Literature thesis
By:
Tom Besseling
(11873639)
31st December 2019
Research Institute: Van t’Hoff institute for molecular sciences
Research group: Homogeneous, Supramolecular and Bio-Inspired Catalysis
Supervisor: Prof. Dr. Joost N.H. Reek
Daily supervisor: Tessel Bouwens MSc.
Second examiner: Prof. Dr. Jan H. van Maarseveen
Out-of-equilibrium driven
Self-assembled Structures
and Molecular Machines.
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Abstract
For 50 years now, supramolecular chemistry has made its entrance in the research spectrum. This has changes research from purely fixed covalent bonds into focusing on weak non-covalent interactions between molecules. These interactions can be used to form dynamic structures, containing as well covalent bonds as non-covalent interactions. Nature already shows multiple of these interesting systems and functions. The synthesis of these systems depends on the
self-organization of molecules that undergo these interactions. An interesting method is the use of active self-organization, in which generating the architectures under out-of-equilibrium conditions takes place. These conditions means that the kinetics of the reactions play a much bigger role than the thermodynamics. This means that a different view is necessary, compared to other parts of chemistry, like synthetic organic chemistry, where the thermodynamics are usually the main
parameter for the reactions. To use these conditions, a source of energy or fuel needs to be added to a reaction all the time. This prevents the reaction from reaching an equilibrium and destroying the desired conditions and products. This also means that new mechanisms should be used. Two of the frequently used mechanisms are the information ratchet and the power stroke. This literature thesis deals with the question how these mechanisms work and to what extent they can be used in the current systems. These systems can be divided into two groups, depending on the type of source they use: the fuel-driven systems and the energy-driven systems. These two groups can be divided again in molecular machines and self-assembled structures.
Based on a review of the literature some very interesting examples of these kind of systems have been found. Some of them were actually based on biological systems like a ribosome, that is able to connect certain amino acids in the human body. All the found examples are using fuel or energy as a source to stay out-of-equilibrium, and they all used an information ratchet- or power stroke
mechanism. If possible, applications are considered. However, most of the energy-driven systems use UV-light as energy source and the fuel-driven systems use harmful chemicals al fuel source. This means that these kind of systems cannot be used for potential medical applications, at the moment. In the end, the principles of the mechanisms have been proved for as well the fuel-driven- as the energy-driven machines. The importance of a kinetic view on these kind of systems, to work under out-of-equilibrium conditions, has been emphasised and current applications have been explained. However, it should be more important to synthesise more machines, inspired by biological systems, that can be used for applications in our medical / chemical advantage.
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Table of contents
Abstract ... 2
List of abbreviations ... 5
1. Introduction ... 6
2. Fuel-driven machines ... 9
2.1 Introduction ... 92.2 Examples of fuel-driven machines / motors. ... 11
2.2.1. Mechanic rotor, steered unidirectional by the attachment or cleavage of bulky groups. ... 11
2.2.2. Mechanic motor, directed by the oxidation state of the palladium complex. ... 13
2.2.3. Sequence-specific peptide synthesis by an artificial machine... 15
2.3 Comparison of the mechanisms of the discussed examples. ... 17
3. Fuel-driven Assemblies ... 18
3.1. Introduction ... 18
3.2. Examples of fuel-driven self-assemblies ... 20
3.2.1. Bottom-up self-assembly of Liesegang rings. ... 20
3.2.2. Formation of a hydrogel using a fibrous structure. ... 22
3.3. Comparison of the described examples. ... 23
4. Energy-driven machines ... 24
4.1 Introduction ... 24
4.2 Found examples of energy-driven machines ... 25
4.2.1. Energy-driven pump, using redox potential. ... 25
4.2.2. Development of Feringa’s nobel prize winning nanocar, through the years. ... 27
4.3 Comparison of the mechanism and function of the discussed examples... 32
5. Energy-driven assemblies ... 33
5.1. Introduction ... 33
5.2. Examples of energy-driven self-assemblies ... 34
5.2.1. Self-assembly of hydrogen-bonded cyclic structures, using UV-light irradiation. ... 34
5.2.2. Writing and self-erasing images using UV-light on nanoparticle “inks”. ... 35
5.3. Comparison of the mechanism of the discussed examples ... 37
6. Conclusion and outlook ... 38
7. References ... 39
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List of abbreviations
ATP: Adenosinetriphosphate
C=C-bond: Carbon-carbon double bond
C-H-bond: Carbon-Hydrogen bond
CBPQT4+: Cyclobis(paraquat-p-phenylene) tetra cation
DBFV: Dibenzofulvene
DDA: Dodecylamine
DMAP: Dimethylaminopyridine
DMS: Dimethylsulfate
DNA: Deoxyribonucleic acid
Fmoc-Cl: Fluorenylmethyloxycarbonyl chloride
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H-NMR: Proton nuclear magnetic resonance
IPP: Isopropylphenylene
MUA: 4-(11-mercaptoundecanoxy)azobenzene
NBS: N-bromosuccinimide
NEt3: Triethylamine
NESA: Non-equilibrium self-assemblies
NP: Nanoparticles
PY+: 3,5-dimethylpyridinium
sPMMA: syndiotactic poly(methylmethacrylate)
STM: Scanning tunneling micropscope
THI: Thermal helix inversion
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1. Introduction
The field of chemistry has been dominated for a long time by the exclusive focus of forming covalent bonds and analysing the structure of these specific instruments. For 50 years now, supramolecular chemistry has made its entrance in the research spectrum. This has changed research, from purely fixed covalent bonds into focusing on weak non-covalent interactions between molecules, their nature and the possibility to exploit these interactions to construct dynamic non-covalent
structures1. Nature already shows interesting systems and functions that can result from chemical complexity. In these biological systems, the self-assemblies and machines are powered by chemical fuels that keep living systems from death. Mostly ATP is used as such a fuel. Examples2 of these systems are F1-ATPase3, DNA polymerase4 and riosomes5. The presence of these biological,
molecular machines has long suggested that building a bridge between machines in the macroscopic world and the synthetic molecular systems, can result in great opportunities6. However, research to many more biological systems can and will provide new insights and will make us increasingly understand the chemistry behind it. Finally, these insights and knowledge, could be used in our advantage. Due to learning and mastering the underlying chemistry and analysing this in order to design new structures, like synthetic machines or self-assemblies, these structures become more complex. This will give emergent properties, deriving from this complexity and the interaction of their molecules. These emergent properties are novel properties that exist after the connection of multiple components. Those components can enhance or slow down each other. This means that the interconnection never really sums up linearly: 1 + 1 ≠ 21,7. Components that enhance the interactions are called synergy and will count as 1 + 1 > 2. Slowing down, due to the components, is called
interference and sums up like 1 + 1 < 2.
Most of the newly found supramolecular compounds are arranged via self-organization. Such a compound is a well-defined complex held together by (non-)covalent bonds, which takes place without guidance or management from an outside source. Self-organization can proceed in 2 forms:
Passive self-organization
active self-organization7,8,9
Passive self-organization (also known as static self-organization) involves the generation of organized covalent or non-covalent functional architectures from components under thermal equilibrium conditions. This means that the ordered state forms as a system approaches an equilibrium1. During the process, the complex reduces its free energy to form the thermodynamic and most stable product (see fig. 1). To form this thermodynamic product, a reaction can run for a longer time, since it is the final and most stable product. Such an equilibrium can be best understood with the principle of microscopic reversibility7,10. This states that any molecular processes in an equilibrium and the reverse of that process occur at the same rate. This means that the forward reaction proceeds at the same rate as the backward reaction, keeping a steady state between the reagents and the product, while the forward and backward reaction keep on going.
The second and more interesting method is the active organization (also known as dynamic self-organization). This method will be the main topic of this thesis. This involves the generation of organized functional architectures under out-of-equilibrium conditions. This means the kinetics play a much bigger role in the synthesis of these compounds, than thermodynamics do. This means that the desired, kinetic, product will be formed first in the reaction, because of the lower activation barrier (see Fig. 1). These syntheses have a dynamic character. The reversible reactions that occur during the reaction, due to this character, make sure that the, more stable, thermodynamic product will be formed as well, as the reaction runs for a longer time11. This will then be in equilibrium again, what makes the reaction time-dependent12.
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To prevent this from happening, the reaction has to be terminated at the right time. Therefore, these architectures are often dissipative7, which means that the system is open. In other words, the system can exchange free energy with the environment, becoming irrecoverable and unavailable for the reversed reaction, so an equilibrium cannot be reached.
A second way to prevent the reaction from reaching the equilibrium is to add an energy source to the reaction continuously. This can be a fuel (chemical agent), as will be discussed in chapters 2 and 3, or another external energy source, like UV-light, which will be discussed in chapters 4 and 5.
Self-organization8 drives towards systems of increasing complexity under the pressure of
information, towards more and more complex forms of matter. Complexity8 is, in general terms, the result from three features: Multiplicity, interconnection and integration. Multiplicity represents chemical diversity in constitution, function and motion. Interconnection stands for the type of bond, covalent and non-covalent and their dynamics. Integration indicates all features through networks with feedback and regulation.
Higher complexity8 to the system can be provided by a combination of three basic types of dynamic chemistry processes:
1) Reactional/interactional dynamics. These dynamics concern the making and breaking of chemical bonds on the molecular level and of intermolecular interactions on the supramolecular level. 2) Motional dynamics. This contains molecular motions and reversible changes in shape. 3) Constitutional dynamics. Involves reversible changes in the constitution of molecular and supramolecular entities by component exchange.
Figure 1: Kinetic product vs. thermodynamic product13. a) the energy level at the start of a reaction. b) the energy level of the
kinetic product. c) The energy level of the thermodynamic product. The activation barrier of the kinetic product is lower, to firstly form this product. When the reaction runs over time, the thermodynamic product will be formed most. To obtain the kinetic product, a reaction must be monitored and terminated at the right time.
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Complexity is intimately linked to adaptation14. This implements the ability of a system to undergo adjustments in response to external stimuli, like phase exchange / protons (chemical) or temperature / pressure changes (physical). The effects of these stimuli are described in the article of Klajn et al15. He provides an overview of various available stimuli to reflect the importance of surface chemistry for the dynamic self-assembly of nanoparticles and how they react on each change. For instance the reaction of the assembly on the change of pH of the solution.
In pursuit to these studies and newly published systems, the following research question is formulated;
Which interesting state of the art self-assemblies and molecular machines have been published and what are the used mechanisms behind out-of-equilibrium?
To address the research question, this thesis is divided into four parts. First, a distinction has been made between fuel-driven and energy-driven systems. These systems were divided again in synthetic molecular machines and self-assembled structures. The first two chapters will cover, respectively, the fuel-driven machines and the self-assembled structures. The last two chapters will discuss the
energy-driven machines (chapter 4) and self-assembled structures (chapter 5). Their mechanisms will be described and compared to each other, since the mechanisms of both the fuel-driven as the energy-driven systems will be different. Thereafter a conclusion will be drawn, about these used mechanisms, their out-of-equilibrium character and the possibility to use the knowledge of these kind of systems in our advantage.
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2. Fuel-driven machines
2.1 Introduction
Molecular machines are among the most complex of all molecules. They lie at the heart of nearly every biological process. In biology, motion is in many cases chemically fuelled with energy deriving from ATP, hydrolysis or chemical gradients. Development of synthetic systems operating by the same principle has been achieved recently. Synthetic small-molecule machines have been developed including molecular muscles16, synthesizers6, pumps17 and transporters18. These motors are perfectly suited to introduce dynamic behaviour, reach metastable states and ultimately drive molecular systems away from thermal equilibrium. The design of nanometre-scale motors in which the components incessantly rotate with the net directionality has tantalized scientists. Providing
directional rotation in molecular motors is challenging for them, not at least because each rotational cycle returns to its starting positions.
In fuel-driven machines, a molecular machine is in continuous motion, driven by the continuous input of a fuel19. This can be a chemical agent, required for the reaction or as supporting solvent. For instance the input of FMOC chloride in the rotor of Leigh and Wilson (2.2.1.). This continuous addition of fuel to the reaction, gives the reaction an out-of-equilibrium character. This means that the reaction is continuously directed into the desired direction to prevent the reaction from reaching the equilibrium, without human interference.
This motion can be divided into two groups20. Translational and rotary motion. Translational motion means that the moving part of the machine, mostly a macrocycle, moves in a linear direction over a track. It migrates preferentially to the end of the track, but should be able to perform multiple cycles. An example of this kind of motion is described in 2.2.3.. The second group is rotary motion. This is a rotation around a covalent bond as the axle. When the machine is chemically fuelled, this will be around a single bond. Light fuelled motors can also rotate around a double bond, as will be discussed in chapter 4.
To make these machines work, two main mechanisms are described in the published machines. These are the information ratchet and power stroke. All chosen examples contain one of those mechanisms:
1. Information ratchet21, 22,23: Mechanism by which directionality is achieved by controlling energy barriers, either by raising or lowering the barrier depending on the state of the system, or by engineering the energy landscape to kinetically favour a specific pathway through the states and then provide chemical energy to allow directional motion on that pathway by mass action.
2. Power stroke7: An external energy source lifts the macromolecular machine into a high-energy state from which it undergoes directional relaxation thereby producing torque or force. Light-driven systems generally do operate by a power-stroke mechanism.
In this chapter, three fuel-driven machines will be described. Their mechanism and their function will be discussed, as well as their main differences. Finally, these mechanisms will also be compared to the driven machines to find the differences in the two approaches, fuel-driven and energy-driven.
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In the first example, a motor will be discussed, published by Leigh et al. Their article was cited multiple times, and some articles have used their machine as example. In these articles, a discussion has risen about the motion and function of the motor, and the conclusion drawn by the authors. This made it an interesting example for this thesis. Secondly, a motor will be discussed, published by Feringa et al. This example makes use of palladium complexes and the changing oxidation state of the palladium centre during a C-H activation and an oxidative addition.
The last example was published by Leigh et al. as well. The machine is basically inspired on the human ribosome, which is able to connect amino acids. This made this example interesting for this article to discuss. As well as the first example, this machine makes use of translation, since the macrocycle moves in one direction over the strand. In the contrary, the second example makes use of rotation in their machine. This made these 3 machines a nice comparison, showing the different types of motion: translation around a ring, translation over a strand and rotation around a single bond.
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2.2 Examples of fuel-driven machines / motors.
2.2.1. Mechanic rotor, steered unidirectional by the attachment or cleavage of bulky groups. The first example described is a fuel-driven motor published by Wilson, Leigh et al.24 In 2016 they described a small molecular ring, transported directionally around a cyclic molecular track. This is all powered by irreversible reactions of 9-fluorenylmethoxycarbonyl chloride (Fmoc)24. This fuel is used for the motion of the macrocycle. During this cycle, due to the triethylamine (NEt3), dibenzofulvene
(DBFV) is released. The authors state that the motor makes use of an information ratchet mechanism moving clockwise around the bigger cycle. However, there has been some controversy about this statement, which is also explained in the paper of Astumian7.
Figure 2: Operation of a chemically fuelled [2]catenane rotary motor published by Leigh et al.1,21,241,7,20,21,24. A cyclic track
containing two fumaramide sites(green) and a benzylic amide macrocycle (blue) that is steered into a direction by the presence and absence of the bulky Fmoc groups(red) and DBFV (orange).
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The benzylic amide macrocycle (blue) binds to one of the two green sites (fumaramide) of the track. The red bulky Fmoc groups are bound, and sterically block the macrocycle from moving to the other fumaramide site. Cleavage of one of the bulky groups through a chemical reaction, driven by triethylamine (NEt3), as dibenzofulvene (DBFV), allows the ring to shuttle between both green sites
along the unblocked pathway. Attachment of a new Fmoc-Cl group at the, during the cleavage, formed, OH-group, locks in any change of location of the macrocycle to prevent the small ring from moving back. This attachment is possible, due to the continuous addition of Fmoc-Cl to the mixture. As well the cleavage of dibenzofulvene (DBFV) as the re-attachment of the Fmoc group are
irreversible processes under the same conditions.
The ring can go clockwise and counter-clockwise. This requires the cleavage of a bulky
dibenzofulvene (orange) on the track. This occurs at such a fast rate that it’s independent of the position on the ring (kfar-cleave = kclose-cleave). However, the FMOC-groups are re-attached through the
continuous addition of FMOC chloride. This re-attachment is dependent on the position, since it occurs faster when the blue ring is further away from the reaction site (kfar-attach > kclose-attach) due to
steric reasons. This means the small ring will the rotate directionally around the larger cycle. In this track, the counter-clockwise site is always more remote than the clockwise site. This results in an overall clockwise motion of the ring. They proved this theory, by using an rotaxane model to demonstrate the favourite far-attachment of the Fmoc-groups.
Next to this, the group of Leigh verified the directional rotation, through the information ratchet, experimentally. Under the used conditions, both the attachment and the cleavage of the fmoc-group occur. This has been determined by labelling experiments with D2-Fmoc groups. They were switched
to non-deuterated Fmoc-groups during the process. This allowed 1H-NMR to determine the location of the small macrocycle. The second determination, they could make using these deuterated
compounds, was the clockwise rotation. The also determined that a full rotation of 360˚ takes around 12 hours (determined with 1H-NMR as well). The authors conclude by stating that they have
published an synthetic chemically fuelled motor, with a proven clockwise motion, which can be enhanced by raising the temperature or the concentration of Fmoc-groups.
However, according to Astumian, published in 20197, the authors had a plausible but wrong hypothesis for this cycle. Their approach was purely based on a thermodynamic view rather than a kinetic view, while, due to the continuous addition of Fmoc-Cl, the motor is out-of-equilibrium. This means that the operational principle is dictated by kinetics rather than thermodynamics. To prove the group of Leigh was wrong, Astumian performed an kinetic analysis on the machine. He
determined that the machine actually prefers the counter-clockwise pathway as Wilson et al.24 explains as well. For the attachment of F-moc groups, the reaction is hindered next to the proximal green recognition site, in comparison to the distal recognition site. For DBFV however, the release occurs at the site several bonds removed from the recognition site, making these rates less strongly influenced. This means that the rate constants predict counter-clockwise rotation. Next to this, Astumian determined that the machine prefers kinetic gating over ‘pushing’ the ring by electrostatic interactions. This gating, during which a kinetic asymmetry arises, is owing to the steric interaction between the small macrocycle and the protecting group. This way the backward-reaction is hindered, leading to a counter-clockwise rotation around the larger macrocycle.
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2.2.2. Mechanic motor, directed by the oxidation state of the palladium complex.
A second molecular motor is reported by Feringa25. The system makes clever use of the fact that palladium can react selectively with C-H and C-Br bonds. This depends on the oxidation state of the metal. In this system, it is important that the introduction and removal of Pd is out of equilibrium and occurs through irreversible steps. The position of the Pd centre is dictated by the chiral sulfur centre. In the design, as basis of a rotary motor a simple biaryl molecule with three functional groups is taken, based on the biaryl sulfoxides, published by Colobert and coworkers26,27.
There are three key factors that govern the system:
1) Selective binding of the two different pairs of ortho functional groups with the two different metals.
2) Lowering the barrier to biaryl rotation on complexation of the metal
3) Transfer of chiral information across the metal centre between the central chirality at A and the biaryl axis leading to diastereomeric complexes with sufficient energy differences to ensure selective unidirectional rotation of the upper aryl ring.
Their design for a unidirectional molecular motor is based on biaryl 3, that exists as two atopisomers, where S denotes the fixed central chirality at sulfur and M and P denote the chirality over the biaryl axis, with a ground-state preference for (S,P)-3 (Δ‡G = 155kJ mol-1). Starting from (S,M)-3, the first step was a selective reaction of the palladium centre of a Pd(II) complex with the ortho C-H bond of the upper aryl ring in a C-H activation. The barrier to atropisomerization is greatly reduced and the biaryl axis becomes configurationally labile, allowing the interconversion of Pd[(R,P)-4]XL and Pd[(R,M)-4]XL. To complete the 180˚ unidirectional rotation, the C-Pd bond was transformed into a C-H bond, which was accomplished via reductive elimination and the formation of a Pd(0) complex. To start the second half of the rotation, The Pd(0) complex was added, and via a oxidative addition, complex Pd[(R,P)-5]BrL was formed. Hereafter the complex was treated with N-bromosuccinimide (NBS) to form the starting complex (S,M)-3.
Figure 3: Palladium-mediated 360˚ unidirectional rotation of biaryl 11,20,21,25. 360˚ rotation in a clockwise sense of the
upper aryl ring with respect to the lower aryl ring (red). In total, four key steps mediate the rotation: (i) C-H activation, (ii) reintroduction of the C-H bond, (iii) oxidative addition, (iv) reintroduction of the C-Br bond.
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To prove this mechanism, they first added (S,M)-3 to the palladium (II) complex under C-H activation conditions, followed by ligand exchange with LiCl. The obtained yellow solid was insoluble in a broad range of common organic solvents. The authors hereby postulated that the solid was a mixture of the desired {Pd[(R,M)-4]Cl}2 and the related bridged complex as shown in figure 3. One and
two-dimensional NMR confirmed the unidirectional transformation of the reaction using a derivative in which the upper aromatic ring was replaced by a deuterated pyridine.
To confirm the second half of the mechanism, the authors solved (S,P)-3 in a mixture of THF,
tricyclohexylposphine and bis(dibenzylideneacetone)palladium(0). Analysis with 19F NMR showed the formation of a broad signal at -118.5 ppm, that could be assigned to the desired Pd[(R,M)-5]BrL complex with PCy3 as neutral ligand.
These experiments showed that the individual steps in the mechanism worked, but now they had to find a pathway to make the machine work without human intervention. In the end, the found that they had to alternatively add sodium triacetoxyborohydride and NBS as chemical fuels. Next to this, they expect that the presence of the electron-rich phosphine will prelude C-H activation. Further, modifying the ligands at palladium, is required to achieve multiple cycles.
The authors conclude by stating they developed a molecular motor that rotates 360˚ unidirectional when combined with palladium and treated with the mentioned chemical fuels, and envision that the development of this machine will be continued by choosing the reaction conditions and ligands more specific.
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2.2.3. Sequence-specific peptide synthesis by an artificial machine.
The third example is a small-molecule machine that performs a sequence-specific peptide synthesis. It has been published by Leigh et al. in 20136. In biology, the ribosome builds proteins by linking amino acids to order to determine by messenger RNA. The authors wanted to synthesize a machine, to mimic this biological process. In their design, a molecular strand had three peptides attached to it via weak phenolic ester linkages. Via this process, milligram quantities of a peptide should be generated.
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A macrocycle was threaded onto the peptide-bearing strand, via a click reaction. Then a reactive side arm containing a protected cysteine derivative was attached to the ring. When the cysteine moiety and the amino acids on the strand where deprotected under basic conditions, the cycle was put in motion. The thiolate residue reacts with the first amino acid phenolic ester to form a thioester, according a transacylation. This thioester reacted further, via chemical ligation, to transfer the amino acid onto the reactive arm of the machine. At the same time, a catalytic thiolate group, ready for the cleavage and transfer of further building blocks, was regenerated. This was repeated with the second and third amino acids, until the macrocycle was detached from the strand. The newly formed peptide was attached to the cycle. In the end, the final peptide product was released by hydrolysis.
Some limitations are still present. For instance, it does take more than 12 hours to form each amide bond, while a ribosome makes 15-20 bonds per second. Furthermore, the size of oligopeptide that can be produced may ultimately be restricted by the size of the cyclic transition states involved in S-to-N acyl transfer.
The function of this machine appears dynamic. However, there is a major conceptual difference. In these cycles, the activating and deactivating reactions operate simultaneously, The inputs and
outputs of chemical energy in the rotaxane system are separated in time. First, energy is expended to assemble the machine which is then trapped in the high-energy state. Second, the deprotection removes the kinetic barrier and all the reactions are energetically downhill. However, there still are some hurdles to overcome, to make sure, the reaction can proceed more than one cycle.
Comparison of the examples. Nevertheless, the synthesized machine, shows that small, artificial molecular machines can be designed and operate on itself, when it is started, for one cycle.
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2.3 Comparison of the mechanisms of the discussed examples.
Considering all of these three mechanisms, there are some differences, but most of all, there are a lot of similarities. One of those similarities is the fact that all of the discussed examples make use of an information ratchet, in which the direction of motion of the examples are determined by chemical interactions. As described in the first example, the anti-clockwise motion was determined by the addition and cleavage of steric Fmoc groups onto the cycle. In the second example the rotation (clockwise) was determined by the alternative addition of triacetoxyborohydride and NBS and the presence of PCy3. As well as in the first two examples, the motion of the third machine was directed
by chemical interactions. As described, the macrocycle was locked onto the strand and after the connection and deprotection of a cysteine moiety and the amino acids, the cycle only had one way to go in which the thiolate continuously reacts with the next amino acid on the peptide-bearing strand. One of the differences of these three examples is the continuous motion. In the first example, as told before, due to the fast addition of Fmoc and cleavage of DBFV, the cycle can go on, without human interference in the reaction. This has also been the concept of the second reaction. Unfortunately, at this moment, the motor is unable to achieve multiple rotary cycles, without interfering, however, research is still going on to this machine.
The third machine is a bit different, compared to the other machines. This is because of the concept. The first two machines are built to be able to make multiple rotary cycles without human
interference. This was not the case in the third example. This example was especially made to show that small, artificial machines can be designed and mimic a biological system, like in this case a ribosome. This machine is able to link amino acids like ribosomes. However, it takes this machines 12 hours to make 1 bond via transacylation, while the ribosome produces 15-20 bonds per second. In the end, it’s interesting to see the way the authors approach their own machine. As told before, the authors of the first example had a thermodynamically based explanation of how their machine functioned. This was followed by the conclusion of a clockwise rotation, while Astumian ended up with the opposite conclusion of a anti-clockwise motion. This was because of his kinetically-based explanation. The other authors however, took more account of the kinetics instead of the
thermodynamics, in their explanation. Which is, as told before, the way to go, using out-of-equilibrium systems.
In the next chapter, the fuel-driven self-assemblies will be discussed. The differences of their mechanisms will be compared to each other and to the mechanisms of these machines.
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3. Fuel-driven Assemblies
3.1. Introduction
Over the last couple of decades, some interesting assemblies have been published. In specific, the evolution of self-assembled structures have been a great part of interest. These self-assembled structures can be divided into two groups. The molecular structures and the supramolecular structures. The group of the molecular structures are assemblies that only contain covalent bonds. These bonds are formed following a reaction mechanism in which two electrons are shared to form a bond. This can be enhanced by fuel or light. When enhanced with fuel, the reaction proceeds, while the compound keeps in place.
The supramolecular structures contain covalent bonds as well as non-covalent bonds. These bonds are not formed by sharing two electrons, but by interactions between functional groups, like hydrogen bonds or dipole-dipole interactions between ketones for instance. Due to these
interactions, the supramolecular structures are highly dynamic. This means, that the bonds can form and break at a high rate, reaching an equilibrium in which both the forward as the backward reaction proceeds at the same rate, according to the microscopic reversibility10. Nevertheless, the fact that these bonds are highly dynamic, doesn’t mean that these structures are weak. These assemblies are as strong as the structures containing only covalent bonds and can result in polymers or gels that can be used.
Some examples of these new supramolecular structures include polymers28,29 and supramolecular gels30. Supramolecular polymers are a kind of polymers from which the monomers are bound via non-covalent interactions, what defines their properties. These polymers are dynamic and reversible, making them able to develop self-healing properties. A good example of these kind of
supramolecular polymers are microtubules31,32,33. These are polymers that contain dimers of α and β-tubulin that bind into linear protofilaments. For further polymerization, polarization plays a role. For the linear polymerization, the alpha-subunit (-) binds end-to-end to the beta-subunit (+) of another dimer. To finally form the macrotubule, 13 of these protofilaments bundle parallel to one another with the same polarity ending up a (+)-end and a (-)-end, surrounding a hollow center. In biology, these kind of structures are used for cell migration of kinesin34 or as motor proteins. This has inspired Hess and coworkers31 , to synthesize these kind structures relevant to the process of cell division, or as testbeds for autonomous chemical robots32.
Second, supramolecular gels are made as well. These gels consist out of agglomerates. They are defined as cross-linked systems with an internal network system, resulting from physical or chemical bonds35. The gelator molecules self-assembles to form fibrous architectures on nanometre scale. These are stabilised by intermolecular non-covalent interactions36. These fibres than build up a micrometer-scale three-dimensional network entrapping molecules of the solvent. This can be organic solvents (organogels), water (hydrogels) and even air (aerogels)35. Paragraph 3.2.2. shows a great example of an hydrogel, while 5.2.2 will show an example of an organogel.
In this chapter, 2 examples of fuel-driven assemblies will be discussed. Their mechanism and their function will be discussed, as well as their main differences. Finally, these mechanisms will also be compared to the energy-driven self-assemblies to find the differences in the two approaches.
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The first example is the bottom-up self-assembly of Liesegang rings, described by Rubi et al. in 201837. The example shows the formation of non-equilibrium self-assembled structures with
predictable, variable sizes, using two electrolytes. The second example is the formation of a hydrogel, by activating the starting blocks with DMS via a methylation process. A hydrogel was formed at the end, before hydrolysis deactivated the compounds. Supramolecular gels30 have been an interesting part of research as well over the last couple of years, which makes this compound a good example to discuss.
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3.2. Examples of fuel-driven self-assemblies
3.2.1. Bottom-up self-assembly of Liesegang rings.The first example, is a self-assembly described by Rubi et al. in 201837. In their article, they propose a model to show the formation of Liesegang rings. These Liesegang patterns have been exhaustively studied because of their theoretical importance in chemistry and potential application to material science38. They were first discovered by R.E. Liesegang in 189639,40. They are composed out of mono-dispersed nano and micro-structures, with variable sizes from ring to ring. These variabilities are predictable. To obtain these rings, a reaction-diffusion process is taking place inside a gelatin matrix. Here periodical precipitation of a suspension of insoluble solids gives rise to the appearance of these Liesegang patterns as shown in figure 9.
Currently in material science, there is a high interest in the design and control of these structures to yield mesoparticles at a defined size. These patterned structures have been used in micro- and nanotechnology over the last few years41,42. The method described, in which these meso-structures of different sizes are obtained, is known as the bottom-up self-assembly. This bottom-up approach43 is used to synthesize non-equilibrium self-assembly (NESA) structures from well-defined small units and chemical fuel. These NESA structures then dissipate matter and energy until they have reached a stationary, metastable or stable state. Examples of this approach are gelation and
reactive-crystallization. Here, the small units suffer sequential transformation to obtain metastable, kinetically trapped structures. In the synthesis, two electrolytes act as fundamental components that trigger the self-assembly process, forming stable NESA structures.
Figure 6: Illustration of the experimental setup and sketch of the Liesegang rings37. The electrolyte (E) diffuses into the
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At the beginning, electrolyte E is placed inside a gelatin matrix containing electrolyte B, separated by a membrane. When this membrane is removed, electrolyte E (the activator) diffuses into the gelatin matrix. In there, it reacts with the fundamental component B. This ends up in a more energetic component. However, this product is thermodynamically unstable, and therefore, it would like to separate from the solution. This ends up in non-soluble nuclei. When the concentration of these nuclei reaches a certain level, the nuclei starts to agglomerate, producing clusters. These clusters precipitate or remain suspended in the gel phase. As a reaction, new nuclei are formed, since their concentration decreases. When the threshold is reached again, new agglomerations are formed. This process goes on and on until one of the electrolytes (mostly E, but it can be B as well) is completely consumed. This model is a nice representation of an information ratchet mechanism, since the reaction starts at the moment that electrolyte E (the fuel) diffuses into the gelatin matrix. From here it first makes the nuclei, and at a certain threshold, the agglomeration begins. When the
concentration of the nuclei decreases, the agglomeration is stopped. When the threshold is reached again, new clusters will be formed. This way, the mechanisms proceeds on and on, until one of the electrolytes (fuels) is completely consumed. This easily takes 5 to 10 cycles.
Using a classical mechanism, potassium dichromate (K2Cr2O7) and silver nitrate (AgNO3) were used as
electrolytes in water. They dissolve, where the anionic dichromate reacts with water to anionic chromate, due to addition of sodium hydroxide (NaOH). This triggers the formation of silver chromate (Ag2CrO4). This is the non-soluble product. From here the NESA processes start, forming
agglomerations of solid silver chromate in the solution. These processes involve two fundamental ingredients: enabling the self-assembly by activation of the components and the presence of forces to trigger the assembly mechanisms. This mechanism does not consider intermediates, dis-assembly or re-dissolution.
The new model, described by Rubi et al.37 is based on the mesoscopic non-equilibrium thermodynamic formalism, described above, in which the kinetics of activation processes are subjected to the second law, the entropy production. They describe specific formulas for mass and energy balances and the structure size during the process. They performed the same experiment as shown in the classical mechanism and showed that the error between the suspected values, based on their model, and the results of their experiments where just 6,4% for the estimated position and 4,8% for the expected diameter, as long as they performed the experiments non-isothermal.. In the end they state that the results show, that they proposed a model that reproduces the main characteristics of Liesegang rings with high accuracy. This model also shows a dependency for temperature, as well as it let the authors rationalize how non-homogeneous conditions may end up in the formation of self-assembled structures and give rise to macroscopic spatial patterns. This lead to the ultimate conclusion that pattern features and particle size modifications can be controlled by electric fields and thermal gradients.
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3.2.2. Formation of a hydrogel using a fibrous structure.
As discussed in the introduction, fuel-driven assemblies are formed using a fuel. The moment the fuel runs out, the assembly will fall apart. Understanding the kinetics at play allows the user to determine the lifetime of the material by the amount of fuel added44. To show this, some examples has been published by van Esch et al45,46. Here, one of them will be discussed. In their article45 they showed a general approach toward self-assembling molecular materials, driven by chemical fuels. The system consists of simple chemicals that are commercially available. The starting blocks need to be activated in the first step. The ester building blocks were molecularly engineered to assemble to fibres that, in turn, formed a dense network that entrapped the aqueous environment forming a hydrogel.
As shown in figure 2, the system was tested with 3 different starting blocks (6a, 7a, 8a). These
building blocks were solved into a buffer-solution, followed by the addition of dimethylsulfate (DMS). This results into the methylation of the starting compounds, ending up with methyl esters. These activated building blocks self-assemble into fibrous structures and due to their environment turn into a hydrogel. From here, they focussed more on compound 7, since it resulted into the best hydrogel. In the backwards reaction, over time, the solution was hydrolysed with hydroxide ions. Some experiments were performed to determine the critical gelation concentration of 7b and the optimal pH value to perform the reaction.
Figure7: A typical reaction cycle and the tested molecular gelators45. In A, the three tested gelators are shown. a is the
carboxylated form before the addition of DMS. B is the methylated form, in which the methyl esters can self-assemble into fibrous gelating structures.
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The lifetime of these gels could be controlled by the kinetics of the reactions involved. For instance, the methylating agent, used in the reaction. DMS is much more reactive than methyl iodide. This can lead to sufficient concentrations of 7b. The lifetime of these gels could be further modified by altering the pH. Using a buffer solution at pH 9 gave gels that persisted for more than a week. At pH 11, these gels were only present for hours. A second effect of the pH is the concentration of 7b. The higher the pH, the faster the hydrolysis. This ends up in a lower concentration of 7b, before
hydrolysis proceeds47. However, a high enough concentration has to be reached to make sure the fibres undergo a self-assembly. The mechanism looks like an information ratchet, but unfortunately, the methylating agent has to be added manually. If an automatic way for this addition has been found, the information ratchet mechanism will be complete.
In the end, the authors state that the showed a far-from-equilibrium self-assembly of molecular building blocks driven by a chemical fuel. This lead to the formation of an active material. Reaction kinetics and fuel levels determine the lifetime, stiffness and self-regeneration in these kind of materials.
3.3. Comparison of the described examples.
In both of these examples, a fuel was used to obtain a self-assembled structure. The second example also needs the fuel, to keep the assembly in place. As described, the first example uses two
components to form the assembled rings. Electrolyte E, can be seen as the fuel, since this component diffuses into the gelatin matrix to react with the other electrolyte. This will eventually stop when E has been totally consumed. Therefore, component E should be added all the time. In the second example, the fibres will be formed and kept in place, when DMS is added as fuel. However, the starting material will always be obtained at the end of the cycle. As shown, some other effects (like change in pH) will also play a role in this self-assembly.
The exact mechanism behind both experiments are not clear. They both tend to be an information ratchet mechanism. However, in the first example, both the electrolytes can be fully consumed, so they need to be added manually. In the contrary, the fact that the agglomeration starts at a certain threshold and stop at a lower level again, makes it an interesting information ratchet. The second example looks like a nice information ratchet as well, since addition of DMS results in fibrous structures. Unfortunately, the addition of DMS needs to be started and stopped manually at the moment. When further research introduces a way to do this automatically, a full information ratchet mechanism is made.
In the next 2 chapters, the energy-driven machines and self-assemblies will be discussed. Their mechanisms will be described and compared, starting with the energy-driven machines.
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4. Energy-driven machines
4.1 Introduction
Not only fuel-driven machines were published. Energy-driven machines have been published as well. External modulation of the environment is used to drive the system away from a thermodynamic equilibrium. This external modulation means changing the reaction conditions by external means. These external agents can consist of reducing or oxidizing the compounds, constantly adding energy to the reaction mixture by means of heat, or by exciting electrons using UV radiation. In the contrary to the fuel-driven machines, no extra chemical agents were directly added to the reaction mixture at the beginning of the reaction, nor continuously during the reaction. As described in the previous chapter, energy-driven machines are basically using a power stroke mechanism, in which an external energy source, lifts the machine into a high-energy state. From here, it undergoes directional
relaxation.
What is often used with energy-driven machines are oscillators1,44. These are chemical reaction networks in which (in chemical fashion) the concentration of one or more reagents or (in energy-driven machines) the amount of energy input changes in a periodic fashion. Naturally, oscillators are out-of-equilibrium systems driven by the conversion of chemical fuel / energy. Their periodically changing reactant concentrations can be used to drive machines. The oscillation enables the system to go through multiple cycles, without human intervention1. An example of these oscillations can be an energy source, that changes the pH of a reaction. This will then be reverted when all energy has been dissipated. In this case, the self-assembly can be coupled to the oscillation in pH. A second example is the use of redox potential as will be discussed in the first machines, published by Cheng, Stoddart et al21.
During this chapter, energy-driven machines will be described. Their mechanisms and their functions will be discussed, as well as their main differences. Finally these mechanisms will also be compared to the fuel-driven machines to find the differences in the two approaches.
The first example is an energy-driven pump, in which the compounds are alternatively reduced and oxidized. This was published by Cheng and coworkers in 201521, inspired by carrier proteins in nature. Since this machine was directly inspired on a biological system, this example is interesting to discuss here.
The second example is actually a set of machines, al published by Feringa and coworkers. This set begins with the explanation of a rotation around a double bond, and then proceeds with their further articles leading to Ben Feringa winning the Nobel Prize in 2016. Since the complex nature of these systems and the achievement of winning the Nobel Prize, these are very interesting machines to discuss in this chapter.
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4.2 Found examples of energy-driven machines
4.2.1. Energy-driven pump, using redox potential.The first energy-driven machine is a redox-driven pump. This pump was published by Cheng, Stoddart et al.21 in 2015. They were inspired by carrier proteins in nature. These proteins consume fuel in order to pump ions or molecules across cell membranes, creating concentration gradients. This is done entirely through noncovalent bonding interactions. In this mechanism, these interactions are used to pump positively charged rings from a solution and kinetically trap them around a
collecting chain. This pump uses energy from externally driven oscillations of the redox potential to concentrate several rings on a dumbbell component. This machine is a clear dissipative, out-of-equilibrium structure. This means that if the redox potential is lost, (the redox oscillations are stopped) the system falls apart.
Figure 8: Schematic illustration of the free-energy profile during the movement of a CBPQT4+ ring along a dumbbell DB3+.21 The top profile describes the energy profile under reduced conditions. The bottom profile describes the energy profile when the ring and the recognition site are oxidised.
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This machine (fig. 8) is made of a cyclobis(paraquat-p-phenylene) tetra cation (CBPQT4+) ring that threads onto a dumbbell (DB3+). This dumbbell contains on one end a viologen (V2+) recognition site and a 3,5-dimethylpyridinium (PY+) group. This serves as an electrostatically switchable barrier for threading the ring onto the dumbbell. On the other end of the dumbbell, a bulky
2,6-diisopropylphenyl stopper was placed. These two ends where separated in the middle by an isopropylphenylene (IPP) group which serves as a steric obstacle. Figure 8 shows the energy landscape for threading the ring onto the dumbbell. This depends on whether the ring and the dumbbell are reduced (upper profile) or oxidised (lower profile).
As shown in figure 9, the placement of the ring onto the dumbbell is depending on the
oxidised/reduced conditions. By externally changing the redox potential back and forth between reducing and oxidising conditions, the energy profile switches between the upper and lower state, giving rise to stochastic pumping48. This means that the final product won’t be clear before the machine starts. However, due to the specific groups on the strand, this machine gets steered into the right product, according an information ratchet. Figure 9 clearly describes these changes and their consequences. At first, the macrocycle and the strand need to be in reduce conditions, to make sure the ring can pass the PY+ group49 at the beginning of the strand and connect to the V2+ group (Dred to
Ired). Under oxidised conditions, this is impossible, due to kinetic blocks by large energy barriers. The
same counts for the following step. Due to the large energy barrier, the transition Ired to Ared is
impossible. To reach the final Aox state, the compounds have to be oxidised first. This way, the ring
can pass the IPP group on the strand.
This design feature simplifies the calculation of the ratio between assembled and disassembled states since there is then only one path we need to consider.
Dox ↔ Dred Ired ↔ Iox Aox ↔ Ared
In this pathway, the double headed arrow indicates transitions that can be pumped by external oscillation of the redox potential. In the presence of these oscillations of the redox potential the system equilibrates between Dred and Ired under reduced conditions and between Iox and Aox under
oxidised conditions.
The artificial molecular pump, described by the authors, demonstrates the ability to perform work by transporting small positively charged rings from one environment to another. A big advantage of this pump is its ability to repetitively function for multiple cycles. If artificial machines are able to
compete with their natural counterparts in elegance and utility, more of these non-equilibrium complexes can be synthesized, based on compact simple components.
Figure 9: Kinetic diagram describing the assembly of a ring onto the collecting chain when driven by external oscillation of the redox potential17,21. Under reducing conditions, an equilibrium between Dred and Ired arises. Under oxidizing conditions, the system equilibrates between Iox and Aox. Continual cycling between oxidizing and reducing condition pumps several rings onto the collecting chain where they are meta-stable for even a month14.
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4.2.2. Development of Feringa’s nobel prize winning nanocar, through the years.
The second set of examples are some of the machines published by the group of Ben Feringa. His group showed multiple motors driven by UV-light with the nobelprize winning nanocar as their highlight. Already in 1999, Feringa et al.50 published a light-driven monodirectional molecular motor. The structure of the molecular motor features two identical halves connected by a central double bond, which is able to rotate around this double bond. The mechanism works in 4 steps. Two light-induced cis-trans isomerizations, followed by thermally controlled helicity inversions, that block reverse rotation. This way, the four steps add up to one full rotation into on direction. In the mechanism, P stands for the right-handed helicity. M denotes the left-handed helicity.
First a light-induced trans to cis isomerization occurs. This is an extremely fast and reversible process, with irradiation at a wavelength of 280nm at -55˚C, and a 180˚ rotation around the C=C bond. During this process, the two axial positioned methyl groups (E-isomer) turn into their new equatorial position (Z-isomer) . This leads to the new left-handed helicity of the compound. Then, the
temperature was raised to 20˚C and the selective conversion to the stable (P,P)-cis-10 was observed. Irradiation, than, again takes care of a isomerization. This time, it’s cis to trans. Increasing the
temperature to 60˚C, brings back the first compound. During these four isomerization steps, one half of the compound completed a 360˚ rotation relative to the other half of the compound. The
structures of trans-9 and cis-10 were confirmed52.
Figure 1050,51: Rotation of (P,P)-trans-1 via a isomerization process. 2 Photochemical processes using a 280nm Xe-lamp
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To achieve this completed rotation, the mechanism makes use of a power stroke mechanism, using UV-light, to excite the compound into a higher energy. The complete energy profile is shown in fig. 11.
In the first step, the energetically uphill E-Z isomerization drives the system out of equilibrium, forming the unstable Z-isomer. This is followed by a Thermal Helix Inversion (THI), which is
energetically downhill. This ensures that the motor returns to its stable form, from where it can be excited again. This leads to a repetitive process as long as the UV-light at 280 nm is supplied. There was however, a big disadvantage in the first generation. As shown in figure 11, the activation barriers are not similar, meaning the second half of the rotation proceeds faster, resulting in an irregular rotation. This was later remedied by the use of an almost symmetric stator, to make sure, the barriers for both THIs where similar. A more uniform rotation was obtained, as can be seen in figure 13 of the nanocar, where the “tires” of the car are symmetrical.
In 2006, The group of Feringa54 published a molecular motor using light to turn much larger items around. This compound was doped onto a liquid-crystal film. A submillimetre-sized glass rod was placed onto the doped film. Than UV-light was used to rotate the motor-compounds. After pictures were token in a periodically fashion, the rotation of the glass rod and thus the compound was confirmed.
Further on in 201155, Feringa again published a UV-dependent rotor containing a stator B with a terminal thiourea group and a rotor A with a terminal dimethylaminopyridine (DMAP), connected by a alkene moiety. Due to an external signal, light, the chiral space in which a catalytic reaction takes place can be controlled. During the individual steps of this cycle, the stereochemistry changes several times. As well as in the first example, this compound was able to rotate around the double bond. In the first step, irradiation at 312 nm, (P,P)-trans-9 was isomerized into (M,M)-cis-10 with a helix inversion from P to M. During this rotation, the two catalytic groups are brought into close proximity. In the second step, a solution of the compound in THF/isopropanol, was heated to 70˚C. A thermal helix inversion provides (P,P)-cis-10. In step three and four, the photochemical and thermal
isomerizations reset the compound via intermediate (M,M)-trans-10. However, these reactions are cooled down to -60 ˚C in step 3 and -10 ˚C in step 4.
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This molecular motor was then used as catalyst in the Michael addition. This asymmetric Michael addition can be switched on in situ by irradiating the catalyst at 312 nm, in the presence of a thiol and an enone. This reaction proceeds faster when the motor was isomerized to the cis-configuration in the first step already. This is, because of the close proximity of the two functional groups and their unfavourable position in the trans-configuration. As a second advantage of the cis-configuration (as well the right-, P, as left-handed helicity, M, ), produce the final product in a much higher
enantioselectivity ((M,M): S/R, 75/25 and (P,P): S/R, 23/77) than the trans-configuration (S/R, 49/51). The authors stated that the helicity of the motor dictates the spatial orientation of the catalytic groups and, as a consequence, the configuration of the newly formed chiral centre in the product of the enantioselective catalytic event.
Finally, in the end of 2011, Feringa et al55. published an electrically driven directional four-wheeled molecule on a metal surface. This new development has finally earned Feringa the Nobel Prize of 2016. In this molecular motor, also known as nanocar, they used their previously published work of a light-driven rotation around a double bond as shown is the first two examples, where it has been studied in solution54 and liquid crystalline films/phases54. They state that this mechanism contains four functional units, that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation56. One of the main questions for the authors was: how to convert rotational motion into translational motion.
The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. To obtain linear translational motion across the surface, all four of the motors on the molecule should rotate in the same direction. This requirement is only met by the meso-(R,S-R,S)-isomer as shown in figure 13a and 13b.
Figure 12: Schematic illustration of an integrated unidirectional UV-light-driven motor55. The first two steps of the
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Figure 13a and 13b shows the molecular machine with its four chiral units based on the
unidirectional rotary motors and the distinctive design features that allow it to move upon electronic excitation using a scanning tunnelling microscope (STM). The stereocentre in the cyclopentane ring determines the stability of each conformer and the direction of rotation of the motor. In figure 13c, a schematic representation of the 360˚ rotation, involving two double bond isomerization steps and two helix inversions.
To start the motion, the STM tip is positioned above the centre of the molecule to apply a voltage pulse larger than 500mV. This movement is then observed by rescanning the area under mild STM imaging conditions. Induced movement, with 10 excitation steps, of the nanocar lets the molecule move for 6 nm. This electronic excitation induces double-bond isomerization that is followed by helix inversion. This induces motion to push the entire molecule one step forward on a Cu(111) surface57.
Figure 13: Structure of the four wheeled molecule56. a) structure of the meso-(R,S-R,S) isomer. b) structural details of
the rotary motor units. The red double bond functions as the axle. It undergoes trans-to-cis isomerization when electronically excited. c) schematic representation of the 360˚ rotation.
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In the end, when the meso-(R,S-R,S) isomer is adsorbed in the proper orientation (correct landing), the four motor units act parallel. This way the molecule moves along the surface. On the other hand, when the ‘wrongly landed’ isomer is formed, the combined effects of the units cancel out to
translational movement. These movements, shows the consequences of the design. This provides evidence that the translational movement originates from the concerted action of the molecular units. The authors stated that this design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.
Figure 14: Movement of a single molecule along the surface56. Side view of the paddlewheel-like motion of the
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4.3 Comparison of the mechanism and function of the discussed examples.
In the contrary of what was discussed in the introduction, the first mechanism makes use of an information ratchet mechanism, instead of a power stroke, since the redox potential was changed periodically over time. The specific functional groups on the strand steered the macrocycle in the right direction under the correct conditions, making the machine use an information ratchet mechanism powered by redox energy. The second example does make use of a power strokemechanism, while UV-light was used to excite the compound, starting the machine to complete 360˚ rotations.
In both the mechanisms, energy was used to excite the compounds . In the first example, to translationally move the macrocyclic ring over the strand, to be, finally, placed at the threshold. In the second example, the energy was used for rotational motion around a double bond, to isomerize the compound from the E-isomer into the Z-isomer and back again. This means that the examples use different energy sources to both excite the compounds. When excited, the motion of both compounds is different, meaning the compounds use the same mechanism, while being very different respective to each other.
A second big difference is the function of the machine. The first compound must be used as a pump. It can take compounds from one part to another, like carrier proteins in nature. This could be used in over a couple of years, however, the use of the redox potential makes this harder. The second example, till now, has no clear function, when compared with biological systems. It has been made to demonstrate single molecule motion and more important for the authors, the conversion of rotary motion into translational motion.
In the following chapter the fuel-driven self-assemblies will be discussed. Their mechanism will be compared to the mechanisms of this chapter, since both make use of energy to drive the assembly.
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5. Energy-driven assemblies
5.1. Introduction
As well as the fuel-driven self-assemblies, the energy-driven ones were a great part of interest. It has recently emerged as one of the most efficient methods to create new materials with controlled properties. For this energy, UV-light has been used as a source in many systems. However, UV-light is not the only source. Some possible sources can be43:
1. Light induced assembly: Light is the most important source to obtain a self-assembly. It may induce reversible switching of a molecular system to obtain an aggregated state. This can lead to the emergence of NESA structures.
2. Self-assembly on surface: NESA can be observed on surfaces. Functional groups that are able to participate in directed non-covalent interactions, can form designs and constructions absorbed on surfaces in a wide range of supramolecular architectures.
3. Redox energy induce assembly: The energy that is obtained during a redox reaction (redox potential) can be used to switch a compound. A second option is reducing or oxidising the compounds during the reaction to activate them and make sure the desired supramolecular architecture is obtained.
The light-induced assemblies are used most of the times. The mechanism of these synthesises is the power stroke as discussed before in chapter 2 and 4. A great example of such a mechanism is described in 5.2.1., where the electrons of the trans form are excited to make a rapid isomerization into the cis form possible. This is reversed dissipatively over time, by losing energy as heat.
In this chapter, 2 examples of energy-driven assemblies will be discussed. Their mechanism and their function will be discussed, as well as their main differences. Finally, these mechanisms will also be compared to the fuel-driven self-assemblies to find the differences in the two approaches.
The first example is a cyclic structure, published by Sleiman and coworkers58 in 2003. They synthesised a compound, able to switch from trans to cis using UV-light irradiation. During this switch, the compounds can form a cycle, kept together by hydrogen bonds. Here they show the use of UV-light to activate the compound by adding sufficient energy to pass the barrier. In the second example, the same technique was actually used. However, here they used coated gold and silver nanoparticles. When irradiated these nanoparticles aggregate and change colour. This way, messages and images can be written on the organogel film. This is an interesting technique, making it
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5.2. Examples of energy-driven self-assemblies
5.2.1. Self-assembly of hydrogen-bonded cyclic structures, using UV-light irradiation. The first example is a macrocycle, described by Sleiman et al. in 200358. In their example,
photoresponsive carboxylic acid-derived azobenzenes are used as supramolecular building blocks. These compounds are able to make extended linear tapes, held together by hydrogen bonds between the carboxylic acids. Due to UV-light irradiation, an isomerization occurs to form the cis-isomer of the azobenzenes59. New hydrogen bonds are formed between the carboxylic acids of separate building blocks to form new compounds, where this reaction tends to cyclic structures.
The starting compound 12 is the trans-form of this compound. In this compound, the carboxylic acids are para placed to the N=N linkage. These carboxylic acids make sure, the hydrogen bonds are formed. This compound is formed via a 4-step synthesis from 3-hydroxy-4-nitrobenzoic acid. This trans-compound is expected to be aligned and form linear aggregates via the hydrogen bonds. Irradiating the building block with UV-light, according a power stroke mechanism, leads to the cis-form as seen in compound 13, because of a absorbance near 360nm originating from the π-π* state36. In this new building block, the ortho alkoxy chains sterically favour the formation of cyclic structures. From here, the compounds are oriented in a near perpendicular shape.
Figure 75: UV-light induced, hydrogen bonded self-assembly of trans-1 and cis-2 azodibenzoic acid. The macrocycle was
formed by self-assembly of compound 2, the cis-form of the building block. Due to hydrogen bonds, the macrocycle keeps in place. Based on ref. 58.
