SubjectsSubjects(version: 902)
Course, academic year 2021/2022
Organic Chemistry II - B110004
Title: Organická chemie II
Guaranteed by: Department of Organic Chemistry (110)
Actual: from 2021 to 2021
Semester: both
Points: 6
E-Credits: 6
Examination process:
Hours per week, examination: 3/2 [hours/week]
Capacity: winter:70 / 48 (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
For type: Bachelor's
Additional information: http://předmět je vyučován pouze v zimním semestru
Note: deregister from the exam date if a requisite was not fulfilled
course can be enrolled in outside the study plan
enabled for web enrollment
you can enroll for the course in winter and in summer semester
Guarantor: Budka Jan doc. Ing. Ph.D.
Pre-requisite : {x}
Interchangeability : N101006, Z110005
In complex pre-requisite: B110009
This subject contains the following additional online materials
Annotation -
Last update: Kubová Petra Ing. (04.12.2017)
This course is continuation of Organic chemistry I. The course of Organic chemistry II is based on the description of organic reactions according to the mechanistic principles. It also includes chemistry of natural compounds (carbohydrates, amino acids, peptides, nucleic acids) as well as basics of heterocyclic chemistry.
Aim of the course -
Last update: Kubová Petra Ing. (04.12.2017)

Students will be able to:

write mechanisms of reactions in organic chemistry

describe stereochemistry of chemical transformations

estimate reactivity of polyfunctional compounds on the bases of structure

plan two- or three-step synthesis of target compound

know chemical properties of basic building blocks of natural and heterocyclic compounds

Literature -
Last update: Kubová Petra Ing. (04.12.2017)

R: J. McMurry: Organic Chemistry, 8. Edition, Brooks/Cole, Belmont, CA, USA, 2012. 9780840054449

Learning resources -
Last update: Kubová Petra Ing. (04.12.2017)

Electronic workbook:

Requirements to the exam -
Last update: Budka Jan doc. Ing. Ph.D. (02.08.2022)


1. Organic reactions. Basic classification (addition, substitution, elimination, rearrangements), oxidation and reduction in organic chemistry, oxidation numbers, chemical bonds, the ways of the splitting of chemical bond, reaction mechanism, reaction intermediates, the theory of transition state, reaction coordinate, DG a DG# and their influence on the reaction rate and on the reaction equilibrium. Acido-basic equilibrium.

2. Nucleophilic substitution on saturated carbon atom. Mechanism and stereochemistry and their dependence on the structure of substrate, nucleophile, leaving group and solvent. Nucleophility vs. Basicity. Competitive reactions. Application of SN reactions in alcohols, ethers, epoxides, esters, thiols and sulfides synthesis, alkylation of ammonia, emines and sulfides, azide and Gabriel synthesis of amines. Formation of C-C bond by SN reactions – preparation and application of nitriles and alkynes. Formation of C-C bond by reaction of organocooper reagents with alkyl-, alkenyl- and arylhalides. - Application of alcohols in SN reactions: Synthesis of alkylhalides from alcohols (by using of hydrogen halides and halides of inorganic acids, transformation of alcohols to alkyl sulfonates (mesylates and tosylates), sulfonates as leaving group, cleavage of ethers, opening of an epoxide ring.

3. Elimination reactions. E1 and E2 mechanism, relation to the nucleophilic substitution, dehydrohalogenation, Zaitsev's rule, influence of the bulkiness of the base, stereochemistry of the elimination reactions, dehalogenation. Hofmann elimination, Cope cleavage. Formation of alkynes and dienes. Dehydratation of alcohols and diols. Pinacol and retropinacol rearrangement. - Introduction in oxygen derivatives – oxidation levels, redox reactions. - Hydrocarbon derivatives containing carbonyl group – classification and reactivity tovards nucleophiles.

4. Aldehydes and ketones: Nucleophilic addition to unsaturated carbon atom - H – nucleophiles (complex hydride reduction), O – nucleophiles (hydratation of carbonyl group, acetals, ketals, C – nucleophiles (cyanhydrines and aminonitriles, Grignard reagents, Wittig reaction). N – nucleophiles (addition of ammonia and amines (+ reductive amination), hydrazine and hydroxylamine to aldehydes and ketones). Reaction of oximes – dehydratation of aldoximes, Beckmann rearrangement of ketoximes. Conjugate addition to α,β-unsatzrated carbonyl compounds – addition of hydrogen halides, alcohols, thiols and amines. Addition of organometal compounds: Grignard and Gilman reagents.

5. Carboxylic acids and their derivatives - Nucleophilic substitution on the unsaturated carbon atom. Transformation of carboxylic acids derivatives (halides, esters, anhydrides). Lactones and lactames. Baeyer-Villiger oxidation. Pyrolysis of acetates. Amides of carboxylic acids – Hofmann degradation, heterocumulenes (isocyanates, ketenes) and addition of nucleophiles. Reaction of carboxylic acids derivatives with organometal compounds and complex hydrides. Hydrolysis of carboxylic acids derivatives and nitriles – synthesis of carboxylic acids, amino- a hydroxyacids. Reaction of amino- a hydroxyacids. Basic derivatives of carbonic acid.

6. Reaction including α-hydrogen: Acidic and basic catalysed enolisation, stability of enoles, consequences of enolisation (exchange of α-hydrogen with solvent, racemisation of stereogenic centre on α-carbon). Reactions of enoles and enolates with electrophiles (α-halogenation of aldehades and ketones, Lieben reaction, Hell-Volhart-Zelinskij reaction, alkylation of enolates. Michael additio). Aldol-type reactions (aldolisation of aldehydes, aldol condensation of ketones, cross-aldol condensation. Claisen and cross-Claisen condensation, condensation of esters with ketones, Dieckmann condensation). Acetoacetic and malonate synthesis.

7. Electrophilic addition to unsaturated systems. Addition of hydrogen halides to alkenes and alkynes, hydration of alkenes and alkynes (revision and extension), hydroxymercuration, hydroboration/oxidation, addition of halogens, formation of halohydrines, epoxidation, dihydroxylation and ozonolysis of alkenes. Carbenes and cyclopropanation including Simmons-Smith reaction. Dienes – 1,2- vs. 1,4-electrophilic addition, Diels-Alder cycloaddition.

8. Electrophilic substitution on unsaturated carbon atom. Aromaticity. Aromatic electrophilic substitution. Wolff-Kizhner and Clemmensen reduction. Influence of substituent on introduction of second substituent (mechanism), Reactivity of naphthalene, kinetic and thermodynamic control.

9. Nucleophilic substitution on aromatic compounds. Preparation and reactivity of aromatic diazonium salts, their use in organic synthesis. Aromatic nucleophilic substitution - addition-elimination and elimination-addition (benzyne) mechanism.

10. Heterocycles - basic types of five- and six-membered heterocycles. Comparison of reactivity of benzene and aromatic heterocycles. Pyridine – basicity, reaction on nitrogen atom, electrophilic and nucleophilic substitution reactions. Reactivity of five-membered heterocycles. Electrophilic substitution of condensate nitrogen heterocycles – quinoline, isoquinoline and indole. Principles of aromatic heterocycles synthesis.

11. Radical reactions. Formation of radicals, structure and stability of radicals. Radical halogenation of alkanes and its selektivity, Halogenation to allylic and benzyl position. Radical addition of HBr (revision) and RSH to alkenes.

12. Oxidation and reduction (revision and extension). Oxidation of side chain on the aromatic ring, spliting of 1,2-diols with HIO4, formation of quinones. Reduction of alkenes and alkynes, partial reduction of alkynes to alkenes, Birch reduction. Reductive dimerization - pinacol reaction, acyloin condensation. Cannizzaro reaction.

Oxidation of sulphur and nitrogen compounds Reduction of nitro compounds to amines, disulfides and sulfonic acids to thiols.

13. Amino acids and peptides. Classification of amino acids, synthesis (Strecker synthesis, alkylation of acetamidomalonate), stereochemistry of alfa-amino acids. Coded amino acids, structural types of natural amino acids, acido-basic equilibrium, isoelectric point. Peptide synthesis – protective groups (Z, Boc, ester), formation of peptide bond (DCCI), solid phase synthesis..Protein classification. Peptide analysis (total hydrolysis, detetermination of C- and N-ends, sequence analysis - Sanger's reagent, dansylation, Edman degradation). - Principles of nucleobases, nucleotides, nucleic acids; base pairing.

14. Carbohydrates. Structure, stereochemistry, configuration, cyclic forms, mutarotation, Kiliani–Fischer synthesis, Wohl degradation, oxidation and formation of lactones, reduction, epimerization, esters, ethers of carbohydrates, glycosides. Disaccharides - reducing and non-reducing, polysaccharides (starch, cellulose).

Syllabus -
Last update: Budka Jan doc. Ing. Ph.D. (12.09.2021)

1. Organic reactions, types, mechanisms, acid-base equilibrium.

2. Nucleophilic substitution on saturated carbon. Mechanism, stereochemistry, applications.

3. Elimination E1 and E2. Mechanism, stereochemistry, application.

4. Nucleophilic addition on unsaturated carbon.

5. Nucleophilic substitution on unsaturated carbon.

6. Chemistry of enoles and enolates.

7. Electrophilic additions on unsaturated systems.

8. Electrophilic substitution on unsaturated systems.

9. Nucleophilic substitution on aromatic compounds.

10. Heterocycles. Basic types of five and six membered heterocycles, synthesis and reactivity.

11. Radical reactions, halogenation, additions of HBr and thiols.

12. Oxidation and reduction.

13. Aminoacids, peptides. Structure, chemical properties, synthesis.

14. Carbohydrates. Structure, stereochemistry, chemical properties.

Registration requirements -
Last update: Kubová Petra Ing. (04.12.2017)

Organic Chemistry I

Course completion requirements - Czech
Last update: Kundrát Ondřej Ing. Ph.D. (16.02.2018)

Předmět je zakončen zkouškou, která se skládá z písemné a ústní části. Student může přistoupit ke zkoušce z Organické chemie II poté, co získal zápočet na cvičeních z Organické chemie II.

Teaching methods
Activity Credits Hours
Účast na přednáškách 1,5 42
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1,5 42
Příprava na zkoušku a její absolvování 2 56
Účast na seminářích 1 28
6 / 6 168 / 168