Stefan-S. Jester

Fluctuating exciton localization in giant π -conjugated spoked-wheel macrocycles

Conjugated polymers offer potential for many diverse applications, but we still lack a fundamental microscopic understanding of their electronic structure. Elementary photoexcitations (excitons) span only a few nanometres of a molecule, which itself can extend over microns, and how their behaviour is affected by molecular dimensions is not immediately obvious. For example, where is the exciton formed within a conjugated segment and is it always situated on the same repeat units? Here, we introduce structurally rigid molecular spoked wheels, 6 nm in diameter, as a model of extended π conjugation. Single-molecule fluorescence reveals random exciton localization, which leads to temporally varying emission polarization. Initially, this random localization arises after every photon absorption event because of temperature-independent spontaneous symmetry breaking. These fast fluctuations are slowed to millisecond timescales after prolonged illumination. Intramolecular heterogeneity is revealed in cryogenic spectroscopy by jumps in transition energy, but emission polarization can also switch without a spectral jump occurring, which implies long-range homogeneity in the local dielectric environment.

Mechanically interlocked DNA nanostructures for functional devices

CONSPECTUS: Self-assembled functional DNA oligonucleotide based architectures represent highly promising candidates for the creation of nanoscale devices. The field of DNA nanotechnology has emerged to a high level of maturity and currently constitutes one of the most dynamic, creative, and exciting modern research areas. The transformation from structural DNA nanotechnology to functional DNA architectures is already taking place with tremendous pace. Particularly the advent of DNA origami technology has propelled DNA nanotechnology forward. DNA origami provided a versatile method for precisely aligning structural and functional DNA modules in two and three dimensions, thereby serving as a means for constructing scaffolds and chassis required for the precise orchestration of multiple functional DNA architectures. Key modules of these will contain interlocked nanomechanical components made of DNA. The mechanical interlocking allows for performing highly specific and controlled motion, by reducing the dimensionality of diffusion-controlled processes without restrictions in motional flexibility. Examples for nanoscale interlocked DNA architectures illustrate how elementary functional units of future nanomachines can be designed and realized, and show what role interlocked DNA architectures may play in this endeavor. Functional supramolecular systems, in general, and nanomachinery, in particular, self-organize into architectures that reflect different levels of complexity with respect to their function, their arrangement in the second and third dimension, their suitability for different purposes, and their functional interplay. Toward this goal, DNA nanotechnology and especially the DNA origami technology provide opportunities for nanomechanics, nanorobotics, and nanomachines. In this Account, we address approaches that apply to the construction of interlocked DNA nanostructures, drawing largely form our own contributions to interlocked architectures based on double-stranded (ds) circular geometries, and describe progress, opportunities, and challenges in rotaxanes and pseudorotaxanes made of dsDNA. Operating nanomechanical devices in a reliable and repetitive fashion requires methods for switching movable parts in DNA nanostructures from one state to another. An important issue is the orthogonality of switches that allow for operating different parts in parallel under spatiotemporal control. A variety of switching methods have been applied to switch individual components in interlocked DNA nanostructures like rotaxanes and catenanes. They are based on toehold, light, pseudocomplementary peptide nucleic acids (pcPNAs), and others. The key issues discussed here illustrate our perspective on the future prospects of interlocked DNA-based devices and the challenges that lay ahead.

Design Strategy for DNA Rotaxanes with a Mechanically Reinforced PX100 Axle

Rotaxanes are interlocked molecular architectures that can be perceived as simple mechanical devices. A macrocycle that is threaded onto an axle and is deterred from dethreading by bulky stoppers can move translationally along the vector of the axle as well as rotate around it. To ensure that these molecular assemblies can carry out directional mechanical motion, the respective components require sufficient dimensional stability, or stiffness, over the entire working space. In case of rotaxanes, it is primarily the axle that needs to exist as a non-deformable unit to efficiently convert the microscopic movement of the macrocycle into mechanical energy and to employ it for power transmission, otherwise the momentum of the moving macrocycle simply leads to a deformation of the axle, and thus cannot be further employed. We have recently described a DNA rotaxane that has a translational amplitude of about 100 base pairs (bp). In a double-stranded DNA, however, the length of persistence of approximately 130 bp is too short to meet the required mechanical stability along the dumbbell axle. Many systematic studies have devised methods in structural DNA nanotechnology that not only allow for the construction of topologically defined architectures by selfassembly of DNA sequences, but also lead to robust twoand three-dimensional objects. Seminal work in this field was established by Seeman, who demonstrated that two DNA double strands that are interwoven by multiple reciprocal strand exchange can lead to molecular assemblies that exhibit increased stiffness. 7] Among them, particularly the so-called paranemic crossover structures PX and JX were often applied for mechanical switching in DNA nanotechnology. PX elements are characterized by a strand exchange that occurs at each contact point of two antiparallel DNA double strands. In a JX element, however, the strand exchange is abrogated at two consecutive positions. What makes the PX and JX elements so special is that two independent DNA double strands can be held together by reciprocal base pairing. Consequently, a paranemic crossover structure always exists in equilibrium with the respective DNA double strands. In presence of Mg ions, the equilibrium is strongly shifted towards the crossover product. For the assembly of dsDNA rotaxanes, we devised a threading strategy that relies on the formation of eight bp between the DNA axle and the macrocycle. The hybridization of these two components occurs highly efficiently, leading to quantitative rotaxane formation. Owing to the highly flexible single-stranded region, the DNA axle is able to easily accommodate its conformation to the geometry inherent to the macrocycle, thus leading to quantitative threading of the axle. However, higher-order DNA architectures like paranemic crossover DNA or even DNA origami 12] do not permit this flexibility anymore. On the contrary: it is precisely their mechanical robustness that accounts for their importance in DNA nanotechnology. Conversely, however, this lack of flexibility constitutes a major challenge for the threading of a rotaxane axle into a macrocycle that necessitates novel design strategies, which we describe herein. To expand the range of application of mechanically interlocked DNA architectures to these higher-order DNA structures, we sought to apply our threading strategy to a robust paranemic crossover system and to assemble the PX100 rotaxane (Figure 1a). The reinforcement of the dumbbell axle is achieved by an extended PX-JX2 crossover system in which two parallel DNA double strands are interwoven by six double crossovers (Figure 1b). A pivotal

Nanopatterning by Molecular Polygons

Molecular polygons with three to six sides and binary mixtures thereof form long-range ordered patterns at the TCB/HOPG interface. This includes also the 2D crystallization of pentagons. The results provide an insight into how the symmetry of molecules is translated into periodic structures.

Syntheses and properties of thienyl-substituted dithienophenazines

Summary A series of dithienophenazines with different lengths of the oligomeric thiophene units (quaterthiophenes and sexithiophenes) was synthesized. The thiophene and phenazine units act as electron donors and acceptors, respectively, resulting in characteristic absorption spectra. The optical spectra were calculated using time-dependent density functional theory at the B3LYP/TZVP level and verify the experimental data. Adsorption of the dithienophenazines on highly ordered pyrolytic graphite (HOPG) was investigated by scanning tunneling microscopy, showing that one of the compounds forms highly organized self-assembled monolayers.

A Giant Molecular Spoked Wheel

The modular synthesis of a defined, rigid molecular spoked wheel structure with the sum formula C1878H2682 and a diameter of about 12 nm is described. The attached 96 dodecyl side chains provide the solubility of the 25 260 Da compound in common organic solvents. At the octanoic acid/highly oriented pyrolytic graphite interface, the molecules self-assemble to form an ordered 2D lattice, which is investigated by scanning tunneling microscopy, displaying their structure with submolecular resolution.

Oligomers and Cyclooligomers of Rigid Phenylene–Ethynylene–Butadiynylenes: Synthesis and Self‐Assembled Monolayers

Nanoscale shape-persistent macrocycles have attracted increasing attention because of their interesting structural, optical, and electronic properties. Moreover, they are able to build up highly organized supramolecular nanostructures in one, two, and three dimensions. Recently, special emphasis has been given to self-assembled monolayers (SAMs) of shape-persistent macrocycles on solid substrates. The ring sizes and distances can be adjusted by the building blocks, and their interior and exterior can synthetically be addressed independently. Together, this allows a surface functionalization with atomic-level precision. In several cases, such patterns could be used for the epitaxial deposition of admolecules. The driving forces for the self-assembly are the molecule– substrate and molecule–molecule interactions, which are dominated by van der Waals forces. Although rigid macrocycles and rigid linear oligomers have come into the focus of recent scanning tunneling microscopy (STM) studies, a systematic investigation of rigid rods connected by freely jointed or freely rotating linkers and their corresponding closed-loop structures on a solid substrate have been rarely reported, if at all. In our own ongoing studies, we have prepared arylene– ethynylene–butadiynylene macrocycles with a variety of symmetries, sizes, and functionalities. In most cases, the final ring closure towards our target structures is achieved by an oxidative coupling of rigid bisacetylenes. This transformation typically proceeds by Glaser, Glaser–Eglinton, Hay, or palladium-mediated homocoupling reactions, and has been used numerous times for the formation of macrocyclic structures. 7] Oxidative acetylene coupling reactions are easy to perform and tolerate a wide variety of functional groups. Notwithstanding, the actual reaction outcome strongly depends not only on the catalyst/oxidant mixture but also on the solvent and reaction temperature, and of course on the specific substrate structure. Sometimes cyclic and acyclic reaction products are formed simultaneously. In other cases, a catalyst discrimination between different macrocyclic or between acyclic and cyclic reaction products was observed. Herein, we present a series of acyclic and cyclic phenylene–ethynylene–butadiynylene(PEB) oligomers prepared by oxidative acetylene oligomerization. These oligomers are based on the same constitutional repeating units (CRUs), in which the rigid elements of the target structures are connected by freely rotating linkers bearing pyridyl functions. Our study was motivated by the question as to whether these oligomers can form stable SAMs at the solid/liquid interface that can be investigated by STM. We wanted to determine the behavior of oligomers of different length and compare directly acyclic and cyclic structures, a topic that has not yet been addressed. The synthesis of the precursors (half-rings) 1a and 4 a is described in the Supporting Information. They were coupled using CuCl/TMEDA (1:1) as catalyst and base, air oxygen as oxidant, and dichloromethane as solvent (Scheme 1, left). Analytical gel permeation chromatography (GPC) of the crude product indicated the formation of dimers along with higher oligomers (see Figure 2A(a)). Similarly, the palladium-catalyzed oxidative acetylene coupling of 1a and 1b and of 4a and 4b using [Pd(PPh3)2Cl2] and CuI as catalysts, I2 as oxidant, and iPr2NH as base in THF as solvent (Scheme 1, right) produced again an oligomer mixture. However, the peak molecular weights of the oligomers were significantly lower (see Figure 2B (a)). Recycling GPC (recGPC) allowed an efficient separation and detailed analysis of the different products. From the copper-catalyzed coupling of 4a, we separated acyclic oligomers [5a]n from the dimer (n = 2) up to the hexamer (n = 6) in yields between 15 % and 4%; from the palladium-catalyzed coupling, cyclic oligomers [6a]n from the dimer (n = 2) to the hexamer (n = 6) were obtained in yields between 19 % and 2%. From the copper-promoted coupling reaction of 1a, we isolated the acyclic oligomers ([2a]n ; n = 2–6) in yields between 22 % and 6%. Under palladium catalysis, both 1a and 1b only gave cyclodimers [3a]2 and [3b]2; higher oligomers show the presence of defects (Supporting Information). However, the pure acyclic and the cyclic oligomers are slightly yellow and show a strong blue fluorescence in solution. With oligomers [5a]n and [6a]n (n = 2–6) now available, we were able to systematically investigate not only the adsorption behavior of defined, monodisperse oligomers of different lengths (and compare them with the monomer, 4a), but could also directly compare cyclic and acyclic compounds of the same chain length. An STM image of the monomer adsorbed at the interface of highly oriented pyrolytic graphite (HOPG)/1,2,4-trichlorobenzene (TCB) is shown in Figure 1a, [*] Dr. S.-S. Jester, Dr. N. Shabelina, S. M. Le Blanc, Prof. Dr. S. H ger Kekul -Institut f r Organische Chemie und Biochemie Rheinische Friedrich-Wilhelms-Universit t Bonn Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany) Fax: (+ 49)228-73-5662 E-mail: stefan.jester@uni-bonn.de hoeger@uni-bonn.de

Nanostructuring the graphite basal plane by focused ion beam patterning and oxygen etching

Ga+ focused ion beam (FIB) patterning was used to structure highly oriented pyrolytic graphite surfaces with square, periodic arrays of amorphous carbon defects (mesh sizes: 300 nm–2 µm). Controlled oxygen etching of these arrays leads to matrices of uniform, orientationally aligned, nm-sized, hexagonal holes. The properties of the resulting hole assembly (hole depths and lateral hole dimensions) have been investigated by means of atomic force microscopy, scanning electron microscopy and FIB sectioning. The hole dimensions and uniformity both depend on the FIB parameters and etching conditions. Etching temperatures from 500 to 700 °C were applied. Initial etch rates of up to 106 C s−1 per individual hole were observed when using oxygen pressures of 200 mbar. For an etch temperature of 590 °C the rate of etching of individual holes was found to depend measurably on the inter-hole separation. This confirms that the associated reaction kinetics is mediated by the finite diffusion length of reactive oxygen species along the graphite basal plane. Prolonged etching results in hole–hole contact and generation of mesa arrays of controllable size and shape.

Solid C58 films

A new solid material has been created in ultra high vacuum by utilizing the aggregation process of C58 molecules deposited onto highly oriented pyrolytic graphite from a mass selected low-energy ion beam comprising C58+. Cluster fluxes of up to 3x10(11) ions s-1 cm-2 with impinging kinetic energies of 6+/-0.5 eV were typically applied. Growth of the solid C58 phase proceeds according to the cluster-aggregation-based Volmer-Weber scenario where initially ramified 2D islands transform into 3D pyramid-like structures at higher coverages. The C58 films created exhibit much higher thermal stability than the C60 solid phase. Sublimation of C58 sets in at a temperature of 700 K. Ultraviolet photoionization spectra (He I, 21.2 eV) yield a molecular ionization potential in the range between 6.6 and 7 eV. Density functional and Hartree-Fock theories suggest that the formation of C58 dimers and higher multimers upon deposition/aggregation gives rise to the high thermal stability and unique electronic properties of this material.

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures

Abstract We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double‐stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo‐DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.