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Carbonyl compounds (aldehydes, ketones, carboxylic acids, esters, amides, thioesters), nitriles, and their pKa. Amines, and imines. Enols and enolates, and their reactivity (aldol reaction, Claisen condensation, Michael addition); enamines (Stork reaction). Biomolecules: Saccharides (function and stereochemistry), glycosides and their synthesis; amino acids, peptides, proteins; aromatic heterocycles; nucleic acids; lipids; isoprenoids (steroids and terpenes); antibiotics; alkaloids; neurotoxins; and selected vitamins.
Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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Textbook
J. E. McMurry: Organic Chemistry, 10th Edition 2023 (or earlier editions) https://assets.openstax.org/oscms-prodcms/media/documents/OrganicChemistry-SAMPLE_9ADraVJ.pdf
Further Reading
J. Clayden, N. Greeves, S. Warren: Organic Chemistry, 2nd Edition, Oxford University Press, 2012 Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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Organic chemistry II(b) is completed by a Class Test and final Exam, according to the rules of the Faculty of Science of Charles University. Chapter 14 (and also 13) may be moved here from OCH I(b), if some of the lecture slots in the winter semester are cancelled due to the state holidays and/or the rector’s and dean’s days.
Attendance at lectures and tutorials is not mandatory but highly recommended. Homework, assigned every week, is not mandatory but highly recommended.
Class Test: Required is achieving the score of at least 60% mark (60/100) in total. There are two options: (1) One Combined Class Test to be sat at the end of the semester; or (2) two Partial Class Tests (2 x 30/50), one in the middle of the semester and the other at its end. In case of the failure to obtain at least 30/50 marks in the first Partial Class Test, the candidate will be required to sit the Combined Class Test (60/100). There will be several dates allocated for the Combined Class Test; however, there will only be one date for each of the Partial Class Tests.
Exam: The exam is in a written form and is available for the candidates who have successfully passed the Class Test. Required score to pass the Exam is at least 60% mark (60/100). Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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Outline of the lectures on Organic Chemistry II(b) for undergraduate study at the Faculty of Science of Charles University, Prague.
15. Aldehydes and ketones: Structure, nomenclature, and properties. Synthesis: oxidation of alcohols (including NAD+). Reactivity: nucleophilic additions (addition of water, alcohols, amines, hydrazine, hydrogen cyanide, and Grignard reagents); reduction; Michael addition to α,β-unsaturated aldehydes and ketones; organocuprate addition; biochemical nucleophilic addition (e.g., NADH). 16. Carboxylic acids and nitriles: Structure, properties, nomenclature, and substituent effects on pKa. Synthesis: oxidation of aldehydes and hydrolysis of nitriles. Reactivity: reduction. Chemistry of nitriles. 17. Derivatives of carboxylic acids: Acid halides, anhydrides, esters, thioesters (coenzyme A), phosphates, and polyamides; esterification and transesterification.. 18. Substitution reaction at the α-position of carbonyl compounds: Keto-enol tautomers, pKa, α-halogenation and alkylation of enolates and enamines (Stork Reaction). Aldol reaction, Claisen and Dieckmann condensation, Michael addition, and Robinson annulation. 19. Amines: Structure, properties, nomenclature, acid-base properties, solubility. Synthesis: Reductive amination, reduction of amides and nitriles. Reactivity. 20. Saccharides: Classification, stereochemistry, nomenclature, cyclic structures (acetals), epimers, anomers, anomeric effect. Glycosides (including synthesis), disaccharides, polysaccharides. Biological function of saccharides. 21. Amino acids, peptides, and proteins: Structure, nomenclature, configuration, isoelectric point, synthesis. Peptides: Merrifield synthesis, protecting groups, biological function. Proteins: brief introduction to the structure and function. 22. Heterocycles: Basic aromatic heterocycles (pyrrole, furan, thiophene, pyridine, indole). Structure and reactivity: electrophilic and nucleophilic reactions. Medicinal applications. 23. Nucleic acids and nucleotides: Structure and function: base-pairing (Watson-Crick model), DNA replication, transcription to RNA, and translation (mechanism of protein biosynthesis). 24. Lipids: Fat, soap, phospholipids, structure of cell membranes. 25. Isoprenoids: Terpenes, steroids (cholesterol, vitamin D, sexual hormones, corticoids, bile acids, cardenolides), ubiquinones (coenzyme Q). Isoprenoid biosynthesis and its inhibition. 26. Antibiotics, alkaloids, substances influencing CNS, neurotoxins, and selected vitamins: Structure and function (a brief introduction). Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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By the end of the course, students should be able to:
1. Design the synthesis of aldehydes, ketones, carboxylic acids, and their derivatives 2. Apply the addition of nucleophiles to aldehydes and ketones (including the formation of acetal, aminal, imines, and enamines, and reactions with Grignard reagents and Michael addition) in organic synthesis. 3. Interpret the substituent effect on the acidity of carboxylic acids. 4. Compare the chemical properties of carboxylic acid derivatives (acid halides, anhydrides, esters, amides, and thioesters) and use this knowledge for organic synthesis. 5. Analyze the substitution reaction at the α-position of carbonyl compounds, including the keto-enols tautomers. 6. Apply aldol reactions, Claisen and Dieckmann condensation, and related reactions in organic synthesis. Identify their role in biochemical reactions and in biosynthesis of natural products. 7. Design the synthesis of amines via reductive amination, reduction of amides and nitriles, and other methods. 8. Recognise saccharides according to their configuration and predict their behaviour. 9. Design a stereocontrolled synthesis of glycosides and disaccharides with the use of neighbouring group effects and protecting groups. 10. Describe the structure and function of di-, oligo-, and poly-saccharides. 11. Design the synthesis of amino acids and peptides using a solid-state synthesis and protecting groups. Utilize methods for separation of amino acid mixrures 12. Define the structure of proteins. 13. Analyze the structure and reactivity of aromatic heterocycles. 14. Describe the structure of nucleic acids and their role in replication and proteosynthesis, including the mechanism of replication and translation. 15. Describe the properties and biosynthesis of isoprenoids and the role of steroids in living organisms. 16. Understand the structure and biological role of antibiotics, alkaloids, substances influencing CNS, neurotoxins, and selected vitamins: Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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