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Lecture Course "Physical Organic Chemistry"

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

Please choose a topic for your seminar talk on the "Seminar Topics" page, where you also find information on the topics and links to relevant literature.


Lecture Course Contents - Further Reading - Old Exams
Seminar Topics - Google Spreadsheet - Tips for Good Talks

Dates and Locations

Lecture Course: Thursdays 12 am - 2 pm; start date: Apr 21, 2022
Thursdays 2 pm- 4 pm; start date: Apr 21, 2022

Location: Arnimallee 22, Lecture Theater A (Room B.006)

No course/seminar on May 26, 2020 (Ascension day)


Organizational Matters

Registration: Registration in Campus Management is required. Choosing a seminar topic does not replace CM registration.

Regular participation: You are required to participate in at least 11 sessions. 

Active participation: You need to provide a talk and to participate in the discussion of quickies.

Exam: You must pass a 30 min oral exam.

Lecture Course Material: The lecture course slides, questions and exercises are provided as Powerpoint files with audio trace on Blackboard and are made available one week prior to the session, in which it is discussed. Solutions to the quickies will become available after the session, in which they are discussed.


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)

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 SN2 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

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 SN2 reaction up to 10 to the power of 15 times faster in the gas phase (double minimum potential, what is a "negative barrier"?)?


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

5.2 Basic Principles in Supramolecular Chemistry

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

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

5.4 Examples for Architectures based on Non-Covalent Bonds

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

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.

5.5 Implementing Function in Non-Covalently Bound Complexes

molecular devices, logic gates, molecular motors


Old Exams

Earlier, the exam has been a written exam. You find the old 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


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

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

  • 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

  • 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)
  • 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