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 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.     

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 analysis of o-phenylenes: helical oligomers with frayed ends

The o-phenylenes represent a fundamental class of conjugated polymers that, unlike the isomeric p-phenylenes, should exhibit rich conformational behavior. Recently, we reported the synthesis and characterization of a series of o-phenylene oligomers featuring unusual electronic properties, including surprisingly long-range delocalization as measured by UV-vis spectroscopy and hypsochromic shifts in fluorescence maxima with increasing length. To rationalize these properties, we hypothesized that the oligomers predominantly assume a stacked helical conformation in solution. This assertion, however, was supported by only indirect evidence. Here we present a thorough investigation of the conformational behavior of this series of o-phenylenes by dynamic NMR spectroscopy and computational chemistry. EXSY experiments, in combination with other two-dimensional NMR techniques, provided full (1)H chemical shift assignments for at least the two most prevalent conformers for each member of the series (hexamer to dodecamer). GIAO density functional theory calculations were then used to relate the NMR data to specific molecular geometries. We have found that the o-phenylenes do indeed assume stacked helical conformations with disorder occurring at the ends. Thus, the o-phenylene motif appears to have great potential as a means to organize arenes into predictable three-dimensional arrangements. Our results also illustrate the power of (1)H NMR GIAO predictions in the solution-phase conformational analysis of oligomers, particularly those with a high density of aromatic subunits.     

Conformational behavior of some hydroxamic acids

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.     

Conformational behavior of 1,1,1-trifluoroethane in nanotubes

According to DFT PBE/3z calculations, conformational transformations of 1,1,1-trifluoroethane molecule in model single-walled carbon nanotubes are determined primarily by the diameter of the latter. Reduction of the nanotube diameter is accompanied by displacement of the conformational equilibrium toward the eclipsed structure.     

Conformational behavior of polymers adsorbed on nanotubes

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.     

Conformational behavior of nylon 6 in mixed solvents

The intrinsic viscosity [η], Huggins constant (K_H), laser light scattering, UV and IR measurements of Nylon 6 are made in m‐cresol and its mixture with 1,4‐dioxane at 20–60 °C. The intrinsic viscosity, R_g, A₂, (<S>²)^1/2 (calculated from viscosity data), R_H, and UV absorbance initially increase and then decrease with the rise in 1,4‐dioxane contents. The K_H and the transmittance of ? OH group in IR spectra show an opposite trend to that of [η]. The dielectric constant calculated from the refractive index of the solvent (m‐cresol with 1,4‐dioxane) and polymer solution shows a continuous decrease with the amount of 1,4‐dioxane. Activation energy shows a minimum while linear expansion coefficient (α³) maximum with the addition of 1,4‐dioxane. Change in [η], K_H, and other characteristics of the polymer solutions with alterations in solvent composition and temperature are the result of variation in the thermodynamic quality of the solvent, its selective adsorption, hydrogen bonding, and conformational transitions. It has been concluded that the addition of 1,4‐dioxane first enhances the quality of the solvent, encourages hydrogen bonding, and specific adsorption, and then deteriorates, bringing conformational transitions in the polymer molecules. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 534–541, 2005     

Synthesis and thermal behavior of chiral oligomers derived from cholesterol

Synthesis and thermal properties of a series of Schiff base oligomers derived from naturally occurring cholesterol are described. In particular, four of them show smectic A and/or chiral nematic phase/s or an unknown mesophase, while the other is non-mesomorphic. Molecular packing in the SmA phase has been determined by the HRXRD experiment.     

Conformational preferences of chondroitin sulfate oligomers using partially oriented NMR spectroscopy of 13C-labeled acetyl groups

A new method is presented for the retrieval of information on the conformation of glycosaminoglycan oligomers in solution. The method relies on the replacement of acetyl groups in isolated native oligomers with 13C labeled acetyl groups and the extraction of orientational constraints from residual dipolar couplings (RDCs) and chemical shift anisotropy (CSA) offsets observed in NMR spectra of partially oriented samples. A novel method for assignment of resonances based on the correlation of resonance intensities with isotope ratios determined from mass spectrometric analysis is also presented. The combined methods are used in conjunction with more traditional NMR structural data to determine the solution structure of a pentasaccharide, GalNAc6S(beta1-4)GlcA(beta1-3)GalNAc4S(beta1-4)GlcA(beta1-3)GalNAc4S-ol, derived by enzymatic hydrolysis of chondroitin sulfate. The geometry derived is compared to that for similar molecules that have been reported in the literature, and prospects for use of the new types of data in the study of protein-bound oligosaccharides are discussed.     

Stability against enzymatic hydrolysis of endomorphin-1 analogues containing beta-proline

The enantiomer of endomorphin-1 (Tyr-Pro-Trp-PheNH2) and the analogues containing (S)- or (R)-beta-proline have been synthesized, and their affinities towards mu-opioid receptors have been measured. As expected, the incubations of the different peptides with some commercially available enzymes showed that the presence of D-residues gave strong resistance towards digestion. The presence of beta-proline alone is sufficient to confer good resistance against the hydrolysis of the biologically strategic Pro-Trp bond.     

Conformational behavior of ethane molecule encapsulated in a nanotube

Investigation of conformation transformations of ethane molecule in single-wall carbon nanotubes by the hybrid DFT method PBE/3z showed that the parameters and the character of the nanotube (length, diameter, open, closed, or semiopened) affect the conformational behavior of the encapsulated molecule leveling the difference in the energy or even resulting in the inversion of the relative stability of the staggered and eclipsed forms.     

Conformational behavior of simple furanosides studied by optical rotation

Experimental and theoretical specific optical rotations (OR) of anhydro, epithio, and epiminoderivatives of methyl tetrofuranosides in chloroform solutions have been compared and used as a tool for exploring their conformational behavior. The potential energy surfaces of these saccharides with reduced flexibility were examined with the density functional theory and the MP2 and CCSD(T) wavefunctions methods. Theoretical ORs were obtained by Boltzmann averaging of values calculated for local minima. Resultant rotations could be used to assess the quality of the DFT and MP2 relative conformer energies. OR values calculated for equilibrium geometries in vacuum were significantly improved when the solvent was accounted for by a polarizable continuum model and first and diagonal second OR derivatives were used for an anharmonic vibrational averaging. The DFT used as a default method reproduced the experimental data fairly well. A modified B3LYP functional containing 70% of HF exchange further improved the results. Because of the strong dependence of OR on the conformation, not only the absolute configuration could be determined, but also the conformational populations were estimated. Likewise, the predicted dependence of OR on the light wavelength well agreed with experiment. The increasing precision of the contemporary computational methods thus makes it possible to relate the specific rotation to more detailed features in molecular structure. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Temperature sensitivity trends and multi-stimuli sensitive behavior in amphiphilic oligomers

A series of oligomers, containing oligo(ethylene glycol) (OEG) moieties, with the same composition of amphiphilic functionalities has been designed, synthesized, and characterized on the basis of their temperature-sensitive behavior. The non-covalent amphiphilic aggregates, formed from these molecules, influence their temperature sensitivity. Covalent tethering of the amphiphilic units also has a significant influence on their temperature sensitivity. The lower critical solution temperatures of these oligomers show increasingly sharp transitions with increasing numbers of OEG functional groups, indicating enhanced cooperativity in dehydration of the OEG moieties when they are covalently tethered. These molecules were also engineered to be concurrently sensitive to enzymatic reaction and pH. This possibility was investigated using porcine liver esterase as the enzyme; we show that enzymatic action on the pentamer lowers its temperature sensitivity. The product moiety from the enzymatic reaction also gives the amphiphilic oligomer a pH-dependent temperature sensitivity.