Seminar Accompanying the Lecture Course "Physical Organic Chemistry"
Course No. 21 221a/b - Modulbeschreibung (Deutsch)
Tips for the Preparation of Good Talks
Each student in the course needs to give a ca. 20 minutes seminar talk in English (not including the following discussion of the topic) to fulfill the requirements of of active participation. Please choose a semiar topic by inserting your name and matriculation number in this Google Spreadsheet. Below you find some introductory information for each topic and literature to start with.
For the preparation of an excellent talk, you may follow this advice:
A scientific talk is not merely bringing knowledge to someone else's attention. Go beyond a mere fact-after-fact presentation. The function of a talk is at least as much to fascinate about science. Thus, tell us a scientific story with a clear storyline and a climax close to the end. Of course, it is not a political speech either. This is similar with scientific manuscripts not being only a collection of data and facts. It is important to go beyond that and to fine-tune what you write - until it has become a dense piece of scientific literature, where every single word has found exactly the position where it belongs and none of it is superfluous. A paper should be a joy to read and a talk should be a joy to listen to…When you prepare a talk, follow the following steps:
Part I: How to Work Out a Good and Clear Structure of Your Talk
- Get an overview of the topic that you are going to talk about. Read the literature that I cited on the homepage and search additional literature, if you feel uncertain, whether everything is clear.
- Consider for what audience you are preparing the talk. The general public is different from the audience in a specialized master course, which again differs from that of a group of true, world-leading experts of a small subfield in your specialized area of research work as you may meet it on a conference. For the course, you may need to give a more detailed introduction of the background than you would do for the expert audience. On the other hand, you do not need to explain anymore, what a carbon atom is.
- Distill the major core idea out of what you have read and about which you wish to talk. Note it in writing as clearly as possible.
- Now work backwards: What do you need to introduce as the background/state-of-the art to make this core idea understandable to the audience? How can you start from knowledge that your audience already has to anchor the new aspects to it. This is absolutely important for learners. This goes into the introduction of the talk
- Starting from that background, in which logical steps can you unfold the core idea so that the logical sequence of arguments is as easy to follow as possible? Anything that you need to explain as the basis of the core idea needs to be explained before, never afterwards. It is extremely difficult for the audience to follow your arguments, if you say: “We will see that three slides ahead…” Much more easily, the audience can follow, when you say “As explained three slides ago.” This will be the main part of your talk, which culminates in the core idea, which everyone should look at with awe.
- Note the main conclusions, in particular think about conclusions beyond a mere summary. A short summary is useful for the audience to see everything in context again at the end, but there should be one or two more general points detailing, why the topic is important, which impact is has generated or something similar.
- Write down a detailed point-by-point structure of the talk.
- Check this structure: Is there something like an interesting storyline? If not, check, whether you can improve the storyline by rearranging some parts. This would then improve the structure significantly.
Once you have read the literature, all this should take maybe 60 or 90 minutes at maximum.
PART II: How to Design Good Slides
- Once you have considered all these steps from Part I, start preparing the slides by entering one slide for each point of your structure. The only thing that you fill in at this stage is the slide title, no contents yet. This way, you have good control whether your talk reflects properly your intended structure. If there is one aspect, which finally turns out to require two slides, you can still add a few. If you need to add many, the structure hasn’t been good and you may go back to rethink the structure of the talk (see Part I). Then, start to fill in the contents in each slide.
- Text in slides has different functions: On one hand, it reminds you of what you wanted to say. Thus, putting some key words into the slides helps avoiding to have additional paper in your hands and makes it easier for you, because you do not have to look back and forth from the slides to your notes to your slides. On the other hand, imagine that you wish to learn for the exam and have a talk which contains only half-illustrative images. You will have difficulties to learn from that. So, the second function of text is to clearly name the major arguments/conclusions of each slide. Thus, there is no problem to have some text, but do not overdo it. Don’t take my lecture course as an example. It contains too much text to make it easier to follow.
- Each slide should contain only one message. It can contain some data, some experimental results, some remarks on the interpretation of these elements, but all this should lead to only one message on each slide. This is important to avoid overloading of the slides and it enables you to put one line at the bottom of the slide, in which this message is clearly stated.
- Each slide should contribute a new aspect. For example, when issuing reviews, I quite frequently am confronted with talks trying to summarize all the examples mentioned in the review article and we end up with four or five slides for one aspect showing different examples that all illustrate the same point. In talk you should carefully select the most illustrative example and then restrict yourself to it. The next slide may have a different message and a different example may be best to explain that message then, but one slide, one example, one message. This keeps the talk clear and focused, moves forward along your line of arguments and is time-saving.
- Images should be illustrative. Thus, they should be straight to the point that you wish to illustrate. Make sure that you use the literature that you read to get an overview of the topic to identify potential candidates for such images at an early stage. Then, when you organize the structure of your talk you already have examples available that you know you can easily illustrate with images, graphics, data plots etc.
- Develop your own design idea, before you assembly everything. Choose a suitable background, choose a suitable letter fond and letter size, restrict letter sizes to two at maximum three (larger letters for the title, smaller letters for the contents). Keep these settings throughout the whole talk. You can also choose two, but not more than two different fonds, e.g. Calibri for the text on the slides and Arial for the text in the images.
- Assemble all elements (e.g. text, graphics, tables) on each slide in a way that allows you to group according to context (so, for example, the distance between a line of text and an image illustrating this text is smaller than that between two lines of text that belong to different arguments). Don’t waste empty space. Quite frequently, I see slides with a superlarge heading, one tiny little small, but overcrowded image with 6 pt size text in there and two square feet of empty white space around it. This is not useful.
- Also consider imaginary lines. If a line of text belongs to an image, then the image and the text should start e.g. at the same height with the image, if it is left or right of it. It makes a slide unclear, if the text is half a line above the image. So, a good feeling for graphical relations between the elements on your slides may finally help the audience as such arrangements guides their eyes as well.
- Finally, think of a useful series of animations so that not the whole slide is there with the first click. You can more easily develop a thought, of you let different elements appear in a logical sequence.
PART III: The Art of Giving a Talk
- Before you start the talk, decide, where you wish to stand so that everyone can see you AND your slides. Choose a place, which gives you enough freedom to move as you may wake up sleeping audiences, if you decide to change position during the talk. Decide, what you wish to do with your hands (if there is no other option, use the Merkel-Raute as an emergency solution…). Typically, you may have a laser pointer (one hand) and the other hand can then be used for gestures (which normally flow automatically, when you talk). Do not block that second hand by putting it into one of your trouser pockets.
- Breathe deep into the bottom of your lungs. The pressure comes from your diaphragm (Zwerchfell), not from your chest. You will automatically talk louder then with less effort. Pressurizing your breath from your chest even may block some of the bloodstream into your brain and in extreme cases can cause dizziness. Definitively, you feel more comfortable when you do it like a singer or like an oboist and use the diaphragm.
- Avoid monotonous voice. Imaging that what you present might be your own results. You have obtained them in months of hard work, you have put together the complicated puzzle that finally led you to a unified concept which is a breakthrough advancement of chemical science. The audience should thus feel your fascination, your joy, your pride of what you have accomplished. Speak slowly (what appears too slow to you is typically still a little bit too fast for the audience). Pronounce important things more heavily than others. Speak clearly (rather use simple sentences in a somewhat colloquial language than ready-for-print sentences that run over half a page). Most importantly: Avoid pretending to be a scientist! Many people appear to believe that a scientist is an expert, who is able to speak in a severely non-understandable and difficult language full of fancy technical terms and winding sentences and that others would then see and believe and admire the enormous scientific quality of that person. The opposite is true. The audience will appreciate, if you can make yourself understandable in an easy-to-follow way.
- Once you have advanced into a state of “talk-giving” that makes you able to also observe your audience, check whether the audience has glassy eyes. Then, you may interrupt yourself, ask a question in between to wake them up again. It is good to keep eye contact with the audience. Of course you cannot keep eye-contact with everyone, but if you look into the back left corner, then into the center of the middle row, then into the front left corner, then into the middle right, everybody will have the feeling that you are in “silent communication” with them.
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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Cytochrome P-450: two-state-reactivity as a new mechanistic paradigm
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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Reaction Dynamics of Reactive Intermediates: Synergy of Theory
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.
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Frontier Molecular Orbitals
Introduction in detail of Fukui's FMO theory, provide examples for the control of radical reactions as well as polar reactions of nucleophile and electrophile.
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Part II: Thermochemistry
High-Pressure Chemistry: What do Activation Volumes Tell?
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
preparation, geometric and electronic structure of fullerenes, properties (e.g. chirality for higher fullerenes, cavity inside that can be filled with atoms/ions), reactivity (e.g. Bingel reaction, cycloadditions)
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preparation, structure and properties, ways to functionalize
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Non-classical Cations, Superacids and Superelectrophiles
norbornyl-, methylcyclopropyl cations, mono- and diprotonated methane, ethylene dication, structures and properties
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Wanzlick and Arduengo carbenes, which factors make a carbene stable? the use of stable carbenes as ligands for transition metals
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reactions that involve sextett rearrangements (concerted or non-concerted) and intermediates such as carbenes and nitrenes, e.g. Wolff rearrangement (carbenes), Curtius acid degradation to isocyanates (nitrenes), Beckmann rearrangement of oximes (nitrenes), Bayer-Villiger oxidation (oxigen analogue), give an overview with some examples presented in greater detail and compare reactions
- organic chemistry textbooks
Li2CF2 calculations, Zr/Al compounds, fenestranes
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Evidence for Short-Lived Intermediates from Neutralization-Reionization Mass Spectrometry
NRMS principle, vertical electron transfers, Franck-Condon factors, examples may include: carbonic acid, ylides
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go into detail with the experiment how to show evidence for water oxide by NRMS (reviews on the method, see talk above), intro into water oxide vs. hydrogen peroxide, energy difference, barrier height for intramolecular rearrangement, the NRMS experiment, why formation of the radical anion is proof of water oxide and not of hydrogen peroxide.
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Evidence for Short-Lived Intermediates from Matrix-Isolation Spectroscopy
the principle of matrix isolation spectroscopy, examples may include: didehydro benzene, dioxiranes, tetrahedrane
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Part IV: Stereochemistry
Origin of Homochirality
Biotic and Abiotic Theories, statistical fluctuations with autocatalysis, chirality through non-symmetric processes on elementary particle level?
- W.A. Bonner, Top. Stereochem. 1988, 18, 1
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- M. Avalos, R. Babiano, P. Cintas, J.L. Jimenez, J.C. Palacios, Chem. Commun. 2000, 887
molecules and graph theory, topology, topological chirality e.g. with catenanes, rotaxanes, and knotanes
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Chiral Shift Reagents for EE Determination by NMR Spectroscopy
what are NMR shift reagents? How do they help in EE determination?
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Dynamic NMR Spectroscopy for the Investigation of Racemization Processes
describe the basics of temperature-dependent NMR spectroscopy (coalescence phenomenon, coalescence temperature, how to determine the activation barrier in a simple case), then a nice example as e.g. the following:
- S. Belviso, E. Santoro, F. Lelj, D. Casarini, C. Villani, R. Franzini, S. Superchi, Eur. J. Org. Chem. 2018, 4029
- for the basics of dynamic NMR, see NMR textbooks
Non-Linear Effects in Asymmetric Catalysis
what are non-linear effects in asymmetric catalysis? models for their description and a few interesting examples
- C. Girard, H.B. Kagan, Angew. Chem. 1998, 110, 3088
- M. Avalos, R. Babiano, P. Cintas, J.L. Jimenez, J.C. Palacios, Tetrahedron: Asymmetry 1997, 8, 2997
Part V: Aromaticity and Pericyclic Reactions
how can one understand, how can one experimentally demonstrate that there are aromatic systems which carry sp3hybridized carbons in their ring structure? prototypical example: the homotropylium ion
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- R. V. Williams, Chem. Rev. 2001, 101, 1185
Three Dimensional Aromaticity
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
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Bullvalene: A Molecular Shape-Shifter
explain bullvalene, its synthesis, dynamic NMR studies that show that it is dynamic, then present the results from the following paper on a chiral bullvalene
- M. He, J. W. Bode, Proc. Natl. Akad. Sci. USA, 2011, 108, 14752
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Reactions with Coarctate Transition Structures
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
what is organocatalysis? which mechanisms exist? organocatalysis through hydrogen bonding, organocatalysis through covalent intermediates, a few interesting and useful examples
- P. Schreiner, Chem. Soc. Rev. 2003, 32, 289
- B. List, Chem. Rev. 2007, 107, 5413
Modern Radical Reactions
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
Molecular Recognition of Anions
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
- special issue: Coord. Chem. Rev. 2006, 250
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Multivalent and Cooperative Binding
intro: docking of influenza virusses to cells by multivalent binding, the advantages of multivalent binding (enhancement of binding strength and geometric control which for influenza virusses leads to endocytosis), multivalent binding and cooperativity, the different types of cooperativity (allosteric and chelate cooperativity), ways to determine them (double mutant cycle analysis), one nice example
- for influenza docking: C. Fasting, C. A. Schalley, M. Weber, O. Seitz, S. Hecht, B. Koksch, J. Dernedde, C. Graf, E.-W. Knapp, R. Haag, Angew. Chem. Int. Ed. 2012, 51, 10472
- review on cooperativity: L. K. S. von Krbek, C. A. Schalley, P. Thordarson, Chem. Soc. Rev. 2017, 46, 2622
Templated Synthesis: Crown Ethers, Catenanes, Rotaxanes, molecular Knots
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
Self-Assembly and Self-Organization: Creating Complexity from Simple Building Blocks
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.
Hydrogen-Bonded Molecular Capsules and Molecular Tennis Balls
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
Subcompoinent-Self Assembly of MetalloSupramolecular Cages
Nitschke's sub-component self-assembly approach, properties, function and applications of these cages
- D. Zhang, T. K. Ronson, J. R. Nitschke, Acc. Chem. Res. 2018, 51, 2423
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.
Helix Bundles: Folding Mechanisms of Peptides
peptide bond, primary, secondary, tertiary and quatenary structure of proteins, helix bundles, how can we template peptide folding in artificial systems
- C.P.R. Hackenberger, Chem. unserer Zeit 2006, 40, 174
- J. Schneider, J.W. Kelly, Chem. Rev. 1995, 95, 2169
- G. Trojandt, U. Herr, K. Polborn, W. Steglich,Chem. Eur. J. 1997, 3, 1254
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.
- W. Jiang, C.A. Schalley, Proc. Natl. Akad. Sci. USA2009, 106, 10425.
Part IX: Molecules with Function
Fluorescence Resonant Energy Transfer
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 based on fluorescent rreceptors, quartz-microbalance-based gravimetric sensors, Sauerbrey equation, pattern recognition, a few nice examples
- A.P. de Silva, N.D. McClenaghan, Chem. Eur. J. 2004, 10, 574
- A.P. de Silva, H.Q.N. Gunaratne, C.P. McCoy, Nature 1993, 364, 42
- M. Schlupp, T. Weil, A.J. Berresheim, U.-M. Wiesler, J. Bargon, K. Müllen, Angew. Chem. Int. Ed. 2001, 40, 4011
Europium- and Terbium-Containing Luminescent Complexes:
Replacement for Radioimmunoassays?
radioimmunoassays: how do they work? where are they used?, disadvantages, Europium luminescence, time-resolved luminiscence spectroskopie antenna molecules, properties requires for medical purposes
- S. Pandya, J. Yu, D. Parker, Dalton Trans. 2006, 2757
- N. Sabbatini, M. Guardigli, J.-M. Lehn, Coord. Chem. Rev. 1993, 123, 201
- F.S. Richardson, Chem. Rev. 1982, 82, 541
Azobenzenes: Switching Back & Forth by Light
mechanism of optical pumping of azobenzenes depending on substituentand solvent, some nice example for applications
- H. M. Dhammika Bandara, S. C. Burdette, Chem. Soc. Rev. 2012, 41, 1809
- D. Samanta, H. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, R. Klain, Proc. Natl. Akad. Sci. USA. 2018, 115, 9379
Molecular Machines: A True Light Driven Molecular Motor
overloaded double bonds as photchemical motors: their synthesis, working principle and applications (e.g. nanocars)
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- B. Feringa, Angew. Chem. Int. Ed. 2017, 56, 11060
Molecular Machines: Rotaxane-Based Shuttles Driven By Light and Redox Stimuli
rotaxanes as switches, molecular shuttles driven by light and redox chemistry, logic gates based on them
- V. Balzani, M. Gomez-Lopez, J.F. Stoddart, Acc. Chem. Res. 1998, 31, 405
- J.-P. Collin, P. Gavina, V. Heitz, J.-P. Sauvage, Eur. J. Inorg. Chem. 1998, 1
Part X: Bioorganic-Chemistry- and Materials-Related Topics
Logic Gates Based on Supramolecular Gels
describe what a supramolecular gel is, how it is characterized and show an example for logic gates that are implemented in such a gel
- Z. Qi, P. Malo de Molina, W. Jiang, Q. Wang, K. Nowosinski, A. Schulz, M. Gradzielski, C. A. Schalley, Chem. Sci. 2012, 3, 2073
Origin of Life: Self-Replication and Autocatalysis?
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
- L.E. Orgel, Nature 1992, 358, 203
- G. von Kiedrowski, Bioorg. Chem. Frontiers 1993, 3, 113
Aquaporins and Ion Pumps
active and passive transport, dependence on energy supply, how does water go through a membrane pore without letting protons pass?
- P. Agre, Angew. Chem. Int. Ed. 2004, 43, 4278
- 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!)
- J. Kurreck, D. Niethammer, H. Kurreck,Chem. unserer Zeit 1999, 33, 72
- 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
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
- R.A. Lerner, S.J. Bencovic, P.G. Schultz, Science, 1991, 252, 659
- P.G. Schultz, R.A. Lerner, Acc. Chem. Res., 1993, 26, 391
- C. Rader, B. List, Chem. Eur. J., 2000, 6, 2091