Rise of the Molecular Machines

The authors thank the EPSRC, ERC, and the Leverhulme Trust for supporting our research programs on molecular machines. E.R.K. is a Royal Society of Edinburgh/Scottish Government Personal Research Fellow.


Introduction
" When we get to the very,very small world …wehave alot of new things that would happen that represent completely new opportunities for design …Atthe atomic level we have new kinds of forces and new kinds of possibilities, new kinds of effects. The problem of manufacture and reproduction of materials will be quite different …i nspired by biological phenomena in which chemical forces are used in arepetitious fashion to produce all kinds of weird effects (one of which is the author) … " Richard P. Feynman (1959) [2] It has long been appreciated that molecular motors and machines are central to almost every biological process.T he harvesting of energy from the sun, the storing of energy, transporting cargoes around the cell, the movement of cells, generation of force (at both the molecular and macroscopic levels), replication, transcription, translation, synthesis,d riving chemical systems away from equilibrium, etc.-virtually every biological task involves molecular machines. [1] Given the success of mankinds machines in the macroscopic world, from the Stone-Age wheel to the modern-day smart phone,it was inevitable that we should one day seek to achieve the ultimate in machine miniaturization. However,i th as taken some time to gain sufficient mastery over the necessary synthetic and supramolecular chemistry (and related physics) for this field to begin to flourish.
Richard Feynmans classic 1959 lecture Theres plenty of room at the bottom [2] outlined some of the promise that manmade molecular machines might hold, as cientific "taster" that Eric Drexler embraced for his controversial [3] vision of "nanobots" and "molecular assemblers". [4] However,w hilst inspirational in general terms,itisdoubtful whether either of these manifestos had much practical influence on the development of artificial molecular machines. [5] Feynmans talk came at atime before chemists had the synthetic methods and analytical tools available to be able to consider how to make molecular machines;D rexlers somewhat nonchemical view of atomic construction is not shared by the majority of experimentalists working in this area. In fact, "mechanical" movement within molecules has been part of chemistry since conformational analysis became established in the 1950s. [6] As well as being central to advancing the structural analysis of complex molecules,t his was instrumental in chemists beginning to consider dynamics as an intrinsic aspect of molecular structure and hence ap roperty they could aspire to control. Artificial systems were designed to exhibit particular conformational behavior, such as the "cog-wheeling"-correlated motions of aromatic "blades" in triptycenes and related structures constructed by the groups of Ō ki, Mislow,a nd Iwamura in the 1970s and 1980s (e.g. 1,F igure 1a). [7] Before long,stimuli-induced changes in conformation had been used to control molecular recognition properties;t wo of the seminal examples being Rebeks use of allostery [8] (binding at one site influencing binding affinity at as econd site; 2, Figure 1b)a nd Shinkais azobenzene photoswitch [9] for modulating the cation-binding properties of crown ethers (3, Figure 1c). However,t he field of synthetic molecular machines really began to take off with developments that occurred in the early 1990s.

Architectures for Well-Defined Large-Amplitude Molecular-Level Motions
In many ways the field of artificial molecular machinery began with J. Fraser Stoddarts invention of a" molecular shuttle" (4)in1991 ( Figure 2). [10] In this rotaxane (a molecule with ar ing mechanically locked onto an axle by bulky stoppers), the ring (shown in blue) moves between two preferred binding sites (the two hydroquinone units,shown in red) by random thermal motion (Brownian motion). Theuse of template effects to assemble mechanically linked molecules (catenanes and, later,r otaxanes) had been introduced by Jean-Pierre Sauvage in the early 1980s; [11] Stoddarts great insight was to recognize that the threaded (mechanically interlocked) architecture of ar otaxane could allow for the large-amplitude motion of molecular-level components in aw ell-defined and potentially controllable manner. The authors of the 1991 JACS paper noted:"Insofar as it becomes possible to control the movement of one molecular component with respect to the other in a [2]rotaxane,the technology for building molecular machines will emerge." [10] This statement turned out to be highly prescient and the paper hugely influential. Although mechanically interlocked structures are not necessary to construct molecular machines (see below), they provided the first practical synthetic molecular architecture through which well-defined largeamplitude molecular-level motions could be selectively addressed, studied, and utilized. [1b-g] This gave an exciting and compelling reason to make rotaxanes and catenanes,and the area burgeoned from these molecules being academic curiosities in the 1960s (when catenanes and rotaxanes were first made by long and/or inefficient synthetic routes [12] )through to 1989 (when Stoddart and co-workers made their first catenane, [13] six years after Sauvage and co-workers revolutionized the strategy for their synthesis through the use of template methods [11] )tothe mainstream area it is now, [14] with hundreds of groups active in this field from the mid-1990s onwards.

Switching the Relative Positions of Molecular Components-From Molecules to Machines
By desymmetrizing ar otaxane thread to have two different potential binding sites,o r" stations", whose relative affinity for the ring could be switched, Stoddart, Kaifer, and co-workers arguably invented the first artificial molecular Brownian motion machine (5,F igure 3). [15] Thec ationic ring (shown in dark blue) prefers to reside over the benzidine group (shown in light blue) rather than the biphenol site (shown in orange). However,protonation (or electrochemical oxidation) of the benzidine station (now in purple) renders the biphenol group the preferred binding site for the cationic ring, thereby causing anet displacement of the ring along the track. This system marks the first example of al argeamplitude,w ell-defined, controlled switching of the position of acomponent along amolecular track.
Theg roups of Stoddart and others (notably those of Sauvage,B alzani, Fujita, Hunter,V çgtle,S anders,B eer, and Leigh) contributed to the development of many other rotaxane-and catenane-forming motifs and strategies over the period 1992-2007, [1b,f,g] and invented many different ways of switching the positions of the components in rotaxane and catenane architectures with various stimuli (light, electrochemistry,p Hvalue,p olarity of the environment, cation binding,a nion binding,a llosteric effects,t emperature,r eversible covalent-bond formation, etc). [1b,f,g] Then ext key advance needed was-and in some respects still is-to find ways to use the change of the position of the components of amolecular machine to perform useful tasks (see below).

The Invention of Rotary Molecular Motors
In 1999, two papers appeared back-to-back on the subject of controlling the direction of rotary motion. [16,17] Theg roup of T. Ross Kelly used chemical reactions-urethane formation followed by hydrolysis-to bias a1 208 8 rotation of at riptycene residue in one direction (6,F igure 4). [16] Unfortunately,K elly was never able to extend this approach to asystem where 3608 8 rotation occurs directionally.
Thep aper that followed it in the same issue of Nature, however, described an over-crowded alkene molecule (7)i n which the components,u pon irradiation with light, rotate directionally all the way around the alkene axis. [17] This molecule,f rom the Feringa group,w as the first example of as ynthetic rotary molecular motor and, indeed, the first example of an artificial molecular motor of any kind (Figure 5). Not only does this elegant design-which exploits, alternately,p hotoisomerization followed by as train-induced diasteromeric helix inversion-achieve complete 3608 8 rotation of one half of the molecule with respect to the other, it does so continuously as long as the compound is irradiated with photons and is above ac ritical temperature.    [16] . .

Angewandte Essays
Over the next decade,m any structural improvements were made to this type of motor molecule,d ramatically increasing the rate of rotation [18] and using them to perform tasks,such as rotating amacroscopic object on the surface of aliquid-crystal medium (8, Figure 6), [19] switching the chirality of an organocatalyst (9,F igure 7), [20] and acting as the "motorized wheels" of a" nanocar". [21] Brownian Ratchet Mechanisms Thep roblem of constructing am otor by using molecular components which move through random thermal motions distils down to achieving directional motion of Brownian particles.This issue has,atvarious times,intrigued some of the greatest physicists of the past 150 years:i ti st he essential process behind the celebrated thought experiments known as Maxwells demon (1871), [22] Smoluchowskis trapdoor (1912), [23] and Feynmans ratchet-and-pawl (1963) [24] (for adiscussion of their relevance to artificial molecular machine design, see Ref. [1f]). In the last two decades of the 20th century,these superficially abstract deliberations gave way to af lourishing field of (mostly theoretical) studies that established ar ange of Brownian ratchet mechanisms through which directional motion of Brownian particles can be achieved. [25] These provide the mechanistic framework for the operation of all molecular motors-whether biological or artificial. [26] Unfortunately,h owever,c hemists failed to appreciate these findings until the mid-2000s;m ost systems described as "motor-molecules" in the 1990s and 2000s were actually switches incapable of doing work cumulatively (i.e. any task performed is undone by the action of resetting the switch). [1f] Thefirst application of ratchet mechanisms to the de novo design of artificial molecular machines resulted in acatenanebased rotary motor [27] and was subsequently developed further over the next few years in as eries of rotaxane-based machines that could pump macrocycles to higher-energy (non-equilibrium) distributions or states. [28] Yet, few synthetic linear small-molecule motors have been prepared to date.The first small molecule able to "walk" along tracks (reminiscent of the mode of transport of kinesin and other motor proteins) was reported in 2010, [29] with directional versions employing ratchet mechanisms introduced shortly afterwards (10,F igure 8). [30] Unlike rotaxane switches (e.g. 4,F igure 2), these walkers move along their tracks progressively,e ach cycle in which fuel is consumed potentially causing the motor to take as tep further along the track. Such devices are,i np rinciple, capable of transporting cargoes directionally.H owever, current systems are only efficient enough to take afew steps along short tracks and are not yet sufficiently robust to walk across surfaces or along polymers.
An umber of molecular walker-track systems that are either largely or entirely assembled from DNAb uilding blocks have been described. [31] Many of these DNAwalkers are genuine motors,s ince they exhibit all four of the fundamental characteristics of molecular motors:r epetitive, progressive (that is,multiple operations of the motor do work cumulatively), processive (that is,take multiple steps without dissociating), and directionally biased transport of amolecular fragment (walker unit) along at rack. [32] However,s ynthetic DNAwalkers are generally of asimilar size to,oreven larger than, biological motor proteins such as kinesin-I, and their applications are likely to be more limited than that of wholly synthetic systems as they are restricted in terms of both operating conditions and chemical stability.D espite these limitations,the ease with which complex DNAconstructs can be designed and made by automated synthesizers (often carried out to order by commercial suppliers), has meant that some enormous (250 000-500 000 Da) DNA-derived molecular machines have been prepared that can perform sophisticated tasks,s uch as transporting gold nanoparticles from place-to-place in ap rogrammable "nano-assembly line". [33] These systems benefit from the tremendous advances being made in other areas of DNAn anotechnology,s uch as DNA origami, DNAt iles,and DNAcomputing. [34] Figure 5. The first light-powered rotary molecularm otor (Feringa and co-workers;1 999). [17] Figure 6. Rotating amacroscopic object with amolecularmachine (Feringa and co-workers;2 006). Modified from Ref. [19] with permission. Richard P. Feynman (1959) [2] Over the last two decades,v arious types of molecular architectures have been used to make molecular "pistons", [35] "clutches", [36] "windmills", [37] "elevators", [38] "wheelbarrows", [39] and even "nanocars", [40] taking the appearance and modes of operation of macroscopic machines as their inspiration. However,just because aspace-filling representation of am olecule looks like am acroscopic piston or automobile does not mean that the molecule can necessarily perform as imilar function at the molecular level. Matter behaves very differently at different length scales,a nd random thermal motion, heat dissipation, solvation, momentum, inertia, gravity,e tc. take on very different significances for the operating environment at the molecular level compared to what is important for macroscopic machine mechanisms. [1f,g, 41] Machines need to be designed according to the environment they are intended to operate in (for example, ac ar, intended for transport on solid ground, would not perform well either on water or in outer space!).H owever, mimicking biology is certainly not the only way to achieve complex functionality:c omputer chips are manufactured from silicon wafers rather than being wet and carbon-based like our brains.T od ate,i tr emains unproven as to whether making iconic molecular representations of macroscopic objects or following the principles of biological machines will be the most effective route for designing molecular machines with useful functions.I ndeed, perhaps the most productive solutions will be found by following neither of these approaches too closely.
Thetasks that molecular machines are best suited to carry out also need careful consideration: " Ican't see exactly what would happen, but Ican hardly doubt that when we have some control of the arrangement of things on asmall scale we will get an enormously greater range of possible properties that substances can have, and of different things that we can do. " Richard P. Feynman (1959) [2]

1) Molecular Machines for Molecular Electronics
In as eries of controversial [42] and ground-breaking [43] experiments from about 1997 to 2007, the groups of Stoddart and Jim Heath interfaced switchable rotaxanes and catenanes with silicon-based electronics in an effort to try to use molecular shuttles in solid-state molecular electronic computing devices (Figure 9a). Competing with the electronic movements in silicon and other semiconductors (which intrinsically occur billions of times faster than the change of position of the components in rotaxanes) seems somewhat counterintuitive as ap roblem suited for solving with abacuslike positional changes within molecular machines.However, adecade of effort and progress culminated in the fabrication and testing of aremarkable 160-kbit memory at 10 11 bits cm À2 based on am onolayer of switchable rotaxanes as the datastorage elements. [44] Whether rotaxanes will ever be effectively employed in electronics remains an open question, but an important legacy of this pioneering research program is the vast amount learnt regarding how to interface complex functional molecules with silicon. These efforts also served to inspire the use of rotaxane-based switches to induce other types of macroscopically observable property changes Figure 8. As mall molecule that walks directionally along amolecular track using alight-fueled energy ratchet (flashing ratchet) mechanism (Leigh and co-workers;2011). [30] through mechanical movement, including chiroptical switching (2003), [45] fluorescence switching (2004), [46] writing of information in polymer films (2005), [47] and in controlledrelease delivery systems (Figure 9b,2005). [48] 2) Molecular Machines that CanDoMechanical Work:"Molecular Muscles" Using controlled molecular-level motion to generate force in the macroscopic world is an appealing task for molecular machines because this is,o fc ourse,h ow muscles work. In 2005, the groups of Leigh and Stoddart each reported artificial molecular machines capable of doing mechanical work. Leighs group used the light-induced shuttling of as urface-bound rotaxane to mask ap olarophobic fluorocarbon unit. Thec hange in surface properties could be used to propel ad roplet along as urface and up as lope,a gainst the force of gravity (Figure 10 a). [49] Stoddarts group used the contraction of ar otaxane as am olecular actuator to bend ag old microcantilever beam (Figure 10 b). [50] Recently,G iuseppone and co-workers described the use of light-driven molecular rotary motors to bring about macroscopic contraction of ag el (11,F igure 10 c). [51] 3) Molecular Machines that CanM ake Molecules " Ultimately,wecan do chemical synthesis. Achemist comes to us and says, 'Look, Iw ant amolecule that has the atoms arranged this and so;make me that molecule.' " Richard P. Feynman (1959) [2] From polyketide synthase to DNAp olymerases and the ribosome,o ne of the key uses of molecular machines in biology is for the construction of other molecules.In2013 an artificial small-molecule machine was invented that assembled at ripeptide of specific sequence by travelling along at rack loaded with amino acid building blocks (12,F igure 11). [52] This is a( very!) primitive analogue of the task performed by the ribosome in cells,b ut arguably one of the most sophisticated performed by an artificial molecular machine to date.F or as ynthetic molecular machine it has at ruly complex mechanism of operation, requiring the integrated interaction of several functional component parts: ar eversibly attached reactive "arm" with ar egenerable catalytic site and apeptide-elongation site,aring that threads the track catalytically with no residual ring-track interactions to retard the machines action, and at rack with amino acid building blocks in ap redetermined sequence separated by rigid spacers.S ystems with integrated mechanisms of operations are likely to lead to increasingly ambitious and Figure 9. a) Rotaxane-based moleculars witch tunnel junctions (Stoddart,H eath, and co-workers;2 007). [44] b) Controlled release of guest molecules using arotaxanev alve (Stoddart,Z ink, and co-workers;2 005). [48] Angewandte Chemie potentially useful applications of synthetic molecular machines.

Outlook
" 'Who should do this and why should they do it?' Well, Ipointed out af ew of the economic applications, but Ik now that the reason that you would do it might be just for fun ……have some fun! " Richard P. Feynman (1959) [2] Thef uture for the field of artificial molecular machines appears very bright. There is already aworking nanotechnology based on molecular machines that perform numerous useful tasks:i ti sc alled Biology.T he natural world shows us just how exquisite and diverse the functions are that can be carried out with molecular machines.A dvances in artificial systems over the past 25 years mean that chemists now have the know-how and synthetic tools available to enable them to make suitable machine architectures (e.g.c atenanes,r otaxanes,o ver-crowded alkenes,m olecules that walk upon tracks). They can switch the position of components (often by clever manipulation of noncovalent interactions between the various parts), they understand how to use ratchet mechanisms to create motor mechanisms,a nd are learning how to introduce them into more complex molecular machine systems.

Angewandte
Essays proton gradients,t here are as yet no chemically driven synthetic small-molecule motors that can operate autonomously (i.e.aslong as ac hemical fuel is present), the closest counter-examples being the over-crowded alkene motors designed by Feringa and co-workers that rotate continuously under irradiation with light. Furthermore,a lthough there have been some notable successes in using artificial molecular machines to bring about property changes,f ew have been shown to perform useful tasks that cannot be accomplished by conventional chemical means.T his contrasts with the essential roles played by biological machines in numerous cellular processes.W hen this last step happens-and the rapid advances of the last few years suggest that that time is not too far away-then artificial molecular machines will start to become the extraordinary nanotechnology that Feynman predicted. Making that happen, as he suggested, [2] will doubtless be fun!