OVERVIEW

The course includes the continuation and deepening of the concepts taught in Organic Chemistry I. The topics covered allow for the acquisition of a more complete view of the basic concepts of organic chemistry. Furthermore, they are largely chosen in such a way as to be preparatory for subsequent courses such as Biochemistry and Pharmaceutical Chemistry.

AIMS AND CONTENT

LEARNING OUTCOMES

Further insight into the reactivity of organic molecules through the study of difunctional molecules. Carbon-carbon bond forming reactions with particular emphasis on the costruction of cyclic systems. Heterocycles. Natural organic substances.

AIMS AND LEARNING OUTCOMES

The aim of the Organic Chemistry II course is to provide more advanced concepts of the subject, compared to those learned in the previous Organic Chemistry I course. At the end of the course, the student will have acquired theoretical knowledge on the structure and reactivity of bifunctional compounds, polycyclic aromatic compounds and heterocyclic compounds (aromatic and non-aromatic). They will also have deepened the fundamental strategies for the formation of carbon-carbon bonds and will have learned the basic structures and properties of the main classes of biomolecules.

This knowledge is fundamental to face future studies in the biochemical and chemical-pharmaceutical fields.

Specifically, the student will be able to:

• know the main classes of synthetic and natural organic compounds;
• apply the fundamental rules of the IUPAC nomenclature, in particular in the field of heterocycles;
• apply basic stereochemical knowledge also to more complex systems;
• reason critically in order to apply the reactions studied to simple synthetic sequences for the production of required molecules, arguing the choices.

PREREQUISITES

Basic knowledge of the main topics of organic chemistry.

TEACHING METHODS

The lessons are given in the traditional way (64 hours in the classroom). The attendance is highly recommended.

SYLLABUS/CONTENT

1.     FURTHER INSIGHT INTO THE REACTIVITY AND PREPARATION OF BIFUNCTIONAL COMPOUNDS (24 hours, Prof. Ginoble Pandoli)

• A1 Polyunsaturated and polycyclic systems and bicarboxylic compounds
  • A1.1 Conformations of cycloalkanes and bicycloalkanes
    • A1.1.2 Conformation of fused bicyclic alkanes
    • A1.1.1 Conformations of monocyclic alkanes
    • A1.1.3 Nomenclature and properties of bridged bicyclic systems
  • A1.2 Dienes
    • A1.2.1: Conjugation and UV-visible absorption
    • A1.2.2: Electrophilic addition to conjugated dienes
    • A1.2.3: Pericyclic cycloadditions: the Diels-Alder reaction
    • A1.2.4 Ring-closing metathesis
    • A1.2.5 Allenes
  • A1.3 Bicarboxylic acids
  • A1.4 Aromatic polycyclic systems
    • A1.4.1: Nomenclature and properties
    • A1.4.2: Fullerenes, graphite, graphene, carbon nanotubes
    • A1.4.3: Arene oxides
    • A1.4.4: Electrophilic substitutions on naphthalene
  • A1.5 Biaryl systems
    • A1.5.1 Chirality in biaryls
    • A1.5.2 Suzuki reaction for the synthesis of biaryls and dienes
• A2 Compounds with two oxygenated functions or one oxygenated function and an unsaturation
  • A2.1 Conjugated carbonyl and carboxylic compounds
    • A2.1.1 Preparation through: halogenation/elimination, crotonic condensation, Knoevenagel reaction; intramolecular metathesis; Wittig and Horner-Wadsworth-Emmons reactions
    • A2.1.2 Synthetic equivalence
    • A2.1.3 Conjugated nucleophilic additions: reactions with mild nucleophiles, with organometallic reagents, with hydrides, Michael reaction.
    • A2.1.4 Robinson annulation
    • A2.1.5 Conjugated additions in biology
    • A2.1.6 Conjugated additions and other reactions of enamines
  • A2.2 1,3-Dioxygenated compounds
    • A2.2.1: Cross aldol reactions with enolate preformation
    • A2.2.2: Cross alsol reactions with synthetic equivalents of aldehydes
    • A2.2.3 Oxidations with diacetoxyiodobenzene and Swern oxidation
    • A2.2.4 Claisen and Dieckmann condensations
    • A2.2.5 Aldol additions and Claisen condensations in biology
  • A2.3 1,2-Dioxygenated compounds
    • A2.3.1 Retrosynthetic strategies: logical and illogical disconnections
    • A2.3.2 Cyanide anion as acyl anion equivalent
    • A2.3.3 Isocyanides: Passerini reaction
    • A2.3.4 Dithianes
    • A2.3.5 1,2-Diols
    • A2.3.6 Cyclic acetals
• A3 Radical reactions, phenols, quinones
  • A3.1 Radical reactions
    • A3.1.1: Generality
    • A3.1.2: Radical polymerizations
    • A3.1.3 Autooxidations   
    • A3.1.4 Anti-oxidants
  • A3.2 Phenols as natural anti-oxidants
  • A3.3 Quinones

2.     HETEROCYCLIC COMPOUNDS (21 h, Prof. Riva).

• B1 Classification and nomenclature of heterocyclic compounds
• B2 Electronrich aromatic heterocycles
  • B2.1 General features
  • B2.2 Synthesis and reactivity of pyrrole, furan, thiophene and related benzo-fused compounds
• B3 Electronpoor aromatic heterocycles
  • B3.1 General features
  • B3.2 Synthesis and reactivity of pyridine, quinoline, isoquinoline, pyrimidine, pyrazine, pyridazine
• B4 Aromatic penta-atomic heterocycles with two heteroatoms
  • B4.1 General features
  • B4.2 Synthesis and reactivity of imidazole, oxazole, isoxazole
• B5 Saturated strained heterocycles: structure, synthesis and reactivity of oxiranes, aziridines, oxetanes, azetidines

3.    BIOMOLECULES (19 h, Prof. Riva).

• C1 Carbohydrates
  • C1.1 Monosaccharides
    • C1.1.1 Stereochemical families
    • C1.1.2 Fischer and Haworth formulas, pyranose and furanose conformations
    • C1.1.3 Anomeric effect
    • C1.1.4 Mutarotation
    • C1.1.5 Behavior of monosaccharides in acids and in bases
    • C1.1.6 Reduction and oxidation reactions; reducing sugar assays
    • C1.1.7 Glycosides: structure, properties and synthesis of simple glycosides
    • C1.1.8 Synthetic strategies for the synthesis of complex glycosides through chemical means (use of protecting groups and activation of glycosyl donor). Enzymatic synthesis
    • C1.1.9 Osazones
    • C1.1.10 Kiliani-Fischer synthesis
    • C1.1.11 Ruff and Wohl degradationsC1.1.12 Determination of relative and absolute configuration of main monosaccharides
  • C1.2 Disaccharides: maltose, cellobiose, saccharose and lactose
  • C1.3 Polysaccharides: structure and properties of main polysaccharides (starch, glycogen, cellulose, chitin, pectin, hyaluronic acid)
  • C1.4 Antigene determinants of cells; blood groups
  • C1.5 Glycoconjugates
    • C1.5.1 glycolipids
    • C1.5.2 glycoproteins
• C2 Lipids
  • C2.1 Fatty acids and derivatives (amides, waxes)
  • C2.2 Eicosanoides (prostaglandins etc.)
  • C2.3 Glycerolipids (triglycerides: fats, oils)
  • C2.4 Soaps and tensioactive compounds
  • C2.5 Glycerophospholipids
  • C2.6 Sphingolipids
  • C2.7 Terpenes, Terpenoids and their biosynthesis
  • C2.8 Steroids
• C3 Amino acids
  • C3.1 Nomenclature
  • C3.2 Structure and classification
  • C3.3 Acid-base properties
  • C3.4 Isoelectric point
  • C3.5 Synthesis of alpha-amino acids (from alpha-haloacids, from acylaminomalonic esters, through reducing amination, through enantioselective reduction of alpha-acylaminoacrylic acids, through Strecker reaction)
  • C3.6 Resolution of racemic alpha-amino acids
• C4 Peptides and proteins
  • C4.1 Primary structure, disulfide bonds.
  • C4.2 Protein denaturation
  • C4.3 Determination of primary structure
    • C4.3.1 Through exhaustive hydrolysis coupled with ion exchange chromatography and visualization with ninhydrin
    • C4.3.2 Through Edman method
    • C4.3.3 Through use of cyanogen bromide
    • C4.3.4 Through enzymatic methods
  • C4.4 Chemical synthesis in solution (from left to right and from right to left; use of protecting groups; activation of carboxylic function) and in solid phase (Merrifield resins)
• C5 Nucleic acids
  • C5.1 Nitrogen bases
  • C5.2 Sugars
  • C5.3 Nucleosides
  • C5.4 Nucleotides
  • C5.5 Oligonucleotides and Nucleic acids
  • C5.6 Secondary and tertiary structure of DNA
  • C5.7 Examples of genetic mutations

RECOMMENDED READING/BIBLIOGRAPHY

• Chimica Organica AA. VV. a cura di B. Botta Edi-Ermes
• Chimica Organica di M. Loudon, EdiSES
• Chimica Organica di J. McMurry, Piccin
• Chimica Organica di P. Y. Bruice, EdiSES
• Chimica Organica di P. C. Vollhardt e N. E. Schore, Zanichelli
• Chimica Organica di W. H. Brown, B. L. Iverson, E. V. Anslyn, C. S. Foote, EdiSES
• Chimica dei Composti Eterociclici di D. Sica, F. Zollo - EdiSES (l'ultima edizione)
• Chimica degli Eterocicli di G. Broggini, G. Zecchi – vol. 1 LaScientifica

TEACHERS AND EXAM BOARD

Exam Board

RENATA RIVA (President)

OMAR GINOBLE PANDOLI

LUCA BANFI (Substitute)

LESSONS

LESSONS START

The lessons will begin February 27, 2023.

Class schedule

ORGANIC CHEMISTRY II (PCT)(MD)

EXAMS

EXAM DESCRIPTION

There will be a preliminary written exam consisting in 12 questions. The students will have 90 minutes for answering. The written exam will be followed, the same day, by an oral exam. At least one question for each of the three parts will be asked at the oral. Only the students who get a sufficient grade at the written exam will be admitted to the oral. The oral exam must be given the same day than the written one and if a student fails to pass the oral, will have to repeat also the written part. In general, the grade of the written exam in not influential on the final vote. Only in particular cases, when the written exam has a very high mark, it can positively influence the final grade.

ASSESSMENT METHODS

The oral exam is always carried out by two members of permanent teaching staff and lasts at least 30 minutes. The students will demonstrate to have reached a sufficient knowledge both by answering to questions, and by drawing at the blackboard formulas, reaction equations, mechanisms and so on. Therefore, also taking into account the preliminary written part, the commission is definitely able to verify, with high accuracy, the fullfilment of learning outcomes. If the commission decides that the learning outcomes have not been met, the student will be invited to try again the exam in a following date.

Exam schedule

FURTHER INFORMATION

Only the students who have already passed Organic Chemistry 1 are admitted to the exam. The professors will check the observance of this rule just before the written exam.