Sundus Erbas-Cakmak

Artificial Molecular Machines

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

Towards Unimolecular Luminescent Solar Concentrators: Bodipy‐Based Dendritic Energy‐Transfer Cascade with Panchromatic Absorption and Monochromatized Emission

Today, efficient and effective utilization of solar energy is a high-priority target and is expected to be even more so in the near future. For the large-scale exploitation of the stellar energy source, cost is always the major prohibitive item. The use of polycrystalline silicon, amorphous thin films of silicon, or alternative semiconducting materials such as Cu(In,Ga)Se2 (CIGS), [4] together with dye-sensitized solar cells already have or are expected to have big impacts on the production costs, but more effort in all aspects of the solar energy transduction is needed. One approach is to break down this massive problem into relatively easily addressable components, such as absorption of solar photons and conversion of absorbed solar energy into electricity. Installation and transmission of the produced electrical energy are two other components, which are essentially engineering problems. For the efficient absorption of the solar radiation component, it has been known for some time that even without major changes in solar cell design, it should be possible to obtain substantial enhancements by making use of solar concentrators. Optical solar concentrators have been around for the last four or five decades, however, overheating is always a troublesome issue, with an additional need for solar tracking with most optical concentrators. Luminescent solar concentrators on the other hand seem to be more promising. Conversion of the incident solar radiation into monochromatized light is expected to lead to a large enhancement in the efficiency of solar cells. Key features of the luminescent solar concentrators are the dispersed dye or dyes in a transparent waveguide. Through total internal reflection, reemitted light is trapped within a plastic or glass matrix, and photovoltaic units are fixed to the sides through which the light is channelled out. The advantages are striking: no tracking or cooling is needed and much smaller areas have to be covered by expensive solar-cell components. However, such concentrators are not free from problems; self absorption of the emitted light is a major problem. Recently a different luminescent concentrator design that made use of a mixture of dyes in amorphous thin films placed in a tandem design with one terminal absorber was reported. The other two dyes absorb light at different wavelengths and are expected to transfer the excitation energy to the terminal absorber. The intermolecular Fçrster energy transfer (FRET) was invoked as the operational mechanism of the energy transfer. With the assumption of efficient intermolecular energy transfer in the solid (gel) phase, the only emission will be at the longer wavelength region with large pseudo-Stokes shifts, thus minimizing self-absorption. The intermolecular energy-transfer efficiency is an important limiting factor that requires high concentrations of the dyes for optimal results, but higher concentrations will lead to larger losses caused by self-absorption. Herein, we propose that this apparent dilemma can be addressed at least in principle, by replacing a cocktail of dyes with a dendritic lightharvesting energy gradient with a core molecule as the terminal absorber and emitter. In the dendritic system, energy-transfer efficiency will remain high, regardless of its concentration within the matrix. Unimolecular energy gradients have been reported previously with a number of peripheral antenna molecules and a core chromophore absorbing at a longer wavelength. Typically, they are characterized in solution. In this work however, we explicitly targeted an energy cascade system SC composed of bodipy dyes (see below) with varying degrees of substitution with styryl groups. This approach will ensure strong absorption in most parts of the visible spectrum, however, through efficient energy-transfer processes, emission is expected to originate only from the terminal absorber. An optimal solar cell placed on the sides of the matrix is expected to produce efficient and cost-effective conversion. In addition, we wanted to demonstrate the efficiency of every single step of cascading energy transfers; to that end we synthesized energy-transfer modules of ET-1, ET-2, and ET-3. Bodipy dyes are highly versatile chromophores and can be conveniently derivatized to span the entire visible spectrum and beyond, showing exceptional photochemical and photophysical qualities. These properties of Bodipy dyes, including sharp absorption and emission maxima, were previously exploited in energy-transfer modules. In our design, the goals were to optimize the absorption in a large part of the visible spectrum and also the conversion to emission centered at 672 nm, which is ideally suited for [*] Dr. O. Altan Bozdemir, S. Erbas-Cakmak, O. O. Ekiz, Dr. A. Dana, Prof. Dr. E. U. Akkaya UNAM-Institute of Materials Science and Nanotechnology Bilkent University, Ankara 06800 (Turkey) E-mail: eua@fen.bilkent.edu.tr

Cascading of Molecular Logic Gates for Advanced Functions: A Self‐Reporting, Activatable Photosensitizer

Logical progress: Independent molecular logic gates have been designed and characterized. Then, the individual molecular logic gates were coerced to work together within a micelle. Information relay between the two logic gates was achieved through the intermediacy of singlet oxygen. Working together, these concatenated logic gates result in a self-reporting and activatable photosensitizer. GSH=glutathione.

Proof of principle for a molecular 1 : 2 demultiplexer to function as an autonomously switching theranostic device

Guided by the digital design concepts, we synthesized a two-module molecular demultiplexer (DEMUX) where the output is switched between emission at near IR, and cytotoxic singlet oxygen, with light at 625 nm as the input (I), and acid as the control (c). In the neutral form, the compound fluoresces brightly under excitation at 625 nm, however, acid addition moves the absorption bands of the two modules in opposite directions, resulting in an effective reversal of excitation energy transfer direction, with a concomitant upsurge of singlet oxygen generation and decrease in emission intensity.

Asymmetric Catalysis with a Mechanically Point-Chiral Rotaxane

Mechanical point-chirality in a [2]rotaxane is utilized for asymmetric catalysis. Stable enantiomers of the rotaxane result from a bulky group in the middle of the thread preventing a benzylic amide macrocycle shuttling between different sides of a prochiral center, creating point chirality in the vicinity of a secondary amine group. The resulting mechanochirogenesis delivers enantioselective organocatalysis via both enamine (up to 71:29 er) and iminium (up to 68:32 er) activation modes.

Toward Singlet Oxygen Delivery at a Measured Rate: A Self-Reporting Photosensitizer

A Bodipy-based energy transfer cassette with a singlet oxygen reactive linker between the donor and acceptor modules has an interesting emergent property, if the acceptor module is also a photosensitizer. Singlet oxygen produced by the photosensitizer reacts rapidly with the molecule itself to liberate the energy donor, resulting in an enhanced fluorescence emission. The result is a self-reporting photosensitizer providing an assessment of the singlet oxygen production rate under the operational conditions.

Rotary and linear molecular motors driven by pulses of a chemical fuel

Acid fuels the motion of a threaded ring A central goal in the construction of molecular-scale machines is the efficient achievement of one-way motion. Erbas-Cakmak et al. developed a class of machines that transmit pH changes into the two-stage guided motion of molecular rings threaded on a linear or cyclic axle. The design relies on temporary blocking groups and landing sites along the axle that toggle between active and passive states in response to acid or base. Trichloroacetic acid initiates the first stage of motion until it is decomposed by base in the solution, spurring the second phase. Science, this issue p. 340 Acid- and base-sensitive components in molecular machines transmit pH changes into directed motion of a threaded ring. Many biomolecular motors catalyze the hydrolysis of chemical fuels, such as adenosine triphosphate, and use the energy released to direct motion through information ratchet mechanisms. Here we describe chemically-driven artificial rotary and linear molecular motors that operate through a fundamentally different type of mechanism. The directional rotation of [2]- and [3]catenane rotary molecular motors and the transport of substrates away from equilibrium by a linear molecular pump are induced by acid-base oscillations. The changes simultaneously switch the binding site affinities and the labilities of barriers on the track, creating an energy ratchet. The linear and rotary molecular motors are driven by aliquots of a chemical fuel, trichloroacetic acid. A single fuel pulse generates 360° unidirectional rotation of up to 87% of crown ethers in a [2]catenane rotary motor.

Near-IR-triggered, remote-controlled release of metal ions: a novel strategy for caged ions.

A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal-ion affinity upon irradiation with low-energy red/near-IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions.