Unconventional Secondary Structure Mimics: Ladder-Rungs

Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype ( 1 ) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.     

Molecular and colloidal self-assembly at the oil–water interface

Self-assembly is a versatile bottom-up approach for fabricating novel supramolecular materials with well-defined nano- or micro-structures associated with functionalities. The oil-water interface provides an ideal venue for molecular and colloidal self-assembly. This paper gives an overview of various self-assembled materials, including nanoparticles, polymers, proteins, and lipids, at the oil-water interface. Focus has been given to fundamental principles and strategies for engineering the self-assembly process, such as control of pH, ionic strength and use of external fields, to achieve complex soft materials with desired functionalities, such as nanoparticle surfactants, structured liquids, and proteinosomes. It has been shown that self-assembly at the oil-water interface holds great promise for developing well-structured complex materials useful for many research and industrial applications.     

Numerical investigation of particle lateral migration in straight channel flows using a direct-forcing immersed boundary method

Inertia-induced cross-stream migration has been recently exploited for precise position of particles in confined channel flows. In this work, a three-dimensional finite volume based immersed boundary method has been developed to study the lateral migration and hydrodynamic self-assembly of neutrally-buoyant particles in pressure-driven flows. Simulation results show that, in 2D channel flows, the equilibrium position for a circular particle is closer to the centreline for larger particle Reynolds number due to the increasing flow rate, while in 3D square duct flow, the equilibrium position for a spherical particle is near a face centre and is closer to the wall for larger particle Reynolds number. Self-assembly of a pair of particles is observed in 3D square duct flows but not in 2D channel flows. Mechanisms for the self-assembly are discussed.     

A new strategy for synthesis of branched cyclic peptide by Asn side-chain hydrazide ligation

Here, we report a new strategy for rapid synthesis of branched peptide by side-chain hydrazide ligation at Asn. The hydrazide was converted to thioester at Asn side chain by NaNO₂ and thiol reagent, and sequential ligation with an N-terminus Cys-peptide efficiently afforded the branched peptide. A branched cyclic peptide was successfully synthesized by side-chain ligation with a two-Cys-peptide and formation of a disulfide bond. This approach provides a new way for expeditious synthesis of branched peptides and facilitates the design of neopeptides as functional bio-mimics.     

Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid-Crystalline-Based Medium

Residual dipolar coupling (RDC), a robust anisotropic NMR parameter for structural elucidation of organic molecules, is only accessible in an anisotropic environment. Herein, we introduce a novel alignment medium based on the molecular self-assembly of oligopeptide amphiphile (OPA). This medium is compatible with different intermediate and polar solvent systems, such as CD₃OD, [D₆]DMSO, and D₂O. The preparation of the OPA-based medium is simple and rapid, while only very weak background signals were observed from OPAs. Furthermore, we show that the purity of OPA has only a minor influence on the quality of the RDC data. These advantages allow RDC measurements of organic molecules with different polarities and solubilities with high efficiency and accuracy.     

A convenient semicarbazide resin for the solid-phase synthesis of peptide ketones and aldehydes

Use of a semicarbazide resin for the solid-phase preparation of peptide ketones and aldehyde led to optimal results in terms of both purity of the final product and overall yield. This resin was prepared without complication by activation of the commercial available aminomethyl polystyrene with CDI at room temperature, followed by treatment with tert-butyl carbazate. Furthermore, the TNBSA colorimetric assay has been adapted for checking the incorporation of the carbonyl moiety onto hydrazine-based resins.     

Towards molecular-scale electronics and biomolecular self-assembly

This paper provides an overview of recent research developments in the field of nanoelectronics with organic materials such as carbon nanotubes and DNA-templated nanowires. Carbon nanotubes and gold electrodes are chemically functionalized in order to contact carbon nanotubes by self-assembly. The transport properties of these nanotubes are dominated by charging effects and display clear Coulomb blockade behaviour. A different approach towards nanoscale electronics is based on the molecular recognition properties of biomolecules such as DNA. As an example, DNA is stretched between electrodes using a molecular combing technique. A two-step metallization procedure leads to the formation of highly conductive gold nanowires.     

Long range one-dimensional ordering of lead phthalocyanine monolayer on InSb(1 0 0) (4 × 2)/c(8 × 2)

Sub-monolayer and monolayer of lead phthalocyanine deposited on InSb(1 0 0) (4 × 2)/c(8 × 2) surface have been investigated by scanning tunneling microscopy and low energy electron diffraction. Molecules first adsorb on the indium rows of the (4 × 2)/c(8 × 2) structure in the [1 1 0] direction and diffuse at the surface in order to form two-dimensional islands. The molecule-substrate interaction stabilizes the PbPc molecules on the In rows. It weakens the interaction between molecules located in adjacent rows resulting in numerous gliding planes between the molecular chains, in the direction parallel to the rows. At monolayer completion, a long-range one-dimensional order is adopted by the molecules in the [1 1 0] direction.     

Isosteres of peptides: boron analogs as dipolar forms of α‐amino acids – a theoretical study

Modification of peptides to produce peptidomimetics is of great interest, with the aim of designing potent, selective, and metabolically stable analogs having certain conformational properties. Organoboranes have been reported in the literature with a wide range of therapeutic applications. One of the therapeutically important class of molecules is amine‐carboxyboranes derived from amino acids by replacement of the Cα atom of an amino acid/peptide by boron. The conformational preferences of these peptides, with respect to backbone ω, ?, and ψ torsion angles, have been investigated by theoretical calculations. The amide bond in these molecules has the same geometry in the ground and transition states as the natural peptides. However, the boron isosteres of glycine and alanine peptides are less structured than their natural derivatives, but are distinguished by structures with a positive value for the ? angle, which is normally disfavored for natural peptides. This property could be used to build peptides with a geometry not usually seen in natural peptides. Copyright © 2007 John Wiley & Sons, Ltd.     

Self-assembly of nanoparticles on the surface of ionic crystals: Structural properties

With a suitable combination of ligand-stabilised nanoparticle suspension and ionic salt solutions, it is possible to produce microcrystals that are coated with nanoparticles. The self-assembly process of coating microcrystals by gold nanoparticles (NP) is mediated by the crystal lattice. This is the so-called CLAMS process - a generic process for self-organisation of nanoparticles on the surface of crystals [M. Murugeshan, D. Cunningham, J.-L. Martnez-Albertos, R. Vrcelj, B.D. Moore, Chem. Commun. (2005) 2677]. We are exploring here the structural properties of these self-assembled structures by using different imaging techniques.