Catenane Structure Research Articles

Folding and cutting DNA into reconfigurable topological nanostructures

Topology is the mathematical study of the spatial properties that are preserved through the deformation, twisting and stretching of objects. Topological architectures are common in nature and can be seen, for example, in DNA molecules that condense and relax during cellular events. Synthetic topological nanostructures, such as catenanes and rotaxanes, have been engineered using supramolecular chemistry, but the fabrication of complex and reconfigurable structures remains challenging. Here, we show that DNA origami can be used to assemble a Möbius strip, a topological ribbon-like structure that has only one side. In addition, we show that the DNA Möbius strip can be reconfigured through strand displacement to create topological objects such as supercoiled ring and catenane structures. This DNA fold-and-cut strategy, analogous to Japanese kirigami, may be used to create and reconfigure programmable topological structures that are unprecedented in molecular engineering.

Introduction of useful peripheral functional groups on [2]catenanes by combining Cu(i) template synthesis with “click” chemistry

Two protocols based on Cu(I) template synthesis and “click” reactions for the synthesis of functionalized [2]catenanes are described. A straightforward procedure, involving high dilution conditions at high temperatures (70 °C), affords [2]catenanes bearing two identical peripheral groups in high yields. For the preparation of non-symmetrically functionalized [2]catenanes, a second milder and simpler protocol was developed, generalizing and extending the method. The introduction of peripheral functional groups into the catenane structure opens up possibilities of using [2]catenanes as building blocks for preparation of even more complex structures.

ChemInform Abstract: Interlocked Host Rotaxane and Catenane Structures for Sensing Charged Guest Species via Optical and Electrochemical Methodologies.

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Onset of Double Helical Structure in Small-Sized Homoleptic Gold Thiolate Clusters

Low-lying isomers of homoleptic gold thiolate clusters (AuSR)(N) (N = 6-12) are studied by using a global-minimum search method. Besides previously known zigzag crown structures for (AuSR)(N) (N = 6-12) and catenane structures for (AuSR)(N) (N = 10, 12), onset of a new structural family of double helical structures in small-sized gold thiolate clusters and the separate-ring structures in larger clusters is revealed. At N = 6-9, the double helical structures are predicted to be the global minima. The onset of double helical structures suggests a new folding way for flexible gold thiolate clusters. The simulated UV-vis spectra and XRD patterns for all low-lying clusters are ready to compare with future experiments.

Interlocked hostrotaxane and catenane structures for sensing charged guest species via optical and electrochemical methodologies

The potential of interlocked host rotaxane and catenane structures as innovative optical and electrochemical sensors is highlighted. Interlocked structures can be engineered to bind specific guests within the topologically constrained three dimensional cavities created during their template-driven syntheses. This binding ability, when coupled to the signal transduction capabilities associated with appended reporter groups and their dynamic structures, make catenanes and rotaxanes highly promising candidates for the development of molecular sensors. With the ultimate challenge of fabricating highly selective anion sensing configurations, a three-staged strategy has been followed. First, we developed a general anion templation methodology for the construction of a variety of interpenetrated and interlocked molecular structures. [2]Rotaxanes and [2]catenanes synthesised using this novel protocol show, after template removal, favourable selective anion binding characteristics distinct from their separate components. At the second stage, the incorporation of redox- and photo-active groups into these interlocked frameworks converts them into electrochemical/optical molecular sensors. In the final third stage, the confinement of interlocked anion receptors at surfaces results in the fabrication of devices exhibiting highly selective binding and electrochemical and/or optical sensing behaviour.

Multiple catenanes based on tetraloop derivatives of calix[4]arenes

Four novel tetraarylurea calix[4]arenes ( 4a– d) have been synthesized, substituted by ω-alkenyloxy residues in 3,5-positions of the arylurea residues. The eight alkenyl groups were pairwise connected by olefin metathesis and subsequent hydrogenation. The ring-closure reaction was carried out with heterodimers exclusively formed by 4 with a tetratosylurea calix[4]arene 1, which serves as a template in this reaction step. The potential trans-cavity bridging is entirely suppressed in this way. Bis- and tetraloop calix[4]arenes cannot form dimers due to overlapping loops. However, they readily form heterodimers with open-chain tetraureas, as long as their urea residues can pass through the loops. Thus, five heterodimeric capsules 8a– e with bis[3]catenane structure were synthesized using again the olefin metathesis followed by hydrogenation. Two different strategies were compared for this reaction sequence, starting with heterodimers formed either by tetraloop derivatives 5 with tetraalkenyl tetraureas 6 (pathway A) or by bisloop derivatives 7 with octaalkenyl tetraureas 4 (pathway B). A distinct advantage of one of these pathways was not observed; the bis[3]catenanes were obtained with yields of 20–60%. Heterodimers formed by tetraloop derivatives 5b– d and octaalkenyl ureas 4b– d were converted analogous to three novel cyclic [8]catenanes 9a– c in 30–42% yield. The structure of the novel catenanes was unambiguously proved by 1H NMR and ESI MS, and for 8a and 9a additionally by single crystal X-ray analysis.

Coupling across a DNA helical turn yields a hybrid DNA/organic catenane doubly tailed with functional termini.

We describe the synthesis of a hybrid DNA/organic macrocycle that is prepared by formation of an amide linkage across one full turn of DNA. Formation of a catenane proved that the linkage crossed a turn rather than running along the phosphodiester backbone contour. The product, a doubly tailed catenane, contains 5'- and 3'-termini that can be functionalized further or used to incorporate the catenane structure into other DNA assemblies.

Two Classes of Alongside Charge-Transfer Interactions Defined in One [2]Catenane

A [2]catenane, which incorporates hydroquinone (HQ) and a sterically bulky tetrathiafulvalene (TTF) into a bismacrocycle, has been designed to probe the alongside charge-transfer (CT) interactions taking place between a TTF unit and one of the bipyridinium moieties in the tetracationic cyclophane cyclobis(paraquat-p-phenylene) (CBPQT4+). A template-directed strategy employs the HQ unit as the primary template for formation of the tetracationic cyclophane CBPQT4+, affording the desired [2]catenane structure but as an uncharacteristic green solid. The X-ray crystal structure and detailed 13C NMR assignments have identified a stereoselective preference for catenation about the cis isomer. The 1H NMR spectroscopy, electrochemistry, and X-ray crystallography all confirm that the CBPQT4+ cyclophane encircles the HQ unit, thereby defining a structure which would normally determine a red color. The visible-NIR region of the absorption spectrum displays a band at approximately 740 nm that is unambiguously assigned to a TTF --> CBPQT4+ CT transition on the basis of resonance Raman spectroscopy using 785 nm excitation. The profile of the CT band changes depending on the ratio of the cis- to trans-TTF isomers in the [2]catenane for which the molar absorptivity of each isomer is estimated to be significantly different at epsilon max = 380 and 3690 M-1 cm-1, respectively. Molecular modeling studies confirmed that the observed difference in the absorption spectroscopic profile can be accounted for by both a better overlap of the HOMO(TTF) and LUMO+1(CBPQT4+) as well as a more stable face-to-face (pi...pi) conformation in the trans isomer compared to the edge-to-face cis isomer of the [2]catenane. The latter is arranged for pi-orbital overlap through the sulfur atoms of the TTF unit, thereby defining an [Spi...pi] interaction.

Anion Templated Assembly of Mechanically Interlocked Structures

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Anion templated assembly of mechanically interlocked structures

This tutorial review describes the evolution of the field of chemical templation, in particular, emphasising the impact its application has made to the synthesis of mechanically interlocked structures. Recent advances in the use of negatively charged template species for the synthesis of interlocked structures are detailed, with the main focus of this review describing the development of a general anion templation strategy that combines anion recognition with ion-pairing. The versatility of this methodology is demonstrated by the chloride anion templated synthesis of a series of interpenetrated pseudorotaxane, rotaxane and catenane structures. Upon template removal, the mechanically interlocked rotaxanes and catenanes are shown to bind anions within their topologically unique anion binding clefts by virtue of electrostatic and hydrogen bonding interactions, exhibiting a strong selectivity for the chloride halide anion template. The incorporation of the photo-active rhenium(I) bipyridyl signalling group into the rotaxane structural framework highlights the potential of these interlocked systems in future chemical sensor design.

Model Carbyne vs. Ideal and DNA Catenanes.

The structure and stability of two-component carbyne catenanes, viewed as model compounds for DNA catenanes, have been estimated by molecular mechanics (MM) calculations. The carbyne catenane molecules studied were composed from interwined cyclic molecules constituted solely from carbon atoms bonded by alternating single and triple bonds. The total number of carbon atoms in molecules studied was set to 60, and the complementary sizes of the catenane components varied. The component cycles were entangled by 2, 4, ..., 11 crossings. For the catenanes with the number of crossings equal to six and seven more than one catenane topological type was considered. The calculated MM strain energy of carbyne catenanes was correlated with the averaged crossing number and length-to-diameter ratio of ideal catenanes as well as the electrophoretic mobility and sedimentation coefficient of DNA catenanes. To observe these correlations, for each topological type of carbyne catenane, it was necessary to find the proportion of the sizes of the two catenane components at which the MM strain energy is the lowest. Then, the values of these energies were correlated with characteristics of ideal and real DNA catenanes. The fits are significant and nonlinear.

Model Carbyne vs Ideal and DNA Catenanes

The structure and stability of two-component carbyne catenanes, viewed as model compounds for DNA catenanes, have been estimated by molecular mechanics (MM) calculations. The carbyne catenane molecules studied were composed from interwined cyclic molecules constituted solely from carbon atoms bonded by alternating single and triple bonds. The total number of carbon atoms in molecules studied was set to 60, and the complementary sizes of the catenane components varied. The component cycles were entangled by 2, 4, ..., 11 crossings. For the catenanes with the number of crossings equal to six and seven more than one catenane topological type was considered. The calculated MM strain energy of carbyne catenanes was correlated with the averaged crossing number and length-to-diameter ratio of ideal catenanes as well as the electrophoretic mobility and sedimentation coefficient of DNA catenanes. To observe these correlations, for each topological type of carbyne catenane, it was necessary to find the proportion of the sizes of the two catenane components at which the MM strain energy is the lowest. Then, the values of these energies were correlated with characteristics of ideal and real DNA catenanes. The fits are significant and nonlinear.

Anion-Templated Assembly of a [2]Catenane

The first example of a [2]catenane structure to be synthesized using anion templation is described. The nature of the anion template is demonstrated to be crucial to the assembly process, with only chloride anion producing the [2]catenane in acceptable yield. Anion binding studies reveal a dramatic catenation effect on anion selectivity properties as compared to a noncatenated acyclic receptor.

Recent studies on alkynyl complexes of the Group 11 and 12 metals

Although alkynyl complexes of Group 11 and 12 metals have been known for many years, recent crystallographic studies have revealed some interesting and novel structural features. These result from the combination of the alternative bonding modes available to the alkynyl ligand and the occurrence of weak metal–metal interactions. These come together to favour the formation of polynuclear ring and polyhedral structures. For example, the seemingly simple isoleptic compound [Au(C 2 t Bu)] has a catenane structure based on two interweaving Au 6 rings and within each ring the alkynyl ligands displaying a range of bonding modes which involve σ- and π-bonding. The study of the reactions of the corresponding silver compound has revealed the formation of a complex with a cation which has a regular rhombohedral structure which is based on a halide anion encapsulated by 14 silver atoms. This compound results from the incorporation of halide anions in the interstitial site in the work-up process. The reactions between the mercury–dialkynyl complexes [Hg(C 2R) 2] (R=Ph, Tol or t Bu) and silver(I) and copper(I) ions have led to complexes where the Group 11 metal ions are π-coordinated to the alkynyl π-bonds. This leads to an interesting series of structures and, for example, {[Hg(C 2Tol) 2Ag][BF 4]} n has a polymeric structure with helices cross linked by CH⋯π-interactions.

PM3 treatment of certain catenanes having cyclacenes and cyclotriacontene units

The results of PM3 (RHF) type semiempirical quantum chemical treatment of certain catenanes which consisted of all- trans cyclotriacontene shaft and the cyclacene shuttle, having R benzenoid rings ( R=6–9) were reported. The results have indicated that the cryptoannulenic effect which is the characteristic property of cyclacenes is almost lost when they are incorporated into the structures of catenanes considered.

Synthesis and X-ray Structure of Amide-Based Macrocycles, Catenanes and Pretzelane

The syntheses and crystal structure studies of amide-based catenanes derived from m-phenylene diacrylic acid and 5-acetoxy isophthalic acid (17% and 3% yield of 4a and 4b resp.) and octalactam macrocycles (21% yield of 3) are described. Hydrogen bonding patterns play a key role in the formation of the different conformations of octalactam 3. The crystal structures of 3 reveal a number of hydrogen-bonding interactions between the macrocycle and two different solvent molecules, which are presumably responsible for the different conformations. Furthermore, we report the X-ray structure of a catenane, which was converted into a “pretzelane” by bridging two phenolic hydroxy groups with a p-xylylene unit.

Novel [2]catenane structures introducing communication between transition metal centers via pi...pi interactions.

[2]Catenane systems containing copper(II) and nickel(II) as metal centers have been self-assembled using tetraazamacrocyclic complexes and benzo-24-crown-8 as building blocks. A variety of methods, including X-ray crystallography, ESI mass spectrometry, (13)C and (1)H NMR, and electrochemistry, were applied to characterize these new face-to-face bismacrocyclic systems. Weak pi...pi interactions introduced by interlocking transition metal complexes with benzocrown moieties were shown to increase the communication (cooperativity) of metal centers. Introduction of the benzocrown increases the stability of the mixed valence state of the macrocyclic complex, which is reflected in high values of conproportionation constants. Moreover, this effect was found to be stronger than that obtained by shortening the length of the spacer between the two tetraazamacrocyclic subunits in the parent bismacrocycles. The extent of communication is larger for the nickel catenane than for the copper one.

Cyclodextrin-based molecular machines.

Cyclodextrins have been used as a cyclic component in the construction of supramolecular architectures. Recently they have been studied as a component in the construction of rotaxanes and catenanes. A cyclodextrin ring can translocate in some rotaxane and catenane structures. Therefore, much attention has been given to cyclodextrins as a component of molecular shuttles, motors, and machines. Attempts to design and synthesize molecular-level machines using cyclodextrins as a cyclic component are described.

水素結合を利用したインターロックト分子の高効率合成 ロタキサン，カテナン合成の最近の進歩

Due to the marked progress in control of intermolecular interactions that assemble component molecules, directed synthesis of interlocked molecules such as rotaxanes and catenanes has recently developed greatly. This review summarizes the efficient synthesis of interlocked compounds based on hydrogen-bonding interaction. Various synthetic methods including threading followed by end-capping, clipping, slipping, entering, and polyslipping are discussed. Synthesis under thermodynamic control is also discussed. Various amide-based catenanes and rotaxanes have been synthesized using the template effect based on amide-amide hydrogen-bonding or anion-recognition by macrolactam. The strong hydrogen-bonding between cucurbituril and ammonium salts allowed to prepare various structures of catenanes, rotaxanes, and polyrotaxanes. Further, secondary ammonium salts can be captured into the rings of crown ethers consisting at least 24 ring member to give pseudorotaxanes. A wide variety of end-capping techniques have been developed to give crown ether-based rotaxanes. Control of intramolecular hydrogen-bonding interaction in the interlocked compounds are briefly discussed.

Template effects and kinetic selection in the self-assembly of crown ether cyclobis(paraquat-p-phenylene)

The template effects exerted by bis(p-phenylene)[34]crown-10 (3) and by 1,5-dinaphto[38]crown-10 (4) in the ring-closure reaction of the trication 2(3+) to yield the [2]catenanes 7(4+) and 8(4+) have been quantitatively evaluated in acetonitrile at 62 degrees C by UV/visible spectroscopy. The rate of ring closure of the trication 2(3+) dramatically increases in the presence of the templates 3 and 4, up to approximately 230 times at [3] approximately equals 0.1 molL(-1), and up to approximately 1,900 times at [4] approximately equals 0.01 molL(-1). The outcome of kinetic selection experiments, in which the two crown ethers compete for the incorporation into the catenane structure, has been discussed in the light of the obtained results. It has been shown that the product ratio of catenanes obeys the Curtin-Hammett principle only if the concentrations of the templates are equal and much greater than that of the substrate. Analysis of the rate profiles has shown that the 1,5-dioxynaphthalene unit, present in the template 4, has a greater affinity than the 1,4-dioxybenzene unit, present in the template 3, for the electron-deficient pyridinium rings present in both the transition-state and substrate structures. Ab initio calculations at the 3-21G and 6-31G(d) levels of theory indicate that the greater affinity of the 1,5-dioxynaphthalene unit cannot be explained on the basis of greater pi-pi stacking and [C-H...pi] interactions, but rather on the basis of the model of apolar complexation in which the solvent plays a major role.