Conformational behavior of beta-proline oligomers

Conformations of the monomer, dimer, and hexamer of beta-proline ((S) pyrrolidine-3-carboxylic acid) were determined using ab initio molecular orbital calculations at the RHF/6-31G level of theory. The calculated minima are in good agreement with experimental data for the system and imply that the conformations could be controlled through chemical modification at Calpha, Cgamma, or Cdelta. The monomer and dimer are small and flexible with many low-energy minima. In the hexamer, two forms of regular secondary structure are preferred: left-handed helices with cis-peptide bonds and right-handed helices with trans-peptide bonds. This is similar to the behavior of alpha-proline helices, except that the relationship between the peptide rotamer and the handedness of the helix is reversed. Therefore, helices of the enantiomer of beta-proline ((R)-pyrrolidine-3-carboxylic acid) should exhibit the same behavior as alpha-proline helices. Through understanding the conformational behavior of beta-proline in various environments, it may be possible to use these protein mimics to inhibit various protein-protein recognition events. To estimate these effects, SCRF energies for the conformers were determined in dielectrics corresponding to water, methanol, and chloroform. It appears that the cis helices are more favorably solvated than the trans helices, but the cause is not clear.     

Conformational properties of thiophene oligomers

The molecular geometries and the torsional potentials about the inter‐ring C‐C bond in α‐oligothiophenes (α‐nTh, n=2–4) have been calculated by means of conventional ab initio and density functional theory (DFT) calculations employing the hybrid B3LYP and BH&HLYP functionals. The position and the energetics of the critical points in the potential energy curve generated by rotation about the inter‐ring C? C bond are shown to be dependent on the computational method. DFT calculations, in comparison with MP2 calculations, favour conjugative interactions, while steric and coulombic interactions are equally treated by both methods. On oligomerization the electron delocalisation increases slightly, the p‐charge being preferentially confined within the rings, although it is sufficient to move the molecular structure towards co‐planarization and to increase the barrier through the perpendicular conformation. The IR and Raman spectra on the relevant rotamers of α‐2Th have been computed at HF/6–31G* and B3LYP/6–31G* levels. The comparison with the experiment is excellent. It has been found that small twisting from the planar conformation has no apparent effects, while 90° twisting and isomerization to the syn‐gauche form produce significant frequency and intensity variations which could be useful probes in conformational studies. The simulated IR and Raman spectra of the α‐2Th rotamers are consistent with a smallπ‐electron delocalisation between the rings.     

Conformational analysis of chiral helical perfluoroalkyl chains by VCD

Vibrational circular dichroism (VCD) technique successfully revealed the absolute configuration of the biased helix of perfluoroalkyl chains in solution with the aid of theoretical calculations, which was supported by an X-ray crystallographic study.     

Mimicking helical antibacterial peptides with nonpeptidic folding oligomers

Unnatural oligomeric scaffolds designed to adopt defined secondary structures (e.g., helices), while retaining the chemical diversity of amino acid side chains, are of practical value to elaborate functional mimetics of bioactive alpha-polypeptides. Enantiopure N,N'-linked oligoureas as short as seven residues long have been previously shown to fold into a stable helical structure, stabilized by 12- and 14-membered H-bonded rings. We now report that eight-residue oligoureas designed to mimic globally amphiphilic alpha-helical host-defense peptides are effective against both gram-negative and gram-positive bacteria (including methicillin-resistant Staphylococcus aureus [MRSA]) and exhibit selectivity for bacterial versus mammalian cells. Circular dichroism (CD) spectroscopy studies suggest enhanced helical propensity of oligoureas in the presence of phospholipid vesicles. The utility of this new class of nonpeptidic foldamers for biological applications is highlighted by high resistance to proteolytic degradation.     

Synthesis of telechelic methacrylate oligomers with carboxyl ends through radical polymerization-chemical modification

A new method used to obtain α,ω-carboxyl terminated oligo(butyl methacrylate) (di-CTBMA) is introduced in this paper, which combines a conventional solution free-radical polymerization and a chemical modification, i.e. saponification. Here, a ω-carboxyl terminated oligo(butyl methacrylate) (CTBMA) is firstly synthesized by a solution polymerization in tetrahydrofuran, where 4,4^′-azobis(4-cyanovaleric acid) is used as radical initiator, and thioglycolic acid as chain transfer agent. Then, CTBMA is transferred into di-CTBMA via saponifying CTBMA in an organic solvent/H₂O/KOH solution. The influence of important reaction parameters, such as the type of organic solvent and reaction time are studied by acid-base titration and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. It is experimentally shown that a saponified CTBMA with a functionality of about two, i.e. di-CTBMA could be obtained under a certain experimental condition.     

Photomodulated chiral induction in helical azobenzene oligomers

Appending L-alanine to the terminal positions of a helical azobenzene oligomer produced a P helical bias, which increased with oligomer length. Irradiation gave rise to E-->Z isomerization of the terminal azo linkages, which displaced the stereogenic center of L-Ala from the helix backbone and suppressed chiral induction. Theoretical simulations of the CD spectrum of the P helical conformation are in qualitative agreement with the experimental spectra.     

Development of synthetic double helical polymers and oligomers

There is growing interest in the design and synthesis of artificial helical polymers and oligomers, in connection with biological importance as well as development of novel chiral materials. Since the discovery of the helical structure of isotactic polypropylene, a significant advancement has been achieved for synthetic polymers and oligomers with a single helical conformation for about half a century. In contrast, the chemistry of double helical counterparts is still premature. This short review highlights the recent advances in the synthesis, structures, and functions of double helical polymers and oligomers, featuring an important role of supramolecular chemistry in the design and synthesis of double helices. Although the artificial double helices reported to date are still limited in number, recent advancement of supramolecular chemistry provides plenty of structural motifs for new designs. Therefore, artificial double helices hold great promise as a new class of compounds. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5195–5207, 2009     

Conformational analysis of alkylated biuret and triuret: evidence for helicity and helical inversion in oligoisocyanates

The conformations of several oligoisocyanates have been investigated by NMR in order to study the onset and dynamics of helicity in polyisocyanates. Pentaethylbiuret and hexaethyltriuret were found to adopt turns and helices in solution. For hexaethyltriuret, symmetric and asymmetric helices are present. Not only is an interconversion of these forms observed (DeltaG(SA)(double dagger) = 9.3 +/- 0.4 kcal/mol) but also a reversal of helicity (DeltaG(PM)(double dagger) = 9.0 +/- 0.4 kcal/mol). The coalescence pattern for the latter process provides direct evidence for a concerted, conrotatory helical inversion.     

Conformational ordering of apolar, chiral m-phenylene ethynylene oligomers

A series of m-phenylene ethynylene oligomers containing nonpolar, (S)-3,7-dimethyl-1-octanoxy side chains have been synthesized and studied. In apolar alkane solvents, oligomers of sufficient length (n > 10) were found to adopt a helical conformation with a large twist sense bias. In contrast, in chloroform the oligomers adopt a random coil conformation. Surprisingly, the strong twist sense bias was determined to be highly time dependent and is partially attributed to intermolecular aggregation.     

Self-assembly of folded m-phenylene ethynylene oligomers into helical columns

Circular dichroism spectroscopy has been used to study the self-assembly of two series of m-phenylene ethynylene oligomers in highly polar solvents. The helical conformation of shorter oligomer lengths was found to be stabilized in aqueous acetonitrile solutions, while longer oligomers began to interact intermolecularly. The intermolecular aggregation of the oligomers in aqueous solutions revealed a chain length dependent association that required the presence of a stable helical conformation. Evidence for intermolecular interactions is provided by Sergeants and Soldiers experiments in which the twist sense bias of a chiral oligomer is transferred to an achiral oligomer.     

Conformational studies of the oligomers of L-lysine in reversed micelles

The effect of the chain length on the conformation of oligo-L-lysines (Lys-n, n= 9, 12 and 15) was examined in the reversed micelles of bis(2-ethylhexyl)sodium sulfosuccinate (AOT) in octane by the circular dichroism (CD) measurements. These oligomers seem to take a-structure in these systems. The structure-inducing effect of the reversed micelles is enhanced as the molar ratio of water to AOT (w₀=[H₂O]/[AOT]) becomes smaller. On the other hand, in the aqueous solutions the oligomers having 12 and 15 residues show the conformational transition from random coil to-helical structure by the addition of AOT, but the short oligomer of 9 residues does not show such a conformational transition.     

Conformational stability of helical peptides containing a thioamide linkage

[structure: see text] Thioxo peptide analogues of the alpha-helical peptide GCN4-p1 were synthesized and evaluated for helicity and oligomeric state. Sedimentation equilibrium and CD measurements indicate that the thioxo peptides fold into parallel alpha-helical coiled coil structures essentially identical to the native structure. This work marks the first incorporation of a thioamide linkage into the backbone of an alpha-helix and demonstrates that a thioamide linkage is compatible with positions within the helix as well as near the C-terminus.     

De novo design of non-hydrogen-bonded helical pseudopeptides composed of oxanipecotic acid oligomers

Ab initio calculation and circular dichroism experiments reveal that Oxa-oligomers adopted pronounced non-hydrogen-bonded helical structures.     

Saccharide recognition-induced transformation of pyridine-pyridone alternate oligomers from self-dimer to helical complex

Co-oligomers involving (1H)-4-pyridone and 4-alkoxypyridine rings were studied, and it was found that their supramolecular transformation was caused by saccharide recognition. In the co-oligomers, pyridone and pyridine rings are alternately linked at their 2,6-position with an acetylene bond. The pyridine rings behave as a hydrogen bonding acceptor, and the pyridone rings and tautomerized 4-pyridinol work as a donor. Pyridine-pyridone-pyridine 3-mer was found to self-dimerize on the basis of vapor pressure osmometry in CHCl(3), and the association constant was obtained as 2.3 x 10(3) M(-1) by (1)H NMR titration. Longer 5-, 7-, 9-, and 11-mer oligomers showed considerable broadening and anisotropy in the (1)H NMR spectra due to self-association. These longer oligomers recognized octyl beta-D-glucopyranoside and changed their form into a chiral helical complex, showing characteristic circular dichroism.     

Theoretical investigation of the second-order nonlinear optical properties of helical pyridine-pyrimidine oligomers

The structure and second-order nonlinear optical properties of a series of helical pyridine-pyrimidine oligomers recently synthesized by Barboiu and Lehn have been investigated theoretically by combining molecular mechanics and quantum chemistry approaches. In the absence of substituents, the hyper-Rayleigh scattering response (betaHRS) and the projection of the first hyperpolarizability on the dipole moment (beta||) exhibit periodic variations with chain length, but these nonlinear optical responses remain small. The first hyperpolarizabilities can, however, be enhanced by adding substituents. The greatest enhancement is obtained by substituting the pyrimidine groups by donor groups. Moreover, regular distributions of the donor groups around the helices enable the design of supramolecular structures exhibiting dipolar, octupolar or Lambda-shaped nonlinear optical characters, evident from the values of the depolarization ratios in hyper-Rayleigh scattering. Therefore this theoretical investigation demonstrates the potential of helical structures for the organization of chromophores in such a way that they exhibit large and specific second-order nonlinear optical responses.