Elements of Chemistry - ELEMENTI DI CHIMICA ORGANICA (2019/2020)

Course code
Name of lecturer
Mariapina D'Onofrio
Number of ECTS credits allocated
Academic sector
Language of instruction
II semestre dal Mar 2, 2020 al Jun 12, 2020.

To show the organization of the course that includes this module, follow this link * Course organization

Lesson timetable

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Learning outcomes

Knowledge and understanding: Students will acquire basic notions of organic chemistry.
The knowledge of organic compounds and their reactivity is the basis for addressing issues for the knowledge of biological and biomolecular phenomena.

Ability to apply knowledge: the students will have the ability to understand and analyze structural and chemical properties of the biomolecules and their transformations. From a chemical point of view, the student will have the ability to deal with the structures and the chemical properties and typical reactions of the organic molecules and must be able to apply such knowledge to describe the reaction mechanisms. The basic concepts learned during the course will will be applied to develope bioinformatics tools for the study of the relationship between structure and function of biological macromolecules and strategies for regulating their functions.


- Bond angles and carbon hybridisations, polarity of the molecules in relation to the electronegativity of the atoms of the molecule, the concept of resonance and different ways of representing the bonds, representation of the electron displacement in a reaction.
- Acids and bases in organic chemistry: definitions according to Bronsted / Lowry and Lewis, how to predict the strength of an acid and the equilibrium position in an acid-base reaction, the relationship between molecular structure and acidity (resonance and relocation of the charge, inductive effect and electronegativity).
- Saturated hydrocarbons: alkanes and cycloalkanes, nomenclature and structure, mention of combustion reaction and radical substitution, constitutional isomerism of alkanes, cis-trans isomers of cycloalcans, chair and boat conformations, equatorial and axial substitutions.
- Unsaturated hydrocarbons: alkenes and alkynes, nomenclature, structure, characteristic reactions of alkenes: addition reactions and Markovnikov’s rule, regioselectivity, hydro-halogenation, hydration, halogenation, hydrogenation.
- Chirality of the molecules: stereoisomers, enantiomers, diasteroisomers, optical activity and R / S configuration of a stereocentre, meso compounds and racemic mixtures, polarimeter and polarized light.
- Alogenoalcans: nomenclature, structure, nucleophilic substitution and elimination reactions. Mechanisms SN1, SN2, E1, E2, stability of exiting groups, relative efficacy of nucleophiles, stability of carbocations, solvent effect, differences between intermediate and transition states, competition between nucleophilic substitution and elimination reactions, energy diagrams of a reaction.
- Alcohols, phenols, ethers and thiols: structure, nomenclature and chemical properties, oxidation and dehydration reactions, secondary and tertiary primary alcohols, acidity comparisons.
- Benzene and aromatic compounds: resonance and Huckel's rule, nomenclature and structure, aromatic molecules of biological interest. General overview of reactions (aromatic electrophilic substitution)
- Aldehydes, ketones: nomenclature and structure, physical properties, reactivity, reduction and oxidation of aldehydes and ketones, nucleophilic addition, reaction with Grignard reagents, formation of emiacetals and acetals, formation of an immine from an aldehyde or ketone, keto–enol tautomerism, alpha-substitution reactions, acidity, condensation reactions.
- Amine: nomenclature, basicity.
- Carboxylic acids and derivatives: nomenclature, structure, properties and acidity, acyl nucleophilic substitution, Carboxylic acids derivatives reactivity, amide bond properties, thioester and acyl phosphate.
- Carbohydrates: classification and configuration, mutarotation, reducing sugars, Fischer and Haworth projections, disaccharides and polysaccharides of biological interest.
- Lipids: Classification and structure of fatty acids, phospholipids, prostaglandins, terpenoids and steroids.
- Amino acids: structure, basic-acidity properties, isoelectric point determination, overview on the protein structural characteristics, polypeptide bond, secondary structure.
- Nucleic Acids: DNA RNA, nucleosides and nucleotides, overview on DNA transcription and translation.
- Software for bi and three-dimensional visualization of the structures of organic molecules, molecular representation systems.
- Codes for molecules representation used in databases.

Reference books
Author Title Publisher Year ISBN Note
Bruice Elementi di chimica organica (Edizione 2) EdiSES 2017 9788879599276
L. G. Wade Jr. Fondamenti di Chimica Organica PICCIN 2014 978-88-299-2300-7
J. G. Smith Fondamenti di chimica organica, 3/e (Edizione 3) McGraw Hill 2018
Brown Poon Introduzione alla chimica organica (Edizione 5) EdiSES 2014 9788879598255

Assessment methods and criteria

Written exam: 6 exercises, available time 1 and a half hours.
The obtained grade will be averaged with the one obtained in the module of "General Chemistry Elements"
The exam consists of a written verification of the level of knowledge acquired on organic chemistry. The student should be able to correctly represent the molecules using the conventions in use, recognize isomers, identify reactive groups, and describe in detail the reaction mechanisms. It is moreover verified the knowledge of molecule codes used in databases.
The test consists of a written exam divided into six open-ended exercises (time available 90 minutes). The final grade is given by the sum of the scores obtained in the individual exercises. If the outcome of the written exam is ≥ 16/30 it is possible to scheduled the oral exam.