SubjectsSubjects(version: 955)
Course, academic year 2019/2020
Organic Reaction Mechanisms - AM110006
Title: Organic Reaction Mechanisms
Guaranteed by: Department of Organic Chemistry (110)
Faculty: Faculty of Chemical Technology
Actual: from 2019 to 2021
Semester: winter
Points: winter s.:5
E-Credits: winter s.:5
Examination process: winter s.:
Hours per week, examination: winter s.:2/2, Ex [HT]
Capacity: 20 / 20 (unknown)
Min. number of students: unlimited
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Tobrman Tomáš doc. Ing. Ph.D.
Examination dates   Schedule   
The course is focused on mechanistic interpretation of reactions and processes in organic chemistry and their application in prediction of reaction parameters, product composition and stereochemistry of synthetically useful organic reactions.
Last update: Kovaříček Petr (16.12.2023)

R: R. B. Grossman, The Art of Writing Reasonable Organic Reaction Mechanisms, Springer, Berlin 2006. 978-0-387-21545-7

A: F. A. Carey & Richard J. Sundberg, Advanced Organic Chemistry - Part A: Structure and Mechanisms, Springer, Boston, MA 2007. 978-0-387-44899-2

A: M. B. Smith, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Wiley 2006, 9780470084960, DOI:10.1002/0470084960

Last update: Kovaříček Petr (16.12.2023)

1. Historical introduction to the structure of matter and theory of chemical bond. Overview of graphical formalism used in organic chemistry. Repetition of atomic and molecular orbitals. Introduction to QMOT theory (qualitative molecular orbital theory). Classification of transformation and mechanism classes. Acid/base concept of organic compounds, acidobasic organic reactions. Recognition of respective mechanism classes based on structure and reaction conditions.

2. Mechanisms SN2, SRN1, metal insertion, elimination E2 and E1cb, elimination-addition mechanisms, α-elimination, carbenes and carbenoids, Zaitsev and Hoffman rules for elimination. Decision factors for substitution vs. elimination.

3. Addition to carbonyl, Burgi-Dunitz a Felkin-Ahn models, aldolization, kinetic and thermodynamic enolates, Knoevenagel and aldol condensation, carbonyl reactions with (formal) hydride shift (benzoin, Canizzaro, Tishchenko, Oppenauer, Meerwein-Ponndorf-Verlay), adice hydride na carbonyl, Michael addition, substitution at carbonyl, addition-elimination mechanism, Stetter synthesis, haloform (Lieben) reaction.

4. Substitution at alkene and arene substrates under basic conditions, Michael substitution, Morita-Baylis-Hillman, nucleophilic substitution on aromates, addition-elimination and elimination-addition mechanisms, Meisenheimer complex, SRN1, metalation and halogen-lithium exchange on aromates and sp2 carbon, reaction at sp carbon. Baldwin rules for cyclization. Rearrangements under basic conditions: benzylic acid, Favorsky, Wolff, Curtius, Hoffmann, Lossen, Smiles, Stevens, Pummerer, Sommelet-Hauser, Nierenstein reaction, Arndt-Eistert homologation.

5. Stability and formation of carbocations, carbocation geometry, resonance, mechanisms SN1 and E1, Decision factors for substitution vs. elimination under acidic conditions, examples of SN1, E1 and SN2 under acidic conditions, carbocation rearrangements, electrophilic addition to multiple bonds, Markovnikov rules, halonium and halolactonization, electrophilic addition to multiple bonds. Mechanism SEAr, regioselectivity explained by induction and resonance effects. Family of Friedel-Crafts mechanisms (alkylations, acylations, Houben-Hoesch, Bischler-Napieralski), formylations (Gattermann, Gattermann-Koch, Vilsmeier-Haack, Duff), Sommelet reaction, ipso- and α-substitutione, reactivity of diazonium salts, Meerweinova arylation, Gomberg-Bachmann, Pschorr, Japp-Klingemann, Sandmayer, Schiemann), reaktivitity of aliphatických diazonia.

6. Reactivity of carbonyl compounds, formation of acetals, aminals and imines, enolization under acidic conditions, microscopic reversibility principle, reactions: aldol, Michael, Mukaiyama, Robinson, Mannich, Hell-Vollhardt-Zelinski, reactivity of triple bonds under acidic conditions, rearrangements under acidic conditions (Wagner-Meerwein, 1,2-hydride and alkyl shift, pinakole), Baeyer-Villiger oxidations, rearrangements: Beckmann, Stieglitz, Bambergerer.

7. Comparison of polar mechanisms under basic vs acidic conditions sorted by functional groups and transformation classes, comparison of acidic vs basic rearrangements (Tiffenau-Demjanov, Hofmann-Martius, Fisher-Hepp, Ries, Ramberg- Bäcklund, Tiemann, Neber, α-ketol, Fritsch–Buttenberg–Wiechell, Seyferth–Gilbert homologation. Esterification and ester hydrolysis, Ingold classification of esterification mechanisms. The most common reactions occurring on phosphorus (Mitsunobu, Arbuzov, Staudinger, Wittig, Horner-Wadsworth-Emmons, Appel, Corey-Fuchs, Pudovik, Kabachnik-Fields), sulfur (ylides, Johnson-Corey-Chaykovsky, Julia olefination) a silicon (Peterson olefination, Brook rearrangement, (de)protection of alcohols). Multicomponent reactions (Paal-Knorr, Strecker, Bucherer-Bergs, Hantzsch, Biginelli, Petasis, Gewald, Passerini, Ugi). Deductive diagrams for rationalization of mechanisms.

8. Fundamental classification of pericyclic reactions, QMOT theory and symmetry of frontier molecular orbitals in pericyclic reactions, reversibility, thermic vs photochemical control of pericyclic reactions. Electrocyclic reactions, Favroskii rearrangement, oxyallyl-cyclopropanon equilibrium, Nazarov cyclization. Stereospecificity of pericyclic reactions, conrotation vs disrotation in transition state, Woodward-Hoddmann rules, Bergman cyclization. Cycloadditions and their classification, Diels-Alder reaction, inverse-demand Diels-Alder, cycloadditions of singlet oxygen, stereospecificity, regio- and stereo-selectivity of cycloadditions, suprafacial vs antarafacial approach, Sharpless dihydroxylation, dipolar cycloadditions, Huisgens cycloaddition and CuAAC, [2+2] cycloadditions (Wittig, Paterno-Büchi, cumulenes), cheletropic reactions, pericyclic hydrogenations and hydroborations.

9. Sigmatropic rearrangements and their classification, Cope, aza-Copem and Claisen rearrangements, stereochemistry of sigmatropic rearrangements and Woodward-Hoffmann rules. Prominent examples involving sigmatropic rearrangements (Fisher indole synthesis, Overman, Sommelet-Hauser, [2,3]-Wittig rearrangements). Ene reactions, metalla-ene reactions, retro-hetero-ene reactions, mechanism Ei, Cope and Chugaev elimination, Swern oxidation and oxidation by SeO2.

10. Radical and photochemical reactions, electronic structure of radicals and excited states, principles of light-matter interactions, stability of radicals, persistent radicals and spin traps, radical initiation by thermal and photochemical stimuli, the use of metals and their salts, typical faith of a radical, reductions by metals (Clemmensen, Birch, Bouveault-Blanc), ketyl radicals and their reactions (pinacol, McMurry, acyloin, Dowd-Beckwith), [1,2]-Wittig rearrangement, thiol-ene click reaction, propagation in chain mechanisms, autooxidation. Norrish type I and type II, photo-(de)caging, photo-Fries rearrangement, Barton and Hofmann-Löffler-Freytag reaction, isomerization of double bonds and photoswitches, Feringa’s motors.

11. Brief introduction to mechanisms running in the coordination sphere of transition metals, the most basic mechanistic steps, brief overview of cross-coupling reactions, Crabbe and Pauson-Khand reactions, Tebbe olefination.

12. Brief introduction to methods used to study mechanisms of organic reactions: isotope effects, kinetics, calculations, correlative methods, and analytical toolbox overview.

Last update: Kovaříček Petr (16.12.2023)
Registration requirements


Last update: Kovaříček Petr (16.12.2023)
Course completion requirements

It is compulsory to present a miniproject at seminar, pass two mid-term tests and the exam. Exam consist of a written test and an interview.

Last update: Kovaříček Petr (16.12.2023)
Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0.5 14
Účast na přednáškách 1 28
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1 28
Příprava na zkoušku a její absolvování 1.5 42
Účast na seminářích 1 28
5 / 5 140 / 140
Coursework assessment
Form Significance
Regular attendance 10
Continuous assessment of study performance and course -credit tests 30
Oral examination 60