Nicolas Daugey

Quantitative label-free RNA detection using surface-enhanced Raman spectroscopy

Surface-Enhanced Raman Spectroscopy (SERS) was performed to detect label-free RNA. We defined conditions which make it possible to probe the four bases of RNA, in single strands of polyadenosine (pA), polyuridine (pU), polycytosine (pC) and polyguanosine (pG). We therefore present below a quantitative analysis of mixtures of non-hybridized single strands, based on the deconvolution of the SERS mixture spectrum into the relative contributions of the SERS spectra of each constituent.

Reaction kinetics to low temperatures. Dicarbon + acetylene, methylacetylene, allene and propene from 77 ≤ T ≤ 296 K

The temperature dependence of the reactions of the dicarbon molecule in its ground singlet (X1Sigma(g)+) and first excited triplet (a 3Pi(u)) states with acetylene, methylacetylene, allene and propene has been studied using a recently constructed continuous supersonic flow reactor. Four Laval nozzles have been designed to access specified temperatures over the range of 77 < or = T < or = 220 K and measurements have been performed at 296 K under subsonic flow conditions. C2 was produced in its two lowest electronic states via the in situ multiphoton dissociation of C2Br4 at 266 nm. The time dependent losses of C2 in these two states in the presence of an excess of co-reagent species were simultaneously followed by laser-induced fluorescence in the Mulliken and Swan bands for the detection of singlet and triplet state C2, respectively. The rate coefficients were measured to be very fast, with values larger than 10(-10) cm3 molecule(-1) s(-1) and up to 5 x 10(-10) cm3 molecule(-1) s(-1). The reactions of 1C2 are seen to be essentially temperature independent from 77 < or = T < or = 296 K whereas the rate coefficients for the 3C2 reactions are seen to increase until they are equivalent to the 1C2 values at 77 K.

PM-IRRAS Investigation of Self-Assembled Monolayers Grafted onto SiO2/Au Substrates

Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) was used to characterize self-assembled monolayers (SAMs). Novel ester-terminated organosilicon coupling agents possessing a trialkoxysilyl headgroup and a urea group in the linear alkyl chains (4) were synthesized and grafted onto SiO(2)/Au substrates (SiO(2) film of 200 Å thickness deposited on gold mirror). This composite substrate allowed the anchoring of SAMs and preserved the high reflectivity for infrared radiation. PM-IRRAS spectra with very high signal-to-noise ratios have been obtained in the mid-infrared spectral range allowing monitoring of the grafted SAMs. Quantitative analysis of the measured signal is described to compare PM-IRRAS and conventional IRRAS spectra. This quantitative analysis has been validated since the band intensities in the corrected PM-IRRAS and conventional IRRAS spectra are identical. Orientation information on the different functional groups has been obtained comparing the corrected PM-IRRAS spectrum with the one calculated using isotropic optical constants of ester-terminated organosilicon coupling agents 4. The carbonyls of the urea groups are preferentially parallel to the substrate surface favoring intermolecular hydrogen bonding and consequently a close packing of the molecules attached to the surface. By contrast, the alkyl chains present gauche defects and are poorly oriented.

A low temperature investigation of the N(4S degrees) + NO reaction.

The kinetics of the N((4)S degrees) + NO(X(2)Pi) reaction have been studied in a continuous supersonic flow reactor over the range 48 K <or= T <or= 211 K. Nitrogen atoms were produced by microwave discharge upstream of the Laval nozzle and were probed in the vacuum ultraviolet by resonance fluorescence. The reaction has been found to exhibit a small negative temperature dependence, with a rate coefficient decreasing from (5.8 +/- 0.3) x 10(-11) cm(3) molecule(-1) s(-1) at 48 K to (3.3 +/- 0.2) x 10(-11) cm(3) molecule(-1) s(-1) at 211 K with the statistical uncertainties cited at the level of a single standard deviation from the mean.

Nitrobenzene Detection by One-Color Laser-Photolysis/Laser-Induced Fluorescence of NO (v” = 0–3)

Combined one-color laser-photolysis/laser-induced fluorescence methods have been applied to photodissociate nitrobenzene (NB) molecules and to detect the resulting nitric oxide (NO) photofragments. A one-color laser is used to induce photodissociation and detection of NO via the A(v‘ = 0)–X(v” = 0–4) transitions. A strongly wavelength-dependent signature is obtained due to the population of v” = 0–3 of NO. The ratios of the peak heights of the P12 bandhead are (v” = 0):(v” = 1):(v” = 2):(v” = 3) = 1:0.3:0.1:0.02. A detection limit of ∼500 ppb by weight of NB in air at pressures of 10 and 100 Torr is achieved by monitoring NO X(v” = 2). This is the first attempt to use an excited NO vibrational level for NB detection, and the method can be extended to detection of other nitro compounds. It has the advantage that background of ambient ground-state NO is precluded.

Quantitative determination of band distortions in diamond attenuated total reflectance infrared spectra.

Due to its unmatched hardness and chemical inertia, diamond offers many advantages over other materials for extreme conditions and routine analysis by attenuated total reflection (ATR) infrared spectroscopy. Its low refractive index can offer up to a 6-fold absorbance increase compared to germanium. Unfortunately, it also results for strong bands in spectral distortions compared to transmission experiments. The aim of this paper is to present a methodological approach to determine quantitatively the degree of the spectral distortions in ATR spectra. This approach requires the determination of the optical constants (refractive index and extinction coefficient) of the investigated sample. As a typical example, the optical constants of the fibroin protein of the silk worm Bombyx mori have been determined from the polarized ATR spectra obtained using both diamond and germanium internal reflection elements. The positions found for the amide I band by germanium and diamond ATR are respectively 6 and 17 cm(-1) lower than the true value dtermined from the k(nu) spectrum, which is calculated to be 1659 cm(-1). To determine quantitatively the effect of relevant parameters such as the film thickness and the protein concentration, various spectral simulations have also been performed. The use of a thinner film probed by light polarized in the plane of incidence and diluting the protein sample can help in obtaining ATR spectra that are closer to their transmittance counterparts. To extend this study to any system, the ATR distortion amplitude has been evaluated using spectral simulations performed for bands of various intensities and widths. From these simulations, a simple empirical relationship has been found to estimate the band shift from the experimental band height and width that could be of practical use for ATR users. This paper shows that the determination of optical constants provides an efficient way to recover the true spectrum shape and band frequencies of distorted ATR spectra.

Non-threshold, Threshold, and Nonadiabatic Behavior of the Key Interstellar C + C2H2 Reaction

The C + C2H2 reaction is a key process in interstellar cloud chemistry. In a crossed-beam scattering experiment approaching the low-collision energies that characterize these environments, we determined relative differential cross sections by detecting the H-atom product. High-level ab initio calculations of the reaction energies of two competing pathways, leading to cyclic and linear C3H, were also performed. Both channels are clearly distinguishable: the integral cross section of the c-C3H + H channel monotonically decreases with increasing relative translational energy whilst the l-C3H + H channel exhibits a translational energy threshold. Moreover, a comparison of the H-atom yields from the C + C2H2 and C + C2H4 reactions shows that the C3 + H2 nonadiabatic channel dominates. These results are consistent with the calculated enthalpies and corroborate earlier low-temperature kinetic experiments. Branching ratios of the three reaction pathways are given in the T = 15-300 K temperature domain for inclusion in astrochemical databases.

Dynamics of the Reactions of C(3PJ) Atoms with Ethylene, Allene, and Methylacetylene at Low Energy Revealed by Doppler-Fizeau Spectroscopy

The dynamics of the H-atom elimination reactions of C((3)P(J)) atoms with ethylene, allene, and methylacetylene have been investigated in experiments conducted with pulsed supersonic beams using a variable beam crossing angle configuration at relative translational energies, E(T), in the range of 0.7 to 5.5 kJ mol(-1). H((2)S(1/2)) atoms were detected by time-of-flight mass spectrometry after sequential excitation to the (2)P(o)(J) state using a laser beam tuned to the Lyman-alpha transition around 121.57 nm and ionization by a second laser beam at 364.7 nm. Doppler-Fizeau spectra of the recoiling H atoms were recorded in two configurations, with the Lyman-alpha laser beam oriented either parallel or perpendicular to the relative velocity vector of the reagents. A mathematical model developed to account for the density-to-flux transformation and to extract angular and recoil energy distribution functions from the experimental spectra by a forward convolution procedure is fully described. The model, applied to the C + C(2)H(4) reaction, gives an excellent agreement with differential cross sections already determined in a previous combined study, thus providing a good test for its validity. All three processes are seen to pass through single pathways, identified by the comparison of the recoil energy distribution functions with the calculated reaction enthalpies, yielding H(2)CCCH + H (for the C + ethylene reaction) and H(2)CCCCH + H (for the C + allene and methylacetylene reactions). These results are discussed in the context of earlier experimental measurements performed at much higher collision energies.

Raman optical activity of enantiopure cryptophanes.

Raman optical activity (ROA) and density functional theory (DFT) calculations were used to determine the absolute configuration of enantiopure cryptophane molecules and to obtain conformational information about their three ethylenedioxy linkers. ROA spectra recorded in chloroform solution for the two resolved enantiomers of cryptophanes derivatives bearing five (2), six (1), nine (3 and 4), and 12 (5) methoxy substituents are presented for the first time. The number of methoxy substituents (cryptophanes 1, 3, and 5) and the arrangement of the three linkers (anti for 3 and syn for 4) are two important parameters that significantly affect the ROA spectra. DFT calculations, at the B3PW91/6-31G** level, for cryptophane bearing six methoxy substituents establish, besides the absolute configuration, the preferential all-trans conformation of the ethylenedioxy linkers of the chloroform-cryptophane complex. This study shows that the ROA/DFT approach exhibits a higher selectivity for the conformation of the linkers than vibrational circular dichroism (VCD) associated with theoretical calculations.

How stereochemistry influences the taste of wine: Isolation, characterization and sensory evaluation of lyoniresinol stereoisomers.

Wine expresses its beauty by sending a sensory message to the taster through molecules coming from grapes, yeast metabolism or oak wood. Among the compounds released during barrel aging, lyoniresinol has been recently reported as a relevant contributor to wine bitterness. As this lignan contains three stereogenic carbons, this work aimed at investigating the influence of stereochemistry on wine taste by combining analytical and sensorial techniques. First, an oak wood extract was screened by Liquid Chromatography-High Resolution Mass Spectrometry to target isomers separable in a symmetric environment and a diastereoisomer called epi-lyoniresinol was isolated for the first time. Then, an original racemic resolution based on natural xylose-derivatives was carried out to obtain lyoniresinol enantiomers. Chiroptical spectroscopic measurements associated with theoretical calculations allowed the unambiguous determination of their absolute configuration. The taste properties of all these stereoisomers revealed that only one lyoniresinol enantiomer is strongly bitter whereas the other one is tasteless and the diastereoisomer is slightly sweet. The presence of these three compounds was established in an oaked Bordeaux wine by chiral and non-chiral chromatography, suggesting the significant influence of stereochemistry on wine taste.