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Molecular Machines Nobel Prize Conference Groningen 19-22 November 2017

Molecular Machines Nobel Prize ConferenceConference

Contributed speakers

Raymond Astumian

Stochastic pumping of non-equilibrium steady-states: How molecules adapt to their fluctuating environment    
In the absence of input energy, a chemical reaction in a closed system ineluctably relaxes toward an equilibrium state governed by a simple Boltzmann distribution. The addition of a catalyst to the system provides a way for more rapid equilibration toward this distribution, but the catalyst can never, in and of itself, drive the system away from equilibrium. In the presence of external fluctuations, however, a macromolecular catalyst (e.g., an enzyme) can absorb energy and drive formation of a steady state between reactant and product that is not determined solely by their relative energies. Due to the ubiquity of non-equilibrium steady states in living systems, the development of a theory for the effects of external fluctuations on chemical systems has been a longstanding focus of non-equilibrium thermodynamics. Work on the effects of externally driven fluctuations on enzyme catalysed reactions, including molecular transport across biological membranes, has provided new insight into the mechanisms by which energy absorbed by an enzyme from non-equilibrium fluctuations can be used to drive and maintain a non-equilibrium steady-state in the presence of dissipation and kinetic assymetry. This effort has been greatly enhanced by a confluence of experimental and theoretical work on synthetic molecular machines designed explicitly to harness external energy to drive non-equilibrium transport and self-assembly.

Massimo Baroncini          

Photoinduced reversible phase change in porous molecular crystals based on star-shaped azobenzene tetramers        

The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of high interest for separation, catalysis, optoelectronics, holography, mechanical actuation, and solar energy conversion. Here we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, whose porosity can be tuned by changing the peripheral substitutents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties, such as birefringence, and of the capture of carbon dioxide from the gas phase. The linear design, the structural versatility and the synthetic accessibility make this new family of materials extremely interesting for technological applications.

M. Baroncini, S. d’Agostino, G. Bergamini, P. Ceroni, A. Comotti, P. Sozzani, I. Bassanetti, F. Grepioni, T. M. Hernandez, S. Silvi, M. Venturi, A. Credi, Nat. Chem.

Chiara Biagini          

Carboxylic Acids as Chemical Fuels for a Catenane Based Molecular Switch: Tuning the Motion Rate

In this work, activated carboxylic acids are presented as new chemical fuels for a catenane based, bistable chemical switch composed of two identical macrocycles incorporating a 1,10-phenanthroline unit. While the transition between two different states of a molecular switch has often been made possible by the sequential addition of a fuel and a proper antifuel, here one only chemical species, 2-cyano-2-phenylpropanoic acid 2, X=H is employed to drive the whole cyclic operation.

Decarboxylation of acid 2, X=H is fast and quantitative when carried out in the presence of 1 molar equivalent of the chemical switch and, when decarboxylation is over, all of the catenane molecules have experienced large-amplitude motions from state A (neutral) to state B (protonated), then to state A again.

In this communication, the principle at the basis of the above system will be illustrated. Furthermore, it will be shown that is possible to control the rate of the cyclic motion of the switch (ranging from 100 s to 50 h timescale) by a fine tuning of the fuel chemical structure.

Fred Brouwer          

How far and how fast can rings move in rotaxane molecular shuttles?              

Rotaxane molecular shuttles are archetype elements of molecular machines. In virtually all cases known, they are typical of the softness of molecular machines as opposed to macroscopic machinery: the molecular architecture invariably contains floppy structural elements. This allows for a multitude of microscopic shuttling pathways. In hydrogen bond-based molecular shuttles we have previously assumed a diffusive process for the reversible migration of the macrocyclic ring between two stations,[1,2] but the flexibility of the linker also allows a "harpooning" mechanism, in which the ring binds both stations in the transition state of the shuttling process.[3]

In another type of rotaxane, based on the pillar[5]arene macrocycle and triazole binding stations, the finding of practically linker-length independent kinetics points to a different mechanism: the macrocycle unbinds from the bis-triazole, moves onto the thread, and then has time to travel back and forth until it crosses the barrier for re-binding either to the initial station or to the (equivalent) second station. The scope and limits of this mechanism will be highlighted.[4]

[1] A. M. Brouwer, C. Frochot, F. G. Gatti, D. A. Leigh, L. Mottier, F. Paolucci, S. Roffia, G. W. H. Wurpel, Science 291 (2001) 2124.

[2] M. R. Panman, P. Bodis, D. J. Shaw, B. H. Bakker, A. C. Newton, E. R. Kay, A. M. Brouwer, W. J. Buma, D. A. Leigh, S. Woutersen, Science 328 (2010) 1255.

[3] J. Baggerman, N. Haraszkiewicz, P. G. Wiering, G. Fioravanti, M. Marcaccio, F. Paolucci, E. R. Kay, D. A. Leigh, A. M. Brouwer, Chem. Eur. J. 19 (2013) 5566.

[4] T. Ogoshi, D. Kotera, S. Nishida, T. Kakuta, T.-A. Yamagishi, A. M. Brouwer, submitted (2017).

Ryan Chiechi

Conductance Switching in Tunneling Junctions Comprising Self-Assembled Monolayers

The properties of molecular tunneling junctions can vary exponentially to minute structural and/or electronic changes at the molecular level. Conductance switching by photoisomerization and rectification are of particular interest as they form the basis of memory and computation, however, practical applications require switching and diode-behavior that is reproducible across multiple switching cycles. Molecules that respond to external stimuli typically contain large π-systems that interfere with efficient packing in self-assembled monolayers (SAMs) of, for example, alkanethiols. Inefficient packing leads to fragile SAMs that readily short and intermolecular interactions that drive side-reactions and degradation.

This talk will focus on our efforts to maximize conductance switching and overcome the rapid fatigue of spiropyran/merocyanine switches in self-assembled monolayers on metallic electrodes through the use of in-place exchange to form mixed monolayers.1 We follow the switching ex-situ via XPS and in-situ in tunneling junctions using eutectic Ga-In (EGaIn) top-contacts. Our goal is to extend the number of switching cycles to 100 without signs of fatigue and without any decrease in the conductance ratio and to generalize our approach to any system that exhibits switching behavior.

(1) Kumar, S.; van Herpt, J. T.; Gengler, R. Y. N.; Feringa, B. L.; Rudolf, P.; Chiechi, R. C. "Mixed Monolayers of Spiropyrans Maximize Tunneling Conductance Switching by Photoisomerization at the Molecule-Electrode Interface in EGaIn Junctions." J. Am. Chem. Soc. 2016, 138, 12519–12526.

Karl-Heinz Ernst    

Driving molecular machines with electrons on surfaces: rotors, walkers and nanocars

Molecules can, for example under influence of light, fulfill work. Such functional molecules are believed to have a large potential and it is expected that they become useful some days in nanomedicine or as intelligent materials. Inelastic tunneling electrons, emanating from a sharp tip of a scanning tunneling microscope (STM), travelling through single molecules can, among other action modes, induce motor action, like unidirectional rotation or translation on a surface.

After a brief introduction into artificial devices based on natural motor proteins and the principles of inelastic electron tunneling through molecules, I will present our involvement in the realization of the first successful electric current-driven, unidirectional motion of a synthetic molecule designed and synthesized by the Feringa group. Excited by tunneling electrons, the motor molecules perform different action modes on a copper surface. Depending on the stereochemical design of the four rotors of a 'nanocar' either induces unidirectional motion on a surface or causes spinning motion [1]. Recent results of electrically driven achiral walkers show a lack of unidirectionality, but exhibit the same action features, like STM contrast change due to switching and moving on the surface. The differences in vibrational and electronic excitations of the action modes will be discussed.

[1] T. Kudernac et al. Nature


Strategies to Control Antibacterial Activity with Visible Light  

Photopharmacology offers exciting properties to control biological function with light.[1] In this presentation, we will discuss the synthesis of red-shifted antibacterial agents, utilizing a newly developed synthetic methodology,[2] to control bacterial growth, in vitro, with visible light. Furthermore, a light controlled Trojan horse strategy will be discussed in which a siderophore native to Pseudomonas aeruginosa is connected, via a photocleavable linker, to a quinolone antibiotic. This allows the spatiotemporal control, with visible light, of antibacterial activity while attaining both an increased uptake and potency in Gram-negative bacteria.

[1] M. M. Lerch, M. J. Hansen, G. M. van Dam, W. Szymanski, B. L. Feringa,.

[2] M. J. Hansen, M. M. Lerch, W. Szymanski, B. L. Feringa,

Nathalie Katsonis

Molecular motors and switches for life-like adaptive matter    

The sophistication reached by organic chemistry has enabled the design and synthesis of a wide range of dynamic molecules that display controlled shape changes with an ever-increasing refinement. However, amplifying these molecular-shape dynamics to support shape-transformation, motility, and eventually a broad range of macroscopic functions remains a key challenge.

To address this challenge, I draw inspiration from living materials where molecular machines maintain out of equilibrium operation by ingenious coupling with their anisotropic supramolecular environment, and ultimately promote the appearance of emergent properties on higher levels of organisation.  


Strain-driven disassembly of supramolecular tubules    

Inspired by biology, chemists have created a wealth of molecular switches, motors and ratchets. While assemblies of these molecular machines have been used to reshape materials, harnessing their work to perform molecular-scale mechanics remains elusive. Here, we report synthetic supramolecular tubules that disassemble under irradiation with light [1]. Because the dynamic exchange between the tubules and the solution is slower than photo-switching, the light-driven disassembly follows a complex mechanism in water, that is similar to the conformational wave disassembly of cellular microtubules. These results pave the way towards the development of supramolecular machines and generation of directional forces at the nanoscale.

[1] J. W. Fredy, A. Méndez-Ardoy, S. Kwangmettatam, D. Bochicchio, B. Matt, M. C. A. Stuart, J. Huskens, N. Katsonis, G. M. Pavan, T. Kudernac

Jérémie Léonard

Vibrationally coherent optomechanical energy transduction in biomimetic molecular switches.  

Ultrafast C=C double bond photoisomerization converts light energy in mechanical energy at the molecular scale and may therefore be exploited in molecular devices for functional switching or rotary motion. In the rhodopsin protein (Rh), the sensor for vision, the ultrafast photoisomerization of the protonated Schiff base of retinal (PSBR) triggers the protein activity. This photoreaction has outstanding speed and quantum yield and it appears to be vibrationally coherent, meaning that the energy of the absorbed photon is efficiently funneled into the isomerization coordinate on a time scale faster than energy dissipation to the environment. This unique property is the promise for an optimum photomechanical energy conversion. Following a biomimetic approach, the N-alkylated indanylidene–pyrrolinium (NAIP) molecular framework was designed and synthesized such that its π-electron system would mimic that of PSBR in Rh. Consequently, its photoreaction dynamics in solution was shown to be very similar to that of Rh, including signatures of low-frequency vibrational coherence in the photoproduct ground state.

Here we apply a recently built experimental set-up utilizing sub-8fs UV-vis pulses to perform vibrational coherence spectroscopy on the NAIP compounds. The objective is to reveal the signatures of the vibrational dynamics that drives the system through the conical intersection from the initial (Franck Condon) structure to the photoproduct. Importantly, the vibrational activity and photoreaction dynamics are critically influenced by the intramolecular steric hindrance imposed by a simple methyl substitution. Hence, we demonstrate that the appropriate chemical design may turn on or off this vibrationally coherent mechanism in the NAIP compounds. Computational quantum chemistry allows us to rationalize the underlying steric-electronic effect. We discuss the possible implications of this finding on the mechanism engineered by Rh to enhance the retinal isomerization yield, and on the future design of synthetic molecular switches targeting enhanced photoreaction yield.

Jovana Milic              

Photoredox-Switchable Grippers: Radical Control of Molecular Machinery  

Molecular grippers feature a binary conformational switch in response to external stimuli that results in reversible encapsulation of smaller molecules. This behavior makes them potentially applicable as delivery systems, sensors, receptors, or elements in nanorobotics.[1,2] However, the control of molecular machinery by physical stimuli, such as electrical charge or light, is a prerequisite to their application.[2] We therefore developed photoredox-switchable molecular grippers based on resorcin[4]arene cavitand platforms equipped with alternating quinone (Q) and quinoxaline walls carrying hydrogen bond donating groups, which were inspired by the role of semiquinones (SQ) in natural photosynthesis (Figure 1).[2,3] The SQ state was generated electrochemically via cyclic voltammetry and photochemically by using [Ru(bpy)3]2+ as a photocatalyst. The properties were studied by UV-Vis spectroelectrochemistry, EPR, ENDOR, and transient absorption spectroscopy, in conjunction with DFT calculations.[2,3] It was shown that these systems adopt an open conformation in the oxidized Q state until redox interconversion to the paramagnetic SQ radical anion provides the stabilization of the closed form through hydrogen bonding.[3] The tunable magnetic properties and enhanced binding affinities of the grippers, along with high reversibility and responsiveness to electrical and electromagnetic stimuli, set the stage for a new generation of artificial molecular machines and devices based on this switching concept in the future.

[1] I. Pochorovski, J. Milić, D. Kolarski, C. Gropp, W. B. Schweizer, F. Diederich,

[2] J. Milić, M. Zalibera, I. Pochorovski, N. Trapp, J. Nomrowski, D. Neshchadin, L. Ruhlmann, C. Boudon, O. S. Wenger, A. Savitsky, W. Lubitz, G. Gescheidt, F. Diederich, J. Phys.

[3] J. Milić, M. Zalibera, D. Talaat, N. Trapp, J. Nomrowski, L. Ruhlmann, C. Boudon, O. S. Wenger, A. Savitsky, W. Lubitz, F. Diederich,

Tomoki Ogoshi      

Supramolecular Assemblies Based on Pillar-Shaped Macrocyclic Compounds “Pillar[n]arenes”    

Macrocyclic compounds play a major role in supramolecular chemistry because of their beautiful shape, nano-scale size and molecular recognition ability. In 2008, we reported a new class of macrocyclic hosts named “pillar[n]arenes”.[1] We have constructed various dimensional assemblies such as porous 1D channels, 2D sheets and 3D spheres by assembly of pillar[n]arenes. The 1D porous channels on the surface were constructed by layer-by-layer assembly based on the pillar-shaped structure.[2] The 2D porous sheets were prepared by 2D supramolecular assemblies by chemical oxidation of hexagonal pillar[6]arene containing six hydroquinones.[3] Electrochemical oxidation of the pillar[6]arene on an electrode surface resulted in formation of the 2D porous sheets on the surface.[4] The 3D vesicles having two different pore sizes were produced by co-assembly of pillar[5]quinone with pillar[6]arene in a 12:20 feed ratio of cyclic pentagonal pillar[5]quinone to cyclic hexagonal pillar[6]arene. Incorporation of pentagonal pillar[5]arene molecules into the 2D pillar[6]arene sheets by charge-transfer complexation provided curvature, resulting in the formation of highly ordered spherical structures like C60.[5]

[1] T. Ogoshi, S. Kanai, S. Fujinami, T. Yamagishi, Y. Nakamoto, Y. J. Am. Chem. Soc. 2008, 130, 5022–5023; Ogoshi, T. Yamagishi, Y. Nakamoto, Y. Chem. Rev. 2016, 116, 7937–8002.

[2] T. Ogoshi, S. Takashima, T. Yamagishi, J. Am. Chem. Soc. 2015, 137, 10962–10964.

[3] T. Ogoshi, K. Yoshikoshi, R. Sueto, H. Nishihara, T. Yamagishi, Angew. Chem. Int. Ed. 2015, 54, 6466–6469.

[4] Tsuneishi, C.; Koizumi, Y.; Sueto, R.; Nishiyama, H.; Yasuhara, K.; Yamagishi, T.; Ogoshi, T.; Tomita, I. Inagi, S. Chem. Commun. 2017, 53, 7454–7456.

[5] T. Ogoshi, R. Sueto, Y. Yoshikoshi, K. Yasuhara, T. Yamagishi, J. Am. Chem. Soc. 2016, 138, 8064–8067.

Douglas Philp        

Integrating replication processes with mechanically interlocked molecular architectures

The development of autonomous, functional chemical systems requires network densities that demand a large number of interconnections between network components. However, the lexicon of intermolecular interactions is relatively limited and therefore it will be necessary to establish orthogonal instructional frameworks that can encode system-level actions independently and without interference.

We have started to address this issue through the integration of replication processes with the assembly of mechanically-interlocked architectures. [2]Rotaxanes provide a perfect platform with which to explore such orthogonal instructional frameworks. Their construction relies on the programmed, sequential application of a series of recognition and reaction events that constitute an assembly algorithm. Replication processes also rely on an algorithm to effect auto- or crosscatalytic template formation. The maintenance of interactional orthogonality when combining these two algorithms should give rise to a [2]rotaxane that is capable of replication. Our group has established the design requirements for non-enzymatic, recognition-mediated replication and these design elements are now well understood. However, the requirements for integrating self-replication with other recognition-mediated processes, such as those required for assembly of mechanically-interlocked architectures, remains an underexplored area.

We have identified three potential designs (Figure 1) for the implementation of a replicating [2]rotaxane — Model 1 (Chem. Sci. 2016, 7, 2592) in which rotaxane assembly was possible, but cross talk between the recognition-directed algorithms was problematic, Model 2 (J. Am. Chem. Soc. 2015, 137, 16074), where unproductive complexes limited replication efficiency in the rotaxane, and Model 3 in which replication is only possible through one correctly assembled structure by partitioning replication and rotaxane assembly into two completely orthogonal pathways.

This presentation will focus on the experimental implementation of each of these three models.

Jan van Maarseveen    

Inverted spiro compounds: synthesis of an unprecedented quasi[1]catenane via a covalent scaffold        

Spiro compounds are well defined three-dimensional structures present in a wide variety of natural molecules. Owing to the rigidity of the spiro connectivity, many of these compounds display high activity and selectivity. However, from the tetrahedral sp3-carbon atom an inverted spiro connectivity may also be envisioned. In this backfolded structure the rings are intertwining, similar to a catenane. Besides their fascinating and aesthetic shape, these inverted spiro compounds display increased compactness and polarity compared to the regular spiro. In our lab we have successfully synthesized a inverted spiro molecule, dubbed a quasi [1]catenane by us due to their structural similarity to these mechanically interlocked compounds. For comparison reasons the isomeric normal spiro compound was synthesized. Based on NMR data and X-ray crystallographic analysis the interlocked nature of the rings in the quasi [1]catenane was determined. To expand the scope of these unprecedented molecules, we also synthesized the structurally similar quasi [1]rotaxane and its non-interlocked analogue. Crucial in the syntheses of these four molecules was the use of a temporary covalent scaffold that pre-organized the components for the desired cyclizations

Ernst Sudholter    

Porous organic frameworks containing platinum nanoparticles for silicon nanowire based chemical sensing              

Porous organic frameworks (POFs) have been discovered recently, and are promising new materials for molecular separations, chemical sensing and catalysis. In this study we show the successful development of a chemical sensor, which is based on the covalent immobilisation of melamine-terephthaldehyde POFs on amino propyl modified silicon nanowires (SiNW). These nanowires were made by top down photo-lithography and act as a (nano-sized) field effect transistor (FET). Changes in the chemical composition of the immobilised POF (the selector layer) is directly monitored by the FET (the transducer) as a change of source-drain current or as a change of gate potential.

The POFs on top of the SiNW was post-synthesis functionalised by uniformly distributed platinum nanoparticles (PtNP) through impregnation using chloroplatinic acid, followed by in situ sodium boron hydride reduction. The obtained PtNP@POF-SiNW chemical sensor showed enhanced sensitivity for methanol vapor detection.

Anping Cao, Meixia Shan, Laura Paltrinieri, Wiel Evers, Liangyong Chu, Lukasz, Poltorak, Johan H. Klootwijk, Beatriz Seoane, Jorge Gascon, Ernst J. R. Sudhölter, and Louis C. P. M. de Smet, Enhanced vapor sensing using silicon nanowire devices coated with Pt nanoparticle functionalized porous organic frameworks, manuscript under review (2017).

Kingo Uchida            

Photoresponsive diarylethene crystals      

We present a new aspect of the photoresponsive diarylethenes. Diarylethenes are thermally irreversible photochromic molecules with fatigue resistance. We have studied the photo-induced crystal growth of versatile shapes of diarylethene derivatives via eutectic mixtures. In this presentation, we will show the photo-control of the surface topographical changes accompanied with surface properties of wetting, forming superhydrophobic and superhydrophilic surfaces. The superhydrophobic surface mimicking the natural lotus leaf having double roughness structures, and another structure mimicking a termite wing which consists of two different sizes were generated. They demonstrated the specific wetting properties of the surface. In parallel, we found also a diarylethene derivative form a hallow crystal and it showed photosalient effect. This is due to the large structure changes of the molecule in the crystal; hence the unit cell also changes the size to induce the crystal break. Such phenomena are the new aspect in the photoresponsive materials.

Sander Wezenberg            

Photomodulation of anion binding affinity and selectivity

Because of the important role that anionic species play in many biological processes (e.g. signalling, osmosis, metabolism), a large number of artificial anion receptors has been developed over the last decades. Interestingly, certain synthetic anion receptors are able to mimic the function of natural protein carriers and therefore have therapeutic potential. However, where proteins can switch between high and low affinity states in response to stimuli, integrating responsive behavior into artificial anion receptors is still extremely challenging.

We have developed bis-urea anion receptors that can be switched between distinct affinity modes using light. These receptors are based on molecular motor and stiff-stilbene scaffolds and selectively bind dihydrogen phosphate. Furthermore, the two possible cis-isomers in the molecular motor isomerization cycle hold opposite enantioselectivity in the binding of chiral phosphates. Currently, their potential application as anion carriers for the regulation of transmembrane transport is investigated.

Laatst gewijzigd:06 december 2017 13:55