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Lecture Course Physical Organic
and Supramolecular Chemistry

 

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Addressees

Chemistry master students interested in physical organic and supramolecular chemistry. The course language will be German, if no foreign student is participating. If desired, we can switch to English.

 

Dates and Locations

 

Organizational Matters

Registration: By choosing a seminar topic, you will be automatically registered for the lecture course. A list with topics will be made available in front of my office (room 32.05) after the first lecture course date (Apr 16th, 2008). Please sign up with name and matriculation number. If you want to step back from the course, you must do that before April 30th, 2009. After this date, registration is fixed. Not giving your talk after that date without unregistering will mean that you don't pass the course.

Attendance: It is completely up to you to attend the lecture course. If you feel that you can learn the topics of the course better on your own, please feel free to use the time in any way beneficial to you. However, I expect that all participants attend the seminar. It is not quite fair, if you only show up for your own talk. Your fellow students tend to put quite some effort into their talks and constantly not being in the audience is - at least in my opinion - a sign of disrespect. Anyway, at the end you need to be fit for the exam...

Seminar: The seminar will expand the topics of the lecture course in seminar talks given by the participating students. The seminar topics provide additional examples for the concepts discussed in the lecture course. The list of topics is available below.

Seminar Dates: When you choose your seminar topic, please make sure that you are available at the date of your talk. The lecture course, seminar, and excercises are scheduled to fit as perfectly together as possible.

Materials: I will use the chalkboard for most of the lecture course, except if I need more complex transparencies, which are then available for download below. I will make your talks accessible for all participants (password-protected, of course). Please send me your presentations as a pdf by email. The headlines of the seminar talks below will be linked to the corresponding file.

Excercises (Quickies): In order to prepare for the written exam, we will talk about one excercise at the beginning of each lecture course and/or seminar. Since they should only take a couple of minutes, I call them Quickies. The excercises will be added to this page during the course. Please download them and prepare them for the next lecture. You will not benefit from them, if you don't try to solve them on your own first.

Examination: The examination consists of two parts: The seminar talk you give and the written exam at the end of the lecture course. Both grades contribute equally to the final grade and each part of the exam must be successfully passed. Not passing either one means you have not passed the lecture course.

 

Results of Written Exams

Here, you find the old exams and the results. You need to login with the same password as for the other material associated to this lecture course to access both.

Summer term 2008:
PDF of Exam (English) - PDF of Exam (German) - Grades

Summer term 2009:
PDF of Exam (English) - PDF of Exam (German) - Grades

 

Lecture Course Contents

1. Fundamentals

1.1 Potential Energy Surfaces

identity reaction of H + H₂ to H₂ + H , discussion of the connection of potential energy surfaces to vibrations, to the reaction path, to the imaginary frequency in quantum chemical calculations etc. How many dimensions does a PES have? What exactly is a reaction coordinate?

1.2 Thermodynamics

energy units, factors that affect entropy, connection of free enthalpies and equilibria, connection to potential energy surfaces

1.3 Kinetics

simple rate laws for unimolecular and bimolecular reactions, Arrhenius equation, Eyring equation, transition state theory, kinetic vs. thermodynamic control, pressure effects (activation volumes and their meaning), catalysis, enzyme kinetics (Michaelis-Menten)

Materials I: Deslipping Kinetics of Rotaxanes

1.4 Linking Kinetics to Thermodynamics

Hammond postulate, Curtin-Hammett principle, linear-free enthalpy correlations (Hammett equation, the meaning of sigma and rho, substituent effects, direct conjugation)

1.5 Investigation of Reaction Mechanisms and Short-Lived Intermediates

kinetic isotope effects, crossover experiments (reaction trajectories; example: Eschenmoser's intra- versus intermolecular S_N2 reaction), characterization of short-lived intermediates by three-phase test, matrix-isolation spectroscopy etc., examples for reactive species (dioxiranes, tetrahedrane, o,m,p-didehydrobenzene (including the Bergman cyclization), water oxide)

1.6 Short Summary of Stereochemistry

euclidean and topological chirality, central, axial, helical, planar chirality, chirality and symmetry

 

2. Bonding and Structure

2.1 Molecular Orbital Theory

how to qualitatively construct molecular-orbitals (knot rule etc.), frontier orbitals and why one often can restrict the discussion to the FOs, molecular orbital basis for HSAB principle, nucleophilicity, electrophilicity

Materials II: MO scheme of methane without hybridized carbon

Materials III: How to construct molecular orbitals?

2.2 Aromaticity

Hückel theory (qualitatively), molecular orbital schemes of cyclobutadiene, benzene and cyclooctatetraene, Jahn-Teller theorem, aromaticity - nonaromaticity - antiaromaticity, homoaromaticity, in plane aromaticity, through-space aromaticity, fullerenes

2.3 Conformational Analysis (strain, alicyclics, cyclics, stereoelectronic effects)

strain, stereoelectronic effects

 

3. Reactivity

3.1 Classification of Reaction Types

polar reactions (nucleophiles, electrophiles), radical reactions, photochemical reactions, pericyclic reactions (this part is meant to provide a brief overview as an introduction mainly into pericyclic reactions)

3.2 Classification of Pericyclic Reactions and Woodward-Hoffman Rules

cycloadditions (allowed - forbidden), electrocyclic reactions (conrotatory - disrotatory), sigmatropic rearrangements (suprafacial - antarafacial), cheletropic reactions (side-on - end-on), aromatic transition structures

3.3 Cycloaddition and Cycloreversion Reactions

introduction to correlation diagrams (1 example for [4+2], 1 example for [2+2]) for deriving the Woodward-Hoffman rules from a molecular orbital approach, comparison to FO method, examples (Diels-Alder, exo/endo, 1,3-dipolar cycloadditions)

3.4 Electrocyclic Reactions

correlation diagrams (1 example for con-, 1 example for disrotatory reaction), comparison to FO method, examples

3.5 Sigmatropic Rearrangements

FO analysis in a simple and qualitative way, examples (e.g. vitamin D, bullvalene)

3.6 Cheletropic Reactions

FO analysis, examples (e.g. carbene addition to double bonds, loss of SO₂ from cyc-CH₂CH=CHCH₂SO₂ or benzoid analoga thereof)

3.7 Group Transfer Reactions

transfer hydrogenations, ene-reaction (e.g. with singlet oxygen)

3.8 Orbital Coefficient Controlled Regioselectivity in Cycloadditions

3.9 Orbital Energy Controlled Reaction Rates of Cycloadditions

Diels-Alder with normal and inverse electron demand

3.10 Carbenes/Carbenoids, Nitrenes/Nitrenoids, and Oxenoids

generation, rearrangements, insertion, and addition

3.11 Radicals

ESR and CIDNP, rearrangements and bimolecular reactions

3.12 Photochemistry

excited states, Jablonski term scheme, energy transfer, photoinduced electron transfer, synthetically useful photochemical reactions

 

4. The Influence of the Environment

4.1 Solvatochromic Behaviour

4.2 Gas-Phase Acidities and Gas-Phase Nucleophilicities

inductive effects of alkyl chains: fact or fiction?, why is the S_N2 reaction up to 10 to the power of 15 times faster in the gas phase (double minimum potential, what is a "negative barrier"?)?

Materials IV: All thermodynamic values used in this chapter can be looked up at the NIST database which is freely available on the net

Materials V: Gas-Phase Acidities - An Absolute Acidity Scale

Materials VI: Gas-Phase Nucloephilic Substitutions

Materials VII: Alkali ion/crown ether binding - is there a best fit in the gas phase?

 

5. Non-Covalent Interactions

5.1 Classification

Charge-charge attraction/repulsion, charge-dipole, dipole-dipole interactions, hydrogen bonds, pi-stacking, C-H-pi, cation-pi interactions, pi-donor-pi-acceptor interactions, Van-der-Waals forces, hydrophobic effect

Materials VIII: The Properties of Non-Covalent Bonds - Some Tables

5.2 Basic Principles in Supramolecular Chemistry

lock-and-key principle, induced fit, preorganisation, self-assembly versus self-organization, template effects, cooperativity, multivalency

Materials IX: Host-Guest Chemistry, Molecular Recognition

Materials X: Self-Assembly, Self-Sorting

5.3 Host-Guest Chemistry

Methods for the investigation of dynamically bound species, one example: coffein receptor and its examination by NMR, IR, UV/VIS spectroscopies, mass spectrometry and crystallography

Materials XI: Characterization of a caffeine receptor

5.4 Examples for Architectures based on Non-Covalent Bonds

self-assembled metallo-supramolecular systems (helicates, grids, capsules), hydrogen bonded capsules, mechanically locked molecules

Materials XII: Molecular Tennis: Self-Assembling Capsules

Materials XIII: Mesoscale Self-Assembly

Self-assembly and self-organization belong to the area of "emergent properties", i.e. a small set of well-defined rules plus simple building blocks make much more complex patterns evolve which are often almost unpredictable. New properties emerge which none of the building blocks have. For a very simple implementation with intriguing consequences, take a look at Conway's Game of Life (also see the related Wikipedia pages)

Materials XIV: Emergent Properties - Conway's Game of Life

5.5 Implementing Function in Non-Covalently Bound Complexes

molecular devices, logic gates, molecular motors

Materials XV: Natural molecular motors
For links to the animations used in the talk, which do not work in the pdf version, see:

• Kenneth Holmes, MPI Heidelberg
• Wolfgang Junge, Universität Osnabrück
• Hong Wang & Georg Oster, UC Berkeley/USA
• Katsuhiko Kinosita, Jr., Waseda University/Japan

 

Seminar

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 brief discussion of the topic. The seminar language can be German or English. Those of you who want to give English a try are encouraged to do so, but it is not a must. The seminars will be graded and your final grade for this lecture course is the average of the grade for the seminar talk and the written exam. Choosing a semiar topic counts as registration for this lecture course. If you want to unsubscribe from the course you need to do that before May 2nd, 2008 in order to avoid malus points.

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 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 ...

• Prepare a handout for your fellow students. One page is sufficient, if it contains the most important statements of your talk in a very shorrt summary plus the relevant literature you used.

 

Seminar Topics

Part I: Potential Energy Surfaces and Molecular Orbitals

• Singlet Oxygen

  singlet and triplet states, generation of singlet oxygen, reactivity, typical synthetically useful reactions

  • W. Adam, Chem. unserer Zeit 1981, 15, 190
  • W. Adam, Chemiker-Zeitung 1975, 99, 142

   

• 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

  • S. Shaik, M. Filatov, D. Schröder, H. Schwarz, Chem. Eur. J. 1998, 4, 193
  • S. Shaik, S.P. de Visser, F. Ogliaro, H. Schwarz, D. Schröder, Curr. Opin. Chem. Biol. 2002, 6, 556

   

• Reaction Dynamics of Reactive Intermediates: Synergy of Theory
  and Experiment

  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. If you wish, we can show some of the animations from the Carpenter homepage.

  • B.K. Carpenter, Angew. Chem. 1998, 110, 3532

   

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

  • F.-G. Klärner, Chem. unserer Zeit 1989, 23, 53
  • M.K. Diedrich, D. Hochstrate, F.-G. Klärner, B. Zimny, Angew. Chem. 1994, 106, 1135
  • W.J. le Noble, Chem. unserer Zeit 1989, 17, 152
  • R. van Eldik, T. Asano, W.J. le Noble, Chem. Rev. 1989, 89, 549

   

Part III: Short-Lived Intermediates and Funny Molecules

• Non-classical Cations, Superacids, Superelectrophiles

  norbornyl-, methylcyclopropyl cations, mono- and diprotonated methane, ethylene dication, structures and properties

  • G.A. Olah, Angew. Chem. 1993, 105, 805
  • G.A. Olah, Angew. Chem. 1995, 107, 1519
  • G.A. Olah, Acc. Chem. Res. 1976, 9, 41

   

• Square-planar Carbon?

  Li₂CF₂ calculations, Zr/Al compounds, fenestranes

  • R. Hoffmann, R.W. Alder, C.F. Wilcox, Jr., J. Am. Chem. Soc. 1970, 92, 4992
  • G. Erker, D. Roettger, Angew. Chem. 1997, 109, 840
  • D.R. Rasmussen, L. Radom, Angew. Chem. 1999, 111, 3052

   

• Fullerenes

  C60: discovery, generation, Euler rule, endohedral complexes, proof for aromaticity, examples for chemistry on fullerene surfaces

  • H. Schwarz, Angew. Chem. 1992, 104, 301
  • H.W. Kroto, Angew. Chem. 1992, 104, 113
    
  • T. Weiske, T. Wong, W. Krätschmer, J.K. Terlouw, H. Schwarz, Angew. Chem. 1992, 104, 242
    
  • M. Saunders, H.A. Jimenez-Vazques, B.W. Bangerter, R.J. Cross, J. Am. Chem. Soc. 1994, 116, 3621

   

• Evidence for Short-Lived Intermediates from Neutralization-Reionization Mass Spectrometry

  NRMS principle, vertical electron transfers, Franck-Condon factors, examples may include: carbonic acid, ylides, water oxide

  • J.K. Terlouw, H. Schwarz, Angew. Chem. 1987, 99, 829
  • N. Goldberg, H. Schwarz, Acc. Chem. Res. 1994, 27, 347
  • C.A. Schalley, G. Hornung, D. Schröder, H. Schwarz, Chem. Soc. Rev. 1998, 27, 91
  • D. Schröder, C.A. Schalley, N. Goldberg, J. Hrusak, H. Schwarz, Chem. Eur. J. 1996, 2, 1235

   

• Evidence for Short-Lived Intermediates from Matrix-Isolation Spectroscopy

  the principle of matrix isolation spectroscopy, examples may include: didehydro benzene, dioxiranes, tetrahedrane

  • W. Sander, Acc. Chem. Res. 1999, 31, 669
  • W. Sander, C. Kötting, Chem. Eur. J. 1999, 4, 24
  • C. Kötting, W. Sander, J. Breidung, W. Thiel, M. Senzlober, H. Bürger, J. Am. Chem. Soc. 1998, 120, 219
  • I. Norman, G. Porter, Nature 1954, 174, 508
  • E. Whittle, D.A. Dows, G.C. Pimentel, J. Chem. Phys. 1954, 22, 1943

   

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
  • W. Thiemann, Naturwissenschaften 1974, 61, 476
  • R.A. Hegstrom, D.K. Kondepudi, Spektrum der Wissenschaft 1990, 56
  • M. Avalos, R. Babiano, P. Cintas, J.L. Jimenez, J.C. Palacios, Chem. Commun. 2000, 887

   

• 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

   

• Topological Chirality

  molecules and graph theory, topology, topological chirality e.g. with catenanes, rotaxanes, and knotanes

  • J.-C. Chambron, C. Dietrich-Buchecker, J.-P. Sauvage, Top. Curr. Chem. 1993, 165, 131
  • A. Sobanski, R. Schmieder, F. Vögtle, Chem. unserer Zeit 2000, 34, 160

   

• Chiroptical Methods

  CD spectroscopy, linearly and circularly polarized light, why do chiral substances turn the plane of the light?

  • G. Snatzke, Chem. unserer Zeit 1981, 15, 78; 1982, 16, 160
  • 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

• 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
  • R.B. King, Chem. Rev. 2001, 101, 1119

   

• Woodward Hoffmann Rules: Correlation Diagrams for Electrocyclic Ring Opening Reactions

  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

   

• Reactions with Coarctate Transition Structures

  what are coarctate transition structures?, comparison to pericyclic reactions, topology and symmetry, predictive rules, mechanisms, stereochemistry

  • R. Herges, Angew. Chem. 1994, 106, 261
  • H.E. Zimmerman, Acc. Chem. Res., 1971, 4, 272

   

Part VI: A Few Concepts Relating to Synthesis

• Umpolung of Reactivity

  the principle, examples (should focus on advanced topics): thiazolium salts and their role in biochemical processes, e.g. pyruvate dehydrogenase multienzyme complex, decarboxylation of amino acids

  • D. Seebach, Angew. Chem. 1979, 91, 259
  • Biochemistry textbooks for thiazolium-mediated reactions
  • F. Diederich, H.D. Lutter, J. Am. Chem. Soc. 1989, 111, 8348

   

• Organocatalysis

  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

   

• Modern Photochemistry

  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
  • S. Shinkai, T. Nakaji, Y. Nishida, T. Ogawa, O. Manabe, J. Am. Chem. Soc. 1980, 102, 5860
  • S. Shinkai, T. Nakaji, T. Ogawa, K. Shigematsu, O. Manabe, J. Am. Chem. Soc. 1981, 103, 111
  • H. Hopf, H. Greiving, P.G. Jones, P. Bebenitschek, Angew. Chem. 1995, 107, 742

   

Part VII: Solvent Effects

• Perfluorinated Solvents

  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

• 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.

   

Part IX: Molecules with Function

• 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?

  • F. Schmidtchen, Top. Curr. Chem. 2005, 255, 1
  • special issue: Coord. Chem. Rev. 2006, 250
  • C. Seel, A. Galan, J. de Mendoza, Top. Curr. Chem. 1995, 175, 101

   

• 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)

   

• Container Molecules, 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

   

• 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

   

• Molecular Machines

  catenanes, rotaxanes as switches, molecular shuttles, light-driven machines, logic gates

  • special issue: Acc. Chem. Res. 2001, 34
  • 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
  • A.P. de Silva, H.Q.N. Gunaratne, C.P. McCoy, Nature 1993, 364, 42

   

• 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

   

Part X: Bioorganic-Chemistry-Related Topics

• Catalytic Antibodies

  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

   

• 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

   

• Artificial Photosynthesis

  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

 

Quickies

The Quickies are short excercises to be discussed in the first few minutes of each lecture course or seminar. I expect you to be prepared to provide the solution on the board! The dates below define for which course date you need to prepare the Quickie.

 

 

Further reading

Besides the references given under each seminar topic, the following literature references extend the scope of the lecture course and provide some more examples which cannot all be discussed. They provide access to more in-depth information and recent applications of the topics presented in the course. Please also see the literature references provided on the seminar page.

1. Textbooks

Physical Organic Chemistry:

• N. Isaacs, Physical Organic Chemistry, Longman, Harlow 1995

Supramolecular Chemistry:

• J.W. Steed, J.L. Atwood, Supramolecular Chemistry, Wiley, New York 2000
• C.A. Schalley (ed.), Analytical Methods in Supramolecular Chemistry, Wiley-VCH, Weinheim, 2007
• G. A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press, Oxford 1997

2. Thermodynamics and Kinetics

Catalysis within molecular capsules

• J. Kang, J. Santamaria, G. Hilmersson, J. Rebek, Jr., J. Am. Chem. Soc. 1998, 120, 7389
• J. Kang, G. Hilmersson, J. Santamaria, J. Rebek, Jr., J. Am. Chem. Soc. 1998, 120, 3650
• T. Heinz, D. M. Rudkevich, J. Rebek, Jr., Nature 1998, 394, 764
• S. K. Körner, F. C. Tucci, D. M. Rudkevich, T. Heinz, J. Rebek, Jr., Chem. Eur. J. 2000, 6, 187

Hammett equation

• P. Sykes, Reaktionsmechanismen der Organischen Chemie, Wiley-VCH, Weinheim

Steric isotope effects

• D. Wade, Chem.-Biol. Interact. 1999, 117, 191
• H. C. Brown, G. J. McDonald, J. Am. Chem. Soc. 1966, 88, 2514
• S. A. Sherrod, R. L. da Costa, R. A. Barnes, V. Boekelheide, J. Am. Chem. Soc. 1974, 96, 1565
• K. Mislow, R., Graewe, A. J. Gordon, G. H. Wahl, Jr., J. Am. Chem. Soc. 1964, 86, 1733
• L. Melander, R. E. Carter, J. Am. Chem. Soc. 1964, 86, 295
• D. Wade, Chem.-Biol. Interact. 1999, 117, 191
• T. Felder, C. A. Schalley, Angew. Chem. 2003, 115, 2360

3. Reactive Intermediates

Three-phase test

• J. Rebek, F. Gaviña, J. Am. Chem. Soc. 1974, 96, 7112
• J. Rebek, D. Brown, S. Zimmerman, J. Am. Chem. Soc. 1975, 97, 454
• J. Rebek, F. Gaviña, J. Am. Chem. Soc. 1975, 97, 3221

Matrix isolation spectroscopy (examples for reactive intermediates)

• G. Maier, H. P. Reisenauer, H. Pacl, Angew. Chem. 1994, 106, 1347 (silacyclopropyne)
• W. Sander, Angew. Chem. 1994, 106, 1522 (triple bonds in small cycles)
• G. Maier, Angew. Chem. 1988, 100, 317 (tetrahedrane)
• G. Maier, H. P. Reisenauer, T. Sayrac, Chem. Ber. 1982, 115, 2192

Neutralisation reionisation mass spectrometry (NRMS)

• G. Hornung, C.A. Schalley, M. Dieterle, D. Schröder, H. Schwarz, Chem. Eur. J. 1997, 3, 1866 (Barton reaction of alkoxy radikals)

4. Aromaticity - Non-Aromaticity - Antiaromaticity

Reviews

• P. Garratt, P. Vollhard, Aromatizität , Thieme, Stuttgart 1973 (excellent small book providing a great overview)
• P.v.R. Schleyer, H. Jiao, Pure Appl. Chem. 1996, 68, 209
• Sonderheft der Chemical Reviews: Chem. Rev. 2001, 101 (very extensive!)

Resonance energies

• M.J.S. Dewar, C. de Llano, J. Am. Chem. Soc. 1969, 91, 789
• L.J. Schaad, B.A. Hess, Jr., Chem. Rev. 2001, 101, 1465

Nucleus-independent chemical shifts (NICS)

• P.v.R. Schleyer, C. Maerker, A. Dransfeld, H. Jiao, N.J.R. van Eikema Hommes, J. Am. Chem. Soc. 1996, 118, 6317

Aromaticity of Fullerenes

• M. Bühl, W. Thiel, H. Jiao, P.v.R. Schleyer, M. Saunders, F.A.L. Anet, J. Am. Chem. Soc. 1994, 116, 6005
• M. Bühl, A. Hirsch, Chem. Rev. 2001, 101, 1153

Homoaromaticity

• R.V. Williams, Chem. Rev. 2001, 101, 1185

Sigma-aromaticity

• D. Moran, M. Manoharan, T. Heine, P.v.R. Schleyer, Org. Lett. 2003, 5, 23
• M.J.S. Dewar, J. Am. Chem. Soc. 1984, 106, 669
• D. Cremer, J. Gauss, J. Am. Chem. Soc. 1986, 108, 7467

3D aromaticity

• M. Bremer, P.v.R. Schleyer, K. Schötz, M. Kausch, M. Schindler, Angew. Chem. 1987, 99, 795
• M.S.W. Chan, D.R. Arnold, Can. J. Chem. 1997, 75, 192

Antiaromaticity

• F.-G. Klärner, Angew. Chem. 2001, 113, 4099
• K.B. Wiberg, Chem. Rev. 2001, 101, 1317

Historical perspective on the development of the term "aromaticity"

• P. Garratt, Endeavour 1987, 11, 36
• J.A. Berson, Angew. Chem. 1996, 108, 2922

5. Pericyclic Reactions

Basics (in german, but they are also available in english)

• Ian Fleming, Grenzorbitale und Reaktionen organischer Verbindungen, VCH, Weinheim 1990
• R.B. Woodward, R. Hoffmann, Die Erhaltung der Orbitalsymmetrie, VCH, Weinheim 1970

Aromaticity and pericyclic reactions

• M.J.S. Dewar, Angew. Chem. 1971, 83, 859
• K.-W. Shen, J. Chem. Educ. 1973, 50, 238

Transition structures (theoretical calculations)

• K.N. Houk, Y. Li, J.D. Evanseck, Angew. Chem. 1992, 104, 711
• F. Bernardi, M. Olivucci, M.A. Robb, Acc. Chem. Res. 1990, 23, 405

Pericyclic reactions in organic synthesis:

• B.M. Trost, Angew. Chem. 1986, 98, 1
• J. Mulzer, Nachr. Chem. Tech. Lab. 1984, 32, 882 + 961
• A. Ichihara, Synthesis 1987, 207
• W. Oppolzer, Angew. Chem. 1977, 89, 10
• S. Blechert, Synthesis 1989, 71

6. Two-state Reactivity

Reviews

• D. Griller, K.U. Ingold, Acc. Chem. Res. 1980, 13, 317 (radical clocks)
• P.R. Ortiz de Montellano, J.J. De Voss, Nat. Prod. Rep. 2002, 19, 477 (cytochrome P-450)

Original literature

• J.T. Groves, G.A. McClusky, R.E. White, M.J. Coon, Biochem. Biophys. Res. Commun. 1978, 81, 154 (oxygen rebound mechanism)
• J.I. Manchester, J.P. Dinnocenzo, L.-A. Higgins, J.P. Jones, J. Am. Chem. Soc. 1997, 119, 5069 (isotope effect profiles)
• M. Newcomb, M.-H. Le Tadic, D.A. Putt, P.F. Hollenberg, J. Am. Chem. Soc. 1995, 117, 3312 (ultrafast radical clocks)
• M. Newcomb, M.-H. Le Tadic-Biadatti, D.L. Chestney, E.S. Roberts, P.F. Hollenberg, J. Am. Chem. Soc. 1995, 117, 12085

7. Photochemistry and Artificial Photosynthesis

Books

• H.G.O. Becker, Einführung in die Photochemie , Akademie Verlag
• C.H. DePuy, O.L. Chapman, Molekül-Reaktionen und Photochemie, VCH, Weinheim 1977
• M. Klessinger, J. Michl, Excited States and Photochemistry of Organic Molecules, Wiley-VCH, Weinheim 1995
• V. Balzani, M. Venturi, A. Credi, Molecular Devices and Machines, Wiley-VCH, Weinheim 2003

Artificial photosynthesis

• G. Steinberg-Yfrach, P.A. Liddell, S.-C. Hung, A.L. Moore, D. Gust, T.A. Moore, Nature 1997, 385, 239
  
• Y.-Z. Hu, S. H. Bossmann, D. van Loyen, O. Schwarz, H. Dürr, Chem. Eur. J. 1999, 5, 1267

8. Solvent Effects

Solvatochromic behaviour

• Lowry, Richardson, Mechanismus und Theorie in der Organischen Chemie, VCH, Weinheim
• Reichard, Dimroth, Angew. Chem. 1979, 91, 119

Gas-phase acidities, gas-phase nucleophilicities

• F. Strohbusch, Chem. unserer Zeit 1982, 16, 103
• W.N. Olmstead, J.I. Brauman, J. Am. Chem. Soc. 1977, 99, 4219
• M.J. Pellerite, J.I. Brauman, J. Am. Chem. Soc. 1980, 102, 5993

9. Non-covalent Bonds, Supramolecular Chemistry

Individual non-covalent interactions

• R. D. Hancock, J. Chem. Ed. 1992, 69, 615 (chelate effect)
• W.L. Jorgensen, J. Pranata, J. Am. Chem. Soc. 1990, 112, 2008 (secondary effects)
• T.J. Murray, S.C. Zimmerman, J. Am. Chem. Soc. 1992, 114, 4010 (secondary effects)
• J.C. Ma, D.A. Dougherty, Chem. Rev. 1997, 97, 1303 (cation-pi interaction)
• C.A. Hunter, J.K.M. Sanders, J. Am. Chem. Soc. 1990, 112, 5525 (pi-pi interaction)
• D.B. Smithrud et al., Pure Appl. Chem. 1990, 62, 2227 (solvent effects, hydrophobic effect)

Determination of binding constants

• K. A. Connors, Binding Constants , Wiley, New York 1987
• S.R. Waldvogel, R. Fröhlich, C.A. Schalley, Angew. Chem. 2000, 112, 2580 (caffeine receptor)

Preorganization

• D.J. Cram, Angew. Chem. 1988, 100, 1041 (Nobel lecture)
• J. Rebek, Jr. et al., J. Am. Chem. Soc. 2001, 123, 11519 ("flexiballs")

Allosteric behaviour

• A. Lützen, O. Haß. T. Bruhn, Tetrahedron Lett. 2002, 43, 1807

10. Molecular Devices

Natural molecular motors

• Biochemistry textbooks(z.B. Voet, Voet)
• P. D. Boyer, Angew. Chem. 1998, 110, 2424
• J. E. Walker, Angew. Chem. 1998, 110, 2438

Artificial molecular "motors"

• C. A. Schalley, K. Beizai, F. Vögtle, Acc. Chem. Res. 2001, 34, 465
• J.-P. Collin, C. Dietrich-Buchecker, P. Gaviña, M. C. Jimenez-Molero, J.-P. Sauvage, Acc. Chem. Res. 2001, 34, 477
• V. Balzani, M. Gómez-López, J. F. Stoddart, Acc. Chem. Res. 1998, 31, 405
• A. M. Brouwer, C. Frochot, F. G. Gatti, D. A. Leigh, L. Mottier, F. Paolucci, S. Roffia, G. W. H. Wurpel, Science 2001, 291, 2124
• P. R. Ashton, V. Balzani, O. Kocian, L. Prodi, N. Spencer, J. F. Stoddart, J. Am. Chem. Soc. 1998, 120, 11190
• J. K. Gimzewski, C. Joachim, R. R. Schlittler, V. Langlais, H. Tang, I. Johannsen, Science 1998, 281, 531
• T. R. Kelly et al., Nature 1999, 401, 150
• B. L. Feringa et al., Nature 1999, 401, 152