The course aims to provide students with a basic knowledge of organic chemistry, with particular regard to biological implications of organic molecules. The basic concepts of structure and bonding are introduced, the structure and reactivity of the main functional groups, with a sketch of the fundamental reaction mechanisms. The last part regards the chemistry of biomolecules (lipids, carbohydrates, amino acids, peptides and proteins, nucleic acids).
Course Content - Last names M-Z
The course aims to provide students with a basic knowledge of organic chemistry, with particular regard to biological implications of organic molecules. The basic concepts of structure and bonding are introduced, the structure and reactivity of the main functional groups, with a sketch of the fundamental reaction mechanisms. The last part regards the chemistry of biomolecules (lipids, carbohydrates, amino acids, peptides and proteins, nucleic acids).
J. Clayden, N. Greeves, S. Warren and P. Wothers. Organic Chemistry. Oxford University Press
P. Y. Bruice Chimica Organica Edises Università
W. H. Brown, T. Poon Introduzione alla chimica organica Edises Università
Learning Objectives - Last names A-L
Knolewdge acquired:
The course is aimed to provide the students with a basic knowledge of organic chemistry. The knowledge of this subject is a fundamental requirement for understanding the complex biochemical mechanisms found in living organisms, such as metabolism and energetic balance, formation of secondary metabolites, action of enzymes and biologically active substances, etc.
Competence acquired:
Ability to recognize the main classes of organic compounds according to the functional groups linked in the molecule. Evaluation of the possibility of transforming the existing functional groups and adding new groups in order to increase the reactivity and/or carry out the preparation of a target compound. General view of the most important classes of organic reactions and related reaction mechanisms.
Skills acquired (at the end of the course):
At the end of the course the students will acquire the ability of writing the structures of organic molecules on the basis of both trivial and IUPAC names. The students, on the basis of the structure of a given compound, will be able to predict its properties, such as acidity, basicity, electrophilic and/or nucleophilic character, optical activity, etc. Furthermore, they will acquire the capability of understanding the general problems related to reactivity of organic compounds, such as formation of by-products, stereo- and regioisomers, etc...
Learning Objectives - Last names M-Z
Knolewdge acquired:
The course is aimed to provide the students with a basic knowledge of organic chemistry. The knowledge of this subject is a fundamental requirement for understanding the complex biochemical mechanisms found in living organisms, such as metabolism and energetic balance, formation of secondary metabolites, action of enzymes and biologically active substances, etc.
Competence acquired:
Ability to recognize the main classes of organic compounds according to the functional groups linked in the molecule. Evaluation of the possibility of transforming the existing functional groups and adding new groups in order to increase the reactivity and/or carry out the preparation of a target compound. General view of the most important classes of organic reactions and related reaction mechanisms.
Skills acquired (at the end of the course):
At the end of the course the students will acquire the ability of writing the structures of organic molecules on the basis of both trivial and IUPAC names. The students, on the basis of the structure of a given compound, will be able to predict its properties, such as acidity, basicity, electrophilic and/or nucleophilic character, optical activity, etc. Furthermore, they will acquire the capability of understanding the general problems related to reactivity of organic compounds, such as formation of by-products, stereo- and regioisomers, etc..
Prerequisites - Last names A-L
Courses to be used as requirements
Courses required: General and Inorganic Chemistry
Prerequisites - Last names M-Z
Courses to be used as requirements
Courses required: General and Inorganic Chemistry
Courses recommended: Mathematics, Physics
Teaching Methods - Last names A-L
CFU: 6
Total hours of the course (including the time spent in attending lectures, seminars, private study, examinations, etc...): 150
Hours reserved to private study and other indivual formative activities:102
Contact hours for: Lectures (hours): 48
Contact hours for: Laboratory (hours): 0
Contact hours for: Laboratory-field/practice (hours): 0
Seminars (hours): 0
Stages: 0
Intermediate examinations: 0
Teaching Methods - Last names M-Z
CFU: 6
Total hours of the course (including the time spent in attending lectures, seminars, private study, examinations, etc...): 150
Hours reserved to private study and other indivual formative activities:102
Contact hours for: Lectures (hours): 48
Contact hours for: Laboratory (hours): 0
Contact hours for: Laboratory-field/practice (hours): 0
Seminars (hours): 0
Stages: 0
Intermediate examinations: 0
Further information - Last names A-L
Frequency of lectures, practice and lab:
Highly recommended
Teaching tools:
Molecular models.
Office hours:
By e-mail contact with the teacher.
Further information - Last names M-Z
Frequency of lectures, practice and lab:
Highly recommended
Teaching tools:
Molecular models.
Office hours:
By e-mail contact with the teacher.
Type of Assessment - Last names A-L
Oral exam. Discussion on the general properties of a class (more classes)of organic compounds. Solving of problems related to the reactivity, reaction mechanisms. Regio- and stereoisomerism.
Type of Assessment - Last names M-Z
Exam modality: Discussion on the general properties of a class (more classes)of organic compounds. Solving of problems related to the reactivity, reaction mechanisms. Regio- and stereoisomerism.
Programme (short version for Diploma Supplement):
Hybridization and shapes of the molecules. Acidity, basicity, electrophilic and nucleophilic character of organic compounds. Redox reactions. Main classes of organic compounds: their synthesis and reactivity. Addition, elimination, and substitution reactions. Structural and stereoisomerism. Biologically relevant organic compounds: amino acids, peptides, proteins, mono- di-, and polysaccharides, lipids.
Course program - Last names A-L
- Structure of organic molecules: Lewis structures, formal charge, resonance, VSEPR, representation of organic molecules
- The link: Hybridization, Length and bond strength, Polarity and electronegativity, dipolar moment
- Acids and bases: Bronsted-Lowry, Lewis; electrophiles and nucleophiles
- Classification of organic compounds: Hydrocarbons, Compounds containing C-Z groups, Compounds containing the C = O group; Intermolecular forces and physical properties
- Alkanes: structural characteristics, modes of representation, physical properties, nomenclature, conformational analysis (ethane, butane, cyclohexane), reactivity (oxidation, radical halogenation)
- Stereochemistry: isomerism and stereoisomerism, chirality, absolute configuration assignment, diastereoisomerism and meso forms, optical isomerism, polarimetry
- General principles of reactions: equations and modes of representation, types of reactions, break-formation of bonds, energy (thermodynamics and kinetics, catalysts, energy diagrams)
- Alkenes: structural characteristics, nomenclature, physical properties, main reactions and mechanism: addition of HX, hydration, addition of halogens, hydrohalogenation, hydroboration, hydrogenation, oxidation reactions (hydroboration-oxidation, hydroxylation of alkenes, epoxidation, ozonolysis)
- Alkynes: structural characteristics, nomenclature, physical properties, main reactions: acetylide ion chemistry, HX addition, halogen addition, water addition, keto-enol tautomerism, hydroboration, catalytic hydrogenation, oxidation reactions
- Dienes, polyenes and terpenes, conjugation, 1,3-butadiene resonance and in allyl systems, electrophilic addition 1,2 and 1,4, kinetic and thermodynamic control, Diels-Alder cycloaddition
- Aromatic compounds: benzene structure, aromaticity, benzene resonance energy, nomenclature, aromatic electrophilic substitution (Friedel and Crafts alkylation, Friedel and Crafts acylation, halogenation, nitration, sulphonation), mechanism and effect of substituents
- Alkyl halides: structural characteristics, nomenclature, physical properties; Nucleophilic substitution: mechanisms and stereochemistry, role of the solvent, reagent and alkyl substrate
- Elimination reactions: mechanisms and energy profile; Radical halogenation: mechanism and energy profile
- Alcohols, ethers, epoxides: structural characteristics, nomenclature, physical properties, reactions and mechanism (dehydration, formation of halides, oxidation, preparation of epoxides, opening of epoxides)
- Aldehydes and ketones: structural characteristics, nomenclature, physical properties, keto-enol tautomerism, reactions and mechanism (nucleophilic addition, reduction, organometallic reagents, hydration, formation of hemiacetals and acetals, enols and enolates, alpha carbon halogenation, direct alkylation of enolates, simple and mixed aldol condensation)
- Amines: structural characteristics and stereochemistry, nomenclature, physical properties and basicity (pyrrole-pyridine, pyridine-piperidine, aniline-cyclohexylamine), preparation of amines and mechanism (direct nucleophilic substitution, Gabriel synthesis, reduction, reductive amination), reactivity and mechanism: formation of imines and enamines
- Carboxylic acids: structural characteristics, nomenclature, physical properties and acidity of the OH bond, reactions and mechanism (formation of acyl halides, Fischer esterification, ester hydrolysis, formation of amides with carbodiimides)
- Derivatives of carboxylic acids: structural characteristics, nomenclature, physical properties, reactivity and mechanism: nucleophilic acyl substitution, reactivity of anhydrides and acyl halides, hydrolysis of esters and amides, hydrolysis and reduction of nitriles, malonic synthesis, synthesis of the acetic vinegar ester, synthesis of Claisen, crossed aldolic reaction
- Amino acids: structure of proteinogenic amino acids, Strecker synthesis, acid-base and isoelectric point properties, peptides and peptide bond structure, protecting groups in peptide synthesis, protein structure (primary, secondary: tertiary alpha-helix and beta-sheet and quaternary)
- Carbohydrates: monosaccharides, structure of aldoses and ketoses, stereochemistry, Fischer and Haworth projections, Kiliani-Fischer synthesis, cyclic form of carbohydrates, glycosides, acetylation, sugar reduction and oxidation (Tollens, Fehling, nitric acid reagents); disaccharide structure: maltose, lactose, sucrose; polysaccharides: amylose, cellulose, glycogen.
- Lipids: Structure and physical properties, triglycerides (saponification or hydrolysis reactions, hydrogenation, oxidation), fatty acids, phospholipids, steroids and cholesterol
- Nucleic acids: purine and pyrimidine bases, nucleosides, nucleotides, phosphodiester bond, DNA structure.
Course program - Last names M-Z
Electronic structure of the elements and the chemical bond: electronic distribution, electronegativity, Lewis structures, atomic and molecular orbitals, VSEPR moled, hybrid orbitals and molecular geometry, electronegativity and polarity of the chemical bonds. Molecular structures: Lewis, Kékulé, condensed structures. Acids and bases. Acid dissociation costant, pH and pKa, acid-base equilibria, influence of structure on the acidity of a compound. Acidity of alcohols and carboxylic acids: electronic delocalization and resonance in the carboxylate ion. Buffer solutions and their importance in biology. Lewis acids and bases. Introduction to organic compounds. Classification of organic compounds. hydrocarbons, compounds containing C-Z groups. Compounds containing the C = O group. Functional groups. Nomenclature, relationship between physical properties and structure. Aliphatic compounds: alkanes and cycloalkanes. IUPAC nomenclature, physical properties. Rotation around the C-C bond and compound conformation. 6-mer rings in nature. Isomerism: geometic isomers, chirality : stereogenic centers. simmetry. C.I.P. rules. Priority rules and assignement of the configuration. R/S descriptors. Molecules with more than one stereocenter. Racemic mixtures, diastereoisomers, meso mers. Fischer projection. Optical properties of enantiomers. Polarimeter and measurement of the optical rotation. Alkenes and alkynes: nomenclature, structure and physical properties. Structural isomers and stereoisomers. Chemical reactions, reaction coordinate diagram, transition state and activation energy. Definition of nucleophiles and electrophiles. Addition reactions to double and triple bonds (addition of hydrogen halides, acid-catalyzed addition of water. Regioselectivity (Markovnikov’s rule and stability of carbocations) . Reduction of akenes to alkanes: heat of hydrogenation and stability. Acidity of alkynes. Polarity of C-X bonds: electrophilicity of the carbon atom. Nucleophilic aliphatic substitution SN1 and SN2, beta-elimination E1 and E2. Competition between nucleophilic substitution and elimination. Nucleophilicity vs basicity. Alcohol. Ethers and thiols: structure, physical properties and reactivity. Amines: nomenclature, structure, reactivity as bases and as nucleophiles. Carbonyl compounds: aldehydes and ketones. Structure of the carbonyl group, polarity, resonance structure and electrophilicity of the carbonyl carbon. Reaction of the carbonyl group with nucleophyles. Acid and base catalysed formation of hemiacetals (mechanism). Acid-catalyzed formation of acetals. Synthesis of imines (Schiff’s bases) mechanism, acid catalyzed hydrolysis. Keto-enol tautomerism. Acidity of the alpha-carbons to a carbonyl. Carboxylic acids: properties, nomenclature, physical properties. Acid-base behaviour. Resonance hybrid. Reactions of carboxylic acids: acid- catalyzed esterification (Fischer’s esterification). Structure, properties and scale of reactivity of the derivatives of carboxylic acids. Reactions of acyl halides, esters, amides. Aromatic compounds. Benzene and its derivatives. Reactivity. Kékulé’s structures. Resonance energy. Hückel rule. Aromatic electrophilic substitution. Activating and deactivating groups. Orientation and selectivity. Heterocyclic aromatic compounds. Dienes, terpenes and polyenes. 1,2 and 1,4 electrophilic addition: kinetic and thermodynamic control. Diels-Alder cycloaddition. Amino acids: structure of the proteinogenic alpha amino acids. Acid-base properties and isoelectric point. Non natural amino acids. Peptides and structure of the peptide bond. Protecting groups in peptide synthesis. Synthesis of peptide on solid phase: the brilliant idea of the Nobel laureate Robert Bruce Merrifield. Oxytocin and Insulin. Proteins: structure ( primary, secondary: alpha-helix, beta-sheet, tertiary and quaternary), non-covalent interactions, importance of amino acid side chains in determining protein folding. Examples of peptide drugs. Carbohydrates: definition and classification. Monosaccharindes, aldoses and ketoses. Epimers. Fischer’s and Haworth’s projection. D,L configuration. Cyclic structure of monosaccharides, glycosydes, acetylation, reduction and oxidation(Tollens’ and Fehling’s reagents, nitric acid). Glucose: anomeric forms. Mutarotation of glucose. Disaccharides: cellobiose, saccharose, lactose, maltose. Polysaccharides: amylose, cellulose, glycogen, structure and properties. Glycans and glycoproteins. Glycation and glycosylation of proteins. Nucleic acids, purine and pyrimidine bases, nucleosides, nucleotides, phosphodiester bond. DNA and RNA, primary and secondary structure of nucleic acids. Lipids: structure and physical properties, triglycerides (saponification, and hydrolysis, hydrogenation, oxidation), fatty acids, phospholipids, steroids and cholesterol.