The proposal follows the SNF advice of a single project per applicant in division II. It is divided in five subprojects, each being the subject of a PhD thesis. In spite of the different research targets, they have enough overlap enabling the fruitful exchange of knowledge and mutual developments required to build up a joint group identity. All five projects focus on current challenges in nanotechnology, molecular devices, and supramolecular materials, which are addressed by novel strategies and innovative molecular designs of functional structures. The five subprojects are briefly described in the following: (I) «Geländer»-molecules and helical architectures: «Geländer»-molecules consist of two periodically interlinked oligomers which compensate their length mismatch by wrapping the longer one helically around the shorter one, resembling the shape of the banister (Geländer in German) of a spiral staircase. The here promoted new designs profit from right-angled connections resulting in a simplified symmetry of the building blocks which should make longer oligomers synthetically accessible. A second strategy based on o-tetraphenylene building blocks is geared towards helical «plait»-type oligomers. (II) mechanosensitive model compounds for molecular junctions are based on cyclophane-type architectures enabling to tune the extent of the coupling between their subunits mechanically. With small [2.2]paracyclonaphthane derivatives the effect of torque motion shall be explored, while a polycyclic porphyrin hexamer will be assembled with two stacked states with large difference in their expansion. Based on a «upended» porphyrin type structure, even the coupling of the single electrons of two parallel radical planes might be investigated. (III) B-field sensitive macrocyclic model compounds are loop-shaped macrocycles consisting of a conjugated periphery decorated with terminal anchor groups enabling their integration in single molecule junction experiments. The intention is to detect the contribution of the Lorentz force to the molecules transport current. With a compact and twisted OPE type macrocycle, the axial chirality of the immobilized structure might become specifiable in the transport experiment. (IV) synthesis of an armchair carbon nanotube (CNT) is an interesting synthetic strategy for the controlled wet chemical assembly of an armchair CNT. A belt fragment of a CNT shall be obtained from a macrocycle by a reaction sequence, which can subsequently be repeatedly applied to control the length of the CNT. (V) approaches towards molecular textiles are based on the development of a cross-type junction acting a covalent template arranging the precursors at the water/air interface. Upon interlinking within the LB-film and cleavage of the template, textile-type interwoven molecular films should be obtained. The potential of the cross-type junction for superstructures will be investigated as well.

SuperMaMa is an EU-FET OPEN Research & Innovation project working on new technologies for mass spectrometry and analysis of lowly charged and neutral high-mass proteins. It comprises the development of neutral and lowly-charged biomolecular beam generation and detection. To this end arrays of superconducting detectors for molecular ions and neutrals will be designed and installed in a converted mass spectrometer, and methods for charge reduction of biomolecular ions in high vacuum devised. The team includes three academic research groups (M. Arndt, U. Vienna; E. Charbon, EPFL; M. Mayor, U. Basel) and two industrial partner (Single Quantum, Delft; MS Vision, Almere). The contribution from UNIBAS is primarily concerned with the development of suitable tags for biomolecules to enable charge manipulation in the gas phase by photochemical methods.

Molecular Systems Engineering is a National Centre of Competence in Research (NCCR) funded by the Swiss National Science Foundation (SNSF), and headed by the University of Basel and the ETH Zurich. This NCCR combines expertise from chemistry, biology, physics, bioinformatics, and engineering. The overreaching aim is to develop tools and devices to monitor and manipulate off-equilibrium (bio)chemical systems. These may find applications in the synthesis of high added-value products, as innovative diagnostic tools and for the restoration of a desired cellular or organ function.

Our vision is to demonstrate that room-temperature quantum interference effects, measured recently in single molecules, can be exploited in massively-parallel arrays of molecules and used to design ultra-thin-film thermoelectric devices with unprecedented ability to convert waste heat to electricity using the Seebeck effect and to cool at the nanoscale via the Peltier effect. Although the dream of high-performance thermoelectric devices has been discussed for many years, evidence of the room-temperature quantum interference effects needed to realise this dream was achieved experimentally only recently. Building on these indirect demonstrations of quantum interference in single molecules using non-scalable set ups, we anticipate that the next breakthrough will be the implementation of QI functionality these intechnologically-relevant platforms. We shall design molecules with built-in quantum interference functionality, which can be used to engineer the properties of ultra-thin molecular films. Molecules will be designed with robust anchors to metallic and carbon-based nano-gap electrodes, which enhance electron transport and eliminate unwanted phonons.This contacting strategy is scalable from a single junction, with the potential to be replicated billions of times on a single substrate. The ability to exploit quantum interference at room temperature will enable new thermoelectric materials and devices with the ability to scavenge energy with unprecedented efficiency. QuIET is a highly interdisciplinary project that brings together internationally leading scientists from four different countries with proven expertise on synthesis, transport measurements and theoretical modelling.

The determination of the three-dimensional structure of molecules using X-ray diffraction is an invaluable tool of modern chemical research. The prerequisite of such investigations is always the availability of a suitable single crystal. Very high brilliance of the primary X-ray beam in conjunction with an outstanding detector system is the solution in the case where the single crystals obtained are of good quality, but too small for successful structure determination using a conventional X-ray source. The brand new Ga-Metaljet X-ray generator offers a primary beam that is about one order of magnitude more intense than all other X-ray sources that are currently available on the market for laboratory use. The main benefit of this instrument is, that it combines a completely new and innovative setup to produce the X-rays with the well established multilayer optics which results in an extremely intense illumination of very small samples. The anode of this generator consists of a jet of liquid metal inhibiting the problem of the anode melting at higher loads of energy. Together with the single photon counting detectors produced by Dectris in Baden, Switzerland, which market their products under the brand names Pilatus and Eiger, this setup offers the most advanced X-ray detection technology available today. This new solution opens the way for many experiments to be run successfully in house, from small molecule work to macromolecular structures. It is in particular very well suited for small crystals of organic molecules. Its wavelength that is slightly shorter than the wavelength obtained from a Cu-anode makes it possible to collect more data, while the spot separation for long unit cell axes is still ways better than with Mo-radiation. In the following pages it will be demonstrated how this new device increases the possibilities of the investigation and elucidation of the structure of samples for which it would not be possible to measure them successfully using a standard laboratory X-ray source.

The proposal follows the future SNF rules of one project per applicant in division II. It is divided in five subprojects, each being the subject of a PhD thesis. Even though these five topics have very different aims, they have in common that current challenges in nano-technology are tackled by bottom-up assembly of functional molecular structures by organic synthesis. The five subprojects are: (I) Helical Oligomers, (II) Molecular Junctions, (III) Electrode Functionalization, (IV) Coated Nanoparticles, and (V) Supramolecular Preorganized Reactants. (I) Helical Oligomers: Molecular rods resembling a "molecular screw" will be developed. They consist of two interlinked oligomers with different spacing of the repeat unit, resulting in the helical wrapping of the longer oligomer around the shorter one which acts as axis. These appealing helical architectures are particular interesting due to their chiroptical properties and as model compounds to investigate molecular racemization mechanisms. (II) Molecular Junction: Molecular rods as functional units of carbon nano-tube (CNT) based molecular junctions will be synthesized. Model compounds enabling single molecule electroluminescence experiments with a central Ir(III) terpy as emitting subunit will be investigated. A molecular turnstile responding on the applied electric field shall be assembled and investigated in CNT-junctions. Interestingly the mechanical switching should be detectable in the junction's transport characteristic. (III) Electrode Functionalization: An electrochemically addressable acetylene protection group shall be developed, enabling to differentiate between electrodes by their electrification. The working principle will be investigated in solution as well as on electrodes by in situ functionalization of the deprotected acetylene groups by alkyne-azide "click" chemistry. (IV) Coated Nanoparticles: As continuation of our studies providing mono-functionalized gold particles in good yields, new motives for thioether based olgomers as multidentate macromolecular ligands shall be investigated. The focus is set on making processible gold nanoparticles with diameters of 2 nm and larger in order to increase their attractiveness for sensing applications based on optical read outs. (V) Supramolecular Preorganized Reactants: Supermolecules are used to spatially arrange molecular building blocks which are subsequently covalently interlinked. Examples of various dimensions are investigated ranging from a small (0-d) caged Fe(II) terpy complex to tune its spin state in transport experiments, over mechanically interlinked daisy chain oligomers (1-d) to interwoven 1-d polymers resembling a "molecular textile" (2-d) which shall be obtained by preorganizing the building blocks in metal organic framework.

Many photophysical and photochemical processes which are relevant for light-to-chemical energy conversion occur on very rapid timescales. Time-resolved UV-Vis absorption spectroscopy has become an indispensable tool in modern photochemistry. Several ongoing Ph. D. theses and postdoctoral research projects in the main applicant's group ask for a transient absorption spectrometer with picosecond time resolution and an appropriate laser source. Among these projects are for example the investigation of photoinduced multi-electron transfer reactions in order to spatially separate multiple electrons from multiple holes, which is of key importance for producing chemical fuels with sunlight as energy input (projects 1 and 2). Similarly, picosecond transient absorption spectrosocopy will permit mechanistic studies of photoinduced proton-coupled electron transfer (PCET) reactions which will greatly further our current fundamental understanding of this important class of reactions (project 3). The activation of small inert molecules such as H 2 O, CO 2 or N 2 will invariably rely on multi-electron, multi-proton chemistry hence the proposed photochemical studies are important in the greater context of solar energy conversion.

Tailor-Made Proteins and Peptides for Quantum Interference Experiments In recent years synthetic chemistry and quantum optics have teamed up with three major objectives in mind and are now in an encouraging position for the inclusion of molecular biology: 1 st : we face the open research challenge to test the linearity of quantum mechanics in the regime of high masses - and with it the concepts of quantum delocalization, quantum superposition and matter-wave interference. Matter-wave interferometry creates refined molecular nanopatterns that are sensitive to external fields and can be used to retrieve internal molecular properties in the presence of known forces. In the past, this has allowed us to determine molecular polarizabilities, vibrationally induced dipole moments, molecular fragmentation or to distinguish structural isomers. 3 rd : by carefully tailoring the molecular properties we were able to demonstrate the evolution of the diffraction pattern molecule by molecule and thus to unambiguously demonstrate the wave nature of the moving molecular particle. We aim to translate these achievements with tailor-made molecules into the world of biomolecular physics. Quantum experiments are expected to be compatible with neutral biomolecular beams that stay beyond a momentum of p=30.000 amu×30m/s. A key challenge is to generate a beam of slow, directed, velocity and mass-selected biomolecules in high vacuum. Peripheral chemical functionalization with perfluoroalkyl chains has proven to facilitate the promotion of intact massive molecules via thermal and laser assisted desorption methods. In this interdisciplinary approach between synthetic chemistry and bio-engineering, we propose the stepwise development of amino-acid based biomolecules for interference experiments. While the design and synthesis of these model compounds is based within the SNI at the University of Basel, the investigation of their physical properties is performed in close cooperation with the group of Markus Arndt at the University of Vienna. With the final goal of proving the wave nature of proteins, the initial challenges are mainly of chemical and biochemical nature. In particular we aim at the stepwise development of biomolecules with increasing size for interference experiments. Starting with small peptides, their volatilization (suitability for slow molecular beam formation) and ionization (detection after scattering) features shall be optimized. Profiting from these small bio-oligomers as proxy, we subsequently apply the design principles to bio-polymers of increasing size and hope to be able to push the mass limit up to suitably functionalized proteins. The sublimability of molecules is increased by reducing their intermolecular interactions and thus, peptides exposing fluorinated groups are at the focus of interest. As a starting point, lysine rich model peptides were selected for the decoration with fluorous tags. The exposed primary amino group of lysine is ideally suited for post-functionalization. Suitable electrophiles (e.g. NHS esters) enable the peripheral functionalization with groups exposing fluorous alkyl chains. The complementary conversion of carboxylic residues further permits the introduction of a photo-ionizable label to facilitate the peptide's detection by mass spectrometry. Initially we would like to investigate the number of peripheral perfluorinated alkyl groups required for the volatilization of model peptides. The modular assembly of peptides is ideally suited to study the correlation between their molecular mass and number of fluorous chains required. The features introduced by the tag can also be combined for example with a porphyrin tag exposing long perfluorinated alkyl chain. Of particular interest are photo-cleavable tags which enable future interference experiments based on optical gratings. The developed technology will subsequently be adapted to surface engineered proteins. Heterologous expression in E. coli allows control of surface residue composition by technically facile site directed mutagenesis. The outlined bio-chemical approach of protein modification also enables the global manipulation of surface charges, a particular important feature as only neutral bio-molecules are suited for interference experiments. To what extent these manipulations will interfere with the folding of the protein core will be subject of the here performed investigations. [1] S. Eibenberger, S. Gerlich, M. Arndt, M, Mayor, J. Tüxen, PhysChemPhys 2013 , 15 , 14696 [2] S. Gerlich, S. Eibenberger, M. Tomandl, S. Nimmrichter, K. Hornberger, P. Fagan, J. Tüxen, M. Mayor, M. Arndt, Nature Commun . 2011 , 2 , 263. [3] T. Juffmann, A. Milic, M. Müllneritsch, P. Asenbaum, A. Tsukernik, J. Tüxen, M. Mayor, O. Cheshnovsky, M. Arndt, Nature Nanotech. 2012 , 7 , 297. [4] P. Schmid, F. Stöhr, M. Arndt, J. Tüxen, M. Mayor, J. Am. Soc. Mass Spectr . 2013 , 24 , 602

The interplay between electrical transport and optical stimulation in tunable nanoscale molecular junctions is the focus of this project. Starting with metal contacts, the investigations will be extended to graphene contacts where better mechanical stability and enhanced control and can be implemented.

The NCCR Molecular Systems Engineering combines competences from life sciences, chemistry, physics, biology, bioinformatics and engineering sciences. More than 100 researchers and support personnel distributed into four work packages and 31 projects work together to address systems engineering challenges by integrating novel chemical and biological modules into molecular factories and cellular systems for the production of high added-value chemicals and applications in medical diagnostics and treatment. Molecular systems engineering relies on the combination of both chemical- and biological modules. In this approach, complex dynamic phenomena emerge as the result of the integration of molecular modules designed to interact in a programmed way with their complex environment. In this manner, it should be possible to create molecular factories and cellular systems whose properties are more than the sum of the attributes of the individual modules. The commitments of the leading houses, the University of Basel and ETH Zurich, also include new (joint) professorships, and extensive training of a new generation of scientists and technologists, leading to a long-term paradigm shift in molecular sciences and a new structure of the Swiss research landscape.