Time-resolved gas-phase kinetic, quantum chemical and RRKM studies of reactions of silylene with cyclic ethers

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with oxirane, oxetane, and tetrahydrofuran (THF). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at four or five temperatures in the range 294-605 K. All three reactions showed pressure dependences characteristic of third-body-assisted association reactions with, surprisingly, SiH2 + oxirane showing the least and SiH2 + THF showing the most pressure dependence. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equations where the error limits are single standard deviations: log(k(oxirane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.03 +/- 0.07) + (5.70 +/- 0.51) kJ mol(-1)/RT In 10 log(k(oxetane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.17 +/- 0.11) + (9.04 +/- 0.78) kJ mol(-1)/RT In 10 log(k(THF)(infinity)/cm(3) molecule(-1) s(-1)) = (-10.59 +/- 0.10) + (5.76 +/- 0.65) kJ mol(-1)/RT In 10 Binding-energy values of 77, 97, and 92 kJ mol(-1) have been obtained for the donor-acceptor complexes of SiH2 with oxirane, oxetane, and THF, respectively, by means of quantum chemical (ab initio) calculations carried Out at the G3 level. The use of these values to model the pressure dependences of these reactions, via RRKM theory, provided a good fit only in the case of SiH2 + THF. The lack of fit in the other two cases is attributed to further reaction pathways for the association complexes of SiH2 with oxirane and oxetane. The finding of ethene as a product of the SiH2 + oxirane reaction supports a pathway leading to H2Si=O + C2H4 predicted by the theoretical calculations of Apeloig and Sklenak.

Peroxy radical partitioning during the AMMA radical intercomparison exercise

Peroxy radicals were measured onboard two scientific aircrafts during the AMMA (African Monsoon Multidisciplinary Analysis) campaign in summer 2006. This paper reports results from the flight on 16 August 2006 during which measurements of HO2 by laser induced fluorescence spectroscopy at low pressure (LIF-FAGE) and total peroxy radicals (RO2* = HO2+ΣRO2, R = organic chain) by two similar instruments based on the peroxy radical chemical amplification (PeRCA) technique were subject of a blind intercomparison. The German DLR-Falcon and the British FAAM-BAe-146 flew wing tip to wing tip for about 30 min making concurrent measurements on 2 horizontal level runs at 697 and 485 hPa over the same geographical area in Burkina Faso. A full set of supporting measurements comprising photolysis frequencies, and relevant trace gases like CO, NO, NO2, NOy, O3 and a wider range of VOCs were collected simultaneously. Results are discussed on the basis of the characteristics and limitations of the different instruments used. Generally, no data bias are identified and the RO2* data available agree quite reasonably within the instrumental errors. The [RO2*]/[HO2] ratios, which vary between 1:1 and 3:1, as well as the peroxy radical variability, concur with variations in photolysis rates and in other potential radical precursors. Model results provide additional information about dominant radical formation and loss processes.

The north Atlantic marine oundary layer experiment (NAMBLEX): Overview of the campaign held at Mace Head, Ireland, in summer 2002

The North Atlantic Marine Boundary Layer Experiment (NAMBLEX), involving over 50 scientists from 12 institutions, took place at Mace Head, Ireland (53.32° N, 9.90° W), between 23 July and 4 September 2002. A wide range of state-of-the-art instrumentation enabled detailed measurements of the boundary layer structure and atmospheric composition in the gas and aerosol phase to be made, providing one of the most comprehensive in situ studies of the marine boundary layer to date. This overview paper describes the aims of the NAMBLEX project in the context of previous field campaigns in the Marine Boundary Layer (MBL), the overall layout of the site, a summary of the instrumentation deployed, the temporal coverage of the measurement data, and the numerical models used to interpret the field data. Measurements of some trace species were made for the first time during the campaign, which was characterised by predominantly clean air of marine origin, but more polluted air with higher levels of NOx originating from continental regions was also experienced. This paper provides a summary of the meteorological measurements and Planetary Boundary Layer (PBL) structure measurements, presents time series of some of the longer-lived trace species (O3, CO, H2, DMS, CH4, NMHC, NOx, NOy, PAN) and summarises measurements of other species that are described in more detail in other papers within this special issue, namely oxygenated VOCs, HCHO, peroxides, organo-halogenated species, a range of shorter lived halogen species (I2, OIO, IO, BrO), NO3 radicals, photolysis frequencies, the free radicals OH, HO2 and (HO2+Σ RO2), as well as a summary of the aerosol measurements. NAMBLEX was supported by measurements made in the vicinity of Mace Head using the NERC Dornier-228 aircraft. Using ECMWF wind-fields, calculations were made of the air-mass trajectories arriving at Mace Head during NAMBLEX, and were analysed together with both meteorological and trace-gas measurements. In this paper a chemical climatology for the duration of the campaign is presented to interpret the distribution of air-mass origins and emission sources, and to provide a convenient framework of air-mass classification that is used by other papers in this issue for the interpretation of observed variability in levels of trace gases and aerosols.

Time-resolved gas-phase kinetic study of the germylene addition reaction, CH3C CCH3

Time-resolved kinetic studies of the reaction of germylene, GeH2, generated by laser. ash photolysis of 3,4-dimethyl-1-germacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with 2-butyne, CH3C CCH3. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at five temperatures in the range 300-556 K. The second order rate constants obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.46 +/- 10.06) + (5.16 +/- 10.47) kJ mol(-1)/ RT ln 10 Calculations of the energy surface of the GeC4H8 reaction system were carried out employing the additivity principle, by combining previous quantum chemical calculations of related reaction systems. These support formation of 1,2-dimethylvinylgermylene (rather than 2,3-dimethylgermirene) as the end product. RRKM calculations of the pressure dependence of the reaction are in reasonable agreement with this finding. The reactions of GeH2 with C2H2 and with CH3CRCCH3 are compared and contrasted.

Gas-phase kinetics of chlorosilylene reactions. I. ClSiH + Me3SiH: absolute rate measurements and theoretical calculations for prototype Si−H insertion reactions

Time-resolved studies of chlorosilylene, CISiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane, Me3SiH, in the gas phase. The reaction was studied at total pressures up to 100 torr (with and without added SF6) over the temperature range 297-407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-13.97 +/- 0.25) + (12.57 +/- 1.64) kJ mol(-1)/RT In 10. The Arrhenius parameters are consistent with a mechanism involving an intermediate complex, whose rearrangement is the rate-determining step. Quantum chemical calculations of the potential energy surface for this reaction and also the reactions of CISiH with SiH4 and the other methylsilanes support this conclusion. Comparisons of both experiment and theory with the analogous Si-H insertion processes of SiH2 and SiMe2 show that the main factor causing the lower reactivity of ClSiH is the secondary energy barrier. The calculations also show the existence of a novel intramolecular H-atom exchange process in the complex of ClSiH with MeSiH3.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations

Time-resolved kinetic studies of the reactions of silylene, SiH2, and dideutero-silylene, SiD2, generated by laser. ash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH3C CCH3. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(-1)/RTln10 log(k(D)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTln10 Additionally, pressure-dependent rate coefficients for the reaction of SiH2 with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC4H8 reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH2C(CH3)=C(CH3)-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH3CH=C(CH3)SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H - D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Direct time-resolved study of the kinetics of the reaction of silylene with phenylsilane in the gas phase. Does SiH2 react with the aromatic ring?

Laser flash photolysis studies of silylene, SiH2, generated by the 193 nm laser flash photolysis phenylsilane, PhSiH3, have been carried out to obtain rate constants for its bimolecular reaction with PhSiH3 itself, in the gas phase. The reaction was studied in SF6 (mostly at 10 Torr total pressure) over the temperature range 298-595 K. The rate constants (also found to be pressure independent) gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-9.92 +/- 0.04) + (3.31 +/- 0.27) kJ mol(-1)/RT ln 10 Similar investigations of the reaction of silylene with benzene, C6H6, (295-410 K) gave data suggestive of the fact that SiH2 might be reacting with photochemical products of C6H6 as well as with C6H6 itself. However, in the latter system, apparent rate constants were sufficiently low to indicate that in the reaction of SiH2 with PhSiH3 addition to the aromatic ring was unlikely to be in excess of 3% of the total. Quantum chemical calculations of the energy surface for SiH2 + C6H6 indicate that 7-silanorcaradiene and 7-silacycloheptatriene are possible products but that PhSiH3 formation is unlikely. RRKM calculations suggest that 7-silanorcaradiene should be the initial product but that it cannot be collisionally stabilized under experimental conditions

Unusual isotope effect in the reaction of chlorosilylene with trimethylsilane-1-d: Absolute rate studies and quantum chemical and Rice–Ramsperger–Kassel–Marcus calculations provide strong evidence for the involvement of an intermediate complex

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1- silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane-1-d, Me3SiD, in the gas phase. The reaction was studied at total pressures up to 100 Torr (with and without added SF6) over the temperature range of 295−407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log[(k/(cm3 molecule−1 s−1)] = (−13.22 ± 0.15) + [(13.20 ± 1.00) kJ mol−1]/(RT ln 10). When compared with previously published kinetic data for the reaction of ClSiH with Me3SiH, kinetic isotope effects, kD/kH, in the range from 7.4 (297 K) to 6.4 (407 K) were obtained. These far exceed values of 0.4−0.5 estimated for a single-step insertion process. Quantum chemical calculations (G3MP2B3 level) confirm not only the involvement of an intermediate complex, but also the existence of a low-energy internal isomerization pathway which can scramble the D and H atom labels. By means of Rice−Ramsperger−Kassel−Marcus modeling and a necessary (but small) refinement of the energy surface, we have shown that this mechanism can reproduce closely the experimental isotope effects. These findings provide the first experimental evidence for the isomerization pathway and thereby offer the most concrete evidence to date for the existence of intermediate complexes in the insertion reactions of silylenes.

Review of the formulation of present‐generation stratospheric chemistry‐climate models and associated external forcings

The goal of the Chemistry‐Climate Model Validation (CCMVal) activity is to improve understanding of chemistry‐climate models (CCMs) through process‐oriented evaluation and to provide reliable projections of stratospheric ozone and its impact on climate. An appreciation of the details of model formulations is essential for understanding how models respond to the changing external forcings of greenhouse gases and ozonedepleting substances, and hence for understanding the ozone and climate forecasts produced by the models participating in this activity. Here we introduce and review the models used for the second round (CCMVal‐2) of this intercomparison, regarding the implementation of chemical, transport, radiative, and dynamical processes in these models. In particular, we review the advantages and problems associated with approaches used to model processes of relevance to stratospheric dynamics and chemistry. Furthermore, we state the definitions of the reference simulations performed, and describe the forcing data used in these simulations. We identify some developments in chemistry‐climate modeling that make models more physically based or more comprehensive, including the introduction of an interactive ocean, online photolysis, troposphere‐stratosphere chemistry, and non‐orographic gravity‐wave deposition as linked to tropospheric convection. The relatively new developments indicate that stratospheric CCM modeling is becoming more consistent with our physically based understanding of the atmosphere.

Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modelled using RRKM theory, based on Eo values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k∞ values in the range 1.9 to 4.5 × 10-10 cm3 molecule-1 s-1. These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16 and 67% of the collision rates for these reactions. In the reaction of SiH2 + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalysed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H2O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

The reaction between silylene and ammonia: some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH3. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ/pulse) fitted the Arrhenius equation: log(k/cm3 molecule-1 s-1) = (-10.37 ± 0.17) + (0.36 ± 1.12 kJ mol-1)/RTln10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10-100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ/pulse. Ab initio calculations at the G3 level of theory, show that SiH2 + NH3 should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH2 + NH3 should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH2 decays are better explained by reaction of SiH2 with the amino radical, NH2, formed by photodissociation of NH3 at 193 nm. The mechanism of this previously unstudied reaction is discussed.

Comparison of polar ozone loss rates simulated by one-dimensional and three-dimensional models with Match observations in recent Antarctic and Arctic winters

Simulations of ozone loss rates using a three-dimensional chemical transport model and a box model during recent Antarctic and Arctic winters are compared with experimental loss rates. The study focused on the Antarctic winter 2003, during which the first Antarctic Match campaign was organized, and on Arctic winters 1999/2000, 2002/2003. The maximum ozone loss rates retrieved by the Match technique for the winters and levels studied reached 6 ppbv/sunlit hour and both types of simulations could generally reproduce the observations at 2-sigma error bar level. In some cases, for example, for the Arctic winter 2002/2003 at 475 K level, an excellent agreement within 1-sigma standard deviation level was obtained. An overestimation was also found with the box model simulation at some isentropic levels for the Antarctic winter and the Arctic winter 1999/2000, indicating an overestimation of chlorine activation in the model. Loss rates in the Antarctic show signs of saturation in September, which have to be considered in the comparison. Sensitivity tests were performed with the box model in order to assess the impact of kinetic parameters of the ClO-Cl2O2 catalytic cycle and total bromine content on the ozone loss rate. These tests resulted in a maximum change in ozone loss rates of 1.2 ppbv/sunlit hour, generally in high solar zenith angle conditions. In some cases, a better agreement was achieved with fastest photolysis of Cl2O2 and additional source of total inorganic bromine but at the expense of overestimation of smaller ozone loss rates derived later in the winter.

Spectral absorption properties of aerosol particles from 350-2500nm

The aerosol spectral absorption efficiency (alpha(a) in m(2)/g) is measured over an extended wavelength range (350-2500 nm) using an improved calibrated and validated reflectance technique and applied to urban aerosol samples from Sao Paulo, Brazil and from a site in Virginia, Eastern US, that experiences transported urban/industrial aerosol. The average alpha(a) values (similar to 3m(2)/g at 550 nm) for Sao Paulo samples are 10 times larger than a a values obtained for aerosols in Virginia. Sao Paulo aerosols also show evidence of enhanced UV absorption in selected samples, probably associated with organic aerosol components. This extra UV absorption can double the absorption efficiency observed from black carbon alone, therefore reducing by up to 50% the surface UV fluxes, with important implications for climate, UV photolysis rates, and remote sensing from space. Citation: Martins, J.V., P. Artaxo, Y.J. Kaufman, A.D. Castanho, and L.A. Remer (2009), Spectral absorption properties of aerosol particles from 350-2500nm, Geophys. Res. Lett., 36, L13810, doi: 10.1029/2009GL037435.

Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues

Unveiling the mechanisms of energy relaxation in biomolecules is key to our understanding of protein stability, allostery, intramolecular signaling, and long-lasting quantum coherence phenomena at ambient temperatures. Yet, the relationship between the pathways of energy transfer and the functional role of the residues involved remains largely unknown. Here, we develop a simulation method of mapping out residues that are highly efficient in relaxing an initially localized excess vibrational energy and perform site-directed mutagenesis functional assays to assess the relevance of these residues to protein function. We use the ligand binding domains of thyroid hormone receptor (TR) subtypes as a test case and find that conserved arginines, which are critical to TR transactivation function, are the most effective heat diffusers across the protein structure. These results suggest a hitherto unsuspected connection between a residue`s ability to mediate intramolecular vibrational energy redistribution and its functional relevance.

Tryptophan photooxidation promoted by new hybrid materials prepared by condensation of naphthalene imides with silicate by the sol-gel process

Three novel hybrid organic/inorganic materials were synthesized from 4-substituted (NO(2), Br, H) 1,8-naphthalene imide-N-propyltriethoxysilane by the sol-gel process. These materials were obtained as a xerogel and partially characterized. The ability to photosensitize the oxidation and degradation of tryptophan indole ring by these materials was studied through photophysical and photochemical techniques. Although the derivatives containing Br and NO(2) as substituent do not cause efficient tryptophan photodamage, the hybrid material obtained from 1,8-naphthalic anhydride is very efficient to promote tryptophan photooxidation. By using laser flash photolysis it was possible to verify the presence of naphthalene imide transient radical species. The presence of oxygen causes an increase of the yield of radical formation. These results suggest that the mechanism of photodegradation of tryptophan occurs by type I, i.e. the transient radical (TrpH(center dot+)) formed by the direct reaction of the triplet state of the naphthalene imide moiety with tryptophan. Thus a inorganic-organic hybrid material that can be used to promote the oxidation of biomolecules was obtained. (C) 2009 Elsevier B.V. All rights reserved.