Bulky Stopper Research Articles

A double-stranded DNA rotaxane

Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

Stoddart−Heath [2]Rotaxane Molecular Switch Made Simple: A Density Functional Theory Study on Model Junction Devices

The essential components of the Stoddart−Heath-type [2]rotaxane molecular switch tunnel junction devices are the aromatic shuttle and stations, which are attached to other components, such as linkers, stoppers, and anchors. In this study, we explored a possibility of whether the molecular switch can be made simple by leaving only the π-stacked aromatic key components between two metal electrodes. The current−voltage (I−V) characteristics of these simplest model devices were calculated from density functional theory using the nonequilibrium matrix Green’s function formalism. When the aromatic components are in direct contact with the surfaces, the I−V characteristics depend dramatically on the orientation of the π stacks, and spatial or temporal changes in the orientation can decrease the device robustness. The robustness can be restored by introducing a buffer layer or a covalent bond (say bulky stoppers and anchors as well as titanium adhesion layers) between the π stack and the electrodes, and this is, ...

Synthesis of linked symmetrical [3] and [5]rotaxanes having an oligomeric phenylene ethynylene (OPE) core skeleton as a π-conjugated guest via double intramolecular self-inclusion

Linked symmetrical [3] and [5]rotaxanes consisting of an oligomeric phenylene ethynylene (OPE) framework as a π-conjugated guest moiety and lipophilic permethylated α-cyclodextrins (PM α-CDs), as macrocyclic hosts have been prepared by double intramolecular self-inclusion of an OPE guest unit carrying two PM α-CDs followed by capping with bulky stopper groups using click azide–alkyne Huisgen cycloaddition or Sonogashira coupling. The structures of these linked rotaxanes were determined by MALDI-TOF mass spectrum and two-dimensional NMR spectroscopy.

Novel main-chain polyrotaxanes synthesized via ATRP of HEMA initiated with polypseudorotaxanes comprising BriB–PEG–iBBr and α-CDs

A novel strategy for the preparation of main-chain polyrotaxanes with lengthily tunable PHEMA as outer bulky stoppers was described in the present study. Polypseudorotaxanes made from the self-assemblies of a distal 2-bromoisobutyryl end-capped PEG with a varying amount of α-CDs in aqueous media were used as macroinitiators in situ to initiate the ATRP of HEMA catalyzed by Cu(I)Br/PMDETA at room temperature. The resulting polyrotaxanes were characterized in virtue of 1H NMR, GPC, FTIR, XRD and DSC analyses. It demonstrated that the target polyrotaxanes were successfully synthesized and both the in-chained number of HEMA and the threaded number of α-CDs were adjustable to some extent. As the active Br groups held at two terminals and combining the unique properties of general polyrotaxanes with that of block copolymers, these supramolecular polymers show the potential as macroinitiators used for new ATRP polymerizations.

Synthesis and Photophysical Investigation of Squaraine Rotaxanes by “Clicked Capping”

Pseudorotaxane complexes of squaraine dyes and tetralactam macrocycles are converted into permanently interlocked rotaxane structures using copper-catalyzed and copper-free cycloaddition reactions with bulky stopper groups. The photophysical properties of the encapsulated squaraine depend on the structure of the macrocycle. In one case, squaraine rotaxanes are produced in near-quantitative yields and with intense near-IR fluorescence. In another case, squaraine fluorescence is greatly diminished upon macrocyclic encapsulation but the signal can be restored by dye displacement with anions.

Relative Rotational Motion between α-Cyclodextrin Derivatives and a Stiff Axle Molecule

Novel [2]rotaxanes bearing alpha-cyclodextrin (alpha-CD) derivatives and a diphenylacetylene axis molecule with trinitrobenzene as a bulky stopper have been prepared to investigate the relative rotary movement of a ring relative to an axis molecule and that of an axis molecule in a ring by NMR techniques. [2]Rotaxanes 2 and 3 were composed of alpha-CD derivatives (2: 6-phenyl-amide-alpha-CD; 3: 6-stilbene-amide-alpha-CD). The protons of alpha-CDs in rotaxanes were thoroughly assigned by the two-dimensional NMR techniques (TOCSY, COSY, ROESY, HMQC, and HMBC). The protons of alpha-CD in rotaxane 1 did not show splitting, whereas the resonance peak shifts and splitting for the corresponding protons of alpha-CD derivatives in rotaxanes 2 and 3 were observed by the shielding and deshielding effects from a diphenylacetylene axis molecule. The splitting of resonance peaks was closely related to the rotary movements of alpha-CDs and an axis molecule. We supposed that alpha-CD in rotaxane 1 rotates freely around a diphenylacetylene axis molecule, and vice versa, whereas the rotary movement of alpha-CD derivatives and the axis molecules of rotaxanes 2 and 3 were restricted by the steric repulsion between the substituent group of alpha-CD and the stopper group of an axis molecule. To estimate the relative rotary movement of CDs and an axis molecule in rotaxanes, the rotational correlation time (tauc) of rotaxanes was measured by 13C NMR. The results indicate that the corresponding rotary movement of the modified alpha-CD and the axis molecules in rotaxanes 2 and 3 depends on the size of the substituent group.

Enzyme-Responsive Snap-Top Covered Silica Nanocontainers

Mesoporous silica nanoparticles, capable of storing a payload of small molecules and releasing it following specific catalytic activation by an esterase, have been designed and fabricated. The storage and release of the payload is controlled by the presence of [2]rotaxanes, which consist of tri(ethylene glycol) chains threaded by α-cyclodextrin tori, located on the surfaces of the nanoparticles and terminated by a large stoppering group. These modified silica nanoparticles are capable of encapsulating guest molecules when the [2]rotaxanes are present. The bulky stoppers, which serve to hold the tori in place, are stable under physiological conditions but are cleaved by the catalytic action of an enzyme, causing dethreading of the tori and release of the guest molecules from the pores of the nanoparticles. These snap-top covered silica nanocontainers (SCSNs) are prepared by a modular synthetic method, in which the stoppering unit, incorporated in the final step of the synthesis, may be changed at will to target the response of the system to any of a number of hydrolytic enzymes. Here, the design, synthesis, and operation of model SCSNs that open in the presence of porcine liver esterase (PLE) are reported. The empty pores of the silica nanoparticles were loaded with luminescent dye molecules (rhodamine B), and stoppering units that incorporate adamantyl ester moieties were then attached in the presence of α-cyclodextrin using the copper-catalyzed azide−alkyne cycloaddition (CuAAC), closing the SCSNs. The release of rhodamine-B from the pores of the SCSN, following PLE-mediated hydrolysis of the stoppers, was monitored using fluorescence spectroscopy.

Monitoring the thermodynamically-controlled formation of diimide-based resin-attached rotaxanes by gel-phase HR MAS1H NMR spectroscopy

The thermodynamically controlled self-assembly of rotaxane and pseudorotaxane systems consisting of (i) a naphthodiimide thread unit terminated at one end with a pyridine ligand, and covalently linked at the other to a gel-phase polystyrene resin support, (ii) a dinaphtho-crown ether shuttle unit, and (iii) a ruthenium carbonyl metalloporphyrin stopper unit, is investigated by high resolution magic angle spinning proton (HR MAS 1H) NMR spectroscopy. The effects of variable concentration of the solution-phase components, the temperature, and added Li+ and Na+ ions are described, and the limitations of the technique are addressed. The dynamic behaviour is compared directly to the solution-phase analogues, where a bulky stopper group is substituted for the polystyrene resin bead.

Face‐Selective [2]‐ and [3]Rotaxanes: Kinetic Control of the Threading Direction of Cyclodextrins

New [2]- and [3]pseudorotaxanes containing alpha-cyclodextrin (alpha-CDs) molecules as rotors and alkyl pyridinium derivatives as axles were prepared by a slipping process. The inclusion behavior of these rotaxanes was investigated by using one- and two-dimensional NMR spectroscopy. The methyl group at the 2-position of the pyridinium moiety at the end of each axle molecule was found to control the rates of threading of the alpha-CD onto the axle molecules. alpha-CD can approach axle molecules from a particular direction to form inclusion complexes. Axle molecules that contain a 2-methylpyridinium moiety at one end and a bulky stopper at the other end can regulate the direction of approach to give a [2]pseudorotaxane such as 2 b-alpha-CD. A [3]pseudorotaxane in which two alpha-CD molecules are arranged facing in the same direction at two stations of the tetracationic axle molecule was also obtained. These face-selective behaviors are dominated by kinetic processes rather than thermodynamic processes.

Highly Selective and High-Yielding Rotaxane Synthesis via Aminolysis of Prerotaxanes Consisting of a Ring Component and a Stopper Unit

A highly rotaxane-selective synthesis via aminolysis of prerotaxanes, which were composed of a phenolic pseudo-crown ether as a ring component and a bulky stopper unit, was developed. The best result was obtained in the case of aminolysis of 3b with 3,5-dimethylbenzylamine which proceeded quantitatively with ca. 100% rotaxane selectivity forming the corresponding rotaxane 5b. The rotaxanes were formed by kinetically controlled attack of the amine from the backside of the ring component of the prerotaxanes.

Synthesis and characterization of a persistent paramagnetic rotaxane based on α-cyclodextrin and α,ω-alkyl disulfides

A new synthetic strategy for the preparation of persistent paramagnetic cyclodextrin-based rotaxanes is described. The method consists in the formation of inclusion complexes between α-cyclodextrin (α-CD) and α,ω-dithiols containing an octamethylene chain covalently trapped by bulky stoppers composed of 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) radical fragments. Interaction of α-CD (the bead) and 1,8-octanedithiol (the thread) occurs in aqueous alkaline media and encapsulation is obtained by nucleophilic substitution at both termini of the linear component with a bulky paramagnetic iodide [2,2,6,6-tetramethyl-4-(2-iodoacetamide)piperidine-N-oxyl]. Structure determination of the new [2]rotaxane by 1H NMR is reported and the spectroscopic data are discussed.

Preparation and Properties of Rotaxanes Formed by Dimethyl-β-cyclodextrin and Oligo(thiophene)s with β-Cyclodextrin Stoppers

Novel cyclodextrin rotaxanes with oligothiophene as an axis molecule have been prepared by the Suzuki coupling reaction of 6-O-(4-iodophenyl)-beta-CD (6-I-Ph-beta-CD) with di(1,3,2-dioxaborolan-2-yl)-oligothiophene (oligothiophene diboric ethylene glycol esters) in aqueous solutions of dimethyl-beta-cyclodextrin (DM-beta-CD). These reactions gave [2]rotaxanes and [3]rotaxanes, which were isolated by reversed phase chromatography. The fluorescence intensities of rotaxanes are higher than those of dumbbell-shaped molecules (without DM-beta-CD) in aqueous solutions. The inclusion ratio and chain length of rotaxanes have been found to relate to the emission properties and emission intensities of oligothiophene. In aqueous solutions, fluorescence quantum yields of rotaxanes are higher than those of dumbbell-shaped molecules. The increase in the fluorescence efficiency of rotaxane is caused by suppression of intermolecular interactions, indicating the effect of insulated oligothiophene with DM-beta-CD. beta-CD at the both ends of rotaxanes functions not only as bulky stoppers but also as the recognition site for guest molecules, as verified by fluorescence quenching experiments.

Novel triblock copolymers synthesized via radical telomerization of N-isopropylacrylamide in the presence of polypseudorotaxanes made from thiolated PEG and α-CDs

A protocol for the preparation of novel triblock copolymers comprising a polyrotaxane center block and outer blocks of poly(N-isopropylacrylamide) (PNIPAAm) as bulky stoppers was developed, in which N-isopropylacrylamide was allowed to telomerize in the presence of polypseudorotaxanes made from the self-assembly of thiol end-capped PEG with a varying amount of α-CDs under UV irradiation in aqueous solution. The molecular structure of the resulting copolymers was characterized in detail by 1H NMR, FTIR, XRD, TG and DSC analyses. It was demonstrated that the PNIPAAm blocks are successfully attached to the two terminals of the polypseudorotaxanes and each block having the minimum 7 NIPAAm units seems long and bulky enough to efficiently impede the dethreading of α-CDs from the PEG axle to give rise to the triblock polyrotaxane-containing copolymers.

Deslipping of Rotaxanes with Axle Center Pieces of Different Lengths

A series of rotaxanes equipped with tetralactam wheels and di-t-butyl stopper groups, which differ only with respect to the length of the alkyl chain serving as the axle center piece, are examined with respect to their deslipping behavior at elevated temperatures. 1H NMR experiments are used to follow the deslipping reactions kinetically, and it is found that the axle length does not have a significant influence on the rate of deslipping. In accordance with expectation, this result confirms that the rate-determining step of the reaction is the passage of the wheel over the stopper group. It also sheds new light on earlier results on rotaxanes bearing ester groups in the axle center piece. The deslipping reaction rate for these rotaxanes was extremely dependent on the choice of solvent and the orientation of the ester groups. The rotaxanes presented here do not contain functional groups in their center pieces and no such effects are observed. For these rotaxanes, the simple model of a thin thread inside a macrocycle mechanically trapped by bulky stopper groups is valid.

Assembly of an electronically switchable rotaxane on the surface of a titanium dioxide nanoparticle.

This paper describes the self-assembly of a heterosupramolecular system consisting of a tripodal [2]rotaxane adsorbed at the surface of a titanium dioxide nanoparticle. The tripodal [2]rotaxane consists of a dumbbell-shaped molecule, incorporating two electron-poor viologens, threading an electron-rich crown ether. The [2]rotaxane also incorporates a bulky tripodal linker group at one end and a bulky stopper group at the other end. The [2]rotaxane is adsorbed, via the tripodal linker group, at the surface of a titanium dioxide nanoparticle. The structure and function of the resulting hetero[2]rotaxane have been studied in detail by (1)H NMR spectroscopy and cyclic voltammetry. A key finding is that it is possible to electronically address and switch the above hetero[2]rotaxane.

Chemically induced contraction and stretching of a linear rotaxane dimer.

Copper(I)-induced assembly of two self-complementary identical units, which consist of a ring that incorporates a 1,10-phenanthroline group attached to a small filament containing a second 1,10-phenanthroline (phen) group, leads quantitatively to a doubly threaded complex. Each copper(I) center is four-coordinate and is located inside a ring and bound to a phen from the macrocyle. The two other coordination sites are occupied by a phen from the filament connected to the other ring. An X-ray structure of the dicopper(I) complex unambiguously demonstrates the doubly threaded nature of the system. The molecule has C(2) symmetry in the crystal. This is an extended form with a Cu small middle dot small middle dot small middle dotCu separation of 18.3 A and an overall length close to 40 A. Further synthetic work, which utilizes the two terminal phenolic functions of the previous dicopper(I) complex, gives rise to a more complex system in which both filaments have been prolonged in opposite directions by 2,2':6',2"-terpyridine (terpy) motifs and bulky stoppers. The organic backbone is that of a rotaxane dimer. Although redox cycling of Cu(I) to Cu(II) did not lead to intramolecular rearrangement, simple chemical reactions induced large conformational changes. The rotaxane dimer was set in motion as follows. The dicopper(I) complex, which is in an extended conformation, was demetallated by using KCN. From the free ligand, the dizinc complex was formed quantitatively at room temperature. (1)H NMR data show that a new conformation is obtained: each Zn(II) is five-coordinate (phen + terpy), and the molecule is in a contracted conformation. This process is reminiscent of biological muscles in the sense that the two filaments of this system can be moved along one another in a gliding motion that keeps the whole system together, but which converts a stretched compound (overall length approximately equal to 83 A) into a contracted species (overall length approximately equal to 65 A, according to CPK models). The motion is quantitatively reversed by the addition of an excess of copper(I) to the dizinc complex; this regenerates the extended starting form. Although the motivation of the present contribution was to illustrate that a muscle-like molecule may be stretched or contracted using electrochemistry and coordination chemistry, the main body of the work is organic synthesis. This is testified by the fact that the dicopper(I) rotaxane dimer was obtained in 23 steps from commercially available compounds.

A stopperless tetrathiafulvalene based [2]pseudorotaxane molecular shuttle

The first stopperless TTF containing molecular shuttle is described.

Optical and electroemission properties of thin films of supermolecular anthracene-based rotaxanes

Rotaxanes are a new class of functional materials. They consist of mechanically interlocked supermolecular systems where a central linear thread passes through the cavity of a macrocyclic ring. The ring is constrained within the two extremities of the thread by two bulky stoppers. In this work, we report on spectroscopic characterisation of an anthracene-based novel rotaxane (EPAR-Me) and on the electroemission (EL) from a basic rotaxane component (ANTPEP). An OLED has been prepared using the anthracene-based thread (ANTPEP) of the EPAR-Me rotaxane in polycarbonate matrices. Spectroscopic measurements are reported, supporting excimer-like EL and field dependent electroexcimer for the ANTPEP thin film. Tentative assignment of emitting species of EPAR-Me are also discussed.

Fabrication and Transport Properties of Single-Molecule-Thick Electrochemical Junctions

A V-shaped compound incorporating two bipyridinium units, which emanate from a central hydrophilic core and bear hydrophobic tetraarylmethane-based stoppers at each end, was designed and synthesized. In a thermodynamically controlled self-assembly process in solution, either one or two 1,4-dioxybenzene-based macrocyclic polyethers can be slipped over the bulky stoppers of the V-shaped compound, affording either a [2]rotaxane or a [3]rotaxane, respectively. The parent V-shaped compound and the two rotaxanes incorporate two redox-active bipyridinium units that can be reduced reversibly and two redox-active phenoxy groups in the stoppers that can be oxidized irreversibly. Furthermore, these three compounds have amphiphilic character and, as a result, form stable monolayers at the air/water interface. Langmuir−Blodgett monolayers of these compounds were sandwiched between two electrodes to afford molecule-based solid-state switches. In forward bias mode, the I−V characteristics of the junction are reversible,...

A Transition Metal Containing Rotaxane in Motion: Electrochemically Induced Pirouetting of the Ring on the Threaded Dumbbell

Fast spinning motion is observed in a copper(I) rotaxane. This “motor-like” molecule consists of an axle, bearing two bulky stoppers at its ends, and a ring containing two differrent coordination sites, each of them corresponding to the preferred situation for copper(I) or copper(II). Thus, using electrochemistry, the axle can be forced to oscillate inside the wheel.