Artificial nanomachines based on interlocked molecular species: recent advances

Advancements and strategic approaches in catenane synthesis

Catenanes, a distinctive category of mechanically interlocked molecules composed of intertwined macrocycles, have undergone significant advancements since their initial stages characterized by inefficient statistical synthesis methods. Through the aid of molecular recognition processes and principles of self-assembly, a diverse array of catenanes with intricate structures can now be readily accessed utilizing template-directed synthetic protocols. The rapid evolution and emergence of this field have catalyzed the design and construction of artificial molecular switches and machines, leading to the development of increasingly integrated functional systems and materials. This review endeavors to explore the pivotal advancements in catenane synthesis from its inception, offering a comprehensive discussion of the synthetic methodologies employed in recent years. By elucidating the progress made in synthetic approaches to catenanes, our aim is to provide a clearer understanding of the future challenges in further advancing catenane chemistry from a synthetic perspective.

Coordination-Driven Selective Formation of D2 Symmetric Octanuclear Organometallic Cages

The coordination-driven self-assembly of organometallic half-sandwich iridium(III)- and rhodium(III)-based building blocks with asymmetric ambidentate pyridyl-carboxylate ligands is described. Despite the potential for obtaining a statistical mixture of multiple products, D₂ symmetric octanuclear cages were formed selectively by taking advantage of the electronic effects emanating from the two types of chelating sites - (O,O') and (N,N') - on the tetranuclear building blocks. The metal sources and the lengths of bridging ligands influence the selectivity of the self-assembly. Experimental observations, supported by computational studies, suggest that the D₂ symmetric cages are the thermodynamically favored products. Overall, the results underline the importance of electronic effects on the selectivity of coordination-driven self-assembly, and demonstrate that asymmetric ambidentate ligands can be used to control the design of discrete supramolecular coordination complexes.

A Light-Operated Molecular Cable Car for Gated Ion Transport

Inspired by the nontrivial and controlled movements of molecular machines, we report an azobenzene-based molecular shuttle PR2, which can perform light-gated ion transport across lipid membranes. The amphiphilicity and membrane-spanning molecular length enable PR2 to insert into the bilayer membrane and efficiently transport K⁺ (EC₅₀ =4.1 μm) through the thermally driven stochastic shuttle motion of the crown ether ring along the axle. The significant difference in shuttling rate between trans-PR2 and cis-PR2 induced by molecular isomerization enables a light-gated ion transport, i.e., ON/OFF in situ regulation of transport activity and single-channel current. This work represents an example of using a photoswitchable molecular machine to realize gated ion transport, which demonstrates the value of molecular machines functioning in biomembranes.

Translational isomers of N-sulfonylated [3]catenane: synthesis and isomerization

N-Sulfonylated [3]catenanes, which exist as two translational isomers, were synthesized. The X-ray crystal structure of the distal isomer of [3]catenane, which has higher symmetry, revealed hydrogen bonds involving the carboxylic acid moieties on the terminal rings. The thermodynamic parameters of the isomerization revealed that this hydrogen bonding influenced the isomerization process.

A switchable [2]rotaxane with two active alkenyl groups

A novel functional [2]rotaxane containing two alkenyl bonds was designed, synthesized and characterized by ¹H, ¹³C NMR spectroscopy and HRESI mass spectrometry. The introduction of alkenyl bonds endowed the [2]rotaxane a fascinating ability to react with versatile functional groups such as alkenyl and thiol functional groups. The reversible shuttling movement of the macrocycle between two different recognition sites on the molecular thread can be driven by external acid and base. This kind of rotaxane bearing functional groups provides a powerful platform for preparing stimuli-responsive polymers.

Photoinduced Release of a Chemical Fuel for Acid-Base-Operated Molecular Machines

Back and forth motions of the acid-base-operated molecular switch 1 are photo-controlled by irradiation of a solution, which also contains the photolabile pre-fuel 4. The photo-stimulated deprotection of the pre-fuel produces controlled amounts of acid 2, the base-promoted decarboxylation of which fuels the back and forth motions of the Sauvage-type [2]-catenane-based molecular switch. Because switch 1 and pre-fuel 4 do not interact in the absence of irradiation, an excess of the latter with respect to 1 can be added to the solution from the beginning. In principle, photocontrol of the back and forth motions of any molecular machine, the operation of which is guided by protonation/deprotonation, could be attained by use of pre-fuel 4, or of any other protected acid that undergoes deprotection by irradiation with light at a proper wavelength, followed by decarboxylation under conveniently mild conditions.

Synthesis and Isomerization Behavior of a Macrocycle with Four Photoresponsive Moieties

The macrocycle 1 containing four photoresponsive fluorenylidene moieties was designed. The EZEZ form of 1, 1 _EZEZ, was selectively produced. Reversible photochemical isomerization between 1 _EZEZ and 1 _ZZZZ was achieved, the extent of which was dependent on the light source used. Furthermore, the intermediate 1 _EZZZ was selectively isomerized to 1 _ZZZZ thermally and photochemically.

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.

Synthesis of rotaxanes and catenanes using an imine clipping reaction

Supramolecular chemistry and self-assembly provide a valuable chance to understand the complicated topological structures on a molecular level. Two types of classical mechanically interlocked molecules, rotaxanes and catenanes, possess non-covalent mechanical bonds and have attracted more attention not only in supramolecular chemistry but also in the fields of materials science, nanotechnology and bioscience. In the past decades, the template-directed clipping reaction based on imine chemistry has become one of the most efficient methods for the construction of functionalized rotaxanes and catenanes. In this review, we outlined the main progress of rotaxanes and catenanes using the template-directed clipping approach of imine chemistry. The review contains the novel topological structures of rotaxanes and catenanes, functions and applications.

Artificial Molecular Machines in Nanotheranostics

Due to their dynamic nature and excellent stimuli-responsiveness resulting from noncovalent driving forces, artificial molecular machines (AMMs) show great promise in cancer theranostics. In this Perspective, we introduce the potential applications of AMMs in controlled drug delivery, bioorthogonal catalysis, imaging, and cell membrane permeabilization, with the goal of enhancing cancer diagnosis and therapy. We expect this preliminary discussion will garner multidisciplinary interest from scientists to advance AMMs and to expand their future clinical applications.

Bistable [2]rotaxane encoding an orthogonally tunable fluorescent molecular system including white-light emission

By combining a rotaxane-type molecular switch and traditional fluorescent switch, an orthogonally tunable fluorescent molecular system was constructed, which can generate multicolor fluorescence including white light.

Variations in the fuel structure control the rate of the back and forth motions of a chemically fuelled molecular switch

Moderate variations in the fuel structure cause large changes in the rate of the back and forth motions experienced by a chemically fuelled catenane-based switch.

This work deals with the use of 2-cyano-2-arylpropanoic acids as chemical fuels for an acid–base operated molecular switch that consists of a Sauvage-type catenand composed of two identical macrocycles incorporating a phenanthroline unit. When used as a base promoter of the decarboxylation of propanoic acid derivatives, the switch undergoes large amplitude motion from the neutral catenand to a protonated catenate and back again to the neutral state. The rate of back proton transfer, which determines the rate of the overall process, was markedly affected by para-substituents in the order Cl > H > CH₃ > OCH₃ (ρ = +5.2). Thus, the time required to complete a full cycle was almost two days for the OCH₃ derivative and dropped to a few minutes for the Cl derivative. These results show for the first time that the rate of operation of a molecular switch can be regulated by variations in the fuel structure.

Construction of a Molecular Switch and Selector under Electrochemical Control

In this work, we designed and synthesized a special axle guest hexyldimethyl(ferrocenylmethyl)ammonium (1 ⁺ ) bromide. The binding interactions of 1 ⁺ and its oxidized form 1 ²⁺ with cucurbit[7]uril (Q[7]) and cyclohexanocucurbit[6]uril (Cy6Q[6]) were investigated by ¹H NMR, cyclic voltammogram, and isothermal titration calorimetry techniques. Our data indicate that both hosts Cy6Q[6] and Q[7] can form stable [2]pseudorotaxanes with 1 ⁺ in their different redox states. Most importantly, the combination and dissociation of the hosts with the guest as well as the binding location can be controlled by electrochemical means, which develops a special molecular switch and selector.

Displacement assay methodology for pseudorotaxane formation in the millisecond time-scale

Rotaxanes, formed by an axis through the cavity of a macrocycle, are promising systems for the construction of molecular machines. A very limited number of experimental techniques are available for mechanistic studies since only mechanical bonds are formed, being NMR one of the most widely used. The major inconvenience derived from NMR use is the time-scale for threading/dethreading processes lasting a few minutes in the case of faster processes. In the present manuscript, we report the application of a new kinetic methodology based on a displacement assay for cyclodextrin-based pseudorotaxane formation. By coupling a very fast (microseconds time-scale) binding/dissociation of nitrophenol to α-CD with a dicationic axle threading/dethreading process, we have been able to study kinetic processes taking place in the millisecond time-scale.

Antibody-powered nucleic acid release using a DNA-based nanomachine

A wide range of molecular devices with nanoscale dimensions have been recently designed to perform a variety of functions in response to specific molecular inputs. Only limited examples, however, utilize antibodies as regulatory inputs. In response to this, here we report the rational design of a modular DNA-based nanomachine that can reversibly load and release a molecular cargo on binding to a specific antibody. We show here that, by using three different antigens (including one relevant to HIV), it is possible to design different DNA nanomachines regulated by their targeting antibody in a rapid, versatile and highly specific manner. The antibody-powered DNA nanomachines we have developed here may thus be useful in applications like controlled drug-release, point-of-care diagnostics and in vivo imaging.

Responsive molecular machines can perform specific tasks triggered by environmental or chemical stimuli. Here, the authors show that antibodies can be used as inputs to modulate the binding of a molecular cargo to a designed DNA-based nanomachine, with potential applications in diagnostics and drug delivery.

Selective synthesis of iridium(iii)-derived molecular Borromean rings, [2]catenane and ring-in-ring macrocycles via coordination-driven self-assembly

Unprecedented iridium(iii) derived molecular Borromean rings, 2[catenane] and ring-in-ring metallacycles were synthesizedviacoordination driven self-assembly using an iridium(iii)-based acceptor and dipyridyl donors.

Kinetic Study of [2]Pseudorotaxane Formation with an Asymmetrical Thread

Kinetic and thermodynamic studies on cyclodextrin (CD)-based [2]pseudorotaxane formation have been carried out by a combination of NMR and calorimetric techniques using bolaform surfactants as axles. Experimental evidence of the formation of an external complex between the trimethylammonium head groups of the axle and the external hydrogen atoms of α-cyclodextrin (α-CD) is reported. Inclusion of this external complex in the reaction pathway allows us to explain the kinetic behavior as well as the nonlinear dependence of the observed rate constant on CD concentrations. The equilibrium constant for [2]pseudorotaxane formation is strongly affected by the spacer length of the axle. This effect is a consequence of increasing rotaxane stability because the threading rate constant is almost independent of the spacer length, but dethreading strongly decreases on increasing the axle size. Using a nonsymmetrical axle with tripropyl and trimethylammonium cations precludes CD threading by the large head side. CDs will thread this asymmetrical bolaform by both their wide and narrow sides, yielding two isomeric [2]pseudorotaxanes. Threading by the wide side of the CD is 60% more favorable than that by the narrow one, but dethreading rate constants are the same for both isomers.

Ferrocene-containing non-interlocked molecular machines

Ferrocene is chemically robust and readily functionalized which enables its facile incorporation into more complex molecular systems. This coupled with ferrocene's reversible redox properties and ability to function as a “molecular ball bearing” has led to the use of ferrocene as a component in wide range of non-interlocked synthetic molecular machine systems.

A tristable [2]rotaxane that is doubly gated by foldamer and azobenzene kinetic barriers

Hydrogen bonded foldamer and azobenzene units have been incorporated into a donor–acceptor-type [2]rotaxane to assemble a doubly gated switching system.

Dual absorption spectral changes by light-triggered shuttling in bistable [2]rotaxanes with non-destructive readout

The photochromic [2]rotaxanes have dual spectral variation characteristics: the spectral changes of the azobenzene (AB) unit and the charge-transfer band. By employing the CT bond region as output signal, non-destructive readout of optical information could be achieved.

Active-Metal Template Synthesis of a Halogen-Bonding Rotaxane for Anion Recognition

The synthesis of an all-halogen-bonding rotaxane for anion recognition is achieved by using active-metal templation. A flexible bis-iodotriazole-containing macrocycle is exploited for the metal-directed rotaxane synthesis. Endotopic binding of a Cu(I) template facilitates an active-metal CuAAC iodotriazole axle formation reaction that captures the interlocked rotaxane product. Following copper-template removal, exotopic coordination of a more sterically demanding rhenium(I) complex induces an inversion in the conformation of the macrocycle component, directing the iodotriazole halogen-bond donors into the rotaxane's interlocked binding cavity to facilitate anion recognition.

Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines

A simple model for a chemically driven molecular walker shows that the elastic energy stored by the molecule and released during the conformational change known as the power-stroke (i.e., the free-energy difference between the pre- and post-power-stroke states) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Further, the apportionment of the dependence on the externally applied force between the forward and reverse rate constants of the power-stroke (or indeed among all rate constants) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Arguments based on the principle of microscopic reversibility demonstrate that this result is general for all chemically driven molecular machines, and even more broadly that the relative energies of the states of the motor have no role in determining the directionality, stopping force, or optimal efficiency of the machine. Instead, the directionality, stopping force, and optimal efficiency are determined solely by the relative heights of the energy barriers between the states. Molecular recognition--the ability of a molecular machine to discriminate between substrate and product depending on the state of the machine--is far more important for determining the intrinsic directionality and thermodynamics of chemo-mechanical coupling than are the details of the internal mechanical conformational motions of the machine. In contrast to the conclusions for chemical driving, a power-stroke is very important for the directionality and efficiency of light-driven molecular machines and for molecular machines driven by external modulation of thermodynamic parameters.

Controllable Coordination Self-Assembly Based on Flexible Tripodal Ligands: From Finite Metallocages to Infinite Polycatenanes Step by Step

This article describes the developments in coordination self-assembly based on flexible tripodal ligands with different metal species. Various finite metallocages such as M3 L2 , M6 L8 , M6 L4 , M4 L4 and different catenanes based on discrete metallocages constructed from flexible tripodal ligands with suitable metal species are presented here. Many M3 L2 metallocages based on ligands L(1) -L(12) and different two-coordinated metal species have been prepared, in which various Ag(I) salts and other metal species that have been protected by suitable groups, such as Zn(OAc)2 , ZnBr2 , and PdBr2 , have been used as effective acceptors. All of the M6 L8 -type metallocages are constructed from ligands L(2) or L(12) -L(20) and different four-coordinated metal species, such as various palladium(II) salts or NiCl2 , and have similar topological structures. Only a few discrete M6 L4 -type metallocages, based on ligands L(21) -L(24) , have been reported, using different strategies such as protecting groups and steric hindrance. All of the M4 L4 -type cages have similar topological structures and are constructed from ligands L(25) -L(29) with multiple donor sites. More intriguing interlocking ensembles constructed from discrete metallocages are also described here in detail, namely, three [2]catenanes based on ligands L(30) -L(32) and four polycatenanes based on ligands L(33) -L(34) .

Nitrate anion templated synthesis of a [2]catenane for nitrate recognition in organic-aqueous solvent media

The first example of a catenane synthesised using a nitrate anion template is demonstrated. Removal of the templating anion reveals a mechanically interlocked molecular host system which is capable of recognising nitrate selectively over a range of more basic mono-anionic oxoanions in a competitive organic-aqueous solvent mixture.

Tunable Electrochemical and Catalytic Features of BIAN- and BIAO-Derived Ruthenium Complexes

This article deals with a class of ruthenium-BIAN-derived complexes, [Ru(II)(tpm)(R-BIAN)Cl]ClO4 (tpm = tris(1-pyrazolyl)methane, R-BIAN = bis(arylimino)acenaphthene, R = 4-OMe ([1a]ClO4), 4-F ([1b]ClO4), 4-Cl ([1c]ClO4), 4-NO2 ([1d]ClO4)) and [Ru(II)(tpm)(OMe-BIAN)H2O](2+) ([3a](ClO4)2). The R-BIAN framework with R = H, however, leads to the selective formation of partially hydrolyzed BIAO ([N-(phenyl)imino]acenapthenone)-derived complex [Ru(II)(tpm)(BIAO)Cl]ClO4 ([2]ClO4). The redox-sensitive bond parameters involving -N═C-C═N- or -N═C-C═O of BIAN or BIAO in the crystals of representative [1a]ClO4, [3a](PF6)2, or [2]ClO4 establish its unreduced form. The chloro derivatives 1a(+)-1d(+) and 2(+) exhibit one oxidation and successive reduction processes in CH3CN within the potential limit of ±2.0 V versus SCE, and the redox potentials follow the order 1a(+) < 1b(+) < 1c(+) < 1d(+) ≈ 2(+). The electronic structural aspects of 1a(n)-1d(n) and 2(n) (n = +2, +1, 0, -1, -2, -3) have been assessed by UV-vis and EPR spectroelectrochemistry, DFT-calculated MO compositions, and Mulliken spin density distributions in paramagnetic intermediate states which reveal metal-based (Ru(II) → Ru(III)) oxidation and primarily BIAN- or BIAO-based successive reduction processes. The aqua complex 3a(2+) undergoes two proton-coupled redox processes at 0.56 and 0.85 V versus SCE in phosphate buffer (pH 7) corresponding to {Ru(II)-H2O}/{Ru(III)-OH} and {Ru(III)-OH}/{Ru(IV)═O}, respectively. The chloro (1a(+)-1d(+)) and aqua (3a(2+)) derivatives are found to be equally active in functioning as efficient precatalysts toward the epoxidation of a wide variety of alkenes in the presence of PhI(OAc)2 as oxidant in CH2Cl2 at 298 K, though the analogous 2(+) remains virtually inactive. The detailed experimental analysis with the representative precatalyst 1a(+) suggests the involvement of the active {Ru(IV)═O} species in the catalytic cycle, and the reaction proceeds through the radical mechanism, as also supported by the DFT calculations.

DNA-based machines

The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

Fluctuation theorem for partially masked nonequilibrium dynamics

We establish a generalization of the fluctuation theorem for partially masked nonequilibrium dynamics. We introduce a partial entropy production with a subset of all possible transitions, and show that the partial entropy production satisfies the integral fluctuation theorem. Our result reveals the fundamental properties of a broad class of autonomous as well as nonautonomous nanomachines. In particular, our result gives a unified fluctuation theorem for both autonomous and nonautonomous Maxwell's demons, where mutual information plays a crucial role. Furthermore, we derive a fluctuation-dissipation theorem that relates nonequilibrium stationary current to two kinds of equilibrium fluctuations.

A molecular pulley based on a triply interlocked [2]rotaxane

A novel triply interlocked [2]rotaxane was designed and synthesized, which showed pulley-like shuttling motion controlled by acid and base.

Synthesis of a double-stranded spiroborate helicate bearing stilbene units and its photoresponsive behaviour

The sodium ion-triggered extension and contraction motions along with photo-induced cis–trans isomerisation of a photoresponsive spiroborate-based double-stranded helicate were investigated.