Seminar Accompanying the Lecture Course "Physical Organic Chemistry"
Course No. 21 221a/b - Modulbeschreibung (Deutsch)
Each student who signs up to the lecture course on "Physical Organic and Supramolecular Chemistry" is required to give a seminar talk of ca. 15 minutes length plus a discussion of the topic. The seminar language is English. The seminars are one of the requirements of active participation in the course, without which you cannot finish the module. So, please choose a semiar topic after the first lecture course. The list of topics and the dates are fixed to my office door.
I offer help for the preparation of your seminars. In order to be able to help, it would be useful, if you would come and see me early on, at least three weeks before the seminar to discuss a concept for the talk. If you wish, we can discuss the direction into which you could go even earlier than that. Approximately one week before the scheduled seminar, it would be advisable to discuss your transparencies.
Please make sure that you take into account the following points to make your seminar interesting and beneficial for all others:
Be absolutely clear: Don't expect your audience to know too much about the topic. In view of the time, reduce the seminar to the really important arguments and concepts. Rather restrict yourselves to a good selection of important points and discuss them in greater detail than trying to make a superficial summery of everything. Choose really illustrative examples. Organize your talks clearly: What argument builds on which other one? How do I introduce each one of them at the appropriate moment? Direct the audience through your talk with (only a couple) of structuring remarks.
Clarity should also be found in your transparencies: Large enough letter size (usually not below 14 pt), not too much text, easy to grasp graphics, if schematic cartoons help to reduce complexity, you can show a molecule, discuss its properties briefly and then explain the concept using cartoons. Nevertheless, don't forget that we are chemists and need to see how the molecules you discuss look like. A cartoon-only talk would not be sufficient!
If you want to use a sheet of paper with short remarks to remind you of what you wanted to say, prepare it in a clear way so that you easily find your way through it. My suggestion would be to prepare the transparencies in a way that they also guide you through the talk.
Use the appropriate scientific language. It is part of your science and you need to be able to use it actively and passively. Name the molecules and things on your transparency by their appropriate names. Reduce for example, IUPAC names to the functional group important in that particular moment. But don't say: "This thing here...", if the molecule can be easily given a more suitable name.
Restrict yourselves to a small number of well-chosen examples. They should perfectly illustrate your points. Don't try to make the collection complete (even if that would match the Germans' need for "Gründlichkeit"). Your audience will be able to transfer the things learnt with the help of a well-chosen and well-explained example to others they encounter. A too large number of examples reduces the time for going into detail and makes the discussion superficial. You have then seen many examples without really understanding a single one ...
You do not need to prepare a handout for your fellow students, if you agree to send my your presentation by email as a pdf file after your talk. I will make it available below by linking the titles to your presentations so that everyone can download them.
- It is expected that you search for more up-to-date literature of your topic. Below you will find a few key words and some introductory literature references for your orientation. This alone is certainly not enough, though.
Part I: Potential Energy Surfaces and Molecular Orbitals
singlet and triplet states, generation of singlet oxygen, reactivity, typical synthetically useful reactions
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what mechanistic ideas exist of Cytochrome P-450-catalyzed reactions: oxygen rebound mechanism, radical clocks, oxen mechanism, the principle of spin conservation, two state reactivity under spin inversion
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concerted, synchronous, and stepwise reactions, what are reaction trajectories, energy redistribution within a molecule, refinement of the static model of potential energy surfaces by invoking dynamic effects, their threoretical prediction and how to demonstrate them experimentally.
- B.K. Carpenter, Angew. Chem. 1998, 110, 3532
Part II: Thermochemistry
how to measure activation enthalpies and entropies, definition: activation volume, how to determine it, comparison of temperature and pressure dependence of chemical reactions, electrostriktion, a good example for illustrating are pericyclic reactions
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Part III: Short-Lived Intermediates and Funny Molecules
norbornyl-, methylcyclopropyl cations, mono- and diprotonated methane, ethylene dication, structures and properties
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properties of fullerenes (e.g. structure, redox chemistry, aromaticity), synthesis, reactivity (e.g. Bingel reaction, cycloadditions), endohedral complexes
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Li2CF2 Wanzlick and Arduengo carbenes, which factors make a carbene stable? the use of stable carbenes as ligands for transition metals
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Li2CF2 calculations, Zr/Al compounds, fenestranes
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Principles of femtosecond chemistry, examples of simple reactions
NRMS principle, vertical electron transfers, Franck-Condon factors, examples may include: carbonic acid, ylides, water oxide
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the principle of matrix isolation spectroscopy, examples may include: didehydro benzene, dioxiranes, tetrahedrane
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Part IV: Stereochemistry
Biotic and Abiotic Theories, statistical fluctuations with autocatalysis, chirality through non-symmetric processes on elementary particle level?
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- M. Avalos, R. Babiano, P. Cintas, J.L. Jimenez, J.C. Palacios, Chem. Commun. 2000, 887
what are non-linear effects in asymmetric catalysis? models for their description and a few interesting examples
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molecules and graph theory, topology, topological chirality e.g. with catenanes, rotaxanes, and knotanes
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CD spectroscopy, linearly and circularly polarized light, why do chiral substances turn the plane of the light?
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- A.B. Buda, T. Auf der Heyde, K. Mislow, Angew. Chem. 1992, 104, 1012
- The program emanim can be used to animate electromagnetic waves. Please also see the animated tutorial! Should the program not be available anymore, I can provide it as well.
Part V: Aromaticity and Pericyclic Reactions
how can one understand aromatic stabilization of systems extended in three dimensions? the tetradehydroadamantane dication diradical is such a molecule
- A.A. Fokin, B. Kiran, M. Bremer, X. Yang, H. Jiao, P.v.R. Schleyer, P.R. Schreiner, Chem. Eur. J. 2000, 6, 1615
- R.B. King, Chem. Rev. 2001, 101, 1119
detailed explanation of the construction of correlation diagrams for dis- and conrotatory electrocyclic ring opening of cyclobutene, why can one restrict the discussion to the frontier molecular orbitals, experimental proof of principle through sterochemical effects
- R.B. Woodward, R. Hoffmann, Die Erhaltung der Orbitalsymmetrie, VCH, Weinheim 1970
- T.L. Gilchrist, R.C. Storr, Organic Reactions and Orbital Symmetry, Cambridge University Press, Cambridge 1979
what are coarctate transition structures?, comparison to pericyclic reactions, topology and symmetry, predictive rules, mechanisms, stereochemistry
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Part VI: A Few Concepts Relating to Synthesis and Catalysis
how can the kinetics of a catalytic reaction be described? what do parameter such as kcat, KM and vmax mean?
- Biochemistry textbooks
what is organocatalysis? which mechanisms exist? organocatalysis through hydrogen bonding, organocatalysis through covalent intermediates, a few interesting and useful examples
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how can selectivity be obtained with highly reactive radicals? are there stereocontrolled radical reactions?
- T. Linker, M. Schmittel, Radikale und Radikalionen in der Organischen Synthese, Wiley-VCH, Weinheim 1998
- D.P. Curran, N.A. Porter, B. Giese, Stereochemistry of Radical Reactions, Wiley-VCH, Weinheim, 1996
- K.C. Nicolaou, E.J. Sorensen, Classics in Total Synthesis, Wiley-VCH, Weinheim, 1996, therein Chapter 23 - total synthesis of hirsutene and capnellene
- C.P. Jasperse, D.P. Curran, T.L. Fevig, Chem. Rev. 1991, 91, 1237
short summary of radiative and non-radiative processes, chromophores, absorption and emission spectroscopy, energy/elektron transfer processes e.g. in Ru/Os complexes (FRET), cis/trans isomerzation of stilbene and azobenzene, preparative applications
- G. v. Bünau, T. Wolff, Photochemie, Wiley-VCH, Weinheim 1987
- M. Volgraf, P. Gorostiza, R. Numano, R.H. Kramer, E.Y. Isacoff, D. Trauner, Nat. Chem. Biol. 2005, 2, 47
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Part VII: Solvent Effects
phase transfer catalysis: crown ethers, tetraalkylammonium salts, perfluorinated solvents (two-phase system organic-perfluorinated), their use for purification and in homogenous catalysis
- B. Betzemeier, P. Knochel, Top. Curr. Chem. 1999, 206, 61
- E. Dehmlow, Angew. Chem. 1974, 86, 187
- D.P. Curran, Angew. Chem. 1998, 110, 1230
Part VIII: Supramolecular Synthesis
definition of "Template", examples: synthesis of crowns and interlocked molecules with template effects based on metal coordination and hydrogen bonding (Sauvage/Stoddart/Vögtle)
- F. Diederich, P.J. Stang, Templated Organic Synthesis, Wiley-VCH, Weinheim 2000
- C.A. Schalley, T. Weilandt, J.Brüggemann, F. Vögtle, Top. Curr. Chem. 2004, 248, 141
- D.H. Busch, Top. Curr. Chem. 2005, 249, 1
definition of "self-assembly" and "self-organization: where are the differences (ask me about them...)?, metallo-supramolecular compounds are interesting and useful examples here (e.g. helicates, grids, tetrahedra etc.)
- J.S. Lindsey, New J. Chem. 1991, 15, 153
- G.M. Whitesides, J.P. Mathias, C.T. Seto, Science 1991, 254, 1312.
Applying the principles of molecular self-assembly to larger objects from a micrometer to centimeter scale
- G.M. Whitesides, B. Grzybowski, Science 2002, 295, 2418
- N.B. Bowden, M. Weck, I.S. Choi, G.M. Whitesides, Acc. Chem. Res.2001, 34, 231.
How self-assembly reactions can be controlled: Programming molecules by self-sorting processes, narcissistic and the two types of social self-sorting, programmed pseudorotaxanes
- P. Mukhopadhyay, A. Wu, L Isaacs, J. Org. Chem. 2004, 69, 6157
- K. Mahata, M.L. Saha, M. Schmittel, J. Am. Chem. Soc.2010, 132, 15933.
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Multivalency, cooperativity, how does a repetition of binding sites around a molecular tether increase binding strength? Why does entropy usually interfere in a negative way making multivalent binding negatively cooperative? Stoddarts molecular elevator and its assembly kinetics, how to assess chelate cooperativity by double mutant cycles
- J.D. Badjic, S.J. Cantrill, J.F. Stoddart, J. Am. Chem. Soc. 2004, 126, 2288
- J.D. Badjic, A. Nelson, S.J. Cantrill, W.B. Turnbull, J.F. Stoddart, Acc. Chem. Res.2005, 38, 723.
- C.A. Hunter, H.L. Anderson, Angew. Chem. Int. Ed.2009, 48, 7488.
Part IX: Molecules with Function
non-covalent binding of anions to receptor molecules, solvent effects (e.g. water versus other less polar solvents), why is anion binding more difficult as compared to cation binding and the binding of neutrals?, Hofmeister series
- F. Schmidtchen, Top. Curr. Chem. 2005, 255, 1
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basic principles of FRET, what questions can be answered? determination of binding constants, determination of distances, artificial light-harvesting complexes
- V. Balzani, M. Venturi, A. Credi, Molecular Devices and Machines, Wiley-VCH, Weinheim 2003
- C.-C. You, C. Hippius, M. Grüne, F. Würthner, Chem. Eur. J. 2006, 12, 7510
- A.L. Belvin, Y. Creeger, G.W. Fisher, B. Ballou, A.S. Waggoner, B.A. Armitage, J. Am. Chem. Soc.2007, 129, 2025
- Internet-based calculation tools for photochemistry (incl. FRET calculator)
Fluorescent sensors with optical readout, molecular logic gates, quartz-microbalance-based gravimetric sensors, Sauerbrey equation, pattern recognition, a few nice examples
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- M. Schlupp, T. Weil, A.J. Berresheim, U.-M. Wiesler, J. Bargon, K. Müllen, Angew. Chem. Int. Ed. 2001, 40, 4011
Cram's carcerands, Rebek's self-assembling and self-complementary hydrogen bonded capsules, dynamic guest encapsulation, catalysis of Diels-Alder reactions inside the cavity
- C.A. Schalley, Chem. unserer Zeit 2001, 35, 166
- D.J. Cram, M.E. Tanner, Angew. Chem. 1991, 103, 1048
- R. Warmuth, J. Inclusion Phenom. Macrocyc. Chem. 2000, 37, 1
- M.M. Conn, J. Rebek, Jr., Chem. Rev. 1997, 97, 1647
- J. Rebek, Jr., Chem. Soc. Rev. 1996, 255
DNA replication, RNA world, self-replication of oligonucleotides, peptides and organic minimal replicators, kinetic analysis: square-root-law, prion proteine: self-replication of conformations?
- E.A. Wintner, M.M. Conn, J. Rebek, Jr., Acc. Chem. Res. 1994, 27, 198
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- G. von Kiedrowski, Bioorg. Chem. Frontiers 1993, 3, 113
catenanes, rotaxanes as switches, molecular shuttles, light-driven machines, logic gates
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radioimmunoassays: how do they work? where are they used?, disadvantages, Europium luminescence, time-resolved luminiscence spectroskopie antenna molecules, properties requires for medical purposes
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Part X: Bioorganic-Chemistry-Related Topics
the principle: how do we get antibodies to reduce the barrier of a chemical reaction, transition state analoga, preparation of monoclonal antibodies, nice examples for chemical reactions catalyzed by antibodies
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- P.G. Schultz, R.A. Lerner, Acc. Chem. Res., 1993, 26, 391
- C. Rader, B. List, Chem. Eur. J., 2000, 6, 2091
peptide bond, primary, secondary, tertiary and quatenary structure of proteins, helix bundles, how can we template peptide folding in artificial systems
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- G. Trojandt, U. Herr, K. Polborn, W. Steglich,Chem. Eur. J. 1997, 3, 1254
active and passive transport, dependence on energy supply, how does water go through a membrane pore without letting protons pass?
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- J.C Skou, Angew. Chem. Int. Ed. 1998, 37, 2320
a very brief introduction into the natural photosynthesis center (only those features which are needed for the explanation of the artificial one!!! Don't loose yourselves in the details!!!), artificial photosynthetic molecules and their work principles (the Moore article below delivers a particularly nice example!)
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- H. Kurreck, M. Hüber, Angew. Chem. 1995, 107, 929
- G. Steinberg-Yfrach, J.-L.Rigaud, E.N. Durantini, A.L. Moore, D. Gust, T.A. Moore, Nature 1998, 392, 479