Interconversion of single and double helices formed from synthetic molecular strands

Aromatic delta-peptides

Oligoamides of 8-amino-2-carboxy-quinoline adopt a very stable helical conformation characterized in solution by 1H NMR and in the solid state by single-crystal X-ray diffraction. The helix comprises only 2.5 units per turn, which represents the highest curvature achieved by aromatic oligoamides until now. Monomers possessing alkoxy substituents in position 4 are easily available from 2-nitroaniline and dimethyl acetylenedicarboxylate.

Self-assembly in palladium(II) and platinum(II) chemistry: the biomimetic approach

The self-assembly of complex cationic structures by combination of cis-blocked square planar palladium(II) or platinum(II) units with bis(pyridyl) ligands having bridging amide units has been investigated. The reactions have yielded dimers, molecular triangles, and polymers depending primarily on the geometry of the bis(pyridyl) ligand. In many cases, the molecular units are further organized in the solid state through hydrogen bonding between amide units or between amide units and anions. The molecular triangle [Pt(3)(bu(2)bipy)(3)(mu-1)(3)](6+), M = Pd or Pt, bu(2)bipy = 4,4'-di-tert-butyl-2,2'-bipyridine, and 1 = N-(4-pyridinyl)isonicotinamide, stacks to give dimers by intertriangle NH.OC hydrogen bonding. The binuclear ring complexes [[Pd(LL)(mu-2)](2)](CF(3)SO(3))(4), LL = dppm = Ph(2)PCH(2)PPh(2) or dppp = Ph(2)P(CH(2))(3)PPh(2) and 2 = NC(5)H(4)-3-CH(2)NHCOCONHCH(2)-3-C(5)H(4)N, form transannular hydrogen bonds between the bridging ligands. The complexes [[Pd(LL)(mu-3)](2)](CF(3)SO(3))(4), LL = dppm or dppp, L = PPh(3), and 3 = N,N'-bis(pyridin-3-yl)-pyridine-2,6-dicarboxamide, and [[Pd(LL)(mu-4)](2)](CF(3)SO(3))(4), LL = dppm, dppp, or bu(2)bipy, L = PPh(3), and 4 = N,N'-bis(pyridin-4-yl)-pyridine-2,6-dicarboxamide, are suggested to exist as U-shaped or square dimers, respectively. The ligands N,N'-bis(pyridin-3-yl)isophthalamide, 5, or N,N'-bis(pyridin-4-yl)isophthalamide, 6, give the complexes [[Pd(LL)(mu-5)](2)](CF(3)SO(3))(4) or [[Pd(LL)(mu-6)](2)](CF(3)SO(3))(4), but when LL = dppm or dppp, the zigzag polymers [[Pd(LL)(mu-6)](x)](CF(3)SO(3))(2)(x) are formed. When LL = dppp, a structure determination shows formation of a laminated sheet structure by hydrogen bonding between amide NH groups and triflate anions of the type NH-OSO-HN.

To fold or to assemble?

We introduce a new class of foldable oligomers consisting of alternating rigid and flexible regions. The rigid segments overlap to give pi-stacked folded conformers whose formation is driven mostly by pi-pi molecular orbital overlaps. As the oligomer concentration increases, the folded molecular structures further self-assemble into larger nanostructures. The dynamic processes of folding and self-organization are monitored with absorption, fluorescence, and NMR spectroscopies. Our results show that folding dominates at low concentrations (< approximately 1 mM) and precedes self-assembly, which occurs over the initial concentration range of approximately 1-100 mM.

Aromatic oligomers that form hetero duplexes in aqueous solution

The electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) and electron-rich 1,5-dialkoxynaphthalene (Dan) have been shown to complex strongly with each other in water due to the hydrophobic effect as modulated through the electrostatic complementarity of the stacked dimer. Previously, oligomers of alternating Ndi and Dan units, termed aedamers, were the first foldamers to employ intramolecular aromatic stacking to effect the formation of secondary structure of nonnatural chains in aqueous solution. Described here is the use of this aromatic-aromatic (or pi-pi) interaction, this time in an intermolecular format, to demonstrate the self-assembly of stable hetero duplexes from a set of molecular strands (1a-4a) and (1b-4b) incorporating Ndi and Dan units, respectively. A 1-to-1 binding stoichiometry was determined from NMR and isothermal titration calorimetry (ITC) investigations, and these experiments indicated that association is enthalpically favored with the tetra-Ndi (4a) and tetra-Dan (4b) strands forming hetero duplexes (4a:4b) with a stability constant of 350 000 M-1 at T = 318 K. Polyacrylamide gel electrophoresis (PAGE) also illustrated the strong interaction between 4a and 4b and support a 1-to-1 binding mode even when one component is in slight excess. Overall, this system is the first to utilize complementary aromatic units to drive discrete self-assembly in aqueous solution. This new approach for designing assemblies is encouraging for future development of duplex systems with highly programmable modes of binding in solution or on surfaces.

Dendronized molecular knots: selective synthesis of various generations, enantiomer separation, circular dichroism

For the first time, knot molecules (of the amide type) are synthesized, which bear one to three dendritic units of various generations at their periphery. They were obtained through two different routes: i) attachment of dendritic wedges to new mono-, di- and trihydroxy functionalized dodecaamide knots that have been obtained by selective debenzylation of oligobenzyloxy substituted knots, or ii) cyclization of already dendron substituted pyridine-2,6-dicarbonyl dichlorides with an "extended diamine" to directly yield the "tri-dendroknots". The derivatization of knot molecules by functional substituents and even large dendritic units is an important advance in the synthesis and property variation of molecular knots. This holds true in particular for substitution of the pyridine units of the knots, whereas the isophthalic acid units seem not to tolerate larger substitutents, as reflected in lower knot yields. These syntheses also demonstrate knots to be accessible indirectly by substitution of the corresponding mono-, di- and tri-functionalized knot skeleton. An advantage of dendritic "decoration" is the control of solubility and chromatographic behaviour of the molecular knots (knotanes). Suggestions are made about the threading mechanism by supramolecular template effects leading to the formation of amide-based molecular knots. The topological chirality of the new "dendroknots" is shown by efficient enantioseparations (separation factor alpha between 1.22 and 1.48). For this purpose (commercially unavailable) chiral column material of the Chiralpak type was used, in which the chiral component is covalently bonded to the silica gel support. The racemate splittings provide additional evidence for the knotted structure, as all other conceivable isomers such as macromonocyclic or catenated dodecaamides would not be chiral. The pure enantiomers obtained exhibit pronounced Cotton effects in their circular dichroism spectra. By comparison with the unsubstituted knot, the absolute configuration (Lambda, Delta) of all new knots is derived.

Self-assembly of dipeptidyl ureas: a new class of hydrogen-bonded molecular duplexes

The dipeptidyl urea 1 composed of two dipeptide chains bearing the C-terminal pyridyl moiety (-L-Ala-L-Pro-NHPy) was prepared. Two molecules of 1 are revealed to be held together by six intermolecular hydrogen bonds to form a hydrogen-bonded duplex by the single-crystal X-ray structure determination. Proton magnetic resonance nuclear Overhauser effect (NOE) study indicates the hydrogen-bonded duplex even in solution. Furthermore, a shuttle-like molecular dynamics based on recombination of the hydrogen bonds was observed. The dipeptidyl urea composed of two dipeptide chains bearing the C-terminal pyrenyl moiety (-L-Ala-L-Pro-NHCH(2)Pyr) exhibited both monomer and eximer emissions in the fluorescence spectra, supporting the formation of a duplex. A combination of the C-terminal amide NH function in each side and the designed sequence of hydrogen-bonding sites are considered to be a crucial factor for the duplex formation.

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

Folding-driven synthesis of oligomers

The biological function of biomacromolecules such as DNA and enzymes depends on their ability to perform and control molecular association, catalysis, self-replication or other chemical processes. In the case of proteins in particular, the dependence of these functions on the three-dimensional protein conformation is long known and has inspired the development of synthetic oligomers and polymers with the capacity to fold in a controlled manner, but it remains challenging to design these so-called 'foldamers' so that they are capable of inducing or controlling chemical processes and interactions. Here we show that the stability gained from folding can be used to control the synthesis of oligomers from short chain segments reversibly ligated through an imine metathesis reaction. That is, folding shifts the ligation equilibrium in favour of conformationally ordered sequences, so that oligomers having the most stable solution structures form preferentially. Crystallization has previously been used to shift an equilibrium in order to indirectly influence the synthesis of small molecules, but the present approach to selectively prepare macromolecules with stable conformations directly connects folding and synthesis, emphasizing molecular function rather than structure in polymer synthesis.

Crescent oligoamides: from acyclic "macrocycles" to folding nanotubes

Oligoarylamides whose backbones are rigidified by intramolecular hydrogen bonds (H-bonds) are found to adopt well-defined conformations in both solution and solid state. Depending on the length of their backbones, these folding oligoamides are crescents, broken macrocycles, or helices. A large (approximately 10 A) interior cavity is associated with the "macrocycles" and helices. The folded conformations are independent of chain length and are found in both nonpolar and polar solvents. This strategy is being extended to the construction of folding acyclic "macrocycles" and nanotubes with larger tubular cavities.

The covalent casting of one-dimensional hydrogen bonding motifs: toward oligomers and polymers of predefined topography

The covalent casting of noncovalent architectures serves to define large covalent constructs that express well-defined modes of aggregation. In the case of one-dimensional hydrogen-bonding motifs, covalent casting yields molecular strands that adopt a duplex mode of aggregation. The effectiveness of this design principle is illustrated through the casting of the aminotriazine hydrogen-bonding motif. These studies have led to the conception of a new family of topographically defined oligomers, which, akin to DNA, self-assemble in the form of a duplex through the action of interstrand hydrogen bonds.