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Course, academic year 2023/2024
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Physical Organic Chemistry I - MC270P95
Title: Fyzikální organická chemie I
Czech title: Fyzikální organická chemie I
Guaranteed by: Department of Organic Chemistry (31-270)
Faculty: Faculty of Science
Actual: from 2020
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:2/1, C+Ex [HT]
Capacity: unlimited
Min. number of students: 3
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
Guarantor: doc. RNDr. Jindřich Jindřich, CSc.
Teacher(s): RNDr. Tomáš Slanina, Ph.D.
Incompatibility : MC270P03
Annotation -
Last update: PharmDr. Eliška Matoušová, Ph.D. (19.08.2019)
The course is composed from lectures and seminars that are complementary to each other. Students will learn how to understand the relationship between the structure of organic compounds and their reactivity. The aim is to gain knowledge about the use of physicochemical methods for practical examples where students will learn how to propose, study and optimize mechanisms of organic reactions. Gained knowledge will help students to get orientation in contemporary chemical literature and to interpret the results of experimental and theoretical studies.
Literature -
Last update: PharmDr. Eliška Matoušová, Ph.D. (19.08.2019)

Required literature

E.V. Anslyn, D.A. Dougherty: Modern Physical Organic Chemistry, University Science Books 2006. ISBN 1891389319

Recommended literature

I. Fleming: Molecular orbitals and organic chemical reactions. John Wiley & Sons, 2010. ISBN 9780470746585

P. Klán, J. Wirz: Photochemistry of Organic Compounds: From Concepts to Practice. John Wiley & Sons Ltd., 2009. ISBN 978-1-4051-9088-6
Requirements to the exam -
Last update: PharmDr. Eliška Matoušová, Ph.D. (19.08.2019)

Requirements for the seminar: attendance (min. 75 %), min. 75 % of homework handed in, mid-term test (min. 60 % of correct answers).

Requirements for the examination: successful completion of the seminar, final written examination (min. 60 %) and oral examination.

Requirements for written and oral examination: knowledge of basic principles between structure and reactivity, ability to apply the physicochemical principles on studies of model examples of organic reactions, ability to propose key experiments for investigation of reaction mechanisms and optimization of their parameters.
Syllabus -
Last update: PharmDr. Eliška Matoušová, Ph.D. (19.08.2019)

1. Introduction. Definition of Physical Organic Chemistry. Basic methodological concepts. Empirical rules for determination of organic reaction mechanisms. Dimension, time, rate and energy in chemistry. Chemical bond. Lewis structures. Valence bond theory. Resonance. Electronegativity. Hybridization. VSEPR. Dipoles, quadrupoles, polarizability.

2. Molecular Orbitals and Reactivity. Construction of molecular orbitals. Salem-Klopman equation. MO-LCAO for H2, CH4, water, ethane, ethylene, formaldehyde. Walsh orbitals for cyclopropane. Hückel approximation. Correlation diagrams. Woodward-Hoffmann, Dewar-Zimmerman, Fukui (FMO) models. Selection rules.

3. Aromaticity. Aromaticity. Antiaromaticity. Homoaromaticity. Hückel, Woodward-Hoffmann, Baird, Clar rules. NICS, ACID methods. Aromatic ions and dipoles. Polycyclic aromatic compounds. Pericyclic reactions: Electrocyclizations, cycloadditions (Diels-Alder, ketenes), sigmatropic rearrangements, ene reactions, atom transfer reactions.

4. Stability of Molecules. Thermochemical calculations. Bond dissociation energy. Benson tables. Conformation of acyclic and cyclic hydrocarbons and their derivatives. Torsion and stereoelectronic effects. A-values. Bredt rule. Hyperconjugation. Anomeric effect. FMO rationalization of stereoelectronic effects. Baldwin rules. Thorpe-Ingold effect.

5. Noncovalent Interactions and Solvation. Chemistry and phases. Solvent effects. Solvent cage effect. Solvatochromism. Hughes-Ingold model. Hydrogen bonding. Halogen bonding. Cation-π-Interaction, π-π-Interaction. Hydrophobic effect. CT interaction. Molecular recognition. Supramolecular interactions. Ionic liquids. Chiral solvation.

6. Acids and Bases. Acid-base equilibria in different solvents and phases. Acidity function. Brønsted equation, Substituent effects and strengths of Brønsted acids and bases. Kinetic acidity. Superacids. Preparation of thermodynamically unstable acids. Photoacidity.

7. Chemical Reactivity. Hard and soft acids, bases, nucleophiles and electrophiles (HSAB theory). Ambident nucleophiles/electrophiles. Reactivity indices. Rate constants and transition state. Activation and driving force of reactions. Activation enthalpy and entropy. Kinetics. Arrhenius and Eyring equation and its connection to statistical thermodynamics. Hammond postulate. Bell-Evans-Polanyi principle. O'Ferrall-Jencks diagrams. Curtin-Hammett principle

8. Thermodynamics and Kinetics and other Tools to Study Mechanisms. Linear free energy relationship (LFER): Hammett equation. Taft equation. QSAR. Kinetic isotope effects. Singleton experiment. Isotopic labelling. Cross experiments. Stereochemical analysis. Kinetic analysis, reaction order determination, experimental kinetic methods, differential least squares fitting.

9. Catalysis. Thermodynamic cycle. Specific and general acid-base catalysis. Brønsted coefficients. Lewis acid and base catalysis. Intramolecular catalysis. Transition metal catalysis. Immobilized and heterogenous catalysts. Langmuir model. Phase transfer catalysis. Asymmetric catalysis.

10. Photochemistry. Electronic excitation. Photophysical and photochemical processes. Jabłoński diagram. Energy transfer. Stern-Volmer analysis. Tools to study photochemical processes.

11. Electron Transfer. Koopmans theorem. Ionization potential, electron affinity and CT complexes. Marcus theory. Electron transfer in SN reactions. Non-equilibrium electron transfer. PeT, conPeT. Photoredox catalysis.

12. Effects of external factors on reactivity: temperature, pressure, concentration, Le Chatelier-Brown principle, non-classical Activation of Chemical Reactions. Spin chemistry. Magnetic field effect. Magnetic isotope effect. Microwave chemistry. Sonochemistry. Mechanochemistry. Radiation chemistry. Plasma chemistry. Chemistry in space. Mode-specific photochemistry (VIPER).
 
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