Molecular Biology, Medicinal Chemistry and Computer Science for Pharmaceutical Applications

Structure and bond. Lewis structures. The shape of the molecules. Representation of organic structures. Hybridization. Ethane, ethylene, acetylene. Bond length and bond strength. Electronegativity and polarity of the bond. Polarity of molecules. Resonance. Acids and bases. Brønsted-Lowry acids and bases. Reactions of Brønsted-Lowry acids and bases. Acid strength and pKa. Equilibrium. Factors that determine acidity. Lewis acids and bases Organic molecules and functional groups. Functional groups. Intermolecular forces. Physical properties. Functional groups and reactivity. Alkanes and cycloalkanes. Introduction. Nomenclature of alkanes and cycloalkanes. Common names. Physical properties. Conformation of acyclic alkanes (ethane, butane). Cycloalkanes. Cyclohexane (chair conformation, ring inversion) Substituted cycloalkanes (mono- and di-substituted). Oxidation and reduction of alkanes (combustion). Stereochemistry. The main classes of isomers. Chiral and achiral molecules. Stereogenic centers. Absolute configuration R/S. Diastereoisomers. Compounds with two or more stereogenic centers. Meso forms. Physical properties of enantiomers (optical activity, racemic mixtures, specific rotation, enantiomeric excess) and diastereoisomers. Chemical properties of enantiomers. Organic reactions. Type of organic reactions (substitution, elimination, addition). Breakage and formation of bonds (radicals, carbocations, carbanions). Bond dissociation energy. Thermodynamics (equilibrium constant and free energy changes). Enthalpy and entropy. Energy diagrams. Kinetics (activation energy, velocity equation). Catalysts. Radical reactions. Introduction. General features. Halogenation of alkanes: mechanism. Alkyl halides and substitution reactions. Introduction. Nomenclature. Physical properties. Polarity of the C-halogen bond. Nucleophilic substitution (halide, leaving group, nucleophilie, solvent effect). SN2 and SN1 mechanism (kinetics, stereochemistry, nature of the halide, effect of the solvent). Stability of carbocations. Factors determining the SN2 or SN1 mechanism. Vinyl and aryl halides. Alkyl halides and elimination reactions. General characteristics of the elimination. Alkenes (C = C bond, cis / trans isomers, stability). E2 and E1 elimination mechanism (kinetics, nature of the halide). Zaitsev's rule (selective and stereoselective regio reactions. Factors determining the E2 or E1 mechanism. E2 in the synthesis of alkynes. Substitution / elimination competition. Alkenes. Nomenclature (use of the prefixes cis / trans and E / Z). Physical properties. Preparation of alkenes. Addition reactions: hydrohalogenation (Markovnikov rule, stereochemistry); hydration; halogenation (stereochemistry). Free radical addition to double bonds. Conjugation, resonance and dienes. Conjugation. Resonance and allyl carbocations. The resonant hybrid. Delocalization of electrons, hybridization and geometry. Conjugated dienes. Electrophilic addition 1,2 and 1,4. Kinetic and thermodynamic control Alkynes. Nomenclature. Physical properties. Preparation. Reactivity: terminal alkynes as acids; hydrohalogenation; halogenation; hydration (keto-enol tautomerism). Reactions of acetylide anions. Alcohols, ethers and epoxides. Structure, Nomenclature, Physical Properties. Preparations. Reactivity of alcohols: dehydration, reaction with HX. Reactivity of ethers with strong acids. Reaction of epoxides with nucleophiles and acids. Oxidations and reductions. Reducing agents. Reduction of alkenes and alkynes. Oxidizing agents. Epoxidation, dihydroxylation, oxidative cleavage of alkenes and alkynes. Oxidation of alcohols. Amines. Structure and bonds. Nomenclature. Preparation by direct nucleophilic substitution, by reduction of functional groups containing nitrogen; hydration; halogenation (stereochemistry). Introduction to carbonyl chemistry. General reactivity of carbonyls Aldehydes and ketones. Nomenclature. Preparation. Reactivity: nucleophilic addition of H- and R-, of –CN, of primary and secondary amines, of water, of alcohols (acetals). Nucleophilic substitution of RCOZ. Cyclic hemiacetals. Reduction of aldehydes and ketones (stereochemistry). Oxidation of aldehydes. Organometallic reagents of lithium, magnesium and copper (as bases and as nucleophiles). -unsaturated carbonyl compounds: 1,2 and 1,4 addition. Carboxylic acids and their derivatives - Nucleophilic acyl substitution. Structure and bond. Nomenclature. Nucleophilic acyl substitution: reaction of acid chlorides, anhydrides, acids, esters, amides Carboxylic acids and the acidity of the O-H bond. Structure and nomenclature. Preparation. Acidity. Inductive effects in aliphatic and aromatic acids. Sulphonic acids. Carboxylic acids and their derivatives - Nucleophilic acyl substitution. Structure and bond. Nomenclature. Nucleophilic acyl substitution: reaction of acid chlorides, anhydrides, acids, esters, amides. Substitutions of carbonyl compounds at C in αEnols and enolates. Keto-enol tautomerism, direct alkylation of enolates. Malonic synthesis. Acetacetic synthesis. The aldol reaction. α, β- unsaturated aldehydes and ketones. Michael's reaction. Benzene and aromatic compounds. The structure of benzene. Nomenclature. Stability of benzene. Hückel's rule. Polycyclic aromatic compounds. Aromatic heterocycles (pyridine, pyrrole). Charged aromatic compounds (cyclopentadienyl anion and tropylium cation). Electrophilic aromatic substitution. General mechanism. Halogenation. Nitration and sulfonation. Friedel-Crafts alkylation and acylation. Electrophilic aromatic substitution of substituted benzenes (effect of substituents on speed and orientation). Introduction to Biomolecules. Carbohydrates. Peptides and proteins. Lipids. Nucleic acids.

For an easy approach to the course, it is advisable to have acquired the knowledge of General and Inorganic Chemistry.

• Organic Chemistry, 9th Edition ( L.G. Wade) • TEST BANK FOR ORGANIC CHEMISTRY, 9th Edition (L.G. Wade) • CHIMICA ORGANICA ESSENZIALE EDI ERMES 2018 (B. Botta)

Attendance to the course is optional, but recommended.

The first evaluation test, in which the student can participate, is held at the end of the course. There are no intermediate tests. At each exam, the evaluation is subject to passing a mandatory written and an oral test. The elements analyzed for the assessment are: knowledge of the subject, the use of an appropriate language, active participation during lectures, the reasoning ability demonstrated during the exam, and the ability to study autonomously.

The teaching of Organic Chemistry consists of face-to-face lessons with students. The lessons are interactive, and the teacher stimulates the students with questions to which they, by virtue of what has been explained, can give answers. The student will be able to find the slides and teaching material (exam program, recommended texts) useful for preparing the exam on the e-learning platform. The slides are a guide to the exam topics, but they cannot replace the recommended texts and lectures held by the teacher.