Molecular design and synthesis of artificial double helices

This account describes novel artificial double helices recently developed by our group. We have designed and synthesized the double helices consisting of two complementary, m-terphenyl-based strands that are intertwined through chiral amidinium-carboxylate salt bridges. Due to the chiral substituents on the amidine groups, the double helices adopted an excess one-handed helical conformation in solution as well as in the solid state. By extending the modular strategy, we have synthesized double helices bearing Pt(II) linkers, which underwent the double helix-to-double helix transformations through the chemical reactions of the Pt(II) complex moieties. In addition, artificial double-stranded metallosupramolecular helical polymers were constructed by combining the salt bridges and metal coordination. In contrast to the design-oriented double helices based on salt bridges, we have serendipitously developed a spiroborate-based double helicate bearing oligophenol strands. The optical resolution of the helicate was successfully attained by a diastereomeric salt formation. We have also unexpectedly found that oligoresorcinols consisting of a very simple repeating unit self-assemble into double helices with the aid of aromatic interactions in water. Furthermore, a bias in the twist sense of the double helices can be achieved by incorporating chiral substituents at both ends of the strands.     

Two luminescent enantiomorphic 3D metal-organic frameworks with 3D homochiral double helices

Two enantiomorphic Cd(II) coordination polymers with three-dimensional homochiral double helices have been assembled respectively from two tripodal enantiopure amino acid derivatives, which exhibit (3,4)-connected (6(3))(6(3).10(3)) topology and strong purple fluorescence.     

Design of Aromatic Helical Polymers for STM Visualization: Imaging of Single and Double Helices with a Pattern of π–π Stacking

From scanning tunneling microscopy (STM) images of rationally designed helical polymers with a pattern of π–π stacking, we successfully identified the single‐ and double‐helical superstructures. The STM images of the helical structures revealed the smallest helical architecture (diameter ca. 1.3 nm) that has been seen so far. Furthermore, the interconversion of single and double helices was further underpinned by experimental analyses. Significantly, the formation of double helices induced different supramolecular chirality to that observed for the single helices.     

Thermodynamics and structural aspect of the gelling process in the gellan gum/metal salt aqueous solutions

Gellan gum undergoes gelation by forming domains composed of associated double helices. Here the further random aggregation of associated double helices seems necessary for the formation of the network in the case of Na-gellan with adding NaCl. Gellan gum aqueous solutions were prepared with or without adding various concentrations of NaCl, and their gel-sol transitions were observed by the differential scanning calorimetry (DSC) and the small-angle X-ray scattering (SAXS). The DSC endothermic peaks are attributed to the dissociation of the ordered domains, and the network dissociation in the case of gel samples. The SAXS results are analyzed in terms of the molecular models of associated double helices. This revised version was published online in July 2006 with corrections to the Cover Date.     

Formation of double helix self-assembled monolayers of ethynylhelicene oligomer disulfides on gold surfaces

Optically active ethynylhelicene pentamers and hexamers linked by disulfide bonds were synthesized. They formed self-assembled monolayers (SAMs) with double helix structure on gold surfaces, which were analyzed by infrared reflection-absorption spectroscopy (IR-RAS), quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and circular dichroism (CD). Double helix SAMs could be formed on gold surfaces either from double helices or random coils in solution. The double helices on the surface were more stable than in solution. This result suggested the presence of strong intercomplex interactions between double helix complexes on the surface.     

Synthesis of complementary double-stranded helical oligomers through chiral and achiral amidinium-carboxylate salt bridges and chiral amplification in their double-helix formation

A series of complementary molecular strands from 2-mer to 5-mer that are composed of m-terphenyl units bearing chiral/achiral amidine or achiral carboxyl groups linked via Pt(II) acetylide complexes were synthesized by sequential stepwise reactions, and their chiroptical properties on the double-helix formation were investigated by circular dichroism (CD) and (1)H NMR spectroscopies. In CHCl(3), the "all-chiral" amidine strands consisting of (R)- or (S)-amidine units formed preferred-handed double helices with the complementary achiral carboxylic acid strands through the amidinium-carboxylate salt bridges, resulting in characteristic induced CDs in the Pt(II) acetylide complex regions, indicating that the chiral substituents on the amidine units biased a helical sense preference. The Cotton effect patterns and intensities were highly dependent on the molecular lengths. The complementary double-helix formation was also explored using the chiral/achiral amidine strands with different sequences in which a chiral amidine unit was introduced at the center (center-chiral) or a terminus (edge-chiral) of the amidine strands. The effect of the sequences of the chiral and achiral amidine units on the amplification of chirality (the "sergeants and soldiers" effect) in the double-helix formation was investigated by comparing the CD intensities with those of the corresponding all-chiral amidine double helices with the same molecular lengths. Variable-temperature CD experiments of the all-chiral and chiral/achiral amidine duplexes demonstrated that the Pt(II)-linked complementary duplexes are dynamic and their chiroptical properties including the chirality transfer from the chiral amidine unit to the achiral amidine ones are significantly affected by the molecular lengths, sequences, and temperatures. On the basis of the above results together with molecular dynamics simulation results, key structural features of the Pt(II)-linked oligomer duplexes and the effect of the chiral/achiral amidine sequences on the amplification of chirality are discussed.     

Thermodynamic and kinetic stabilities of complementary double helices utilizing amidinium-carboxylate salt bridges

A series of dimer strands consisting of m-terphenyl backbones bearing complementary chiral or achiral amidines and achiral carboxylic acid residues connected by various types of linkers, such as diacetylene, Pt(II)-acetylide, and p-diethynylbenzene linkages, were synthesized by a modular strategy, and their chiroptical properties on the complementary double helix formations were investigated by absorption, circular dichroism (CD), and (1)H NMR spectroscopies. The thermodynamic and kinetic stabilities of the complementary double helices assisted by amidinium-carboxylate salt bridges are highly dependent on their linkages, and the thermodynamic analyses of the dimer duplexes revealed that the association constants increased in the order: Pt(II)-acetylide linker < p-diethynylbenzene linker < diacetylene linker, which is in agreement with the reverse order of their bulkiness. The substituents on the amidine groups were also found to affect the stabilities on the duplexes and the association constants increased in the order: isopropyl < (R)-1-phenylethyl < cyclohexyl. In addition, the introduction of electron-donating and/or electron-withdrawing substituents at the phenyl groups of the p-diethynylbenzene linkers connecting the amidine and carboxylic acid units, respectively, tends to stabilize the complementary double helices, especially in polar solvents, such as DMSO, due to the attractive charge-transfer interactions between the aromatic linkers, although the salt bridge formation is hampered in DMSO. Furthermore, the kinetic analyses of the chain exchange reactions for the duplexes bearing diacetylene and p-diethynylbenzene linkages showed that these were slow processes with negative ΔS([symbol: see text]) values, meaning that the chain exchange reactions proceed via direct exchange pathways. In contrast, those for the duplexes bearing Pt(II)-acetylide linkages were fast processes supported by positive ΔS([symbol: see text]) values, suggesting that the chain exchange reactions proceed via dissociation-exchange ones. The helix-inversion kinetics investigated for the racemic dimer duplexes composed of achiral amidines based on variable-temperature (1)H NMR measurements indicated that the barriers for the helix-inversion increased in the order: Pt(II)-acetylide linker, p-diethynylbenzene linker < diacetylene linker.     

Enantioselective Assembly of a Ruthenium(II) Polypyridyl Complex into a Double Helix

Evolution can increase the complexity of matter by self‐organization into helical architectures, the best example being the DNA double helix. One common aspect, apparently shared by most of these architectures, is the presence of covalent bonds within the helix backbone. Here, we report the unprecedented crystal structures of a metal complex that self‐organizes into a continuous double helical structure, assembled by non‐covalent building blocks. Built up solely by weak stacking interactions, this alternating tread stairs‐like double helical assembly mimics the DNA double helix structure. Starting from a racemic mixture in aqueous solution, the ruthenium(II) polypyridyl complex forms two polymorphic structures of a left‐handed double helical assembly of only the Λ‐enantiomer. The stacking of the helices is different in both polymorphs: a crossed woodpile structure versus a parallel columnar stacking.     

Detailed investigation of gel–sol transition temperature of κ-carrageenan studied by DSC, TMA and FBM

A broad temperature range of the gel–sol transition of κ-carrageenan was precisely examined by differential scanning calorimetry (DSC), thermomechanical analysis (TMA) and the falling ball method (FBM). κ-Carrageenan the transition temperature of which ranged from 290 to 350 K was used as a representative sample of a thermo-reversible hydrogel. The starting of transition attributed to dissociation of the weak cross-linking zone of aggregated double helices was detected as a change of expansion coefficient by TMA and as an endothermic deviation by DSC. Peak temperature of endotherm by DSC agreed well with the temperature where expansion changed from positive to negative value and this temperature was attributed to gel–sol transition caused by dissociation of double helices’ assembly. Transition temperature measured by FBM was observed at a temperature higher than those obtained by DSC and TMA, which was attributed to decomposition of double helices.     

Oligoresorcinols fold into double helices in water

We report the first double helices with a controlled helicity in water based on oligoresorcinols as a new, simplest water-soluble structural motif. The molecular strands of the oligoresorcinols self-assemble into double helices with the aid of aromatic interactions in water as characterized by 1H NMR and absorption spectroscopies together with the X-ray crystallographic study of the pentamer. The double helix formation is sensitive to the chain length, solvent composition, and temperature. Moreover, a bias in the screw sense of the double helices was achieved by covalently attaching chiral substituents to both ends of the molecular strands.     

A ternary copper(II) complex for supramolecular assembly with double helices: synthesis,crystal structure,DNA-binding and DNA-cleavage properties

A ternary Cu(II) complex, [Cu(naph-ser)(bipy)]·0.125CH₂Cl₂ (naph-ser = a Schiff base derived from 2-hydroxy-1-naphthaldehyde and l-serine, bipy = 2, 2′-bipyridine), has been synthesized and structurally characterized. In the crystal structure, a supramolecular assembly with left-handed double helices is formed by O–H···O hydrogen bonding interactions. The DNA-binding properties and DNA-cleavage activity of the Cu(II) complex have been investigated by spectroscopic methods and agarose gel electrophoresis. The results indicate that the Cu(II) complex can bind to CT-DNA via an intercalative mode and shows efficient cleavage activity in the absence and presence of reducer.     

Thermoreversible gelation strongly coupled to coil-to-helix transition of polymers

This paper theoretically studies thermoreversible gelation driven by aggregation of helices formed on the polymer chains. Two fundamentally different cases of (i) multiple association of single helices and (ii) association by multiple helices with multiplicity k (such as double helices (k=2), triple helices (k=3), etc.) are treated on the basis of different equations. The helix length distribution on a polymer chain (or assemble of chains for multiple helices) is derived as a function of polymer concentration and temperature. Theoretical calculation of the total helix content in the solution is compared with experimental data of optical rotation in iota-carrageenan solutions at different polymer concentrations. It is shown that at low temperature there is a sharp transition from network to bundle state (pair, triplet, etc.). To confirm such a network/pairing transition, we carried out Monte Carlo simulation of polymer solution in which hydrogen-bonded zipper-like cross-links are formed.     

Halogen Bonding Directed Supramolecular Quadruple and Double Helices from Hydrogen‐Bonded Arylamide Foldamers

Halogen bonding has been used to glue together hydrogen‐bonded short arylamide foldamers to achieve new supramolecular double and quadruple helices in the solid state. Three compounds, which bear a pyridine at one end and either a CF₂I or fluorinated iodobenzene group at the other end, engage in head‐to‐tail N???I halogen bonds to form one‐component supramolecular P and M helices, which stack to afford supramolecular double‐stranded helices. One of the double helices can dimerize to form a G‐quadruplex‐like supramolecular quadruple helix. Another symmetric compound, which bears a pyridine at each end, binds to ICF₂CF₂I through N???I halogen bonds to form two‐component supramolecular P and M helices, with one turn consisting of four (2+2) molecules. Half of the pyridine‐bearing molecules in two P helices and two M helices stack alternatingly to form another supramolecular quadruple helix. Another half of the pyridine‐bearing molecules in such quadruple helices stack alternatingly with counterparts from neighboring quadruple helices, leading to unique quadruple helical arrays in two‐dimensional space.     

A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern

A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.     

Double‐Stranded Helical Oligomers Covalently Bridged by Rotary Cyclic Boronate Esters

Novel double helices covalently bridged by cyclic boronate esters were synthesized from complementary dimers with an m ‐terphenyl backbone joined by a chiral or achiral phenylene linker bearing diethyl boronates and diols, respectively. The X‐ray crystallographic analysis and variable‐temperature NMR and circular dichroism measurements, along with theoretical calculations, revealed that the double helices function as a “molecular rotor” in which the cyclic boronate ester units rotate, yielding two stable rotamers at low temperatures. Moreover, our data indicates that the covalently bonded double helices can undergo a unique helix‐inversion simultaneously with a rotational motion of the boronate esters.     

Chiral tether-mediated stabilization and helix-sense control of complementary metallo-double helices

A series of novel Pt^II-linked double helices were prepared by inter- or intrastrand ligand-exchange reactions of the complementary duplexes composed of chiral or achiral amidine dimer and achiral carboxylic acid dimer strands joined by trans-Pt^II–acetylide complexes with PPh₃ ligands using chiral and achiral chelating diphosphines. The structure and stability of the Pt^II-linked double helices were highly dependent on the diphosphine structures. An interstrand ligand exchange took place with chiral and achiral 1,3-diphosphine-based ligands, resulting in trans-Pt^II-bridged double helices, whose helical structures were quite stable even in dimethyl sulfoxide (DMSO) due to the interstrand cross-link, whereas a 1,2-diphosphine-based ligand produced non-cross-linked cis-Pt^II-linked duplexes, resulting from an intrastrand ligand-exchange that readily dissociated into single strands in DMSO. When enantiopure 1,3-diphosphine-based ligands were used, the resulting trans-Pt^II-bridged double helices adopted a preferred-handed helical sense biased by the chirality of the bridged diphosphines. Interestingly, the interstrand ligand exchange with racemic 1,3-diphosphine toward an optically-active Pt^II-linked duplex, composed of chiral amidine and achiral carboxylic acid strands, was found to proceed in a diastereoselective manner, thus forming complete homochiral trans-Pt^II-bridged double helices via a unique chiral self-sorting.     

Electron attachment induced proton transfer in a DNA nucleoside pair: 2'-deoxyguanosine-2'-deoxycytidine

To elucidate electron attachment induced damage in the DNA double helix, electron attachment to the 2'-deoxyribonucleoside pair dG:dC has been studied with the reliably calibrated B3LYP/DZP++ theoretical approach. The exploration of the potential energy surface of the neutral and anionic dG:dC pairs predicts a positive electron affinity for dG:dC [0.83 eV for adiabatic electron affinity (EAad) and 0.16 eV for vertical electron affinity (VEA)]. The substantial increases in the electron affinity of dG:dC (by 0.50 eV for EAad and 0.23 eV for VEA) compared to those of the dC nucleoside suggest that electron attachment to DNA double helices should be energetically favored with respect to the single strands. Most importantly, electron attachment to the dC moiety in the dG:dC pair is found to be able to trigger the proton transfer in the dG:dC- pair, surprisingly resulting in the lower energy distonic anionic complex d(G-H)-:d(C+H).. The negative charge for the latter system is located on the base of dC in the dG:dC- pair, while it is transferred to d(G-H) in d(G-H)-:d(C+H)., accompanied by the proton transfer from N1(dG) to N3(dC). The low energy barrier (2.4 kcal/mol) for proton transfer from dG to dC- suggests that the distonic d(G-H)-:d(C+H). pair should be one of the important intermediates in the process of electron attachment to DNA double helices. The formation of the neutral nucleoside radical d(C+H). is predicted to be the direct result of electron attachment to the DNA double helices. Since the neutral radical d(C+H). nucleotide is the key element in the formation of this DNA lesion, electron attachment might be one of the important factors that trigger the formation of abasic sites in DNA double helices.     

Control of helix formation in vinylogous gamma-peptides by (E)- and (Z)-double bonds: a way to ion channels and monomolecular nanotubes

[structure: see text] A complete overview on the alternative and competitive helices in vinylogous gamma-peptides is given, which was obtained on the basis of a systematic conformational analysis at various levels of ab initio MO theory (HF/6-31G*, DFT/B3LYP/6-31G*, PCM/HF/6-31G*). Contrary to the parent gamma-peptides, there is a strict control of helix formation by the configuration of the double bond between the C(alpha) and C(beta) atoms of the monomer constituents. (E)-Double bonds favor helices with larger pseudocycles beginning with 14- up to 27-membered hydrogen-bonded rings, whereas the (Z)-configuration of the double bonds supports a distinct preference of helices with smaller seven- and nine-membered pseudocycles showing interactions between nearest-neighbor peptide bonds. The rather stable helices of the (E)-vinylogous peptides with 22-, 24-, and 27-membered hydrogen-bonded pseudocycles have inner diameters large enough to let molecules or ions pass. Thus, they could be interesting model compounds for the design of membrane channels and monomolecular nanotubes. Since (E)- and (Z)-vinylogous gamma-amino acids and their oligomers are synthetically accessible, our study may stimulate structure research in this novel field of foldamers.     

Thermoreversible gelation strongly coupled to polymer conformational transition

Thermoreversible gelation of polymers driven by the coil-to-helix transition in chain conformation is theoretically studied. For pairwise association of single helices, there are three fundamental types of self-assemblies as a result of competition between helix growth and helix association: Type I network (random coils connected by paired short helices), Type II network (helices connected by short random coils) and pairing (pairs of long helices without branching). Two distinct phase diagrams showing sol/gel transition and coil/helix transition are derived for weak and strong association.