PHYSICS

Master Degree

ORGANIC CHEMISTRY

Teachers: 
CASNATI Alessandro
Credits: 
6
Site: 
PARMA
Year of erogation: 
2020/2021
Unit Coordinator: 
Disciplinary Sector: 
Organic Chemistry
Semester: 
Second semester
Language of instruction: 

Italian

Learning outcomes of the course unit

To introduce the student to the basic concepts of Organic Chemistry and to the properties and reactivity of the different classes of organic compounds.

Knowledge and understanding: aim of the course is to give to the student the fundamentals of Organic Chemistry and the essential instruments to understand the biochemistry phenomena and processes. The most important classes of organic compounds and of organic chemistry reactions for students in Biology will be especially discussed, highlighting the connections with the biological world. The thermodynamic and kinetic aspects of organic reactions will be also discussed together with the notational and stereochemical terms of organic compounds and reactions. The main classes of macromolecules of biological interest will be also presented and discussed in terms of structure and reactivity.

Applying knowledge and understanding: in parallel to theoretical explanations, the student will be guided through the resolution of organic chemistry problems also in order to train the student to apply and reinforce the concepts acquired. This will allow him to apply knowledge and understanding, correlating the structure of organic molecules to their properties and reactivity.

Making judgements: The student will become independent in the evaluation and interpretation of the experimental data which deal with the properties and reactivity of organic molecules. The student will be possibly acquire a complete autonomy in the classification of organic compounds and an elementary ability to understand the properties and reactivity of organic and biological molecules. The student will also be able to evaluate the didactics.

Communication: at the end of the course, the student should be able to properly communicate using the typical terminology of organic chemistry and shouild also be able to discuss problems of stereochemistry and reactivity of the main classes of organic compounds.

Learning skills: To acquire a methodology of study wich allows the prosecution of the universitary formation.

Prerequisites

To successfully follow the course and pass the examination it is
fundamental to
possess most of the knowledge and concepts treated in the course of
'Chimica
Generale'. In particular, fundamental are the concepts related to the
electronic
structure of the atoms, to the chemical bond, to thermodynamics (with
special
regard to the chemical equilibria and to acid-base equilibria) and to the
chemical
kinetics. It is not compulsory to have passed the examination of Chimica Generale,
but it is
strongly recommended to be in possess of most of the concepts related
to such
course before attending the lectures of Chimica Organica.

Course contents summary

The students will be first introduced to the basic theories of VSEPR and of
the
valence bond for the description of organic molecules. Some basic
concepts of
chemical thermodynamics and kinetics will be also reminded with
particular
attention to 1st and 2nd order reactions, to chemical catalysis and to
competitive
reactions. The concepts of nucleophile and electrophile will be compared
with those
of Brønsted-Lowry and Lewis acid and base. The concepts of organic
stereochemistry will be described together with the stereochemical
nomenclature
and properties of the stereoisomers with particular attention to biological
and
pharmaceutical world.
A systematic survey of the structure, properties and reactivity of organic
molecules,
divided by functional groups, will be undertaken. In particular this
analysis will
include the following classes of organic compounds: Alkanes snd
Cycloalkanes;
Alkenes and Alkynes; Alkyl halides; Alcohols, Ethers and Thiols; Benzenes
and
Aromatic compounds; Amines; Ketones and Aldehydes; Carboxylic acids
and their
derivatives.
In parallel to this theoretical part, a series of exercises will be presented
and solved
during separate tutoring lectures aiming at applying the concepts learnt
and to
provide a constructivist approach to learning organic chemistry.

Course contents

Introduction
Introduction to Organic Chemistry; The C atom as central atom in organic
compounds; electronic and Lewis structures of atoms; Lewis bond model;
electronegativity; Lewis structures of molecules and ions; bond angles
and distances: shape of molecules according to the VSEPR theory; dipole
moment of bonds and molecules; resonance. Covalent bonds according
to the valence bond theory: hybridation of atomic orbitals. Introduction to
the functional group theory. Intermolecular forces (dipole-dipole
interactions, Hydrogen bonds, van der Waals forces); polarizability;
solubility and physical properties of organic compounds; properties of
solvents (apolar, dipolar aprotic and protic solvents); dielectric constants
of solvents.
Fundamentals of kinetics. First and second order reactions. Molecularity
of a reaction. Effect of the temperature on the rate of a reaction:
Arrhenius equation.
Thermodynamics and kinetics of organic reactions
Enthalpy and entropy of reaction. Kinetics of reactions: mechanism of a
reaction, rate determing steps, reaction intermediates, transition states
and activation energy; rate of a reaction and specific rate constant;
molecularity; Eyring equation. Chemical catalysis. Reactions under kinetic
or thermodynamic control. Competitive reactions. Hammond postulate.
Brønsted-Lowry acids and bases. Nucleophiles and electrophiles.
Structure analysis: properties and reactivity according to functional group
theory.
Alkanes. Nomenclature. Cycloalkanes. Nomenclature. Conformation of
alkanes. Conformation of cycloalkanes and substituted cycloalkanes.
Physical properties of alkanes and cycloalkanes. Sources of alkanes.
Reactivity of alkanes. Oxydation and combustion. Halogenation reaction.
Homolytic cleavage. Radical species. Hyperconjugation. Orientation in
halogenation reactions. Statistical and reactivity factors.
Reactivity/selectivity in organic reactions. Regiochemsitry in radical
reactions. Exercises.
Chirality. Chiral and achiral molecules. Definition of stereocenters.
Stereoisomers. R/S designation. Fischer projections. Enantiomers.
Molecules having more than one chiral center: diastereomers and meso mixtures and their resolution. Enantiomeric and diastereomeric excess.
Chirality in the biological world. Enantiomers in biology and drugs. Origin
of chiral homogeinity in nature.
Alkenes and alkynes. Structure and nomenclature. Geometric isomerism
(cis/trans and E/Z). Cycloalkenes. Terpenes. Alkenes reactions.
Electrophile addition to the double bonds and polymerization reactions.
Addition of halogenidric acids. Carbocation stability. Alkene hydration.
Chlorine and bromine addition to alkenes: the bromonium ion.
Stereoselective and stereospecific reactions. Glycols formation.
Reduction of alkenes: heats of hydrogenation and stability of alkenes.
Stereochemistry in the addition reactions to alkenes. Structure and
acidity of alkynes. Reactivity of alkynes. Addition of H2, X2, HX e H2O.
Isolated, conjugated and cumulated dienes. Heats of hydrogenation.
Polymerization of alkenes and dienes.
Halogenoalkanes: structure and nomenclature. Nucleophilic aliphatic
substitution. Nucleophiles and bases, electrophiles and acids. SN2 and
SN1 mechanisms: differences in the kinetics, in the mechanism and in
the stereochemistry of the products. Stereoselectivity and
stereospecificity of the reactions. Factors influencing the rates of SN2 and
SN1 reactions: structure of the nucleophile, of the RX, of the leaving
group and of the solvent. Examples of SN2 and SN1 reactions. Betaelimination
and dehydroalogenation reactions. Saitzev’s rule, E2 and E1
mechanisms. E2 vs E1. Stereochemistry of E2 reactions. Biosynthesis of
terpenes.
Alcohols, ethers and thiols: structure, nomenclature and physical
properties. Acidity of the alcohols according to the inductive effects of
substituents. Acidity of methanol, ethanol, iso-propanol and terz-butanol.
Reaction with active metals, conversion into halogenoalkanes.
Mechanism of the reaction of alcohols and thionyl chlorids. De-hydration
reaction in acidic catalysis. Oxydation of 1° and 2° alcohols. Ether bond
formation via Williamson reaction. Crown ether and cryptands. Epoxydes
and their reactivity in basic and acid catalysis. Reaction of thiols: acidbase
and oxydation reactions.
Benzenes and their derivatives. Resonance energy and aromaticity.
Heterocyclic aromatic compounds and the nucleic acid bases.
Nomenclature. Mono- di- and poly-substituted benzenes. Phenols: acidity
and acid base reactions. Introduction to the Aromatic Electrophilic
Reaction. Acidity of substituted phenols. Separation of phenols from
alcohols and of acids from phenols.
Amines. Classification of the amines. pKb and pKa of amines. Henderson-
Hasselbach equation. Structure-basicity relationship in aliphatic, aromatic
and heterocyclic aromatic amines. Reactions with acids. Stereochemistry
at the nitrogen atoms of amines and quaternary ammonium salts.
Ketones and aldehydes. Structural characteristics of the carbonyl group.
Nomenclature. Reactions of the cabonyl group. Addition of oxygen
nucleophiles: emiacetals and acetals. Addition of nitrogen nucleophiles:
the imines or Schiff bases. Keto-enolic tautomerism and racemization of a
carbon atom alfa to the carbonyl group. Oxydation and reduction of
aldehydes and ketones.
Carboxylic acids: structure and nomenclature. Physical properties. Acidity
and effects of the substituents in acetic and benzoic acids. Separation
alcohols/phenols/carboxylic acids. Reduction of carboxylic acids.
Esterification of Fischer. Conversion into acyl chlorides. Decarboxylation
of beta-ketoacids and malonic acids.
Derivatives of carboxylic acids: acyl chlorides, anhydrides, esters and
amides. Structure and nomenclature. Lactons, lactams and phosphoric
acid esters. Nucleophilic acyl substitution: similarity and differences with
the reactivity of the carbonyl groups f aldehydes and ketones.
Differences in reactivity of the derivatives of carboxylic acids on the type
of leaving group and of the electrophilicity of carboxy group. Hydrolysis,
reaction with alcohols, ammonia and ammines. Reduction of esters and
amides.
Enolate anions. Acidity of the H atoms in alfa position to a carbonyl
group. Formation of enaolates. Enolizable ketones and aldehydes. Formation of enols by acidic catalysis. Aldol condensation: mechanism of
the reaction under basic or acidic catalysis. Symmetric and crossed aldol
condensations. Intramolecular aldol condensations. Claisen and
Dieckmann Condensation. Hydrolysis and decarboxylation of betaketoesters.
Claisen and aldol condensation in the biological world.
Biological important molecules
Carbohydrates: classification. D- and L-monosaccharides: Fischer
representations. Aminosugars. Emiacetalic cyclic structure: Haworth
projection and chair conformation. Epimers and anomers. Mutarotation.
Monosaccharide reactions: glucoside formation, reduction of alditols,
oxydation of aldonic acids, glucose test. Ascorbic acid. Disaccharides:
Maltose, Lactose, Saccharose. Blood group substances. Polysaccharides:
starch, glycogen and cellulose.
Amino acids. Classification. Natural alfa-amino acid. Acid-base properties.
Isoelectric point. Polypeptide and proteins: primary, secondary (alfa helix
and beta-sheets), tertiary and quaternary structures. Chemical synthesis
of polypeptides: protective and activating groups. Solid-phase synthesis.
Biosynthesis of proteins.
Lipids: classification. Triglycerids: saturated and unsaturated fatty acids.
Oils and fats. Soaps and detergents. Phospholipids: lipidic double layer
and mosaic model of the cell membranes. Liposoluble vitamines.
Steroids: cholesterol, steroid hormons, bile acids. Cholesterol
biosynthesis. Prostaglandines.
Nucleic acids. Nitrogenous bases, nucleosides, nucleotides. DNA: primary,
secondary structures. RNA.

Recommended readings

Main textbook
· W. Brown, T. Poon: Introduzione alla Chimica Organica, 3^ Edizione,
EdiSES,
Napoli.
To be consulted
· N. L. Allinger, M. P. Cava, D. C. De Jongh, C. R. Johnson, N. A. Lebel, C. L.
Stevens, Chimica Organica, 2^ Edizione, Zanichelli, Bologna.
· W. H. Brown, C. S. Foote: Chimica Organica, 2^ Edizione, EdiSES,
Napoli.
· J. McMurry, Chimica Organica, 1^ Edizione, Zanichelli, Bologna.

Teaching methods

Oral lectures and practice on organic chemistry problems

Applying knowledge and understanding: Ability to analyse organic compounds and biomolecules in terms of functional groups and stereocenters. Ability to classify and to give a systematic name to the compounds belonging to the main classes of organic compounds. Ability to understand the mechanisms of the main organic chemistry reaction also via the use of curley arrows. To understand the connections between structure and properties/reactivity of organic molecules and of complex biological macromolecules such as peptide, carbohydrates, lipids and nucleic acids.

Exercises guided by the teacher in the class will start to make the student able to develop a judgement on the relationship between structure and reactivity.

Assessment methods and criteria

The examination consists of a written (2 hs time) and an oral proof. At the half and at the end of the semester, it is possible to attend two
intermediate written proofs regarding the first and second part of the programme, respectively.
Who will pass both the intermediate proofs can directly access the oral examination.
The written hexam consists of 6 exercises of organic chemistry at open answers. Each of these exercises will be evaluted with 5 points.

The final votation is a media of the written and oral proofs.

Written and oral exams. At the half and at the end of the semester, it is possible to attend two intermediate written tests related to the first and second part of the programme. Who will pass both the intermediate tests can directly access the oral examination.

Written and oral examinations will verifying the knowledge of the student through the discussion of organic chemistry problems with the aim to evaluate the ability to apply the competence acquired by the student on the structure and reactivity of organic and bio-organic compounds.

The exam is passed if the student is able to analyse the organic and bio-organic compounds in terms of functional groups and stereocenters present and if he is able to classify and assign the systematic IUPAC name to molecules belonging to the main classes of organic compounds.

The ability to describe the stereochemistry and the properties of stereoisomers will be also evaluated in details (up to further 3 points) toghether with the knowledge of the reactivity of the main classes of organic compounds (up to further 3 points).

It will be also evaluated the ability to correlate the molecular properties and reactivity of organic compounds with their molecular structures (structure-property relationship) and to describe the mechanism of the main organic reactions by using the curley arrows (up to further 3 points).

The ability to properly discuss the organic chemistry reaction in terms of kinetics and thermodynamics will allow to gain up to further 3 points.

Other informations

Theoretical explanations (4 hours/week during 13 weeks) together with
tutoral
activity (2 hours/week) consisting in exercises solved in classroom by the
students
and aimed at applying and reinforce the concepts learned.
The examination consists of a written and an oral proof.
At the half and at the end of the semester, it is possible to attend two
intermediate
written proofs regarding the first and second part of the programme,
respectively.
Who will pass both the intermediate proofs can directly access the oral
examination.