Double versus single helical structures of oligopyridine-dicarboxamide strands. Part 1: Effect of oligomer length

Oligoamides of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid were previously shown to fold into single helical monomers and to hybridize into double helical dimers. A new series of these oligomers comprising 5 to 15 pyridine units, 4-decyloxy residues, and benzylcarbamate end groups were synthesized using a new convergent scheme that involves an early disymmetrization of the diamine and of the diacid. The hybridization of these compounds into double helices was studied by ¹H NMR spectroscopy in chloroform solutions at various temperatures. Somewhat unexpectedly, these studies revealed that dimerization increases with oligomer length up to a certain point, and then decreases down to undetectable levels for the longest strands. NMR studies show that both double helices and single helices become more stable when strand length increases. The measured values of enthalpy and entropy of hybridization for oligomers of various length show that the enthalpic gain constantly decreases with strand length. This can be interpreted as being the result of an increasing enthalpic price of the spring-like extension that the strand undergoes upon hybridization as its length increases. On the other hand, the entropic loss of hybridization also constantly decreases with strand length. Presumably, the helical preorganization of the monomers increases with strand length, which allows the longer strands to hybridize with a minimal loss of motional freedom, that is to say at a low entropic price. The competiton between these two factors results in a maximum of hybridization for the strands having an intermediate length.     

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.     

Chain-length-dependent helical motifs and self-association of beta-peptides with constrained side chains

Homo-oligomers constructed by using trans-2-aminocyclohexanecarboxylic acid monomers without protecting groups were studied. Both ab initio theory and NMR measurements showed that the tetramer tends to adopt a 10-helix motif, while the pentamer and hexamer form the known 14-helix. It was concluded that the conformationally constrained backbone is flexible enough to afford both 10-helical and 14-helical motifs, this observation in turn providing evidence of the true folding process. Self-association of the helical units was also detected, and the results of variable-temperature diffusion NMR measurements strongly suggested the presence of helical bundles in methanol solution.     

Stable helical beta 3-peptides in water via covalent bridging of side chains

An on-bead cyclization protocol of beta 3-peptides was developed, providing easy access to cyclic beta 3-peptides. With this methodology, a small library of helical cyclic beta 3-peptides was synthesized and investigated with CD spectroscopy. Covalent bridging of two side chains in beta 3-peptides significantly stabilized their helical conformation in aqueous solutions and turned out to be superior to the previously described electrostatic interactions.     

A bridge between pillared-layer and helical structures: a series of three-dimensional pillared coordination polymers with multiform helical chains

Rational self-assembly of a long V-shaped 3,3',4,4'-benzophenonetetracarboxylate (bptc) ligand and metal salts in the presence of linear bidentate ligand yield a series of novel pillared helical-layer complexes, namely, [Cu2(bptc)(bpy)2] (1), [M3(Hbptc)2(bpy)3(H2O)4].2 H2O (M = Fe(2) and Ni(3)), [Co2(bptc)(bpy)(H2O)].0.5 bpy (4), [Cd2(bptc)(bpy)(H2O)2].H2O (5), [Mn2(bptc)(bpy)1.5(H2O)3] (6) and [M2(bptc)(bpy)0.5(H2O)5].0.5 bpy (M = Mn(7), Mg(8) and Co(9), bpy=4,4'-bipyridine). Their structures were determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, and thermogravimetric (TG) analyses. The structure of 1 consists of two types of chiral layers, one left-handed and the other right-handed, which are connected by bpy pillars to generate a novel 3D open framework featuring four distinct helical chains. Compounds 2 and 3 are isostructural and feature 3D structures formed from the interconnection of arm-shaped helical layers with bpy pillars. Compound 4 is a pillared helical double-layer complex containing four different types of helices, among which the nine-fold interwoven helices constructed from triple-stranded helical motifs are unprecedented. Compound 5 exhibits a novel 3D covalent framework which features nanosized tubular channels. These channels are built from helical layers pillared by bptc ligands. The structure of 6 is constructed from {Mn(bptc)(H2O)}n2n- layers, which consist of left- and right-handed helical chains, pillared by [Mn2(bpy)3(H2O)4]4+ complexes into a 3D framework. To the best of our knowledge, compounds 1-6 are the first examples of pillared helical-layer coordination polymers. Compounds 7-9 are isostructural and exhibit interesting 2D helical double-layer structures, which are constructed from {M(bptc)(H2O)2}n2n- ribbons cross-linked by [M2(bpy)(H2O)6]4+ complexes. Furthermore, the 3D supramolecular structures of 7-9 are similar to the 3D structure of 6, and the 2D structure of 7 can be transformed into the 3D structure of 6 at higher reaction temperature. By inspection of the structures of 1-9, it is believed that the V-shaped bptc ligand and V-shaped phthalic group of the bptc ligand are important for the formation of the helical structures. The magnetic behavior of compounds 1, 2, 4, 6, and 9 was studied and indicated the existence of antiferromagnetic interactions. Moreover, compound 5 shows intense photoluminescence at room temperature.     

Dielectric relaxations in bilayer structures of comb-like copolymers: Perfluoralkyl and liquid-crystalline side chains

Abstract : A series of comb-like copolymers and homopolymers containing different liquid-crystalline and perfluoralkyl side chains was studied by frequency and temperature dependent dielectric measurements. The structure and the phase behaviour of the systems were characterized by X-ray scattering and differential scanning calorimetry. The dielectric relaxation spectra of these polymers reflect the molecular mobility in bilayer structures formed by the mesogenic or crystalline side chains. By changing temperature it was possible to investigate the molecular motions in the different phases of the copolymers (smectic-crystalline, smectic-isotropic, and isotropic). The homopolymer containing perfluoralkyl side chains and all copolymers show a β-relaxation at low temperatures, which is assigned to local molecular motions. Above the glass transition temperature, all samples exhibit a segmental (α) relaxation with WLF-like temperature dependence in the activation plots. For the polymers forming LC structures only one relaxation process was detected in all phases, i.e. in the smectic, nematic, and isotropic structure or, in case of the copolymers, in the smectic-crystalline and smectic-isotropic double structures. This process was attributed always to the segmental motions, assisted by tumbling motions of the mesogens. The phase transitions are clearly indicated by discontinuities in the dielectric relaxation times and changes in the relaxation strength Δϵ. The dipole reorientations of the mesogens seem to be more restricted by the crystalline layers in the copolymers as by the smectic order of the LC homopolymers.     

Spectroscopic evidence for the formation of helical structures in gas-phase short peptide chains

Aminoisobutyric acid (Aib) is a synthetic amino acid known to favor the formation of 3(10) helical structures in condensed phases, namely, crystals. The intrinsic character of these helicogenic properties has been investigated on the Ac-Aib-Phe-Aib-NH2 molecule under isolated conditions, namely, in the gas phase, both experimentally by double-resonance IR/UV spectroscopy and theoretically by quantum chemistry. A convergent set of evidence, based on energetic, IR, and UV spectroscopic data as well as on analogies with the similar peptide Ac-Ala-Phe-Ala-NH2 previously studied, enables us to conclude the formation of an incipient 310 helix in these isolated systems.     

Ferrocenoyl peptides with sulfur-containing side chains: synthesis, solid state and solution structures

The synthesis and full characterization of a number of amino acid and dipeptide derivatives with sulfur-containing side chains derived from ferrocene carboxylic acid and ferrocene-1,1′-dicarboxylic acid is presented. In particular, compounds Fc-CO-(Aaa)_n-OMe (4) and Fe[C₅H₄-CO-(Aaa)_n-OMe]₂ (3) with (Aaa)_n = Cys(Bzl) (a), Cys(Bzl)-Cys(Bzl) (b), Cys(p-OMe-Bzl) (c), Cys(p-OMe-Bzl)-Cys(p-OMe-Bzl) (d), Met (e), and Met-Met (f) were prepared. Also, the free acid derivatives Fe[C₅H₄-CO-Met-OH]₂ (6e) and Fc-CO-Met-OH (7e) were prepared and characterized. The solid state structures of 3a, 4b, and 4e were determined by single crystal X-ray diffraction. Compound 3a shows a 1,3′ substitution pattern on the Cp rings in the solid state. Structures in solution were determined by NMR, IR and CD spectroscopy, with particular emphasis on the question of hydrogen bonding and helical chirality of the metallocene. As an example, the full assignment for the Cp signals in the disubstituted derivative 3a was achieved by simulation of the ¹H NMR signals from the cyclopentadienyl ring in combination with 2D-NOESY spectra. In solution, 3a has the known 1,2′ substitution pattern, which is stabilized by intramolecular hydrogen bonds.     

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.     

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.     

Influence of single versus double hydrogen-bonding motif on the crystallization and morphology of self-assembling carbamates with alkyl side chains: model system for polyurethanes

The difference in the morphology and crystallization aspects of hydrogen-bond-mediated self-assembling systems with single and double hydrogen-bonding motifs is studied here with carbamates as an example. These carbamates have alkyl side chains of various lengths, from C(4) to C(18). The biscarbamates with double hydrogen-bonding sites and symmetric substitution of alkyl segments show a significantly different morphological behavior as compared to the N-octadecyl carbamate alkyl esters (ref 5, referred to as simple carbamates henceforth) with a single hydrogen-bond motif and asymmetric substitution of alkyl side chains. In contrast to the simple carbamates in which no significant difference was found in the spherulite size from C(4) to C(12), with the biscarbamates we find that the spherulitic size, rate of growth of spherulites, and rate of crystallization show a maximum with an alkyl chain length of C(8). This is rationalized in terms of the relative contributions of the hydrogen-bond and van der Waals interaction energies. Oriented X-ray diffraction patterns from the fibrils of the spherulites lead to a model for the growth patterns of the hydrogen-bond planes and the molecular orientation in the spherulites.     

Absorption by DNA single strands of adenine isolated in vacuo: the role of multiple chromophores

The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (~3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.     

Self-consistent electronic band structures of extended polydiacetylene chains with realistic model side groups

Self-consistent semi-empirical band structure calculations for isolated extended polydiacetylene chains with a variety of realistic model side groups have been performed. For side groups with a CH₂ group next to the chain backbone the predicted band gap Δ ≈ 0.5 eV is substantially independent of the detailed structure of the side group and much smaller than the optical absorption thresholds experimentally observed. These results support the hypothesis that the low energy electronic excitations of these systems are better described by an excitonic, rather than an electronic, band model.     

Surface properties and structures of diblock copolymer and homopolymer with perfluoroalkyl side chains

The surface free energy of diblock copolymer, composed of methyl methacrylate and 2-perfluorooctylethyl methacrylate (PMMA-b-PFEMA), was compared with that of PFEMA homopolymer (P-PFEMA) in correlation with their structures in the solid state and in the solution using dynamic contact angle, X-ray photoelectron spectroscopy, X-ray diffraction, and dynamic light scattering. The PMMA-b-PFEMA film cast from chloroform solution was found to possess very low surface free energy (7.8 mJ/m(2)) compared with the surface free energies of the P-PFEMA (8.5 mJ/m(2)) and the PMMA-b-PFEMA (9.8 mJ/m(2)) films cast from CF(3)CF(2)CHCl(2) solutions. These differences in the surface free energy were brought about by the variations in their surface structures. The very low surface free energy was considered to have originated from the surface segregation of the PFEMA segments highly self-assembled by the presence of chloroform.     

Calculation of the glass transition temperatures of polymers. Part I. Homopolymers and copolymers with alkyl side chains

Four equations, relating the glass transition temperatures T_g of homopolymers and copolymers to invariant additive temperature parameters (ATP) associated with their constituent groups, but weighted in different ways, have been applied to the calculation of the T_g of seven series of polymers having alkyl side chains. It is shown that the T_g of the 32 polymers considered may be calculated, within 7°K of the observed values, without the use of interaction coefficients from 15 independent variables, representing summations of the ATP's. The present calculations are confined to those structures which may be formed by a recombination of the structures corresponding to these independent variables. It is an essential feature of the approach that a distinction is made between groups with different nearest neighbors. Alternative methods of calculation are considered. The temperature parameter for a sequence of three or more methylene groups is estimated as 141°K, in conformity with the transition in polyethylene at 148°K. Nearest-neighbor interactions, stereoregularity, and crystallinity effects are discussed.     

The synthesis of pyridoquinolines with dialkylaminopropylamine side chains

Several new pyridoquinolines with dimethylaminopropyl side chain including 4,7-bis(3′-dimethylaminopropylamino)-1,10-phenanthroline ( 1 ), 4,10-bis(3′-dimethylaminopropylamino)-1,7-phenanthroline ( 2 ), 4,10-bis(3′-dimethylaminopropylamino)-6-methyl-1,7-phenanthroline ( 3 ), 4,6-bis(3′-dimethylaminopropylamino)-10-methylpyrido[3,2-g]quinoline ( 4 ) and 4-(3′-dimethylaminopropyl)pyrrolo[lmn][4,7]phenanthroline (5) have been prepared. The compounds were prepared by a multi-step synthesis which begins with Michael type addition of dimethyl acetylenedicarboxylate or diethyl ethoxymethylenemalonate to the appropriate phenylenediamine. The enamines obtained from the Michael addition were cyclized on heating at elevated temperatures to form the corresponding pyridoquinoline-diester-diones. The diester-diones were saponified decarboxylated and converted into dichloropyridoquinolines which on reaction with dimethylaminopropylamine yielded the title compounds.