ORGANIC CHEMISTRY BASICS
Learning outcomes of the course unit
At the end of the course, the student is expected to acquire knowledge and competence on basic organic chemistry.
In particular, the student will be on the following targets:
1. Knowledge of the basic functional groups and applying this knowledge for the classification of simple organic molecules (knowledge and understanding; applying knowledge and understanding).
2. Knowledge of, understanding and applying the structural representation of simple organic molecules and their visualization in the three-dimensional space also with the help of molecular models (knowledge and understanding; applying knowledge and understanding).
3. Knowledge of, and understanding the basic physical-chemistry principles (chemical equilibria, structural theory, thermodynamics and kinetics of organic reactions, acids and bases, nucleophiles and electrophiles) (knowledge and understanding).
4. Knowledge, understanding and prevision of the relationship between the structure of simple organic molecules (containing the functional groups detailed in the contents section) and their physical properties, in particular their solubility in aqueous or non-aqueous solvents (knowledge and understanding; applying knowledge and understanding).
5. Knowledge, understanding and prevision of the relationship between the structure of simple organic molecules (containing the functional groups detailed in the contents section) and their reactivity (chemical behavior), also by carrying out suitable exercises (knowledge and understanding; applying knowledge and understanding).
6. Knowledge of, and understanding the methods of synthesis (preparation) and interconversion of simple organic molecules (containing the functional groups detailed in the contents section) and applying these methods for the synthesis and transformation of unknown organic molecules, also by carrying out suitable exercises (knowledge and understanding; applying knowledge and understanding).
7. Knowledge of the international rules for the nomenclature of simple organic molecules (containing the functional groups detailed in the contents section) and applying them for the nomenclature of unknown molecules, also by carrying out suitable exercises (knowledge and understanding; applying knowledge and understanding).
8. Ability to convey the contents of the course to a specialized audience using appropriate scientific language (both written and oral) (communication skills).
9. Understanding the role of organic chemistry basics in the study of drugs and living organisms. Ability to link the contents of the course to those of neighboring chemical disciplines (making judgements; learning skills).
To fully appreciate the content of the course, it is necessary to acquire knowledge of general and inorganic chemistry in a previous course. To access the final examination, it is necessary to pass the “General and Inorganic Chemistry” exam.
Course contents summary
The introduction of the course is devoted to a general presentation of organic chemistry as a scientific discipline, with a brief overview of its historical background and an highlight of the significance and impact of organic chemistry on contemporary science, culture, and life. Basic principles are then given emphasizing the key connections between the structure of organic compounds and their physico-chemical properties, recalling some general concepts from the General Chemistry course including thermodynamics principles, the kinetics and the structural theories. The key concepts of covalent and ionic bonds, molecular geometry, resonance, acids and bases in organic chemistry, and isomerism are given (conformational and configurational isomers) and an emphasis is placed to stereoisomerism. The second part of the course comprises the systematic study of basic organic compounds including the structure, nomenclature, natural occurrence, physical properties, reactivity, and synthetic methods of alkanes, cycloalkanes, halogeno-alkanes, alkenes, alkynes, alcohols, polyols, ethers, epoxides, thiols.
During the course, a series of exercises are proposed and solved at the blackboard, with the purpose to applying the principles and concepts into a “real-world” context. These exercises are open for free discussion between teacher and students and they are considered an essential part of the course.
Genesis and development of the science of organic chemistry. Functional groups of the main organic compounds. The carbon atom as a key element in organic chemistry: its electronic configuration, hybrid orbitals, oxidation number within a molecule, valence, electronegativity. Classification of the main classes of organic compounds based on the functional groups and the oxidation number of the carbon atom within them. Radical carbon atom, carbocation, carbanion.
Configurational and conformational isomers. Conformational analysis of linear alkanes and cycloalkanes, in particular mono- and polysubstituted cyclohexanes. Graphical representation of organic molecules (zig-zag modality, pseudocyclic, Fisher projection, Newman projection along carbon-carbon bond axis). Constitutional isomers and stereoisomers. Chirality of organic molecules, enantiomers, diastereoisomers, compounds possessing two or more stereocenters, R and S descriptors, meso compounds, geometric isomerism. Separation of racemates. Significance of chirality in biology and drugs.
Recalling the concepts of chemical equilibrium, equilibrium constants and relationship with the variation of free energy in a given reaction. Reaction kinetics, activation energy, energy profile of a reaction. Thermodynamic vs kinetic control of an organic reaction. Catalysis: general concepts.
Reaction mechanisms, use of curly arrows for their representation. Resonance structures. Representation of radical or ionic reaction mechanisms. Nucleophiles and electrophiles: definition, classification, factors influencing their behavior.
Acid and basic organic compounds. Definition according to Bronsted-Lowry and Lewis. Acid-base equilibria, pKa, equilibria position, dependence of the position of the equilibria upon pH. Factors influencing their behavior.
Classification of main solvents in organic chemistry. Relationship between the molecular structure of a simple organic compound and its solubility in aqueous/non-aqueous, protic/aprotic, polar/apolar solvents.
Monomolecular and bimolecular nucleophilic substitution reactions at saturated carbon atoms. Monomolecular and bimolecular elimination reactions. Regioselectivity, stereoselectivity, stereospecificity aspects.
Radical halogenation of alkanes. Regioselectivity aspects.
Brief introduction to organometallic compounds; Grignard reagents.
Electrophilic addition reaction to the carbon-carbon double and triple bonds: mechanisms, regioselectivity, stereoselectivity.
Aliphatic domain. Structure, nomenclature, natural occurrence, physical properties, reactivity, and synthesis of: alkanes, cycloalkanes, alkyl halides, alkenes, alkynes, alcohols, vicinal diols, aliphatic ethers. Structure, nomenclature, and synthesis of epoxides.
Choose one of the following textbooks (mandatory) (the same for both modules):
-W.H. Brown, B. L. Iverson, E. V. Anslyn, C.S. Foote, “Chimica Organica”, V Edizione, EdiSES, Napoli, 2014
-Autori vari, “Chimica Organica” (a cura di B. Botta), Seconda Edizione, Edi.Ermes, Milano, 2016.
-J. Gorzynski Smith, Fondamenti di Chimica Organica, Terza Edizione, McGraw Hill Education, Milano, 2018.
-J. McMurry, “Chimica Organica”, IX Edizione, Piccin, Padova, 2017.
- P.Y. Bruice, “Chimica Organica”, Terza Edizione, EdiSES, Napoli, 2017.
Choose one of the following exercise books (mandatory) (the same for both modules):
-M. V. D’Auria, O. Taglialatela Scafati, A. Zampella, “Guida Ragionata allo Svolgimento di Esercizi di Chimica Organica”, seconda Edizione, Loghia Ed., Napoli, 2011.
-B. Iverson, S. Iverson, “Guida alla soluzione dei problemi da Brown, Foote, Iverson – Chimica Organica”, 4° Ed., EdiSES, Napoli, 2014.
-T.W.G. Solomons, C.B. Fryhle, R.G. Johnson, “La chimica organica attraverso gli esercizi”, Seconda Edizione, Zanichelli, Bologna, 2010.
-S. Cacchi, F. Nicotra, “Esercizi di Chimica Organica”, Casa Editrice Ambrosiana, 1998
Further readings available at the Library of the Food and Drug Department (as a suggestion for specific subjects, not mandatory) (the same for both modules):
-J. Clayden, N. Greeves, S. Warren, P. Wothers, “Organic Chemistry”, Oxford Edition, 2001
-R. Norman, J.M. Coxon, “Principi di Sintesi Organica”, 2a Edizione Italiana, Piccin Editore, Padova, 1997
-L. Kürti, B. Czakó, “Strategic Applications of Named Reactions in Organic Synthesis”, Elsevier Academic Press, 2005.
Many copies of the text of written examinations (in some cases with solutions) of the past academic years are loaded and updated in the Elly platform, to provide further tools in preparation of the examination.
The course is carried out through frontal oral lessons at the blackboard (total 40 hours corresponding to 5 CFU) including exercises. The exercises are carried out by either the teacher or the students and are considered an essential part of the course in order to:
-applying the theory to solve practical problems dealing with the contents of the course;
-verifying the status of knowledge before passing to the subsequent subject;
-acquire a method for the execution of exercises.
The student is expected to read and study the contents of the lessons by him/herself by using notes and textbook, and applying this knowledge in the execution of exercises, including 1) the exercises made in classroom, 2) exercises in the textbook and study guides, and 3) exercises assigned during lessons and loaded weekly on the Elly platform.
The teacher is available for further explanations about theory and exercises at the end of the lesson, during the break or in office on e-mail appointment.
The teacher may sometimes use additional teaching material (slides) loaded on the Elly platform; this material is considered optional and does not replace the textbook and the exercise study guide, which are mandatory.
Many copies of the text of written examinations of the past academic years are loaded and updated in the Elly platform, to provide further tools in preparation of the examination.
Assessment methods and criteria
To verify the level of knowledge and learning of the student, a written examination is mandatory (1 hour and 45 minutes maximum length) consisting of 7 or 8 open-answer questions having different weight and corresponding to a score detailed in the text. The result is marked in thirtieth, with a minimum pass of 18; it contributes for the 45% of the final quotation of the whole examination.
To access the final oral examination and subsequent recording, it is also necessary to pass the written examination of the second module (Organic Chemistry). It is possible to carry out the written examination of both modules (Organic Chemistry Basics and Organic Chemistry) in the same date since they are at different (and subsequent) times.
To access the written examination, the student must register on-line (via Essetre) in the dates according to the official examination schedule of the Food and Drug Department.
The written exam is judged positive (superior or equal to 18/30) when the student demonstrates knowledge and learning of the nomenclature of basic organic molecules, acid-base reactions, writing the structure of simple organic molecules including different conformations and configurations.
The laude (30/30 cum laude) is assigned as a maximum quotation when all questions are correctly answered and when specialized language is used.
While carrying out the examination, as a rule, no books, notes nor whatever information system must be available.
The result of the written examination is given within one week from the date of the same exam and anyway before the date of the oral examination of the same session via Essetre portal. The student is expected to view his/her work (either successful or failed) which is consigned the day of the oral session. If the student cannot be present that day, he/she has to inform the teacher by e-mail; the teacher will show the work to the student on another date, to be fixed with the student.