Pascal Pernot

A KINETIC DATABASE FOR ASTROCHEMISTRY (KIDA)

We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry (KIDA), this database consists of gas-phase reactions with rate coefficients and uncertainties that will be vetted to the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will be studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar medium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. Each year, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the chemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named Nahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar sources.

Tholinomics—Chemical Analysis of Nitrogen-Rich Polymers

The polymeric composition of Titans tholins--laboratory analogues of Titans aerosols--is elucidated using high-resolution mass spectrometry. This complex organic matter is produced by plasma discharge in a gaseous nitrogen-methane mixture and analyzed with a hybrid linear trap/orbitrap mass-spectrometer. The highly structured mass spectra are treated with tools developed for petroleomics (Kendrick and van Krevelen diagrams), with original adaptations for nitrogen-rich compounds. Our goal is to find the best chemical basis set to describe the compositional space that these polymers occupy, to shed light onto the chemical structure of tholins. We succeeded in assigning the molecules identified in the mass spectra of tholins to a small number of regularly distributed X-(CH(2))(m)(HCN)(n) families, where the balanced copolymer (m = n) is determined to play a central role. Within each family, the polymer lengths n and m present Poisson-type distributions. We also identify the smallest species of a subset of families as linear and cyclic amino nitrile compounds of great astrobiological interest: biguanide, guanidin, acetamidine, aminoacetonitrile, and methylimidazole.

CRITICAL REVIEW OF N, N+, N-2(+), N++, And N-2(++) MAIN PRODUCTION PROCESSES AND REACTIONS OF RELEVANCE TO TITAN'S ATMOSPHERE

This paper is a detailed critical review of the production processes and reactions of N, N+, N+ 2, N++, and N++ 2 of relevance to Titans atmosphere. The review includes neutral, ion-molecule, and recombination reactions. The review covers all possible active nitrogen species under Titans atmospheric conditions, specifically N2 (A3Σ+ u), N (4 S), N (2 D), N (2 P), N+ 2, N+ (3 P), N+ (1 D), N++ 2, and N++ species, and includes a critical survey of the reactions of N, N+, N+ 2, N++, and N++ 2 with N2, H2, D2, CH4, C2H2, C2H4, C2H6, C3H8 and the deuterated hydrocarbon analogs, as well as the recombination reactions of N+ 2, N+, N++ 2, and N++. Production processes, lifetimes, and quenching by collisions with N2 of all reactant species are reviewed. The N (4 S) state is reactive with radicals and its reactions with CH2, CH3, C2H3, and C2H5 are reviewed. Metastable states N2(A3Σ+u), N (2 D), and N (2 P) are either reactive or quenched by collisions with the target molecules reviewed. The reactions of N+ (1 D) have similar rate constants as N+ (3 P), but the product branching ratios differ significantly. Temperature effects and the role of the kinetic energy content of reactants are investigated. In all cases, experimental uncertainties of laboratory data are reported or estimated. Recommended values with uncertainties, or estimated values when no data are available, are given for rate constants and product branching ratios at 300 K and at the atmospheric temperature range of Titan (150-200 K for neutral reactions and 150 K for ion reactions).

Complex fluorescence of the cyan fluorescent protein: comparisons with the H148D variant and consequences for quantitative cell imaging.

We have studied the fluorescence decays of the purified enhanced cyan fluorescent protein (ECFP, with chromophore sequence Thr-Trp-Gly) and of its variant carrying the single H148D mutation characteristic of the brighter form Cerulean. Both proteins exhibit highly complex fluorescence decays showing strong temperature and pH dependences. At neutral pH, the H148D mutation leads (i) to a general increase in all fluorescence lifetimes and (ii) to the disappearance of a subpopulation, estimated to be more than 25% of the total ECFP molecules, characterized by a quenched and red-shifted fluorescence. The fluorescence lifetime distributions of ECFP and its H148D mutant remain otherwise very similar, indicating a high degree of structural and dynamic similarity of the two proteins in their major form. From thermodynamic analysis, we conclude that the multiexponential decay of ECFP cannot be simply ascribed, as is generally admitted, to the slow conformational exchange characterized by NMR and X-ray crystallographic studies [Seifert, M. H., et al. (2002) J. Am. Chem. Soc. 124, 7932-7942; Bae, J. H., et al. (2003) J. Mol. Biol. 328, 1071-1081]. Parallel measurements in living cells show that these fluorescence properties in neutral solution are very similar to those of cytosolic ECFP.

Dose rate effect on size of CdS clusters induced by irradiation

Abstract Size-controlled CdS clusters, with subnanometric radii, have been produced by γ-irradiation of aqueous solution containing Cd 2+ and thiol. Absorption and fluorescence spectra show that the mean CdS cluster size increases in the distribution with the dose or the post-irradiation time. On the contrary, at a given dose, the effect of the dose rate has been clearly demonstrated to lower the cluster size. The mechanism of CdS cluster growth is discussed via coalescence reactions. A numerical simulation taking into account the coalescence reactions between monomers produced by irradiation and then between clusters of any size is presented. Calculations show how the final nuclearity depends on the dose rate effect. The observation of isosbestic points during the slow coalescence (100 M −1 s −1 ) allowed us to derive the absorption spectra of oligomeric CdS clusters, successively formed with maxima at 270, 282 and 320 nm, respectively. At high dose rate and low dose, only the smallest clusters of CdS absorbing at 270 nm (and never observed previously) are formed.

Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation

Calibration of forcefields for molecular simulation should account for the measurement uncertainty of the reference dataset and for the model inadequacy, i.e., the inability of the force-field/simulation pair to reproduce experimental data within their uncertainty range. In all rigour, the resulting uncertainty of calibrated force-field parameters is a source of uncertainty for simulation predictions. Various calibration strategies and calibration models within the Bayesian calibration/prediction framework are explored in the present article. In the case of Lennard-Jones potential for Argon, we show that prediction uncertainty for thermodynamical and transport properties, albeit very small, is larger than statistical simulation uncertainty.

Determination of the absolute photoionization cross sections of CH3 and I produced from a pyrolysis source, by combined synchrotron and vacuum ultraviolet laser studies.

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(i)(CH3) = 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., 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(i)(CH3I) = (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 2P(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(i)(I2P(3/2)) = 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. and is also compared to an earlier calculation of the iodine cross section by Robicheaux and Greene. 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.

Laboratory Studies of Molecular Growth in the Titan Ionosphere

Experimental simulations of the initial steps of the ion-molecule reactions occurring in the ionosphere of Titan were performed at the synchrotron source Elettra in Italy. The measurements consisted of irradiating gas mixtures with a monochromatic photon beam, from the methane ionization threshold at 12.6 eV, up to and beyond the molecular nitrogen dissociative ionization threshold at 24.3 eV. Three gas mixtures of increasing complexity were used: N(2)/CH(4) (0.96/0.04), N(2)/CH(4)/C(2)H(2) (0.96/0.04/0.001), and N(2)/CH(4)/C(2)H(2)/C(2)H(4) (0.96/0.04/0.001/0.001). The resulting ions were detected with a high-resolution (1 T) FT-ICR mass spectrometer as a function of time and VUV photon energy. In order to interpret the experimental results, a Titan ionospheric model was adapted to the laboratory conditions. This model had previously allowed the identification of the ions detected in the Titan upper atmosphere by the ion neutral mass spectrometer (INMS) onboard the Cassini spacecraft. Comparison between observed and modeled ion densities validates the kinetic model (reactions, rate constants, product branching ratios) for the primary steps of molecular growth. It also reveals differences that we attribute to an intense surface chemistry. This result implies that heterogeneous chemistry on aerosols might efficiently produce HCN and NH(3) in the Titan upper atmosphere.

Distance dependence of the reaction rate for the reduction of metal cations by solvated electrons: a picosecond pulse radiolysis study.

The decay of the solvated electron generated by picosecond electron pulse radiolysis is studied by broad-band transient absorption measurements in ethylene glycol solutions containing decimolar concentrations of Cu(2+), Ni(2+), and Pb(2+) metal cations. Analysis of the nonexponential kinetics of the decays reveals molecular parameters of the electron transfer reaction. It is found that the reaction occurs at long distance for Cu(2+) solutions and is only limited to contact distance in the case of Ni(2+) solutions. The distribution of reaction distance strongly depends on the free enthalpy change of the reactions.

Time-Dependent Radiolytic Yield of OH Radical Studied by Picosecond Pulse Radiolysis

Picosecond pulse radiolysis measurements using a pulse-probe method are performed to measure directly the time-dependent radiolytic yield of the OH(•) radical in pure water. The time-dependent absorbance of OH(•) radical at 263 nm is deduced from the observed signal by subtracting the contribution of the hydrated electron and that of the irradiated empty fused silica cell which presents also a transient absoption. The time-dependent radiolytic yield of OH(•) is obtained by assuming the yield of the hydrated electron at 20 ps equal to 4.2 × 10(-7) mol J(-1) and by assuming the values of the extinction coefficients of e(aq)(-) and OH(•) at 782 nm (ε(λ=782 nm) = 17025 M(-1) cm(-1)) and at 263 nm (ε(λ=263 nm) = 460 M(-1) cm(-1)), respectively. The value of the yield of OH(•) radical at 10 ps is found to be (4.80 ± 0.12) × 10(-7) mol J(-1).