Unprecedented Chain‐Length‐Dependent Conformational Conversion Between 11/9 and 18/16 Helix in α/β‐Hybrid Peptides

α,β‐Hybrid oligomers of varying lengths with alternating proteogenic α‐amino acid and the rigid β^2,3,3‐trisubstituted bicyclic amino acid ABOC residues were studied using both X‐ray crystal and NMR solution structures. While only an 11/9 helix was obtained in the solid state regardless of the length of the oligomers, conformational polymorphism as a chain‐length‐dependent phenomenon was observed in solution. Consistent with DFT calculations, we established that short oligomers adopted an 11/9 helix, whereas an 18/16 helix was favored for longer oligomers in solution. A rapid interconversion between the 11/9 helix and the 18/16 helix occurred for oligomers of intermediate length.     

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes

Recent experimental investigation (Reitzenstein and Lambert,Macromolecules, 2009, 42, 773) indicated that the quite different optical properties of 2,7- and 3,6-linkage triarylboryl carbazole oligomers may arise from the different nature of their low-lying excited states: a low-lying delocalized within-backbone excitation in longer 2,7-linked oligomers vs a backbone-to-sidechain charge-transfer (CT) excitation independent of the polymerization length in 3,6-linked oligomers. Here in this paper, two long-range corrected functionals, CAM-B3LYP and ωB97X, are applied together with the traditional B3LYP functional in time-dependent density functional theory (TDDFT) calculations to systematically investigate the low-lying electronic excitations in both oligomers. Our calculations indicate that an extensive conjugation exists between monomer molecular orbitals in 2,7-linked oligomers, which is absent in those of 3,6-linked structures, resulting in a considerable narrowing of the HOMO-LUMO gap of their backbone moiety, while having little effect on the side-chains. CAM-B3LYP and ωB97x calculations confirm that the lowest-energy absorption is a within-backbone excitation in longer 2,7-linked oligomers as opposed to a backbone to side-chain charge transfer excitation in 2,7-linked oligmers of shorter length and 3,6-linked oligomers of any length. All these findings are consistent with the experimental findings and the qualitative energy diagram proposed by Reitzenstein and Lambert.     

Radical polymerization of tetrafluoroethylene in solutions of trimethoxysilanes: Formation of colloidal solution and gel of oligomers

Radical polymerization of tetrafluoroethylene (TFE) in solutions of trimethoxysilanes leads to the formation of fluoroalkoxysilane oligomers and the products of their subsequent hydrolysis and dimerization that occur when methoxyl groups are replaced by hydroxyl groups and Si–O–Si links to bind the oligomers are subsequently formed. The chain length of the oligomers increases with the initial TFE concentration, thereby leading to the formation of colloidal solutions. Colloid particles contain oligomers and solvent molecules, the number of which per TFE unit decreases as the chain length grows to 4–6. Partial replacement of the starting solvents, which are also capable of creating a silicone skeleton during polycondensation, makes it possible to control the number of fluoroalkyl chains attached to this skeleton.     

Synthesis of Amphiphilic Oligomers of Acrylic Acid

Synthesis of amphiphilic oligomers of acrylic acid via radical polymerization in the presence of thiols as molecular mass regulators is described. The effect of the length of the introduced hydrophobic terminal group on the critical micellization concentration of the acrylic acid oligomers has been elucidated. It has been shown that the incorporation of an antituberculous drug (prothionamide) in the micelles of acrylic acid oligomers is enhanced with the increase in the length of the hydrophobic moiety. The preparation of hydroxyapatite-filled calcium-polycarboxylate bone cements containing prothionamide (promising for the sealing of postoperative cavities) is described.     

Synthesis and properties of a series of well-defined and polydisperse benzo[1,2-b:4,3-b']dithiophene oligomers

Monodisperse and polydisperse oligomers of benzo[1,2-b:4,3-b']dithiophene (BDT) (1-14), including three types of oligomers with different spacers combining BDT units (direct linkage, vinylene spacers, and ethynylene spacers), were synthesized, and their thermal, optical, and electrochemical properties were investigated. The oligomers were synthesized using Suzuki, Stille, Wittig, and Sonogashira coupling reactions. All of the monodisperse oligomers showed high melting points and 5% weight loss temperatures (T(d) > 400 degrees C). The fluorescence maxima of all oligomers were red-shifted, and the emission colors varied from blue to yellow as the chain lengths-and thus the conjugation lengths-increased. The vinylene-bridged oligomers emitted at longer wavelengths than the direct-linked and ethynylene-bridged oligomers. UV-vis absorption spectra in toluene solution indicated an effective conjugation length of about six BDT units for polydisperse oligomer 5. Cyclic voltammetry measurement indicated that tetramer 3 had high electrochemical stability. Although tetramer 3 and vinylene-bridged tetramer 8 exhibited reversible oxidation waves, ethynylene-bridged tetramer 13 showed an irreversible oxidation process. Each type of monodisperse oligomer exhibited higher HOMO levels with increasing chain length.     

Unexpected chain length dependence on a chiral memory effect of ‘meta-ethynylpyridine’ oligomers

The chain length dependence involving a chiral memory effect of 2,6-pyridylene ethynylene oligomers ‘meta-ethynylpyridines’ was investigated. The meta-ethynylpyridine oligomers associated with octyl β-d-glucopyranoside form a helical complex giving induced CD; the induced chirality could be memorized with the help of Cu(OTf)₂ as an additive. Contrary to our expectations, the study of the length dependence revealed that the 12-meric oligomer showed a more sustainable chiral memory effect than those observed in both of the shorter 6-meric and longer 18-meric oligomers.     

Heme peroxidase clothing and inhibition with polyphenolic substances revealed by molecular modeling

Molecular modeling techniques were applied to study oligomeric derivatives of phenols, which are produced during peroxidase-catalyzed oxidation. The interaction of substrates and oligomers with Arthromyces ramosus peroxidase (ARP) was analyzed by docking and molecular dynamics methods. The most possible interaction site of oligomers is the active center of the peroxidase. The affinity of oligomers increases with increasing length of oligomers. However, the complexed oligomers produce non-productive complexes with the peroxidase. Molecular dynamics studies showed that oligomer-peroxidase complexes are stable. It seems likely that strong and stable, but non-productive docking of the oligomers determinates peroxidase inhibition during the reaction by preventing the access of regular substrates to the active center of the enzyme.     

Synthesis, structure, and nonlinear optical properties of cross-conjugated perphenylated iso-polydiacetylenes

Monodisperse, cross-conjugated perphenylated iso-polydiacetylene (iso-PDA) oligomers, ranging from monomer 15 to pentadecamer 25, have been synthesized by using a palladium-catalyzed cross-coupling protocol. Structural characteristics elucidated by X-ray crystallographic analysis demonstrate a non-planar backbone conformation for the oligomers due to the steric interactions between alkylidene phenyl groups. The electronic absorption spectra of the oligomers show a slight red-shift of the maximum absorption wavelength as the chain length increases from dimer 17 b to pentadecamer 25, a trend that has saturated by the stage of nonamer 22. Fluorescence spectroscopy confirms that the pendent phenyl groups present on the oligomer framework enhance emission, and the relative emission intensity consistently increases as a function of chain length n. The molecular third-order nonlinearities, gamma, for this oligomer series have been measured via differential optical Kerr effect (DOKE) detection and show a superlinear increase as a function of the oligomer chain length n. Molecular modeling and spectroscopic studies suggest that iso-PDA oligomers (n>7) adopt a coiled, helical conformation in solution.     

Through versus cross electron delocalization in polytriacetylene oligomers: a computational analysis.

Herein, we report a systematic theoretical investigation of the molecular and electronic properties of unsubstituted polytriacetylene (PTA) and iso-polytriacetylene (iso-PTA) oligomers, which are characterized by through and cross pi-conjugation pathways, respectively. The goal of the study is to compare through versus cross conjugation on the basis of the computed molecular geometries of the neutral, anionic, and cationic species, the electron affinities, ionization potentials, excitation energies, and nonlinear optical properties for oligomers up to the nonamer. Differences in the effective conjugation length are directly related to electron delocalization in cross- and through-conjugated pathways. As in the through-conjugated oligomers, that is, the PTAs, the frontier orbitals of the iso-PTA oligomers are delocalized along the entire carbon backbone, suggesting that pi-delocalization can extend through cross-linked carbon atoms. However, in contrast to the PTA oligomers, the bond lengths remain strictly constant and the reduction of the energy gap beyond the trimer is completely due to the correlation contribution. On the other hand, in the anions and cations, the bond lengths do change significantly with increasing chain length. Therefore, oxidation or reduction of the iso-PTA oligomer appears to switch on delocalization through cross-linked carbon atoms. Obviously, the effective conjugation length is specific and depends on the observable considered.     

Theoretical study of spectroscopic properties of dimethoxy-p-phenylene-ethynylene oligomers: planarization of the conjugated backbone

The optical spectra of the dimethoxy-p-phenylene-ethynylene oligomers (up to n = 10) are calculated by DFT and TD-DFT methods. It is found that the conformational rotations around the cylindrical triple-bonded carbon links impact significantly the optical spectrum. The effective conjugation length (ECL) of the oligomer is obtained by extrapolating the HOMO-LUMO gap to infinite chain length with an alternative exponential function. The spectral shift is mainly dependent on the high pi-conjugation segment of oligomers, resulting from the planarization of the backbone. Although the rotational barrier is very low, the calculated results further indicate that rotation about the cylindrical triple bond still interrupts the conjugation of rod-like oligomers to some extent, and leads to an angle-dependent HOMO-LUMO gap. The results are helpful to interpret the conformational-dependent spectroscopic phenomena of p-phenyleneethynylene oligomers and polymers (PPEs) observed in ensemble and single molecule spectroscopy.     

Role of charge transfer interaction and conjugation length on electrical polarizability of doped trans-polyacetylene oligomers

The effects of charge transfer and molecular chain length on the electrical polarizability of doped trans-polyacetylene oligomers have been investigated using a series of quantum chemical methods ranging from Hartree-Fock to current density functional theory. Polarizability tensors of pristine and metal-doped trans-polyacetylene oligomers have been estimated. The nature of variations of polarizability tensor components are quite different for pristine and doped oligomers. For doped samples, distinct minima in the average static polarizabilities per acetylene unit have been observed. The results suggest that the competitive role of charge-transfer interaction and oligomer chain length are responsible for the observed minima. To simulate the ab initio results on polarizability variation, we propose a mathematical model that describes the minima quite satisfactorily.     

m-Phenylene ethynylene sequences joined by imine linkages: dynamic covalent oligomers

Imine metathesis between m-phenylene ethynylene oligomers of various lengths was performed in acetonitrile, a solvent in which oligomers containing eight or more repeat units adopt a compact helical conformation. The equilibrium constants and corresponding free energy change for the imine metathesis reactions were estimated. The results showed that the magnitude of equilibrium shifting measured by the free energy change for the formation of imine-containing oligomers increases linearly below a critical product chain length and grows asymptotically above it. The linear region is ascribed to the constant increase in contact area between monomer units of adjacent helical turns as the product chain grows to the 12-mer. Once the ligation product is 12 units in length, full contact is made between adjacent helical turns. On the other hand, for imine metathesis between oligomers leading to products having more than 12 units, the driving force is the difference between the folding energy of products and that of reactants. The additional stabilizing energy is roughly constant, regardless of the chain length, since the contact area between adjacent helical turns is unchanged. Consistent with the notion that the imine bond only minimally destabilizes the helical conformation, the position of the imine bond in the ligation product has been observed to have no significant effect on the folding stability. The magnitudes of equilibrium shifting are similar for ligation products of the same length but having the imine at various positions along the sequence. This suggests that the imine bond is compatible with the m-phenylene ethynylene backbone, regardless of the position in the sequence. Imine metathesis of m-phenylene ethynylene oligomers could allow a quick access to an unbiased, dynamic library of oligomer sequences joined by imine linkages.     

Blue/red-shift of the p-Phenylene-ethynylene Oligomers Absorption Spectra

The absorption spectra of the p-phenylene-ethynylene(p-PPE) oligomers(up to n = 12) were estimated by DFT and TD-DFT methods. The effective conjugation length(ECL) of the corresponding polymer was obtained by extrapolating the first excitation energies of the oligmers to infinite chain length with an alternative exponential function. The absorption spectral red-shift mainly depends on the ?-conjugation segment of oligomers resulting from the planarization of the backbone. The excitation mechanism of the rotamer has been investigated sufficiently by analyzing the orbital density variation upon the conformational rotations around the cylindrical triple-bonded carbon which is believed to impact significantly on the optical spectrum. The calculated results further indicate that rotation about the cylindrical triple bond interrupts the conjugation of rod-like oligomers to lead an angle-dependence of the corresponding excitation energy. The results are helpful to interpret the conformational-dependent spectroscopic phenomena of p-phenyleneethynylene and derivatives oligomers and polymers observed in ensemble and single molecule spectroscopy.     

High-performance liquid chromatography of in vitro synthesized poly(ADP-ribose) on ion-exchange columns, separation of oligomers of varying chain length and estimation of apparent branching

Separated macromolecular fractions of in vitro synthesized poly(ADP-ribose) by liver nuclei were subjected to ion-exchange chromatography in a programmed high-performance liquid chromatographic elution system. The effects of ionic strength, pH and temperature on the separation of poly(ADP-ribose) chains were determined. Short chain oligomers (up to n = 11) were fractionated into individual components by baseline separation. Each fraction was analyzed for chain length. Trace amounts of Ado(P)Rib(P)Rib(P) found in phosphodiesterase digests were taken as indication of apparent branching. In phosphodiesterase digests of the shorter oligomers, besides traces of the above component, two other digestion products were also observed, presumably representing oligomer termini, one terminal fragment being dominant in short oligomers. Medium and long chain oligomers were partly resolved to individual components, and especially the long oligomers exhibited marked temperature dependent elution patterns. Apparent branching increased with increasing chain length up to about 3% for n = 44 and components presumably indicating termini diminished to mere traces. The adenine spectra of all fractions identified individual components.     

Study of hopping transport in long oligothiophenes and oligoselenophenes: dependence of reorganization energy on chain length

Internal reorganization energies for self-exchange hole-transfer process were calculated at the B3LYP/6-31G(d) level of theory for a series of oligothiophenes and oligoselenophenes up to the 50-mers. This is the first study of reorganization energy in very long pi-conjugated systems. We observed a linear correlation between reorganization energy and the reciprocal chain length for these long pi-conjugated heterocyclic oligomers, which can be explained by the changes in bond length that occur between the neutral and cation radical species and by the charge distribution in the cation radicals. In contrast to the saturation behavior observed for the HOMO-LUMO gaps of long pi-conjugated heterocyclic oligomers, the reorganization energy does not show saturation behavior for any length of the oligomers in this study, even up to the 50-mers. Interestingly, the reorganization energy approaches zero for infinite numbers of oligomer units (at the B3LYP/6-31G(d) level of theory), that is, for polythiophene and polyselenophene. The absolute values of the reorganization energies of oligoselenophenes, and the changes that occur in those energies with chain length, are similar to those found for oligothiophenes.     

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.     

Synthesis of end-functionalized π-conjugated porphyrin oligomers

4-(S-Acetylthiomethyl)phenyl- and pyrenyl-functionalized π-conjugated porphyrin oligomers were synthesized. The distribution of the length of the oligomers could be controlled by changing the ratio of the starting porphyrin to the capping molecules. Oligomers from dimers to heptamers were isolated using size exclusion chromatography. The spectroscopic properties of these oligomers were measured to determine the influences of the number of porphyrin units and capping molecules on the absorption and emission spectra.     

Crystallization of carboxylic acid salts in poly(ethylene oxide) oligomers at higher temperatures

Many alkali metal carboxylates when dissolved in poly(ethylene oxide) (PEO) oligomers, are phaseseparated by heating. These were revealed to be the crystals of the initially dissolved corresponding salts from the X-ray diffraction patterns. Some acetate salts achieve the lower limit of the lattice energy for phase separation of ordinary inorganic salts by heating in PEO oligomers. These carboxylate salts were therefore expected to show crystallization behavior in PEO oligomers by heating. The effects of cation size, alkyl chain length and molecular weight of PEO on the solubility are summarized. Negative temperature dependence of solubility of these acetate salts is seen in the PEO oligomers only when the salts have long alkyl chains. The salts containing larger cations needed a longer chain length of PEOs for crystallization by heating. These salts with longer alkyl chains showed positive temperautred dependence in lower molecular weight polyethers, but negative temperature dependence in solubility in PEO with molecular weights higher than 400. In PEO₄₀₀, all the carboxylates with longer alkyl chains were phase separated by heating.     

Free solution mobility of small single-stranded oligonucleotides with variable charge densities

The free solution mobilities of six single-stranded 16-nucleotide DNA oligomers with the same sequence, containing up to 11 neutral phosphoramidate internucleoside linkages, have been measured by capillary electrophoresis. The mobilities of the partially charged oligomers increase linearly with the logarithm of increasing charge density, as predicted by the Manning theory of electrophoresis (G. S. Manning, J. Phys. Chem. 1981, 85, 1506-1515). For comparison, the mobilities of eight fully charged single-stranded oligomers containing similar numbers of charged phosphate residues have also been measured. The mobilities of the variable length, fully charged oligomers increase more rapidly with the increasing number of charged phosphate residues than the mobilities of the constant size, partially charged phosphoramidate derivatives, because of the larger diffusion coefficients of the modified oligomers.     

Synthesis of homoconjugated oligomers derived from 7,7-diphenylnorbornane

A methodology for the synthesis of monodisperse homoconjugated oligomers (dimer, trimer, and tetramer) derived from cofacial 7,7-diphenylnorbornane (DPN) is described. Extended aromatic homoconjugation is observed in these oligomers as revealed by the electronic spectra. The effective homoconjugation length (EHL) is in the range of 4-5 DPN subunits.