Introduction to the internship and description of experiments

Interfacial Systems Chemistry Compulsory internship for master students in the first term of their master studies

Winter term 2010/2011

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1. Introduction to the internship Research Department Interfacial Systems Chemistry (IFSC)

The Research Departments are an integrated part of the institutional Research Campus

strategy of the Ruhr-University Bochum, developed to promote excellent research using a

unique interdisciplinary approach which encourages the independence of scientist.

The Research Department IFSC is one of the thematic priorities of the Natural Sciences and

Engineering faculties. It is a joint, interdisciplinary approach of chemistry and its neighbouring

disciplines, aimed to gain a basic and systemic understanding of the structural and dynamic

complexity of hierarchically structured assemblies at interfaces.

Several of the most important, but also less understood processes occur at interfaces. The

Research Department aims to investigate these problems through the interplay (synergy) of

synthetic chemistry, analytical and computational methods. Starting from intermolecular

interactions and the aggregation of small molecules, our vision is to achieve a general

understanding of the evolution of chemical complexity. Projects in the Research Department

will lead to the development of smart drug carriers, adaptive biosensors, and novel materials

for energy conservation.

Internship Interfacial Systems Chemistry (IFSC)

The practical course Interfacial Systems Chemistry is a compulsory internship for master

students in the first term of their master studies. Within the framework of the course, students

will gain an overview of the whole field of research and the interdisciplinary research

activities available within the Faculty of Chemistry and Biochemistry and the Research

Department IFSC. One of the central scientific areas researched within the faculty is the

investigation of chemistry on interfaces from molecules to complex systems. Therefore the

name of the internship is related to the name of the research department Interfacial Systems

Chemistry (RD IFSC) established in 2008. The mission of this interdisciplinary research

facility is to pool the competencies in the area of chemistry on interfaces, in order to gain a

deeper understanding of the processes behind it and to achieve a general understanding of

the evolution of chemical complexity. These processes will be investigated using different

approaches, combining synthetical, physical and theoretical chemistry. This internship will

give students an overview of current experimental and theoretical approaches of importance

within, but also beyond, this research focus.

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2. General information about the internship IFSC

The course will start in the first week of the winter term 2010/2011 and will end with a poster

presentation and a final discussion on December 12th, 2010. Every student has to perform

two experiments, each of which will last two weeks. Four slots of two weeks will be offered

within this course. Once registered for the course (registration is binding), students will

choose two experiments from the list described on the next pages and they will then be

assigned appropriate slots, according to availability. Regarding this procedure, time slots can

not be chosen by the students It will be possible for students to begin the course in the

second week, providing that places are vacant.

1. Slot 11.10 - 22.10.2010

2. Slot 25.10 - 05.11.2010

3. Slot 08.11 - 19.11.2010

4. Slot 22.11 - 03.12.2010

Additionally two obligatory seminars will be given which will introduce the topics of scientific

presentation techniques and poster preparation..

Grading system for the internship

In total six credit points (CP) are available for the internship. Students will get three points for

writing an experimental report, providing that the report is graded with at least a pass and is

submitted before the deadline (deadline: 03.12.2010, to the IFSC office, Room NC

02/168).Three CP will be assigned for the preparation and presentation of one poster from

the second experiment and a short oral presentation about an experiment of choice within

the framework of the poster session on 03.12.2010.

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Contact for questions:

Dr. Andres Schützendübel Science Manager Research Department Interfacial Systems Chemistry (IFSC) Ruhr-University Bochum Universitaetsstr. 150 Building NC 02/168 D-44801 Bochum Phone: ++49 (0) 234 32-24374 Fax: ++49 (0) 234 32-14378 Email: Andres.Schuetzenduebel@rub.de

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3. List of experiments 1. Fourier-transform infrared spectroscopy and microscopy

2. Characterization of structured and functionalized surfaces with an atomic force microscope

3. Introduction to matrix isolation

4. Introduction to ESR spectroscopy

5. Introduction to methods for quantum chemical calculations

6. Dynamics of the unfolding of a photoswitchable Foldamer in solution

7. Corrosion of metal surfaces: structure and stability of surface oxides

8. Computational chemical kinetics and thermodynamics

9. Atomic Layer Deposition (ALD) of Functional Metal Oxides

10. Phosphatidylinositol mediated assembly of protein complexes at lipid membranes and analysis of protein induced membrane deformation

11. Redox-active monolayers – Self assembly and electrochemical characterization.

12. Synthesis of Short Metallo-Peptides

13. Immobilization of reagents and bioactive molecules on polymers

14. Investigations on the kinetics of the so called SOAI reaction

15. Circular Dichroism and protein folding

16. Synthesis, characterization and modeling of porous coordination polymers

17. Ion clustering of ionic liquids in weakly polar solvents

18. Microfluidic investigation of a DNA amplification system

19. Synthesis of a task specific ionic liquid

20. Application and characterization of a task-specific ionic liquid

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1. Fourier-transform infrared spectroscopy and microscopy Required skills: Basic knowledge in infrared spectroscopy (e.g. from PCIII lecture) Short description of the experiment: Infrared spectroscopy is one of the most important analytical techniques for identification and investigation of organic compounds. An infrared vibrational spectrum of a molecule represents a molecular fingerprint of the compound due to its characteristic pattern of absorption bands. Positions and intensities of vibrational bands can be used to confirm or identify the presence of particular functional groups, whereas spectral correlations can be used to access structural and environmental information on selected functional groups. One of the great advantages of infrared spectroscopy is the large diversity of sample states that can be studied, ranging from gas to liquids and solutions to surfaces, powders, and even molecular thin films. Furthermore infrared spectroscopy is particulary non-intrusive, requires small amount of sample and can be easily coupled with microscopy providing spatial localized spectral information in order to gain knowledge of the spatial distribution of a substance. A combination of infrared spectroscopy and microscopy is called Fourier transform infrared (FT-IR) microspectroscopy. Using this technique, chemical maps of samples can be generated providing an infrared spectrum at each pixel. The importance of FT-IR microspectroscopy is reflected in the wide range of applications in different research fields such as material sciences, agriculture, biology, pharmaceutics and medicine. Also in industrial laboratories infrared microspectroscopy is an indispensible tool for failure analysis, contaminant identification, quality control, and quality assurance for many years. Materials and products of interest include semiconductors (e.g. determination of dopants and contaminants, or characterization of amorphous and crystalline dielectrics), packaging materials, ceramics, polymers, adhesives, magnetic media and lubricants. Furthermore the FTIR methodology is also intensively used in context of crime scene investigations. This practical course offers a theoretical and practical introduction to FT-IR spectroscopy and microscopy. The students will gain experience in FTIR methodology, in particular sample preparation and handling, as well as basic spectral interpretation. Advantages and limitations of the FTIR technique are outlined. In the first part the basics of the FTIR methodology are demonstrated by acquiring and analyzing qualitative and quantitative measurements of different solvents and solutions. Advanced issues will be addressed in the following microscopic part. Students will learn how to generate chemical maps of diverse samples (e.g. polymer blends and/or onion cells) in different measurement modes. Computer based multivariant statistic data evaluation will create false colour images providing information on spatial distribution of chemical signatures. Further reading: Recommended to refresh your knowledge:

„Physical Chemistry“ P. W. Atkins; Wiley-VCH

„Spektroskopische Methoden in der organischen Chemie“ M. Hesse, H. Meier, B. Zeeh; Thieme Verlag

„Methoden der Biophysikalischen Chemie“ R. Winter, F. Noll; Teubner Studienbücher Advanced literature: „Infrared and Raman Spectroscopic Imaging“ R. Salzer, H. W. Siesler; Wiley-VCH (Probekapitel und Google Vorschau:

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http://www.wiley-vch.de/publish/dt/books/bySubjectCH00/ISBN3-527-31993- X/?sID=p3m58ufcvnri95viabfnvsu1a4)

„Infrared Spectroscopy – Fundamentals and Applications“ B. H. Stuart; Wiley

„Infrared Microspectroscopy and Imaging“ Lisa M. Miller

“Non-Invasive Fourier Transform Infrared Microspectroscopy and Imaging Techniques: Basic Principles and Applications” P. Garidel, M. Boese

“Chemical Imaging of Plant Cells”, C. Hyett,et al., Canadian light Source(110), 2007

“FT-IR imaging of polymers: an industrial appraisal”, J.Chalmers et. Al, vibrational Spectroscopy, 30, 2002, 43-52.

Multivariant Statistic:

“A tutorial on Principal Component Analysis” J. Shlens

“Analytische Chemie” M. Otto; Wiley-VCH; Kapitel Chemometrie Webpages:

- SpectroscopyNOW.com --> Guide to Infrared Spectroscopy http://www.spectroscopynow.com --> “IR” --> “Education” or “Links”->”Education”

- Spectral Database for Organic Compounds: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

- (fast) Alles über die IR-Spektroskopie http://www.ir-spektroskopie.de/

Persons involved: Prof. Dr. Martina Havenith-Newen, Marlena Filimon, Dr. Ilona Kopf, Dr. Erik Bründermann and scientific assistants

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2. Characterization of structured and functionalized surfaces with an atomic force microscope Required skills: This experiment is based on experiment F10 of the Physikalisch-chemische Praktikum für Fortgeschrittene. Short description of the experiment: The first two days of the practical course the students have to become familiar with the different modes of operation of scanning probe microscopes and important sample preparation methods in the field of scanning probe microscopy. The experimental part starts at the third day: With the help of a suitable sample the atomic force microscope (AFM) has to be calibrated and then force-distance curves has to be measured for samples with different hardnesses. A lateral structured sample prepared by microcontact printing consisting of two different thiols having similar length but a different functional group is measured at the fourth day of the experiment to demonstrate differences in the friction force qualitatively and to define a method to calibrate the measured signals with respect to different sample friction coefficients. Alternatively to these experiment measurements of a structured Biotin-Streptavidin system are possible to compare height differences of a monolayer of Streptavidin molecules which occur if tapping mode AFM measurements are carried out in air or in a liquid. At the fifth day of the experiment a sample from a running scientific project has to be measured with the AFM. In the second week of the experiment the students have time to become familiar with the image processing software and they have to process the AFM data in a way it is necessary for scientific publications. Furthermore the students have to write the report for the AFM experiment during the second week. Further reading:

G. Binnig, H. Rohrer, Ch. Gerber, E. Weibel, Phys. Rev. Lett. 49 (1982) 57-61 H. Fuchs, Physikalische Blätter 45 (1989) 105-115 G. Binnig, C.F. Quate and Ch. Gerber, Phys. Rev. Lett. 56 (1986) 930-933 G. Friedbacher und H. Fuchs, Angew. Chem. 115 (2003) 5804-5820 H. Fuchs, Physikalische Blätter 50 (1994) 837-843 U.D. Schwarz und H. Hölscher, Physikalische Blätter 54 (1998) 1127-1130 Y. Xia, X.-M. Zhao, E. Kim, and G.M. Whitesides, Chem. Mater. 7 (1995) 2332-2337 Persons involved: Dr. A. Birkner, N.N. (Physical Chemistry 1)

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3. Introduction to matrix isolation Required skills: Basic knowledge on spectroscopy Short description of the experiment: The spectroscopic detection of reactive intermediates often requires low temperatures and embedding of these molecules in an unreactive environment such as noble gas atoms which form a solid phase at temperatures near absolute zero. This technique is called matrix isolation. In many cases stable precursors are first diluted in the gas phase with a noble gas (argon, neon, nitrogen) and deposited on a cold window and then reactive intermediates can be generated by photochemical means upon irradiation with UV or visible light. The experiments must be performed under a high vacuum to prevent contaminates from unwanted gases freezing to the cold window. Because of the broad optical transparency of the matrix material, the reactive intermediates can be detected by infrared or UV/VIS spectroscopy. By warming up the matrix below the boiling point of the noble gas (“annealing”), the matrix loses rigidity and reactions or the formation of aggregates are possible. This experiment will provide an introduction to this technique. Within the framework of this experiment also quantum chemical calculations will be performed to calculate the geometry and the infrared spectra of simple systems. These theoretical results will be compared to the experimental spectra. Persons involved: Dr. Dirk Grote (NC4/132), N.N.

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4. Introduction to ESR spectroscopy Required skills: Short description of the experiment: ESR spectroscopy is a convenient method to study paramagnetic systems such as radicals or high-spin systems (two or more electrons with parallel spin). The benefit of applying ESR spectroscopy here is that it provides a method to selectively detect paramagnetic systems while diamagnetic products do not appear in the spectra. Since organic paramagnetic systems are generally very reactive, ESR spectroscopy is often performed at low temperatures and can be combined with matrix isolation techniques. This experiment will provide an introduction to the theory and technique of ESR spectroscopy by measuring and analyzing ESR spectra of simple paramagnetic systems. Further reading: A short introduction to ESR spectroscopy can be found in several physical chemistry textbooks and in the dissertation of Hans Henning Wenk (http://www.ruhr-uni-bochum.de/oc2/dissertations.html , Chapter 2). Additional literature will be provided by the organizers of this experiment. Persons involved: Dr. Dirk Grote (NC4/132), Patrik Neuhaus, Klaus Gomann

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5. Introduction to methods for quantum chemical calculations Required skills: This experiment is intended only for students, which have NOT participated in the practical course "Theoretische Chemie und Biochemie" in the 6th semester of the BSc studies. Short description of the experiment: The aim of this theory experiment is an introduction to basic quantum chemical methods using a widely distributed software package (Gaussian) and the critical evaluation of the obtained results. First, using a common visualization tool (Molden) the structures of some amino acids will be constructed and then optimized by Gaussian employing various quantum chemical methods (Hartree-Fock, MP2, DFT) and basis sets. The influence of the chosen method and basis sets will be critically evaluated and the reliability of the results will be discussed. A further goal of this experiment is the visualization and interpretation of the canonical and localized molecular orbitals as well as the investigation of the electrostatic potential of the zwitterionic and the neutral forms of the amino acids. The applied methods are standard tools in quantum chemistry and thus of general relevance for many other applications. Further reading: A. Szabo, N.S. Ostlund, "Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory", Dover Publications, 1996. J.B. Foresman, "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian", Gaussian Inc., 1996. F. Jensen, "Introduction to Computational Chemistry", Wiley, 2008. Persons involved: Dr. Behler, Prof. Hättig, Prof. Marx and coworkers.

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6. Dynamics of the unfolding of a photoswitchable Foldamer in solution Required skills: A necessary condition for carrying out this experiment is the successful participation in the “Theoretisch-Chemisches Praktikum” in the 6th semester of the BSc studies or equivalent experience in carrying out theoretical calculations. Short description of the experiment: The formation of secondary structures of proteins can be mimicked by foldamers that adopt a helical conformation in solution. Of special interest in the BioNano border area of material sciences are photoswitchable foldamers that can be switched reversibly between two states of secondary structure. This experiment's focus is on the system of Hecht and coworkers (Angew. Chem. Int. Ed. 45 (2006) 1878), that for the first time instantiates a photoswitchable foldamer by using azobenzene as the switch in the centre of an oligomer of meta-phenylene ethynylene (mPE). In this theory experiment, first a MD simulation of an oligo-(mPE) foldamer in the solvent acetonitrile will be performed in the E-azo confomation and analysed in detail with respect to the interface of the stable helical molecule and the solvent. In a second step, the azo group will be switched in a computer experiment to the Z conformation. The resulting unfolding dynamics of the foldamer and the qualitatively altered molecule/solvent interface of the unfolded oligomer (“random coil”) will be analysed in detail in this second part of the experiment. Further reading: S. Hecht and I. Huc (eds), "Foldamers. Structure, Properties, and Applications", Wiley-VCH 2007. A. Khan, C. Kaiser, and S. Hecht, Angew. Chem. Int. Ed. 45, 1878-1881 (2006). M. T. Stone, J. M. Heemstra, and J. S. Moore, Acc. Chem. Res. 39, 11-20 (2006). Persons involved: Prof. Marx and coworkers

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7. Corrosion of metal surfaces: structure and stability of surface oxides Required skills: A necessary condition for carrying out this experiment is the successful participation in the “Theoretisch-Chemisches Praktikum” in the 6th semester of the BSc studies or equivalent experience in carrying out theoretical calculations. Short description of the experiment: In this theory experiment the formation of oxide films at metal surfaces is studied by density-functional theory calculations. First, the stable structures of ideal, adsorbate-free metal surfaces are determined. Then the adsorption of oxygen at these metal surfaces is studied. Several properties will be addressed: the stable adsorption sites of oxygen atoms, adsorbate-induced structural changes at the surface, and adsorption energies. Further, the dependence of these quantities on the surface coverage will be calculated and the first steps of the oxide formation by the occupation of subsurface sites will be studied. Finally, the obtained results will be compared to data of the bulk oxide. Further reading: W. Koch, M.C. Holthausen, "A Chemist's Guide to Density Functional Theory", Wiley-VCH 2007.

A. Kiejna, B.I. Lundqvist, Phys. Rev. B 63, 85405 (2001).

A. Kiejna, B.I. Lundqvist, Surf. Sci. 504, 1 (2002).

Persons involved: Dr. Behler and coworkers

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8. Computational chemical kinetics and thermodynamics Required skills: Successful participation at the „Theoretisch-Chemisches Praktikum“ (optional course in 6. semester of the program for a bachelor in chemistry) or an equivalent practical course in computation or theoretical chemistry. Short description of the experiment: You will use computational electronic structure methods to determine a reaction path and the transition state for a typical reaction from organic or inorganic chemistry. By visualising and analysing the frontier orbitals you will investigate in detail the reaction mechanism. Modern computational chemistry techniques will then be used to compute the Gibbs free enthalpies of the educt, product and the transition state and to predict as accurate as possibly the reaction and activation enthalpies of the reaction. To calibrate the accuracy of the computed results it will be investigated how the results depend on the employed electronic structure methods and basis sets. For a spectroscopic characterisation of the products and educts you will compute there vibrational normal modes and frequencies and simulate their IR spectra. The aim of this computer experiment is to learn how chemical reactions can be modeled with quantum chemical electronic structure methods and to apply the most important methods at a typical example. Further reading: Chapters 11,12 & 14 in: F. Jensen, Introduction to Computational Chemistry, Verlag J. Wiley, Weinheim. Persons involved: Prof. C. Hättig and coworkers

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9. Atomic Layer Deposition (ALD) of Functional Metal Oxides Required skills: (i) Experience in handling air sensitive compounds, (ii) basic knowledge in handling vacuum apparatus, (iii) basic understanding of surface analysis/spectroscopy Short description of the experiment: ALD is a chemical process for the deposition of ultrathin layers on surfaces. It has growing importance in many areas of surface and interfacial nanochemistry. In particular, ALD plays a major role in the fabrication of microelectronic and nanoelectronic devices. ALD relies on sequential and saturating surface reactions of the alternatively applied precursors. Suitable volatile molecular precursors are pulsed with a carrier gas in a computer controlled process at reduced pressure onto the substrate surface. In contrast to chemical vapour deposition (CVD), this is a surface controlled process where the substrate is alternately and separately exposed to different vapour phase precursors. The precursor pulses are separated by inert gas purges to eliminate gas-phase reactions and remove volatile by-products. Growth proceeds in a cyclic manner, which makes the thickness control accurate and simple. The basic principle of ALD is the self-limiting surface reaction that takes place between two precursors (typically). ALD is now a mature technique and is closely linked with heterogeneous catalysis. Adsorption, reaction and desorption are the typical steps involved. However, at the gas/solid interface a coating or thin film is left behind as a reaction product and the by-products are desorbed with a purge gas and removed. The strength of ALD technology lies in its capability to produce high-quality, dense and pinhole-free films on large and complex surfaces with excellent conformality and uniformity as well as thickness and composition control at an atomic level. ALD is particularly suitable for materials such as metal oxides (for e.g. Al2O3, HfO2, Ln2O3, and ternary oxides), which find applications as dielectrics for MOSFET and related devices. In the context of a concrete research-based case study, a completely developed ALD experiment (e.g. HfO2, Gd2O3) will be performed on an ASM-F-120 Research Reactor including the characterisation of the obtained layers using different surface analytical techniques with partners within the IFSC-RD. Objectives: ALD principle, reactor design, experimental setup, programming, sample preparation, analytical characterisation: XRD, XRR, SEM, AFM, Ellipsometry. Perspective: The experiment also offers the option of introducing the field of ALD with research partners in the Netherlands or in Forschungszentrum Jülich. Further reading: Chem. Rev. 2010, 110, 111–131 Angew. Chem. 2003, 42, 5548, Phys. Stat. Sol. (a) 2004, 201, 1443 Persons involved: Jun. Prof. Dr. Anjana Devi, Ke Xu.

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10. Phosphatidylinositol mediated assembly of protein complexes at lipid membranes and analysis of protein induced membrane deformation Required skills: Curiosity Short description of the experiment: Phosphatidylinositols are an integral part of natural lipid membranes. Phosphatidylinositols are characterized by different phosphorylation-patterns of the inositol head group. Several protein domains (PH-, PDZ-, Phox-domains) have evolved being able to bind selectively to specific phosphatidylinositols.

Given the fact that within a cell different phosphatidylinositols are localized at different membrane compartments, phosphatidylinositols are main regulators of selective protein complex assembly on membranes. Within this experiment we will demonstrate the selective binding of proteins to lipid membranes mediated by phosphatidylinositols in vitro and in vivo. For the in vitro experiments we will perform liposome-binding assays and for in vivo analysis we will apply Fluorescence-microscopy. In order to show phosphatidylinositol dynamics we will purify a phosphatidylinositol-phosphatase and determine its activity in an in vitro dephosphorylation assay. In the second part of the experiment we address the fundamental question how nature bends (shapes) lipid membranes into such important structures like tubes or vesicles. Again phosphatidylinositols play here a crucial role contributing to the assembly of certain membrane deforming proteins containing BAR or F-BAR domains. In this experiment we will also analyze these properties by in vitro and in vivo experiments. Further reading:

Di Paolo, G. and De Camilli, P. Phosphoinositides in cell regulation and membrane dynamics Nature, 443, 651-657 (2006)

Erdmann, K.S., Mao, Y., McCrea, H.J., Zoncu, R., Lee, S.Y., Summer, P., Modregger, J., Biemesderfer, D., Toomre, D., and De Camilli, P. A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway. Dev. Cell, 13, 377-390 (2007) Itoh, T., Erdmann, K.S., Roux, A., Habermann, B., Werner, H., and De Camilli, P. Dynamin and the actin cytoskeleton cooperatively regulate plasma membrane invagination by BAR and F-BAR proteins. Dev. Cell, 9, 791-804 (2005) Persons involved: PD Dr. Erdmann, Nina Hagemann, Nadine Ackermann

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11. Redox-active monolayers – Self assembly and electrochemical characterization. Required skills: Chemistry background Short description of the experiment: Immobilisation of redox enzymes in their active form on an electrode surface is of keen interest in bioelectrocatalysis, biosensors, biofuelcells and nanobiotechnology. In this experiment, redox-active biocatalytic systems will be tethered in a controlled orientation on electrode surfaces via affinity binding or click chemistry. The electrode surface modification will involve 4 steps. The affinity binding constants, the surface concentrations and the kinetics of electron transfer within the self-assembled monolayers will be determined by cyclic voltammetry. Further reading: (1) Chaga, G. S. J. Biochem. Biophys. Methods 2001, 49, 313-334. (2) Blankespoor, R.; Limoges, B.; Schöllhorn, B.; Syssa-Magalé, J.-L.; Yazidi, D. Langmuir 2005, 21, 3362–3375. (4) Balland, V.; Lecomte, S.; Limoges B. Langmuir 2009, 25, 6532-6542. (5) Balland, V.; Hureau, C.; Cusano, A. M.; Liu, Y.; Tron, T.; Limoges B. Chem. Eur. J. 2008, 14, 7186-7192. (5) Demin, S.; Hall, E. A. H. Bioelectrochemistry 2009 76 19–27. Persons involved: Dr. Nicolas Plumeré, Dr. Magdalena Gebala.

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12. Synthesis and characterisation of Short Metallo-Peptides Required skills: None Short description of the experiment: We know many naturally occurring peptides which exhibit antibacterial activity. Usually these are oligo-peptides with at least 20 amino acids or cyclic peptides. Many of these peptide antibiotics disrupt the function or structure of the bacterial membrane. A few years ago it was shown that comparably short peptides can have significant antibacterial activity. However, little is known about their mechanism of action. In analogy to naturally occurring antibiotic peptides interactions with the bacterial membrane were suspected, with some evidence that positively charged and sterically demanding amino acids are critical to the peptides' activity. We could show that the introduction of metal complexes not only increased antibacterial activity of small peptides, but altered the activity profile regarding specificity for Gram-positive and Gram-negative bacteria. We were not yet able to define a coherent structure activity relationship. In this experiment, using a computer controlled peptide synthesizer, two peptides will be synthesized, one of which will be modified with a metallocene at the N-terminus. After cleavage and lyophilization, the peptides will be purified by HPLC and characterized by mass spectrometry (MALDI-MS using the new IFSC instrument) and 2D- NMR spectroscopy (Metzler-Nolte Lab). In the laboratory of Prof. Bandow peptides will be tested for their minimal inhibitory concentration (MIC) against different bacterial strains and compared to classical antibiotics. Further reading: S.I. Kirin, F. Noor, N. Metzler-Nolte, W. Mier, Manual solid phase peptide synthesis, J. Chem. Educ. 2007, 84, 108-111. J.M. Andrews, Determination of minimum inhibitory concentrations, J. Antimicrob. Chemother. 2001, 48 (Suppl. 1), 5-16. J. Chantson, M.V. Varga Falzacappa, S. Crovella, N. Metzler-Nolte, Solid phase synthesis, characterisation and anti-bacterial activity of metallocene-peptide bioconjugates, ChemMedChem 2006, 1, 1268-1274. Persons involved: Prof. Nils Metzler-Nolte (Fak. für Chemie und Biochemie) and coworkers Jun. Prof. Dr. Julia Bandow

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13. Immobilization of reagents and bioactive molecules on polymers Required skills: Basic organic chemistry laboratory as well as analytical skills. Short description of the experiment: Reagents and scavenging agents immobilized on polymers are powerful tools for solution phase organic and combinatorial chemistry. In fact, an immobilized reagent can be filtered off after reaction completion (scheme 1a), or excess reagent can be sequestered by an immobilized scavenger and easily removed from the reaction mixture by filtration (scheme 1b). The strengths of the immobilization approach are (a) the advantage of the solution phase, (b) the convenience of the solid phase, and (c) no chromatography. However, there are some limitations such as the low loading of the polymer. Moreover, the strategy for covalent immobilization should be efficient and not alter the chemical properties and reactivity of the compound.´Bioactive molecules such as peptides and proteins can also be covalently attached to polymers and used for affinity chromatography, molecular recognition and biomedical applications. One example is given by the bulk or surface modification of polyurethanes with signalling proteins or peptides to obtain biomimetic materials with good biocompatibility and suitable for long term medical implants. Some of the immobilization strategies simplified in scheme 1c as well as polymer functionalizations will be investigated during the practical.

Scheme 1. Use of polymer-immobilized reagents (1a) and scavengers (1b), and chemical strategies for polymer functionalization (1c). Further reading: Kirschning, A. et al. Functionalized Polymers - Emerging Versatile Tools for Solution-Phase Chemistry and Automated Parallel Synthesis. Angew. Chem. Int. Ed. 2001, 40, 650. Fournier, D., Du Prez, F. “Click” Chemistry as a Promising Tool for Side-Chain Functionalization of Polyurethanes. Macromolecules 2008, 41, 4622. Bonnet, D. et al. Solid-Phase Organic Tagging Resins for Labeling Biomolecules by 1,3-Dipolar Cycloaddition: Application to the Synthesis of a Fluorescent Non-Peptidic Vasopressin Receptor Ligand. Chem. Eur. J. 2008, 14, 6247. Persons involved: Prof. Dr. C. Cabrele, F. Zanta (PhD student)

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14. Investigations on the kinetics of the so called SOAI reaction Required skills: Profound knowledge of synthetic organic chemistry in theory and practice Short description of the experiment: The addition of diisopropylzinc to pyrimidinecarb-aldehydes, presented by Kenso Soai in 1987[1,2] leads to spontaneous chiral symmetry breaking. This behaviour was long time only known from this example, until 2007 Tsogoeva et al. reported on the same effect in Asymmetric Mannich and Aldol Reactions"[1]. By now it seems that this finding could be of a general nature. Many reactions, so far considered as "boring simple", exhibit interesting behaviour in the sense of chemical systems. The practical will consist of three parts: 1. Synthesis of the precursors (synthetic organic chemistry) 2. Performing of reactions and monitoring kinetics and possible chiral imbalances via NMR and polarimetry 3. Analysis of the data using computer simulation and fitting (SIMFIT) and statistics Further reading: K. Soai, S. Niwa, H. Hori, J. Chem. Soc. Chem. Commun, 1990, 982. Singleton D. A., Vo L. K., J. Am. Chem. Soc. 2002; 124, 10010. M. Mauksch, S. B. Tsogoeva, S. Wei, I. M. Martynova, Chirality 2007, 19, 816. Persons involved: Prof. Dr. G. von Kiedrowski, Arne Dieckmann

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15. Circular Dichroism and protein folding Required skills: Some background in protein biochemistry Short description of the experiment: The aim of the present practical course is to provide an overview on the molecular basis of optical activity and, mainly, on its application to the circular dichroism (CD) of proteins. The course will help the students understand the theory behind the analysis of secondary and tertiary structure, stability and interactions of proteins by use of CD spectroscopy. More, the interplay between structure and function will be analyzed, by investigating the activity of enzymes under identical conditions, using UV/VIS or fluorescence-based assays. Special topics:

Investigation of protein secondary/tertiary structure from far-UV/near-UV CD.

Study of thermal and/or chemical unfolding and refolding in terms of thermodynamics and kinetics by using steady-state and stopped-flow CD.

Investigation of association-induced structural change and determination of binding constants.

Analysis of mutation-induced changes in protein structure.

Influence of different co-solvents on protein structure and stability.

Enzyme activity and the influence of structural changes.

The students will have the opportunity perform several types of investigations from the ones mentioned above, depending on their ability to accumulate the information and perform the experiments, but also on their particular/special interests. More, the students are welcome to propose/ask for new issues that would be interesting for them and the supervisor will try to answer their requests. Thus, the students are encouraged to communicate and to get involved in the experiments. Nevertheless, at the end of the practical course, the student should be able to perform different types of CD measurements, to deconvolute the far-UV CD-spectra in terms of secondary structure elements and to analyze the influence of different factors on protein structure, stability and function in terms of thermodynamics and kinetics. Further reading: C.P.M. van Mierlo et al. (2000) Circular Dichroism of Proteins in Solution and at Interfaces, Applied Spectroscopy Reviews, 35, 277-313.

Brenda A. Bondesen and Merlyn D. Schuh (2001) Circular Dichroism of globular proteins, Journal of Chemical Education, 78, 1244-1247.

Sharon M. Kelly and Nicholas C. Price (1997) The application of circular dichroism to studies of protein folding and unfolding, Biochimica et Biophysica Acta, 1338, 161-185.

Persons involved: Dr. Diana Constantinescu, Prof. Christian Herrmann

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16. Synthesis, characterization and modeling of porous coordination polymers Required skills: • Experience in basic inorganic and organic synthesis • Knowledge in physical chemistry (spectroscopy etc.) Short description of the experiment: The students will work in a lab rotation style in a collaborative research environment between groups in Technical and Inorganic Chemistry on new fascinating porous coordination polymers, aka MOFs. These systems have tunable pore space which can be filled with guest molecules. The students will accompany the researches in their work, allowing them an insight into the actual research from different points of view. This includes synthesis of MOF materials including the basic characterization, the computational modeling of such systems with respect to structure, dynamic and hot-guest interactions and the in depth spectroscopic characterization by IR methods. Further reading: Ferey, G. “Hybrid porous solids: past, present, future”, Chem. Soc. Rev. 2008, 37, 191. Tafipolsky, M.; Amirjalayer, S.; Schmid, R. “Atomistic Theoretical Models for Nanoporous Hybrid Materials”, Micropor. Mesopor. Mater. 2010, 129, 304. Wang, Y.; Glenz, A.; Muhler, M.; Wöll, Ch. “A new dual-purpose ultrahigh vacuum infrared spectroscopy apparatus optimized for grazing-incidence reflection as well as transmission geometries”, Rev. Sci. Intruments 2009, 80, 113108. Prestipino, C.; Regli, L.; Vitillo, J. G.; Bonino, F.; Damin, A.; Lamberti, C.; Zecchina, A.; Solari, P. L.; Kongshaug, K. O.; Bordiga, S. “Local Structure of Framework Cu(II) in HKUST-1 Metallorganic Framework: Spectroscopic Characterization upon Activation and Interaction with Adsorbates”, Chem. Mater. 2006, 18, 1337. Persons involved: PD Dr. Rochus Schmid (AC) Prof. Dr. Roland A. Fischer (AC) Dr. Yuemin Wang (TC) Prof. Martin Muhler (TC)

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17. Ion clustering of ionic liquids in weakly polar solvents Required skills: Some background in Physical Chemistry II Short description of the experiment: The aim of the present practical course is to provide an overview on modern techniques in solution chemistry and their application to the study of ion clustering in solution. The course will help the students understand elementary steps of chemical reactions in solutions of charged species. Specifically, the ion clustering and ion dynamics will be analyzed by investigating the interplay between the viscosity, electrical conductivity and dielectric response of ionic liquids in solution.

Special topics:

Understanding properties of ionic liquids.

Understanding the interplay between viscosity and electrical conductivity and the underlying molecular processes in an electrolyte solution.

Understanding ion pair formation and ion clustering in solutions and its effect on chemical reactions.

Understanding the principles of dielectric spectroscopy. The students will have the opportunity perform several types of experiments, determining transport coefficients at the macroscopic level (electrical conductance, viscosity) and at the microscopiy level observing picosecond ion dynamics (dielectric spectroscopy). The results will be combined to obtain a comprehensive understanding of the species distribution of ionic liquids in weakly polar solvents. Further reading:

1. H. Weingärtner, “Zum Verständnis ionischer Flüssiglkeiten auf molekularer Ebene”, Angew. Chemie, 2008, 120, 664-682; or English version: “Understanding ionic liquids at the molecular level”, Angew. Chemie Int. Ed., 2008, 47, 654-670.

R. Buchner and G. Hefter, “Interactions and dynamics in electrolyte solutions by dielectric spectroscopy”, Phys. Chem. Chem. Phys., 2009 Persons involved: Prof. Weingärtner and Coworkers

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18. Microfluidic investigation of a DNA amplification system Required skills: A basic understanding of chemical kinetics and autocatalysis, DNA hybridization in solution, some prior experience with electrophoresis (e.g. biochemistry practical) and fluorescence spectroscopy and/or microscopy are required. Additionally some exposure to fluid dynamics, electrokinetics or electrochemistry might be helpful. Short description of the experiment: The aim of the experiment is to investigate a chemical system (without enzymes) that allows exponential amplification of oligonucleotides under isothermal conditions using microfluidics and online fluorescence monitoring as a function of starting template concentration and reaction conditions and to validate the reaction cycle products by use of Capillary Gel Electrophoresis (CGE). The reaction will be performed in parallel in microfluidically generated droplets or under flow conditions in microchannels. The reaction cycle for conformational autocatalytic amplification of DNA complexes was recently published by Zhang et al. (Science 318, 1121 (2007)). In our implementation, an autocatalyst (34mer oligomer) interacts with a substrate consisting of a terplex (50mer “template”, 34mer “autocatalyst” and 36mer “signal”-oligomer) releasing a free “signal”-oligo (36mer). This signal then combines with the “reporter” (duplex, one 20mer labelled with Alexa 488 and one 30mer labelled with Dabcyl) leading to an increase of fluorescence as the signal displaces the Alexa labelled oligonucleotide. In the next step the newly formed terplex (template, 2 x autocatalyst) releases both autocatalysts as the fuel (a 44mer) combines with the template. So in each reaction cycle the amount of autocatalyst is doubled and the consequence is an exponential increase in fluorescence intensity.

The schematic view shows the selected part of one microfluidic structure that has been used for the measurements of the autocatalytic reaction. The red colored squares inside the blow-up fluorescence snapshot taken after 1600 s under stop flow conditions indicate the used measuring fields within the optical field of view. The diagram shows the progress of the reaction cycle at 37°C with different flow rates. Channel 1 (substrate): 2*10-7 M (Poly T

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Oligo AF 647): 1*10-6 M; Channel 2 (fuel): 2.6*10-7 M, (autocatalyst) 2.0*10-7 M, (reporter AF 488, Dabcyl) 4.0*10-7 M (Poly T Oligo) 2*10-6 M

Further reading: David Yu Zhang, Andrew J. Turberfield, Bernard Yurke and Erik Winfree, Science Vol. 318. no. 5853 (2007) pp. 1121 – 1125. Microfluidic integration of an autocatalytic amplification system: http://www.istpace.org/Web_Final_Report/WP_6_microfluidic_complementation/microsystem_implementation_/replication/microfluidic_integration_of_2.html Persons involved: Prof. Dr. John S. McCaskill and Dr. Patrick Wagler

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19. Synthesis of a task specific ionic liquid

Required skills: General safety knowledge and lab skills Short description of the experiment: Ionic Liquids (ILs) are salts with a melting point below 100°C. Many of them are even liquid at room temperature and below. They are composed of organic cations and organic or inorganic anions. By the choice of the cation/anion combination many of the chemical and physicochemical properties such as melting point, thermal stability, salvation power etc. can be tuned. Die most prominent IL cations are alkylphosphonium, alkylammonium, N,N‘-dialkylimidazolium as well as N-dialkylpyridinium cations. Frequently used anions include [BF4]

-, [PF6]- und [SbF6]

-, alkylsulfates and alkylsulfonates and often perfluorinated anions such as triflate, [CF3SO3]

- or bis(trifluoromethylsulfonyl)amide [(CF3SO2)2N]-. An important property of many ILs is their negligible vapour pressure. Virtually no toxic

or harmful vapours are evaporated and the loss of solvent becomes unimportant. Furthermore ILs have an extremely low flammability. Many transition metal catalysts have quite a high solubility in ILs and can be immobilized in the IL. In contrast dissolution of organic compounds can be low. This allows to run a two-phase reaction or to distil off the volatile reaction products. The IL can be easily recycled after the reaction. Thus, ILs might be safe and environmentally begnin („green“) replacements of conventional volatile organic solvents. An example of such an eco-certified process is the BASF´s BASIL-process.

Carefully chosen ions and ion combinations allow tuning the properties of an IL for a desired application. We are interested in such task-specific ionic liquids which are / can be used for:

- luminescent ILs - magnetic ILs - liquid crystalline ILs - synthesis of phosphors for lightning applications - Synthesis and stabilization of nanoparticles - Synthesis of metal/metalloxide catalysts

The aim of the experiment is to synthezise an ionic liquid for one of those applications.

1

2

3

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Further reading: Introductory and seminal papers: T. Welton, Chem. Rev., 1999, 99, 2071. P. Wasserscheid, W. Kleim, Angew. Chem. 2000, 112, 3926. C. Chiappe, D. Pieraccini, J. Phys. Org. Chem., 2005, 18, 275. P. Wasserscheid, T. Welton: Ionic Liquids in Synthesis, Wiley VCH, Weinheim, 2007 BASIL-Process: http://www.basionics.com/en/ionic-liquids/ http://www.basf.com/group/corporate/en/innovations/innovation-award/2004/basil Task-specific ILs: J. H. Davis, Chem. Lett. 2004, 33, 1072. Luminescent ILs: S.-F. TANG, A. BABAI, A.-V. MUDRING: Low melting europium ionic liquids as luminescent soft materials, Angew. Chem. Int. Ed. 2008, 120, 7631. S. TANG, A.-V. MUDRING: Terbium-β-diketonate based highly luminescent soft materials, 2009, Eur. J. Inorg. Chem. in press. Magnetic ILs: B. MALLICK, B. BALKE, C. FELSER, A.-V. MUDRING: Dysprosium room temperature ionic liquids exhibiting strong luminescence and response to magnetic fields, Angew. Chem. Int. Ed. 2008, 120, 7635. Nanoparticle Synthesis: K. RICHTER, T. BÄCKER, A.-V. MUDRING: Facile, environmentally friendly fabrication of porous silver monoliths using the ionic liquid N-(2-hydroxyethyl)ammonium formate, Chem. Commun. 2009, 301. T. ALAMMAR, A.-V. MUDRING: Facile ultrasound-assisted synthesis of ZnO nanorods in an ionic liquid, Mat. Lett. 2009, 63, 732. T. ALAMMAR, A.-V. MUDRING: Ultrasound assisted synthesis of CuO nanorods in a neat room temperature ionic liquid, Eur. J. Inorg. Chem. 2009, in press. Ionic Liquid Crystals: A. GETSIS, A.-V. MUDRING: Imidazolium Based Ionic Liquid Crystals:Structure, Photophysical and Thermal Behaviour of [Cnmim]Br•xH2O (n = 12, 14; x=0, 1), Cryst. Res. Technol. 2008, 43, 1187. A. GETSIS, B. BALCKE, C. FELSER, A.-V. MUDRING: Luminescent, magnetic and liquid crystalline behavior of [C12mim]3[DyBr6] and structural characterisation of [C12mim]3[DyBr6]•2CH3CN, Crystal Growth & Design, 2009, in press. Persons involved: Prof. Dr. Anja-Verena Mudring mit MSc. Tobias Bäcker, MSc. Nina v. Prondzinski, Mei Yang, Dr. Sifu Tang

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20. Application and characterization of a task-specific ionic liquid

Tb(III)

ILIL

377 nm

9 C12mimBr : TbBr3

Required skills: General safety knowledge and lab skills Short description of the experiment: Ionic Liquids (ILs) are salts with a melting point below 100°C. Many of them are even liquid at room temperature and below. They are composed of organic cations and organic or inorganic anions. By the choice of the cation/anion combination many of the chemical and physicochemical properties such as melting point, thermal stability, salvation power etc. can be tuned. Die most prominent IL cations are alkylphosphonium-, alkylammoniumionen, N,N‘-dialkylimidazolium as well as N-dialkylpyridinium cations. Frequently used anions include [BF4]

-, [PF6]- und [SbF6]

-, alkylsulfates and alkylsulfonates and often perfluorinated anions such as triflate, [CF3SO3]

- or bis(trifluoromethylsulfonyl)amide [(CF3SO2)2N]-. Carefully chosen ions and ion combinations allow tuning the properties of an IL for a

desired application. We are interested in such task-specific ionic liquids which can be used for the synthesis of phophors and catalysts or have magnetic, luminescent or liquid crystalline properties. The aim of the experiment is to use an ionic liquid for the synthesis of

- Luminescent nanoparticles - Magnetic nanoparticles - Catalytical active nanoparticles - Framework structures

and the subsequent characterization of the reaction product with respect to its materials properties. Further reading: Introductory and seminal papers: T. Welton, Chem. Rev., 1999, 99, 2071. P. Wasserscheid, W. Kleim, Angew. Chem. 2000, 112, 3926. C. Chiappe, D. Pieraccini, J. Phys. Org. Chem., 2005, 18, 275. P. Wasserscheid, T. Welton: Ionic Liquids in Synthesis, Wiley VCH, Weinheim, 2007 Task-specific ILs: J. H. Davis, Chem. Lett. 2004, 33, 1072. Luminescent ILs:

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S.-F. TANG, A. BABAI, A.-V. MUDRING: Low melting europium ionic liquids as luminescent soft materials, Angew. Chem. Int. Ed. 2008, 120, 7631. S. TANG, A.-V. MUDRING: Terbium-β-diketonate based highly luminescent soft materials, 2009, Eur. J. Inorg. Chem. in press. Nanoparticle Synthesis: K. RICHTER, T. BÄCKER, A.-V. MUDRING: Facile, environmentally friendly fabrication of porous silver monoliths using the ionic liquid N-(2-hydroxyethyl)ammonium formate, Chem. Commun. 2009, 301. T. ALAMMAR, A.-V. MUDRING: Facile ultrasound-assisted synthesis of ZnO nanorods in an ionic liquid, Mat. Lett. 2009, 63, 732. T. ALAMMAR, A.-V. MUDRING: Ultrasound assisted synthesis of CuO nanorods in a neat room temperature ionic liquid, Eur. J. Inorg. Chem. 2009, in press. Ionic Liquid Crystals: A. GETSIS, A.-V. MUDRING: Imidazolium Based Ionic Liquid Crystals:Structure, Photophysical and Thermal Behaviour of [Cnmim]Br•xH2O (n = 12, 14; x=0, 1), Cryst. Res. Technol. 2008, 43, 1187. A. GETSIS, B. BALCKE, C. FELSER, A.-V. MUDRING: Luminescent, magnetic and liquid crystalline behavior of [C12mim]3[DyBr6] and structural characterisation of [C12mim]3[DyBr6]•2CH3CN, Crystal Growth & Design, 2009, in press. Persons involved: Prof. Dr. Anja-Verena Mudring mit MSc. Tarek Alammar, Dr. Joanna Cybinska, MSc. Kai Richter, Dr. Guangmei Wang