Shaun A. Carl

Early Aggregation Steps in α-Synuclein as Measured by FCS and FRET: Evidence for a Contagious Conformational Change

The kinetics of aggregation of alpha-synuclein are usually studied by turbidity or Thio-T fluorescence. Here we follow the disappearance of monomers and the formation of early oligomers using fluorescence correlation spectroscopy. Alexa488-labeled A140C-synuclein was used as a fluorescent probe in trace amounts in the presence of excess unlabeled alpha-synuclein. Repeated short measurements produce a distribution of diffusion coefficients. Initially, a sharp peak is obtained corresponding to monomers, followed by a distinct transient population and the gradual formation of broader-sized distributions of higher oligomers. The kinetics of aggregation can be followed by the decreasing number of fast-diffusing species. Both the disappearance of fast-diffusing species and the appearance of turbidity can be fitted to the Finke-Watzky equation, but the apparent rate constants obtained are different. This reflects the fact that the disappearance of fast species occurs largely during the lag phase of turbidity development, due to the limited sensitivity of turbidity to the early aggregation process. The nucleation of the early oligomers is concentration-dependent and accompanied by a conformational change that precedes beta-structure formation, and can be visualized using fluorescence resonance energy transfer between the donor-labeled N-terminus and the acceptor-labeled cysteine in the mutant A140C.

A highly sensitive method for time-resolved detection of O(1D) applied to precise determination of absolute O(1D) reaction rate constants and O(3P) yields

We demonstrate detection, in the gas-phase, of O(1D2) at concentrations down to 10(7) cm(-3) and develop this new method for time-resolved kinetic studies allowing both the total removal rate of O(1D2), of up to 1.5 x 10(6) s(-1), and the fraction quenched to O(3P(J)) by species X, k(q)/k(X), to be determined precisely from a single time profile: at 295 K we find, k(O(1D2) + N2O) = (1.43 +/- 0.08) x 10(-10) cm3 s(-1) with k(q)/k(N2O) = 0.056 +/- 0.009; k(O(1D2) + C2H2) = (3.1 +/- 0.2) x 10(-10) cm3 s(-1) with k(q)/k(C2H2) = 0.020 +/- 0.010; k(q)/k(H2O) < 0.003 for O(1D2) + H2O.

Pulsed laser photolysis and quantum chemical-statistical rate study of the reaction of the ethynyl radical with water vapor

The rate coefficient of the gas-phase reaction C(2)H + H(2)O-->products has been experimentally determined over the temperature range 500-825 K using a pulsed laser photolysis-chemiluminescence (PLP-CL) technique. Ethynyl radicals (C(2)H) were generated by pulsed 193 nm photolysis of C(2)H(2) in the presence of H(2)O vapor and buffer gas N(2) at 15 Torr. The relative concentration of C(2)H radicals was monitored as a function of time using a CH* chemiluminescence method. The rate constant determinations for C(2)H + H(2)O were k(1)(550 K) = (2.3 +/- 1.3) x 10(-13) cm(3) s(-1), k(1)(770 K) =(7.2 +/- 1.4) x 10(-13) cm(3) s(-1), and k(1)(825 K) = (7.7 +/- 1.5) x 10(-13) cm(3) s(-1). The error in the only other measurement of this rate constant is also discussed. We have also characterized the reaction theoretically using quantum chemical computations. The relevant portion of the potential energy surface of C(2)H(3)O in its doublet electronic ground state has been investigated using density functional theory B3LYP6-311 + + G(3df,2p) and molecular orbital computations at the unrestricted coupled-cluster level of theory that incorporates all single and double excitations plus perturbative corrections for the triple excitations, along with the 6-311 + + G(3df,2p) basis set [(U)CCSD(T)6-311 + + G(3df,2p)] and using UCCSD(T)6-31G(d,p) optimized geometries. Five isomers, six dissociation products, and sixteen transition structures were characterized. The results confirm that the hydrogen abstraction producing C(2)H(2)+OH is the most facile reaction channel. For this channel, refined computations using (U)CCSD(T)6-311 + + G(3df,2p)(U)CCSD(T)6-311 + + G(d,p) and complete-active-space second-order perturbation theory/complete-active-space self-consistent-field theory (CASPT2/CASSCF) [B. O. Roos, Adv. Chem. Phys. 69, 399 (1987)] using the contracted atomic natural orbitals basis set (ANO-L) [J. Almlof and P. R. Taylor, J. Chem. Phys.86, 4070 (1987)] were performed, yielding zero-point energy-corrected potential energy barriers of 17 kJ mol(-1) and 15 kJ mol(-1), respectively. Transition-state theory rate constant calculations, based on the UCCSD(T) and CASPT2/CASSCF computations that also include H-atom tunneling and a hindered internal rotation, are in perfect agreement with the experimental values. Considering both our experimental and theoretical determinations, the rate constant can best be expressed, in modified Arrhenius form as k(1)(T) = (2.2 +/- 0.1) x 10(-21)T(3.05) exp[-(376 +/- 100)T] cm(3) s(-1) for the range 300-2000 K. Thus, at temperatures above 1500 K, reaction of C(2)H with H(2)O is predicted to be one of the dominant C(2)H reactions in hydrocarbon combustion.

Laser-induced fluorescence of nascent CH from ultraviolet photodissociation of HCCO and the absolute rate coefficient of the HCCO+O2 reaction over the range T=296–839 K

The absolute rate coefficient of the gas-phase reaction HCCO+O2 was determined over the temperature range 296–839 K and at a pressure 7±1 Torr helium. The experiments were performed in a slow-flow kinetic apparatus employing pulsed photolysis of CH2CO at 193 nm as a source of HCCO radicals. Reaction time profiles of [HCCO] were constructed using a newly developed, sensitive spectroscopic technique in the visible spectral region to detect this radical: laser—induced fluorescence of nascent CH(X 2Π) photofragments following HCCO photodissociation at 266 nm. Photodissociation of HCCO at this wavelength was found to produce rotationally excited CH(X) populated to N″⩾26. The rate coefficient for the title reaction was found to be described by k(T)(HCCO+O2)=(2.6±0.3)×10−12 exp[−(325±80)K/T] cm3 s−1 molecule−1 (2σ errors). The absorption cross section of HCCO at 266 nm, σHCCO(266 nm), was also determined relative to that of CH2CO at 193 nm as σHCCO(266 nm)=0.07−0.05+0.20σCH2CO(193 nm).

Kinetics of O(1D) + H2O and O(1D) + H2: absolute rate coefficients and O(3P) yields between 227 and 453 K

The rate coefficients for the crucial atmospheric reactions of O((1)D) with H(2)O and H(2), k(1) and k(2), were measured over a wide temperature range using O((1)D) detection based on the chemiluminescence reaction of O((1)D) with C(2)H. Analyzing the decays of the chemiluminescence intensities yielded a value for k(1)(T) of (1.70 x 10(-10)exp[36 K/T]) cm(3) s(-1). Multiplying or dividing k(1)(T) by a factor f(T) = 1.04 exp(5.59(|1 K/T- 1/287|)), gives the 95% confidence limits; our new determination, in good agreement with previous studies, further reduces the uncertainty in k(1). An extended study of k(2) yielded a temperature independent rate constant of (1.35 +/- 0.05) x 10(-10) cm(3) s(-1). This precise value, based on an extended set of determinations with very low scatter, is significantly larger than the current recommendations, as were two other recent k(2) determinations. Secondly, the fractions of O((1)D) quenched to O((3)P) by H(2)O and H(2), k(1b)/k(1) and k(2b)/k(2), were precisely determined from fits to chemiluminescence decays. A temperature-independent value for k(1b)/k(1) of 0.010 +/- 0.003 was found. For the quenching fraction k(2b)/k(2) a value of 0.007 +/- 0.007 was obtained at room temperature. Both determinations are significantly smaller than values and upper limits from previous studies.

An experimental and theoretical study of the reaction of ethynyl radicals with nitrogen dioxide (HC≡C+NO2)

A pulsed laser photolysis/chemiluminescence (PLP/CL) technique was used to determine absolute rate constants of the reaction C2H+NO2→products over the temperature range 288–800 K at a pressure of 5 Torr (N2). The reaction has a large rate constant that decreases with increasing temperature. It may be expressed in simple Arrhenius form as k1(T)=(7.6±1.0)×10−11 exp[(130±50) K/T], although there is an indication of a downward curvature for T>700 K. A three-parameter Arrhenius fit to the data, which takes this into account gives k1(T)=(9.7±1.5)×10−9T−0.68 exp[(158±65) K/T]. Our experiments also show that the 293 K rate constant is invariant to pressure between 2 and 11 Torr (N2). We have also characterized the C2H+NO2 reaction theoretically. A large portion of the potential energy surface (PES) of the [C2,H,N,O2] system has been investigated in its electronic (singlet) ground-state using DFT with the B3LYP/6-311++G(3df,2p) method and MO computations at the CCSD(T)/6-311++G(d,p) level of theory. Seventeen isom...

INFLUENCE OF STELLAR FLARES ON THE CHEMICAL COMPOSITION OF EXOPLANETS AND SPECTRA

More than 3000 exoplanets have been detected so far, and more and more spectroscopic observations of exoplanets are performed. Future instruments are eagerly awaited as they will be able to provide spectroscopic data with a greater accuracy and sensitivity than what is currently available. An important aspect to consider is temporal stellar atmospheric disturbances that can influence the planetary composition, and hence spectra, and potentially can lead to incorrect assumptions about the steady-state atmospheric composition of the planet. We focus on perturbations that come from the host star in the form of flare events that significantly increase the photon flux impingement on the exoplanet atmosphere. In some cases, and particularly for M stars, this sudden increase may last for several hours. We aim at answering the question to what extent a stellar flare is able to modify the chemical composition of the planetary atmosphere and, therefore influence the resulting spectra. We use a 1D thermo-photochemical model to study the neutral atmospheric composition of two hypothetic planets located around the star AD Leo. This active star has already been observed during a flare. We use the spectroscopic data from this flare event to simulate the evolution of the chemical composition of the atmospheres of the two hypothetic planets. We compute synthetic spectra to evaluate the implications for observations. The increase of the incoming photon flux affects the chemical abundances of some important species down to altitudes associated with an atmospheric pressure of 1 bar, that can lead to variations in planetary spectra if performed during transit.

Oh kinetics and photochemistry of HNO3 in the presence of water vapor

Abstract The pulsed-laser-photolysis technique was used to determine the rate constant of the gas-phase reaction between the hydroxyl radical (OH) and HNO 3 for the first time under conditions of high relative humidity at (295±3) K. The value obtained, at a total pressure of 200 Torr N 2 , was 1.64 −0.20 +0.11 ×10 −13 cm 3 s −1 (error limits include assessment of systematic errors), in excellent agreement with the most recent determinations [J. Phys. Chem. 103 (1999) 3031], and was invariant with relative humidity up to 0.50. The shape of the HNO 3 absorption bands between 210 and 350 nm also showed negligible variation with relative humidity.

Experimental determination of the temperature dependence of the absolute rate coefficients of the HCCO + NO2 and HCCO + H2 reactions

The absolute rate coefficients of the gas-phase reactions HCCO+NO2 and HCCO+H2 were experimentally determined for the first time over extended temperature ranges: 293 K to 769 K and 438 K to 761 K, respectively. HCCO radicals were generated by pulsed-laser photolysis of CH2CO at 193 nm. Their subsequent decay, under pseudo-first-order conditions, was monitored in real-time using a laser-photofragment/laser-induced fluorescence technique. The rate coefficient of HCCO+NO2 exhibits a negative temperature dependence similar to that of the HCCO+NO reaction, but the Arrhenius A-factor is 1.4 times larger; k(T)(HCCO+NO2)=(2.3±0.4)×10−11 exp (340±40) K/T) cm3 s−1. It is argued that, if the major product channels yield N, NH or NCO, the HCCO+NO2 reaction should be a significant removal route of NOx in stationary combustion systems under fuel-rich conditions at temperatures below ca. 1300 K. The rate coefficient for the HCCO+H2 reaction was determined as k(T)(HCCO+H2)=(2.2±1.4)×10−11 exp(−2000±400)K/T). In fuel-rich combustion environments, given the high concentrations of H2, this reaction is likely to be a significant loss process for HCCO radicals: k(1500 K)HCCO+H2=(6+0.4−0.2)×10−12 cm−3 s−1, a factor of three greater than k(1500 K)HCCO+O2.

Theoretical study of the reaction of the ethynyl radical with ammonia (C2H + NH3): hydrogen abstraction versus condensation

Portions of the potential energy surface (PES) related to the reaction between the ethynyl radical and ammonia (C2H + NH3) have been investigated in detail using both MO and DFT methods up to geometry optimizations using the coupled-cluster theory with large basis sets. Several (C2H4N) intermediates and transition structures for unimolecular rearrangements between them have been characterized. Calculations at the CCSD(T)/6-311++G(3df,2p) + ZPE level show that the C2H + NH3 reaction has two main entrance channels: H-abstraction and condensation. The relative energies (kcal mol−1) along the H-abstraction pathway are as follows: 1 C2H + NH3 (0) → pre-reaction complex CO2 (−2.9) → TS (−1.8) → post-reaction complex CO3 (−28.4) → HCCH + NH2 (−26.6). This channel thus starts by formation of a weak complex HCC…H3N, which after H-atom transfer gives rise to another weak complex between the products, HCCH⋯NH2. The energies (kcal mol−1) along the condensation pathway are: 1 C2H + NH3 (0) → pre-association complex CO1 (−6.1) → TS (−3.0) → adduct HCC–NH3 (−7.6) → TS (4.3) → H2N–CCH + H (−14.2). Although both complex CO1 and primary adduct HCC–NH3 are slightly more stable than CO2 and CO3, the transition structure for conversion of the adduct has a substantially higher energy than the reactants and is fairly rigid, whereas the transition state for H-abstraction lies below the reactant limit and is rather loose. Therefore, H-abstraction is calculated to be clearly favored over condensation at all temperatures. The predicted barrier-free main channel is consistent with recent experimental results showing the title reaction to be a fast process exhibiting a negative temperature dependence. In view of the small energy barrier related to the novel condensation pathway, it might contribute at high temperatures in a significant way to the products formation.