D. Fisher

Adsorption site determination for oxygen on Al(111) using normal incidence standing X-ray wavefield absorption

Abstract The structure of the chemisorption phase of oxygen on Al(111) has been studied using normal incidence standing X-ray wavefield absorption (NISXW) at the (111) and the ( 1 11) Bragg reflection conditions. The resulting Oue5f8Al layer spacings in these two directions gives a measure of both the absorbate-substrate layer spacing perpendicular the surface, and the adsorption site. At the lowest coverages of oxygen, the results indicate that the adsorbed oxygen atoms occupy “fcc” hollow sites (i.e. directly above Al atoms in the third layer of the substrate) at a layer spacing of 0.70 A. This result agrees well with previous SEXAFS results and with later LEED work, and reinforces the view that early LEED results giving much larger layer spacings were in error. The new results also indicate that this site is occupied at the lowest coverages of the chemisorbed phase, and that there is no evidence for a previously proposed precursor underlayer. Similar NISXW measurements taken from a surface containing a significant fraction of the subsequent surface oxide phase indicate that the oxygen atoms in this structure retain the same coordination, as well as bondlength, relative to the Al substrate, and favour a model in which the majority of the overlayer oxygen atoms of the chemisorbed phase retain their overlayer sites.

Characterization of a Nudix hydrolase from Deinococcus radiodurans with a marked specificity for (deoxy)ribonucleoside 5'-diphosphates

BackgroundNudix hydrolases form a protein family whose function is to hydrolyse intracellular nucleotides and so regulate their levels and eliminate potentially toxic derivatives. The genome of the radioresistant bacterium Deinococcus radiodurans encodes 25 nudix hydrolases, an unexpectedly large number. These may contribute to radioresistance by removing mutagenic oxidised and otherwise damaged nucleotides. Characterisation of these hydrolases is necessary to understand the reason for their presence. Here, we report the cloning and characterisation of the DR0975 gene product, a nudix hydrolase that appears to be unique to this organism.ResultsThe DR0975 gene was cloned and expressed as a 20 kDa histidine-tagged recombinant product in Escherichia coli. Substrate analysis of the purified enzyme showed it to act primarily as a phosphatase with a marked preference for (deoxy)nucleoside 5-diphosphates (dGDP > ADP > dADP > GDP > dTDP > UDP > dCDP > CDP). Km for dGDP was 110 μM and kcat was 0.18 s-1 under optimal assay conditions (pH 9.4, 7.5 mM Mg2+). 8-Hydroxy-2-deoxyguanosine 5-diphosphate (8-OH-dGDP) was also a substrate with a Km of 170 μM and kcat of 0.13 s-1. Thus, DR0975 showed no preference for 8-OH-dGDP over dGDP. Limited pyrophosphatase activity was also observed with NADH and some (di)adenosine polyphosphates but no other substrates. Expression of the DR0975 gene was undetectable in logarithmic phase cells but was induced at least 30-fold in stationary phase. Superoxide, but not peroxide, stress and slow, but not rapid, dehydration both caused a slight induction of the DR0975 gene.ConclusionNucleotide substrates for nudix hydrolases conform to the structure NDP-X, where X can be one of several moieties. Thus, a preference for (d)NDPs themselves is most unusual. The lack of preference for 8-OH-dGDP over dGDP as a substrate combined with the induction in stationary phase, but not by peroxide or superoxide, suggests that the function of DR09075 may be to assist in the recycling of nucleotides under the very different metabolic requirements of stationary phase. Thus, if DR0975 does contribute to radiation resistance, this contribution may be indirect.

Structural investigation of Rb adsorption on Al(111) using normal incidence standing x‐ray wavefield absorption triangulation

The adsorption site, and adsorbate‐substrate bondlength, has been investigated for the adsorption system Al(111)/Rb, using normal incidence standing x‐ray wavefield absorption (NISXW), over a range of coverages from 0.12 to 0.33 ML including the ordered (2×2) and (√3×√3)R30° phases. By measuring both (111) and (111) Bragg reflections in NISXW we obtain Rb–Al layer spacings in two real space directions and can therefore fully determine the adsorption structure by triangulation. For all phases we find adsorption in the atop sites, with a coverage‐independent bondlength corresponding to an effective radius for the adsorbed Rb of 1.70±0.10 A, significantly closer to the ionic (1.48 A) than the metallic (2.43 A) value. The NISXW results also show that the adsorbed Rb atoms have large vibrational amplitudes parallel to the surface which may be associated with the atop site adsorption.

Measurement of the overlayer-substrate spacing for potassium on Ni{111} as a function of coverage

Abstract The overlayer-substrate distance for potassium adsorbed on Ni{111} was measured for four different coverages by measuring the low-energy electron diffraction (LEED) specular beam intensities and analyzing them using a constant-momentum-transfer averaging (CMTA) technique. The overlayer-substrate spacing was found to be 2.7 ± 0.1 A for the four coverages measured, namely 0.13, 0.20, 0.25 and 0.275. This spacing corresponds to a potassium radius of 1.46 ± 0.10 A for the 0.25 coverage measurement, which is between the ionic and metallic radii for potassium of 1.33 and 2.38 A, respectively. This result suggests that the nature of the bonding of the potassium overlayer atoms to the substrate does not change appreciably in this coverage range. We propose an alternative criterion to replace the labels “ionic”, “covalent” and “metallic” for describing the bonding of the alkali metal adatoms to the substrate which does not depend on the labeling of electrons and which is easy to compare to calculations of the charge densities for these systems.

Characterization of the Mn2+-stimulated (di)adenosine polyphosphate hydrolase encoded by the Deinococcus radiodurans DR2356 nudix gene

The DR2356 nudix hydrolase gene from Deinococcus radiodurans has been cloned and the product expressed as an 18xa0kDa histidine-tagged protein. The enzyme hydrolysed adenosine and diadenosine polyphosphates, always generating ATP as one of the initial products. ATP and other (deoxy)nucleoside triphosphates were also substrates, yielding (d)NDP and Pi as products. The DR2356 protein was most active at pH 8.6–9.0 and showed a strong preference for Mn2+ as activating cation. Mg2+ ions at 15xa0mM supported only 5% of the activity achieved with 2xa0mM Mn2+. Km and kcat values for diadenosine tetra-, penta- and hexaphosphates were 2.0, 2.4 and 1.1xa0μM and 11.4, 28.6 and 12.0xa0s−1, respectively, while for GTP they were 20.3xa0μM and 1.8xa0s−1, respectively. The Km for adenosine 5′-pentaphosphate was <1xa0μM. Expression analysis showed the DR2356 gene to be induced eight- to ninefold in stationary phase and in cells subjected to slow dehydration plus rehydration. Superoxide (but not peroxide) treatment and rapid dehydration caused a two-to threefold induction. The Mn-requirement and induction in stationary phase suggest that DR2356 may have a specific role in maintenance mode metabolism in stationary phase as Mn2+ accumulates.

Electron paramagnetic resonance studies of nitrogen interstitial defects in diamond

We report on electron paramagnetic resonance (EPR) studies of nitrogen doped diamond that has been (15)N enriched, electron irradiated and annealed. EPR spectra from two new nitrogen containing [Formula: see text] defects are detected and labelled WAR9 and WAR10. We show that the properties of these defects are consistent with them being the ⟨001⟩-nitrogen split interstitial and the ⟨001⟩-nitrogen split interstitial-⟨001⟩-carbon split interstitial pair, respectively. We also provide an explanation for why these defects have previously eluded discovery.

Electron paramagnetic resonance of the

Nitrogen is the dominant impurity in the majority of natural and synthetic diamonds, and the family of nitrogen vacancy-type (

\mathrm{N_{2}V^{-}}

mathrm{N_{n}V}

defect in

) defects are crucial in our understanding of defect dynamics in these diamonds. A significant gap is the lack of positive identification of

\mathrm{^{15}N}

mathrm{N_{2}V}^{-}