[3]Pseudorotaxane-like complexes formed between bipyridinium dications and bis-p-xylyl[26]crown-6

Sequential nucleophilic substitution of pseudorotaxanes forms rotaxanes with various linking functionalities and recycling of the surrogate stopper

A sequential nucleophilic substitution method produces rotaxanes from anion-sensitive pseudorotaxanes. First, a nucleophilic bulky tertiary aniline interlocks a pseudorotaxane to form a surrogate rotaxane; this unit then functions as a leaving group for a set of bulky nucleophiles, affording rotaxanes with various linking functionalities, along with the bulky aniline recovered in its original form.

Squaramide-Based Heteroditopic [2]Rotaxanes for Sodium Halide Ion-Pair Recognition

A series of squaramide-based heteroditopic [2]rotaxanes consisting of isophthalamide macrocycle and squaramide axle components are synthesized using an alkali metal cation template-directed stoppering methodology. This work highlights the unprecedented sodium cation template coordination of the Lewis basic squaramide carbonyls for interlocked structure synthesis. Extensive quantitative 1 H NMR spectroscopic anion and ion-pair recognition studies reveal the [2]rotaxane hosts are capable of cooperative sodium halide ion-pair mechanical bond axle-macrocycle component recognition, eliciting up to 20-fold enhancements in binding strengths for bromide and iodide, wherein the Lewis basic carbonyls and Lewis acidic NH hydrogen bond donors of the squaramide axle motif operate as cation and anion receptive sites simultaneously in an ambidentate fashion. Notably, varying the length and nature of the polyether cation binding unit of the macrocycle component dramatically influences the ion-pair binding affinities of the [2]rotaxanes, even overcoming direct contact NaCl ion-pair binding modes in polar organic solvents. Furthermore, the cooperative ion-pair binding properties of the squaramide-based heteroditopic [2]rotaxanes are exploited to successfully extract solid sodium halide salts into organic media.

How Secondary and Tertiary Amide Moieties are Molecular Stations for Dibenzo-24-crown-8 in [2]Rotaxane Molecular Shuttles?

Interlocked molecular machines like [2]rotaxanes are intriguing aesthetic molecules. The control of the localization of the macrocycle, which surrounds a molecular axle, along the thread leads to translational isomers of very different properties. Although many moieties have been used as sites of interactions for crown ethers, the very straightforwardly obtained amide motif has more rarely been envisaged as molecular station. In this article, we report the use of secondary and tertiary amide moieties as efficient secondary molecular station in pH-sensitive molecular shuttles. Depending on the N-substitution of the amide station, and on deprotonation or deprotonation-carbamoylation, the actuation of the molecular machinery differs accordingly to very distinct interactions between the axle and the DB24C8.

Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes

Examples of using two-dimensional shape-persistent macrocycles, i.e. those having noncollapsible and geometrically well-defined skeletons, for constructing mechanically interlocked molecules are scarce, which contrasts the many applications of these macrocycles in molecular recognition and functional self-assembly. Herein, we report the crucial role played by macrocyclic shape-persistency in enhancing multipoint recognition for the highly efficient template-directed synthesis of rotaxanes. Cyclo[6]aramides, with a near-planar conformation, are found to act as powerful hosts that bind bipyridinium salts with high affinities. This unique recognition module, composed of two macrocyclic molecules with one bipyridinium ion thread through the cavity, is observed both in the solid state and in solution, with unusually high binding constants ranging from ∼10¹³ M^-2 to ∼10¹⁵ M^-2 in acetone. The high efficacy of this recognition motif is embodied by the formation of compact [3]rotaxanes in excellent yields based on either a "click-capping" (91%) or "facile one-pot" (85%) approach, underscoring the great advantage of using H-bonded aromatic amide macrocycles for the highly efficient template-directed synthesis of mechanically interlocked structures. Furthermore, three cyclo[6]aramides bearing different peripheral chains 1-3 demonstrate high specificity in the synthesis of a [3]rotaxane from 1 and 2, and a [2]rotaxane from 3via a "facile one-pot" approach, in each case as the only isolated product. Analysis of the crystal structure of the [3]rotaxane reveals a highly compact binding mode that would be difficult to access using other macrocycles with a flexible backbone. Leveraging this unique recognition motif, resulting from the shape-persistency of these oligoamide macrocycles, in the template-directed synthesis of compact rotaxanes may open up new opportunities for the development of higher order interlocked molecules and artificial molecular machines.

Design of [2]rotaxane through image threshold segmentation of electrostatic potential image

An electrostatic potential (ESP)-based image segmentation method has been used to estimate the ability of proton donation and acceptance involved in ring-rod recognition. The relative binding strength of [2]rotaxane has also been further estimated from the difference of the characteristic image-segmentation derived ESP between proton donor and proton acceptor. The size and electrostatic compatibility criteria are introduced to guide the design of interlocked [2]rotaxane. A library of 75 thermodynamically stable [2]rotaxane candidates has been generated, including 16 experimentally known systems. The theoretical results for 16 experimentally known [2]rotaxanes are in good agreement with both the experimental association constants and density functional theory-calculated binding energies. Our ESP-based image segmentation model is also applicable to the tristable [2]rotaxane molecular shuttle as well as [1]rotaxane with self-inclusion function, indicating this simple method is generic in the field of constructing other supramolecular architectures formed with donor/acceptor molecular recognition. © 2016 Wiley Periodicals, Inc.

Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle

The kinetics and thermodynamics of intramolecular electron transfer (IET) can be subjected to redox control in a bistable [2]rotaxane comprised of a dumbbell component containing an electron-rich 1,5-dioxynaphthalene (DNP) unit and an electron-poor phenylene-bridged bipyridinium (P-BIPY(2+)) unit and a cyclobis (paraquat-p-phenylene) (CBPQT(4+)) ring component. The [2]rotaxane exists in the ground-state co-conformation (GSCC) wherein the CBPQT(4+) ring encircles the DNP unit. Reduction of the CBPQT(4+) leads to the CBPQT(2(•+)) diradical dication while the P-BIPY(2+) unit is reduced to its P-BIPY(•+) radical cation. A radical-state co-conformation (RSCC) results from movement of the CBPQT(2(•+)) ring along the dumbbell to surround the P-BIPY(•+) unit. This shuttling event induces IET to occur between the pyridinium redox centers of the P-BIPY(•+) unit, a property which is absent between these redox centers in the free dumbbell and in the 1:1 complex formed between the CBPQT(2(•+)) ring and the radical cation of methyl-phenylene-viologen (MPV(•+)). Using electron paramagnetic resonance (EPR) spectroscopy, the process of IET was investigated by monitoring the line broadening at varying temperatures and determining the rate constant (k(ET) = 1.33 x 10(7) s(-1)) and activation energy (ΔG(‡) = 1.01 kcal mol(-1)) for electron transfer. These values were compared to the corresponding values predicted, using the optical absorption spectra and Marcus-Hush theory.

Synthesis, physicochemical properties, and hydrogen bonding of 4(5)-substituted 1-H-imidazole-2-carboxamide, a potential universal reader for DNA sequencing by recognition tunneling

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6-10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.

Controlling the chair conformation of a mannopyranose in a large-amplitude [2]rotaxane molecular machine

Molecular machines boarding now! Molecular machines containing dibenzo[24]crown-8 (DB24C8) and based on an anilinium and a pyridinium amide station have been prepared. The DB24C8 shuttles upon variation of pH and interacts differently with the pyridinium amide station depending on its substitution. When the DB24C8 sits around the disubstituted amide, the conformation of the pyranose changes from (1)C(4) to (4)C(1).

A [2]rotaxane-based (1)H NMR spectroscopic probe for the simultaneous identification of physiologically important metal ions in solution

We describe a [2]rotaxane molecule that exhibits distinct signals in its (1)H NMR spectra upon the complexation of physiologically important Li(+), Na(+), Mg(2+) and Ca(2+) ions; thus, the identification of these metal ions in solution is possible from the analysis of a single (1)H NMR spectrum of a single molecular sensor.

A chromophoric switch based on pseudorotaxanes

In a three-component system containing dibenzo-24-crown-8 (1), diamino-dibenzo-24-crown-8 (2), and 1,2-bis(4,4(')-dipyridyl)ethane (3(2+)), axle 3(2+) can shuttle between wheels 1 and 2 by acid-base control, accompanying color changes from yellow to red. This system could not only be taken as a chromophoric supramolecular switch, but also exhibit a function as INHIBIT logic gate.