CHIMICA ORGANICA

The course aims to provide a critical and scientific mentality and a rational use of memory skills, favoring the ability to apply theoretical knowledge to problem-solving.

This means overcoming the limit of the mere “mnemonic repetition” of concepts that, in doing so, would be aimed at simple learning. Critical and scientific mentality at the same time constitute a high-level objective; it requires a synthesis between mental operation and actual realization: the first is expressed in the design of an experiment, in the rational-intuitive control of the phases of execution and calculation and in the evaluation phase of the results; the second one is expressed in the real execution of the experiment, also on a virtual level.

Therefore, at the end of the course, the student must be able to:

• recognize that the great number of organic substances is determined by the ability to chain carbon atoms;
• linking the phenomenon of structural isomerism with the physical and chemical properties of isomeric compounds;
• correlate the functional and spatial structure of the molecules with the physical and chemical properties;
• predict the behavior of organic and bio-organic substances under certain reaction conditions, using general reactivity models (reaction mechanisms);
• correlate the structure of organic molecules with biological functions, with particular reference to the catalytic action of enzymes and to enzymatic kinetics;
• solve some exercises on the reactivity and the transformations of the most common functional groups, formulating plausible reaction mechanisms;
• make syntheses of simple compounds;
• carry out separations, purifications, and characterization of the most common organic compounds.

Frontal lessons

MODULE 1. Introduction to the study of organic chemistry

1. Elements of general chemistry: electronic structure and binding

Structure of the atom - Distribution of electrons in the atom - Covalent bonds - Representations of the structure of a compound - Atomic orbitals - Introduction to the theory of molecular orbitals - Formation of single bonds in organic compounds - Formation of the double bond: the bonds of the ethene - Formation of the triple bond: the bonds of the ethyne - The bonds of the methyl cation, of the methyl radical and of the methyl anion - The bonds of ammonia and the ammonium ion - The bonds of water - The bonds of the hydrogen halides - Hybridization and molecular geometry - Summary: hybridization, bond length, bond strength and bonding angles - dipole moments of molecules.

Paragraphs: 1.1-1.16

2. Acids and bases: fundamental concepts in organic chemistry

Introduction to acids and bases, pK and pH - Organic acids and bases - How to predict the outcome of an acid-base reaction - How to determine the position of an equilibrium - Influence of the structure of an acid on its value of pK - Influence of substituents on the strength of an acid - Introduction to the delocalized electrons - Summary of the factors that determine the strength of an acid - Influence of pH on the structure of an organic compound - Buffer solutions - Lewis acids and bases - Acids and bases.

Paragraphs: 2.1-2.12

3. Introduction to organic compounds: nomenclature, physical properties and structure

The alkyl groups - Nomenclature of the alkanes - Nomenclature of the cycloalkanes - Nomenclature of the alkyl halides - Nomenclature of the ethers - Nomenclature of the alcohols - Nomenclature of the amines - The structure of alkyl halides, alcohols, ethers and amines - The non covalent interactions - Solubility of the organic compounds - Rotation around the single carbon-carbon bond - Cycloalkanes and ring tension - Cyclohexane conformations - Conformations of the monosubstituted cyclohexanes - Conformations of the disubstituted cyclohexanes - Condensed cyclohexanes.

Paragraphs: 3.1-3.16

MODULE 2. Electrophile addition, stereochemistry, and electronic delocalization reactions

4. Isomers: the arrangement of atoms in space

Cis-trans isomers - Nomenclature E, Z of alkene isomers - Chirality - An asymmetric center generates chirality in a molecule - Isomers with an asymmetric center - Asymmetric and stereocentric centers - Representation of enantiomers - Naming of enantiomers with descriptors R, S - Optical activity of chiral compounds - Measure of specific rotation - Enantiomeric excess - Compounds containing more than one asymmetric center - Stereoisomers of cyclic compounds - Meso compounds - Nomenclature of compounds containing more than one asymmetric center - Nitrogen and phosphorus may be asymmetric centers - Receptors - The separation of enantiomers.

Paragraphs: 4.1-4.18

5. Alkenes: Structure, nomenclature, and introduction to reactivity • Thermodynamics and kinetics

Molecular formulas and degree of unsaturation - Nomenclature of alkenes - Structure of alkenes - Reactivity of organic compounds and functional groups - Reactivity of alkenes • Use of curved arrows - Thermodynamics: how much product is formed? - Increase the quantity of product in a reaction - Calculate the values of ΔH - Use the values of ΔH to determine the relative stability of alkenes - Kinetic: how fast do the products form? - The speed of a chemical reaction - Diagram of free energy as a function of the reaction coordinate - Catalysis - Enzyme catalysis.

Paragraphs: 5.1-5.14

6. The reactions of alkenes • The stereochemistry of addition reactions

Halogenic acid addition to alkenes - Stability of carbocations - Transitional state structure - Regioselectivity of electrophilic addition reactions - Water addition to alkenes - Alcohol addition to alkenes - Transposition of carbocations - Oxymercuration-Demercuriation - Borane addition to alkenes: hydroboration-oxidation - Halogen addition to alkenes - Addition of a peroxy acid to alkenes - Addition of ozone to alkenes: ozonolysis - Regioselective, stereoselective and stereospecific reactions - Stereochemistry of electrophilic addition reactions - Cyclic alkenes - Stereochemistry of reactions catalyzed by enzymes - Differentiation of enantiomers by biological molecules - Chiral catalysts - Reactions and synthesis - Dihydroxylation sin - Oxidative cleavage.

Paragraphs: 6.1-6.16; Wade 8.5, 8.12 and 8.13

7. The reactions of alkynes • Introduction to multistage synthesis

Nomenclature of alkynes - Nomenclature of compounds containing more than one functional group - Structure of alkynes - Physical properties of unsaturated hydrocarbons - Reactivity of alkynes - Addition of halogens and halogens to alkynes - Addition of water to alkynes – Hydroboration -oxidation of alkynes - Hydrogen addition to alkynes - Acidity of a hydrogen bonded to carbon sp - Use of acetylide ions in organic synthesis - Synthetic Strategy I: Introduction to multistage synthesis. Paragraphs: 7.1-7.128. Electronic relocation and its effect on stability, pK and reaction products • Aromaticity, electronic effects and introduction to benzene reactions. Delocalized electrons explain the structure of benzene - The bonds in benzene - Resonance limit structures and resonance hybrid - How to draw the Resonance limit structures - Predicting the stability of resonance limit structures - Resonant energy - Electronic delocalization increases stability - Stability according to the theory of molecular orbitals - Effect of electronic localization on the pK - Electronic effects - Electronic delocalization can affect the product of a reaction - Reactions of the dienes - Thermodynamic control and kinetic control - Diels-Alder reaction: an addition reaction 1,4 - Retrosynthetic analysis of the Diels-Alder reaction - Benzene is an aromatic compound - The two criteria for aromaticity - Application of aromaticity criteria - Aromaticity according to the theory of molecular orbitals - Aromatic heterocyclic compounds - Benzene reactivity - Classification of the reactivity of organic compounds I.

Paragraphs: 8.1-8.22

MODULE 3. Replacement and elimination reactions

9. Substitution and elimination reactions of alkyl halides S_N2 reaction - Factors influencing S_N2 reactions - S_N1 reaction - Factors influencing S_N1 reactions - Competition between S_N2 and S_N1 reactions - Alkyl halide elimination reactions - E2 reaction - Reaction E1 - Competition between E1 and E2 reactions - Stereoselectivity of E2 and E1 reactions - Elimination from substituted cyclohexanes - Predict the reaction products of an alkyl halide with a nucleophile / base - Benzyl, allyl, vinyl and aryl halides - Solvent effects - Replacement and elimination reactions in organic synthesis - Competition between intermolecular reactions and intramolecular reactions - synthetic strategy ii: How to tackle the problem.

Paragraphs: 9.1-9.17

10. Reactions of alcohols, ethers, epoxides, amines and sulfur-containing compounds

Acidophilic substitution reactions of alcohols: formation of alkyl halides - Lucas assay - Other methods used to convert alcohols into alkyl halides - Conversion of an alcohol into a sulfonic ester - Reaction of alcohol elimination: dehydration - Biological dehydration - Oxidation of alcohols - Nucleophilic substitution reactions of ethers - Nucleophilic substitution reactions of epoxides - Crown ethers: another example of molecular recognition - Corona ethers can be used to catalyze S_N2 reactions - Arsenic oxides - Benzo[a]pyrene and cancer - Chimney sweeps and cancer - Amines do not undergo nucleophilic substitution or elimination reactions - Quaternary ammonium hydroxides undergo elimination reactions - Thiols, sulfides, and sulfonium ions - Gas mustard: a chemical agent of war - Gli alkylating agents such as cancer drugs - Methylating agents - Eliminating termites - S-adenosylmethionine: an anti-repression - Classification of the reactivity of organic compounds II.

Paragraphs: 10.1-10.13

11. Organometallic compounds

Composite organolithium and organomagnesium - Transmetallation - Organocuprates - Palladium-catalyzed coupling reactions - Alkenes metatarsals - Grubbs, Schrock, Suzuki, and Heck receive the Nobel Prize.

Paragraphs: 11.1-11.5

12. Radicals

Reactivity of alkanes - Natural gas and oil - Fossil fuels: a problematic source of energy - Chlorination and bromination of alkanes - Stability of radicals - Distribution of products depends on probability and reactivity - The principle of reactivity-selectivity - Formation of explosive peroxides - Addition of alkenes to radicals - Stereochemistry of radical replacement and addition reactions - Radical replacement of allyl and benzyl hydrogens - Cyclopropane - synthetic strategy iii: Examples of multi-stage synthesis - Radical reactions in biological systems - Radicals and stratospheric ozone.

Paragraphs: 12.1-12.12

MODULE 4. Carbonyl compounds

15. Reactions of carboxylic acids and carboxylic acid derivatives

Nomenclature of carboxylic acids and carboxylic acid derivatives - Structure of carboxylic acids and carboxylic acid derivatives - Physical properties of carbonyl compounds - How carboxylic acids and carboxylic acid derivatives react - Reactivity of carboxylic acids and carboxylic acid derivatives - Acyl halide reactions - Foreign reactions - Hydrolysis and transesterification acid-catalyzed esters - Hydrolysis of esters favored by hydroxide ion - Carboxylic acid reactions - Amide reactions - Hydrolysis and alcoholysis of amides catalyzed by acids - Hydrolysis promoted by hydroxide ions of amides - Hydrolysis of an imide: the synthesis of Gabriel of primary amines - Nitriles - Carboxylic acid anhydrides - Dicarboxylic acids - Chemical activation of carboxylic acids - Biological activation of carboxylic acids.

Paragraphs: 15.1-15.19

16. The reactions of aldehydes and ketones • Further reactions of carboxylic acid derivatives

Nomenclature of aldehydes and ketones - Relative reactivity of carbonyl compounds - Reactivity of aldehydes and ketones - Reactions of carbonyl compounds with carbon nucleophiles - Reactions of carbonyl compost with hydride ion - Focus on reduction reactions - Chemoselective reactions - Reactions of aldehydes and ketones with nitrogen nucleophiles - Reactions of aldehydes and ketones with nucleophiles to oxygen - Protectors groups - Reactions of aldehydes and ketones with sulfur nucleophiles - Reactions of aldehydes and ketones with a peroxyacid - Wittig reaction - SYNTHETIC STRATEGY IV: Disconnections, synthetic syntons and equivalents - Nucleophilic addition to aldehydes and ketones a, b-unsaturates - Nucleophilic addition to carboxylic acid derivatives a, b-unsaturates - Addition reactions conjugated in biological systems.

Paragraphs: 16.1-16.17

17. Carbon reactions

Hydrogen acidity - Keto-enol tautomers - Keto-enolic inter-conversion - Halogenation and ketone carbon halogenation - Carboxylic acid carbon halogenation - Enolate ion formation - Carbon alkylation - Carbon alkylation and acylation through a enamino intermediate - Carbon alkylation in b - Addition of aldolic to b-hydroxyaldehyde or b-hydroxyketone - Dehydration of an aldol addition product forms aldehydes and a,b-unsaturated ketones - Crossed aldolic addition - Claisen condensation: formation of b-ketoesters - Other cross-linked condensation - Intramolecular aldol condensation and addition reactions – Robinson’s annulation - Decarboxylation of b-ketoacids - Malonic synthesis - Acetoacetic synthesis - SYNTHETIC STRATEGY V: Formation of new carbon-carbon bonds - Reactions to carbon in biological systems.

Paragraphs: 17.1-17.22

MODULO 5. Aromatic compounds

18. Reactions of benzene and substituted benzenes

Nomenclature of monosubstituted benzenes - General mechanism of aromatic electrophilic substitution reactions - Benzogen halogenation - Benzene nitrogenation - Benzene sulfonation - Benzyl Friedel-Crafts acylation - Benzyl Friedel-Crafts alkylation - Alkylation of benzene by acylation-reduction - Use of coupling reactions in benzene alkylation - Chemical transformations of substituents on the benzene ring - Nomenclature of disubstituted and polysubstituted benzenes - Effect of substituents on reactivity - Effect of substituents on orientation - The ortho para - Further considerations on the effects of substituents - SYNTHETIC STRATEGY VI: Synthesis of mono and disubstituted benzenes - Synthesis of trisubstituted benzenes - Use of diazonium salts for the synthesis of substituted benzenes - Azobenzenes - Mechanism of the formation of an ion diazonium - Aromatic nucleophilic substitution - SYNTHETIC STRATEGY VII: Synthesis of cyclic compounds.

Paragraphs: 18.1-18.22

19. Reactions of amines and heterocyclic compounds

Nomenclature - Acid-base properties of amines - Reactivity of amines as bases and as nucleophiles - Synthesis of amines - Pentatomic aromatic heterocycles (will be resumed and discussed in the next chapter) - Exatomic aromatic heterocycles (will be taken up and deepened in next chapter) - Heterocyclic amines of biological importance.

Paragraphs: 19.1-19.8

18. The Chemistry of Aromatic Heterocycles

Classification of aromatic heterocycles - Heteroaromaticity - Electrophilic substitution: general aspects – Electron-rich systems: pentatomic heterocycles containing only one heteroatom - Preparation: Paal-Knorr synthesis of furan, pyrrole and thiophene - Knorr synthesis of pyrrole - Synthesis of Feist-Bernary of furan and Hantzsch's synthesis of pyrrole - Reactivity: Acid-base reactions, electrophilic substitution, addition and cycloaddition, oxidation and reduction - Electron-rich systems: pentatomic benzocondensated heterocycles containing only one heteroatom - Preparation: Synthesis of Indole Fischer - Reactivity: Acid-base, electrophilic replacement, oxidation and reduction reactions - Electron-poor systems: hexatomic heterocycles containing only one heteroatom - Preparation: Hantzsch synthesis of pyridine - Reactivity: Acid-base reactions, Reactions of nitrogen with electrophiles, Electro replacement reactions rhodium, nucleophilic substitution, oxidation and reduction - Electron-poor systems: hexahedral benzocondensate heterocycles containing only one neutral heteroatom - Preparation: Quinoline Skraup synthesis, Bischler-Napieralski synthesis of isoquinoline - Reactivity: Main reactions - Preparation of a-aminoquinone - Solvent effect on the basicity of pyridine and ammonia - Pyridine N-oxide and electrophilic substitution.

Paragraphs: Botta 18.1-18.6

MODULO 6. Bioorganic compounds

20. The organic chemistry of carbohydrates

Characterisation of carbohydrates - The notation of - Configuration of aldoses - Configuration of ketosis - Reactions of monosaccharides in basic solution - Oxidation-reduction of monosaccharides - Lengthening of the chain: Kiliani-Fischer synthesis - Chain shortening: Wohl degradation - Glucose stereochemistry: Fischer demonstration - Monosaccharides form cyclic hemiacetals - Glucose is the most stable among aldoses - Glycoside formation - The anomeric effect - Reducing and non-reducing sugars - Disaccharides - Polysaccharides - Some natural products derived from carbohydrates - Carbohydrates on the cell surface - Synthetic sweeteners.

Paragraphs: 20.1-20.19

21. Amino acids, peptides and proteins

Amino acids nomenclature - Amino acids configuration - Acid-base properties of amino acids - Isoelectric point - Amino acid separation - Amino acid synthesis methods - Resolution of a racemic mixture of amino acids - Peptide bonds and disulfide bonds - Some interesting peptides - Peptide synthesis strategies - Automated peptide synthesis - Introduction to protein structure - How to determine the primary structure of a polypeptide or protein - Secondary structure of proteins - Tertiary structure of proteins - Quaternary structure of proteins - Denaturation of proteins.

Paragraphs: 21.1-21.17

22. Catalysis in organic reactions and in enzymatic reactions

Catalysis in organic reactions - Acid catalysis - Basic catalysis - Nucleophilic catalysis - Catalysis with metal ions - Intramolecular reactions - Intramolecular catalysis - Catalysis in biological reactions - A similar enzymatic reaction to hydrolysis of amides catalyzed by acids - Another enzymatic reaction similar to hydrolysis of amides catalyzed by acids - An enzymatic reaction that involves two successive reactions S_N2 - An enzymatic reaction similar to the enediolic transposition catalyzed by bases - An enzymatic reaction similar to retro-aldolic reaction.

Paragraphs: 22.1-22.13

26. The organic chemistry of nucleic acids

Nucleosides and nucleotides - Nucleic acids are made up of nucleotide subunits - The secondary structure of DNA - Because in the DNA there is no 2-OH group - DNA biosynthesis is called replication - DNA and the inheritance - RNA biosynthesis is called transcription - RNAs used for protein biosynthesis - Protein biosynthesis is called translation - Because DNA contains thymine instead of uracil - Antiviral drugs - How to determine the sequence of bases of DNA - genetic engineering.

Paragraphs: 26.1-26.13

• Chimica Organica – P. Y. Bruice – 3^a Ed. EdiSES (include un kit di modelli molecolari).
• Fondamenti di Chimica Organica – L. G. Wade, Jr. – Piccin.
• Chimica Organica – a cura di B. Botta, AA. VV. – 2ª Ed. Edi-Ermes.
• Manuale Virtuale di Chimica Organica: http://organicavirtuale.altervista.org/VirtualText/intro1.html
• Esercizi risolti di Chimica Organica – N. E. Schore e K. P. C. Vollhardt – Zanichelli.