Organic synthesis (specialization) 0600-S2-SP/W-SO
,,Mechanisms of organic reactions'' (lecture). Description of reaction mechanisms: molecularity, transition state, reactions profiles, activation parameters, reaction maps. Investigation of reaction mechanisms: reaction order and rate, kinetic measurements, solvent effects, determination of activation parameters, kinetic isotope effects, thermodynamic and kinetic control stoichiometry and product analysis and linear free energy relationships. Reactive intermediates: free radicals, carbonium ions, non-classical carbocations, carbanions, carbenes, nitrenes - formation, identification, structures, conversions.The use of isotopes for investigation of the reactions mechanisms. Spectroscopic methods in investigation of the reaction mechanisms. Steric difficulty of delocalization.
Nucleophilic substitution, additions to the C=C, C=N and C=N double bonds. Elimination reactions. Molecular rearrangements. Acidity and basicity of organic compounds.
Mass spectrometry. Ionization methods used in MS (FAB, LSIMS, MALDI, desorption methods, e.g. PD, LD, FD; thermo-(TSP) and electro-(ES, ESI)spray; chemical ionisation under atmospheric pressure (APCI)), analyzers, methods of sample insertion. LC- and GC-MS. Tandem Mass Spectrometry (MS-MS). The theory of fragmentation reactions.
Nuclear magnetic resonance. Advanced one- and two-dimensional methods (TOCSY, NOE effect, ROESY, INADEQUATE), dynamic NMR (DNMR), shift reagents – application of these methods to structure elucidation of organic compounds. Magnetic resonance of 11B, 14N, 15N, 31P, and 19F.
,,Retrosynthetic analysis in organic chemistry'': The course covers the following topics: introduction of basic concepts of retrosynthetic analysis. Acquaint with the fundamental disconnection rules of organic compounds (target molecule structure analysis), synthons generated in the process retrosynthetic analysis and their synthetic counterparts. Comparison of linear and convergent syntheses. Discussion of selected methods of C-C bond formation and transformation of functional groups, and chemo-, regio- and stereoselective reactions. Demonstrate by example of multistep syntheses of organic compounds the rules governing of retrosynthesis. The student analyzes the structure of target molecules and design of simple structures of organic synthesis.
,,Chemistry of drugs'': Historical survey of drug chemistry. Drug nomenclature. Pharmacological and chemical drug classification. Influence of physicochemical factors on stability, absorption, and distribution of drugs. Theory of receptors. Mechanism of drug action at enzymes. Drugs biotransformation. Chemical structure versus drug-target interaction. Isolation of drugs from natural products. An overview of the process of drug discovery. Drug design - SAR and QSAR. Synthesis of drugs. Screening of drugs. Selected classes of drugs – anaesthetics; analgesics, anti-inflammatory drugs, antimicrobial drugs, anti-AIDS drugs, and anti-cancer drugs.
Laboratory: Completion of five tasks related to the isolation of substances from biological material and synthesis of structurally simple drugs. Comparative analysis and assessment of purity of synthesized and purchased drugs.
,,Structures of heterocyclic compounds'': Nomenclature of heterocyclic compounds. Non-aromatic heterocyclic compounds with small (three- and four-membered), normal (five- and six-membered) and larger rings - structure, physical properties, synthetic methods, reactivity, biological importance, applications in organic technology. Aromaticity of heterocyclic compounds, electronic structure and reactivity. Strycture, physical properties, synthetic methods, reactiviyu, biological importance, and practical applications of the following classes of compounds: a) six-membered heteroaromatic rings with one heteroatom (pyridines, pyrylium salts, pyrones), b) six-membered heteroaromatic rings with two and three nitrogen atoms (diazynes, triazynes, purines, and pteridines), c. five-membered heteroaromatic rings with one heteroatom (pyrrole, furan, thiophene, porphyrins, phthalocyanines), d) five-membered heteroaromatic rings with two heteroatoms (azoles, mesoionic compounds, benzazoles), e) bicyclic heterocycles (indole, benzofuran, uinoline, isoquiniline).
Course coordinators
Learning outcomes
After completing the course, the student: can recognize basic mechanisms of organic reactions, presents methods of their designation, compare acidity and basicity of various types of organic compounds. Explains differences and reasons of different course of the substitution, addition, elimination and molecular rearrangement reactions. Interprets the results of kinetic investigations of organic reactions. The student can analyze and interpret MS and NMR spectra as well as identifies organic compounds on the basis of their MS and NMR spectra.
The student analyzes the structure of target molecules and design of simple structures of organic synthesis.
The student defines the basic concepts of medicinal chemistry. Selects appropriate methods for the manufacture of medicines and techniques of analysis and evaluation of their purity. Uses literature sources in obtaining and verifying knowledge in medicinal chemistry. The student analyzes the purity of drugs.
The student can recognize typical types of heterocyclic compounds an and connect their properties with a structure.
Assessment criteria
Writting exams.
Laboratory: ending written test
Bibliography
,,Mechanisms of organic reactions'' (lecture): P. A. Sykes, Guidebook to Mechanism in Organic Chemistry, Longman Scientific & Technical, Harlow 1986.
M. G. Moloney, Structure and Reactivity in Organic Chemistry, Blackwell Publishing, Oxford, 2008.
Richard A. Jackson, Mechanizmy reakcji organicznych, Wydawnictwo NaukowePWN, Warszawa 2007. K. C. Nicolaou, R. Hanko, W. Hartwig, Handbook of Combinatorial Chemistry, Wiley-VCH, Weinheim, 2002;
S. R. Wilson, A. W. Czarnik, Combinatorial Chemistry: Synthesis and Application, Wiley-Interscience, New York, 1997;
T. Eichler, S. Hauptmann, The Chemistry of Heterocycles, Wiley-VCH, Weinheim 2003,
J. Młochowski, Chemia związków heterocyklicznych, PWN, Warszawa, 1994.
F. Z. Dörwald, Organic Synthesis on Solid Phase, Wiley-VCH, Weinheim, 2002;
G. Jung, Combinatorial Chemistry: Synthessi, analysis, screening, Wiley-VCH, Weinheim, 2001;
W. Bannwarth, B. Hinzen, Combinatorial Chemistry: From Theory to Application, Wiley-VCH, Weinheim, 2006;
S. Brase, Combinatorial Chemistry on Solid Supports. Topics in Current Chemistry, Springer-Verlag, Berlin-Heidelberg, 2007;
R. A. W. Johnstone, M. E. Rose, Spektrometria mas, Wydawnictwo naukowe PWN, Warszawa, 2001 (in Polish)
F. W. McLafferty, Interpretation of Mass Spectra, University Science Books, Mill Valey 1993;
R. M. Silverstein, F. X. Webster, D. J. Kiemle, Spektroskopowe metody identyfikacji związków organicznych, Wydawnictwo naukowe PWN, Warszawa, 2007 (in Polish);
A. S. Płaziak, Introduction to Mass Spectrometry of Organic Compounds, UAM, Poznań 1997 (in Polish);
H. Friebolin, Basic One- and Two-Dimensional NMR Spectroscopy, VCH, Weinheim 1993;
E. Breitmaier, Structure Elucidation by NMR in Organic Chemistry, J. Wiley, New York 1993.
J. W. Hennel, J. Klinowski, Podstawy magnetycznego rezonansu jądrowego, Wydawnictwo naukowe UAM, Poznań, 2000 (in Polish);
J. H. Gross, Mass Spectrometry, Springer, Berlin, 2004.
1. S. Warren, P Wyatt, Organic Synthesis: The Disconnection Approach, Wiley, Chichester, 2008.
2. J. Clayden, N. Greeves, S. Warren, P. Wothers, Organic Chemistry, Oxford University Press, Oxford, 2001.
3. Ch. Willis, M. Willis, Synteza organiczna, WUJ, Kraków 2004.
4. J. Skarżewski, Wprowadzenie do syntezy organicznej, PWN, Warszawa, 1999.
5. J. Gawroński, K. Gawrońska, K. Kacprzak, M. Kwit, Współczesna synteza organiczna, PWN, Warszawa, 2004.
G. L. Patrick, Chemia leków. Krótkie wykłady, PWN, Warszawa, 2004;
R. B. Silverman, Chemia organiczna w projektowaniu leków, WNT, Warszawa, 2004;
G. L. Patrick, Chemia medyczna. Podstawowe zagadnienia, Wydawnictwa Naukowo-Techniczne, Warszawa, 2003;
G. Thomas, Medicinal Chemistry – An Introduction, John Wiley and Sons Ltd., Chichester, 2000;
A. Zejc, M. Gorczyca, Chemia leków, PZWL, Warszawa, 1999;
Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry, wyd. J. H. Block, J. M. Beale, Jr, Lippincott Williams & Wilkins, Philadelphia, 2004.
Additional information
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