Course No. 21 221a/b - Modulbeschreibung (Deutsch)

Quicklinks:

Lecture Course Contents - Seminar Topics - Seminar schedule - Quickies - Old Exams

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

Lecture Course: Thursdays 12 am - 2 pm; start date: Apr 23, 2020; WebEx video conference

Seminar: Thursdays 2 pm- 4 pm; start date: Apr 23, 2020; WebEx video conference

To participate as efficiently as possible, make sure that you have sufficient internet bandwith, a headset with microphone and a suitable computer/laptop available. I will send the invitations to join the video conferences to all participants.

Because of a Berlin-wide holiday, there will be no course/seminar on May 21, 2020

Organizational Matters

Registration: Please do not forget to register for the course in Campus Management. In addition, you also need to choose a seminar topic from the list which will be made available in front of my office (room 32.05) after the first lecture course date. Please sign up for the desired topic with name and matriculation number. If you want to step back from the course, you must do that before the registration deadline. After this date, registration is fixed.

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 on a second page. After the talks, I will make the pdfs of the presentations available by linking them to the headlines in the list of topics on the seminar page (password protected, of course). Please send me your presentations as a pdf by email after your talk.

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 together as much 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 them accessible to all participants 

Excercises (Quickies): Two of the Quickies below will be discussed in the beginning of each lecture course/seminar day. Please download and prepare them.

Active participation: To pass the course and finish the module, active participation is one requirement, to pass the oral exam is the second one. Active participation means that you give a seminar talk AND participate in the discussion of the quickies.

Exam: The course is completed by an oral exam of ca. 30 minutes which comprises the topics of the lecture course as well as the topics of the seminar. The grade of the oral exam defines the grade for the module. The exam can be individually scheduled with me, but is to be taken before the start of the next term.

Old Exams

Earlier, the exam has been a written exam. You find the exams here for training purposes. 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)

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

Summer term 2011:
PDF of Exam (English) - PDF of Exam with Solutions

Lecture Course Contents

Chapter 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

Chapter 2 - Structure and Bonding

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

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

Chapter 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

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

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

Materials V: Gas-Phase Nucloephilic Substitutions

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

Chapter 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 VII: 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 VIII: Host-Guest Chemistry, Molecular Recognition

Materials IX: 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 X: 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 XI: Molecular Tennis: Self-Assembling Capsules

Materials XII: 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 XIII: Emergent Properties - Conway's Game of Life (Golly Win)

5.5 Implementing Function in Non-Covalently Bound Complexes

molecular devices, logic gates, molecular motors

Materials XIV: 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

Quickies

The Quickies are short excercises to be discussed in the first few minutes of each lecture course or seminar.

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