Strategies and Tactics for the Metal-Directed Synthesis of Rotaxanes, Knots, Catenanes, and Higher Order Links
by Roy McBurney
More than a quarter of a century after the first metal template synthesis of a [2]catenane in Strasbourg, there now... more More than a quarter of a century after the first metal template synthesis of a [2]catenane in Strasbourg, there now exists a plethora of strategies available for the construction of mechanically bonded and entwined molecular level structures. Catenanes, rotaxanes, knots and Borromean rings have all been successfully accessed by methods in which metal ions play a pivotal role. Originally metal ions were used solely for their coordination chemistry; acting either to gather and position the building blocks such that subsequent reactions generated the interlocked products or by being an integral part of the rings or “stoppers” of the interlocked assembly. Recently the role of the metal has evolved to encompass catalysis: the metal ions not only organize the building blocks in an entwined or threaded arrangement but also actively promote the reaction that covalently captures the interlocked structure. This Review outlines the diverse strategies that currently exist for forming mechanically bonded molecular structures with metal ions and details the tactics that the chemist can utilize for creating cross-over points, maximizing the yield of interlocked over non-interlocked products, and the reactions-of-choice for the covalent capture of threaded and entwined intermediates.
A synthetic molecular pentafoil knot
by Roy McBurney
Knots are being discovered with increasing frequency in both biological and synthetic macromolecules and have been... more Knots are being discovered with increasing frequency in both biological and synthetic macromolecules and have been fundamental topological targets for chemical synthesis for the past two decades. Here, we report on the synthesis of the most complex non-DNA molecular knot prepared to date: the self-assembly of five bis-aldehyde and five bis-amine building blocks about five metal cations and one chloride anion to form a 160-atom-loop molecular pentafoil knot (five crossing points). The structure and topology of the knot is established by NMR spectroscopy, mass spectrometry and X-ray crystallography, revealing a symmetrical closed-loop double helicate with the chloride anion held at the centre of the pentafoil knot by ten CH···Cl– hydrogen bonds. The one-pot self-assembly reaction features an exceptional number of different design elements—some well precedented and others less well known within the context of directing the formation of (supra)molecular species. We anticipate that the strategies and tactics used here can be applied to the rational synthesis of other higher-order interlocked molecular architectures.
Cover Picture: A star is born
by Roy McBurney
The cover image features the interlaced 'rho' character from Matthew 1:18 in the Lindisfarne
Gospels as a... more
The cover image features the interlaced 'rho' character from Matthew 1:18 in the Lindisfarne
Gospels as a backdrop for the X-ray crystal structure of the most complex non-DNA molecular knot
synthesized so far. A team led by David Leigh prepared the 160-atom-long pentafoil knot in a one-step reaction from ten organic building blocks and five iron(II) cations. They use a single chloride anion as a template, which, in the solid-state structure, is located at the centre of the pentafoil knot and exhibits ten CH...Cl– hydrogen bonds.
Article p15; News & Views p7
IMAGE: JIM CALLAGHAN (EVOLUTION DESIGN) BASED ON AN IMAGE ©THE BRITISH LIBRARY BOARD. (COTTON NERO D. IV, F.29)
COVER DESIGN: ALEX WING
Download (.tif) Evolution of Dynamic Combinatorial Chemistry
F. B. L. Cougnon, J. K. M. Sanders
Since its inception in the mid-1990s, dynamic combinatorial chemistry (DCC), the chemistry of complex systems under... more
Since its inception in the mid-1990s, dynamic combinatorial chemistry (DCC), the chemistry of complex systems under thermodynamic control, has proved valuable in identifying unexpected molecules with remarkable binding properties and in providing effective synthetic routes to complex species. Essentially, in this approach, one designs the experiment rather than the molecule. DCC has also provided us with insights into how some chemical systems respond to external stimuli. Using examples from the work of our laboratory and others, this Account shows how the concept of DCC, inspired by the evolution of living systems, has found an increasing range of applications in diverse areas and has evolved conceptually and experimentally.
A dynamic combinatorial library (DCL) is a thermodynamically controlled mixture of interconverting species that can respond to various stimuli. The Cambridge version of dynamic combinatorial chemistry was initially inspired by the mammalian immune system and was conceived as a way to create and identify new unpredictable receptors. For example, an added template can select and stabilize a strongly binding member of the library which is then amplified at the expense of the unsuccessful library members, minimizing the free energy of the system. But researchers have exploited DCC in a variety of other ways: over the past two decades, this technique has contributed to the evolution of chemistry and to applications in the diverse fields of catalysis, fragrance release, and responsive materials. Among these applications, researchers have built intricate and well-defined architectures such as catenanes or hydrogen-bonded nanotubes, using the ability of complex chemical systems to reach a high level of organization. In addition, DCC has proved a powerful tool for the study of complex molecular networks and systems.
The use of DCC is improving our understanding of chemical and biological systems. The study of folding or self-replicating macrocycles in DCLs has served as a model for appreciating how complex organisations such as life can emerge from a pool of simple chemicals. Today, DCC is no longer restricted to thermodynamic control, and new systems have recently appeared in which kinetic and thermodynamic control coexist. Expanding the realm of DCC to unexplored and promising new territories, these hybrid systems show that the concept of dynamic combinatorial chemistry continues to evolve.
Templated Synthesis of a [3]Catenane
Fabien B. L. Cougnon, Nicholas A. Jenkins, G. Dan Pantoş, Jeremy K. M. Sanders
Three rings: The self-assembly of a water-soluble [3]catenane from a library composed of two linear building blocks,... more Three rings: The self-assembly of a water-soluble [3]catenane from a library composed of two linear building blocks, both terminated by cysteine components, is promoted either by a high salt concentration or by the presence of spermine. The spermine-templated synthesis of the [3]catenane shows that such structures can exhibit strong binding interactions with a biologically relevant target in water under near-physiological conditions.
18 views
Seen by:
Borinic Acids: A Neglected Class of Organoboron Compounds for Recognition of Diols in Aqueous Solution
Chudzinski, M. G.; Chi, Y.; Taylor, M. S. Australian Journal of Chemistry. 2011, 64, 1466-1469.
Association constants between diphenylborinic acids and representative analytes capable of reversible two-point... more Association constants between diphenylborinic acids and representative analytes capable of reversible two-point covalent binding (diols, catechols, and hydroxy acids) were determined using an indicator-displacement assay. Unlike boronic acids, which have been studied in great detail as receptors for diols and related compounds, borinic acids have effectively been ignored as candidates for such applications. The results of this study indicate that diphenylborinic acid displays high affinity for certain analytes of this type in aqueous solution. Of particular interest are differences between the selectivity of the borinic acid and that of a boronic acid of similar pKa towards the series of analytes studied: the borinic acid displays an unusually high level of discrimination for catechols over carbohydrates. The distinct selectivity observed, and the unique opportunities for steric and electronic tuning of diarylborinic acids, suggest that these compounds hold significant potential for applications in aqueous-phase molecular recognition.
Molecular Recognition Effects in Atomistic Models of Imprinted Polymers
In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in... more In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.
A Novel Supramolecular Organogel Nanotubular Template Approach for Conducting Nanomaterials
by Parambath "Anil " Anilkumar
P. Anilkumar and M. Jayakannan, J. Phys. Chem. B, 2010, 114,728–736
We report a unique supramolecular organogel template approach for conducting polyaniline nanomaterials. A novel... more We report a unique supramolecular organogel template approach for conducting polyaniline nanomaterials. A novel organogel based on sulfonic acid dopant was designed and developed from renewable resource 3-pentadecyl phenol via ring-opening of 1,4-butane sultone. The amphiphilic dopant molecule formed thermo-reversible supramolecular organogel in highly polar solvents like alcohols. The self-assembled fibril network morphology of the gel was confirmed by scanning electron microscopy (SEM) and atomic force microscopy. Transmission electron microscopy (TEM) revealed that the inner part of the fibrous gel is nanotubular with the pore diameter of 75 nm. The organogel nanotubular morphology was retained even in the presence of aniline+dopant complex, and the aniline monomers occupied the hydrophobic nanopockets provided by the amphiphilic dopant. The chemical oxidative polymerization of the dopant+aniline organogel template produced well-defined polyaniline nanofibers. The polymerization was carried out at various temperatures to establish the role of the physical state and stability of the organogel on the morphology. The sulfonic acid molecule acts both as self-assembled molecular template for the synthesis of polymer nanomaterial as well as anionic counterpart for stabilizing the positively charged conducting polymer chains. The gel template played a pivotal role in directing polyaniline chains to form nanofibers and also manipulating the number of other properties such as conductivity, solubility, percent crystallinity, and solid-state ordering, etc. Temperature-dependent electrical conductivity measurements revealed that the nanomaterials showed typical linear ohmic behavior and also followed the 3-D VRH model at elevated temperatures.
Self-Assembled Cylindrical and Vesicular Molecular Templates for Polyaniline Nanofibers and Nanotapes
by Parambath "Anil " Anilkumar
P. Anilkumar, M. Jayakannan, J. Phys. Chem. B, 2009, 113, 11614–11624
We report a soft template approach based on a custom-designed novel surfactant-cum-dopant for size and shape tuning of... more We report a soft template approach based on a custom-designed novel surfactant-cum-dopant for size and shape tuning of polyaniline nanomaterials such as nanofibers and nanotapes via emulsion and dispersion polymerization routes. A new amphiphilic 4-(3-dodecyl-8-enylphenyloxy) butane sulfonic acid was synthesized by ring-opening of butanesultone with renewable resource cardanol. The new amphiphilic dopant forms spherical micelles in water and its critical micelle concentration was determined by dye encapsulation and surface tension methods. In the emulsion route, the amphiphilic dopant complexed with aniline to produce cylindrical micellar aggregates that template exclusively for polyaniline nanofibers. The dispersion of aniline + dopant in water/toluene solvent mixture produces vesicles that selectively template for polyaniline nanotapes. The mechanism of the polyaniline nanomaterials formation was investigated by dynamic light scattering (DLS) and high-resolution transmission electron microscopy (HR-TEM). DLS of the polymerization templates in water proved the presence of micrometer range aggregates, and TEM images confirmed the shape of the cylindrical and vesicular templates. The polyaniline nanomaterials were found soluble in water and polar organic solvents for structural characterization and composition analysis by 1H NMR spectroscopy. Absorbance spectra of the nanomaterials showed free carrier tail above 900 nm in the near IR region for the delocalization of electrons in the polaron band corresponding to expanded conformation of polyaniline chains. Wide angle X-ray diffraction showed two new peaks at low angle region with d-spacing of 26.5 and 13.6 Å corresponding to lamellar ordering of polyaniline chains followed by interdigitations of the amphiphilic dopant in the nanomaterials.
Divergent Nanostructures from Identical Ingredients: Unique Amphiphilic Micelle Template for Polyaniline Nanofibers, Tubes,Rods, and Spheres
by Parambath "Anil " Anilkumar
P. Anilkumar and M. Jayakannan, Macromolecules, 2008, 41, 7706–7715
Here, we report a unique soft templating approach based on an in-built amphiphilic azobenzenesulfonic acid for tuning... more Here, we report a unique soft templating approach based on an in-built amphiphilic azobenzenesulfonic acid for tuning various types of polyaniline nanomaterials such as fibers, rods, spheres, and tubes. The dopant molecule is freely soluble in water, and DLS measurements of the resultant solution revealed that it forms spherical micelles of diameter 4.29 nm. The addition of aniline induces self-organization in the dopant micelles which produce micrometer-sized cylindrical aggregates or layerlike assemblies depending upon the aniline/dopant composition in the feed. In the emulsion route, the oxidation of these cylindrical or layerlike micelle aggregates produce nanofibers and nanotubes, respectively. The dilution of thick emulsion microaggregates led to the formation of uniformly distributed small 175 nm aggregated micelles, which template for the nanorods (dilution route). Alternatively, the dopant micelles form spherical shape aggregates with oxidizing agent ammonium persulfate (APS) in water. Aniline molecules diffuse through the organic/aqueous interface and get absorbed at these spherical aggregates, and subsequent chemical oxidation produces exclusively polyaniline nanospheres (interfacial route). The mechanism of the polyaniline nanomaterials formation was investigated by dynamic light scattering (DLS) and high-resolution transmission electron microscopy (TEM). DLS studies of the polymerization mixtures in water evident for the formation of micrometer range aggregates. TEM analysis confirmed the shape of the template as cylindrical, cylindrical + spherical, and spherical geometry for the complexes of dopant with aniline and APS in the emulsion, dilution, and interfacial routes, respectively. The amphiphilic nature of the dopant solubilizes the nanomaterials in water and organic solvents, and the optical properties of nanomaterials were studied in various solvents by UV−vis spectroscopy. The wide-angle X-ray diffraction studies confirmed the appearance of a new peak at lower angle (d = 13.6 Å) corresponding to the highly crystalline and ordered polyaniline nanomaterials. The solid-state properties of the nanomaterials were found to be highly dependent on the size and shape of polymerization templates employed for the synthesis.
Single-Molecular-System-Based Selective Micellar Templates for Polyaniline Nanomaterials: Control of Shape, Size, Solid State Ordering, and Expanded Chain to Coillike Conformation
by Parambath "Anil " Anilkumar
P. Anilkumar and M. Jayakannan, Macromolecules, 2007, 40, 7311–7319
A single molecular approach has been developed to selectively template polyaniline nanomaterials via interfacial and... more A single molecular approach has been developed to selectively template polyaniline nanomaterials via interfacial and emulsion polymerization routes to control the nanomaterials shape, size, solubility, solid state ordering, and expanded polymer chain to coil-like conformation. A new amphiphilic azobenzenesulfonic acid dopant was designed and developed from renewable resource cardanol which exists in the form of 4.3 nm spherical micelles in water. The amphiphilic micelles selectively undergo spherical or cylindrical aggregation with ammonium persulfate (APS) and aniline in water at ambient conditions. In the interfacial route, aniline molecules diffuse through the interface and get oxidized by the dopant−APS spherical pre-aggregates to produce polyaniline nanospheres of 400 nm in diameter. The oxidations of dopant-aniline cylindrical micelles by APS in the emulsion route produce polyaniline nanofibers of 150−200 nm diameters with length up to 5−8 μM. The mechanistic aspects of the polyaniline nanomaterials formation was investigated by dynamic light scattering to trace the factors which control the morphology of the resultant materials. The aniline/dopant ratio was varied from 100 to 450 to study the effect of reactants composition on the morphology and mechanism of the nanomaterials formation. The presence of hydrophobic tail in the amphiphilic dopant increases the solubility of nanospheres and nanofibers in water as well as organic solvents such as chloroform, n-butanol, chlorobenzene, xylene, and m-cresol, etc. The absorbance spectra of the nanospheres showed a free carrier tail above 950 nm in the near IR region for the delocalization of electrons in the polaron band corresponding to expanded conformation of polyaniline chains whereas the polyaniline nanofibers showed a peak characteristics at 750−850 nm with respect to more coiled-like conformation. The solvent dependent absorption studies revealed that the conformations of the polymer nanomaterials are less influenced by the solvent in which they were suspended. WXRD patterns of nanofibers showed a peak at 2θ = 6.4° (d-spacing = 13.6 Å) for polyaniline chain due to the effective inter-digitations of dopant molecules in the polyaniline crystalline domain. The expanded conformation of polymer chains enhances the solid state ordering of the nanospheres and a new intense peak at 2θ = 6.05° (d-spacing 14.3 Å) is observed, which is absent in the case of nanofibers.
Fluorescent Tagged Probing Agent and Structure-Directing Amphiphilic Molecular Design for Polyaniline Nanomaterials via Self-Assembly Process
by Parambath "Anil " Anilkumar
P. Anilkumar and M. Jayakannan, J. Phys. Chem. C, 2007, 111, 3591–3600
We have designed and developed a unique amphiphilic dopant molecule,... more We have designed and developed a unique amphiphilic dopant molecule, 4-[4-hydroxy-2((Z)-pentadec-8-enyl)phenylazo]-benzenesulfonicacid, from a renewable resource, cardanol, which acts as a fluorescent probe and structure-directing agent for polyaniline nanomaterials. The amphiphilic dopant is fluorescing in water and forms stable emulsion for a wider composition of dopant:aniline ratio from 1:1 to 1:1500 (in moles), which is rarely noticed in the polyaniline synthesis. The azobenzene dopant exists in two supramolecular aggregates, such as bi-layer or micelle, depending upon its concentration in water, and the critical micelle concentration (CMC) is directly obtained from the emission properties. Above the CMC, the dopant−aniline complex exists as either aggregated or isolated micelles, and subsequent oxidation produces polyaniline nanomaterials such as hollow spheres (1−2 μM), dendritic nanofibers, and linear nanofibers of 8−10 μM length with a diameter of 130−180 nm. Below the CMC, the dopant aggregated in the form of bi-layers which produce mixtures of nanotubes plus nanofibers or nanotubes of 60 nm pore and 80 nm wall thicknesses. The WXRD patterns of nanofibers showed a sharp peak at 2θ = 6.4 (d-spacing = 13.6), which corresponds to the highly ordered polyaniline chain followed by the effective interdigitations of dopant molecules. The intensity and percent (%) crystallinity of the ordered peak increase and reach a maximum up to CMC and then decrease gradually. It reveals that above CMC, the dopant effectively penetrates into the polymer interlayer and produces highly three dimensionally ordered solid-state nanofibers. Below the CMC, the dopant molecule loses the collective penetration ability to form highly ordered fibers. The polyaniline nanofibers showed enhanced emission in water, and the amount of the dopant in the nanomaterial plays a crucial role in luminescent intensity and quantum yield of the nanofibers. In a nutshell, by understanding the mechanistic aspects of renewable resource amphiphilic dopant−aniline complex by fluorescent spectroscopy, the properties of polyaniline nanomaterials were precisely controlled in a single system.
Computational Prediction of Salt and Cocrystal Structures - Does a Proton Position Matter?
Co-authored with Sally Price and Derek Tocher
The lattice energy landscape is calculated for three pyridinium carboxylate salts and the corresponding... more The lattice energy landscape is calculated for three pyridinium carboxylate salts and the corresponding pyridine·carboxylic acid cocrystals. Experimentally, one system crystallizes as a salt, another as a cocrystal and the acidic proton in the third is disordered across the Narom·O hydrogen bond vector. A novel structure of a 1:1 4-cyanopyridine·4-fluorobenzoic acid cocrystal (I) was characterized to provide the cocrystal as a system with an isolated carboxylic acid-pyridine heterosynthon. By contrast, the 4-dimethylaminopyridinium maleate salt (GUKVUE) shows the effects of an internal hydrogen bond, and the proton-disordered pyridine·isophthalic acid crystal (IYUPEX) shows the effects of competing intermolecular hydrogen bonds. All three crystal structures were found low in energy on the lattice energy landscape for the correct proton connectivity. For all three systems, comparing the salt and cocrystal energy landscapes shows the importance of the proton position for the relative stabilities of structures, despite the expected similarities between the ionized and neutral forms of the carboxylic acid-pyridine heterosynthon. The systems with additional hydrogen bonds have some hydrogen bonding motifs that are only favourable for the salt or for the cocrystal. This illustrates the sensitivity of the range of thermodynamically plausible crystal structures to whether the molecules are assumed to be ionized or neutral.
Supramolecular variations on a molecular theme: the structural diversity of phosphazenes (RNH)(6)P3N3 in the solid state
Co-authors: J.F. Bickley, R. Bonar-Law, G.T. Lawson, F. Rivals, A. Steiner and S. Zacchini
Source: Dalton Transactions, 2003, Issue: 7 Pages: 1235-1244
Herein, we introduce an extremely ‘soft’ tecton, which interacts via ‘soft’ synthons displaying an unprecedented... more
Herein, we introduce an extremely ‘soft’ tecton, which interacts via ‘soft’ synthons displaying an unprecedented variety of supramolecular architectures in the solid state.
Hexakis(organoamino) cyclotriphosphazene derivatives, (RNH)6P3N3, contain a polar core comprising an equatorial belt of three ring nitrogen atoms and six NH functions which is sandwiched between hemispheres of lipophilic substituents R.
The study shows that subtle modifications of the lipophilic periphery lead to considerable changes in the solid-state aggregation pattern. With the exception of 1 all solid-state structures show intermolecular NHN bonding with motifs containing one, two, three and four H-bridges.
Supramolecular architectures include monomer (1), dimer (2), cyclic hexamer (3), zigzag chain (4, 6), linear chain (5·thf, 7, 8), double chain (9), graphite-type sheet (10), rectangular grid (11) and hexagonal close-packed sheet (12).
The structural variety is due to easy rotation around exocyclic P–N bonds, which allows variable directionalities of all six N–H bonds.
M.O. calculations on the gas phase dimer of (H2N)6P3N3 mirror the H-bridging motifs observed in crystal structures of (RNH)6P3N3 derivatives.
Cyclophosphazenes as nodal ligands in coordination polymers
Co-author: A. Steiner
Inorganic Chemistry, 2004, Volume: 43 Issue: 9 Pages: 2810-2817
Cyclotriphosphazenes carrying organo amino side chains, (RNH)6P3N3 {R = n-propyl (1), cyclohexyl (2), benzyl (3)}, and... more Cyclotriphosphazenes carrying organo amino side chains, (RNH)6P3N3 {R = n-propyl (1), cyclohexyl (2), benzyl (3)}, and (C4H8N)6P3N3 (4) produce supramolecular coordination compounds in conjunction with silver salts by formation of linear N−Ag−N connections via nitrogen centers of the phosphazene ring. The donor ability of the anion and the steric demand of the lipophilic ligand sphere R control the topology of the coordination network. The crystal structures of 3(AgClO4)2 and 3(AgNO3)2 show additional Ag−π(aryl) interactions between the terminally arranged silver ions and benzyl groups. Phosphazene ligands 1−3 have the ability to undergo hydrogen bonding to anions via the six NH groups, and the coordination polymers containing these ligands feature dense networks of NH···O bonds.