass from H to D in a continuous manner. A consequence of this frequency increase in the heavier isotopomer is that the direction of the N-D OP bend is reversed from the N-H OP bend.
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Pirali, O., Galue, H. A., Dahl, J. E., Carlson, R. M. K., & Oomens, J. (2010). Infrared spectra and structures of diamantyl and triamantyl carbocations. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 297(1-3), 55–62.
Résumé: Gas-phase infrared spectra have been recorded for the diamantyl and triamantyl carbocations by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Chemical ionization of the neutral parent diamondoid molecule in an rf ion trap is accompanied by H-atom loss, forming a stable closed-shell carbocation. Comparing the IRMPD spectra with harmonic DFT calculations permits to determine the structures of the species trapped in our set-up. Comparison of experimental and calculated spectra suggests that H-atom abstraction occurs on a tertiary carbon (CH group) rather than on a secondary carbon (CH(2) group), as also indicated by the calculated relative energies of the various isomers. Combining experimental results and DFT calculations, we compare the spectra of neutral and carbocationic forms of adamantane, diamantane and triamantane. Substantial differences are observed between the IR spectra of neutral and ionic species. In the ions, the 3 μm CH stretching modes become much weaker, while the other mid-IR modes strongly gain in intensity. An intense band centered at 1200 cm(-1) due to a CH/CH(2) bending mode appears to be characteristic of the dehydrogenated cationic species. Finally, the intensities of the low frequency modes (<= 900 cm(-1)) associated with carbon cage deformations appear to be most sensitive to the ionization and dehydrogenation state of the molecules. (C) 2010 Elsevier B.V. All rights reserved.
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Smirnova, I. N., Cuisset, A., Hindle, F., Mouret, G., Bocquet, R., Pirali, O., & Roy, P. (2010). Gas-Phase Synchrotron FTIR Spectroscopy of Weakly Volatile Alkyl Phosphonate and Alkyl Phosphate Compounds: Vibrational and Conformational Analysis in the Terahertz/Far-IR Spectral Domain. JOURNAL OF PHYSICAL CHEMISTRY B, 114(50), 16936–16947.
Résumé: The high brilliance of the AILES beamline at the SOLEIL synchrotron facility has been exploited for the study of the gas-phase vibrational spectra of weakly volatile organophosphorous compounds. The propagation of the synchrotron radiation in long path length gas cells allowed improvements in the sensitivity limits and spectral coverage compared with a previous study, performed by our group with conventional thermal sources.' A ppm level detection in the entire IR domain up to terahertz (THz) frequencies has been realized for dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), triethyl phosphate (TEP), and diethyl (2-methylallyl)phosphonate (DEMaP). In the present study, the assignment of the gas-phase vibrational and the conformational analysis of the two most stable conformers of DMMP and TMP have been extended to the torsional THz spectra in the 20-120 cm(-1) range. The improvement of the SIN ratio below 600 cm(-1) has permitted for the first time a gas-phase conformational analysis of the two weakly volatile and highly flexible TEP and DEMaP compounds. The experimental far-infrared (FIR)/THz spectra have been studied taking into account four low-energy conformers determined by means of high level of theory quantum chemistry calculations. Finally, due to its particularly low vapor pressure, the detection of gas-phase tributyl phosphate (TBP) in the FIR domain was unsuccessful. Nevertheless, the mid-IR/near-IR spectra of TBP recorded in a multipass cell heated to 355 K have been assigned with the harmonic vibrational predictions of the most stable conformer.
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Tulej, M., Pino, T., Pachkov, M., & Maier, J. P. (2010). Electronic transitions of the C5H- anion. MOLECULAR PHYSICS, 108(7-9), 865–871.
Résumé: Electronic transitions of the triplet chain C5H- anion were studied using detachment spectroscopy. The system detected in the vicinity of the electron detachment threshold is assigned to the b(3)A <- a(3) A transition with a dipole bound state (DBS) character. The second system measured by autodetachment spectroscopy is attributed to the c(3)A <- a(3)A Feshbach electronic transition. Negative anharmonicity of the vibrational progression built upon the low frequency CCC in-plane bending mode nu(12) is observed in both DBS and Feshbach states. This indicates a barrier to linearity on the potential energy surface in both excited states. The triplet chain C5H- anion exhibits similar electronic properties to C3H-. Renner-Teller and vibronic effects between the (3)A DBS and Feshbach states are inferred and may explain the stabilisation of the DBS. This interaction is weaker in C5H- than C3H- leading to smaller barrier heights on the potential energy surface.
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Yu, S. S., Pearson, J. C., Drouin, B. J., Sung, K., Pirali, O., Vervloet, M., Martin-Drumel, M. A., Endres, C. P., Shiraishi, T., Kobayashi, K., & Matsushima, F. (2010). Submillimeter-wave and far-infrared spectroscopy of high-J transitions of the ground and nu(2)=1 states of ammonia. JOURNAL OF CHEMICAL PHYSICS, 133(17), 174317.
Résumé: Complete and reliable knowledge of the ammonia spectrum is needed to enable the analysis and interpretation of astrophysical and planetary observations. Ammonia has been observed in the interstellar medium up to J = 18 and more highly excited transitions are expected to appear in hot exoplanets and brown dwarfs. As a result, there is considerable interest in observing and assigning the high J (rovibrational) spectrum. In this work, numerous spectroscopic techniques were employed to study its high J transitions in the ground and nu(2) = 1 states. Measurements were carried out using a frequency multiplied submillimeter spectrometer at Jet Propulsion Laboratory (JPL), a tunable far-infrared spectrometer at University of Toyama, and a high-resolution Bruker IFS 125 Fourier transform spectrometer (FTS) at Synchrotron SOLEIL. Highly excited ammonia was created with a radiofrequency discharge and a dc discharge, which allowed assignments of transitions with J up to 35. One hundred and seventy seven ground state and nu(2) = 1 inversion transitions were observed with microwave accuracy in the 0.3-4.7 THz region. Of these, 125 were observed for the first time, including 26 Delta K = 3 transitions. Over 2000 far-infrared transitions were assigned to the ground state and nu(2) = 1 inversion bands as well as the nu(2) fundamental band. Of these, 1912 were assigned using the FTS data for the first time, including 222 Delta K = 3 transitions. The accuracy of these measurements has been estimated to be 0.0003-0.0006 cm(-1). A reduced root mean square error of 0.9 was obtained for a global fit of the ground and nu(2) = 1 states, which includes the lines assigned in this work and all previously available microwave, terahertz, far-infrared, and mid-infrared data. The new measurements and predictions reported here will support the analyses of astronomical observations by high-resolution spectroscopy telescopes such as Herschel, SOFIA, and ALMA. The comprehensive experimental rovibrational energy levels reported here will permit further refinement of the potential energy surface to improve ammonia ab initio calculations and facilitate assignment of new high-resolution spectra of hot ammonia. (C) 2010 American Institute of Physics. [doi:10.1063/1.3499911]
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Actes de Conférences |
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Basire, M., Parneix, P., Calvo, F., Pino, T., & Bréchignac, P. (2010). Simulation of the IR absorption spectrum of the naphthalene molecule. In Proceeding of the international symposium on PAHs and the Universe (Vol. Ed Ch. Joblin and A.G.M. Tielens, Juin 2010).
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Bernhardt, B., Ozawa, A., Jacquet, P., Jacquey, M., Kobayashi, Y., Udem, T., Holzwarth, R., Guelachvili, G., Haensch, T. W., & Picque, N. (2010). Trace gas detection with frequency comb Fourier transform spectroscopy. In 2010 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO) AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (QELS).
Résumé: Dual-comb Fourier transform spectroscopy with cavity enhancement holds much promise for trace gas sensing. Broadband high resolution spectra of ammonia around 1.0 μm are recorded within 18 μs and a noise-equivalent-absorption of 1 10(-10) cm(-1) Hz(-1/2). (C) 2010 Optical Society of America
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Bernhardt, B., Sorokin, E., Jacquet, P., Thon, R., Becker, T., Sorokina, I. T., Haensch, T. W., & Picque, N. (2010). 2.4 μm Dual-Comb Spectroscopy. In 2010 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO) AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (QELS).
Résumé: A proof-of-principle experiment of mid-infrared frequency comb Fourier transform spectroscopy is carried out with two interfering Cr2+:ZnSe femtosecond oscillators, emitting around 2400 nm. Spectra of acetylene are measured within 10 μs with 12 GHz resolution. (C)2010 Optical Society of America
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Brubach, J. B., Manceron, L., Rouzieres, M., Pirali, O., Balcon, D., Tchana, F. K., Boudon, V., Tudorie, M., Huet, T., Cuisset, A., & Roy, P. (2010). Performance of the AILES THz-Infrared beamline at SOLEIL for High resolution spectroscopy. In WIRMS 2009: 5TH INTERNATIONAL WORKSHOP ON INFRARED MICROSCOPY AND SPECTROSCOPY WITH ACCELERATOR BASED SOURCES (Vol. 1214, pp. 81–84).
Résumé: The new THz beamline (AILES) located at the third generation Synchrotron Radiation source SOLEIL., is now operating for applications in a wide variety of research themes. In particular, this source with its adapted optics allows high resolution spectroscopic measurements of molecules in the entire infrared and THz range. This presentation focuses on the performances concerning flux, spectral range and stability for molecular spectroscopy. Thanks to these performances, the coupling of synchrotron radiation from a highly stable third generation source with high resolution FTIR spectrometer and with a long path cell (150 m or more) can be particularly advantageous. This fact is related to the optics of the beamline permitting the entire source to be used without aperture stop (entrance iris), even for measurements at highest-resolution of similar to 0.1 μeV (10(-3) cm(-1)).
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Crepin C., S. N., Chin W., Galaup J.P., M. C. J. G., & Arabei S.M. (2010). Absorption, fluorescence et émission stimulée de AlCl-Phtalocyanine en matrice d’Argon. In PROCEEDINGS of the International Conférence on “ Bases moléculaires, membranaires et cellulaires du fonctionnement des biosystèmes“ (157).
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Cuisset, A., Smirnova, I., Bocquet, R., Hindle, F., Mouret, G., Yang, C., Pirali, O., & Roy, P. (2010). Gas phase THz spectroscopy of toxic agent simulant compounds using the AILES synchrotron beamline. In WIRMS 2009: 5TH INTERNATIONAL WORKSHOP ON INFRARED MICROSCOPY AND SPECTROSCOPY WITH ACCELERATOR BASED SOURCES (Vol. 1214, pp. 85–87).
Résumé: A new study is currently underway aiming at recording and assigning the gas phase rovibrational spectra of several organophosphorus and organosulphur compounds in the THz frequency domain. Thanks to the exceptional properties of flux, brilliance and spectral range of the AILES beamline coupled to the FTIR spectrometer, the gas phase vibrational spectra of low volatility organophosphorous compounds have been recorded across the entire THz frequency range. High resolution FTIR spectroscopy was used to record the pure rotational and the low-frequency rovibrational spectrum of DMSO. A comparison between the spectra measured with the AILES beamline and the spectra obtained with optoelectronic THz sources is possible.
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Gans, B., Boye-Peronne, S., Douin, S., & Gauyacq, D. (2010). TOWARDS A QUANTITATIVE STUDY OF THE VUV PHOTOLYSIS OF METHANE: PRELIMINARY EXPERIMENT ON TRICHLOROMETHANE. In PHYSICS AND ASTROPHYSICS OF PLANETARY SYSTEMS (Vol. 41, pp. 455–458).
Résumé: Photolysis of methane in Titan's stratosphere is the starting point of gas phase carbon chemistry. Quantitative studies of methane photolytic products are of utmost importance for Titan atmosphere models. With this aim, two experimental strategies are presented in this article. Preliminary results demonstrate the possibility of using CRDS absorption coupled with pulsed photolysis on the example of a halogenated derivative of methane: Trichloromethane (CHCl(3)).
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Mandon, J., Jacquet, P., Bernhardt, B., Jacquey, M., Guelachvili, G., Haensch, T. W., & Picque, N. (2010). Sensitive and Simple Frequency Comb Fourier Transform Spectrometer with a Multipass Cell. In 2010 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO) AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (QELS).
Résumé: Multipass cells offer a simple manner to enhance the sensitivity of dual-comb Fourier transform spectrometer. 1.5 μm spectra spanning 125 nm and exhibiting a noise-equivalent absorption coefficient of 4.10(-9) cm(-1)Hz(-1/2) are recorded within 63 μs. (C)2010 Optical Society of America
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Roy, P., Brubach, B., Manceron, L., Rouzieres, M., Pirali, O., Creff, G., Kwabia-Tchana, F., & Peng, W. (2010). The AILES Beamline for THz and IR spectroscopy. In 35TH INTERNATIONAL CONFERENCE ON INFRARED.
Résumé: The infrared beamline (AILES) at the third generation Synchrotron Radiation source SOLEIL is available for users. This beamline exploits infrared and THz synchrotron radiation from both edge emission and the constant field conventional source. The performances including flux, spatial distribution of the photons, spectral range and stability are discussed and the optical system and spectroscopic stations are described. The combined source with the adapted optics for beam transport offers high flux and brilliance for all kinds of infrared experiments. We will briefly review the main research themes and future developments and illustrate the potential use with two examples.
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