Water-soluble J-type rosette nanotubes with giant molar ellipticity

Size Selective Corona Interactions from Self-Assembled Rosette and Single-Walled Carbon Nanotubes

Nanoparticle corona phases, especially those surrounding anisotropic particles, are central to determining their catalytic, molecular recognition, and interfacial properties. It remains a longstanding challenge to chemically synthesize and control such phases at the nanoparticle surface. In this work, the supramolecular chemistry of rosette nanotubes (RNTs), well-defined hierarchically self-assembled nanostructures formed from heteroaromatic bicyclic bases, is used to create molecularly precise and continuous corona phases on single-walled carbon nanotubes (SWCNTs). These RNT-SWCNT (RS) complexes exhibit the lowest solvent-exposed surface area (147.8 ± 60 m^-1 ) measured to date due to its regular structure. Through Raman spectroscopy, molecular-scale control of the free volume is also observed between the two annular structures and the effects of confined water. SWCNT photoluminescence (PL) within the RNT is also modulated considerably as a function of their diameter and chirality, especially for the (11, 1) species, where a PL increase compared to other species can be attributed to their chiral angle and the RNT's inward facing electron densities. In summary, RNT chemistry is extended to the problem of chemically defining both the exterior and interior corona interfaces of an encapsulated particle, thereby opening the door to precision control of core-shell nanoparticle interfaces.

Chiral nanotubes self-assembled from discrete non-covalent macrocycles

Many strategies have been used to construct supramolecular hollow tubes, including helical folding of oligomers, bundling of rod-like structures, rolling-up of sheets and stacking of covalent cycles. On the other hand, controlling chirality at the supramolecular level continues attracting much interest because of its implications in future applications of porous systems. This review article covers the main examples in the literature that use simple molecular structures as chiral units for precise assembly into discrete non-covalent cyclic structures that are able to form chiral supramolecular tubular systems.

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.

Controlling Ultra-Large Optical Asymmetry in Amorphous Molecular Aggregations

Although ultra-large optical asymmetry appears in crystalline materials, distractions from the mesoscopic ordering often causes inauthenticity in chiropticity. In amorphous materials, however, it remains challenging and elusive to achieve large chiropticity. Herein, we report the quantitative control of chiral amplification, on amorphous supramolecular structures of cholesteryl-linked bis(dipyrrinato)zinc(II), to an exceptionally high level. A proper chiral packing of the building block at several molecular scale considerably contributes to the absorptive dissymmetry factor g_abs , although the system is overall disordered. The intense and tunable aggregation strength renders a variable g_abs value up to +0.10 and +0.31 in the solution and in film state. On this basis, a superior ON-OFF switching of chiropticity is realized under external stimuli. This work establishes a general design principle to control over ultra-large optical asymmetry on a wider scope of chiral materials.

Unnatural bases for recognition of noncoding nucleic acid interfaces

The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.

Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors

Rosette nanotubes (RNTs) are a class of materials formed by molecular self-assembly of a fused guanine-cytosine base (G∧C base). An important feature of these self-assembled nanotubes is their precise atomic structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present experimental observations of ion transport across 1.1 nm inner diameter RNT porins (RNTPs) of various lengths in the range 5-200 nm. In a typical experiment, custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl solution indicate ion transport rates of ∼50 ions s^-1 V^-1 m, which for short channels amounts to conductance values of ∼1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-molecule sensors and selective nanofilters with tunable functionality through chemistry.

Guidelines for the assembly of hydrogen-bonded macrocycles

This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.

Hydrogen-bonded rosettes comprising π-conjugated systems as building blocks for functional one-dimensional assemblies

Hydrogen-bonded supermacrocycles (rosettes) are attractive disk-shaped noncovalent synthons for extended functional columnar nanoassemblies. They can serve not only as noncovalent monomer units for supramolecular polymers and discrete oligomers in a dilute solution but also as constituent entities for soft matters such as gels and lyotropic/thermotropic liquid crystals. However, what are the merits of using supramolecular rosettes instead of using expanded π-conjugated covalent molecules? This review covers the self-assembly of photochemically and electrochemically active π-conjugated molecules through the formation of supramolecular rosettes via directional complementary multiple hydrogen-bonding interactions. These rosettes comprising π-conjugated covalent functional units stack into columnar nanoassemblies with unique structures and properties. By overviewing the design principle, characterization, and properties and functionalities of various examples, we illustrate the merits of utilizing rosette motifs. Basically, one can easily access a well-defined expanded π-surface composed of multi-chromophoric systems, which can ultimately afford stable extended nanoassemblies even in a dilute solution due to the higher association constants of supermacrocyclized π-systems. Importantly, these columnar nanoassemblies exhibit unique features in self-assembly processes, chiroptical, photophysical and electrochemical properties, nanoscale morphologies, and bulk properties. Moreover, the stimuli responsiveness of individual building blocks can be amplified to a greater extent by exploiting rosette intermediates to organize them into one-dimensional columnar structures. In the latter parts of the review, we also highlight the application of rosettes in supramolecular polymer systems, photovoltaic devices, and others.

Possible Existence of α-Sheets in the Amyloid Fibrils Formed by a TTR105-115 Mutant

Herein, we combine several methods to characterize the fibrils formed by a TTR105-115 mutant in which Leu111 is replaced by the unnatural amino acid aspartic acid 4-methyl ester. We find that this mutant peptide exhibits significantly different aggregation behavior than the wild-type peptide: (1) it forms fibrils with a much faster rate, (2) its fibrils lack the long-range helical twists observed in TTR105-115 fibrils, (3) its fibrils exhibit a giant far-UV circular dichroism signal, and (4) its fibrils give rise to an unusual amide I' band consisting of four distinct and sharp peaks. On the basis of these results and also several previous computational studies, we hypothesize that the fibrils formed by this TTR mutant peptide contain both β- and α-sheets.

Light-induced unfolding and refolding of supramolecular polymer nanofibres

Unlike classical covalent polymers, one-dimensionally (1D) elongated supramolecular polymers (SPs) can be encoded with high degrees of internal order by the cooperative aggregation of molecular subunits, which endows these SPs with extraordinary properties and functions. However, this internal order has not yet been exploited to generate and dynamically control well-defined higher-order (secondary) conformations of the SP backbone, which may induce functionality that is comparable to protein folding/unfolding. Herein, we report light-induced conformational changes of SPs based on the 1D exotic stacking of hydrogen-bonded azobenzene hexamers. The stacking causes a unique internal order that leads to spontaneous curvature, which allows accessing conformations that range from randomly folded to helically folded coils. The reversible photoisomerization of the azobenzene moiety destroys or recovers the curvature of the main chain, which demonstrates external control over the SP conformation that may ultimately lead to biological functions.

Dynamically controlling the conformations of 1D elongated supramolecular polymers can induce functions comparable to protein folding/unfolding. Here the authors show light-induced conformational changes of azobenzene-based supramolecular polymers from helically coiled to extended/randomly coiled conformations.

Assembled molecular face-rotating polyhedra to transfer chirality from two to three dimensions

In nature, protein subunits on the capsids of many icosahedral viruses form rotational patterns, and mathematicians also incorporate asymmetric patterns into faces of polyhedra. Chemists have constructed molecular polyhedra with vacant or highly symmetric faces, but very little is known about constructing polyhedra with asymmetric faces. Here we report a strategy to embellish a C_3h truxene unit with rotational patterns into the faces of an octahedron, forming chiral octahedra that exhibit the largest molar ellipticity ever reported, to the best of our knowledge. The directionalities of the facial rotations can be controlled by vertices to achieve identical rotational directionality on each face, resembling the homo-directionality of virus capsids. Investigations of the kinetics and mechanism reveal that non-covalent interaction among the faces is essential to the facial homo-directionality.

Protein subunits on the capsids of icosahedral viruses can form patterns with rotational symmetry, which are difficult to recreate in the laboratory. Here the authors report a strategy to construct 3D chiral polyhedra with rotational faces from 2D chiral truxene-based units through dynamic covalent chemistry.

Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces

Cyclization into closed assemblies is the most recurrent approach to realize the noncovalent synthesis of discrete, well-defined nanostructures. This review article particularly focuses on the noncovalent synthesis of monocyclic hydrogen-bonded systems that are self-assembled from a single molecule with two binding-sites. Taking advantage of intramolecular binding events, which are favored with respect to intermolecular binding in solution, can afford quantitative amounts of a given supramolecular species under thermodynamic control. The size of the assembly depends on geometric issues such as the monomer structure and the directionality of the binding interaction, whereas the fidelity achieved relies largely on structural preorganization, low degrees of conformational flexibility, and templating effects. Here, we discuss several examples described in the literature in which cycles of different sizes, from dimers to hexamers, are studied by diverse solution or surface characterization techniques.

Molecular and supramolecular chemistry of rosette nanotubes

Synthetic strategies used to tune the properties of a class of supramolecular 1D nanostructures, the rosette nanotubes, are reviewed herein.

Rosette Nanotubes Alter IgE-Mediated Degranulation in the Rat Basophilic Leukemia (RBL)-2H3 Cell Line

In this study, the effects of rosette nanotube (RNT) exposure on immune cell viability and function were investigated in vitro using the rat basophilic leukemia (RBL)-2H3 cell line. RBL-2H3 viability was decreased in a dose- and time-dependent manner after lysine-functionalized RNT (K-RNT) exposure. In addition, K-RNTs had a significant effect on RBL-2H3 degranulation. When K-RNT exposure was concurrent with IgE sensitization, 50 and 100 mg l(-1) K-RNTs elicited a heightened degranulatory response compared with IgE alone. Exposure to 50 and 100 mg l(-1) K-RNTs also caused degranulation in RBL-2H3 cells not sensitized with IgE (0 ng ml(-1) IgE). Furthermore, in cells preexposed to K-RNTs for 2 h and subsequently washed, sensitized, and stimulated with IgE, a potentiated degranulatory response was observed. Using confocal laser scanning microscopy and a fluorescein isothiocyanate (FITC)-functionalized RNT construct (termed FITC(1)/TBL(19)-RNT), we demonstrated a strong and direct affiliation between RNTs and RBL-2H3 cell membranes. We also demonstrated cellular internalization of RNTs after 2 h of exposure. Together, these data demonstrate that RNTs may affiliate with the cellular membrane of RBL-2H3 cells and can be internalized. These interactions can affect viability and alter the ability of these cells to elicit IgE-FcεR mediated degranulation.

Radiosynthesis of [18F]ATPFU: a potential PET ligand for mTOR

Mammalian target of rapamycin (mTOR) plays a pivotal role in many aspects of cellular proliferation, and recent evidence suggests that an altered mTOR signaling pathway plays a central role in the pathogenesis of aging, tumor progression, neuropsychiatric, and major depressive disorder. Availability of a mTOR-specific PET tracer will facilitate monitoring early response to treatment with mTOR inhibitors that are under clinical development. Towards this we have developed the radiosynthesis of [(18)F]1-(4-(4-(8-oxa-3-azabicyclo[3.2.1]octan-3-yl)-1-(2,2,2-trifluoroethyl)-1H-pyrazolo[3,4-d]pyrimidin-6-yl)phenyl)-3-(2-fluoroethyl)urea [(18)F]ATPFU ([(18)F]1) as an mTOR PET ligand. Synthesis of reference 1 and the precursor for radiolabeling, 4-(4-8-oxa-3-azabicyclo[3.2.1]-octan-3yl)-1-(2,2,2-trifluoroethyl)-1H-pyrazolo[3,4-d]pyrimidin-6yl)aniline (10), were achieved from beta-chloroaldehyde 3 in 4 and 5 steps, respectively, with an overall yield of 25-28%. [(18)F]Fluoroethylamine was prepared by heating N-[2-(toluene-4-sulfonyloxy)ethyl]phthalimide with [(18)F]fluoride ion in acetonitrile. [(18)F]1 was obtained by slow distillation under argon of [(18) F]FCH2CH2NH2 into amine 10 that was pre-treated with triphosgene at 0-5 °C. The total time required for the two-step radiosynthesis including semi-preparative HPLC purification was 90 min, and the overall radiochemical yield of [(18)F]1 for the process was 15 ± 5% based on [(18)F]fluoride ion (decay corrected). At the end of synthesis (EOS), the specific activity was 37-74 GBq/µmol (N = 6).

Chiromers: conformation-driven mirror-image supramolecular chirality isomerism identified in a new class of helical rosette nanotubes

Rosette nanotubes are biologically inspired nanostructures, formed through the hierarchical organization of a hybrid DNA base analogue (G∧C), which features hydrogen-bonding arrays of guanine and cytosine. Several twin-G∧C motifs functionalized with chiral moieties, which undergo a self-assembly process under methanolic and aqueous conditions to produce helical rosette nanotubes (RNTs), were synthesized and characterized. The built-in molecular chirality in the twin-G∧C building blocks led to the supramolecular chirality exhibited by the RNTs, as evidenced by the CD activity. Depending on the motifs and environmental conditions, mirror-image supramolecular chirality due to absolute molecular chirality, solvent-induced and structure-dependent supramolecular chirality inversion, and pH-controlled chiroptical switching were observed.

Light-induced disassembly of self-assembled vesicle-capped nanotubes observed in real time

Molecular self-assembly is the basis for the formation of numerous artificial nanostructures. The self-organization of peptides, amphiphilic molecules composed of fused benzene rings and other functional molecules into nanotubes is of particular interest. However, the design of dynamic, complex self-organized systems that are responsive to external stimuli remains a significant challenge. Here, we report self-assembled, vesicle-capped nanotubes that can be selectively disassembled by irradiation. The walls of the nanotubes are 3-nm-thick bilayers and are made from amphiphilic molecules with two hydrophobic legs that interdigitate when the molecules self-assemble into bilayers. In the presence of phospholipids, a phase separation between the phospholipids and the amphiphilic molecules creates nanotubes, which are end-capped by vesicles that can be chemically altered or removed and reattached without affecting the nanotubes. The presence of a photoswitchable and fluorescent core in the amphiphilic molecules allows fast and highly controlled disassembly of the nanotubes on irradiation, and distinct disassembly processes can be observed in real time using fluorescence microscopy.

Determinants of cyanuric acid and melamine assembly in water

While the recognition of cyanuric acid (CA) by melamine (M) and their derivatives has been known to occur in both water and organic solvents for some time, analysis of CA/M assembly in water has not been reported (Ranganathan, A.; Pedireddi, V. R.; Rao, C. N. R. J. Am. Chem. Soc.1999, 121, 1752-1753; Mathias, J. P.; Simanek, E. E.; Seto, C. T.; Whitesides, G. M. Macromol. Symp.1994, 77, 157-166; Zerkowski, J. A.; MacDonald, J. C.; Seto, C. T.; Wierda, D. A.; Whitesides, G. M. J. Am. Chem. Soc.1994, 116, 2382-2391; Mathias, J. P.; Seto, C. T.; Whitesides, G. M. Polym. Prepr.1993, 34, 92-93; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1993, 115, 905-916; Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1992, 114, 5473-5475; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1990, 112, 6409-6411; Wang, Y.; Wei, B.; Wang, Q. J. Chem. Cryst.1990, 20, 79-84; ten Cate, M. G. J.; Huskens, J.; Crego-Calama, M.; Reinhoudt, D. N. Chem.-Eur. J.2004, 10, 3632-3639). We have examined assembly of CA/M, as well as assembly of soluble trivalent CA and M derivatives (TCA/TM), in aqueous solvent, using a combination of solution phase NMR, isothermal titration and differential scanning calorimetry (ITC/DSC), cryo-transmission electron microscopy (cryo-TEM), and synthetic chemistry. While the parent heterocycles coprecipitate in water, the trivalent system displays more controlled and cooperative assembly that occurs at lower concentrations than the parent and yields a stable nanoparticle suspension. The assembly of both parent and trivalent systems is rigorously 1:1 and proceeds as an exothermic, proton-transfer coupled process in neutral pH water. Though CA and M are considered canonical hydrogen-bonding motifs in organic solvents, we find that their assembly in water is driven in large part by enthalpically favorable surface-area burial, similar to what is observed with nucleic acid recognition. There are currently few synthetic systems capable of robust molecular recognition in water that do not rely on native recognition motifs, possibly due to an incomplete understanding of recognition processes in water. This study establishes a detailed conceptual framework for considering CA/M heterocycle recognition in water which enables the future design of molecular recognition systems that function in water.

Rational construction of perylene bisimide columnar superstructures with a biased helical sense

Discotic supramolecular complexes bearing six perylene bisimide (PBI) chromophores were prepared by mixing monotopically triple-hydrogen-bonding melamines equipped with two PBI chromophores and two 3,7-dimethyloctyl chiral handles with tritopically triple-hydrogen-bonding cyanuric acid (CA). UV/Vis and fluorescence titration experiments demonstrated that the discotic complexes were formed in methylcyclohexane by the 3:1 complexation between the melamines and CA. TEM and AFM studies revealed that the complexes hierarchically organize into fibrous columnar assemblies, which eventually results in the formation of organogels. Circular dichroism (CD) and flash-photolysis time resolved microwave conductivity measurements revealed the presence of extended chiral stacks of PBI chromophores within the columns. The anisotropy factors of the columnar assemblies are remarkably high (g=1.5×10(-3)) when considering the presence of only one 3,7-dimethyloctyl chiral handle per perylene chromophore, suggesting that the columnar structures have a biased helical sense. The fact that the chiral centers are located inside the discotic complexes rather than at their peripheries might be unique structural property responsible for the rather strong optical activities for the assemblies of this chromophore. The effective transcription of the molecular chirality to the extended columnar assemblies through the formation of unique discotic complexes enables the expression of "majority-rules" chiral amplification effect, which is unprecedented for the supramolecular assemblies of PBIs.