Folding of coordination polymers into double-stranded helical organization

Self-assembling coordination polymers based on Pd II and Cu II metal ions were prepared from complexation of a bent-shaped bispyridine ligand and a corresponding transition metal. These coordination polymers were observed to self-assemble into supramolecular structures that differ significantly depending on the coordination geometry of the metal center. The polymer based on Pd II self-assembles into a layer structure formed by bridging bispyridine ligands connected in a trans-position of the square-planar coordination geometry of metal center. In contrast, the polymer based on Cu II adopts a double-helical conformation with regular grooves, driven by interstranded, copper-chloride dimeric interaction. The double-stranded helical organization is further confirmed by structure optimization from density functional theory with aromatic framework, showing that the optimized double-helical structure is energetically favorable and consistent with the experimental results. These results demonstrate that weak metal-ligand bridging interactions can provide a useful strategy to construct stable double-stranded helical nanotubes.     

Helix formation in synthetic polymers by hydrogen bonding with native saccharides in protic media

Water-soluble poly(m-ethynylpyridine)s were designed to realize saccharide recognition in protic media. UV/Vis, 1H NMR, and fluorescence measurements revealed that the polymer forms a helical higher order structure by solvophobic interactions between the ethynylpyridine units in the protic medium. The resulting pore in the helix behaves like a binding pocket in proteins, by taking advantage of inwardly directed hydrogen-bonding functional groups of the polymers. Molecular recognition of native saccharides by the polymers was investigated by circular dichroism (CD). The chirality of the saccharide was transferred to the helical sense of the polymers, accompanied by the appearance of induced CDs (ICDs) in the absorptive region of the polymers. In MeOH/water (10/1), mannose and allose showed intense ICDs, and the apparent association constant between the polymer and D-mannose was 14 M(-1).     

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.     

Self‐assembly of supramolecular polymers into tunable helical structures

There is growing interest in the design of synthetic molecules that are able to self‐assemble into a polymeric chain with compact helical conformations, which is analogous to the folded state of natural proteins. Herein, we highlight supramolecular approach to the formation of helical architectures and their conformational changes driven by external stimuli. Helical organization in synthetic self‐assembling systems can be achieved by the various types of noncovalent interactions, which include hydrogen bonding, solvophobic effects, and metal‐ligand interactions. Since the external environment can have a large influence on the strength and configuration of noncovalent interactions between the individual components, stimulus‐induced alterations in the intramolecular noncovalent interactions can result in dynamic conformational change of the supramolecular helical structure thus, driving significant changes in the properties of the materials. Therefore, these supramolecular helices hold great promise as stimuli‐responsive materials. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1925–1935, 2008     

Diversity of interstrand π—π stacking motifs in the double helices of pyridinedicarboxamide oligomers

Winding of oligoamide strands of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid into molecular duplexes is illustrated by two new crystal structures of double helical dimers. The relative positions of the two strands within the double helices in these two structures are different; they also differ from the structures reported previously. Unlike the single helical structure of the monomeric strands, the double helical motif is not highly stable in the solid state. This implies that the interactions that lead to duplex formation are not directional. It suggests that the two strands have a significant motional freedom in the duplex.     

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.     

Solid-state self-assembly of polymeric double helicates leading to linear arrays of silver(I) ions and reversible strand/double helix interconversion in solution

Reaction of a bent py-hyz-pym-hyz-pym 1 and of a linear py-hyz-py-hyz-pym 3 (py=pyridine; pym=pyrimidine; hyz=hydrazone) ligand strands with silver(I) tetrafluoroborate in CH(3)NO(2) generates double-helical dinuclear 2 and trinuclear 4 complexes. These complexes form polymeric, highly ordered solid-state structures, with wirelike, linear continuous or discontinuous polycationic Ag(n) (+) arrays with Ag--Ag distances of 2.78 to 4.42 A. Ligand 5, an isomer of 1, is found to yield a [2x2] grid-type complex 6. Titration experiments reveal the formation of linear rack-type dinuclear species from 1 and 5. Acid-base modulated, reversible interconversion between strand 1 and double helicate 2 may be achieved by using tren as a competing complexing agent (tren=N(CH(2)CH(2)NH(2))(3)). Progressive addition of silver(I) ions to a 1:1 mixture of 1 and 5 leads to the preferential formation of the double helicate 2 over the grid complex 6, illustrating a process of self-organisation with selection of the correct ligand.     

Polymorphism of hydrogen bonding in the short double helixes of oligonucleotides: Semiempirical quantum chemical study

The origin of heterogeneity of nucleotide steps geometry in short double helixes is studied theoretically. By using the semiempirical MNDO/PM3 technique, the stability of “propeller‐like” and “step‐like” forms of base H‐pairing is examined in the structure of oligonucleotide duplexes of different types. The influence of end effects on the process of nucleotides packing, as well as the dependence of duplex curvature on the nature of bonded oligonucleotides, are examined. It is concluded that the structural polymorphism of base pairs most likely determines the unique packing of complementary pairs and their flexibility in DNA structure. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Messages in molecules: ligand/cation coding and self-recognition in a constitutionally dynamic system of heterometallic double helicates

Double helicates are known to exhibit self-recognition characteristics determined by the coordination geometry of the metal involved as well as by the topicity of the ligands. Combining tridentate (terpyridine, T) or bidentate (bipyridine, B) subunits in a tritopic strand affords a set of ligands able to assemble by pairs to form double helicates, homo- or heterostranded, homo- or heterotopic, depending on the coordination properties of the metals involved. The four ligand strands, BBB, TTT, BBT, and TBT form constitutionally dynamic sets of double helicates with the metal ions Cu(I), Cu(II), and Zn(II); these helicates correspond to the correct coding of the BB, BT, and TT pairs for tetra-, penta-, and hexacoordinate Cu(I), Cu(II), and Zn(II) cations, respectively.     

Effect of stoichiometry on liquid crystalline supramolecular polymers formed with complementary nucleobase pair interactions

We report herein studies on the liquid crystalline behavior of a series of supramolecular materials that contain different ratios of two complementary symmetrically-substituted alkoxy-bis(phenylethynyl)benzene AA- and BB-type monomers. One monomer has thymine units placed at either end of the rigid mesogenic core, while the other has N⁶-(4-methoxybenzoyl)-adenine units placed on the ends. Differential scanning calorimetric and polarized optical microscopy studies have been carried out on these systems. These studies show that the material's behavior is strongly dependent on its thermal history. As a result, the materials can exhibit, on heating, either a liquid crystalline phase, a crystalline phase, or the coexistence of crystalline and liquid crystalline regions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5049–5059, 2006     

DNA-inspired hierarchical polymer design: electrostatics and hydrogen bonding in concert

Nucleic acids and proteins, two of nature's biopolymers, assemble into complex structures to achieve desired biological functions and inspire the design of synthetic macromolecules containing a wide variety of noncovalent interactions including electrostatics and hydrogen bonding. Researchers have incorporated DNA nucleobases into a wide variety of synthetic monomers/polymers achieving stimuli-responsive materials, supramolecular assemblies, and well-controlled macromolecules. Recently, scientists utilized both electrostatics and complementary hydrogen bonding to orthogonally functionalize a polymer backbone through supramolecular assembly. Diverse macromolecules with noncovalent interactions will create materials with properties necessary for biomedical applications.