Photoresponsive peptoid oligomers bearing azobenzene side chains

N-Substituted glycine peptoid oligomers were synthesized to incorporate a photoresponsive azobenzene side chain. The ability of this side chain to undergo reversible photoisomerization was established, and the cis- to trans-azobenzene thermal isomerization of this side chain was investigated. Circular dichroism studies indicated that trans- to cis-azobenzene isomerization does not significantly alter the backbone conformation in a series of peptoids thought to have well-defined structures.     

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.     

Synthesis and circular dichroism spectroscopic investigations of oligomeric beta-peptoids with alpha-chiral side chains

Biomimetic oligomers are of large interest both as targets for combinatorial and parallel synthetic efforts and as foldamers. For example, shorter peptoid derivatives of beta-peptides, i.e., oligo-N-substituted beta-Ala, have been described as potential lead structures. Herein, we describe a solid-phase synthetic route to beta-peptoids with alpha-chiral aromatic N-substituents up to 11 residues long. Furthermore, the folding propensities of these oligomers were investigated by circular dichroism (CD) spectroscopy.     

Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis

Peptoids (N-substituted glycines) are an important class of biomimetic oligomers that have made a significant impact in the areas of combinatorial drug discovery, gene therapy, drug delivery, and biopolymer folding in recent years. Sequence-specific peptoid oligomers are easily assembled from primary amines by the solid-phase submonomer method. However, most amines that contain heterocyclic nitrogens in the side chain do not incorporate efficiently. We present here a straightforward revision of the submonomer method that allows efficient incorporation of unprotected imidazoles, pyridines, pyrazines, indoles, and quinolines into oligomers as long as 15 monomers in length. This improved method uses chloroacetic acid instead of bromoacetic acid in the acylation step of the monomer addition cycle, and allows for the incorporation of new side chains that should enable the synthesis of peptoids with entirely new properties.     

Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.     

Mercury binding by ferrocenoyl peptides with sulfur-containing side chains: Electrochemical, spectroscopic and structural studies

Ferrocenoyl peptides incorporating amino acids derived from either l-methionine, l-cysteine or dl-homocysteine have been synthesised and investigated as agents for heavy metal binding and detection. Heavy metal-peptide interactions have been characterised using cyclic voltammetry to follow changes in the potential of the Fe(II)/Fe(III) redox couple, revealing that these systems interact with mercury(II) ions more strongly than with other thiophilic heavy metals such as cadmium(II), silver(I) and lead(II). Proton NMR experiments have demonstrated 1:1 peptide:mercury binding and enabled quantitative characterisation of this binding interaction. Crystal structures for two of these ferrocenoyl peptide derivatives have been elucidated, revealing that these compounds adopt a P-1,3′ open solid state conformation in the absence of mercury; this arrangement precludes intramolecular hydrogen bonding between chains, while extensive intermolecular hydrogen bonding is evident. The particular affinity of these systems for mercury(II) opens the possibility of incorporating them in new, biologically inspired sensors for detecting this toxic pollutant.     

Characterizing the structure and dynamics of folded oligomers: Pulsed ESR studies of peptoid helices

Helical peptoid oligomers were synthesized in which the positions of nitroxide radical spin probes along the backbone were systematically varied, allowing evaluation of intra-molecular distances and dynamics by electron spin resonance spectroscopy.     

Two-component fibers/gels and vesicles formed from hetero-double-helices of pseudoenantiomeric ethynylhelicene oligomers with branched side chains

A methodology for the formation of fibers/gels and vesicles by molecular assembly and for controlling their properties is presented. Two-component systems of pentamer (P)-5 and tetramer (M)-4 pseudoenantiomeric ethynylhelicenes with decyloxycarbonyl (D) and 4-methyl-2-(2-methylpropyl)-1-pentyloxycarbonyl (bD) side-chains have been examined. Distinct aggregates were formed by changing the solvent for the three combinations of (P)-bD-5/(M)-bD-4, (P)-D-5/(M)-bD-4, and (P)-D-5/(M)-D-4. In toluene, (P)-bD-5/(M)-bD-4, (P)-D-5/(M)-bD-4, and (P)-D-5/(M)-D-4 all formed gels and fibrous assemblies were observed by AFM. The minimum gel-forming concentration (MGC) decreased in the order (P)-bD-5/(M)-bD-4>(P)-D-5/(M)-bD-4>(P)-D-5/(M)-D-4. In diethyl ether, vesicular formation was observed by dynamic light scattering (DLS), AFM, and TEM, and the size of the vesicles decreased in the order (P)-bD-5/(M)-bD-4>(P)-D-5/(M)-bD-4>(P)-D-5/(M)-D-4. Both fiber/gel and vesicle formation were accompanied by enhanced CDs and redshifted UV/Vis absorption bands with a change in color to deep yellow. These are novel two-component oligomeric systems that form assemblies of fibers/gels or vesicles depending on the solvent, and the structures and properties of the assemblies can be fine-tuned by changing the combination of oligomers. In m-difluorobenzene, a homogeneous solution was obtained with (P)-D-5/(M)-bD-4, which again exhibits enhanced CDs and redshifted UV/Vis absorptions. Vapor pressure osmometry analysis showed the formation of a bimolecular heteroaggregate. The study has indicated that pseudoenantiomeric oligomers form hetero-double-helices that hierarchically assemble to form fibers/gels and vesicles.     

A new route for synthesizing cholesterol analogs with fluorocarbon side chains and their liquid-crystalline aliphatic esters

A new and efficient route has been developed to synthesize 17β-(1-methyl-3-perfluoroalkyl)propyl-3β-androsterol (1) in nine steps from hyodeoxycholic acid via selective addition of 1-perfluoroalkyl iodide to 24-norchola-5,22-dien-3β-ol. From (1), the first series of steroidal liquid crystalline aliphatic esters (smectic A) with fluorocarbon side chains has been prepared.     

Structural and spectroscopic studies on 2-pyranones

Experimental methods of infrared, Raman and electronic absorption spectroscopy and DFT calculations using B3LYP functionals and 6-31G** and 6-311++G** basis sets have been used to understand the structural and spectral characteristics of 2-pyranones, 6-phenyl-4-methylsulfanyl-2-oxo-2H-pyran and 6-phenyl-4-methylsulfanyl-2-oxo-2H-pyran-3-carbonitrile in the electronic ground (S₀) and first excited (S₁) states. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Based on TD-DFT calculations using 6-31+G**5D basis set, an assignment of absorption peaks in the UV–VIS region has been suggested. The S₁ state is found to be a ¹(π,π*) state. A complete vibrational analysis has been attempted on the basis of experimental infrared and Raman spectra and calculated frequency and intensity of the vibrational bands and potential energy distribution over the internal coordinates. Characteristic vibrational bands of the 2-pyranone ring and methylsulfanyl and carbonyl groups have been identified.     

Thermal studies on polythiophene containing mesogenic side chains

Series of thiophenes containing mesogenic side chains at the 3^rd position are synthesized. The thermal transitions and thermal stability of the synthesized monomers and polymers are studied. The polarizing microscopic studies of synthesized monomers showed nematic liquid crystalline phase and these mesophases further confirmed by differential scanning calorimetric study. The obtained melting and the isotropic temperatures decrease linearly with the increase of aliphatic chain length. The transition temperatures determined from DSC analysis, overlap well with the temperatures obtained from optical microscopy studies. Thermal stability of the compounds is analysed using thermogravimetric studies. Thermal stability of monomers and polymers has been determined by calculating IPDT values. Structural influence on thermal degradation patterns of monomers and polymers are also discussed.     

Refractometry of dian and aliphatic epoxy oligomers

The refractometric characteristics of dian and aliphatic epoxy oligomers and their mixtures in a wide range of concentrations and temperatures have been investigated. It has been shown that the temperature dependences of the refractive indexes of the oligomers and their mixtures are straight lines. Upon mixing the oligomers, their volume remains unchanged. The molar refractions of individual oligomers and their mixtures are determined from experimental values of refractive indexes and densities and on the basis of calculations of atomic and group contributions using the concentrations of terminal fragments and the ratio of components. The effect of terminal fragments of the oligomers on the refractive index, density, and molar refraction was taken into account using the reduced molecular mass values. Methods for estimating the molecular mass of linear epoxy oligomers on the basis of their refractive indexes are suggested.     

Heterocyclic amines for the construction of peptoid oligomers bearing multi-dentate ligands

Peptoids are oligomers of N-substituted glycine that can be readily assembled using haloacetic acids and primary amines as synthons. Here, we report the synthesis and characterization of three new heterocyclic amines, 2-(2,2′:6′,2″-terpyridine-4′-yloxy)ethylamine, 2-(1,10-phenanthroline-5-yloxy)ethylamine and 8-hydroxy-2-quinolinemethylamine, and their incorporation into a series of different peptoid oligomer sequences. Since the heterocycles are all known to coordinate metal ions, the peptidomimetic products are designed to bind metal species with the potential for applications in catalysis and materials science.     

Structural and spectroscopic studies of silylated cyclo- and bicyclosilanes

A number of cyclo-and bicyclosilanes have been prepared and structurally characterized by X-ray crystallography and Raman spectroscopy. 1,1,4,4- and 1,1,3,3-tetrakis(trimethylsilyl)octamethylcyclohexasilanes were found to exhibit unusual twist- and twisted boat-conformations. The UV absorption properties of all compounds were studied and found to show absorption maxima red shifted compared to the parent compound dodecamethylcyclohexasilane. Dedicated to Prof. Mitsuo Kira on the occasion of his reception of the Wacker Silicon Award 2005 and in recongnition of his numerous outstanding achievements in organosilicon chemistry.     

Synthetic studies toward bicyclic endoperoxides presenting polar side chains

We developed a synthetic strategy for the preparation of tetrahydrofuro[2,3-c][1,2]dioxane and 2,3,8-trioxa[3,3,1]nonanes bearing polar functional groups at C3 and C4, respectively. The synthetic strategy has been applied to the synthesis of 2,3,8-trioxa[3,3,1]nonanes bearing various amides and amines at C3 useful for structure-activity relationships investigation as antiplasmodial compounds. The synthesis of 1 and the reaction conditions identified for its conversion to amides and amines could pose the basis for the use of this class of endoperoxides also in conjugation with other drugs for polypharmacology approaches.     

Synthesis and electrochemical studies of disubstituted ferrocene/dipeptide conjugates with sulfur-containing side chains

A series of 1,1′-disubstituted ferrocenoyl peptides incorporating dipeptide sidearms has been synthesized and studied electrochemically. The target peptides include ferrocene as an electrochemical reporter, sulfur-containing amino acids (l-methionine, S-methyl-l-cysteine, S-trityl-l-cysteine, S-benzhydryl-l-cysteine) as metal binding agents, and amino acids with non-polar side chains (l-alanine, l-valine, l-phenylalanine) as spacers between reporter and metal binding groups. Ferrocene/dipeptide conjugates were prepared using solution phase peptide synthesis methods employing a BOC-protecting group strategy and HBTU- (O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate) mediated peptide coupling. The electrochemical properties of these 1,1′-substituted ferrocenoyl peptides have been characterized using cyclic voltammetry. All exhibit fully reversible one electron oxidation steps; forward sweep half wave peaks (E_F), reverse sweep half wave peaks (E_R), peak separations (ΔE_P) and half wave potentials (E_1/2) are reported. Finally, towards the goal of utilizing ferrocenoyl peptides to detect heavy metals in solution, the response of these ferrocene/dipeptide conjugates to metal cations (zinc(II), mercury(II), cadmium(II), lead(II), silver(I)) has been examined. Monitoring changes in the potential of the Fe(II)/Fe(III) redox couple to follow peptide/metal interactions, we have probed the influence of the spacer unit between the redox reporter and the metal-binding amino acid, and shown that these systems respond to mercury(II) more strongly than to other heavy metal ions.     

Curing of mixtures of diane and aliphatic epoxy oligomers with different reactivities

Curing of diane and aliphatic epoxy oligomers and their blends is studied by DSC. The use of the traditional dynamic procedure and preliminary heating of the samples at a constant temperature are shown to be convenient for estimating the degree of conversion, glass-transition temperature, and activation energy of curing. Curing of diane, aliphatic epoxy oligomers, and blends with aliphatic amine is adequately described by the Kamal—Sourour equation, and the apparent activation energy of curing is 61.4–55.7 kJ/mol according to the Flynn—Wall—Ozawa model and 54.7–48.5 kJ/mol according to the Kissinger model. This value slightly changes with variation in the content of epoxy oligomers.     

Rigid-rod polymers with flexible side chains

Modeling studies were performed for a rigid-rod polyester with hexadecyloxy side chains (n=16) in order to simulate x-ray scattering curves in the medium angle scattering region (s=4 sin / from 0.2 Å^–1 to 2.2 Å^=t–1). The experimental ones were taken from a material obtained by cooling to room temeperature from the smectic mesophase at 150°C. The wide-angle x-ray diffractograms were calculated for given conformations and molecular arrangements using Debye's equation. The theoretical result thus obtained for a great variety of possible packing models and structures was compared to the experimental result. The size of the effective scattering region is found to be 61×18×52=6×10⁴ ų and consists of approximately five layers, each of which is composed of two rigid rods and 20 side chains. The planes form by the rigid rods, together with the side chains, have a distance of 3.6 Å, the distance between the rods being 26 Å. As the main result, it was found that the side chains form regions with a denser ordering (clustering). The interchain distance for side chains decreases in the regions from 5.3 Å to 4.8 Å.