Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains

Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.     

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.     

Synthesis and circular dichroism of tetraarylporphyrin-oligonucleotide conjugates

The preparation and circular dichroic (CD) studies of self-complimentary 8-mer DNA sequences with a porphyrin at the 3' end are presented. Electronic interaction between the two porphyrins (the interchromophoric distance is in the range of 28-40 A), attached to both ends of the double-stranded helix, gives rise to a long-range exciton-coupled CD in the visible region (400-450 nm). The porphyrin chromophores act as sensitive probes of geometrical changes in the DNA backbone and sensitively reflect the double-strand to single-strand transition. This study demonstrates the possibility of using exciton-coupled porphyrin CDs for conformational studies of DNA.     

Solid-phase and solution-phase syntheses of oligomeric guanidines bearing peptide side chains

[reaction: see text] Synthetic strategies for preparing N,N'-bridged oligomeric guanidines bearing peptide side chains both on solid support and in solution are presented. Monomers are prepared from common alpha-amino acids and therefore contain conventionally protected peptide side chains. The side chains include alkyl, aromatic, hydroxyl, amino, carboxylic acid, and amide functional groups. Oligomer elongation utilizes acid-sensitive sulfonyl activated thiourea through the formation of carbodiimide intermediate. With proper preparation of monomers, synthesis of oligomer can be performed in two directions (equivalent to N to C terminal or C to N terminal in a peptide sequence) with excellent efficiency.     

FTIR and circular dichroism spectroscopic study of interaction of 5-fluorouracil with DNA

5-Fluorouracil (5FU) is an anticancer chemotherapeutic drug which exerts cytotoxic effect by inhibiting cellular DNA replication. In the present study, we explore the binding of 5FU with DNA and resulting structural and conformational changes on DNA duplex. UV-visible, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopic techniques were employed to explore these interactions. A constant concentration of calf thymus DNA was incubated with varying concentrations of 5FU. UV-visible and FTIR spectroscopic results revealed that intercalation is the primary mode of interaction between 5FU and nitrogenous bases of the nucleic acid. The binding constant was found to be 9.7×10(4); which is indicative of moderate type of interaction between 5FU and DNA duplex. It was also observed that 5FU intercalates slightly more between AT base pairs compared to GC pairs. FTIR and circular dichroism spectroscopic results revealed that 5FU disturbs native B-conformation of DNA though, DNA remains in its B conformation even at higher concentrations of 5FU.     

Synthesis and luminescence of polyphosphazenes with carbazolyl side chains

Two new blue‐light‐emitting polyphosphazenes ( 1 and 2 ) containing carbazolyl groups as side chains were synthesized from a highly reactive macromolecular intermediate by a nucleophilic substitution reaction. Molecular structural characterization for the polymers was presented by ¹H NMR, IR, and ultraviolet–visible spectra, gel permeation chromatography, and differential scanning calorimetry. The polymers exhibited excellent solubility in common organic solvents and were thermally stable. A fluorescence analysis of the two materials in tetrahydrofuran showed a strong blue light emitting. The quantum yields of the polyphosphazenes were 0.55 for 1 and 0.64 for 2 , relative to quinoline (in 0.1 N H₂SO₄). An electroluminescent diode was fabricated, and a bright blue light was observed; the maximum external quantum efficiency was about 0.026% at an applied forward voltage of 23 V. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3428–3433, 2001     

Synthesis and properties of fluorosilicone with perfluorooctylundecyl side chains

A series of fluorosilicone (FLS) homopolymers with 4,4,5,5,6,6,7,7,8,8, 9,9,10,10,11,11,11‐heptadecafluoroundecylmethylsiloxane [? C₈F₁₇CH₂CH₂CH₂(CH₃) SiO? ; HDFUSiO] and copolymers based on dimethylsiloxane [? (CH₃)₂SiO? ] were prepared by the hydrosilylation of 4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,11‐heptadecafluoro‐1‐undecene (C₈F₁₇CH₂CH?CH₂) with poly(hydromethylsiloxane)s. Thermal characterization showed that the decomposition of fluoroalkyl side chains occurred at about 245 °C. Side‐chain crystallization was observed for FLSs with more than 30 mol % HDFUSiO. The refractive index decreased with increasing HDFUSiO content. The dielectric constant increased with increasing HDFUSiO content. The liquid surface tension of the FLS containing 10 mol % HDFUSiO was as low as that of the highly fluorinated FLSs. FLSs with HDFUSiO and trichlorosilylethyl side chains (Cl₃SiCH₂CH₂? ) were also prepared so that their solid surface tension (surface free energy) could be measured. The surface free energy of these FLSs decreased with increasing Cl₃SiCH₂CH₂? content, but the sliding angle of a water droplet and the contact‐angle hysteresis adversely increased. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2704–2714, 2003     

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism

Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.     

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 of pyridazines functionalized with amino acid side chains

A simple route for the preparation of 3,4,6-substituted pyridazines is described by using Tebbe olefination of esters then Diels–Alder reaction of the resulting enol ethers with tetrazine.     

Configurational assignment of alpha-chiral carboxylic acids by complexation to dimeric Zn-porphyrin: host-guest structure,chiral recognition and circular dichroism

A circular dichroic (CD) excition chirality method based on host-guest chiral recognition has been developed to determine the absolute configuration of carboxylic acids with an alpha-stereogenic center; an amide C = O-->Zn coordination, identified by infrared spectroscopy and computations, is involved in this complexation.     

Synthesis of chromenes with isoprenoid side chains and their selective ozonolysis

The reactions of trimethylhydroquinone with isoprenoid allylic alcohols catalyzed by a Pentasil type zeolite in the H-form gave trimethyl-1,4-benzoquinones with the corresponding isoprenoid group, which were subsequently transformed into the target ³-chromenes on treatment with pyridine. Partial ozonolysis of chromenes proceeded selectively at the -bond of the side chain, resulting in the corresponding chromenes with an -carbonyl group.     

Vibrational circular dichroism: a new spectroscopic tool for biomolecular structural determination

Vibrational circular dichroism (VCD) in the past two decades has developed into a powerful new structural tool. A concise review of the applications of VCD to determine the structures of various biological molecules, namely peptides and proteins, nucleic acids and carbohydrates, is provided.     

Vibrational circular dichroism: a new spectroscopic tool for biomolecular structural determination

Vibrational circular dichroism (VCD) in the past two decades has developed into a powerful new structural tool. A concise review of the applications of VCD to determine the structures of various biological molecules, namely peptides and proteins, nucleic acids and carbohydrates, is provided. Received: 31 August 1999 / Revised: 2 November 1999 / Accepted: 14 November 1999     

Synthesis and mesomorphic structures of comb liquid-crystalline polymers with lipopeptidic side chains

Lipopeptidic macromonomers were synthesized from bi-functional lipids by two methods and transformed into comb copolymers with lipopeptidic side chains by radical polymerization of their acrylate, methacrylate, acrylamide or methacrylamide terminal group. X-ray diffraction and differential scanning calorimetry studies showed that comb copolymers exhibit both a thermotropic and a lyotropic behaviour and present smectic and nematic mesophases. The influence of the solvent concentration, the degree of polymerization of the peptidic chains and the nature of the main chains on the structural parameters of the smectic mesophases were established in the case of copolymers with liposarcosine side chains.     

Theoretical and experimental investigations of circular dichroism and absolute configuration determination of chiral anthracene photodimers

Substituted anthracenes photodimerize to stereoisomeric [4 + 4] cyclodimers, some of which are inherently chiral. Recent supramolecular photochirogenic studies enabled the efficient preparation of specific stereoisomers, the absolute configurations of which should reflect the chiral environment of supramolecular host or scaffold employed but have not been determined, hindering detailed mechanistic elucidation and further host/scaffold design. In this study, we performed the combined experimental and state-of-the-art theoretical analyses of the circular dichroism spectra of chiral cyclodimers of 2-anthracenecarboxylic and 2,6-anthracenedicarboxylic acids to reveal the configurational and molecular orbital origin of the Cotton effects observed, and unambiguously determined the absolute configurations of these chiral cyclodimers. The present results allow us to directly correlate the enantiotopic face-selectivity upon photocyclodimerization with the absolute configuration of the cyclodimer derived therefrom and also to precisely elucidate the chiral arrangement of two cyclodimerizing anthracenes.     

Rigid-rod polymers with polysiloxane side chains. I. Synthesis and characterization of rigid-rod polyimides with polysiloxane side chains and their compatibility with linear polysiloxanes

Rigid-rod aromatic polyimdies having polydimethylsiloxane side chains were prepared for the purpose of dispersing rigid-rod molecules in silicone matrices for molecular reinforcement. The polyimides were obtained by imidizing the polyamide-acids bearing the side chains either thermally or chemically, which were synthesized by reacting 4,4′-diaminobiphenyl-terminated polysiloxane macromonomers with pyromellitic dianhydride in THF. The polyamide-acid films obtained by removing the solvent were soluble in THF, but the polyimides were insoluble in any common solvent. The polyimides showed no melting transition below 350°C on DSC analysis, at which temperature the side chain started decomposing. Although all the polyimides were anisotropic as observed by a polarizing microscope, x-ray diffraction analysis suggested the presence of only limited chain organization. Blends with linear polydimethylsiloxanes were prepared by casting the THF solution containing the polyamide-acid and the polydimethylsiloxane, followed by solvent evaporation and thermal imidization. With relatively longer side chains, the polyimides were proved to be compatibilized with polydimethylsiloxanes. © 1994 John Wiley & Sons, Inc.     

Rigid-rod polymers with polysiloxane side chains. 2. Synthesis and characterization of aromatic polybenzobisoxazoles with polysiloxane side chains and composite formation with polysiloxane matrices

Aromatic polybenzobisoxazoles, having polydimethylsiloxane side chains (SCPBOs), were prepared using terephthaloyl chloride-terminated polydimethylsiloxane macromonomers and 3,3′-bis(trimethylsiloxy)-4,4′-bis(trimethylsilylamino)biphenyl for the purpose of dispersing rigid-rod molecules in silicone matrices for molecular reinforcement. The degree of polymerization of the side chain was varied from 7.8 to 45.4, and a small amount of (3-butenyloxy)terephthaloyl chloride was copolymerized to give the polymers a functionality that can be linked to the matrices. For all the SCPBOs, the WAXD pattern showed only diffuse reflections, suggesting limited structural regularity, although the polymers were optically anisotropic. No melting transition was observed below the side chain decomposition temperature, 350°C. A polydimethylsiloxane/polybenzobisoxazole composite elastomer was obtained first curing the polysiloxane matrix containing the prepolymer of the SCPBO, followed by in situ thermal ring closure of the prepolymer. Some reinforcement was observed, but the presence of plasticizing effect by the unbound SCPBO was suggested at the same time. © 1995 John Wiley & Sons, Inc.