Self-assembly with degenerate prototropy

This work describes a rational approach for addressing the prototropy-related problems in heterocycle-based self-assembling systems by the use of degenerate prototropy. As a proof of principle, the utility of degenerate prototropy is demonstrated herein by developing heterocycle-based AADD-type self-assembling modules that exist as "single set of protameric pair (duplex)" in both solution and solid states. These self-assembling modules are quickly accessible in good yield by reacting 2-amino-5,5-disubstituted-1H-pyrimidine-4,6-diones, available in one step by the condensation of alpha,alpha-dialkyl malonates and free guanidine, with isocyanates. Evidence from NMR spectroscopy, ESI mass spectrometry, and single-crystal X-ray diffraction studies confirmed the formation of molecular duplexes. The effect of electronic repulsion in duplex formation is also investigated. Their ready synthetic accessibility, remarkably high propensity to crystal formation, and the novel property of degenerate prototropy would make these novel self-assembling molecules promising candidates for many proposed applications.     

A novel series of oligomers from 4-aminomethyl-tetrahydrofuran-2-carboxylates with 2,4-cis and 2,4-trans stereochemistry

Two tetrahydrofuran-based γ-amino acids [2,4-cis and 2,4-trans] were subjected to iterative peptide-coupling procedures to afford dimeric, tetrameric and hexameric carbopeptoids in good yield. These homooligomers were prepared for secondary structural study—to ascertain the conformational preference inherent in the monomer units. The l-xylo oligomers were protected with triethylsilyl ethers to increase the range of solvents suitable for structural investigation. Initial secondary structure data indicate the presence of hydrogen-bonded conformations in the l-ribo series.     

Conformationally rigid aromatic amino acids as potential building blocks for abiotic foldamers

This communication describes the development of conformationally constrained unnatural aromatic amino acids, constructed on rigid backbone wherein the carboxyl and amino groups project in two dimensions (planes) on the aromatic framework. Such a feature offers the possibility of design and development of conformationally ordered synthetic oligomers with intriguing structural architectures distinct from those classically observed. Furthermore, such amino acids will have the potential to extend the conformational space available for foldamer design with diverse backbone conformation and structural architectures.     

Helical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding

This communication describes a set of hybrid foldamers that do not feature inter-residual, but intra-residual backbone hydrogen-bonding, yet adopt a preferentially folded conformation displaying right-handed helical architecture. Conformational ordering is apparently due to the combined conformational restrictions imposed by the conformationally restricted individual amino acid residues with which the oligomers are made of.     

Carbohydrate-derived conformationally restricted bicyclic dipeptides as potential hetero foldamer building blocks

Starting from carbohydrate precursors, hetero foldamer building blocks featuring diverse amino acid side chains and stereochemistry have been accessed via a multi-step synthetic protocol. These conformationally restricted bicyclic dipeptide building blocks are characterized by a constrained β-lactam ring fused with a pyrrolidine ring carrying a hydroxyethylamine isostere (HEA) on the backbone. These building blocks offer the possibility of developing foldamers with interesting structural architectures, conspicuously different from those classically observed. Furthermore, such hetero-building blocks have the potential to augment the conformational space available for foldamer design with diverse backbone conformations and structural architectures.     

Synthesis of 4-aminomethyl-tetrahydrofuran-2-carboxylates with 2,4-cis and 2,4-trans relationships

Templated tetrahydrofuran-based γ-azido esters were prepared with the C-2 and C-4 functionalities in cis and trans relative configurations. This was achieved by ring contraction of the suitably protected 2-O-triflates of pentono-1,5-lactones (d-ribose and l-arabinose) with subsequent introduction of the azide via the 4-O-triflate. Access to a corresponding β-azido ester was achieved in good yield. Little elimination product was observed by introduction of the azide via the 3-O-triflate. These azido esters are scaffolds, which may be predisposed to adopt secondary structural motifs, for example, for use as peptidomimetics; they may also be utilised for the preparation of stereodiverse compound libraries.     

Energy spectra for decaying 2D turbulence in a bounded domain

We use results derived in the framework of the replica approach to study the liquid-glass thermodynamic transition. The main results are derived without using replicas and applied to the study of the Lennard-Jones binary mixture introduced by Kob and Andersen. We find that there is a phase transition due to the entropy crisis. We compute both analytically and numerically the value of the phase transition point T(K) and the specific heat in the low temperature phase.     

Enforcing periodic secondary structures in hybrid peptides: a novel hybrid foldamer containing periodic gamma-turn motifs

This note describes the design, synthesis, and conformational studies of a novel hybrid foldamer that adopts a definite compact, three-dimensional structure determined by a combined effect of the special conformational properties of the foldamer constituents. The striking feature of this de novo designed foldamer is its ability to display periodic gamma-turn conformations stabilized by intramolecular hydrogen bonds. Conformational investigations by single-crystal X-ray studies, solution-state NMR, and ab initio MO theory at the HF/6-31G* level strongly support the prevalence of gamma-turn motifs in both the di- and tetrapeptide foldamers, which are presumably stabilized by bifurcated hydrogen bonds in the solid and solution states. The strategy disclosed herein for the construction of hybrid foldamers with periodic gamma-turn motifs has the potential to significantly augment the conformational space available for foldamer design with diverse backbone structures and conformations.     

Synthesis and anticancer activity of conformationally constrained Smac mimetics containing pseudo β turns

Herein, we report synthesis and in vitro anticancer activity of conformationally constrained Smac mimetics containing reverse turn inducing motifs “Ant-Pro” and “^sAnt-Pro”. The synthesis of Smac analogs with diverse hydrophobic groups at the C-terminus was carried out using solution phase peptide synthesis. The synthesis of Ant-Pro containing analogs 3a–j was carried out by ring opening of benzoxazinones 7a–c, whereas, their sulfonamide counterparts 4a–h were synthesized by using routine acid-amine coupling reaction. In vitro anticancer studies against breast cancer cell line MDA-MB-231 revealed that some of the new analogs had better anticancer activity than the standard AVPI Smac tetrapeptide.     

Sheet-forming abiotic hetero foldamers

Abiotic hetero oligomers, adopting a well-defined extended self-assembled sheet-like structure, derived from conformationally constrained aliphatic and aromatic amino acid residues repeating at regular intervals are reported.