The influence of organic acids in relation to acid deposition in controlling the acidity of soil and stream waters on a seasonal basis

Much uncertainty still exists regarding the relative importance of organic acids in relation to acid deposition in controlling the acidity of soil and surface waters. This paper contributes to this debate by presenting analysis of seasonal variations in atmospheric deposition, soil solution and stream water chemistry for two UK headwater catchments with contrasting soils. Acid neutralising capacity (ANC), dissolved organic carbon (DOC) concentrations and the Na:Cl ratio of soil and stream waters displayed strong seasonal patterns with little seasonal variation observed in soil water pH. These patterns, plus the strong relationships between ANC, Cl and DOC, suggest that cation exchange and seasonal changes in the production of DOC and seasalt deposition are driving a shift in the proportion of acidity attributable to strong acid anions, from atmospheric deposition, during winter to predominantly organic acids in summer.

Fibrillisation of hydrophobically modified amyloid peptide fragments in an organic solvent

The self-assembly of a hydrophobically modified fragment of the amyloid beta(A beta) peptide has been studied in methanol. The peptide FFKLVFF is based on A beta(16-20) extended at the N terminus by two phenylalanine residues. The formation of amyloid-type fibrils is confirmed by Congo Red staining, thioflavin T fluorescence and circular dichroism experiments. FTIR points to the formation of beta-sheet structures in solution and in dried films and suggests that aggregation occurs at low concentration and is not strongly affected by further increase in concentration, i.e. the peptide is a strong fibril-former in methanol. UV fluorescence experiments on unstained peptide and CD point to the importance of aromatic interactions between phenylalanine groups in driving aggregation into beta-sheets. The CD spectrum differs from that usually observed for beta-sheet assemblies formed by larger peptides or proteins and this is discussed for solutions in methanol and also trifluoroethanol. The fibril structure is imaged by transmission electron microscopy and scanning electron microscopy on dried samples and is confirmed by small-angle X-ray scattering experiments in solution.

Reactive Halogens in the Marine Boundary Layer (RHaMBLe): the tropical North Atlantic experiments

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv (note the non-IUPAC adoption in this manuscript of pptv and ppbv, equivalent to pmol mol−1 and nmol mol−1 to reflect common practice). Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.

Chemical and aerosol characterisation of the troposphere over West Africa during the monsoon period as part of AMMA

During June, July and August 2006 five aircraft took part in a campaign over West Africa to observe the aerosol content and chemical composition of the troposphere and lower stratosphere as part of the African Monsoon Multidisciplinary Analysis (AMMA) project. These are the first such measurements in this region during the monsoon period. In addition to providing an overview of the tropospheric composition, this paper provides a description of the measurement strategy (flights performed, instrumental payloads, wing-tip to wing-tip comparisons) and points to some of the important findings discussed in more detail in other papers in this special issue. The ozone data exhibits an "S" shaped vertical profile which appears to result from significant losses in the lower troposphere due to rapid deposition to forested areas and photochemical destruction in the moist monsoon air, and convective uplift of ozone-poor air to the upper troposphere. This profile is disturbed, particularly in the south of the region, by the intrusions in the lower and middle troposphere of air from the southern hemisphere impacted by biomass burning. Comparisons with longer term data sets suggest the impact of these intrusions on West Africa in 2006 was greater than in other recent wet seasons. There is evidence for net photochemical production of ozone in these biomass burning plumes as well as in urban plumes, in particular that from Lagos, convective outflow in the upper troposphere and in boundary layer air affected by nitrogen oxide emissions from recently wetted soils. This latter effect, along with enhanced deposition to the forested areas, contributes to a latitudinal gradient of ozone in the lower troposphere. Biogenic volatile organic compounds are also important in defining the composition both for the boundary layer and upper tropospheric convective outflow. Mineral dust was found to be the most abundant and ubiquitous aerosol type in the atmosphere over Western Africa. Data collected within AMMA indicate that injection of dust to altitudes favourable for long-range transport (i.e. in the upper Sahelian planetary boundary layer) can occur behind the leading edge of mesoscale convective system (MCS) cold-pools. Research within AMMA also provides the first estimates of secondary organic aerosols across the West African Sahel and have shown that organic mass loadings vary between 0 and 2 μg m−3 with a median concentration of 1.07 μg m−3. The vertical distribution of nucleation mode particle concentrations reveals that significant and fairly strong particle formation events did occur for a considerable fraction of measurement time above 8 km (and only there). Very low concentrations were observed in general in the fresh outflow of active MCSs, likely as the result of efficient wet removal of aerosol particles due to heavy precipitation inside the convective cells of the MCSs. This wet removal initially affects all particle size ranges as clearly shown by all measurements in the vicinity of MCSs.

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.

Night-time tropospheric chemistry of the unsaturated alcohols (Z)-pent-2-en-1-ol and pent-1-en-3-ol: Kinetic studies of reactions of NO3 and N2O5 with stress-induced plant emissions

The night-time tropospheric chemistry of two stress-induced volatile organic compounds (VOCs), (Z)-pent-2-en-1-ol and pent-1-en-3-ol, has been studied at room temperature. Rate coefficients for reactions of the nitrate radical (NO3) with these pentenols were measured using the discharge-flow technique. Because of the relatively low volatility of these compounds, we employed off-axis continuous-wave cavity-enhanced absorption spectroscopy for detection of NO3 in order to be able to work in pseudo first-order conditions with the pentenols in large excess over NO3. The rate coefficients were determined to be (1.53 +/- 0.23) x 10(-13) and (1.39 +/- 0.19) x 10(-14) cm(3) molecule(-1) s(-1) for reactions of NO3 with (Z)-pent-2-en-1-ol and pent-1-en-3-ol. An attempt to study the kinetics of these reactions with a relative-rate technique, using N2O5 as source of NO3 resulted in significantly higher apparent rate coefficients. Performing relative-rate experiments in known excesses of NO2 allowed us to determine the rate coefficients for the N2O5 reactions to be (5.0 +/- 2.8) x 10(-19) cm(3) molecule(-1) s(-1) for (Z)-pent-2-en-1-ol, and (9.1 +/- 5.8) x 10(-19) cm(3) molecule(-1) s(-1) for pent-1-en-3-ol. We show that these relatively slow reactions can indeed interfere with rate determinations in conventional relative-rate experiments.

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles representative of atmospheric cooking aerosols. We apply and extend the recently developed KM-SUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant time scales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semisolid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

A step toward the wet surface chemistry of glycine and alanine on Cu{110}: destabilization and decomposition in the presence of near-ambient water vapor

The coadsorption of water with organic molecules under near-ambient pressure and temperature conditions opens up new reaction pathways on model catalyst surfaces that are not accessible in conventional ultrahigh-vacuum surfacescience experiments. The surface chemistry of glycine and alanine at the water-exposed Cu{110} interface was studied in situ using ambient-pressure photoemission and X-ray absorption spectroscopy techniques. At water pressures above 10-5 Torr a significant pressure-dependent decrease in the temperature for dissociative desorption was observed for both amino acids, accompanied by the appearance of a newCN intermediate, which is not observed for lower pressures. The most likely reaction mechanisms involve dehydrogenation induced by O and/or OH surface species resulting from the dissociative adsorption of water. The linear relationship between the inverse decomposition temperature and the logarithm of water pressure enables determination of the activation energy for the surface reaction, between 213 and 232 kJ/mol, and a prediction of the decomposition temperature at the solidliquid interface by extrapolating toward the equilibrium vapor pressure. Such experiments near the equilibrium vapor pressure provide important information about elementary surface processes at the solidliquid interface, which can be retrieved neither under ultrahigh vacuum conditions nor from interfaces immersed in a solution.

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles approximating atmospheric cooking aerosols. We apply and extend the recently developed KMSUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant timescales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semi-solid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

Adsorption from aqueous solutions on opened carbon nanotubes: organic compounds speed up delivery of water from inside

We report the results of first systematic studies of organic adsorption from aqueous solutions onto relatively long single walled carbon nanotubes (four tubes, in initial and oxidised forms). Using molecular dynamics simulations (GROMACS package) we discuss the behaviour of tube-water as well as tube-adsorbate systems, for three different adsorbates (benzene, phenol and paracetamol).

A Lagrangian model of air-mass photochemistry and mixing using a trajectory ensemble: the Cambridge Tropospheric Trajectory model of Chemistry And Transport (CiTTyCAT) version 4.2

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

Highly resolved observations of trace gases in the lowermost stratosphere and upper troposphere from the SPURT project: an overview

During SPURT (Spurenstofftransport in der Tropopausenregion, trace gas transport in the tropopause region) we performed measurements of a wide range of trace gases with different lifetimes and sink/source characteristics in the northern hemispheric upper troposphere (UT) and lowermost stratosphere (LMS). A large number of in-situ instruments were deployed on board a Learjet 35A, flying at altitudes up to 13.7 km, at times reaching to nearly 380 K potential temperature. Eight measurement campaigns (consisting of a total of 36 flights), distributed over all seasons and typically covering latitudes between 35° N and 75° N in the European longitude sector (10° W–20° E), were performed. Here we present an overview of the project, describing the instrumentation, the encountered meteorological situations during the campaigns and the data set available from SPURT. Measurements were obtained for N2O, CH4, CO, CO2, CFC12, H2, SF6, NO, NOy, O3 and H2O. We illustrate the strength of this new data set by showing mean distributions of the mixing ratios of selected trace gases, using a potential temperature-equivalent latitude coordinate system. The observations reveal that the LMS is most stratospheric in character during spring, with the highest mixing ratios of O3 and NOy and the lowest mixing ratios of N2O and SF6. The lowest mixing ratios of NOy and O3 are observed during autumn, together with the highest mixing ratios of N2O and SF6 indicating a strong tropospheric influence. For H2O, however, the maximum concentrations in the LMS are found during summer, suggesting unique (temperature- and convection-controlled) conditions for this molecule during transport across the tropopause. The SPURT data set is presently the most accurate and complete data set for many trace species in the LMS, and its main value is the simultaneous measurement of a suite of trace gases having different lifetimes and physical-chemical histories. It is thus very well suited for studies of atmospheric transport, for model validation, and for investigations of seasonal changes in the UT/LMS, as demonstrated in accompanying and elsewhere published studies.

Substitutional and orientational disorder in organic crystals: a symmetry-adapted ensemble model

Modelling of disorder in organic crystals is highly desirable since it would allow thermodynamic stabilities and other disorder-sensitive properties to be estimated for such systems. Two disordered organic molecular systems are modeled using a symmetry-adapted ensemble approach, in which the disordered system is treated as an ensemble of the configurations of a supercell with respect to substitution of one disorder component for another. Computation time is kept manageable by performing calculations only on the symmetrically inequivalent configurations. Calculations are presented on a substitutionally disordered system, the dichloro/dibromobenzene solid solution, and on an orientationally disordered system, eniluracil, and the resultant free energies, disorder patterns, and system properties are discussed. The results are found to be in agreement with experiment following manual removal of physically implausible configurations from ensemble averages, highlighting the dangers of a completely automated approach to organic crystal thermodynamics which ignores the barriers to equilibration once the crystal has been formed.