The main objective of the course is to familiarize students with the basic principles of modern organic chemistry, understanding the structure-activity relationship of organic compounds and application of methods in syntheses of organic compounds in the biosciences and industry.
Enrolment requirements and required entry competences for the course:
Attended lectures and completed exercises of General and inorganic chemistry and Analytical chemistry courses.
Learning outcomes at the level of the study programme to which the course contributes:
1. Ability to identify and solve qualitative problems by applying of appropriate chemical principles and theories,
2. Competences in the estimation, interpretation and synthesis of chemical information and data,
3. Performing of standard laboratory techniques and the use of adequate instrumentation that is used in the preparative purposes and organic systems,
4. Results interpretation of laboratory observations and measurements, their meanings and connection with corresponding theory,
5. Management and planning of time skills, the ability for independent work
Expected learning outcomes at the level of the course (4-10 learning outcomes):
1. To analyze the structure of the compounds of carbon, organic compounds and define the nature of chemical bonds in organic molecules based on molecular orbital theory and hybrid atomic orbitals,
2. To define the basic types of organic reactions and explain their reaction mechanisms with the recognition of reactive intermediates in reaction,
3. To idetify functional groups in molecules and define corresponding class of compounds, to apply IUPAC rules for naming of organic compounds,
4. To explain conformations of alkanes and cycloalkanes, define and name isomers,
5. To define reactions of alkanes, alkenes, alkynes, alcohols, ethers, reactions in which alky halides, alkenes, alkynes, alcohols and ethers are involved,
6. To explain radical reactions.
1. CARBON COMPOUNDS AND INTRODUCTION TO STRUCTURAL THEORY OF ORGANIC CHEMISTRY: introduction to structural theory: the empirical and structural molecular formulas, isomers, tetrahedral structure of methane; chemical bonds-the octet rule, ionic and covalent bonds, Lewis structures, resonance; quantum mechanics, atomic and molecular orbitals; structure of methane and ethane: sp3-hybiridisation; structure of ethene: sp2-hybiridisacija, cis-trans isomerism; structure of ethyne: sp-hybridisation.
2. INTRODUCTION TO ORGANIC REACTIONS: ACIDS AND BASES: Types of chemical reactions and their mechanisms; acid-base reactions, Brönsted, Lowry and Lewis definitions of acids and bases; heterolysis of carbon bond (carbocations and carbanions), the strength of acids and bases, the relationship between structure and function of acid, the acidity of carboxylic acids, organic compounds as base; introduction to the mechanisms of organic reactions.
Seminar examples for acid-base reaction, recognition of acids and bases in reaction and acidity of given compounds.
3. CLASSES OF CARBON COMPOUNDS, FUNCTIONAL GROUPS: Hydrocarbons: alkanes, alkenes, alkynes and aromatic compounds; functional groups in organic molecules, alkyl halides, alcohols, ethers, amines, aldehydes and ketones, carboxylic acids, esters, amides, nitriles. The relationship of the structure and physical properties of the molecules (hydrogen bonding, van der Waals forces)
4. ALKANES - CONFORMATIONAL ANALYSIS AND INTRODUCTION TO SYNTHESIS: Conformational analysis of alkanes, relative stability of cycloalkanes - ring tension, cis- and trans-isomerism of cycloalkanes, syntheses of alkanes and cycloalkanes.
5. STEREOCHEMISTRY AND CHIRALITY I: The biological significance of chirality; isomerism: constitutional isomers and stereoisomers; chiral molecules and enantiomers, enantiomer nomenclature (Cahn-Ingold-Prelog system of rules R, S), relative and absolute configuration, optical activity of enantiomers, molecules with multiple chiral centers, meso-compounds, Fischer projection formula, stereoisomerism of cyclic compounds.
6. STEREOCHEMISTRY AND CHIRALITY II: Heteroatoms as centers of chirality, axial chirality, helical structure, homochirality in nature, pseudochirality, prochirality, diastereomers, preparation of enantiomerically pure compounds (fractional crystallization of racemates, chromatographic separation of enantiomers on chiral stationary phases), chiral drugs interactions of drug enantiomer and receptor.
Seminar examples for determination of relative and absolute configuration of compounds with more than one chiral centers.
7. IONIC REACTIONS - NUCLEOPHILIC SUBSTITUTION REACTIONS OF ALKYL HALIDE: Nucleophilic substitution reactions: nucleophiles, leaving groups; kinetics, mechanism and stereochemistry of SN1 and SN2 reactions (carbocations); examples of organic synthesis by functional group transformation in SN2 reactions.
Seminar examples for the nucleophilic substitution reactions of alkyl halide.
8. IONIC REACTIONS - ELIMINATION REACTIONS OF ALKYL HALIDE: The impact of nucleophile on the elimination and substitution competitive reactions; mechanism of E1 and E2, stereoselectivity and regioselectivity of reaction E1, stereospecifity of substituted cyclohexane in E2 reactions, regioselektvnost in elimination reactions (Hoffman's and Zaitsev's rule), carbanionic mechanism of elimination (E1cB).
Seminar examples for elimination reactions of alkyl halide.
9. ALKENES AND ALKYNES I: SYNTHESIS AND PROPERTIES: Determining of E-and Z-configuration, the relative stability of alkenes, cycloalkenes, synthesis of alkenes by dehydrohalogenation of alkyl halide and dehydration of alcohols, and stability of carbocation and molecular rearrangement, synthesis of alkynes in elimination reactions, acidity of terminal alkynes.
Seminar examples of alkenes and alkynes syntheses and determination of E-and Z-configuration.
10. ALKENES AND ALKYNES II: THE ADDITION REACTION: Hydrogen halides addition to alkenes (Markovnikov's rule), the stereochemistry of ionic addition reaction of alkenes, oksymercuration and demercuration of alkenes (Markovnikov's additions) synthesis of alcohol by hydroboration and oxidation of alkenes (syn-hydration, anti-Markovnikov's rule), hydroboration of alkenes and synthesis of alkyl-borane, halogen addition to alkenes, the stereochemistry of the addition reaction of halogen to alkenes.
11. STRUCTURE DETERMINATION OF ORGANIC COMPOUNDS BY NUCLEAR MAGNETIC RESONANCE AND MASS SPECTROMETRY: Introduction to nuclear magnetic resonance spectroscopy (NMR), the spin of protons, shielding and deshielding effects of protons, chemical shift, chemical equivalent and non-equivalent protons, splitting of signal: the spin-spin coupling, 1H and 13C one- and two-dimensional nuclear magnetic resonance spectroscopy (1D and 2D NMR), introduction to mass spectrometry, ionization and fragmentation of molecular ion, determination of molecular formula and mass, applications of mass spectrometry in biomedicine.
12. RADICAL REACTIONS: Energy of homolitic bond cleavage and relative stability of radicals, selectivity in radical substitution reactions, chlorination of methane - energy activation, halogenation of higher alkanes, the geometry of alkyl radicals, radical additions to alkenes (anti-Markovnikov's addition of hydrogen halide), radical polymerization of alkenes, radicals in biology, medicine and industry.
13. ALCOHOLS: Synthesis of alcohols from alkenes, reactions of alcohols, alcohols as acids, conversion of alcohols to alkyl halides, the reaction mechanism of alcohols with hydrogen halides, alcohol derivatives with leaving groups: tosylates, mesylates and triflates, the reaction of alcohols with aldehydes and ketones - preparation of hemiacetals and acetals, silyl ethers as protecting groups of alcohols, sugar alcohols.
14. ETHERS: synthesis of ethers, silyl protecting groups of ethers, reactions of ethers (cleavage of ethers by strong acids), cyclic ethers (epoxides): synthesis by epoxidation of alkenes, Sharpless asymmetric epoxidation of alkenes; reaction of epoxides (acid-catalyzed ring-opening reaction, crown ethers: phase-transfer catalysts.