Donor-Acceptor Oligorotaxanes Made to Order

Five donor–acceptor oligorotaxanes made up of dumbbells composed of tetraethylene glycol chains, interspersed with three and five 1,5-dioxynaphthalene units, and terminated by 2,6-diisopropylphenoxy stoppers, have been prepared by the threading of discrete numbers of cyclobis(paraquat-p-phenylene) rings, followed by a kinetically controlled stoppering protocol that relies on click chemistry. The well-known copper(I)-catalyzed alkyne–azide cycloaddition between azide functions placed at the ends of the polyether chains and alkyne-bearing stopper precursors was employed during the final kinetically controlled template-directed synthesis of the five oligorotaxanes, which were characterized subsequently by ^1H NMR spectroscopy at low temperature (233 K) in deuterated acetonitrile. The secondary structures, as well as the conformations, of the five oligorotaxanes were unraveled by spectroscopic comparison with the dumbbell and ring components. By focusing attention on the changes in chemical shifts of some key probe protons, obtained from a wide range of low-temperature spectra, a picture emerges of a high degree of folding within the thread protons of the dumbbells of four of the five oligorotaxanes—the fifth oligorotaxane represents a control compound in effect— brought about by a combination of C-H···O and π–π stacking interactions between the p-electron-deficient bipyridinium units in the rings and the π-electron-rich 1,5-dioxynaphthalene units and polyether chains in the dumbbells. The secondary structures of a foldamer-like nature have received further support from a solid-state superstructure of a related [3]pseudorotaxane and density functional calculations performed thereon

Measurement of the ground-state distributions in bistable mechanically interlocked molecules using slow scan rate cyclic voltammetry

In donor–acceptor mechanically interlocked molecules that exhibit bistability, the relative populations of the translational isomers—present, for example, in a bistable [2]rotaxane, as well as in a couple of bistable [2]catenanes of the donor–acceptor vintage—can be elucidated by slow scan rate cyclic voltammetry. The practice of transitioning from a fast scan rate regime to a slow one permits the measurement of an intermediate redox couple that is a function of the equilibrium that exists between the two translational isomers in the case of all three mechanically interlocked molecules investigated. These intermediate redox potentials can be used to calculate the ground-state distribution constants, K. Whereas, (i) in the case of the bistable [2]rotaxane, composed of a dumbbell component containing π-electron-rich tetrathiafulvalene and dioxynaphthalene recognition sites for the ring component (namely, a tetracationic cyclophane, containing two π-electron-deficient bipyridinium units), a value for K of 10 ± 2 is calculated, (ii) in the case of the two bistable [2]catenanes—one containing a crown ether with tetrathiafulvalene and dioxynaphthalene recognition sites for the tetracationic cyclophane, and the other, tetrathiafulvalene and butadiyne recognition sites—the values for K are orders (one and three, respectively) of magnitude greater. This observation, which has also been probed by theoretical calculations, supports the hypothesis that the extra stability of one translational isomer over the other is because of the influence of the enforced side-on donor–acceptor interactions brought about by both π-electron-rich recognition sites being part of a macrocyclic polyether

Mechanically Stabilized Tetrathiafulvalene Radical Dimers

Two donor−acceptor [3]catenanes—composed of a tetracationic molecular square, cyclobis(paraquat-4,4′-biphenylene), as the π-electron deficient ring and either two tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) containing macrocycles or two TTF-butadiyne-containing macrocycles as the π-electron rich components—have been investigated in order to study their ability to form TTF radical dimers. It has been proven that the mechanically interlocked nature of the [3]catenanes facilitates the formation of the TTF radical dimers under redox control, allowing an investigation to be performed on these intermolecular interactions in a so-called “molecular flask” under ambient conditions in considerable detail. In addition, it has also been shown that the stability of the TTF radical-cation dimers can be tuned by varying the secondary binding motifs in the [3]catenanes. By replacing the DNP station with a butadiyne group, the distribution of the TTF radical-cation dimer can be changed from 60% to 100%. These findings have been established by several techniques including cyclic voltammetry, spectroelectrochemistry and UV−vis−NIR and EPR spectroscopies, as well as with X-ray diffraction analysis which has provided a range of solid-state crystal structures. The experimental data are also supported by high-level DFT calculations. The results contribute significantly to our fundamental understanding of the interactions within the TTF radical dimers

Relative contractile motion of the rings in a switchable palindromic [3]rotaxane in aqueous solution driven by radical-pairing interactions

Artificial muscles are an essential component for the development of next-generation prosthetic devices, minimally invasive surgical tools, and robotics. This communication describes the design, synthesis, and characterisation of a mechanically interlocked molecule (MIM), capable of switchable and reversible linear molecular motion in aqueous solution that mimics muscular contraction and extension. Compatibility with aqueous solution was achieved in the doubly bistable palindromic [3]rotaxane design by using radical-based molecular recognition as the driving force to induce switching.National Institute of General Medical Sciences (U.S.) (Award F32GM105403)American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi

Uncovering the Thermodynamics of Monomer Binding for RNA Replication

The nonenzymatic replication of primordial RNA is thought to have been a critical step in the origin of life. However, despite decades of effort, the poor rate and fidelity of model template copying reactions have thus far prevented an experimental demonstration of nonenzymatic RNA replication. The overall rate and fidelity of template copying depend, in part, on the affinity of free ribonucleotides to the RNA primer–template complex. We have now used 1H NMR spectroscopy to directly measure the thermodynamic association constants, Kas, of the standard ribonucleotide monophosphates (rNMPs) to native RNA primer–template complexes. The binding affinities of rNMPs to duplexes with a complementary single-nucleotide overhang follow the order C > G > A > U. Notably, these monomers bind more strongly to RNA primer–template complexes than to the analogous DNA complexes. The relative binding affinities of the rNMPs for complementary RNA primer–template complexes are in good quantitative agreement with the predictions of a nearest-neighbor analysis. With respect to G:U wobble base-pairing, we find that the binding of rGMP to a primer–template complex with a 5′-U overhang is approximately 10-fold weaker than to the complementary 5′-C overhang. We also find that the binding of rGMP is only about 2-fold weaker than the binding of rAMP to 5′-U, consistent with the poor fidelity observed in the nonenzymatic copying of U residues in RNA templates. The accurate Ka measurements for ribonucleotides obtained in this study will be useful for designing higher fidelity, more effective RNA replication systems

Radically enhanced molecular recognition

The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host–guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication

Influence of Constitution and Charge on Radical Pairing Interactions in Tris-radical Tricationic Complexes

The results of a systematic investigation of trisradical tricationic complexes formed between cyclobis(paraquat-p-phenylene) bisradical dicationic (CBPQT2(•+)) rings and a series of 18 dumbbells, containing centrally located 4,4′-bipyridinium radical cationic (BIPY•+) units within oligomethylene chains terminated for the most part by charged 3,5-dimethylpyridinium (PY+) and/or neutral 3,5-dimethylphenyl (PH) groups, are reported. The complexes were obtained by treating equimolar amounts of the CBPQT4+ ring and the dumbbells containing BIPY2+ units with zinc dust in acetonitrile (MeCN) solutions. Whereas UV-VIS-NIR spectra revealed absorption bands centered on ca. 1100 nm with quite different intensities for the 1:1 complexes depending on the constitutions and charges on the dumbbells, titration experiments show that the association constants (Ka) for complex formation vary over a wide range from Ka values of 800 M^(-1) for the weakest to 180000 M^(-1) for the strongest. While Coulombic repulsions emanating from PY+ groups located at the ends of some of the dumbbells undoubtedly contribute to the destabilization of the trisradical tricationic complexes, solid-state superstructures support the contention that those dumbbells with neutral PH groups at the ends of flexible and appropriately constituted links to the BIPY•+ units stand to gain some additional stabilization from C‒H···π interactions between the CBPQT2(•+) rings and the PH termini on the dumbbells. The findings reported in this full paper demonstrate how structural changes implemented remotely from the BIPY•+ units influence their noncovalent bonding interactions with CBPQT2(•+) rings. Different secondary effects (Coulombic repulsions versus C‒H···π interactions) are uncovered and their contributions to both binding strengths associated with trisradical interactions and the kinetics of associations and dissociations are discussed at some length and are supported by extensive DFT calculations at the M06-D3 level. A fundamental understanding of molecular recognition in radical complexes has relevance when it comes to the design and synthesis of non-equilibrium systems

Radically Enhanced Molecular Switches

The mechanism governing the redox-stimulated switching behavior of a tristable [2]rotaxane consisting of a cyclobis(paraquat-p-phenylene) (CBPQT^4+) ring encircling a dumbbell, containing tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) recognition units which are separated from each other along a polyether chain carrying 2,6-diisopropylphenyl stoppers by a 4,4′-bipyridinium (BIPY^2+) unit, is described. The BIPY^2+ unit acts to increase the lifetime of the metastable state coconformation (MSCC) significantly by restricting the shuttling motion of the CBPQTT^4+ ring to such an extent that the MSCC can be isolated in the solid state and is stable for weeks on end. As controls, the redox-induced mechanism of switching of two bistable [2]rotaxanes and one bistable [2]catenane composed of CBPQT^4+ rings encircling dumbbells or macrocyclic polyethers, respectively, that contain a BIPY2+ unit with either a TTF or DNP unit, is investigated. Variable scan-rate cyclic voltammetry and digital simulations of the tristable and bistable [2]rotaxanes and [2]catenane reveal a mechanism which involves a bisradical state coconformation (BRCC) in which only one of the BIPY^•+ units in the CBPQT^2(•+) ring is oxidized to the BIPY2+ dication. This observation of the BRCC was further confirmed by theoretical calculations as well as by X-ray crystallography of the [2]catenane in its bisradical tetracationic redox state. It is evident that the incorporation of a kinetic barrier between the donor recognition units in the tristable [2]rotaxane can prolong the lifetime and stability of the MSCC, an observation which augurs well for the development of nonvolatile molecular flash memory devices

A Radically Configurable Six-State Compound

Most organic radicals possess short lifetimes and quickly undergo dimerization or oxidation. Here, we report on the synthesis by radical templation of a class of air- and water-stable organic radicals, trapped within a homo[2]catenane composed of two rigid and fixed cyclobis (paraquat-p-phenylene) rings. The highly energetic octacationic homo[2]catenane, which is capable of accepting up to eight electrons, can be configured reversibly, both chemically and electrochemically, between each one of six experimentally accessible redox states (0, 2+, 4+, 6+, 7+, and 8+) from within the total of nine states evaluated by quantum mechanical methods. All six of the observable redox states have been identified by electrochemical techniques, three (4+, 6+, and 7+) have been characterized by x-ray crystallography, four (4+, 6+, 7+, and 8+) by electron paramagnetic resonance spectroscopy, one (7+) by superconducting quantum interference device magnetometry, and one (8+) by nuclear magnetic resonance spectroscopy