Self-assembly of a set of hydrophilic-solvophobic-hydrophobic coil-rod-coil molecules based on perylene diimide.

The self-assembly and the resulting morphology of a set of asymmetrically substituted perylene diimide is discussed. We synthesized perylene diimides with hydrophilic Jeffamine® (PEO/PPO co-oligomer) attached to the imide nitrogen on one side and (hydrophobic) alkyl chains of different lengths on the other. Although studies on asymmetrically substituted perylene diimides have been reported by various authors, both side chains in this work are linear and we discuss the effect of the length of the hydrophobic alkyl side chain on the self-assembly in water and aqueous mixtures and the resulting morphology. We find that self-assembly occurs in water in a range of concentrations (from 10(-7) to 10(-4) M), and the mode of packing of the H-stacked molecules changes with concentration for the propyl substitution. Although self-assembly does not occur in non-aqueous solvents such as acetone, it does upon addition of water. While other authors observed nano-belts and nano-fibers with asymmetrically substituted perylene diimides, the morphology of drop-cast films in our work consists of folded sheets and hollow tubes, of a few microns in diameter. Such folding in a non-chiral system such as the present case is attributed to predominant asymmetry of interactions between the molecules in the three directions, as we discussed in our previous work on an hydrogen bonded system (S. Khanna, M. K. Khan and P. Sundararajan, Langmuir, 2009, 25, 13183-13193).

Impact of chaos and Brownian diffusion on irreversibility in Stokes flows.

We study a reversal process in Stokes flows in the presence of weak diffusion in order to clarify the distinct effects that chaotic flows have on the loss of reversibility relative to nonchaotic flows. In all linear flows, including a representation of the baker's map, we show that the decay of reversibility presents universal properties. In nonlinear chaotic and nonchaotic flows, we show that this universality breaks down due to the distribution of strain rates. In the limit of infinitesimal diffusivity, we predict qualitatively distinct behavior in the chaotic case.

CAP: conformation angles package-displaying the conformation angles of side chains in proteins.

SUMMARY: A graphics package has been developed to display all side chain conformation angles of the user selected residue in a given protein structure. The proposed package is incorporated with all the protein structures (solved using X-ray diffraction and NMR spectroscopy) available in the Protein Data Bank. The package displays the multiple conformations adopted by a single amino acid residue whose structure is solved and refined at very high resolution. In addition, it shows the percentage distribution of the side chain conformation angles in different rotameric states. AVAILABILITY: http://144.16.71.146/cap/

Ramachandran plot on the web.

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

Transposable element interactions in insects: crossmobilization of hobo and Hermes.

There are four non-drosophilid insect gene vector systems available that have been constructed from the short inverted repeat-type transposable elements Minos, piggyBac, mariner and Hermes. These elements (with the possible exception of piggyBac) are members of transposable element families that appear to be widespread in nature. Because these transposable element families are large it is possible that an insect species targeted for transformation will contain related transposable elements. The data presented here begin to address directly the question of interaction between diverged but related members of transposable element families. We tested the ability of the hAT elements hobo and Hermes to interact and cause crossmobilization. Using plasmid-based and chromosome-based element mobility assays we found that the terminal sequences of hobo and Hermes were almost equally good substrates for hobo transposase. However, this ability to crossmobilize was not reciprocal. Hermes transposase was only rarely able to cause the excision of hobo elements from plasmids and was never observed from germline chromosomes. These results have important implications for transgenic insect studies in the future.

Chiral poly(beta-hydroxyalkanoates): an adaptable helix influenced by the alkane side-chain.

Bacterial copolyesters of poly(beta-hydroxyalkanoates) (PHA) with average side-chain lengths between C5 and C7 crystallize as a 21 helix in an orthorhombic lattice with two molecules per unit cell. The fibre repeat, or c dimension, is 4.55 A on average, compared with 5.96 and 5.56 A for poly(beta-hydroxybutyrate) (PHB) and poly(beta-hydroxyvalerate) (PHV), respectively. This collapse of the c dimension while maintaining the 21 helical symmetry may be thought of as crystallization driven by side-chain packing influences. This class of PHA with homologous hydrocarbon side-chains must form ordered sheets with the extended alkane branches in polyethylene-like domains. The melting point, glass transition temperature and fibre repeat change regularly as a function of average number of side-chain carbons for the whole family of PHA. X-ray diffraction of a melt-crystallized PHA indicated a maximum crystallinity of about 25%, achieved only after several hours at room temperature. Compared with P(HB-co-HV) polyesters, the stress-strain curves of PHA polyesters studied are typical of elastomers. 13C-n.m.r. spectra and relaxation times of the bulk phase amorphous regions of these polymers demonstrate the high degree of motional freedom of the side-chains and the significantly slower motion for the backbone carbons. 13C n.m.r. was also used to estimate the percentage crystallinity which is in agreement with the X-ray diffraction results. Modelling and conformational analysis of single chains using the virtual bond approach lead to two possible models for the crystalline helix: 'herringbone' versus 'comb-like'.

Conformation of crystalline type III pneumococcal polysaccharide.

The conformation of crystalline Type III pneumococcal polysaccharide, poly[(1 yields 3)-beta-D-GlcpA-(1 yields 4)-beta-D-Glcp], has been studied by X-ray diffraction and stereochemical analysis. The X-ray pattern, recorded at 80% relative humidity, led to a trigonal unit-cell, with alpha = beta = 1.028 nm, c = 2.77 nm, and gamma = 120 degrees. Meridional reflections on the third and the sixth layer-lines show that the chain consists of a three-fold helix, with a repeat of 0.923 nm. Conformational analysis, by the virtual-bond method, shows that one right-handed and two left-handed helices are equally favorable, on the basis of energies of isolated chains. Packing of the three helix models in the unit cell, by contact-distance criteria, ruled out the possibility of the right-handed helical conformation. One of the left-handed helices has intramolecular hydrogen-bonds O-3'...O-5 and O-2...O-6' between the residues in the (1 yields 4) linkage, and O-4'...O-5 between those in the (1 yields 3) linkage. In the other left-handed helix, the O-4'...O-5 hydrogen bond is replaced by an O-2...O-2' hydrogen bond. The choice between the two left-handed helix models is inhibited by the paucity of X-ray intensity data.