Biocomplementary interaction behavior in DNA‐like and RNA‐like polymers

A series of nucleobased polymers and copolymers were synthesized through atom transfer radical polymerization (ATRP). Biocomplementary DNA‐ and RNA‐like supramolecular complexes are formed in dilute DMSO solution through nucleobase recognition. ¹H NMR titration studies of these complexes in CDCl₃ indicated that thymine‐adenine (T‐A) and uracil‐adenine (U‐A) complexes form rapidly on the NMR time scale with high association constants (up to 534 and 671 M^–1, respectively) and result in significant T_g increase. WAXD and differential scanning calorimetry analyzes in the bulk state indicate the presence of highly physical cross‐linked structures and provide further details into the nature of the self‐assembly of these systems. Furthermore, this study is of discussion on the difference in the hydrogen bond strength between T‐A and U‐A base pairs within polymer systems, indicating that the strength of hydrogen bonds in RNA U‐A pairs is stronger than that in DNA T‐A base pairs. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6388–6395, 2009     

1‐[5‐(4,5‐Dimethyl‐1,3,2‐dioxaborolan‐2‐yl)thiophen‐2‐yl]ethanone and 4‐(4,4,5,5‐tetramethyl‐1,3,2‐dioxaborolan‐2‐yl)benzaldehyde

In both title compounds, C₁₀H₁₃BO₃S, (I), and C₁₃H₁₇BO₃, (II), the molecules adopt nearly planar conformations. The crystal packing of (I) consists of a supramolecular two‐dimensional network with a herringbone‐like topology formed by self assembly of centrosymmetric pairs of molecules linked via dipole–dipole interactions. The crystal structure of (II) consists of a supramolecular two‐dimensional network built up from centrosymmetric pairs of molecules viaπ–π interactions. These pairs of molecules are self‐organized in an offset fashion related by a symmetry centre, generating supramolecular ribbons running along the [101] direction. Neighbouring ribbons are stacked via complementary van der Waals and hydrophobic methyl–methyl interactions.     

A Supramolecular Sorting Hat: Stereocontrol in Metal–Ligand Self‐Assembly by Complementary Hydrogen Bonding

A combination of self‐complementary hydrogen bonding and metal–ligand interactions allows stereocontrol in the self‐assembly of prochiral ligand scaffolds. A unique, non‐tetrahedral M₄L₆ structure is observed upon multicomponent self‐assembly of 2,7‐diaminofluorenol with 2‐formylpyridine and Fe(ClO₄)₂. The stereochemical outcome of the assembly is controlled by self‐complementary hydrogen bonding between both individual ligands and a suitably sized counterion as template. This hydrogen‐bonding‐mediated stereoselective metal–ligand assembly allows the controlled formation of nonsymmetric discrete cage structures from previously unexploited ligand scaffolds.     

Controlled Stacking and Unstacking of Peripheral Chlorophyll Units Drives the Spring‐Like Contraction and Expansion of a Semi‐Artificial Helical Polymer

Developing new strategies for controlling polymer conformations through precise molecular recognition can potentially generate a machine‐like motion that is dependent on molecular information—an important process for the preparation of new intelligent nanomaterials (e.g., polymer‐based nanomachines) in the field bordering between polymer chemistry and conventional supramolecular sciences. Herein, we propose a strategy to endow a helical polymer chain with dynamic spring‐like (contraction/expansion) motion through the one‐dimensional self‐assembly (aggregation/disaggregation) of peripheral amphiphilic molecules. In this developing system, we employed a semi‐artificial helical polysaccharide presenting peripheral amphiphilic chlorophyll units as a power device that undergoes contractive motion in aqueous media, driven by strong π–π interactions of its chlorophyll units or by cooperative molecular recognition of bipyridyl‐type ligands through pairs of chlorophyll units, thereby converting molecular information into the regulated motion of a spring. In addition, this system also undergoes expansive motion through coordination of pyridine. We anticipate that this strategy will be applicable (when combined with the established wrapping chemistry of the helical polysaccharide) to the development of, for example, drug carriers (e.g., nano‐syringes), actuators (stimuli‐responsive films), and directional transporters (nano‐railways), thereby extending the frontiers of supramolecular science.     

Nanoarchitectonics beyond Self‐Assembly: Challenges to Create Bio‐Like Hierarchic Organization

Incorporation of non‐equilibrium actions in the sequence of self‐assembly processes would be an effective means to establish bio‐like high functionality hierarchical assemblies. As a novel methodology beyond self‐assembly, nanoarchitectonics, which has as its aim the fabrication of functional materials systems from nanoscopic units through the methodological fusion of nanotechnology with other scientific disciplines including organic synthesis, supramolecular chemistry, microfabrication, and bio‐process, has been applied to this strategy. The application of non‐equilibrium factors to conventional self‐assembly processes is discussed on the basis of examples of directed assembly, Langmuir–Blodgett assembly, and layer‐by‐layer assembly. In particular, examples of the fabrication of hierarchical functional structures using bio‐active components such as proteins or by the combination of bio‐components and two‐dimensional nanomaterials, are described. Methodologies described in this review article highlight possible approaches using the nanoarchitectonics concept beyond self‐assembly for creation of bio‐like higher functionalities and hierarchical structural organization.     

Cooperative Effect of a Classical and a Weak Hydrogen Bond for the Metal‐Induced Construction of a Self‐Assembled β‐Turn Mimic

A novel metal‐induced template for the self‐assembly of two independent phosphane ligands by means of unprecedented multiple noncovalent interactions (classical hydrogen bond, weak hydrogen bond, metal coordination, π‐stacking interaction) was developed and investigated. Our results address the importance and capability of weak hydrogen bonds (WHBs) as important attractive interactions in self‐assembling processes based on molecular recognition. Together with a classical hydrogen bond, WHBs may serve as promoters for the specific self‐assembly of complementary monomeric phosphane ligands into supramolecular hybrid structures. The formation of an intermolecular C? H???N hydrogen bond and its persistence in the solid state and in solution was studied by X‐ray crystal analysis, mass spectrometry and NMR spectroscopy analysis. Further evidence was demonstrated by DFT calculations, which gave specific geometric parameters for the proposed conformations and allowed us to estimate the energy involved in the hydrogen bonds that are responsible for the molecular recognition process. The presented template can be regarded as a new type of self‐assembled β‐turn mimic or supramolecular pseudo amino acid for the nucleation of β‐sheet structures when attached to oligopeptides.     

Specific Intermolecular Interactions in the Supramolecular Structure of 5‐Hydroxy‐6‐Methyluracil: A DFT Study of the Hydrogen‐bonded Dimers

Studying the self‐assembly of uracil derivatives has great importance for biochemistry and nanotechnology. For example, modification of the sorbent surfaces by 5‐hydroxy‐6‐methyluracil (HMU ) enhances their adsorption activity. It is assumed that these changes are caused by the self‐assembly of the network‐like supramolecular associates of the uracil derivative on the sorbent surface. In the present work, the relative stabilities of 15 hydrogen‐bonded dimers HMU have been studied by the TPSSh /TZVP density functional theory method and the strengths of the noncovalent interactions analyzed in terms of the reduced density gradient and natural bond orbital approaches. It was found that the symmetric dimer stabilized by two intermolecular hydrogen bonds N1 –H∙∙∙O–C2 (dimer 1‐1) is the most stable. This suggests that the self‐assembly of HMU should occur through the intermediate formation of the dimer 1‐1. The results may be useful for understanding the processes of self‐assembly of the uracil derivatives and the rationalized design of the uracil‐based supramolecular structures with specific properties.     

Spontaneous Self‐Assembly of a Mono‐Component Polyimide Bearing Terminal Hydrogen‐Bonding Sites in a Single Solvent

A unique example of macromolecular self‐assembly, where a mono‐component homopolyimide bearing carboxy end‐groups spontaneously forms nanopartilces with novel dimple‐like morphology in a single good solvent, is presented. The self‐assembly process is dramatically affected by the solution concentration and the temperature. It is proposed that such an unexpected self‐assembly behavior is a synergistic result of the self‐complementary hydrogen bonding between carboxy end‐groups and the propensity to parallel packing of polyimide chains through aromatic interactions.

     

Photoinduced Triplet–Triplet Energy Transfer in a 2‐Ureido‐4(1H)‐Pyrimidinone‐Bridged,Quadruply Hydrogen‐Bonded Ferrocene–Fullerene Assembly

2‐Ureido‐4(1H)‐pyrimidinone‐bridged ferrocene–fullerene assembly I is designed and synthesized for elaborating the photoinduced electron‐transfer processes in self‐complementary quadruply hydrogen‐bonded modules. Unexpectedly, steady‐state and time‐resolved spectroscopy reveal an inefficient electron‐transfer process from the ferrocene to the singlet or triplet excited state of the fullerene, although the electron‐transfer reactions are thermodynamically feasible. Instead, an effective intra‐assembly triplet–triplet energy‐transfer process is found to be operative in assembly I with a rate constant of 9.2×10⁵ s^?1 and an efficiency of 73 % in CH₂Cl₂ at room temperature.     

Host–Guest Binding‐Site‐Tunable Self‐Assembly of Stimuli‐Responsive Supramolecular Polymers

Despite the remarkable progress made in controllable self‐assembly of stimuli‐responsive supramolecular polymers (SSPs), a basic issue that has not been consideration to date is the essential binding site. The noncovalent binding sites, which connect the building blocks and endow supramolecular polymers with their ability to respond to stimuli, are expected to strongly affect the self‐assembly of SSPs. Herein, the design and synthesis of a dual‐stimuli thermo‐ and photoresponsive Y‐shaped supramolecular polymer (SSP2) with two adjacent β‐cyclodextrin/azobenzene (β‐CD/Azo) binding sites, and another SSP (SSP1) with similar building blocks, but only one β‐CD/Azo binding site as a control, are described. Upon gradually increasing the polymer solution temperature or irradiating with UV light, SSP2 self‐assemblies with a higher binding‐site distribution density; exhibits a flower‐like morphology, smaller size, and more stable dynamic aggregation process; and greater controllability for drug‐release behavior than those observed with SSP1 self‐assemblies. The host–guest binding‐site‐tunable self‐assembly was attributed to the positive cooperativity generated among adjacent binding sites on the surfaces of SSP2 self‐assemblies. This work is beneficial for precisely controlling the structural parameters and controlled release function of SSP self‐assemblies.     

Macroscopic Self‐Assembly Based on Complementary Interactions between Nucleobase Pairs

We have created a selective macroscopic self‐assembly process by using polymer gels modified with complementary DNA oligonucleotides or nucleobases. The hydrogels modified with complementary DNA oligonucleotides adhered to each other by simple contact. The organogels modified with complementary nucleobases selectively formed macroscopic assemblies by agitation in nonpolar organic solvents. The adhesion strength of each gel was estimated semi‐quantitatively by stress–strain measurements. We achieved direct adhesion between macroscopic materials both in water and in organic media, based on complementary hydrogen bonds.     

Hydrogen‐Bonding‐Mediated Vesicular Assembly of Functionalized Naphthalene–Diimide‐Based Bolaamphiphile and Guest‐Induced Gelation in Water

This paper describes the spontaneous vesicular assembly of a naphthalene–diimide (NDI)‐based non‐ionic bolaamphiphile in aqueous medium by using the synergistic effects of π‐stacking and hydrogen bonding. Site isolation of the hydrogen‐bonding functionality (hydrazide), a strategy that has been adopted so elegantly in nature, has been executed in this system to protect these moieties from the bulk water so that the distinct role of hydrogen bonding in the self‐assembly of hydrazide‐functionalized NDI building blocks could be realized, even in aqueous solution. Furthermore, the electron‐deficient NDI‐based bolaamphiphile could engage in donor–acceptor (D–A) charge‐transfer (CT) interactions with a water‐insoluble electron‐rich pyrene donor by virtue of intercalation of the latter chromophore in between two NDI building blocks. Remarkably, even when pyrene was located between two NDI blocks, intermolecular hydrogen‐bonding networks between the NDI‐linked hydrazide groups could be retained. However, time‐dependent AFM studies revealed that the radius of curvature of the alternately stacked D–A assembly increased significantly, thereby leading to intervesicular fusion, which eventually resulted in rupturing of the membrane to form 1D fibers. Such 2D‐to‐1D morphological transition produced CT‐mediated hydrogels at relatively higher concentrations. Instead of pyrene, when a water‐soluble carboxylate‐functionalized pyrene derivative was used as the intercalator, non‐covalent tunable in‐situ surface‐functionalization could be achieved, as evidenced by the zeta‐potential measurements.     

Effect of Head‐Group Chemistry on Surface‐Mediated Molecular Self‐Assembly

Surface molecular self‐assembly is a fast advancing field with broad applications in sensing, patterning, device assembly, and biochemical applications. A vast number of practical systems utilize alkane thiols supported on gold surfaces. Whereas a strong Au? S bond facilitates robust self‐assembly, the interaction is so strong that the surface is reconstructed, leaving etch pits that render the monolayers susceptible to degradation. By using different head group elements to adcust the molecule–surface interaction, a vast array of new systems with novel properties may be formed. In this paper we use a carefully chosen set of molecules to make a direct comparison of the self‐assembly of thioether, selenoether, and phosphine species on Au(111). Using the herringbone reconstruction of gold as a sensitive readout of molecule–surface interaction strength, we correlate head‐group chemistry with monolayer (ML) properties. It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S. We find that the structure of the monolayers can be explained by the geometry of the molecules in terms of dipolar, quadrupolar, or van der Waals interactions between neighboring species driving the assembly of distinct ordered arrays. As this study directly compares one element with another in simple systems, it may serve as a guide for the design of self‐assembled monolayers with novel structures and properties.     

Metal‐Folded Single‐Chain Nanoparticle: Nanoclusters and Self‐Assembled Reduction‐Responsive Sub‐5‐nm Discrete Subdomains

Easy access to discrete nanoclusters in metal‐folded single‐chain nanoparticles (metal‐SCNPs) and independent ultrafine sudomains in the assemblies via coordination‐driven self‐assembly of hydrophilic copolymer containing 9% imidazole groups is reported herein. ¹H NMR, dynamic light scattering, and NMR diffusion‐ordered spectroscopy results demonstrate self‐assembly into metal‐SCNPs (>70% imidazole‐units folded) by neutralization in the presence of Cu(II) in water to pH 4.6. Further neutralization induces self‐assembly of metal‐SCNPs (pH 4.6–5.0) and shrinkage (pH 5.0–5.6), with concurrent restraining residual imidazole motifs and hydrophilic segment, which organized into constant nanoparticles over pH 5.6–7.5. Atomic force microscopy results evidence discrete 1.2 nm nanoclusters and sub‐5‐nm subdomains in metal‐SCNP and assembled nanoparticle. Reduction of metal center using sodium ascorbate induces structural rearrangement to one order lower than the precursor. Enzyme mimic catalysis required media‐tunable discrete ultrafine interiors in metal‐SCNPs and assemblies have hence been achieved.     

Quantifying Hydrogen‐Bond Populations in Dimethyl Sulfoxide/Water Mixtures

Dimethyl sulfoxide (DMSO) disrupts the hydrogen‐bond networks in water. The widespread use of DMSO as a cosolvent, along with its unusual attributes, have inspired numerous studies. Herein, infrared absorption spectroscopy of the S=O stretching mode combined with molecular dynamics and quantum chemistry models were used to directly quantify DMSO/water hydrogen‐bond populations in binary mixtures. Singly H‐bonded species are dominant at 10 mol %, due to strong DMSO–water interactions. We found an unexpected increase in non‐hydrogen‐bonded DMSO near the eutectic point (ca. 35 mol %) which also correlates with several abnormalities in the bulk solution properties. We find evidence for three distinct regimes: 1) strong DMSO–water interactions (<30 mol %), 2) ideal‐solution‐like (30–90 mol %), and 3) self‐interaction, or aggregation, regime (>90 mol %). We propose a “step in” mechanism, which involves hydrogen bonding between water and the DMSO aggregate species.     

Self‐Assembly of Bolaamphiphilic Molecules

The current buzzword in science and technology is self‐assembly and molecular self‐assembly is one of the most prominent fields as far as research in chemical and biological sciences is concerned. Generally, self‐assembly of molecules occurs through weak non‐covalent interactions like hydrogen bonding, π–π stacking, hydrophobic effects, etc. Inspired by many natural systems consisting of self‐assembled structures, scientists have been trying to understand their formation and mimic such processes in the laboratory to create functional “smart” materials, which respond to temperature, light, pH, electromagnetic field, mechanical stress, and/or chemical stimuli. These responses are usually manifested as remarkable changes from the molecular (e. g., conformational state, hierarchical order) to the macroscopic level (e. g., shape, surface properties). Many molecules such as peptides, viruses, and surfactants are known to self‐assemble into different structures. Among them, glycolipids are the new entries in the area of molecules that are being investigated for their self‐assembly characteristics. Among the different classes of glycolipids like rhamnolipids and trehalose lipids, owing to their biological preparations and their structural novelty, sophorolipids (SLs) are evoking greater interest among researchers. Sophorolipids are a class of asymmetric bolas bearing COOH groups at one end and sophorose (dimeric glucose linked by an unusual β(1→2) linkage). The extreme membrane stability of Archaea, attributed to the membrane‐spanning bolas (tetraether glycolipids), has inspired chemists to unravel the molecular designs that underpin the self‐assembly of bolaamphiphilic molecules. Apart from these self‐assembled structures, bolaamphiphiles find applications in many fields such as drug delivery, membrane mimicking, siRNA therapies, etc. The first part of this Personal Account presents some possible self‐assembled structures of bolaamphiphiles and their mechanism of formation. The later part covers our work on one of the typical bolaamphiphiles known as sophorolipids.     

Hydrogen‐Bonding‐Induced Polymorphous Phase Transitions in 2D Organic Nanostructures

The 2D self‐assembly of various 2‐hydroxy‐7‐alkoxy‐9‐fluorenone (HAF) molecules has been investigated by scanning tunneling microscopy (STM) at the liquid/solid interface. A systematic study revealed that HAF molecules with different numbers of carbon atoms in their alkoxy chains could form two or three different kinds of nanostructures, that is, less‐ordered, flower‐like, and zig‐zag patterns, owing to the formation of different types of intermolecular hydrogen bonds. The observed structural transition was found to be driven by molecular thermodynamics, surface diffusion, and the voltage pulse that was applied to the STM tip. The zig‐zag pattern was the most stable of these configurations. An odd–even effect on the flower‐like structure, as induced by the odd and even number of carbon atoms in the side chain, was observed by STM. The influence of the odd–even effect on the melting point has a close relationship with the molecular self‐assembled pattern. Our results are significant for understanding the influence of hydrogen‐bonding interactions on the dominant adsorption behavior on the surface and provide a new visual approach for observing the influence of the odd–even effect on the phase transition.     

Amine‐Directed Hydrogen‐Bonded Two‐Dimensional Supramolecular Structures

Utilizing pure amine hydrogen bonding is a novel approach for constructing two‐dimensional (2D) networks. Further, such systems are capable of undergoing structural modifications due to changes in pH. In this study, we designed a 2D network of triaminobenzene (TAB) molecules that by varying the pH from neutral to acidic, form either ordered or disordered structures on Au(111) surface as revealed in scanning tunneling microscopy images. In near‐neutral solution (pH ≈5.5), protonation of TAB generates charged species capable of forming H‐bonds between amine groups of neighboring molecules resulting in the formation of a 2D supramolecular structure on the electrified surface. At lower pH, due to the protonation of the amine groups, intermolecular hydrogen bonding is no longer possible and no ordered structure is observed on the surface. This opens the possibility to employ pH as a chemical trigger to induce a phase transition in the 2D molecular network of triaminobenzene molecules.     

Hydrogen‐Bonding Induced Alternate Stacking of Donor (D) and Acceptor (A) Chromophores and their Supramolecular Switching to Segregated States

This paper reports comprehensive studies on the mixed assembly of bis‐(trialkoxybenzamide)‐functionalized dialkoxynaphthalene (DAN) donors and naphthalene‐diimide (NDI) acceptors due the cooperative effects of hydrogen bonding, charge‐transfer (CT) interactions, and solvophobic effects. A series of DAN as well as NDI building blocks have been examined (wherein the relative distance between the two amide groups in a particular chromophore is the variable structural parameter) to understand the structure‐dependent variation in mode of supramolecular assembly and morphology (organogel, reverse vesicle, etc.) of the self‐assembled material. Interestingly, it was observed that when the amide functionalities are introduced to enhance the self‐assembly propensity, the mode of co‐assembly among the DAN and NDI chromophores no longer remained trivial and was dictated by a relatively stronger hydrogen‐bonding interaction instead of a weak CT interaction. Consequently, in a highly non‐polar solvent like methylcyclohexane (MCH), although kinetically controlled CT‐gelation was initially noticed, within a few hours the system sacrificed the CT‐interaction and switched over to the more stable self‐sorted gel to maximize the gain in enthalpy from the hydrogen‐bonding interaction. In contrast, in a relatively less non‐polar solvent such as tetrachloroethylene (TCE), in which the strength of hydrogen bonding is inherently weak, the contribution of the CT interaction also had to be accounted for along with hydrogen bonding leading to a stable CT‐state in the gel or solution phase. The stability and morphology of the CT complex and rate of supramolecular switching (from CT to segregated state) were found to be greatly influenced by subtle structural variation of the building blocks, solvent polarity, and the DAN/NDI ratio. For example, in a given D–A pair, by introducing just one methylene unit in the spacer segment of either of the building blocks a complete change in the mode of co‐assembly (CT state or segregated state) and the morphology (1D fiber to 2D reverse vesicle) was observed. The role of solvent polarity, structural variation, and D/A ratio on the nature of co‐assembly, morphology, and the unprecedented supramolecular‐switching phenomenon have been studied by detail spectroscopic and microscopic experiments in a gel as well as in the solution state and are well supported by DFT calculations.     

Thermo/pH Dual Responsive Mixed‐Shell Polymeric Micelles Based on the Complementary Multiple Hydrogen Bonds for Drug Delivery

Thermo/pH dual responsive mixed‐shell polymeric micelles based on multiple hydrogen bonding were prepared by self‐assembly of diaminotriazine‐terminated poly(?‐caprolactone) (DAT‐PCL), uracil‐terminated methoxy poly(ethylene glycol) (MPEG‐U), and uracil‐terminated poly(N‐vinylcaprolactam) (PNVCL‐U) at room temperature. PCL acted as the core and MPEG/PNVCL as the mixed shell. Increasing the temperature, PNVCL collapsed and enclosed the PCL core, while MPEG penetrated through the PNVCL shell, thereby leading to the formation of MPEG channels on the micelles surface. The low cytotoxicity of the mixed micelles was confirmed by an MTT assay against BGC‐823 cells. Studies on the in vitro drug release showed that a much faster release rate was observed at pH 5.0 compared to physiological pH, owing to the dissociation of hydrogen bonds. Therefore, the mixed‐shell polymeric micelles would be very promising candidates in drug delivery systems.