Towards artificial molecular factories from framework-embedded molecular machines

Collective dynamics of molecular rotors in periodic mesoporous organosilica: a combined solid-state 2H-NMR and molecular dynamics simulation study

Molecular rotors offer a platform to realize controlled dynamics and modulate the functions of solids. The motional mechanisms in arrays of rotors have not been explored in depth. Crystal-like porous organosilicas, comprising p-phenylene rotators pivoted onto a siloxane scaffold, were modelled using molecular dynamics (MD) simulations. Long simulations, on a microsecond scale, allowed to follow the reorientation statistics of rotor collections and single out group configurations and frequency distributions as a function of temperature. The motions observed in the MD simulations support a multiple-site model for rotor reorientations. Computed motional frequencies revealed a complex rotatory phenomenon combining an ultra-fast libration motion (oscillation up to 30°) with a slow and fast 180° flip reorientation. Adopting a multiple-site model provides a more accurate simulation of the ²H-NMR spectra and a rationalization of their temperature dependence. In particular, rotators endowed with distinct rates could be explained by the presence of slower rings locked in a T-shaped conformation.

Visible light activated BINOL-derived chiroptical switches based on boron integrated hydrazone complexes

Chiral optical switches, which use light to control chirality in a reversible manner, offer unique properties and fascinating prospects in the areas of molecular switching and responsive systems, new photochromic materials and molecular data processing and storage. Herein, we report visible light responsive chiroptical switches based on tetrahedral boron coordination towards an easily accessible hydrazone ligand and optically pure BINOL. Upon instalment of a non-planar dibenzo[a,d]-cycloheptene moiety in the hydrazone ligand's lower half, the enantiopure boron complex shows major chiroptical changes in the CD read-out after visible light irradiation. The thermal isomerization barrier in these chiroptical switching systems showed to be easily adjustable by the introduction of substituents onto the olefinic bond of the cycloheptene ring, giving profound control over their thermal stability. The control over their thermal stability in combination with excellent reversibility, photochemical properties and overall robustness of the complexes makes these BINOL-derived chiroptical switches attractive candidates for usage in advanced applications, e.g. photonic materials and nanotechnology.

Chiroptical switches, which use light to control chirality in a reversible manner, offer unique properties and fascinating prospects in the areas of molecular responsive systems, new photochromic materials and molecular data processing and storage.

Controlling rotary motion of molecular motors based on oxindole

Molecular motors are essential components of artificial molecular machines, which can be used to manipulate and amplify mechanical motion at the nanoscale to create machine-like function. Since the discovery of light-driven rotary molecular motors, the field has been widely developed, including the introduction of molecular motors based on oxindole by our group in 2019. The rotational properties of molecular motors, e.g. absorption wavelength, quantum yield and rotation speed, often critically depend on substituent effects. Up to now, the substituent effects of oxindole-based molecular motors have not yet been investigated. Herein, we present a family of oxindole-based molecular motors functionalised at three different positions on the motor core, with either CN or OMe groups. The motors prepared in this work retain the favourable features of oxindole-based motors, i.e. simple synthesis and visible light addressability. We find that functionalisation has substantial effects on the absorption wavelength of the motors, meanwhile the rotation speed is unaffected. Furthermore, we found that functionalisation of the oxindole molecular motors increases their quantum efficiency considerably in comparison to previous motors of their class.

We present a new family of oxindole-based functionalised at three positions on the upper and lower halves, with methoxy or cyano groups. We find that this allows the absorption wavelength and quantum yields of these motors to be tuned.

Light-Driven Molecular Motors Embedded in Covalent Organic Frameworks

The incorporation of molecular machines into the backbone of porous framework structures will facilitate nano actuation, enhanced molecular transport, and other out-of-equilibrium host-guest phenomena in well-defined 3D solid materials. In...

Polyrotaxanes and the pump paradigm

The year 2022 marks the 30th anniversary of the first reports of polyrotaxanes in the scientific literature.

Computer-aided design of molecular machines: techniques, paradigms and difficulties

With their development in the past decade, molecular machines, which achieve specific tasks by responding to external stimuli, have gradually come to be regarded as powerful tools for a wide range of applications, rather than interesting molecular toys. This conceptual change in turn motivates scientists to design molecular machines with complex architectures. Due to the lack of general principles bridging the functions and the chemical structures of molecular machines, experience-based design becomes difficult with the increase of size and complexity of the architectures. Computer-aided molecular-machine design, therefore, has attracted widespread attention on account of its ability to model and investigate complex molecular architectures without too much time and expense required for synthetic experiments. Using leading-edge numerical-simulation techniques, the mechanisms underlying achieving tasks through response to external stimuli of a large number of existing molecular machines have been successfully explored. Based on the experience of studying existing molecular machines, generalized methodologies of predicting the properties and working principles of molecular candidates have been established, paving the way for de novo computer-aided design of molecular machines. In this perspective, we introduce cutting-edge techniques that have been applied for investigating and designing molecular machines. We show paradigms of computer-aided design of molecular machines, which can serve as guidelines for the investigation of new supramolecular architectures. Moreover, we discuss the limitations and possible future developments of current techniques and methodologies in the field of computer-aided design of molecular machines.

Active mechanisorption driven by pumping cassettes

[Figure: see text].

Photochemical Energy Conversion with Artificial Molecular Machines

The exploitation of sunlight as a clean, renewable, and distributed energy source is key to facing the energetic demand of modern society in a sustainable and affordable fashion. In the past few decades, chemists have learned to make molecular machines, that is, synthetic chemical systems in which energy inputs cause controlled movements of molecular components that could be used to perform a task. A variety of artificial molecular machines operated by light have been constructed by implementing photochemical processes within appropriately designed (supra)molecular assemblies. These studies could open up new routes for the realization of nanostructured devices and materials capable to harness, convert, and store light energy.

Capturing the Rotation of One Molecular Crank by Single-Molecule Conductance

Unveiling the internal dynamics of rotation in molecular machine at single-molecule scale is still a challenge. In this work, three crank-shaped molecules are elaborately designed with the conformational flipping between syn and anti fulfilled by two naphthyl groups rotating freely along 1,3-butadiynyl axis. By investigating the single-molecule conductance using scanning tunnelling microscope break junction (STM-BJ) technique and theoretical simulation, the internal rotation of these crank-shaped molecules is well identified through low and high conductance corresponding to syn- and anti-conformations. As demonstrated by theoretically computational study, the orbital energy changes with the conformational flipping and influences the intraorbital quantum interference, thus eventually modulating the single-molecule conductance. This work demonstrates single-molecule conductance measurement to be a rational approach for characterizing the internal rotation of molecular machines.

Designing light-driven rotary molecular motors

The ability to induce and amplify motion at the molecular scale has seen tremendous progress ranging from simple molecular rotors to responsive materials. In the two decades since the discovery of light-driven rotary molecular motors, the development of these molecules has been extensive; moving from the realm of molecular chemistry to integration into dynamic molecular systems. They have been identified as actuators holding great potential to precisely control the dynamics of nanoscale devices, but integrating molecular motors effectively into evermore complex artificial molecular machinery is not trivial. Maximising efficiency without compromising function requires conscious and judicious selection of the structures used. In this perspective, we focus on the key aspects of motor design and discuss how to manipulate these properties without impeding motor integrity. Herein, we describe these principles in the context of molecular rotary motors featuring a central double bond axle and emphasise the strengths and weaknesses of each design, providing a comprehensive evaluation of all artificial light-driven rotary motor scaffolds currently present in the literature. Based on this discussion, we will explore the trajectory of research into the field of molecular motors in the coming years, including challenges to be addressed, potential applications, and future prospects.

Three-State Switching of an Anthracene Extended Bis-thiaxanthylidene with a Highly Stable Diradical State

A multistable molecular switching system based on an anthracene-extended bis-thiaxanthylidene with three individually addressable states that can be interconverted by electrochemical, thermal, and photochemical reactions is reported. Besides reversible switching between an open-shell diradical- and a closed-shell electronic configuration, our findings include a third dicationic state and control by multiple actuators. This dicationic state with an orthogonal conformation can be switched electrochemically with the neutral open-shell triplet state with orthogonal conformation, which was characterized by EPR. The remarkably stable diradical shows kinetic stability as a result of a significant activation barrier for isomerization to a more stable neutral closed-shell folded geometry. We ascribe this activation barrier of ΔG^⧧(293 K) = 25.7 kcal mol^-1 to steric hindrance in the fjord region of the overcrowded alkene structure. The folded closed-shell state can be converted back to the diradical state by irradiation with 385 nm. The folded state can also be oxidized to the dicationic state. These types of molecules with multiple switchable states and in particular stable diradicals show great potential in the design of new functional materials such as memory devices, logic gates, and OFETs.

Coordination-directed self-assembly of molecular motors: towards a two-wheel drive nanocar

Designing and constructing hierarchical and stimuli-responsive motorized nanocar systems to perform useful tasks on-demand is highly imperative towards molecular nanotechnology. In this work, a most simplified two-wheel nanocar was successfully prepared through a facile strategy of coordination-directed self-assembly. The nanocar meso-AgL2 features a central pseudo square-planar Ag(I) which was bridged by two enantiomeric motors as the wheels that ensure the car moves in the same direction when observed externally. Thanks to the electronic push-pull characteristic of L and ³ILCT triplet sensitization, this nanocar can be driven by visible light up to 500 nm. Furthermore, it could be disassembled into individual motor elements through the addition of pyridine, thus allowing dynamic regulation over the function of the nanocar. Importantly, our STM imaging results showed very organized tilted layered structures for meso-AgL2 on highly oriented pyrolytic graphite (HOPG) that are quite similar to its crystalline ones, paving the way for future single molecule manipulations. The nanocar reported here represents the first example of integrating individual motors into a hierarchical motorized nanocar system via the facile coordination-directed self-assembly method and may offer a good starting point to realize its robotic functions, e.g., metal transportation and release.

Cascade Dynamics of Multiple Molecular Rotors in a MOF: Benchmark Mobility at a Few Kelvins and Dynamics Control by CO2

Achieving sophisticated juxtaposition of geared molecular rotors with negligible energy-requirements in solids enables fast yet controllable and correlated rotary motion to construct switches and motors. Our endeavor was to realize multiple rotors operating in a MOF architecture capable of supporting fast motional regimes, even at extremely cold temperatures. Two distinct ligands, 4,4′-bipyridine (bipy) and bicyclo[1.1.1]pentanedicarboxylate (BCP), coordinated to Zn clusters fabricated a pillar-and-layer 3D array of orthogonal rotors. Variable temperature XRD, ²H solid-echo, and ¹H T₁ relaxation NMR, collected down to a temperature of 2 K revealed the hyperfast mobility of BCP and an unprecedented cascade mechanism modulated by distinct energy barriers starting from values as low as 100 J mol^–1 (24 cal mol^–1), a real benchmark for complex arrays of rotors. These rotors explored multiple configurations of conrotary and disrotary relationships, switched on and off by thermal energy, a scenario supported by DFT modeling. Furthermore, the collective bipy-ring rotation was concerted with the framework, which underwent controllable swinging between two arrangements in a dynamical structure. A second way to manipulate rotors by external stimuli was the use of CO₂, which diffused through the open pores, dramatically changing the global rotation mechanism. Collectively, the intriguing gymnastics of multiple rotors, devised cooperatively and integrated into the same framework, gave the opportunity to engineer hypermobile rotors (10⁷ Hz at 4 K) in machine-like double ligand MOF crystals.

Evolution of catalytic machinery: three-component nanorotor catalyzes formation of four-component catalytic machinery

The three-component nanorotor [Cu2(S)(R)]2+ (k298 = 46.0 kHz) that is a catalyst for a CuAAC reaction binds the click product at each of its copper centers thereby creating a new platform and a dynamic slider-on-deck system. Due to this sliding motion (k298 = 65.0 kHz) the zinc-porphyrin bound N-methylpyrrolidine is efficiently released into solution and catalyzes a follow-up Michael addition.

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

Radical-pairing-induced molecular assembly and motion

Radical-pairing interactions between conjugated organic π-radicals are relative newcomers to the inventory of molecular recognition motifs explored in supramolecular chemistry. The unique electronic, magnetic, optical and redox-responsive properties of the conjugated π-radicals render molecules designed with radical-pairing interactions useful for applications in various areas of chemistry and materials science. In particular, the ability to control formation of radical cationic or anionic species, by redox stimulation, provides a flexible trigger for directed assembly and controlled molecular motions, as well as a convenient means of inputting energy to fuel non-equilibrium processes. In this Review, we provide an overview of different examples of radical-pairing-based recognition processes and of their emerging use in (1) supramolecular assembly, (2) templation of mechanically interlocked molecules, (3) stimuli-controlled molecular switches and, by incorporation of kinetic asymmetry in the design, (4) the creation of unidirectional molecular transporters based on pumping cassettes powered by fuelled switching of radical-pairing interactions. We conclude the discussion with an outlook on future directions for the field.

Adjusting Rotational Behavior of Molecular Rotors by a Rational Tuning of Molecular Structure

Many crystalline molecular rotors have been developed in the past decades. However, manipulating the rotational gesture that intrinsically controls the physical performance of materials remains a challenge. Herein, we report a series of crystalline rotors whose rotational gestures can be modulated by modifying the structures of molecular stators. In these dynamic crystals, the ox^2- (ox^2- = oxalate anion) behave as molecular rotators performing axial-free rotation in cavities composed of five complex cations, [M^II(en)₃]²⁺ (en = ethylenediamine). The structure of [M^II(en)₃]²⁺ that serves as a molecular stator can be tuned by varying the metal center with different ionic radii, consequently altering the chemical environment around the molecular rotator. Owing to the quasi-transverse isotropy of ox^2- and multiple hydrogen-bond interactions around it, the molecular rotator exhibits unusual motional malleability, i.e., it can rotate either longitudinally in the compound of Zn^II, or with a tilt angle of 42° in the compound of Fe^II, or even laterally in the compound of Cd^II. The atypical dynamic behavior demonstrated here provides a new chance for the development of exquisite crystalline molecular rotors with advanced tunable functionalities.

Enhanced Gearing Fidelity Achieved Through Macrocyclization of a Solvated Molecular Spur Gear

Molecular spur gear dynamics with high gearing fidelity can be achieved through a careful selection of constituent molecular components that favorably position and maintain the two gears in a meshed configuration. Here, we report the synthesis of a new macrocyclic molecular spur gear with a bibenzimidazole stator combined with a second naphthyl bis-gold-phosphine gold complex stator to place two 3-fold symmetric 9,10-diethynyl triptycene cogs at the optimal distance of 8.1 Å for gearing. Micro electron diffraction (μED) analysis confirmed the formation of the macrocyclic structure and the proper alignment of the triptycene cogs. Gearing dynamics in solution are predicted to be extremely fast and, in fact, were too fast to be observed with variable-temperature ¹H NMR using CD₂Cl₂ as the solvent. A combination of molecular dynamics and metadynamics simulations predict that the barriers for gearing and slippage are ca. 4 kcal mol^-1 and ca. 9 kcal mol^-1, respectively. This system is characterized by enhanced gearing fidelity compared to the acyclic analog. This is achieved by rigidification of the structure, locking the two triptycenes in the preferred gearing distance and orientation.

"Texas-Sized" Molecular Boxes: From Chemistry to Applications

The design and synthesis of novel macrocyclic host molecules continues to attract attention because such species play important roles in supramolecular chemistry. However, the discovery of new classes of macrocycles presents a considerable challenge due to the need to embody by design effective molecular recognition features, as well as ideally the development of synthetic routes that permit further functionalization. In 2010, we reported a new class of macrocyclic hosts: a set of tetracationic imidazolium macrocycles, which we termed “Texas-sized” molecular boxes (TxSBs) in homage to Stoddart’s classic “blue box” (CBPQT⁴⁺). Compared with the rigid blue box, the first generation TxSB displayed considerably greater conformational flexibility and a relatively large central cavity, making it a good host for a variety of electron-rich guests. In this review, we provide a comprehensive summary of TxSB chemistry, detailing our recent progress in the area of anion-responsive supramolecular self-assembly and applications of the underlying chemistry to water purification, information storage, and controlled drug release. Our objective is to provide not only a review of the fundamental findings, but also to outline future research directions where TxSBs and their constructs may have a role to play.

Molecular Pumps and Motors

Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.

Molecular-Rotor-Driven Advanced Porous Materials

Advanced porous materials (APMs)-such as metal-organic frameworks (MOFs) and porous organic polymers (POPs)-have emerged as an exciting research frontier of chemistry and materials science. Given their tunable pore size and extensive diversity, APMs have found widespread applications. In addition, adding dynamic functional groups to porous solids furthers the development of stimuli-responsive materials. By incorporating moving elements-molecular rotors-into the porous frameworks, molecular-rotor-driven advanced porous materials (MR-APMs) can respond reversibly to chemical and physical stimuli, thus imparting dynamic functionalities that have not been found in conventional porous materials. This Minireview discusses exemplary MR-APMs in terms of their design, synthesis, rotor dynamics, and potential applications.

Emerging Spacers-Based Ligands for Supramolecular Coordination Complexes

The design and self-assembly of supramolecular coordination complexes (SCCs) i. e., discrete cyclic metalloarchitectures such as cycles, cages, mesocates, and helicates with desired size, shape, and properties have been increasing exponentially owing to their potential applications in molecular sensors, molecular cargos, molecular recognition, and catalysis. The introduction of the organic motifs and metal complexes as a spacer provides functionality to the metalloarchitecture. This review mainly focusses on newly evolving spacer based ligands employed to yield simple to high-order metallosupramolecular assemblies using straight-forward approaches. The new spacers including corannulene, organic cyclic framework, bicyclic organic motifs, aliphatic chain, metalloligands, triarylboron, BODIPY, azaphosphatrane, phosphine, and thio/selenophosphates offer a great set of properties and in-built functionalities to the metalloarchitectures which are discussed in this review.

A Cd(ii) and Zn(ii) selective naphthyl based [2]rotaxane acts as an exclusive Zn(ii) sensor upon further functionalization with pyrene

A new multi-functional [2]rotaxane, ROTX, has been synthesized via a Cu(i) catalysed azide-alkyne cycloaddition reaction between Ni(ii) templated azide terminated pseudorotaxane composed of a naphthalene based heteroditopic wheel, NaphMC, and an alkyne terminated stopper. Subsequently, ROTX has been functionalized with pyrene moieties to develop a bifluorophoric [2]rotaxane, PYROTX, having naphthalene and pyrene moieties. Detailed characterization of these two rotaxanes is performed by utilizing several techniques such as ESI-MS, (1D and 2D) NMR, UV/Vis and PL studies. Comparative metal ion sensing studies of NaphMC (a fluorophoric cyclic receptor), ROTX ([2]rotaxane with a naphthyl fluorophore) and PYROTX ([2]rotaxane having naphthyl and pyrene fluorophores) have been performed to determine the effect of dimensionality/functionalization on the metal ion selectivity. Although NaphMC fails to discriminate between metal ions, ROTX serves as a selective sensor for Zn(ii) and Cd(ii). Importantly, PYROTX shows exclusive selectivity towards Zn(ii) over various transition, alkali and alkaline earth metal ions including Cd(ii).

Hydrazone exchange: a viable route for the solid-tethered synthesis of [2]rotaxanes

Using a hydrazone exchange methodology, resin beads were functionalised with [2]rotaxanes at up to 80% efficiency—higher than using other dynamic or irreversible synthetic approaches to form self-assembled structures on solid supports.

Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle

Metal-organic frameworks (MOFs) are modular and tunable nanoporous materials with applications in gas storage, separations, and sensing. Integrating flexible/dynamic, gas-responsive components into MOFs can give them unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, the position of the wheel, and the differential energy of adsorption depend on temperature, pressure, and the interactions of the gas and wheel with the stations on the strut. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature sensitive and to release more or less heat upon adsorption. The model also uncovers that, if gas-wheel competition for a station is fierce, temperature influences the position of the wheel differently depending on the amount of gas adsorbed.