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. Gorzynski Smith, Fondamenti di Chimica Organica, McGraw-Hill, Milano.
J. McMurry, Fondamenti di Chimica Organica, Zanichelli, Bologna.
W. Brown, T. Poon, Introduzione alla Chimica Organica, EdiSES, Napoli.
Material provided by the teacher
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
Courses recommended: Mathematics, Physics
Prerequisites - Last names M-Z
Courses required: General and Inorganic Chemistry
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: 150
Hours reserved to private study and other indivual formative activities: 102
Contact hours for: Lectures (hours): 48
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
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.
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.
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
Stereochemistry: constitutional isomers, enantiomers and diastereomers.
Elements of symmetry. Stereogenic centers. Chirality. C.I.P. system and priority rules in the assignment of stereocenters. Molecules with many stereocenters. Racemic and diastereomeric mixtures, meso compounds. Fischer projections. Nomenclature of stereoisomers. R/S and D/L descriptors. Optical properties of the enantiomers. Polarimetry and measurement of optical activity. Enantiomeric purity. Resolution of racemates and formation of diastereomers. Enzymatic kinetic resolution.
Alkanes. Definition, nomenclature and physical properties. Structural isomerism. Reactivity: radicalic substitutions, stability of radicals. Radicalic halogenation: mechanism, kinetic and termodynamic data. Kinetic profiles of the reactions,
reaction coordinate, transition states, reaction intermediates. Newman projections. Cycloalkanes: conformational analysis. Alkenes: definition, nomenclature and physical properties. Isomerism. Structure and stability of alkenes: standard entalpies of hydrogenation, constitutional isomerism and stereoisomerism (cis-trans, E-Z). Reactivity. Addition of water under acid catalysis: regioselectivity. Hydroboration-oxidation reaction. Halohydrin formation. Addition of bromine: bromonium ion, stereochemistry of the addition. Oxidation reactions: hydroxylation with OsO4 and KMnO4, stereochemistry of the reaction.
Epoxide formation. Preparation of alkenes: elimination reactions and issues connected to the formation of isomers, partial hydrogenation of alkynes. Polymerization. Dienes: definition, classification, nomenclature. Structural features of 1,2 1,3 and isolated dienes. Stability. Reactions of 1,3 dienes with electrophiles. Addition of HBr on 1,3-butadiene: 1,2 and 1,4 adducts. Kinetic and termodynamic control. Diels-Alder cycloaddition: structural and electronic requirements of dienes and dienophiles, mechanism and stereoselectivity.
Alkynes. Structural features, nomenclature. Acidity. Formation of ionic and covalent acetylides. Analogy between acetylide and cyanide. Additions to the triple bond. Addition of water and keto-enol tautomerism.
Aliphatic nucleophilic substitutions: SN1 and SN2 reactions, nucleophiles and leaving groups, stereochemistry, requirements for the SN1 and SN2 reactions. Competition between substitution and elimination reactions. E1 and E2 reactions.
Halogen derivatives. Definition, nomenclature, physical properties. Methods of preparation from hydrocarbons (saturated and unsaturated) and alcohols. Reactivity: transformations in other functional derivatives via nucleophilic substitutions.
Alcohols. Definition, classification, nomenclature, physical properties. Methods of preparations via addition reactions, substitution reactions, hydrolysis and fermentations. Preparation of 1,2-diols: methods and stereochemical issues. Glycerol. Oxidation of alcohols. Phenols.
Ethers. Definition and physical properties. Formation via alcohol dehydration and the Williamson synthesis.
Aromatic compounds. Historical notes on the structure of benzene and its derivatives.
General reactivity of benzene. Kekulé formulas. Empirical resonance energy, Hückel rules. Electrophilic substitution reactions. Kinetic profile of the aromatic electrophilic substitution (alkylation, acylation, halogenation, sulfonation, nitration). Activating and disactivating groups. Inductive and mesomeric effects. Orientation and selectivity. Heterocyclic and polycyclic compounds: electron-rich and electron-poor heterocycles.
Carbonyl compounds. Definition, nomenclature of aldehydes and ketones, physical properties. Reactivity of the carbonyl bond. Reactions with carbon, oxygen, nitrogen , and hydrogen allo zolfo, nucleophiles. Addition of hydrides. Hemiacetals and acetals. Grignard reagents and organometallic compounds. Reactions involving the carbon atom vicinal to the carbonyl group. Keto-enol tautomerism. Enols and enolates. Aldolic condensation, mixed condensations. Reactivity of alpha-beta unsaturated aldehydes.
Carboxylic acids. Definition, nomenclature and physical properties. Acidity and basicity. Methods of preparation: oxidations, hydrolysis, reductions, malonic synthesis. Reaction of carboxylic acids: esterification and functional derivatives. Reactivity of functional derivatives.
Esters. Preparation, properties and reactivity. Esters of carboxylic acids: Fischer esterification. Acid and base (saponification) hydrolysis. Acyl chlorides: preparation, properties and reactivity. Anhydrides: preparation, properties and reactivity. Amides: preparation, properties and reactivity. Nitriles.
Amines. Definition, classification, nomenclature, physical properties. Basicity of aromatic and aliphatic amines. Preparation and reactions of amines with electrophiles.
Amino acids: types of amino acids. Physicochemical features of the amino acids: solubility, acidity and basicity. Alpha-amino acids. Natural amino acids. Preparation of the amino acids. Isoelectric point. Structure and formation of the peptide bond. Protecting groups. Activators of the carboxylic group. Solid-phase synthesis of peptides.
Nucleic acids: pirimidines and purines. Nucleosides and nucleotides.
Fatty acids: soaps. Lipids. Waxes, triglycerides. Esters of other acids: phospholipids. Terpenes and steroids.
Carbohydrates: definition and classification. Monosaccharides of the D series. Epimers. Fischer and Haworth projections. Glucose: anomeric species. Mutarotation of glucose. Disaccharides: cellobiose, saccharose, lattose, maltose. Polysaccharides: cellulose, starch, amylose, amylopectine, glycogen.
Course program - Last names M-Z
Course Contents (detailed program): Introduction: beginning and development of organic chemistry. Fundamental discoveries. Organic compounds and their interest from economical, social, and cultural points of view.
Hybridization of the carbon atom and shape of the molecules. Bondsethylene and acetylene. Bond length and strength. Acid-base theories. Inductive and resonance effects.
Structure and stability of carbocations. Hyper-conjugative effects.
Classification of the organic chemistry reactions. Electrophiles and nucleophiles: definition, analogies and differences between acid-base and E/N behaviour. Acid (protic and Lewis) attack onto unsaturated species: activation of the carbonyl group and double carbon-carbon bond.
Alkanes: definition, nomenclature and physical properties. Structural isomerism. Reactivity. General remarks on the reactions: kinetic plots, definition of reaction coordinate, transition state, and reaction intermediate. Hammond postulate. Newman projection formulas, conformational analysis. Cycloalkanes: stability and combustion enthalpies, angle bond strains and torsion strains. Conformational analysis of cycloalkanes.
Alkenes: definition, nomenclature, and physical properties. Isomerism. Structure and stability. Structural and stereo- isomerism (cis/trans, E/Z). Reactivity. Markovnikov’s rule.
Dienes: definition, classification, and nomenclature. Structural features of 1,2- and 1,3-dienes. Diels-Alder cycloadditions.
Alkynes: structural features and nomenclature. Acidity.
Aromatic compounds. Meaning of the term. Pioneering studies on benzene and its derivatives. Reactivity of benzene. Kekulé formulas. Empirical resonance energy. Huckel’s rule. Electrophilic substitution reactions. Kinetic plots of the main aromatic electrophilic substitutions. Activating and deactivating groups toward aromatic electrophilic substitution. Analysis of inductive and conjugative effects. Orientation. Ortho/para ratio in disubstituted derivatives of benzene. Elimination-addition reactions via benzene, nucleophilic substitutions SN1Ar and SN2Ar: decomposition of diazonium salts.
Stereoisomerism. Diastereoisomers and enantiomers: definition and examples. Symmetry elements. Concept of chirality. Nomenclature of diastereoisomers (geometric isomers) by means of E/Z method. Principles of polarimetry. Specific rotation and optical purity. Optically active compounds with one stereogenic center: attribution of the stereochemistry by means of the relative method D/L and the absolute method R/S. Compounds with two stereogenic centers. Compounds having two equivalent stereogenic centers: meso isomers. Prochirality. Resolution of racemic mixtures. Chirality in compounds without stereogenic centers.
Aliphatic nucleophilic substitutions SN1 and SN2: features of nucleophiles and leaving groups, stereochemical aspects, circumstances that favor the SN1 and SN2. Substitutions vs. eliminations.
Halohydrocarbons: definition, nomenclature, physical properties. Reactivity.
Grignard’s reagents: preparation and reactions with polar multiple bonds. Reaction with aldehydes, ketones
Alcohols: definition, classification, nomenclature, physical properties. Preparation of 1,2-diols: methods and stereochemical aspects. Glycerol.
Esters: definition. Esters of carboxylic acids. Formation according to Fischer. Acid and alkaline (saponification) hydrolysis. Mechanism of alkaline hydrolysis. Stereochemical proofs of the mechanism. Waxes, oils, and fats. Esters of non-carboxylic acids. Phospholipids.
Ethers: definition, nomenclature, and physical properties. Epoxides: preparation and reactivity.
Phenols: definition, nomenclature, and reactivity. Electrophilic substitutions on the ring by weak electrophiles.
Sulfur-containing compounds. Thiols, thiophenols and thioethers. Oxidation of thiols and thioethers.
Carbonyl compounds: definition, nomenclature of aldehydes and ketones, physical properties. Reactivity of the carbonyl group. Reaction with nitrogen, carbon, oxygen, and sulfur nucleophiles. Addition of hydride ion. Cannizzaro reaction. Reactions involving the carbon adjacent to the carbonyl: aldol reaction and mixed aldol reactions.
Carboxylic acids: definition, nomenclature, and physical properties. Reactions of carboxylic acids: formation of esters and other functional derivatives. Dicarboxylic acids, hydroxyacids and oxoacids.
Amines: definition, classification, nomenclature, and physical properties. Basicity of alkylamines and arylamines in comparison with ammonia. Reactions of amines with electrophiles.
-Amino acids: definition, nomenclature, and physical properties. Classification according to chemical and biological criteria. Structure and amphoteric character, isoelectric point. Stereochemistry. Peptides and their synthesis: use of protecting groups. Proteins.
Carbohydrates: definition and classification. Monosaccharides belonging to D series. Fischer projection formulas. Chain elongation of an aldose (Kiliani-Fischer). Shortening the chain of an aldose (Ruff and Wohl degradations). Ancient and actual meaning of the term epimeric sugars. Reaction of monosaccharides with Tollens, Fehling, and Benedict reactants. Glucose: and forms. Mutarotation. Stability of -and - glucose. Disaccharides and polysaccharides.