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Lecturer(s)
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Pospíšil Jiří, doc. RNDr. PhD.
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Course content
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Content The course focuses on advanced relationships between molecular structure, electronic properties, chemical reactivity, and molecular function. Students are introduced to contemporary concepts of physical organic chemistry, mechanistic analysis of chemical reactions, and modern approaches to predicting chemical behaviour. Topics include molecular structure and conformation, stereoelectronic effects, thermodynamic and kinetic control, mechanistic investigation, frontier molecular orbital theory, conceptual DFT, and computational approaches including machine-learning methods. The course also addresses applications in catalysis, chemical biology, enzymatic transformations, bioorthogonal chemistry, and late-stage functionalization. Emphasis is placed on mechanistic reasoning, interpretation of experimental data, and critical analysis of current scientific literature. Study Materials The primary study materials consist of lectures, recommended textbooks, review articles, and current publications in leading international journals. Students are expected to work extensively with primary scientific literature focusing on mechanistic analysis, structure-reactivity relationships, and modern approaches to predicting chemical behaviour. Selected review papers and case studies from physical organic chemistry, catalysis, chemical biology, and molecular sciences form an integral part of the course.
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Learning activities and teaching methods
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Lecture
- Attendace
- 6 hours per semester
- Semestral Work
- 55 hours per semester
- Preparation for the Exam
- 37 hours per semester
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Learning outcomes
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The course aims to develop an advanced understanding of the relationships between molecular structure, electronic properties, chemical reactivity, and molecular function. Emphasis is placed on mechanistic reasoning, interpretation of experimental and computational data, and the application of modern concepts of physical organic chemistry to explain and predict chemical behaviour. Students learn to critically evaluate scientific evidence, formulate and test mechanistic hypotheses, and analyse structure-reactivity relationships in complex molecular systems. The course promotes independent scientific thinking, effective use of scientific literature, and the ability to address complex research problems in contemporary molecular sciences.
The student is able to independently analyse scientific literature related to structure-reactivity relationships in molecular systems. They can formulate and critically evaluate mechanistic hypotheses, integrate experimental and theoretical evidence, and interpret data relevant to chemical reactivity and molecular behaviour. The student is capable of defending scientific conclusions using evidence-based arguments and communicating complex mechanistic concepts in a professional scientific discussion. The acquired competences can be applied to experimental design, data interpretation, and the solution of complex research problems in chemistry.
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Prerequisites
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Students are expected to possess advanced knowledge of organic chemistry at the Master's level, particularly in molecular structure, chemical reactivity, reaction mechanisms, and the fundamentals of physical organic chemistry. The ability to independently read and critically analyse scientific literature in English is required. Basic familiarity with computational chemistry, catalysis, or chemical biology is advantageous but not mandatory for successful course completion.
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Assessment methods and criteria
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Oral exam, Seminar Work
Active participation in the block course and independent study of scientific literature. Students are required to prepare a written critical analysis (5-10 pages) of a selected structure-reactivity problem based on primary scientific literature. The examination includes a 30-minute scientific presentation followed by a discussion. Students are expected to demonstrate the ability to critically evaluate experimental evidence, formulate mechanistic hypotheses, and interpret contemporary findings within the context of modern molecular science.
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Recommended literature
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Recent publications from: Nature Chemistry, Nature Chemical Biology, Nature Catalysis, ACS Central Science, Chemical Science, Journal of the American Chemical Society, Angewandte Chemie, Accounts of Chemical Research.
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Anslyn, E. V., Dougherty, D. A. (2006). Modern Physical Organic Chemistry. Sausalito.
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Carey, F. A., Sundberg, R. J. (2007). Advanced Organic Chemistry. Part A: Structure and Mechanisms. New York.
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Clayden, J., Greeves, N., Warren, S., Anslyn, E. V. (2025). Organic Chemistry. 3rd ed.
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Mayr, H. (2016). Selected publications on nucleophilicity and electrophilicity scales.
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