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Structure of organic compounds, properties of covalent bonds, non-covalent interactions, reactions of covalent bonds. Carbon skeleton and functional groups. Nomenclature of organic compounds, classification and main groups of organic compounds. Spatial structure of organic molecules, isomers, configuration, conformation, chirality, enantiomers, and diastereoisomers. Electronic and stereoelectronic effects, intermediates, carbocations, carbanions, carbenes, radicals, aromaticity, delocalization, resonance. Mechanisms of reactions: nucleophilic and electrophilic substitution, radical and electrophilic addition, elimination, oxidation, and reduction. Systematic overview of selected compounds: alkanes, alkenes, alkynes, alkyl halides, aromatic compounds, alcohols, phenols, thiols, and sulfides. Other compounds are systematically discussed in the following semester (OCH IIb).
Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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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 I(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 to OCH II(b), if some of the lecture slots are cancelled due to the state holidays and/or the rector’s and dean’s days. This will be announced by the lecturer.
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 I(b) for undergraduate study at the Faculty of Science of Charles University, Prague.
1. Structure and bonding: Orbitals; hybridization; chemical bonding. 2. Polar chemical bonds: electronegativity; dipole moment; formal charges; resonance; Brønsted acids and bases; pKa; Lewis acids and bases. 3. Alkanes and cycloalkanes: Functional groups; nomenclature (discussed mainly in tutorials); properties of alkanes and cycloalkanes. Conformation of alkanes and cycloalkanes; axial and equatorial bonds in cyclohexane; polycyclic molecules. 4. Overview of organic reactions: Reaction types; radical and ionic mechanism; curly arrows; energy diagrams; transition states; intermediates. 5. Stereochemistry: Symmetry, isomerism; chirality; stereogenic centres; enantiomers; diastereoisomers; optical activity; racemates and their resolution; configuration and conformation; R/S and D/L assignment 6. Alkenes 1: Structure and reactivity; cis-/trans-isomers; E/Z-isomers; electrophilic additions; Markovnikov rule; structure and stability of cations; cation rearrangements; Hammond postulate. 7. Alkenes 2: Synthesis of alkenes – elimination reactions. Reactions of alkenes: Halogenation; hydration; hydroboration; dihydroxylation; epoxidation; hydrogenation; ozonization; carbene addition; radical reactions; polymerization; stereoelectronic effect and Fürst-Plattner rule. 8. Alkynes: Structure and reactivity; nomenclature; synthesis; partial hydrogenation; hydration; halogenation; acidity (pKa); acetylide ions and their synthetic use. 9. Alkyl halides 1: Structure; nomenclature; synthesis from alkanes, alkenes, and alcohols; Grignard reagents; organocuprates; Suzuki coupling. 10. Alkyl halides 2: Nucleophilic substitution SN1 and SN2; elimination E1 and E2; Zaitsev rule; elimination in cyclohexane; use of isotope effect in mechanistic studies. 11. Conjugated dienes: Electrophilic addition; allylic cations; polymerization; Diels-Alder reaction; 1,3-dipolar addition and click chemistry. 12. Aromatic compounds: Structure and stability; aromaticity; nomenclature; electrophilic aromatic substitution; substituent effects; nucleophilic aromatic substitution. Aromatic amines: diazonium salts and their reactions (Sandmeyer reaction). 13. Alcohols and phenols: Structure, nomenclature, properties, hydrogen bonding. Synthesis from alkyl halides, alkenes, and carbonyl derivatives. Reactions: dehydration, oxidation, protecting groups. 14. Ethers, thiols, and sulfides: Structure, nomenclature, properties. Synthesis from alkyl halides and alkenes. Reactions: cleavage, Claisen rearrangement. Crown ethers. 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. Explain the structure of the chemical bond based on orbitals and hybridization and their effect on molecular geometry. 2. Identify polar and non-polar chemical bonds using the electronegativity scale, dipole moment, and formal charges. 3. Analyze resonance structures and their impact on the stability and reactivity of molecules. 4. Classify Brønsted acids and bases upon their behaviour in acid-base reactions. 5. Apply nomenclature and character of functional groups in alkanes, cycloalkanes, and their polycyclic derivatives. 6. Compare configuration and conformation isomers of alkanes, alkenes, and cycloalkanes, including axial and equatorial bonds in cyclohexane; asses their relative stability. 7. Rationalize various types of organic reactions, including radical and ionic mechanisms by utilizing curly arrows and energy diagrams. 8. Predict the reactivity of alkenes in hydrogenation, electrophilic additions, namely in hydrohalogenation, hydratation, halogenation, hydroboration, epoxidation, and dihydroxylation and propose the mechanism for these reactions. 9. Apply the Markovnikov and Zaitsev rules in reactions of alkenes and in elimination and rationalize these rules by electronic and stereoelectronic effects. 10. Rationalize the structure and properties of alkynes, their synthesis and reactivity; apply acetylide ions in organic synthesis. 11. Understand the stereochemical terms, namely chirality, enantiomers, diastereoisomers, and racemates (including their resolution). 12. Analyze mechanisms SN1 and SN2, predict the influence of the substrate structure, the leaving group, the nucleophile, and the solvent and the impact on the mechanism and stereochemical outcome. 13. Recognize the E1 and E2 mechanism, its impact on the steric course, and the use of isotope effect in determining the reaction mechanism. 14. Rationalize the course of electrophilic addition to conjugated dienes and its mechanism with a view of kinetic and thermodynamic control of the reaction. 15. Predict the outcome of the Diels-Alder reaction using the endo-rule and design its modifications for chemical biology. 16. Employ the 1,3-dipolar click reaction for the use in chemical biology. 17. Analyze the structure, stability, and reactivity of aromatic compounds, including the principles of aromaticity and mechanistic features of electrophilic and nucleophilic aromatic substitution. 18. Analyze the reactivity of alcohols and phenols (including dehydration, oxidation, and Claisen rearrangement) and design their synthesis from alkenes, alkyl halides, carbonyl compounds, and other starting materials. 19. Apply crown ethers in organic synthesis. 20. Synthesize thiols, sulfides, and disulfides. Last update: Míšek Jiří, doc. RNDr., Ph.D. (31.03.2026)
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