Regular Subgraphs in Graphs and Rooted Graphs and Definability in Monadic Second - Order Logic

We investigate the definability in monadic ∑₁¹ and monadic Π₁¹ of the problems REG_k, of whether there is a regular subgraph of degree k in some given graph, and XREG_k, of whether, for a given rooted graph, there is a regular subgraph of degree k in which the root has degree k, and their restrictions to graphs in which every vertex has degree at most k, namely REG_k^k and XREG_k^k, respectively, for k ≥ 2 (all our graphs are undirected). Our motivation partly stems from the fact (which we prove here) that REG_k^k and XREG_k^k are logspace equivalent to CONN and REACH, respectively, for k ≥ 3, where CONN is the problem of whether a given graph is connected and REACH is the problem of whether a given graph has a path joining two given vertices. We use monadic first - order reductions, monadic ∑₁¹ games and a recent technique due to Fagin, Stockmeyer and Vardi to almost completely classify whether these problems are definable in monadic ∑₁¹ and monadic Π₁¹, and we compare the definability of these problems (in monadic ∑₁¹ and monadic Π₁¹ with their computational complexity (which varies from solvable using logspace to NP - complete).     

Dyad beads and the combinatorial discovery of catalysts

Dyad beads, bearing both a substrate and a catalyst, were prepared to enable direct split and mix bead based screening for catalysis.     

Oxoneptunium(v) as part of the framework of a polyoxometalate

(NH4)14Na4[(Np3W4O15)(H2O)3(BiW9O33)3].62H2O (1) and (NH4)14.5Na3.5[(Np3W4O15)(H2O)3(SbW9O33)3].40.5H2O (2) each contain three neptunyl(v) moieties encapsulated within heteropolyoxotungstate frameworks in which axial {NpO2}+ oxygens form one face of a WO6 octahedron.     

The structures of higher boron halides B8X12(X = F, Cl, Br and I) by gas-phase electron diffraction and ab initio calculations

The structure of B8F12 has been shown by gas electron diffraction and computational methods (up to MP2/6-31+G*) to have the same highly asymmetric form observed in crystalline phases. The structure can be regarded as derived from a central B2 group, bridged by two BF2 groups to give a central B4 core that is folded, not planar, and with a very short bond [164.3 pm calculated, 164.2(19) pm experimental] along the fold line. There are also four terminal BF2 groups. One of the other four bonds in the core is consistently 20-30 pm longer than the others. This asymmetry has been attributed to many intra-molecular B...F interactions, particularly those between core boron atoms and fluorines of the terminal BF2 groups. Calculations for the chloro analogue lead to a structure similar to that for B8F12, but with the long core bond extended so that one of the bridging BCl2 groups may now be regarded as terminal. With bromine as the halogen the structure changes again, with one bromine atom taking up a bridging position. With iodine, this process continues further, and there are three bridging iodine atoms. However, in this case this is not the lowest energy structure, and instead a loosely associated dimer of B4I6 is preferred. In all these cases, and particularly with the heavier halogens, there are huge differences between the results obtained with different computational methods.     

Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.     

The phase behavior of a polymer‐fullerene bulk heterojunction system that contains bimolecular crystals

Polymer:fullerene blends have been widely studied as an inexpensive alternative to traditional silicon solar cells. Some polymer:fullerene blends, such as blends of poly(2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene (pBTTT) with phenyl‐c71‐butyric acid methyl ester (PC₇₁BM), form bimolecular crystals due to fullerene intercalation between the polymer side chains. Here we present the determination of the eutectic pBTTT:PC₇₁BM phase diagram using differential scanning calorimetry (DSC) and two‐dimensional grazing incidence X‐ray scattering (2D GIXS) with in‐situ thermal annealing. The phase diagram explains why the most efficient pBTTT:PC₇₁BM solar cells have 75–80 wt % PC₇₁BM since these blends lie in the center of the only room‐temperature phase region containing both electron‐conducting (PC₇₁BM) and hole‐conducting (bimolecular crystal) phases. We show that intercalation can be suppressed in 50:50 pBTTT:PC₇₁BM blends by using rapid thermal annealing to heat the blends above the eutectic temperature, which forces PC₇₁BM out of the bimolecular crystal, followed by quick cooling to kinetically trap the pure PC₇₁BM phase. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Characterization and genetic manipulation of peptide synthetases in Pseudomonas aeruginosa PAO1 in order to generate novel pyoverdines

PvdD, a nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1, incorporates two L-threonines into the siderophore pyoverdine. A pvdD mutant did not synthesize pyoverdine and lacked a high Mr iron-regulated cytoplasmic protein (IRCP). Analysis of other IRCPs and the P. aeruginosa genome enabled the remaining pyoverdine NRPSs to be identified. The pvdD mutation could be complemented in trans, enabling design of plasmid-based systems for the generation of novel pyoverdines. Introduction of a truncated pvdD gene resulted in attenuated forms of pyoverdine, and introduction of L-threonine-incorporating NRPSs from other organisms restored pyoverdine production to mutant cells. This is the first successful rational in vivo modification of NRPS modules outside of Bacillus subtilis. The systems employed did not allow incorporation of other residues into pyoverdine, indicating that there are multiple elements contributing toward substrate specificity in NRPSs.     

Reactions of N-heterocyclic carbenes (NHCs) with one-electron oxidants: possible formation of a carbene cation radical

One-electron oxidation of N-heterocyclic carbenes (NHCs) has been carried out using oxidising agents such as tetracyanoethylene (TCNE) and ferrocenium [Cp(2)Fe](+); the formation of carbene radical cations is postulated.