The widespread use of molecular machines in biology has long suggested that great rewards could come from bridging the gap between synthetic molecular systems and the machines of the macroscopic world. In the last two decades, it has proved possible to design synthetic molecular systems with architectures where triggered large amplitude positional changes of submolecular components occur. Perhaps the best way to appreciate the technological potential of controlled molecular-level motion is to recognize that nanomotors and molecular-level machines lie at the heart of every significant biological process. Over billions of years of evolution, nature has not repeatedly chosen this solution for performing complex tasks without good reason. When mankind learns how to build artificial structures that can control and exploit molecular level motion and interface their effects directly with other molecular-level substructures and the outside world, it will potentially impact on every aspect of functional molecule and materials design. An improved understanding of physics and biology will surely follow.

The first steps on the long path to the invention of artificial molecular machines were arguably taken in 1827 when the Scottish botanist Robert Brown observed the haphazard motion of tiny particles under his microscope.1,2 The explanation for Brownian motion, that it is caused by bombardment of the particles by molecules as a consequence of the kinetic theory of matter, was later provided by Einstein, followed by experimental verification by Perrin.3,4 The random thermal motion of molecules and its implications for the laws of thermodynamics in turn inspired Gedankenexperiments (“thought experiments”) that explored the interplay (and apparent paradoxes) of Brownian motion and the Second Law of Thermodynamics. Richard Feynman’s famous 1959 lecture “There’s plenty of room at the bottom” outlined some of the promise that manmade molecular machines might hold.5,6 However, Feynman’s talk came at a time before chemists had the necessary synthetic and analytical tools to make molecular machines. While interest among synthetic chemists began to grow in the 1970s and 1980s, progress accelerated in the 1990s, particularly with the invention of methods to make mechanically interlocked molecular systems (catenanes and rotaxanes) and control and switch the relative positions of their components.7−24

Here, we review triggered large-amplitude motions in molecular structures and the changes in properties these can produce. We concentrate on conformational and configurational changes in wholly covalently bonded molecules and on catenanes and rotaxanes in which switching is brought about by various stimuli (light, electrochemistry, pH, heat, solvent polarity, cation or anion binding, allosteric effects, temperature, reversible covalent bond formation, etc.). Finally, we discuss the latest generations of sophisticated synthetic molecular machine systems in which the controlled motion of subcomponents is used to perform complex tasks, paving the way to applications and the realization of a new era of “molecular nanotechnology”.

1.1. The Language Used To Describe Molecular Machines
Terminology needs to be properly and appropriately defined and these meanings used consistently to effectively convey scientific concepts. Nowhere is the need for accurate scientific language more apparent than in the field of molecular machines. Much of the terminology used to describe molecular-level machines has its origins in observations made by biologists and physicists, and their findings and descriptions have often been misinterpreted and misunderstood by chemists. In 2007 we formalized definitions of some common terms used in the field (e.g., “machine”, “switch”, “motor”, “ratchet”, etc.) so that chemists could use them in a manner consistent with the meanings understood by biologists and physicists who study molecular-level machines.14

The word “machine” implies a mechanical movement that accomplishes a useful task. This Review concentrates on systems where a stimulus triggers the controlled, relatively large amplitude (or directional) motion of one molecular or submolecular component relative to another that can potentially result in a net task being performed. Molecular machines can be further categorized into various classes such as “motors” and “switches” whose behavior differs significantly.14 For example, in a rotaxane-based “switch”, the change in position of a macrocycle on the thread of the rotaxane influences the system only as a function of state. Returning the components of a molecular switch to their original position undoes any work done, and so a switch cannot be used repetitively and progressively to do work. A “motor”, on the other hand, influences a system as a function of trajectory, meaning that when the components of a molecular motor return to their original positions, for example, after a 360° directional rotation, any work that has been done is not undone unless the motor is subsequently rotated by 360° in the reverse direction. This difference in behavior is significant; no “switch-based” molecular machine can be used to progressively perform work in the way that biological motors can, such as those from the kinesin, myosin, and dynein superfamilies, unless the switch is part of a larger ratchet mechanism.14

Artificial Molecular Machines

Catalysis is key to the effective and efficient transformation of readily available building blocks into high value functional molecules and materials. For many years research in this field has largely focussed on the invention of new catalysts and the optimization of their performance to achieve high conversions and/or selectivities. However, inspired by Nature, chemists are beginning to turn their attention to the development of catalysts whose activity in different chemical processes can be switched by an external stimulus. Potential applications include using the states of multiple switchable catalysts to control sequences of transformations, producing different products from a pool of building blocks according to the order and type of stimuli applied. Here we outline the state-of-art in artificial switchable catalysis, classifying systems according to the trigger used to achieve control over the catalytic activity and stereochemical or other structural outcomes of the reaction.

/pdf/artificial-switchable-catalysts-1vz85ufdrw.pdf

Artificial switchable catalysts

Acyl transfer is at the heart of functional-group transfers utilized both in nature and in the chemical laboratory. Acylations are part of the natural assembly machinery for the generation of complex molecules and for energy transport in biological systems. The recognition of covalent acyl-enzyme intermediates led to both mechanistic studies as well as the development of biomimetic approaches. Consequently, chemists first used the tools of nature in the form of enzymes and naturally occurring alkaloids as catalysts, before eventually developing a large variety of synthetic small molecules for selective acyl transfer. In contrast to nature, chemists utilize acylation reactions as a practical way for stereoselection and functional-group protection. Indeed, the number of studies concerning acyl transfer has significantly increased over the last 15 years. This Review examines and highlights these recent developments with the focus as given in the title.

Organocatalytic enantioselective acyl transfer onto racemic as well as meso alcohols, amines, and thiols.

Asymmetric catalysis has been revolutionised by the realisation that attractive non-covalent interactions such as hydrogen bonds and ion pairs can act as powerful controllers of enantioselectivity when incorporated into appropriate small molecule chiral scaffolds. Given these tremendous advances it is surprising that there are still a relatively limited number of examples of non-covalent interactions being harnessed for control of regioselectivity or site-selectivity in catalysis, two other fundamental selectivity aspects facing the synthetic chemist. This perspective examines the progress that has been made in this area thus far using non-covalent interactions in conjunction with transition metal catalysis as well as in the context of purely organic catalysts. We hope this will highlight the great potential in this approach for designing selective catalytic reactions.

/pdf/harnessing-non-covalent-interactions-to-exert-control-over-32816ct372.pdf

Harnessing non-covalent interactions to exert control over regioselectivity and site-selectivity in catalytic reactions

Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.

Toward automated oligosaccharide synthesis.

The activation mode of a rotaxane-based organocatalyst with both secondary amine and squaramide catalytic units can be switched with acid or base. The macrocycle blocks whichever of the catalytic sites it is positioned over. The switchable rotaxane catalyst generates different products from a mixture of three building blocks according to the location of the macrocyclic ring in the rotaxane.

/pdf/selecting-reactions-and-reactants-using-a-switchable-4h9rbi6lay.pdf

Selecting reactions and reactants using a switchable rotaxane organocatalyst with two different active sites

Organocatalytic regioselective acylation of mono- and disaccaharides with various functionalized acid anhydrides has been developed. Acylation of octyl beta-D-glucopyranoside with acid anhydrides derived from alpha-amino acids, cinnamic acid, and gallic acid took place at C(4)-OH with 67-94% regioselectivity in the presence of catalyst 1. Regioselective acylation of disaccharides with functionalized acid anhydrides was also achieved with 78-94% selectivity. Especially, a disaccharide with seven free hydroxy groups (X = OH, R' = H) underwent acylation at C(4)-OH with 78% regioselectivity in the presence of 1. Thus, functional group tolerance in the regioselective acylation catalyzed by 1 was found to be high.

Functional group tolerance in organocatalytic regioselective acylation of carbohydrates.

Short total syntheses of natural glycosides (ellagitannins) were performed through sequential and regioselective functionalization of the hydroxy groups of unprotected glucose. The key reactions are β-selective glycosidation of a gallic acid derivative by using unprotected glucose as a glycosyl donor and catalyst-controlled regioselective introduction of a galloyl group into the inherently less reactive hydroxy group of the glucoside.

/pdf/total-synthesis-of-ellagitannins-through-regioselective-1i39r6qn2t.pdf

Total Synthesis of Ellagitannins through Regioselective Sequential Functionalization of Unprotected Glucose

Acylation of lanatoside C in the presence of organocatalyst 5 gave the C(4′′′′)-O-acylate in up to 90% regioselectivity (catalyst-controlled regioselectivity). Various functionalized acyl groups can be introduced at the C(4′′′′)-OH by a mixed anhydride method in the presence of 5 or the related organocatalyst. On the other hand, DMAP-catalyzed acylation of lanatoside C gave the C(3′′′′)-O-acylate in up to 97% regioselectivity (substrate-controlled regioselectivity). Thus, diverse regioselective introduction of acyl groups among eight free hydroxy groups of lanatoside C was achieved.

Kenji Mishiro

Papers

Selecting reactions and reactants using a switchable rotaxane organocatalyst with two different active sites

Functional group tolerance in organocatalytic regioselective acylation of carbohydrates.

Total Synthesis of Ellagitannins through Regioselective Sequential Functionalization of Unprotected Glucose

Regioselective Diversification of a Cardiac Glycoside, Lanatoside C, by Organocatalysis

Perfectly Regioselective and Sequential Protection of Glucopyranosides