Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

The influence of viscous and latent heating on crystal-rich magma flow in a conduit

The flow dynamics of crystal-rich high-viscosity magma is likely to be strongly influenced by viscous and latent heat release. Viscous heating is observed to play an important role in the dynamics of fluids with temperature-dependent viscosities. The growth of microlite crystals and the accompanying release of latent heat should play a similar role in raising fluid temperatures. Earlier models of viscous heating in magmas have shown the potential for unstable (thermal runaway) flow as described by a Gruntfest number, using an Arrhenius temperature dependence for the viscosity, but have not considered crystal growth or latent heating. We present a theoretical model for magma flow in an axisymmetric conduit and consider both heating effects using Finite Element Method techniques. We consider a constant mass flux in a 1-D infinitesimal conduit segment with isothermal and adiabatic boundary conditions and Newtonian and non-Newtonian magma flow properties. We find that the growth of crystals acts to stabilize the flow field and make the magma less likely to experience a thermal runaway. The additional heating influences crystal growth and can counteract supercooling from degassing-induced crystallization and drive the residual melt composition back towards the liquidus temperature. We illustrate the models with results generated using parameters appropriate for the andesite lava dome-forming eruption at Soufriere Hills Volcano, Montserrat. These results emphasize the radial variability of the magma. Both viscous and latent heating effects are shown to be capable of playing a significant role in the eruption dynamics of Soufriere Hills Volcano. Latent heating is a factor in the top two kilometres of the conduit and may be responsible for relatively short-term (days) transients. Viscous heating is less restricted spatially, but because thermal runaway requires periods of hundreds of days to be achieved, the process is likely to be interrupted. Our models show that thermal evolution of the conduit walls could lead to an increase in the effective diameter of flow and an increase in flux at constant magma pressure.

Industrial radioactive barite scale: suppression of radium uptake by introduction of competing ions

Incorporation of radioactive isotopes during the formation of barite mineral scale is a widespread phenomenon occurring within the oil, mining and process industries. In a series of experiments radioactive barite/celestite solid solutions (SSBarite-Celcstite) have been synthesized under controlled conditions by the counter diffusion of Ra-226, Ba2+, Sr24+ and SO42- ions through a porous medium (silica gel), to investigate inhibiting effects in Ra uptake associated with the introduction of a competing ion (Sr2+). From characterization studies, the particle size and the morphology of the crystals appear to be related to the initial [Sr]/[Ba] molar ratio of the starting solution. Typically, systems richer in Sr produce smaller sized crystals and clusters characterized by a lower degree of order. The activity introduced to the system is mainly incorporated in the crystals generated from the barite/celestite solid solution as suggested by the activity profiles of the hydrogel columns analysed by gamma-spectrometry. There is a relationship between the initial [Sr]/[Ba] molar ratio of the starting solution and the activity exhibited by the synthesized crystals. An effective inhibition of the Ra-226 uptake during formation of the crystals (SSBarite-Celestite) was obtained through the introduction of a competing ion (Sr2+): the higher the initial [Sr]/[Ba] molar ratio of the starting solution, the lower the intensity of the activity peak in the crystals. (C) 2003 Published by Elsevier Ltd.

Problems with determining the particle size distribution of chalk soil and some of their implications

Particle size distribution (psd) is one of the most important features of the soil because it affects many of its other properties, and it determines how soil should be managed. To understand the properties of chalk soil, psd analyses should be based on the original material (including carbonates), and not just the acid-resistant fraction. Laser-based methods rather than traditional sedimentation methods are being used increasingly to determine particle size to reduce the cost of analysis. We give an overview of both approaches and the problems associated with them for analyzing the psd of chalk soil. In particular, we show that it is not appropriate to use the widely adopted 8 pm boundary between the clay and silt size fractions for samples determined by laser to estimate proportions of these size fractions that are equivalent to those based on sedimentation. We present data from field and national-scale surveys of soil derived from chalk in England. Results from both types of survey showed that laser methods tend to over-estimate the clay-size fraction compared to sedimentation for the 8 mu m clay/silt boundary, and we suggest reasons for this. For soil derived from chalk, either the sedimentation methods need to be modified or it would be more appropriate to use a 4 pm threshold as an interim solution for laser methods. Correlations between the proportions of sand- and clay-sized fractions, and other properties such as organic matter and volumetric water content, were the opposite of what one would expect for soil dominated by silicate minerals. For water content, this appeared to be due to the predominance of porous, chalk fragments in the sand-sized fraction rather than quartz grains, and the abundance of fine (<2 mu m) calcite crystals rather than phyllosilicates in the clay-sized fraction. This was confirmed by scanning electron microscope (SEM) analyses. "Of all the rocks with which 1 am acquainted, there is none whose formation seems to tax the ingenuity of theorists so severely, as the chalk, in whatever respect we may think fit to consider it". Thomas Allan, FRS Edinburgh 1823, Transactions of the Royal Society of Edinburgh. (C) 2009 Natural Environment Research Council (NERC) Published by Elsevier B.V. All rights reserved.

The role of gypsum in the reactions of phosphate with soils

The aim of this study was to examine the mechanisms by which gypsum increases the sorption of fertilizer-P in soils of and and semi-arid regions. Either gypsum or soil (Usher from the UK; pH 7.8, 7% organic matter, 21% CaCO3: Yasouj from Iran; pH 8.2, 1.4% OM, 18% CaCO3: Ghanimeh from Saudi Arabia; pH 7.8, 1% OM, 26% CaCO3, 13% gypsum) was shaken for 24 It with KH2PO4 solutions in 10 mM CaCl2. With gypsum, grinding increased sorption by a factor of about 3, and increase in pH from 5.6 to 7.5 greatly increased sorption. Scanning electron micrographs (SEM) and EDX quantitative analysis showed that small crystals of gypsum disappeared and roughly spherical particles of dicalcium phosphate (DCPD) were formed. Analysis of equilibrium Solutions showed, using GEOCHEM, that octa-calcium phosphate (OCP) coated the DCPD. For the soils, sorption was in the order Ghanimeh > Yasouj > Usher. Removal of gypsum from Ghanimeh reduced sorption, with precipitated gypsum having a greater effect than gypsum mixed physically with the soil. Addition to Usher had no effect. SEM and EDX could not be used in the soil matrix, but solubility analysis again showed that solutions were close to equilibrium with OCP. Usher was unresponsive to added gypsum, presumably because of its small sorption capacity and high organic matter content. In Ghanimeh and Yasouj soils, gypsum increased sorption by being a source of readily available Ca2+ (c) 2005 Elsevier B.V. All rights reserved.

Earthworms produce granules of intricately zoned calcite

Earthworms of the family Lumbricidae, which includes many common species, produce and secrete up to millimeter-sized calcite granules, and the intricate fine-scale zoning of their constituent crystals is unique for a biomineral. Granule calcite is produced by crystallization of amorphous calcium carbonate (ACC) that initially precipitates within the earthworm calciferous glands, then forms protogranules by accretion on quartz grain cores. Crystallization of ACC is mediated by migrating fluid films and is largely complete within 24 11 of ACC production and before granules leave the earthworm. Variations in the density of defects formed as a byproduct of trace element incorporation during calcite crystall growth have generated zoning that can be resolved by cathodoluminescence imaging at ultraviolet to blue wavelengths and using the novel technique of scanning electron microscope charge contrast imaging. Mapping of calcite crystal orientations by electron backscatter diffraction reveals an approximate radial fabric to the granules that reflects crystal growth from internal nucleation sites toward their margins. The survival within granules of ACC inclusions for months after they enter soils indicates that they crystallize only within the earthworm and in the presence of fluids containing biochemical catalysts. The earthworm probably promotes crystallization of ACC in order to prevent remobilization of the calcium carbonate by dissolution. Calcite granules vividly illustrate the role of transient precursors in biomineralization, but the underlying question of why earth-worms produce granules in volumes sufficient to have a measurable impact on soil carbon cycling remains to be answered.

Radar scattering by aggregate snowflakes

The radar scattering properties of realistic aggregate snowflakes have been calculated using the Rayleigh-Gans theory. We find that the effect of the snowflake geometry on the scattering may be described in terms of a single universal function, which depends only on the overall shape of the aggregate and not the geometry or size of the pristine ice crystals which compose the flake. This function is well approximated by a simple analytic expression at small sizes; for larger snowflakes we fit a curve to Our numerical data. We then demonstrate how this allows a characteristic snowflake radius to be derived from dual wavelength radar measurements without knowledge of the pristine crystal size or habit, while at the same time showing that this detail is crucial to using such data to estimate ice water content. We also show that the 'effective radius'. characterizing the ratio of particle volume to projected area, cannot be inferred from dual wavelength radar data for aggregates. Finally, we consider the errors involved in approximating snowflakes by 'air-ice spheres', and show that for small enough aggregates the predicted dual wavelength ratio typically agrees to within a few percent, provided some care is taken in choosing the radius of the sphere and the dielectric constant of the air-ice mixture; at larger sizes the radar becomes more sensitive to particle shape, and the errors associated with the sphere model are found to increase accordingly.

Model catalyst studies of the strong metal-support interaction: Surface structure identified by STM on Pd nanoparticles on TiO2(110)

Model catalysts of Pd nanoparticles and films on TiO2 (I 10) were fabricated by metal vapour deposition (MVD). Molecular beam measurements show that the particles are active for CO adsorption, with a global sticking probability of 0.25, but that they are deactivated by annealing above 600 K, an effect indicative of SMSI. The Pd nanoparticles are single crystals oriented with their (I 11) plane parallel to the surface plane of the titania. Analysis of the surface by atomic resolution STM shows that new structures have formed at the surface of the Pd nanoparticles and films after annealing above 800 K. There are only two structures, a zigzag arrangement and a much more complex "pinwheel" structure. The former has a unit cell containing 7 atoms, and the latter is a bigger unit cell containing 25 atoms. These new structures are due to an overlayer of titania that has appeared on the surface of the Pd nanoparticles after annealing, and it is proposed that the surface layer that causes the SMSI effect is a mixed alloy of Pd and Ti, with only two discrete ratios of atoms: Pd/Ti of 1: 1 (pinwheel) and 1:2 (zigzag). We propose that it is these structures that cause the SMSI effect. (c) 2005 Elsevier Inc. All rights reserved.

Retrieval of effective ice crystal size in the infrared: sensitivity study and global measurements from TIROS-N Operational Vertical Sounder

The difference between cirrus emissivities at 8 and 11 μm is sensitive to the mean effective ice crystal size of the cirrus cloud, De. By using single scattering properties of ice crystals shaped as planar polycrystals, diameters of up to about 70 μm can be retrieved, instead of up to 45 μm assuming spheres or hexagonal columns. The method described in this article is used for a global determination of mean effective ice crystal sizes of cirrus clouds from TOVS satellite observations. A sensitivity study of the De retrieval to uncertainties in hypotheses on ice crystal shape, size distributions, and temperature profiles, as well as in vertical and horizontal cloud heterogeneities shows that uncertainties can be as large as 30%. However, the TOVS data set is one of few data sets which provides global and long-term coverage. Having analyzed the years 1987–1991, it was found that measured effective ice crystal diameters De are stable from year to year. For 1990 a global median De of 53.5 μm was determined. Averages distinguishing ocean/land, season, and latitude lie between 23 μm in winter over Northern Hemisphere midlatitude land and 64 μm in the tropics. In general, larger Des are found in regions with higher atmospheric water vapor and for cirrus with a smaller effective emissivity.

Barley oxalate oxidase is a hexameric protein related to seed storage proteins: evidence from X-ray crystallography

The oxalate oxidase enzyme expressed in barley roots is a thermostable, protease-resistant enzyme that generates H2O2. It has great medical importance because of its use to assay plasma and urinary oxalate, and it has also been used to generate transgenic, pathogen-resistant crops. This protein has now been purified and three types of crystals grown. X-ray analysis shows that the symmetry present in these crystals is consistent with a hexameric arrangement of subunits, probably a trimer of dimers. This structure may be similar to that found in the related seed storage proteins.

Anthraquinone catalysis in the glucose-driven reduction of indigo to leuco-indigo

Anthraquinone immobilised onto the surface of indigo microcrystals enhances the reductive dissolution of indigo to leuco-indigo. Indigo reduction is driven by glucose in aqueous NaOH and a vibrating gold disc electrode is employed to monitor the increasing leuco-indigo concentration with time. Anthraquinone introduces a strong catalytic effect which is explained by invoking a molecular "wedge effect'' during co-intercalation of Na+ and anthraquinone into the layered indigo crystal structure. The glucose-driven indigo reduction, which is in effective in 0.1 M NaOH at 65 degrees C, becomes facile and goes to completion in the presence of anthraquinone catalyst. Electron microscopy of indigo crystals before and after reductive dissolution confirms a delamination mechanism initiated at the edges of the plate-like indigo crystals. Catalysis occurs when the anthraquinone-indigo mixture reaches a molar ratio of 1:400 (at 65 degrees C; corresponding to 3 mu M anthraquinone) with excess of anthraquinone having virtually no effect. A strong temperature effect ( with a composite E-A approximate to 120 kJ mol(-1)) is observed for the reductive dissolution in the presence of anthraquinone. The molar ratio and temperature effects are both consistent with the heterogeneous nature of the anthraquinone catalysis in the aqueous reaction mixture.

Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport

YcdB is a periplasmic haem-containing protein from Escherichia coli that has a potential role in iron transport. It is currently the only reported haem-containing Tat-secreted substrate. Here, the overexpression, purification, crystallization and structure determination at 2.0 angstrom resolution are reported for the apo form of the protein. The apo-YcdB structure resembles those of members of the haem-dependent peroxidase family and thus confirms that YcdB is also a member of this family. Haem-soaking experiments with preformed apo-YcdB crystals have been optimized to successfully generate haem-containing YcdB crystals that diffract to 2.9 angstrom. Completion of model building and structure refinement are under way.

An in situ time-dependent study of the photodimerisation of chloro-derivatives of trans-cinnamic acid using infrared microspectroscopy with a synchrotron radiation source

The photodimerisation of single crystals of substituted cinnamic acid has been monitored continuously by infrared microscopy using a synchrotron source. The beta-form of 2,4-dichloro-trans-cinnamic acid dimerises under ultraviolet irradiation to form the corresponding beta-truxinic acid derivative in a reaction which follows strictly first order kinetics. By contrast the corresponding reactions in single crystals of beta-2-chloro-trans-cinnamic acid and beta-4-chloro-trans-cinnamic acid deviate somewhat from first order kinetics as a result of solid-state effects. In all three cases the reactions proceed smoothly from monomer to dimer with no hint of any reaction intermediate.

A SAXS study of flow alignment of thermotropic liquid crystal mixtures

We report on the capillary flow behaviour of thermotropic liquid crystal mixtures containing 4-n-octyl-4'-cyanobiphenyl (8CB) and 4-n-pentyl-4'-cyanobiphenyl (5CB). The liquid crystal mixtures are studied in the Nematic (N) and Smectic (SA) phases at room temperature. Polarised optical microscopy (POM), rheology and simultaneous X-ray diffraction (XRD)/capillary flow experiments are performed to characterise the system. Polarised optical microscopy reveals a dramatic change in optical texture when the 5CB content is increased from 20 to 30% in the mixtures. X-ray diffraction results show that the system goes through a SA-N phase transition, such that the mixtures are smectic for 10-20% 5CB and nematic for 30-90% 5CB. Smectic mixtures flow with the layers aligned along the flow direction (mesogens perpendicular to flow) while nematic mixtures flow with the mesogens aligned in the flow direction. Simultaneous XRD/shear flow experiments show that the SA-N transition is independent of the flow rate in the range 1-6 ml min-1. The correlation length of the liquid crystal order decreases with increasing 5CB content. Rheology is used to prove that the correlation length behaviour is related to a reduction in the viscosity of the mixture.

Helices, chirality and interpenetration: the versatility and remarkable interconversion of silver-copper cyanide frameworks

The structural transformations between cesium silver-copper cyanides under modest conditions, both in solution and in the solid state, are described. Three new cesium silver(I) copper(I) cyanides with three-dimensional (3-D) framework structures were prepared as single crystals from a one-pot reaction initially heated under hydrothermal conditions. The first product to appear, Cs3Ag2Cu3(CN)(8) (I), when left in contact with the supernatant produced CsAgCu(CN)(3) (II) and CsAgCu(CN)(3)center dot 1/3H(2)O (III) over a few months via a series of thermodynamically controlled cascade reactions. Crystals of the hydrate (III) can be dehydrated to polycrystalline CsAgCu(CN)(3) (II) on heating at 100 degrees C in a remarkable solid-state transformation involving substantial breaking and reconnection of metal-cyanide linkages. Astonishingly, the conversion between the two known polymorphs of CsAg2Cu(CN)(4), which also involves a major change in connectivity and topology, occurs at 180 degrees C as a single-crystal to single-crystal transformation. Structural features of note in these materials include the presence of helical copper-cyanide chains in (I) and (II), which in the latter compound produce a chiral material. In (II) and (III), the silver-copper cyanide networks are both self- and interpenetrating, features also seen in the known polymorphs of CsAg2Cu(CN)(4).