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Organic Chemistry
First semester
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Learning outcomes of the course unit

At the end of the course students are expected to have gained the following skills:
1. Knowledge and Understanding:
- To recognize nomenclature, structure and reactivity of the main organic compound classes, either linear, carbocyclic, heterocyclic or fused bicyclic
- To explain with useful examples the principles underlying advanced organic reactions allowing the rationally interpretation of reaction mechanisms and understanding of similarities and differences among different reaction pathways
2. Applying Knowledge and Understanding
- To select information and ideas in order to make judgments and apply such information to solve ever emerging problems of organic synthesis, and to propose ways to design and synthesize simple chiral organic compounds.
3. Communication and Learning Skills
- To acquire learning skills and communication skills by employing appropriate language to both specialized and non-specialized audience, in line with the above mentioned objectives.
- To communicate the results of an empirical research writing and discussing a critical essay.
4. Making Judgements
- To critically review a synthetic strategy aimed at the preparation of a small, polyfunctionalized molecule.


To fully appreciate the content of the course, it is necessary to acquire knowledge of general and inorganic chemistry and organic chemistry basics in previous courses. To access the final examination, it is necessary to pass the “Organic Chemistry I” exam.
Nomenclature of functional groups in organic chemistry
Synthesis and reactivity of common functional groups and synthesis of simple functionalized molecules.
Acid-base reactivity and equilibria of organic compounds

Course contents summary

The first part of the course is devoted to recall and advance knowledge acquired in the Organic Chemistry I course. Particular attention will be devoted to the topics related to the formation of new carbon-carbon bonds, functional group interconversion, protecting group insertion and cleavage. The second part of the course allows students to acquire knowledge on retrosynthetic strategies for the total synthesis of bioactive compounds.

Course contents

1. Nomenclature of Aromatic Carbocyclic and Heterocyclic Compounds. Nomenclature of fused bicycles.
2. Reactivity of Benzene and Related Aromatic Compounds
Electrophilic aromatic substitution, synthesis of mono- and di-substituted benzenes, diazonium salts, nucleophilic aromatic substitution, organometallic aromatic compounds
3. Introduction to the Palladium catalyzed coupling reactions
Heck Reaction, Suzuki Reaction, Sonogashira Reaction, Stille Reaction
4. Enol and Enolates
Keto-enol tautomer equilibria, acidity and basicity of enols and enolates; acid- and base-catalyzed enolization; metal enolates, ammonium enolates; silicon-stabilized enolates; kinetic vs thermodynamic enolates; Z/E geometry control of enolates; non cabonylic enolates; ylides.
4a. Aldol Reaction
The “classic” acid- and base-catalyzed aldol reaction, the crossed aldol reaction, the Mukaiyama aldol reaction, the intramolecular aldol reaction, the vinylogous aldol reaction, the Henry reaction, the Nef reaction; Baylis-Hillmann Reaction.
4b. Mannich Reaction
Imines and iminium ions, the direct and indirect Mannich reaction, the vinylogous Mannich reaction.
4c. Other Reactions
Michael reaction, The Claisen and Dieckmann reactions; Knovenagel reaction.
5. Double Bond-Forming Reaction
Stabilized and non stabilized phosphorus Ylides, the Wittig reaction, Horner-Emmons reaction, Still-Gennari variant of the HWE reaction, sulfur ylides and Julia olefination, Peterson reaction.
6 Allylation Reaction
Allyl-silanes, allyl-boranes, allyl-stannanes in organic synthesis. Tsuji-Trost allylation
7. Pericyclic Reactions
Diels Alder Reaction. Sigmatropic Transpositions.

Recommended readings

Suggested textbook:
J. CLAYDEN, N. GREEVES, S. WARREN, "Organic Chemistry", Second edition, Oxford 2012.
Supplementary material:
Scientific articles suggested by the teacher
Reference books:
2. Francis A. Carey, Richard J. Sundberg "Advanced Organic Chemistry. Part A: Structure and Mechanisms", Springer-Verlag; Fifth Ed. 2007.
3. Francis A. Carey, Richard J. Sundberg "Advanced Organic Chemistry. Part B: Reaction and Synthesis", Springer-Verlag; Fifth Ed. 2007.

Teaching methods

According to the abovementioned objectives and contents, the course will be carried out through frontal oral lessons favoring active learning modalities using a heuristic-socratic approach, implying a dialogical relationship with the students. In the second part of each lesson, suitable exercises will be proposed dealing with the design, synthesis, and transformation of simple organic molecules which could be connected with the pharmaceutical and biological domains. These exercises are open for free discussion between teacher and students and they are considered an essential part of the course. Also several “case studies” will be analyzed following those criteria and methods described in the teaching and bibliographical material provided. All teaching slides will be uploaded weekly on Elly web-platform. All students willing to download the slides need to enlist first on the on-line course. These slides are considered to all intents and purposes important teaching material, as the books are. All not-attending students should always check on a regular basis the available material on the Elly-platform.

Assessment methods and criteria

The final examination consists of a colloquium and a written assay on a reported total synthesis to be discussed at the end of the colloquium.
The colloquium deals with the execution of exercises on asymmetric synthesis and reactivity of organic compounds. This test is aimed at verifying whether the student has developed the skill and ability of 1) recognizing the relationship between structure and properties of organic compounds, 2) predicting the behavior of a given organic chemistry transformation among those comprised in the program, 3) selecting and deploying information from the theory study in order to furnish solutions to a given practical organic synthesis problem, and finally 4) acquiring learning skills and communication skills by employing appropriate language to both specialized and non-specialized audience.
The written assay will focus on a critical comment on the published synthesis of a target, as well as on the mechanisms and transition states of key reactions exploited during the synthesis. The student may carry out the work alone or in a group of no more than 5 persons. Each student has to submit its own written assignement within two weeks of the date of the colloquium. All information related to the execution of the assay will be discussed during the course lessons and will be uploaded on the Elly platform.
The colloquium is evaluated on a 0-30 scale and will affect the 80% of the final grade.
The written assay is evaluated on a 0-30 scale and will affect the 10% of the final grade.
The critical discussion on the written assay is evaluated on a 0-30 scale and will affect the 10% of the final grade.
The final grade will be announced just at the end of the colloquium.