A threaded loop conformation adopted by a family of peptoid nonamers

Non-natural polymers with well-defined three-dimensional folds offer considerable potential for engineering novel functions that are outside the scope of biological polymers. Here we describe a family of N-substituted glycine or "peptoid" nonamers that folds into an unusual "threaded loop" structure of exceptional thermal stability and conformational homogeneity in acetonitrile. The structure is chain-length-specific and relies on bulky, chiral side chains and chain-terminating functional groups for stability. Notable elements of the structure include the engagement of the positively charged amino terminus by carbonyl groups of the backbone through hydrogen bonding interactions and shielding of polar groups from and near-complete exposure of hydrophobic groups to solvent, in a manner resembling a folded polypeptide globular domain turned inside-out. The structure is stable in a variety of organic solvents but is readily denatured in any solvent/cosolvent milieu with hydrogen bonding potential. The structure could serve as a scaffold for the elaboration of novel functions and could be used to test methodologies for predicting solvent-dependent polymer folding.     

Homogenization in L

Homogenization of deterministic control problems with L^∞ running cost is studied by viscosity solutions techniques. It is proved that the value function of an L^∞ problem in a medium with a periodic micro-structure converges uniformly on the compact sets to the value function of the homogenized problem as the period shrinks to 0. Our main convergence result extends that of Ishii (Stochastic Analysis, control, optimization and applications, pp. 305-324, Birkhäuser Boston, Boston, MA, 1999.) to the case of a discontinuous Hamiltonian. The cell problem is solved, but, as non-uniqueness occurs, the effective Hamiltonian must be selected in a careful way. The paper also provides a representation formula for the effective Hamiltonian and gives illustrations to calculus of variations, averaging and one-dimensional problems.     

Poly-N-hydroxyethylacrylamide (polyDuramide): a novel,hydrophilic, self-coating polymer matrix for DNA sequencing by capillary electrophoresis

A replaceable polymer matrix, based on the novel monomer N-hydroxyethylacrylamide (HEA), has been synthesized for application in DNA separation by microchannel electrophoresis. The monomer was found by micellar electrokinetic chromatography analysis of monomer partitioning between water and 1-octanol to be more hydrophilic than acrylamide and N,N-dimethylacrylamide. Polymers were synthesized by free radical polymerization in aqueous solution. The weight-average molar mass of purified polymer was characterized by tandem gel permeation chromatography-multiangle laser light scattering. The steady-shear rheological behavior of the novel DNA sequencing matrix was also characterized, and it was found that the viscosity of the novel matrix decreases by more than 2 orders of magnitude as the shear rate is increased from 0.1 to 1000 s(-1). Moreover, in the shear-thinning region, the rate of change of matrix viscosity with shear rate increases with increasing polymer concentration. Poly-N-hydroxyethylacrylamide (PHEA) exhibits good capillary-coating ability, via adsorption from aqueous solution, efficiently suppressing electroosmotic flow (EOF) in a manner comparable to that of poly-N,N-dimethylacrylamide. Under DNA sequencing conditions, adsorptive PHEA coatings proved to be stable and to maintain negligible EOF for over 600 h of electrophoresis. Resolution of DNA sequencing fragments, particularly fragments > 500 bases, in PHEA matrices generally improves with increasing polymer concentration and decreasing electric field strength. When PHEA is used both as a separation matrix and as a dynamic coating in bare silica capillaries, the matrix can resolve over 620 bases of contiguous DNA sequence within 3 h. These results demonstrate the good potential of PHEA matrices for high-throughput DNA analysis by microchannel electrophoresis.     

Determination of the mode and efficacy of the cross-linking of guar by borate using MAS 11B NMR of borate cross-linked guar in combination with solution 11B NMR of model systems

The reaction product of boric acid and the polysaccharide guaran (the major component of guar gum) has been investigated by 11B NMR spectroscopy. By comparison with the 11B NMR of boric acid and phenylboronic acid complexes of 1,2-diols (HOCMe2CMe2OH, cis-C6H10(OH)2, trans-C6H10(OH)2, o-C6H4(OH)2), 1,3-diols (neol-H2), monosaccharides (L-fucose, mannose and galactose) and disaccharides (cellobiose and sucrose) it is found that the guaran polymer is cross-linked via a borate complex of two 1,2-diols both forming chelate 5-membered ring cycles ([B5(2)]), this contrasts with previous proposals. Based upon steric constraints we propose that preferential cross-linking the guaran polymer occurs via the 3,4-diols of the galactose side chain. The DeltaH and DeltaS for complexation of boric acid to cis- and trans-1,2-cyclohexanediol have been determined, from the temperature dependence of the appropriate equilibrium constants, and used in conjunction with ab initio calculations on model compounds, to understand prior conflicting proposals for guaran-boric acid interactions. 11B NMR derived pH dependent equilibrium constants and ab initio calculations have been used to understand the reasons for the inefficiency of boric acid to cross-link guaran (almost 2 borate ions per 3 monosaccharide repeat units are required for a viscous gel suitable as a fracturing fluid): the most reactive sites on the component saccharides (mannose and galactose) are precluded from reaction by the nature of the guar structure; the comparable acidity (pKa) of the remaining guaran alcohol substituents and the water solvent, results in a competition between cross-linking and borate formation; a significant fraction of the boric acid is ineffective in cross-linking guar due to the modest equilibrium (Keq). In contrast to prior work, we present evidence for the reaction of alcohols with boric acid, rather than the borate anion. Based upon the results obtained for phenylboronic acid, alternative cross-linking agents are proposed.     

Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices.

The achiral backbone of oligo-N-substituted glycines or "peptoids" lacks hydrogen-bond donors, effectively preventing formation of the regular, intrachain hydrogen bonds that stabilize peptide alpha-helical structures. Yet, when peptoids are N-substituted with alpha-chiral, aromatic side chains, oligomers with as few as five residues form stable, chiral, polyproline-like helices in either organic or aqueous solution. The adoption of chiral secondary structure in peptoid oligomers is primarily driven by the steric influence of these bulky, chiral side chains. Interestingly, peptoid helices of this class exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have taken advantage of this distinctive spectroscopic signature to investigate sequence-related factors that favor and disfavor stable formation of peptoid helices of this class, through a comparison of more than 30 different heterooligomers with mixed chiral and achiral side chains. For this family of peptoids, we observe that a composition of at least 50% alpha-chiral, aromatic residues is necessary for the formation of stable helical structure in hexameric sequences. Moreover, both CD and 1H-13C HSQC NMR studies reveal that these short peptoid helices are stabilized by the placement of an alpha-chiral, aromatic residue on the carboxy terminus. Additional stabilization can be provided by the presence of an "aromatic face" on the helix, which can be patterned by positioning aromatic residues with three-fold periodicity in the sequence. Extending heterooligomer chain length beyond 12-15 residues minimizes the impact of the placement, but not the percentage, of alpha-chiral aromatic side chains on overall helical stability. In light of these new data, we discuss implications for the design of helical, biomimetic peptoids based on this structural motif.     

Crystal structure of Al(tBu)3(NH2CH2CH2Ph): A molecular “slinky”

The molecular structure of Al(^tBu)₃(NH₂CH₂CH₂Ph) is determined by the crystal packing of the phenyl rings and the pseudo spherical Al(^tBu)₃ units, and may be viewed as a layered structure consisting of double sheets of the phenyl rings and the Al(^tBu)₃ units. The Al–N–C–C linkage shows severe disorder as a result of its flexibility. The structure of Al(^tBu)₃ (NH₂CH₂CH₂Ph) can be likened to a molecular slinky, in which the rigid ends are fixed in space by molecular packing forces, leaving the interior link to adopt multiple orientations. Crystal data: orthorhombic, Cmca,a=13.282(9),b=25.01(1),c=13.210(9), Å,V=4388(10) ų,Z=4,R=0.0957,R _w=0.0957.     

Molecular structure of (tBu)3AlP(nPr)3

The crystal and molecular structure of (^tBu)₃AlP(ⁿPr)₃ has been determined. The Al(1)?P(1) bond distance [2.594(3) Å] is slightly longer than other aluminum-phosphine complexes; however, the geometry about aluminum is similar to that of the [AlCl(^tBu)₃]^? anion, suggesting that the geometry about the aluminum in tri-tert-butylaluminum complexes is defined by the size of thetert-butyl ligands and not as a consequence of the steric bulk of the Lewis base. Crystal data: Monoclinic,P2_t,a=8.932(2),b=16.832(3),c=9.328(2), Å, β=114.36(3)°,V=1277.6(6) ų,Z=4,R.=0.055,R _w =0.053.     

Capacity and entry issues in online exchanges

With the advent of open standards and Internet technologies, the number of sellers who can participate in online exchanges is greatly increased. We model the competition between identical sellers vying for the same business, and find that there exists a mixed-strategy equilibrium in prices. The results help us understand the dynamics between a seller’s capacity and his motivation to participate in an auction.