Metallo-organic domino reactions: C-H versus C-C bond breaking

HL and MeL are prepared by condensing benzil dihydrazone with 2-formylpyridine and 2-acetylpyridine, respectively, in 1:2 molar proportions. While in a reaction with [Ru-(C6H6)Cl-2](2), HL yields the cation [Ru(C6H6){5,6-diphenyl-3-(pyridin-2-yl)- 1,2,4-triazine}Cl](+), MeL gives the cation [Ru(C6H6)(MeL)Cl](+). Both the cations are isolated as their hexafluorophosphate salts and characterised by X-ray crystallography. In the case of HL, double domino electrocyclic/elimination reactions are found to occur. The electrocyclic reaction occurs in a C=N-N=C-C=N fragment of HL and the elimination reaction involves breaking of a C-H bond of HL. Density functional calculations on model complexes indicate that the identified electrocyclic reaction is thermochemically as well as kinetically feasible for both HL and MeL in the gas phase. For a double domino reaction, similar to that operative in HL, to occur for MeL, breaking of a C-C bond would be required in the elimination step. Our model calculations show the energy barrier for this elimination step to be much higher (329.1 kJ mol(-1)) for MeL than that for HL (96.3 kJ mol(-1)). Thus, the domino reaction takes place for HL and not for MeL. This accounts for the observed stability of [Ru(C6H6)-(MeL)Cl](+) under the reaction conditions employed.

Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Coupling aerosol surface and bulk chemistry with a kinetic double layer model (K2-SUB): oxidation of oleic acid by ozone

We present a kinetic double layer model coupling aerosol surface and bulk chemistry (K2-SUB) based on the PRA framework of gas-particle interactions (Poschl-Rudich-Ammann, 2007). K2-SUB is applied to a popular model system of atmospheric heterogeneous chemistry: the interaction of ozone with oleic acid. We show that our modelling approach allows de-convoluting surface and bulk processes, which has been a controversial topic and remains an important challenge for the understanding and description of atmospheric aerosol transformation. In particular, we demonstrate how a detailed treatment of adsorption and reaction at the surface can be coupled to a description of bulk reaction and transport that is consistent with traditional resistor model formulations. From literature data we have derived a consistent set of kinetic parameters that characterise mass transport and chemical reaction of ozone at the surface and in the bulk of oleic acid droplets. Due to the wide range of rate coefficients reported from different experimental studies, the exact proportions between surface and bulk reaction rates remain uncertain. Nevertheless, the model results suggest an important role of chemical reaction in the bulk and an approximate upper limit of similar to 10(-11) cm(2) s(-1) for the surface reaction rate coefficient. Sensitivity studies show that the surface accommodation coefficient of the gas-phase reactant has a strong non-linear influence on both surface and bulk chemical reactions. We suggest that K2-SUB may be used to design, interpret and analyse future experiments for better discrimination between surface and bulk processes in the oleic acid-ozone system as well as in other heterogeneous reaction systems of atmospheric relevance.

Evaluation of a Lagrangian box model using field measurements from EASE (Eastern Atlantic Summer Experiment) 1996

The Cambridge Tropospheric Trajectory model of Chemistry and Transport (CiTTyCAT), a Lagrangian chemistry model, has been evaluated using atmospheric chemical measurements collected during the East Atlantic Summer Experiment 1996 (EASE '96). This field campaign was part of the UK Natural Environment Research Council's (NERC) Atmospheric Chemistry Studies in the Oceanic Environment (ACSOE) programme, conducted at Mace Head, Republic of Ireland, during July and August 1996. The model includes a description of gas-phase tropospheric chemistry, and simple parameterisations for surface deposition, mixing from the free troposphere and emissions. The model generally compares well with the measurements and is used to study the production and loss of O3 under a variety of conditions. The mean difference between the hourly O3 concentrations calculated by the model and those measured is 0.6 ppbv with a standard deviation of 8.7 ppbv. Three specific air-flow regimes were identified during the campaign – westerly, anticyclonic (easterly) and south westerly. The westerly flow is typical of background conditions for Mace Head. However, on some occasions there was evidence of long-range transport of pollutants from North America. In periods of anticyclonic flow, air parcels had collected emissions of NOx and VOCs immediately before arriving at Mace Head, leading to O3 production. The level of calculated O3 depends critically on the precise details of the trajectory, and hence on the emissions into the air parcel. In several periods of south westerly flow, low concentrations of O3 were measured which were consistent with deposition and photochemical destruction inside the tropical marine boundary layer.

Radicals from the atmospheric pressure pyrolysis and oxidative pyrolysis of hydroquinone, catechol, and phenol

The burning of tobacco creates various types of free radicals that have been reported to be biologically active. Some radicals are transient but can initiate catalytic cycles that generate other free radicals. Other radicals are environmentally persistent and can exist in total particulate matter (TPM) for extended periods. In spite of their importance, little is known concerning the precursors of these radicals or under what pyrolysis/combustion conditions they are formed. We performed studies of the formation of radicals from the gas-phase pyrolysis and oxidative pyrolysis of hydroquinone (HQ) and catechol (CT) between 750 and 1000 °C and phenol from 500 to 1000 °C. The initial electron paramagnetic resonance (EPR) spectra were complex, indicating the presence of multiple radicals. Using matrix annealing and microwave power saturation techniques, phenoxyl, cyclopentadienyl, and peroxyl radicals were identifiable, but only cyclopentadienyl radicals were stable above 750 °C.

Kinetics of the reaction between OH radicals and monochlorodimethylsulphide (CH3SCH2Cl)

The gas-phase rate coefficient for the reaction between OH radicals and CH3SCH2Cl (MCDMS) was determined to be (2.5±1.3)×10−12 cm3 molecule−1 s−1 using the discharge–flow kinetic technique. An estimate of ≈10−10 cm3 molecule−1 s−1 was obtained for the rate coefficient for reaction of Cl with MCDMS. It would appear that the reaction with OH is not the main loss process for CH3SCH2Cl in the marine boundary layer. The possible implications for the MBL of halogen-promoted oxidation of dimethylsulphide are considered.

A kinetics and mechanistic study of the atmospherically relevant reaction between molecular chlorine and dimethyl sulfide (DMS)

A gas-phase kinetics study of the atmospherically important reaction between Cl2 and dimethyl sulfide (DMS)Cl2 + CH3SCH3 → productshas been made using a flow-tube interfaced to a photoelectron spectrometer. The rate constant for this reaction has been measured at 1.6 and 3.0 torr at T = (294 ± 2) K as (3.4 ± 0.7) × 10−14 cm3 molecule−1 s−1. Reaction (1) has been found to proceed via an intermediate, (CH3)2SCl2, to give CH3SCH2Cl and HCl as the products. The mechanism of this reaction and the structure of the intermediate were investigated using electronic structure calculations. A comparison of the mechanisms of the reactions between Cl atoms and DMS, and Cl2 and DMS has been made and the relevance of the results to atmospheric chemistry is discussed.

Electron spin resonance study of puff-resolved free radical formation in mainstream cigarette smoke

Puff-by-puff resolved gas phase free radicals were measured in mainstream smoke from Kentucky 2R4F reference cigarettes using ESR spectroscopy. Three spin-trapping reagents were evaluated: PBN, DMPO and DEPMPO. Two procedures were used to collect gas phase smoke on a puff-resolved basis: i) the accumulative mode, in which all the gas phase smoke up to a particular puff was bubbled into the trap (i.e., the 5th puff corresponded to the total smoke from the 1st to 5th puffs). In this case, after a specified puff, an aliquot of the spin trap was taken and analysed; or, ii) the individual mode, in which the spin trap was analysed and then replaced after each puff. Spin concentrations were determined by double-integration of the first derivative of the ESR signal. This was compared with the integrals of known standards using the TEMPO free radical. The radicals trapped with PBN were mainly carbon-centred, whilst the oxygen-centred radicals were identified with DMPO and DEPMPO. With each spin trap, the puff-resolved radical concentrations showed a characteristic pattern as a function of the puff number. Based on the spin concentrations, the DMPO and DEPMPO spin traps showed better trapping efficiencies than PBN. The implication for gas phase free radical analysis is that a range of different spin traps should be used to probe complex free radical reactions in cigarette smoke.

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.

Ozone climatology using interactive chemistry: results from the Canadian Middle Atmosphere Model

The climatology of ozone produced by the Canadian Middle Atmosphere Model (CMAM) is presented. This three-dimensional global model incorporates the radiative feedbacks of ozone and water vapor calculated on-line with a photochemical module. This module includes a comprehensive gas-phase reaction set and a limited set of heterogeneous reactions to account for processes occurring on background sulphate aerosols. While transport is global, photochemistry is solved from about 400 hPa to the top of the model at ∼95 km. This approach provides a complete and comprehensive representation of transport, emission, and photochemistry of various constituents from the surface to the mesopause region. A comparison of model results with observations indicates that the ozone distribution and variability are in agreement with observations throughout most of the model domain. Column ozone annual variation is represented to within 5–10% of the observations except in the Southern Hemisphere for springtime high latitudes. The vertical ozone distribution is generally well represented by the model up to the mesopause region. Nevertheless, in the upper stratosphere, the model generally underestimates the amount of ozone as well as the latitudinal tilting of ozone isopleths at high latitude. Ozone variability is analyzed and compared with measurements. The comparison shows that the phase and amplitude of the seasonal variation as well as shorter timescale variations are well represented by the model at various latitudes and heights. Finally, the impact of incorporating ozone radiative feedback on the model climatology is isolated. It is found that the incorporation of ozone radiative feedback results in a cooling of ∼8 K in the summer stratopause region, which corrects a warm bias that results when climatological ozone is used.

Development and evaluation of an Earth-System model – HadGEM2

We describe here the development and evaluation of an Earth system model suitable for centennial-scale climate prediction. The principal new components added to the physical climate model are the terrestrial and ocean ecosystems and gas-phase tropospheric chemistry, along with their coupled interactions. The individual Earth system components are described briefly and the relevant interactions between the components are explained. Because the multiple interactions could lead to unstable feedbacks, we go through a careful process of model spin up to ensure that all components are stable and the interactions balanced. This spun-up configuration is evaluated against observed data for the Earth system components and is generally found to perform very satisfactorily. The reason for the evaluation phase is that the model is to be used for the core climate simulations carried out by the Met Office Hadley Centre for the Coupled Model Intercomparison Project (CMIP5), so it is essential that addition of the extra complexity does not detract substantially from its climate performance. Localised changes in some specific meteorological variables can be identified, but the impacts on the overall simulation of present day climate are slight. This model is proving valuable both for climate predictions, and for investigating the strengths of biogeochemical feedbacks.

Lithium and oxygen adsorption at the b-MnO2 (110) surface

The adsorption and co-adsorption of lithium and oxygen at the surface of rutile-like manganese dioxide(b-MnO2), which are important in the context of Li–air batteries, are investigated using density functional theory. In the absence of lithium, the most stable surface of b-MnO2, the (110), adsorbs oxygen in the form of peroxo groups bridging between two manganese cations. Conversely, in the absence of excess oxygen, lithium atoms adsorb on the (110) surface at two different sites, which are both tricoordinated to surface oxygen anions, and the adsorption always involves the transfer of one electron from the adatom to one of the five-coordinated manganese cations at the surface, creating (formally) Li+ and Mn3+ species. The co-adsorption of lithium and oxygen leads to the formation of a surface oxide, involving the dissociation of the O2 molecule, where the O adatoms saturate the coordination of surface Mn cations and also bind to the Li adatoms. This process is energetically more favourable than the formation of gas-phase lithium peroxide (Li2O2) monomers, but less favourable than the formation of Li2O2 bulk. These results suggest that the presence of b-MnO2 in the cathode of a nonaqueous Li–O2 battery lowers the energy for the initial reduction of oxygen during cell discharge.

Atmospheric chemistry and physics in the atmosphere of a developed megacity (London): an overview of the REPARTEE experiment and its conclusions

The REgents PARk and Tower Environmental Experiment (REPARTEE) comprised two campaigns in London in October 2006 and October/November 2007. The experiment design involved measurements at a heavily trafficked roadside site, two urban background sites and an elevated site at 160–190 m above ground on the BT Tower, supplemented in the second campaign by Doppler lidar measurements of atmospheric vertical structure. A wide range of measurements of airborne particle physical metrics and chemical composition were made as well as measurements of a considerable range of gas phase species and the fluxes of both particulate and gas phase substances. Significant findings include (a) demonstration of the evaporation of traffic-generated nanoparticles during both horizontal and vertical atmospheric transport; (b) generation of a large base of information on the fluxes of nanoparticles, accumulation mode particles and specific chemical components of the aerosol and a range of gas phase species, as well as the elucidation of key processes and comparison with emissions inventories; (c) quantification of vertical gradients in selected aerosol and trace gas species which has demonstrated the important role of regional transport in influencing concentrations of sulphate, nitrate and secondary organic compounds within the atmosphere of London; (d) generation of new data on the atmospheric structure and turbulence above London, including the estimation of mixed layer depths; (e) provision of new data on trace gas dispersion in the urban atmosphere through the release of purposeful tracers; (f) the determination of spatial differences in aerosol particle size distributions and their interpretation in terms of sources and physico-chemical transformations; (g) studies of the nocturnal oxidation of nitrogen oxides and of the diurnal behaviour of nitrate aerosol in the urban atmosphere, and (h) new information on the chemical composition and source apportionment of particulate matter size fractions in the atmosphere of London derived both from bulk chemical analysis and aerosol mass spectrometry with two instrument types.

Sample preparation: a crucial factor for the analytical performance of rationally designed MALDI matrices

Evidence is presented that the performance of the rationally designed MALDI matrix 4-chloro-α-cyanocinnamic acid (ClCCA) in comparison to its well-established predecessor α-cyano-4-hydroxycinnamic acid (CHCA) is significantly dependent on the sample preparation, such as the choice of the target plate. In this context, it becomes clear that any rational designs of MALDI matrices and their successful employment have to consider a larger set of physicochemical parameters, including sample crystallization and morphology/topology, in addition to parameters of basic (solution and/or gas-phase) chemistry.