Anion Recognition by Aliphatic Helical Oligoureas

Anion binding properties of neutral helical foldamers consisting of urea type units in their backbone have been investigated. ¹H NMR titration studies in various organic solvents including DMSO suggest that the interaction between aliphatic oligoureas and anions (CH₃COO^?, H₂PO₄^?, Cl^?) is site‐specific, as it largely involves the urea NHs located at the terminal end of the helix (positive pole of the helix), which do not participate to the helical intramolecular hydrogen‐bonding network. This mode of binding parallels that found in proteins in which anion‐binding sites are frequently found at the N‐terminus of an α‐helix. ¹H NMR studies suggest that the helix of oligoureas remains largely folded upon anion binding, even in the presence of a large excess of the anion. This study points to potentially useful applications of oligourea helices for the selective recognition of small guest molecules.     

Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles

Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer–peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.

When peptides and helical aromatic foldamers are combined in a macrocycle, an interplay of their properties is observed, including helix handedness bias, helix stabilisation, peptide stretching and peptide resistance to proteolytic degradation.     

Reversible Ligand‐Gated Ion Channel via Interconversion between Hollow Single Helix and Intertwined Double Helix

Ligand responsiveness is one of the typical mechanisms in biological organization to trigger sophisticated channel switching. Here, we report a new type of helical trimer which can undergo transition between a hollow single helix and an intertwined double helix with no cavity by complexation and decomplexation of Cu ions. In addition, the one dimensional (1D) hollow helical tubes spontaneously generated from single helices via π‐π interactions embedded into the lipid bilayers and displayed satisfactory channel stability and efficiency. With the addition of Cu^I ions and further extraction with ammonia, the disassembly and reassembly of 1D hollow helical tubes gave rise to the reversible switching of channel activity in situ inside the bilayers. The synthetic helical system provides the first model of reversible ligand‐gated ion channel by means of dynamic transition between single and double helices, which will be available for developing intelligent artificial nanochannels for potential biological and medicinal applications.     

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA–ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

We present the rational design of photoswitchable DNA glue to trigger the reversible formation of duplex DNA by light. The supramolecular assembly shows a mutual interaction between ligand and DNA, which induces a preferred helicity in the switch.     

Increasing the Size of an Aromatic Helical Foldamer Cavity by Strand Intercalation

The postsynthetic modulation of capsules based on helical aromatic oligoamide foldamers would be a powerful approach for controlling their receptor properties without altering the initial monomer sequences. With the goal of developing a method to increase the size of a cavity within a helix, a single‐helical foldamer capsule was synthesized with a wide‐diameter central segment that was designed to intercalate with a second shorter helical strand. Despite the formation of stable double‐helical homodimers (K_dim>10⁷ M ^?1) by the shorter strand, when it was mixed with the single‐helical capsule sequence, a cross‐hybridized double helix was formed with K_a>10⁵ M ^?1. This strategy makes it possible to direct the formation of double‐helical heterodimers. On the basis of solution‐ and solid‐state structural data, this intercalation resulted in an increase in the central‐cavity size to give a new interior volume of approximately 150 ų.     

Controlling the Helix Handedness of ααβ‐Peptide Foldamers through Sequence Shifting

Peptide foldamers containing both cis ‐β‐aminocyclopentanecarboxylic acid and α‐amino acid residues combined in various sequence patterns (ααβ, αααβ, αβααβ, and ααβαααβ) were screened using CD and NMR spectroscopy for the tendency to form helices. ααβ‐Peptides were found to fold into an unprecedented and well‐defined 16/17/15/18/14/17‐helix. By extending the length of the sequence or shifting a fragment of the sequence from one terminus to another in ααβ‐peptides, the balance between left‐handed and right‐handed helix populations present in the solution can be controlled. Engineering of the peptide sequence could lead to compounds with either a strong propensity for the selected helix sense or a mixture of helical conformations of opposite senses.     

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.     

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.     

Beiträge zur Chemie der Pyrrolpigmente; 64. Mitt.

The title compound was prepared by acid catalyzed condensation of the appropriate pyrrole-2,5-dialdehyde and two equivalents of the corresponding pyrromethenone. Its solution structure was deduced by¹⁵N-,¹³C- and¹H-NMR to be the bislactam form with a fixation as the N₂₇-H-tautomer and configuration (4Z, 9Z, 15Z, 20Z) at the exocyclic double bonds. From NOE measurements and a comparison of its UV-VIS spectrum andPPP-SCF-LCAO-MO-CI spectra calculations an overall helical 5sp, 10sp, 14sp, 19sp-conformation with a dihedral angle of 20° at the exocyclic single bonds was deduced. Judging from spin—lattice relaxation times of the methyl groups its flexibility is lowered as compared to bilatrienes-abc. However, its helix interconversion barrier is still low enough to prohibit an identification of the enantiomeric helices, as shown by means of a chiral shift reagent.

Herrn Prof. Dr.O. Hromatka zum 80. Geburtstag gewidmet.     

Reversible Ligand-Gated Ion Channel via Interconversion between Hollow Single Helix and Intertwined Double Helix

Ligand responsiveness is one of the typical mechanisms in biological organization to trigger sophisticated channel switching. Here, we report a new type of helical trimer which can undergo transition between a hollow single helix and an intertwined double helix with no cavity by complexation and decomplexation of Cu ions. In addition, the one dimensional (1D) hollow helical tubes spontaneously generated from single helices via π-π interactions embedded into the lipid bilayers and displayed satisfactory channel stability and efficiency. With the addition of Cu^I ions and further extraction with ammonia, the disassembly and reassembly of 1D hollow helical tubes gave rise to the reversible switching of channel activity in situ inside the bilayers. The synthetic helical system provides the first model of reversible ligand-gated ion channel by means of dynamic transition between single and double helices, which will be available for developing intelligent artificial nanochannels for potential biological and medicinal applications.     

The underappreciated influence of ancillary halide on metal–ligand proton tautomerism

Syntheses of Vaska-type complexes [IrP₂X(CO)] (P = phosphine, X = halide) with all four common halides (fluoride, chloride, bromide, and iodide) was attempted using a protic and hemilabile imidazolyl di-tert-butyl phosphine ligand. In the solid-state, all four complexes were found to be ionic with the halides in the outer-sphere, and the fourth coordination site of the square plane occupied by the imidazole arm of the ligand. In solution, however, the chloride complex was found to be in equilibrium with an octahedral Ir^III–H species at room temperature. For the bromide and iodide analogs, the corresponding Ir^III–H species were also observed but only after heating the solutions. The neutral Ir^I Vaska''s analogs for X = Cl, Br, and I were obtained upon addition of excess halide salt, albeit heating was required for X = Br and I. The Ir^III–H species are proposed to originate from tautomerization of minor amounts of the electron rich neutral Vaska analog (halide inner-sphere and phosphines monodentate) that are in equilibrium with the ionic species. Heating is required for the larger anions of bromide and iodide to overcome a kinetic barrier associated with their movement to an inner-sphere position prior to tautormerization. For the fluoride analog, the Ir^III–H was not observed, attributable to strong hydrogen bonding interactions of the imidazolyl proton with the fluoride anion.

Ligand protonated Ir^I bisphosphine carbonyl complexes isolated as halide salts equilibrate with their neutral Ir^III–H congeners in solution. The equilibrium constant and energy barrier to interconversion are dependent on the identity of the halide.     

Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states

The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I–K–E–I–A–x–Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.

Systematic de novo design of peptides that form α-helical barrels with functionalisable central channels with a range of internal diameters.     

Amplification of weak chiral inductions for excellent control over the helical orientation of discrete topologically chiral (M3L2)n polyhedra

Superb control over the helical chirality of discrete (M₃L₂)_n polyhedra (n = 2,4,8, M = Cu^I or Ag^I) created from the self-assembly of propeller-shaped ligands (L) equipped with chiral side chains is demonstrated here. Almost perfect chiral induction (>99 : 1) of the helical orientation of the framework was achieved for the largest (M₃L₂)₈ cube with 48 small chiral side chains (diameter: ∼5 nm), while no or moderate chiral induction was observed for smaller polyhedra (n = 2, 4). Thus, amplification of the weak chiral inductions of each ligand unit is an efficient way to control the chirality of large discrete nanostructures with high structural complexity.

Superb control over the helical chirality of highly-entangled (M₃L₂)_n polyhedra (M = Cu(i), Ag(i); n = 2,4,8) was achieved via multiplication of weak chiral inductions by side chains accumulated on the huge polyhedral surfaces.     

Selective covalent capture of collagen triple helices with a minimal protecting group strategy

Collagens and their most characteristic structural unit, the triple helix, play many critical roles in living systems which drive interest in preparing mimics of them. However, application of collagen mimetic helices is limited by poor thermal stability, slow rates of folding and poor equilibrium between monomer and trimer. Covalent capture of the self-assembled triple helix can solve these problems while preserving the native three-dimensional structure critical for biological function. Covalent capture takes advantage of strategically placed lysine and glutamate (or aspartate) residues which form stabilizing charge–pair interactions in the supramolecular helix and can subsequently be converted to isopeptide amide bonds under folded, aqueous conditions. While covalent capture is powerful, charge paired residues are frequently found in natural sequences which must be preserved to maintain biological function. Here we describe a minimal protecting group strategy to allow selective covalent capture of specific charge paired residues which leaves other charged residues unaltered. We investigate a series of side chain protecting groups for lysine and glutamate in model peptides for their ability to be deprotected easily and in high yield while maintaining (1) the solubility of the peptides in water, (2) the self-assembly and stability of the triple helix, and (3) the ability to covalently capture unprotected charge pairs. Optimized conditions are then illustrated in peptides derived from Pulmonary Surfactant protein A (SP-A). These covalently captured SP-A triple helices are found to have dramatically improved rates of folding and thermal stability while maintaining unmodified lysine–glutamate pairs in addition to other unmodified chemical functionality. The approach we illustrate allows for the covalent capture of collagen-like triple helices with virtually any sequence, composition or register. This dramatically broadens the utility of the covalent capture approach to the stabilization of biomimetic triple helices and thus also improves the utility of biomimetic collagens generally.

A minimal protecting group strategy is developed to allow selective covalent capture of collagen-like triple helices. This allows stabilization of this critical fold while preserving charge–pair interactions critical for biological applications.     

The generic geometry of helices and their close-packed structures

The formation of helices is an ubiquitous phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical structures have geometrical constraints analogous to close-packing of three-dimensional crystal structures. For helical packing the geometrical constraints involve parameters such as the radius of the helical cylinder, the helical pitch angle, and the helical tube radius. In this communication, the geometrical constraints for single helix, double helix, and for double helices with minor and major grooves are calculated. The results are compared with values from the literature for helical polypeptide backbone structures, the α-, π-, 3₁₀-, and γ-helices. The α-helices are close to being optimally packed in the sense of efficient use of space, i.e. close-packed. They are also more densely packed than the other three types of helices. For double helices comparisons are made to the A, B, and Z forms of DNA. The helical geometry of the A form is nearly close-packed. The packing density for the B and Z forms of DNA are found to be approximately equal to each other.     

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.     

Dynamic chemical devices: generation of reversible extension/contraction molecular motion by ion-triggered single/double helix interconversion

The polyheterocyclic strands 1-H and 2-H adopt a helical shape enforced by the pyridine-pyrimidine helicity codon. The crystal structure of 2-H shows the formation of stacks of dimers of right- and left-handed individual helices. Treatment of 1-H and 2-H with silver triflate results in the generation of double-helical entities 1-DH and 2-DH, containing two strands and two silver ions. NMR studies and determination of the crystal structure of 2-DH indicate that the duplex is stabilized by coordination of each Ag(+) ion to two terminal bipyridine units, one from each strand, and by pronounced pi-pi stacking interactions between the internal heterocycles of the strands, yielding a very robust double helical structure. Reversible interconversion of the single and double helix may be achieved by addition of a cryptand capable of sequestering Ag(+) and releasing it by protonation. Thus, successive addition of acid and base leads to reversible interconversion between the shorter ( approximately 3.6 A) single helix and the longer ( approximately 10.3 A) double helix, resulting in the generation of pronounced extension/contraction motion. The system 1,2-H/1,2-DH represents a dynamic chemical device undergoing ionic modulation of reversible molecular mechanical motion fueled by acid/base neutralization.     

Mechanically induced single-molecule helicity switching of graphene-nanoribbon-fused helicene on Au(111)

Helicene is a functional material with chirality caused by its characteristic helical geometry. The inversion of its helicity by external stimuli is a challenging task in the advanced control of the molecular chirality. This study fabricated a novel helical molecule, specifically a pentahelicene-analogue twisted aromatic hydrocarbon fused with a graphene nanoribbon, via on-surface synthesis using multiple precursors. Noncontact atomic force microscopy imaging with high spatial resolution confirmed the helicity of the reaction products. The helicity was geometrically converted by pushing a CO-terminated tip into the twisted framework, which is the first demonstration of helicity switching at the single-molecule scale.

Graphene nanoribbon-fused helicene was fabricated via on-surface synthesis. The helicity of the product was reversibly switchable by pushing a CO-terminated scanning-probe-microscopy tip into the protruding helical terminal.     

Recognition competes with hydration in anion-triggered monolayer formation of cyanostar supra-amphiphiles at aqueous interfaces

The triggered self-assembly of surfactants into organized layers at aqueous interfaces is important for creating adaptive nanosystems and understanding selective ion extraction. While these transformations require molecular recognition, the underlying driving forces are modified by the local environment in ways that are not well understood. Herein, we investigate the role of ion binding and ion hydration using cyanosurf, which is composed of the cyanostar macrocycle, and its binding to anions that are either size-matched or mis-matched and either weakly or highly hydrated. We utilize the supra-amphiphile concept where anion binding converts cyanosurf into a charged and amphiphilic complex triggering its self-organization into monolayers at the air–water interface. Initially, cyanosurf forms aggregates at the surface of a pure water solution. When the weakly hydrated and size-matched hexafluorophosphate (PF₆⁻) and perchlorate (ClO₄⁻) anions are added, the macrocycles form distinct monolayer architectures. Surface-pressure isotherms reveal significant reorganization of the surface-active molecules upon anion binding while infrared reflection absorption spectroscopy show the ion-bound complexes are well ordered at the interface. Vibrational sum frequency generation spectroscopy shows the water molecules in the interfacial region are highly ordered in response to the charged monolayer of cyanosurf complexes. Consistent with the importance of recognition, we find the smaller mis-matched chloride does not trigger the transformation. However, the size-matched phosphate (H₂PO₄⁻) also does not trigger monolayer formation indicating hydration inhibits its interfacial binding. These studies reveal how anion-selective recognition and hydration both control the binding and thus the switching of a responsive molecular interface.

The selective binding of anions transform macrocycles into amphiphiles that form monolayers on the surface of water depending upon the relative roles of anion hydration and anion recognition.     

Ni(0)-promoted activation of Csp2–H and Csp2–O bonds

A dinickel(0)–N₂ complex, stabilized with a rigid acridane-based PNP pincer ligand, was studied for its ability to activate C(sp²)–H and C(sp²)–O bonds. Stabilized by a Ni–μ–N₂–Na⁺ interaction, it activates C–H bonds of unfunctionalized arenes, affording nickel–aryl and nickel–hydride products. Concomitantly, two sodium cations get reduced to Na(0), which was identified and quantified by several methods. Our experimental results, including product analysis and kinetic measurements, strongly suggest that this C(sp²)–H activation does not follow the typical oxidative addition mechanism occurring at a low-valent single metal centre. Instead, via a bimolecular pathway, two powerfully reducing nickel ions cooperatively activate an arene C–H bond and concomitantly reduce two Lewis acidic alkali metals under ambient conditions. As a novel synthetic protocol, nickel(ii)–aryl species were directly synthesized from nickel(ii) precursors in benzene or toluene with excess Na under ambient conditions. Furthermore, when the dinickel(0)–N₂ complex is accessed via reduction of the nickel(ii)–phenyl species, the resulting phenyl anion deprotonates a C–H bond of glyme or 15-crown-5 leading to C–O bond cleavage, which produces vinyl ether. The dinickel(0)–N₂ species then cleaves the C(sp²)–O bond of vinyl ether to produce a nickel(ii)–vinyl complex. These results may provide a new strategy for the activation of C–H and C–O bonds mediated by a low valent nickel ion supported by a structurally rigidified ligand scaffold.

A structurally rigidified nickel(0) complex was found to be capable of cleaving both C(sp²)–H and C(sp²)–O bonds.