Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers

The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n‐hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self‐aggregation of unfolded chains, as a minor component, gradually drives the folding–unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH₃OH/H₂O) both folded and unfolded oligomer 2 appear to undergo self‐association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H₂O content, self‐aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded–unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers.     

A novel type of optically active helical polymers: Synthesis and characterization of poly(N‐propargylureas)

This article presents two novel artificial helical polymers, substituted polyacetylenes with urea groups in side chains. Poly( 4 ) and poly( 5 ) can be obtained in high yields (≥97%) and with moderate molecular weights (11,000–14,000). Poly( 4 ) contains chiral centers in side chains, and poly( 5 ) is an achiral polymer. Both of the two polymers adopted helical structures under certain conditions. More interestingly, poly( 4 ) exhibited large specific optical rotations, resulting from the predominant one‐handed screw sense. The helical conformation in poly( 5 ) was stable against heat, while poly( 4 ) underwent conformational transition from helix to random coil upon increasing temperature from 0 to 55 °C. Solvents had considerable influence on the stability of the helical conformation in poly( 4 ). The screw sense adopted by the helices was also largely affected by the nature of the solvent. Poly( 4 ‐co‐ 5 )s formed helical conformation and showed large optical rotations, following the Sergeants and Soldiers rule. By comparing the present two polymers (with one ? N? H groups) with the three polymers previously reported (with two ? N? H groups in side chains), the nature of the hydrogen bonds formed between the neighboring urea groups played big roles in the formation of stable helical conformation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4112–4121, 2008     

A Molecular Orbital Approach to Conformational Study of the Polyisocyanates

A conformational study of poly(alkyl isocyanates) with both non‐chiral and chiral side groups (R) is presented. For this purpose the conformational preferences of model compounds CH₃—(CONR)_m—CH₃, where m is the number of monomers, were investigated by means of quantum mechanical methods. The influence of the number of monomers and the side chain conformation on the relative stability of the different helical minima has been systematically studied. Finally, the influence of the solvent chloroform has been examined by using a self‐consistent reaction‐field. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these compounds.     

Switching of the helical polymer conformation in a solid polymer film

A chiral photochromic polyisocyanate was incorporated into a solid polymer matrix of poly(methyl methacrylate) (PMMA), yielding an isotropic polymer film. Isomerization of the chiral photochromic azo side groups (cis‐trans) triggers a reversible conformational change of the helical polyisocyanate backbone. Thus the chirooptical properties of the film can be switched photochemically. The isomerization of the helix is much slower than the isomerization of the azo side groups. Below T_g , the photochemically modified helix conformation is thus stable, despite thermal relaxation of the azo chromophores.     

Synthesis of polyisocyanide derived from phenylalanine and its temperature‐dependent helical conformation

Screw‐sense‐selective polymerization of the chiral isocyanide monomers derived from phenylalanine with NiCl₂ as a catalyst in methanol to yield helical‐conjugated polyisocyanide was investigated with respect to the thermal stability of its helical conformation. Poly(1‐tert‐butoxycarbonyl‐2‐phenylethyl isocyanide) (poly 1c ) took a stable helical conformer independent of the polymerization temperature. In poly(1‐ethoxycarbonyl‐2‐phenylethyl isocyanide) (poly 2c ), which had slightly smaller side groups, the helical conformation was thermally destabilized. The specific rotation and circular dichroism of poly 2c prepared at temperatures greater than 40 °C were considerably depressed in comparison with the values for poly 2c prepared at or below room temperature. Additionally, poly 2c prepared at low temperatures exhibited reversible temperature‐dependent specific rotation and circular dichroism, whereas poly 1c showed few changes. It is suggested that polyisocyanide derived from phenylalanine takes various helical conformers (i.e., from tightly to loosely coiled helices), the thermal stability of which depends on the size of the side group. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 40: 399–408, 2002     

Helical secondary structures in 2:1 and 1:2 α/γ-peptide foldamers

Oligomers containing both α- and γ-amino acid residues in a 1:1 alternating pattern have recently been shown by several research groups to adopt helical secondary structures. We have begun to explore the folding behavior of oligomers with different α-residue/γ-residue backbone patterns. Previously we reported that the γ-amino acids bearing a cyclohexyl constraint at the C_β–C_γ bond and a variable side chain at C_α strongly promote a helical conformation containing 12-atom CO(i)?H–N(i+3) hydrogen bonds for 1:1 α:γ backbones. Here we report synthesis and crystallographic analysis of 2:1 and 1:2 α/γ-peptides that adopt CO(i)?H–N(i+3) hydrogen-bonded helical conformations.     

Conformation of Azobenzene‐Modified Poly(α‐L‐Glutamate) (AZOPLGA) in Thin Films: Solid State NMR Studies

Abstract

The conformations of azobenzene‐modified poly(α‐L‐glutamate)s (AZOPLGA) with a different degree of functionalization were examined by solid state ¹³C NMR. The polymer main chain conformations in AZOPLGA powders (precipitated from reaction system) changes from α‐helix to β‐sheet when the degree of functionalization increases from 12% to 56%. In addition, the solvent used for fabricating films plays an important role in organizing AZOPLGA backbones into characteristic conformation. For AZOPLGA56 (AZOPLGA with 56% of functionalization) cast films, the polymer backbones can assume conformations ranging from order state (β‐sheet) to random coil by changing the solvent for fabrication. In contrast, the effect of solvent on the conformation of AZOPLGA23 (AZOPLGA with 23% of functionalization) is not so significant. When compared with AZOPLGA23 powder (precipitated from reaction system), the helical conformation increases for AZOPLGA23 film cast from TFA. However, the fractions of α‐helix and β‐sheet conformation in AZOPLGA23 films (cast from DMF or pyridine) are nearly identical to that of AZOPLGA23 power. Moreover, even though the polymer backbones are random coil in AZOPLGA56 films when cast from TFA, some locally ordered domain can be observed. Lastly, the effect of the azo content appears to play a dominant role over the effect of solvents in directing the conformation of these polymers.     

Do Valine Side Chains Have an Influence on the Folding Behavior of β‐Substituted β‐Peptides?

The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3₁₄‐helical propensity of β³‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β³‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3₁₄‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β³‐peptides show a structural preference for 3₁₄‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.     

Helical Ullazine-Quinoxaline-Based Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic azomethine ylides (PAMYs) are powerful building blocks in the bottom-up synthesis of internally nitrogen-containing polycyclic aromatic hydrocarbons (N-PAHs) through 1,3-cycloaddition reactions. In this work, the cycloaddition reaction of PAMYs to asymmetric ortho-quinones is presented, which, in contrast to the addition to symmetric para-quinones, facilitates subsequent condensation reactions and allows the synthesis of three helical N-PAHs with ullazine-quinoxaline ( UQ - 1 – 3 ) backbones. UQ - 1 and UQ - 2 possess two helical centers; however, single-crystal X-ray analysis together with the computational modeling of UQ - 3 elucidate the formation of only the thermodynamically most stable geometry with four helical centers in a (P,P,M,M) configuration. For the series UQ - 1 – 3 , the number of redox steps is directly correlated with the number of ullazine or quinoxaline units incorporated into the targeted molecular backbones. A detailed investigation of the spectroscopic and magnetic properties of the radical cation and anion as well as the dication and dianion species by in situ EPR/UV/Vis-NIR spectroelectrochemistry is provided. The excellent optical and redox properties combined with helical geometries render them possibly applicable as chiral emitter or ambipolar charge transport material in organic electronics.     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Polymorphy in the stereostructure of periodic polymer backbones

We theoretically investigated the polymorphy of the stereostructures of a periodic polymer. Using the polymer's internal conformation parameters of bond lengths, bond angles, and internal rotation angles, we extended the mathematical treatment for designing polymer backbones. We considered those periodic polymers whose unit cell consists of one (m = 1), two (m = 2), or three (m = 3) kinds of atoms. Moreover, for these three types of polymers, we supposed two catenation types for the skeleton atoms; one is a “homorotatory” sequence and the other is a “heterorotatory” one. To specify the backbone's stereostructure, we introduced several conformation parameters such as the helical pitch number n, the translation distance d, and the inclination angle of the skeleton plane Θ. By combining these parameters, we can systematically understand the variety and the possible polymorphy in the stereostructure of a periodic polymer backbone. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2829–2849, 2003     

Energy calculations on helical polypeptides: Structure of polyglycine II

Single chain and packing energy calculations have been made on polyglycine (threefold and fourfold helical structures) with interchain NH…?O hydrogen bonds. In conformation A of polyglycine, in which the NH groups point away from the helix axis and the CO groups are nearer to the helix axis, the conformational energy is nearly the same for threefold and fourfold structures. However, the minimum energy conformation corresponds to a threefold structure of polyglycine with peptide configurations in conformation B in which the CO groups point away from the helix axis and NH groups are nearer to the helix axis. This structure is consistent with the polyglycine II x-ray diffraction data.     

Towards tobacco mosaic virus-like self-assembled supramolecular architectures

This paper discusses the molecular design of selected examples of structural units containing taper shaped exo-receptors and various crown ether, oligooxyethylenic, and H-bonding based endo-receptors, which self-assemble into cylindrical channel-like architectures via principles resembling those of tobacco mosaic virus (TMV). The ability of these structural units to self- assemble via a delicate combination of exo-and endo-recognition processes will be presented. A comparison between various supramolecular (generated via H-bonding, ionic, and electrostatic interactions) and molecular “polymer backbones” will be made. The present limitations concerning the ability to engineer the structural parameters of these supramolecular channel-like architectures and some possible novel material functions derived from them will be briefly mentioned.     

The Propensity of α‐Aminoisobutyric Acid (=2‐Methylalanine; Aib) to Induce Helical Secondary Structure in an α‐Heptapeptide: A Computational Study

We present a molecular‐dynamics simulation study of an α‐heptapeptide containing an α‐aminoisobutyric acid (=2‐methylalanine; Aib) residue, Val¹‐Ala²‐Leu³‐Aib⁴‐Ile⁵‐Met⁶‐Phe⁷, and a quantum‐mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 3₁₀/α‐helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L ‐Ala, D ‐Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L ‐Ala and D ‐Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C₇ and 3₁₀‐helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α‐helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib‐containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.     

Distinct Helical Molecular Orbitals through Conformational Lock**

Several theoretical studies have proposed strategies to generate helical molecular orbitals (Hel-MOs) in [n]cumulenes and oligoynes. While chiral even-[n] cumulenes feature Hel-MOs, odd-[n] cumulenes may also present them if the terminal groups lie in different planes. However, the proposed systems have been either experimentally unfeasible or resulted in opposite pseudo-degenerated Hel-MOs. We hereby demonstrate the introduction of a remarkable energy difference between helical orbitals of opposite twist by fixing the torsion angle between the terminal groups in butadiyne fragments. To experimentally lock the conformation of the terminal groups, we designed and synthesized cyclic architectures by combining acetylenes with chiral spirobifluorenes. The high stability of these systems with distinct helical orbitals allowed their isolation and full characterization. In our view, these results constitute a step further in the development of real systems presenting helical molecular orbitals.     

A Stimuli-Responsive Macromolecular Gear: Interlocking Dynamic Helical Polymers with Foldamers

Herein, macromolecular gears composed of helical poly(phenylacetylenes) (PPAs) bearing short oligopeptides as pendant groups are described, in which the two structural motifs (framework and substituents) are combined. These gears are obtained by polymerization of the acetylene groups introduced at the C-terminus of short oligopeptides formed by achiral (Aib)_n units (n=1–3) derivatized at the N-terminus by a single enantiomer (R or S) of α-methoxy-α-trifluoromethylphenylacetic acid (MTPA, Mosher's reagent). The chiral information of the MTPA is transmitted to the achiral Aib fragments and, through either chiral tele-induction and/or chiral harvesting mechanisms, is further transferred to the polyene backbones, which adopt preferentially P or M helical senses. Moreover, these materials also show dynamic behavior and respond to the action of external stimuli by either inverting the P/M sense and/or modifying the elongation in fully reversible processes.     

Evidence that the β‐Peptide 14‐Helix is Stabilized by β3‐Residues with Side‐Chain Branching Adjacent to the β‐Carbon Atom

Oligomers of β‐substituted β‐amino acids (‘β³‐peptides') are known to adopt a helical secondary structure defined by 14‐membered ring hydrogen bonds ('14‐helix'). Here, we describe a deca‐β³‐peptide, 1 , that does not adopt the 14‐helical conformation and that may prefer an alternative secondary structure. β³‐Peptide 1 is composed exclusively of residues with side chains that are not branched adjacent to the β‐C‐atom (β³‐hLeu, β³‐hLys, and β³‐hTyr). In contrast, an analogous β‐peptide, 2 , containing β³‐hVal residues in place of the β³‐hLeu residues of 1 , adopts a 14‐helical conformation in MeOH, according to CD data. These results illustrate the importance of side‐chain branching in determining the conformational preferences of β³‐peptides.     

A Stimuli‐Responsive Macromolecular Gear: Interlocking Dynamic Helical Polymers with Foldamers

Herein, macromolecular gears composed of helical poly(phenylacetylenes) (PPAs) bearing short oligopeptides as pendant groups are described, in which the two structural motifs (framework and substituents) are combined. These gears are obtained by polymerization of the acetylene groups introduced at the C‐terminus of short oligopeptides formed by achiral (Aib)_n units (n=1–3) derivatized at the N‐terminus by a single enantiomer (R or S) of α‐methoxy‐α‐trifluoromethylphenylacetic acid (MTPA, Mosher's reagent). The chiral information of the MTPA is transmitted to the achiral Aib fragments and, through either chiral tele‐induction and/or chiral harvesting mechanisms, is further transferred to the polyene backbones, which adopt preferentially P or M helical senses. Moreover, these materials also show dynamic behavior and respond to the action of external stimuli by either inverting the P/M sense and/or modifying the elongation in fully reversible processes.     

Temperature induced structural evolution of a fluorene‐thiophene copolymer on rubbed surfaces

The thermal alignment of the liquid crystalline fluorene‐thiophene copolymer (F8T2) on rubbed polyimide surfaces is investigated by ex‐situ and in‐situ X‐ray scattering experiments. The ex‐situ characterization allows an assignment of the observed diffraction peaks to distances between polymer backbones (1.6 nm), distances between the flexible side groups of the polymer chains (0.43 nm), and intramolecular distances of adjacent ring units (0.5 nm). The in‐situ characterization allows a temperature dependent observation of the polymer chain alignment. A gradual alignment process of the polymer backbones is observed for temperatures up to 563 K. Decreasing temperature after the polymer chain alignment is accompanied by a glass transition of the side chains at 380 K. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47:1599–1604, 2009     

Helicoid Shiftamers for the Transport of π‐Clumps and Charges

Hypothetical helical organic polymers with localized electrons, charges, and/or atoms are described, in which these localized substructures can move along the backbones of the polymers via sigmatropic H shifts.