Low energy electron induced damage to plasmid DNA pQE30

Low energy electrons (LEEs) are produced in copious amounts by the primary radiation used in radiation therapy. The damage caused to the DNA by these secondary electrons in the energy range 5-22 eV has been studied to understand their possible role in radiation induced damage. Electrons are irradiated on dried films of plasmid DNA (pQE30) and analysed using agarose gel electrophoresis. Single strand breaks (SSBs) induced by LEE to supercoiled plasmid DNA show resonance structures at 7, 12, and 15 eV for low doses and 6, 10, and ～18 eV at saturation doses. The present measurements have an overall agreement with the literature that LEEs resonantly induce SSBs in DNA. Resonant peaks in the SSBs induced by LEEs at 7, 12, and 15 eV with the lowest employed dose in the current study are somewhat different from those reported earlier by two groups. The observed differences are perhaps related to the irradiation dose, conditions and the nature of DNA employed, which is further elaborated.     

Metalated 1, 3‐Azaphospholes: η1‐(1H‐1, 3‐Benzazaphosphole‐P)M(CO)5 and μ2‐[(1, 3‐Benzazaphospholide‐P)(cyclopentadienide)nickel] Complexes

1H‐1, 3‐Benzazaphospholes react with M(CO)₅(THF) (M = Cr, Mo, W) to give thermally and relatively air stable η¹‐(1H‐1, 3‐Benzazaphosphole‐P)M(CO)₅ complexes. The ¹H‐ and ¹³C‐NMR‐data are in accordance with the preservation of the phosphaaromatic π‐system of the ligand. The strong upfield ³¹P coordination shift, particularly of the Mo and W complexes, forms a contrast to the downfield‐shifts of phosphine‐M(CO)₅ complexes and classifies benzazaphospholes as weak donor but efficient acceptor ligands. Nickelocene reacts as organometallic species with metalation of the NH‐function. The resulting ambident 1, 3‐benzazaphospholide anions prefer a μ₂‐coordination of the η⁵‐CpNi‐fragment at phosphorus to coordination at nitrogen or a η³‐heteroallyl‐η⁵‐CpNi‐semisandwich structure. This is shown by characteristic NMR data and the crystal structure analysis of a η⁵‐CpNi‐benzazaphospholide. The latter is a P‐bridging dimer with a planar Ni₂P₂ ring and trans‐configuration of the two planar heterocyclic phosphido ligands arranged perpendicular to the four‐membered ring.     

Solvent Vapor Annealing of Block Copolymers in Confined Topographies: Commensurability Considerations for Nanolithography

The directed self‐assembly of block copolymer (BCP) materials in topographically patterned substrates (i.e., graphoepitaxy) is a potential methodology for the continued scaling of nanoelectronic device technologies. In this Communication, an unusual feature size variation in BCP nanodomains under confinement with graphoepitaxially aligned cylinder‐forming poly(styrene)‐block‐poly(4‐vinylpyridine) (PS‐b‐P4VP) BCP is reported. Graphoepitaxy of PS‐b‐P4VP BCP line patterns (C_II) is accomplished via topo­graphy in hydrogen silsequioxane (HSQ) modified substrates and solvent vapor annealing (SVA). Interestingly, reduced domain sizes in features close to the HSQ guiding features are observed. The feature size reduction is evident after inclusion of alumina into the P4VP domains followed by pattern transfer to the silicon substrate. It is suggested that this nano­domain size perturbation is due to solvent swelling effects during SVA. It is proposed that using a commensurability value close to the solvent vapor annealed periodicity will alleviate this issue leading to uniform nanofins.

     

Embedding optimization in computational science workflows

Workflows support the automation of scientific processes, providing mechanisms that underpin modern computational science. They facilitate access to remote instruments, databases and parallel and distributed computers. Importantly, they allow software pipelines that perform multiple complex simulations (leveraging distributed platforms), with one simulation driving another. Such an environment is ideal for computational science experiments that require the evaluation of a range of different scenarios “in silico” in an attempt to find ones that optimize a particular outcome. However, in general, existing workflow tools do not incorporate optimization algorithms, and thus whilst users can specify simulation pipelines, they need to invoke the workflow as a stand-alone computation within an external optimization tool. Moreover, many existing workflow engines do not leverage parallel and distributed computers, making them unsuitable for executing computational science simulations. To solve this problem, we have developed a methodology for integrating optimization algorithms directly into workflows. We implement a range of generic actors for an existing workflow system called Kepler, and discuss how they can be combined in flexible ways to support various different design strategies. We illustrate the system by applying it to an existing bio-engineering design problem running on a Grid of distributed clusters.     

Sulfur and selenium derivatives of 2-phosphaindolizines

The 2-phosphaindolizines 1 react with hydrogen sulfide and elemental sulfur to give the new zwitterionic heterocyclic systems 2 of the N-pyridiniomethyl dithiophosphinate type. In contrast, no reaction is observed with sulfur alone. MeI methylates 2e,f at sulfur. The analogous pyridiniodiselenophosphinate 5 results from the reaction of 1a with 1,3,2,4-diselenadiphosphetane-2,4-diselenide, 4a, in the absence of an additional base. As a further product, the perselenophosphinic anhydride 6 is identified. In the presence of triethylamine, 1a reacts with each of the diselenides 4a–c to give the new triethylammonium diselenophosphinates 7a–c, respectively. This reaction can be extended to 1-aza-2-phosphaindolizine, 8, which yields with each of 4a,b and NEt₃ the diselenophosphinates 9a,b, respectively. The anhydride 6 and the diselenophosphinates 7 and 9 result from an electrophilic substitution at the phosphaindolizine ring. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:445–452, 1998     

Synthesis of the 6-O-methyl-D-glycero-α-L-gluco-heptopyranose moiety present in the capsular polysaccharide from Campylobacter jejuni NCTC 11168

The first synthesis of the 6-O-methyl-D-glycero-α-L-gluco-heptopyranose moiety present in the capsular polysaccharide from Campylobacter jejuni NCTC 11168 is reported. The target (1) was synthesized as the 8-aminooctyl glycoside and then conjugated to bovine serum albumin (BSA) for the generation of antibodies recognizing this motif. Heptose 1 was obtained from D-galactose via a series of galactofuranose derivatives.