Dendronized supramolecular polymers self‐assembled from dendritic ionic liquids

The synthesis, structural, and retrostructural analysis of a library of self‐assembling dendrons containing triethyl and tripropyl ammonium, pyridinium and 3‐methylimidazolium chloride, tetrafluoroborate, and hexafluorophosphate at their apex are reported. These dendritic ionic liquids self‐assemble into supramolecular columns or spheres which self‐organize into 2D hexagonal or rectangular and 3D cubic or tetragonal liquid crystalline and crystalline lattices. Structural analysis by X‐ray diffraction experiments demonstrated the self‐assembly of supramolecular dendrimers containing columnar and spherical nanoscale ionic liquid reactors segregated in their core. Both in the supramolecular columns and spheres the noncovalent interactions mediated by the ionic liquid provide a supramolecular polymer and therefore, these assemblies represent a new class of dendronized supramolecular polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4165–4193, 2009     

An unusual three‐dimensional chiral threefold polycatenating network self‐assembled from inclined two‐dimensional (4,4) layer motifs

In the coordination compound poly[diaqua(μ₂‐4,4′‐bipyridine)(μ₂‐4‐carboxylatocinnamato)nickel(II)], [Ni(C₁₀H₆O₄)(C₁₀H₈N₂)(H₂O)₂]_n, both the 4‐carboxylatocinnamate and 4,4′‐bipyridine (4,4′‐bpy) ligands act as bidentate bridges, connecting the Ni^II centres in an octahedral coordination geometry into a two‐dimensional (4,4) layer. Each layer polycatenates two other identical layers, thus giving a rare 2D → 3D polycatenating network (2D and 3D are two‐ and three‐dimensional, respectively), with a mutually parallel arrangement of the layers. The chiral 4,4′‐bpy ligands link the Ni^II centres into chiral chains, thus introducing chirality into the layer and the resulting 3D network.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Spontaneous resolution of chiral polyoxometalate-based compounds consisting of 3D chiral inorganic skeletons assembled from different helical units

Four enantiomerically pure 3D chiral POM-based compounds, [Ni(2)(bbi)(2)(H(2)O)(4)V(4)O(12)]2 H(2)O (1 a and 1 b) and [Co(bbi)(H(2)O)V(2)O(6)] (2 a and 2 b) (bbi=1,1'-(1,4-butanediyl)bisimidazole) based on the achiral ligand, different vanadate chains, and different metal centers have been synthesized by hydrothermal methods. Single-crystal X-ray diffraction analyses revealed that 1 a and 1 b, and 2 a and 2 b, respectively, are enantiomers. In 1 a and 1 b two kinds of vanadate chains with different screw axes link Ni cations to generate 3D chiral inorganic skeletons, which are connected by the achiral bbi ligands to form complicated 3D 3,4-connected chiral self-penetrating frameworks with (7(2)8)(7(2)8(2)9(2))(7(3)8(2)10) topology. They represent the first examples of chiral self-penetrating frameworks known for polyoxometalate (POM) systems. Contrary to 1 a and 1 b, in 2 a and 2 b the vanadate chains link Co(II) cations to generate 3D chiral inorganic skeletons, which are assembled from two kinds of heterometallic helical units of opposite chirality along the c axes. The chiral inorganic skeletons are connected by bbi to form 3D 3,4-connected chiral POM-based frameworks with (6(2)8)(2)(6(2)8(2)10(2)) topology. It is believed that the asymmetrical coordination modes of the metal cations in 1 a-2 b generate the initial chiral centers, and that the formation of the various helical units and the hydrogen bond interactions are responsible for preservation of the chirality and spontaneous resolution when the chirality is extended into the homochiral 3D-networks. This is the first known report of chiral POM-based compounds consisting of 3D chiral inorganic skeletons being obtained by spontaneous resolution upon crystallization in the absence of any chiral source, which may provide a rational strategy for synthesis of chiral POM-based compounds by using achiral ligands and POM helical units.     

Tuning the size of supramolecular single‐chain polymer nanoparticles

In this article we further investigate our recently devised method for folding polymer chains into nanoparticles using intramolecular, supramolecular interactions. Specifically, we show a direct relationship between molecular weight of the parent chain and size of the folded nanoparticle. This is investigated both analytically via the separation and subsequent characterization of a polydisperse nanoparticle sample into high and low molecular weight fractions, and by examining a family of poly(norbornenes) deliberately prepared with varying molecular weights. With these polymer nanoparticles in hand their assembly on surfaces is studied where larger structures are formed as a result of the interplay between the movement of the nanoparticles on the surface and the evaporation of solvent. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Separation of single‐base sequential isomers of single‐stranded DNA by capillary electrophoresis and its application in the discrimination of single‐base DNA mutations

Separation of single‐base substitution sequential DNA isomers remains one of the most challenging tasks in DNA separation by capillary electrophoresis. We developed a simple, versatile capillary electrophoresis technique for the separation of single‐base sequential isomers of DNA having the same chain length. This technique is based on charge differences resulting from the different protonation (acid dissociation) properties of the four DNA bases. A mixture of 13 single‐base sequential isomers of 12‐mer single‐stranded DNA was separated by using an electrophoretic buffer solution containing 20 mM phosphoric acid (pH 2.0) and 8 M urea. We demonstrated that our method could separate all possible mutation patterns under identical experimental conditions. In addition, application of our method to the separation of the polymerase chain reaction product of a 68‐mer gene fragment and its single‐base isomers indicates that in combination with the appropriate genomic DNA extraction techniques, the method can detect single‐base gene mutations.     

Self‐assembled supramolecular microgels: Fractal structure and aggregation mechanism

Multifunctional molecules were designed to produce microgels with specific structures. Both static light scattering and dynamic light scattering were employed to determine the fractal dimension of the microgels. The protein, avidin, was strongly bound to four biotin moieties. Biotin was attached covalently to specifically engineered peptide nucleic acid (PNA) oligomers. Three designed DNA oligomers self‐assembled to produce a trifunctional three‐way junction (TWJ) with single‐stranded ends that were complementary to the PNA sequence. The sizes of the supramolecular aggregates were characterized by dynamic light scattering. The fractal dimension was obtained from the angular dependence of the scattered intensity when the microgels were large enough. When the microgels were formed via cooling from a temperature above the melting point of the PNA–DNA helices, reversible structures with a fractal dimension of approximately 1.86 were formed, which is consistent with a cluster–cluster aggregation mechanism. When the microgels were formed by the slow addition of biotinylated PNA bound to the TWJ to a solution of avidin at room temperature, the observed fractal dimension approached 2.6, which is consistent with a point–cluster aggregation mechanism. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 3037–3046, 2003     

Mirror symmetry breaking and chiral amplification in foldamer-based supramolecular helical aggregates

Spontaneous asymmetric generation of supramolecular chiral fibers was observed in the folding induced self-assembly of a lock-washer shaped foldamer. A secondary nucleation growth mechanism is proposed to explain the observed chiral amplification or deracemization of these supramolecular fibers.     

Self-assembly of helical supramolecular channels from chiral aminopyrimidine hydrogen bonding motifs in the solid state

The H-bond mediated self-assembly of the chiral C₂-symmetric bis-(2-amino-4-chloro-pyrimidines) 3 and 4 allows for the molecular recognition directed generation of helical superstructures. In the former case, unoccupied channel structures defined by the cylindrical interior of the derived supramolecular helix result, as revealed by X-ray crystallographic analysis using a synchrotron source. Upon crystallization, racemic 3 spontaneously resolves to form homochiral crystals exhibiting a helical packing motif identical to that determined for optically pure 3. The data provide insight into the interplay of the different structural and interactional features of the molecular components to the generation of the channel structure and suggest design strategies toward porous organic molecular solids of variable size.     

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     

Kinetically controlled Ag+-coordinated chiral supramolecular polymerization accompanying a helical inversion

We report kinetically controlled chiral supramolecular polymerization based on ligand–metal complex with a 3 : 2 (L : Ag⁺) stoichiometry accompanying a helical inversion in water. A new family of bipyridine-based ligands (d-L1, l-L1, d-L2, and d-L3) possessing hydrazine and d- or l-alanine moieties at the alkyl chain groups has been designed and synthesized. Interestingly, upon addition of AgNO₃ (0.5–1.3 equiv.) to the d-L1 solution, it generated the aggregate I composed of the d-L1AgNO₃ complex (d-L1 : Ag⁺ = 1 : 1) as the kinetic product with a spherical structure. Then, aggregate I (nanoparticle) was transformed into the aggregate II (supramolecular polymer) based on the (d-L1)₃Ag₂(NO₃)₂ complex as the thermodynamic product with a fiber structure, which led to the helical inversion from the left-handed (M-type) to the right-handed (P-type) helicity accompanying CD amplification. In contrast, the spherical aggregate I (nanoparticle) composed of the d-L1AgNO₃ complex with the left-handed (M-type) helicity formed in the presence of 2.0 equiv. of AgNO₃ and was not additionally changed, which indicated that it was the thermodynamic product. The chiral supramolecular polymer based on (d-L1)₃Ag₂(NO₃)₂ was produced via a nucleation–elongation mechanism with a cooperative pathway. In thermodynamic study, the standard ΔG° and ΔH_e values for the aggregates I and II were calculated using the van''t Hoff plot. The enhanced ΔG° value of the aggregate II compared to that of the formation of aggregate I confirms that aggregate II was thermodynamically more stable. In the kinetic study, the influence of concentration of AgNO₃ confirmed the initial formation of the aggregate I (nanoparticle), which then evolved to the aggregate II (supramolecular polymer). Thus, the concentration of the (d-L1)₃Ag₂(NO₃)₂ complex in the initial state plays a critical role in generating aggregate II (supramolecular polymer). In particular, NO₃⁻ acts as a critical linker and accelerator in the transformation from the aggregate I to the aggregate II. This is the first example of a system for a kinetically controlled chiral supramolecular polymer that is formed via multiple steps with coordination structural change.

The nanoparticles were transformed into the supramolecular polymer as the thermodynamic product, involving a helical inversion from left-handed to right-handed helicity.     

Molecular tectonics: from enantiomerically pure sugars to enantiomerically pure triple stranded helical coordination network

The self-assembly between a bis-monodentate tecton based on two pyridine units connected to an enantiomerically pure isomannide stereoisomer and HgCl2 leads to the formation of an enantiomerically pure triple stranded helical infinite coordination network which was structurally characterised by X-ray diffraction on single crystal.     

An antibacterial silver(I) supramolecular network assembled from thiophene-2,5-dicarboxylate and benzimidazole

Abstract

A silver(I) supramolecular network Ag(BIm)₂(HTDC) (1) was assembled from thiophene-2,5-dicarboxylic acid (H₂TDC) and benzimidazole (BIm) ligands and characterized by single-crystal X-ray diffraction, elemental analysis, FT-IR, and thermal gravimetric analysis. Complex 1 possesses a two-dimensional structure with a hydrogen-bonded grid network, in which the adjacent [Ag(BIm)₂]⁺ cations and (HTDC)^– are bridged via N–H···O hydrogen bonds forming undulating ribbons. The antibacterial properties of 1 were investigated by determining the minimal inhibitory concentration (MIC), the growth curve of bacteria and zone inhibition value assays against Gram-negative bacterium, Escherichia coli, and Gram-positive bacterium, Staphylococcus aureus. The MIC of 1 against E. coli and S. aureus are 15-20?ppm and 20-30?ppm which showed that 1 has higher antibacterial activity than commercial silver nanoparticles. The mechanism of antibacterial activity of 1 was also discussed.     

A supramolecular ladder‐like network from trimesic acid and pyrazine N,N′‐dioxide

In the title complex, benzene‐1,3,5‐tricarboxylic acid–pyrazine N,N′‐dioxide (2/1), C₉H₆O₆·0.5C₄H₄N₂O₂, cocrystallized trimesic acid (TMA) and pyrazine N,N′‐dioxide (PNO) molecules form strong O—H...O hydrogen bonds, but also important weak C—H...O and dipole–dipole intermolecular interactions, to generate a densely packed three‐dimensional network. PNO molecules lie on inversion centres where they connect pairs of TMA sheets into distinct two‐dimensional hydrogen‐bonded layers perpendicular to the crystallographic ab diagonal.     

A three‐dimensional cadmium(II) coordination polymer with unequal homochiral double‐stranded concentric helical chains

A homochiral helical three‐dimensional coordination polymer, poly[[(μ₂‐acetato‐κ³O,O′:O)(hydroxido‐κO)(μ₄‐5‐nicotinamido‐1H‐1,2,3,4‐tetrazol‐1‐ido‐κ⁵N¹,O:N²:N⁴:N⁵)(μ₃‐5‐nicotinamido‐1H‐1,2,3,4‐tetrazol‐1‐ido‐κ⁴N¹,O:N²:N⁴:N⁵)dicadmium(II)] 0.75‐hydrate], {[Cd₂(C₇H₅N₆O)₂(CH₃COO)(OH)]·0.75H₂O}_n, was synthesized by the reaction of cadmium acetate, N‐(1H‐tetrazol‐5‐yl)isonicotinamide (H‐NTIA), ethanol and H₂O under hydrothermal conditions. The asymmetric unit contains two crystallographically independent Cd^II cations, two deprotonated 5‐nicotinamido‐1H‐1,2,3,4‐tetrazol‐1‐ide (NTIA⁻) ligands, one acetate anion, one hydroxide anion and three independent partially occupied water sites. The two Cd^II cations, with six‐coordinated octahedral and seven‐coordinated pentagonal bipyramidal geometries are located on general sites. The tetrazole group of one symmetry‐independent NTIA⁻ ligand links one of the independent Cd^II cations into 6₁ helical chains, while the other NTIA⁻ ligand links the other independent Cd^II cations into similar but unequal 6₁ helical chains. These chains, with a pitch of 24.937 (5) Å, intertwine into a double‐stranded helix. Each of the double‐stranded 6₁ helices is further connected to six adjacent helical chains through an acetate μ₂‐O atom and the tetrazole group of the NTIA⁻ ligand into a three‐dimensional framework. The helical channel is occupied by the isonicotinamide groups of NTIA⁻ ligands and two helices are connected to each other through the pyridine N and carbonyl O atoms of isonicotinamide groups. In addition, N—H...O and O—H...N hydrogen bonds exist in the complex.     

Discrimination of single‐stranded DNA homopolymers by sieving out G‐quadruplex using tiny solid‐state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single‐base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G‐quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20‐nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105‐nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore‐based DNA sequencing at single‐base level.     

Sequence‐based separation of single‐stranded DNA at high salt concentrations in capillary zone electrophoresis

DNA separation by fragment length can be readily achieved using sieving gels in electrophoresis. Separation by sequence has not been as simple, generally requiring adequate differences in native or induced conformation between single or hybridized strands or differences in thermal or chemical stability of hybridized strands. Previously, it was shown that four single‐stranded DNA (ssDNA) 76‐mers that differ by only a few A‐G substitutions could be separated based solely on sequence by adding guanosine‐5’‐monophosphate to the running buffer in capillary zone electrophoresis (CZE). The separation was attributed to interactions of the ssDNA with self‐assembled guanine‐tetrad structures; however, subsequent studies of an expanded set of ten 76‐mers showed that the separation was a more general phenomenon that occurred at high salt concentrations. With the long‐term goal of using experimental and computational methods to provide insight into the basis of the separation, a set of ssDNA 15‐mers was designed including a poly(dT) 15‐mer and nine variants. Separations were performed using fluorescent‐labeled ssDNA in CZE with laser‐induced fluorescence detection. Results show that separation improves with increasing buffer concentration and decreasing temperature, due at least in part to longer separation times. Migration times increase with increasing purine content, with A having a much larger effect that G. Circular dichroism spectra of the mixtures of the strands suggest that the separation is not due to changes in conformation of the ssDNA at high salt concentrations.     

Interlocked chiral nanotubes assembled from quintuple helices

Homochiral helical chains were rationally synthesized from C2-symmetric 1,1-binaphthyl-6,6'-bipyridine ligands and linear metal-connecting points, Ni(acac)2. Five such homochiral helices associate in parallel to form nanotubes of 2 x 2 nm in dimensions which further intertwine to form periodically ordered, interlocked nanotubular architectures that possess nanometer-scale open channels and have high affinity for aromatic molecules. Chiral crown ethers have also been successfully incorporated into the walls of these nanotubes, which promises to lead to novel chiral zeolitic materials applicable in enantioselective processes.     

Enzyme responsive supramolecular hydrogels assembled from nonionic peptide amphiphiles

Smart peptide hydrogels are of great interest for their great potential applications. Here, we report a facile approach to prepare a class of enzyme-responsive hydrogels in a scalable manner. These hydrogels self-assemble from a family of nonionic peptide amphiphiles(PAs) synthesized by sequential ring-opening polymerization(ROP) of γ-benzyl-L-glutamate N-carboxyanhydride(BLG-NCA) and L-tyrosine N-carboxyanhydride(Tyr-NCA), followed by subsequent aminolysis. These PA samples can readily form a clear hydrogel with a critical gelation concentration as low as 0.5 wt%. The incorporation of tyrosine residues offers hydrophobicity, hydrogen-bonding interaction and enzyme-responsive properties. The hydrogel-to-nanogel transition is observed under physiological conditions in the presence of horseradish peroxidase(HRP) and hydrogen peroxide(H2 O2). The obtained PA hydrogels are ideal candidates for the new generation of smart scaffolds.     

A chiral pinwheel supramolecular network driven by the assembly of PTCDI and melamine

The mixing of perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and 1,3,5-triazine-2,4,6-triamine (melamine) at room temperature in a ratio of 3 : 4 on Au(111) leads to the formation of a new chiral "pinwheel" structure.