Chemical ligation by ring opening of oxo-thiomorpholines

The invention discloses processes for preparing compounds comprising an #-amino acid motif. The compounds are useful in e.g. the chemical ligation of peptides.

Modulation of visually evoked cortical fMRI responses by phase of ongoing occipital alpha oscillations

Using simultaneous electroencephalography as a measure of ongoing activity and functional magnetic resonance imaging (fMRI) as a measure of the stimulus-driven neural response, we examined whether the amplitude and phase of occipital alpha oscillations at the onset of a brief visual stimulus affects the amplitude of the visually evoked fMRI response. When accounting for intrinsic coupling of alpha amplitude and occipital fMRI signal by modeling and subtracting pseudo-trials, no significant effect of prestimulus alpha amplitude on the evoked fMRI response could be demonstrated. Regarding the effect of alpha phase, we found that stimuli arriving at the peak of the alpha cycle yielded a lower blood oxygenation level-dependent (BOLD) fMRI response in early visual cortex (V1/V2) than stimuli presented at the trough of the cycle. Our results therefore show that phase of occipital alpha oscillations impacts the overall strength of a visually evoked response, as indexed by the BOLD signal. This observation complements existing evidence that alpha oscillations reflect periodic variations in cortical excitability and suggests that the phase of oscillations in postsynaptic potentials can serve as a mechanism of gain control for incoming neural activity. Finally, our findings provide a putative neural basis for observations of alpha phase dependence of visual perceptual performance.

In situ preservation of wetland heritage: hydrological and chemical change in the burial environment of the Somerset Levels, UK.

In Situ preservation is a core strategy for the conservation and management of waterlogged remains at wetland sites. Inorganic and organic remains can, however, quickly become degraded, or lost entirely, as a result of chemical or hydrological changes. Monitoring is therefore crucial in identifying baseline data for a site, the extent of spatial and or temporal variability, and in evaluating the potential impacts of these variables on current and future In Situ preservation potential. Since August 2009, monthly monitoring has taken place at the internationally important Iron Age site of Glastonbury Lake Village in the Somerset Levels, UK. A spatial, stratigraphic, and analytical approach to the analysis of sediment horizons and monitoring of groundwater chemistry, redox potential, water table depth and soil moisture (using TDR) was used to characterize the site. Significant spatial and temporal variability has been identified, with results from water-table monitoring and some initial chemical analysis from Glastonbury presented here. It appears that during dry periods parts of this site are at risk from desiccation. Analysis of the chemical data, in addition to integrating the results from the other parameters, is ongoing, with the aim of clarifying the risk to the entire site.

Normal mode Rossby waves and their effects on chemical composition in the late summer stratosphere

During past MANTRA campaigns, ground-based measurements of several long-lived chemical species have revealed quasi-periodic fluctuations on time scales of several days. These fluctuations could confound efforts to detect long-term trends from MANTRA, and need to be understood and accounted for. Using the Canadian Middle Atmosphere Model, we investigate the role of dynamical variability in the late summer stratosphere due to normal mode Rossby waves and the impact of this variability on fluctuations in chemical species. Zonal wavenumber 1, westward travelling waves are considered with average periods of 5, 10 and 16 days. Time-lagged correlations between the temperature and nitrous oxide, methane and ozone fields are calculated in order to assess the possible impact of these waves on the chemical species. Using Fourier-wavelet decomposition and correlating the fluctuations between the temperature and chemical fields, we determine that variations in the chemical species are well-correlated with the 5- and 10-day waves between 30 and 60 km, although the nature of the correlations depend strongly on altitude. Interannual variability of the waves is also examined.

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.

Correlations of long-lived chemical species in a middle atmosphere general circulation model

Correlations between various chemical species simulated by the Canadian Middle Atmosphere Model, a general circulation model with fully interactive chemistry, are considered in order to investigate the general conditions under which compact correlations can be expected to form. At the same time, the analysis serves to validate the model. The results are compared to previous work on this subject, both from theoretical studies and from atmospheric measurements made from space and from aircraft. The results highlight the importance of having a data set with good spatial coverage when working with correlations and provide a background against which the compactness of correlations obtained from atmospheric measurements can be confirmed. It is shown that for long-lived species, distinct correlations are found in the model in the tropics, the extratropics, and the Antarctic winter vortex. Under these conditions, sparse sampling such as arises from occultation instruments is nevertheless suitable to define a chemical correlation within each region even from a single day of measurements, provided a sufficient range of mixing ratio values is sampled. In practice, this means a large vertical extent, though the requirements are less stringent at more poleward latitudes.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

High resolution simulation of recent Arctic and Antarctic stratospheric chemical ozone loss compared to observations

Simulations of polar ozone losses were performed using the three-dimensional high-resolution (1∘ × 1∘) chemical transport model MIMOSA-CHIM. Three Arctic winters 1999–2000, 2001–2002, 2002–2003 and three Antarctic winters 2001, 2002, and 2003 were considered for the study. The cumulative ozone loss in the Arctic winter 2002–2003 reached around 35% at 475 K inside the vortex, as compared to more than 60% in 1999–2000. During 1999–2000, denitrification induces a maximum of about 23% extra ozone loss at 475 K as compared to 17% in 2002–2003. Unlike these two colder Arctic winters, the 2001–2002 Arctic was warmer and did not experience much ozone loss. Sensitivity tests showed that the chosen resolution of 1∘ × 1∘ provides a better evaluation of ozone loss at the edge of the polar vortex in high solar zenith angle conditions. The simulation results for ozone, ClO, HNO3, N2O, and NO y for winters 1999–2000 and 2002–2003 were compared with measurements on board ER-2 and Geophysica aircraft respectively. Sensitivity tests showed that increasing heating rates calculated by the model by 50% and doubling the PSC (Polar Stratospheric Clouds) particle density (from 5 × 10−3 to 10−2 cm−3) refines the agreement with in situ ozone, N2O and NO y levels. In this configuration, simulated ClO levels are increased and are in better agreement with observations in January but are overestimated by about 20% in March. The use of the Burkholder et al. (1990) Cl2O2 absorption cross-sections slightly increases further ClO levels especially in high solar zenith angle conditions. Comparisons of the modelled ozone values with ozonesonde measurement in the Antarctic winter 2003 and with Polar Ozone and Aerosol Measurement III (POAM III) measurements in the Antarctic winters 2001 and 2002, shows that the simulations underestimate the ozone loss rate at the end of the ozone destruction period. A slightly better agreement is obtained with the use of Burkholder et al. (1990) Cl2O2 absorption cross-sections.

Quantification of chemical and physical processes influencing ozone during long-range transport using a trajectory ensemble

During long-range transport, many distinct processes – including photochemistry, deposition, emissions and mixing – contribute to the transformation of air mass composition. Partitioning the effects of different processes can be useful when considering the sensitivity of chemical transformation to, for example, a changing environment or anthropogenic influence. However, transformation is not observed directly, since mixing ratios are measured, and models must be used to relate changes to processes. Here, four cases from the ITCT-Lagrangian 2004 experiment are studied. In each case, aircraft intercepted a distinct air mass several times during transport over the North Atlantic, providing a unique dataset and quantifying the net changes in composition from all processes. A new framework is presented to deconstruct the change in O3 mixing ratio (Δ O3) into its component processes, which were not measured directly, taking into account the uncertainty in measurements, initial air mass variability and its time evolution. The results show that the net chemical processing (Δ O3chem) over the whole simulation is greater than net physical processing (Δ O3phys) in all cases. This is in part explained by cancellation effects associated with mixing. In contrast, each case is in a regime of either net photochemical destruction (lower tropospheric transport) or production (an upper tropospheric biomass burning case). However, physical processes influence O3 indirectly through addition or removal of precursor gases, so that changes to physical parameters in a model can have a larger effect on Δ O3chem than Δ O3phys. Despite its smaller magnitude, the physical processing distinguishes the lower tropospheric export cases, since the net photochemical O3 change is −5 ppbv per day in all three cases. Processing is quantified using a Lagrangian photochemical model with a novel method for simulating mixing through an ensemble of trajectories and a background profile that evolves with them. The model is able to simulate the magnitude and variability of the observations (of O3, CO, NOy and some hydrocarbons) and is consistent with the time-average OH following air-masses inferred from hydrocarbon measurements alone (by Arnold et al., 2007). Therefore, it is a useful new method to simulate air mass evolution and variability, and its sensitivity to process parameters.

Interaction of anthocyanins with human serum albumin: influence of pH and chemical structure on binding

The affinity of anthocyanins for human serum albumin (HSA) was determined by a fluorescence quenching method. The effects of pH and structure of anthocyanins on the binding constants were studied. The constants for binding of anthocyanins to HSA ranged from 1.08 x 10^5 M-1 to 13.16 x 10^5 M-1. A hydrophobic effect at acidic pH was shown by the relatively high positive entropy values under the conditions studied. Electrostatic interactions including hydrogen bonding contributed to the binding at pH 7.4. The effect of structure of anthocyanins on the affinity was pH dependent, particularly the effect of additional hydroxyl substituents. Hydroxyl substituents and glycosylation of anthocyanins decreased the affinity for binding to HSA at lower pH (especially pH 4), but increased the strength of binding at pH 7.4. In contrast, methylation of a hydroxyl group enhanced the binding at acidic pH, while this substitution reduced the strength of binding at pH 7.4. This paper has shown that changes in anthocyanin structure or reductions in pH, which may occur in the region of inflammatory sites, have an effect of the binding of anthocyanins to HSA.

Complex dynamics in simple systems with periodic parameter oscillations

We study systems with periodically oscillating parameters that can give way to complex periodic or nonperiodic orbits. Performing the long time limit, we can define ergodic averages such as Lyapunov exponents, where a negative maximal Lyapunov exponent corresponds to a stable periodic orbit. By this, extremely complicated periodic orbits composed of contracting and expanding phases appear in a natural way. Employing the technique of ϵ-uncertain points, we find that values of the control parameters supporting such periodic motion are densely embedded in a set of values for which the motion is chaotic. When a tiny amount of noise is coupled to the system, dynamics with positive and with negative nontrivial Lyapunov exponents are indistinguishable. We discuss two physical systems, an oscillatory flow inside a duct and a dripping faucet with variable water supply, where such a mechanism seems to be responsible for a complicated alternation of laminar and turbulent phases.

High-speed Keck spectroscopy of flares and oscillations in AE Aquarii

Using high-time-resolution (72 ms) spectroscopy of AE Aqr obtained with LRIS on Keck II we have determined the spectrum and spectral evolution of a small flare. Continuum and integrated line fluxes in the flare spectrum are measured, and the evolution of the flare is parametrized for future comparison with detailed models of the flares. We find that the velocities of the flaring components are consistent with those previously reported for AE Aqr by Welsh, Horne & Gomer and Horne. The characteristics of the 33-s oscillations are investigated: we derive the oscillation amplitude spectrum, and from that determine the spectrum of the heated regions on the rotating white dwarf. Blackbody fits to the major and minor pulse spectra and an analysis of the emission-line oscillation properties highlight the shortfalls in the simple hotspot model for the oscillations.

Fireballs and oscillations in AE Aqr

From rapid spectroscopy of AE Aqr we determined the variable component of a flare spectrum. The hot spot model is inconsistent with the oscillation amplitude spectra, line oscillations require a more detailed model. This work will be submitted shortly to MNRAS.