Topological stereochemistry

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Toward Electrochemically Controllable Tristable Three-Station [2]Catenanes

Encouraged by the prospect of producing an electrochemical, color-switchable red-green-blue (RGB) dye compound, we have designed, synthesized, and characterized two three-station [2]catenanes. Both are composed of macrocyclic polyethers containing three pi-electron-rich stations, which act as recognition sites for a pi-electron-deficient tetracationic cyclophane. The molecular structures of the two three-station [2]catenanes were characterized fully by mass spectrometry and 1H NMR spectroscopy. To anticipate the relative occupancies of the three stations in each [2]catenane by the cyclophane, model compounds with the same constitutions in the vicinity of the stations were synthesized. The relative ground-state populations of the three stations occupied in both [2]catenanes were estimated from the thermodynamic parameters for 1:1 complexes between all these model compounds and the cyclophane, obtained from isothermal titration calorimetry (ITC). The electrochemical and electromechanical properties of the three-station [2]catenanes were analyzed by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and spectroelectrochemistry (SEC). The first three-station [2]catenane was found to behave like a bistable system, whereas the second can be described as a quasi-tristable system.

Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies

How and why do molecules tangle or thread? Investigations of molecular knots (knotanes) may shed some light on the mechanisms of (supra)molecular templation and the folding of molecules that result in intertwining. The topological chirality of these fascinating molecules leads to new types of isomerism and paves the way to nanosized molecular motors. Their preparation and derivatization makes high demands on modern synthetic methods and analytical separation since molecular knots are formed in a more or less planned design based on metal coordination or hydrogen-bonding patterns. This Review describes the development of templation techniques for the synthesis of knotanes and their chiral resolution as well as their selective functionalization and use as building blocks in the synthesis of higher knotane assemblies. Such assemblies can possess linear, branched, or even macrocyclic structures which, on the one hand, introduce unprecedented isomeric compositions that arise from multiple topological stereogenic units and, on the other, define new types of artificial macromolecules beyond polymers and dendritic species.

Topologically novel multiple rotaxanes and catenanes based on tetraurea calix[4]arenes

Calix[4]arenes bearing at their wide rim four urea residues easily form hydrogen bonded dimeric capsules. This has been used to preorganise alkenyl functions attached to these urea groups for their controlled connection via metathesis reaction. Multimacrocyclic tetraurea derivatives are thus obtained in excellent yields via heterodimers which are formed exclusively with tetratosylurea derivatives. Heterodimerisation of such bis- and tetraloop tetraureas leads analogously to multicatenanes, or to rotaxanes by stoppering. Huge macrocycles are detached from tetraloop derivatives by cleavage of the urea function.

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.

Nanoscale Borromean links for real

Borohydride reduction of a Borromean Ring (BR) complex containing six zinc(II) ions and 12 imine bonds has resulted in its demetallation, producing a neutral BR compound and also its free macrocycle, following cleavage of at least one of the imine bonds in the ethanolic reaction mixture.

Construction of Polymeric δ-Graph: A Doubly Fused Tricyclic Topology

A doubly fused tricyclic polymer architecture, corresponding to a delta-graph, has been constructed effectively through metathesis polymer cyclization (MPC) of an 8-shaped dicyclic polymer precursor having two allyl groups placed at opposite positions of the two rings of the 8-shaped structure. The 8-shaped polymer precursor has been obtained through the covalent conversion of an electrostatic self-assembly (composed of two units of the linear poly(tetrahydrofuran)s, poly(THF)s, having pyrrolidinium salt end groups and having a pendant allyl group at the middle of the chain, carrying a tetrafunctional carboxylate counteranion) by the heating treatment under appropriate dilution to cause the ring-opening reaction of pyrrolidinium salt groups by carboxylate anions.

Exploring Dynamics and Stereochemistry in Mechanically-Interlocked Compounds

The advent of self-assembly and template-directed synthetic protocols has led to a tremendous surge in the number of mechanically-interlocked compounds being prepared and studied. As these investigations are being carried out, it is becoming increasingly apparent that many of these compounds, known as catenanes and rotaxanes, possess unique dynamic and stereochemical properties. In addition, the drive to create molecular switches and machines for nanotechnological applications has generated a need to understand how to control those properties in condensed phases. Here, we present an overview of the field with regard to the solution dynamics and stereochemistry of mechanically-interlocked compounds - as well as to some related structural types - and review the recent results from our own research in some detail. 1H NMR spectroscopy has proven to be a powerful tool for probing both degenerate and nondegenerate dynamic processes in these compounds, as well as for identifying stereoisomers if they are present in solution. The results of several variable temperature NMR investigations on the effects of structural changes upon the dynamic processes and stimulated relative motions of components in catenanes and rotaxanes, as well as in some self-complexes and pretzelanes, are discussed. A review with 90 references.

Nanoscale borromean rings

The molecular expression of topologically interesting structures represents a formidable challenge for synthetic chemists. The nontrivial link known as the Borromean rings has long been regarded as one of the most ambitious targets in this field. Of ancient provenance, this symbol comprises three interlocked rings in an inseparable union, but cut any one of the rings and the whole assembly unravels into three separate pieces. This Account delineates different strategies that can be applied to the formation of molecules possessing this distinctive topology, culminating with two successful syntheses of such compounds, thus cutting the Gordian knot of topological chemistry.

An octanuclear [Co(ii)2–Co(iii)2]2 interlocked grid—example of an inorganic [2]catenane

An oxalic dihydrazide based flexible polydentate amidrazone ligand undergoes spontaneous [2 x 2] grid assembly, followed by partial disassembly, and then reassembly in the presence of Co(NO3)2.6H2O and NH4(NCS) to form a unique octanuclear [Co(II)2-Co(III)2]2 interlocked, single braided 4 + 4 [2]catenane.

Topological polymer chemistry by dynamic selection from electrostatic polymer self-assembly

A collection of recent developments in topological polymer chemistry is presented. First, topological isomerism occurring on randomly coiled, flexible polymer molecules having cyclic and linear structures is discussed. Second, an electrostatic self-assembly and covalent fixation strategy has been developed for the synthesis of polymeric topological isomers. These isomers have double cyclic, manacle-, and theta-shaped constructions, and are prepared by using either linear or star telechelic polymer precursors having moderately strained cyclic ammonium salt groups, which carry multifunctional carboxylate counteranions. A technique of reversed-phase chromatography (RPC) is demonstrated as an effective means to separate polymers with different topologies, especially polymeric topological isomers. A further extension of topological polymer chemistry has been observed by dynamic selection from electrostatic polymer self-assembly to enable the effective formation of tadpole-shaped, cyclic-linear hybrid topologies.

Molecular Borromean Rings

The realization of the Borromean link in a wholly synthetic molecular form is reported. The self-assembly of this link, which is topologically achiral, from 18 components by the template-directed formation of 12 imine and 30 dative bonds, associated with the coordination of three interlocked macrocycles, each tetranucleating and decadentate overall, to a total of six zinc(II) ions, is near quantitative. Three macrocycles present diagonally in pairs, six exo-bidentate bipyridyl and six endo-diiminopyridyl ligands to the six zinc(II) ions. The use, in concert, of coordination, supramolecular, and dynamic covalent chemistry allowed the highly efficient construction, by multiple cooperative self-assembly processes, of a nanoscale dodecacation with an approximate diameter of 2.5 nanometers and an inner chamber of volume 250 A(3), lined with 12 oxygen atoms.

In the Twilight Zone between [2]Pseudorotaxanes and [2]Rotaxanes

A [2]pseudorotaxane, based on a semi-dumbbell-shaped component containing asymmetrically substituted monopyrrolotetrathiafulvalene and 1,5-dioxynaphthalene recognition sites for encirclement by cyclobis(paraquat-p-phenylene) and with a "speed bump" in the form of a thiomethyl group situated between the two recognition sites, has been self-assembled. This supramolecular entity is a mixture in solution of two slowly interconverting [2]pseudorotaxanes, one of which is on the verge of being a [2]rotaxane at room temperature, allowing it to be isolated by employing flash column chromatography. These two [2]pseudorotaxanes were both characterized in solution by UV/Vis and (1)H NMR spectroscopies (1D and 2D) and also by differential pulse voltammetry. The spectroscopic and electrochemical data reveal that one of the complexes behaves wholly as a [2]pseudorotaxane, while the other has some [2]rotaxane character to it. The kinetics of the shuttling of cyclobis(paraquat-p-phenylene) between the monopyrrolotetrathiafulvalene and the 1,5-dioxynaphthalene recognition sites have been investigated at different temperatures. The shuttling processes, which are accompanied by detectable color changes, can be monitored using UV/Vis and (1)H NMR spectroscopies; the spectroscopic data have been employed in the determination of the rate constants, free energies of activation, enthalpies of activation, and the entropies of activation for the translation of cyclobis(paraquat-p-phenylene) between the two recognition sites.