87617 - CHEMISTRY

Course Unit Page

Academic Year 2018/2019

Learning outcomes

The successful student is familiar with basic principles in general and organic chemistry, in order to eventually approach in-depth biochemistry and molecular studies.

Course contents

Module 1. Inorganic chemistry.

The properties of matter. Physical and chemical changes. Elements, compounds and mixtures. Dalton’s atomic theory. Quantum theory. Heisenberg’s uncertainly principle. Schrödinger's equation. Atomic quantum theory. Quantum numbers. Atomic orbitals. Polyelectronic atoms. Periodic table. Periodic properties of the elements. Atomic radius, ionization energy and electronic affinity. Metals and non-metals. The chemical bond. Valence Bond Theory. Sigma and Pi bonds. Hybridization of atomic orbitals. Bonding and non-bonding electrons. Meaning of chemical formulas. Lewis structures. Electronegativity. Molecular dipole. Molecular geometry and VSEPR model. Formal charges and number of oxidation. Resonance formulas. Ionic bond. Atomic and ionic radii. Intermolecular forces. Polarizability. Hydrogen bond. General equation of ideal gases. Phase transitions. Phase diagrams. Vapor pressure. Stoichiometry. Concept of chemical equation. Mass ratios in chemical reactions. The relative atomic mass. The mole and the molar mass. Limiting reagent. Solutions and Dispersions. Concentration Units. Chemical reactions and equilibria. Thermodynamics. Internal energy and enthalpy. Gibbs free energy and spontaneity of a reaction. Reaction quotient. Equilibrium constant. The principle of Le Chatelier. Equilibria in aqueous solution. Self-ionization of water and pH. Definition of acids and bases according to Arrhenius, Brønsted-Lowry and Lewis. Aqueous solutions of acids and bases. Dissolution of weak acids and bases. Hydrolysis of salts. Reactions between an acid and a base. Buffer solutions. Acid-base titrations. Indicators. Oxidation and electrochemical reactions. Electromotive force. Reduction potentials. Nernst’s equation. Spontaneity of a redox reaction. Reaction rate and mechanism. Collisions theory. Activation energy. Arrhenius equation. Multistep reactions. Catalysis.

Module 2. Organic chemistry.

Classification and nomenclature of organic compounds. Functional groups. Drawing chemical structures. Alkanes and Alkane isomers. Alkyl groups. Properties of Alkanes. Conformations and stability of alkanes. Cycloalkanes. Conformation and stability of cycloalkanes. Cyclohexan. Axial and equatorial bonds, conformational mobility. Conformations of Polycyclic Molecules. Structure of alkenes. Degree of unsaturation. Nomenclature, cis-trans isomerism in alkenes. The E, Z designation. Alkene stability and reactions. Conjugated and non conjugated dienes. Polyenes. Conjugated systems in nature. Hydration of Alkynes. Enols. Reduction of Alkynes. Oxidation and reduction in organic chemistry. Properties and reactions of alcohols. Structure, properties and sources of ethers. Cyclic ethers: epoxides. Preparation of epoxides using a peroxyacid. Ring–opening reactions of epoxides. Thiols and Sulphides. Oxidation of thiols to disulphides. Properties and reactions of aldehydes and ketones. Nucleophilic addition reactions. Addition of alcohols: hemiacetals and acetals formation. Chemical and physical properties of carboxylic acids. Dissociation of carboxylic acids. Substituent effect on acidity. Common diacids and their biological role. Naming carboxylic acid derivatives: acid halides, anhydrides, amides, esters. Conversions of carboxylic acids into derivatives. Nucleophilic acyl substitution: general reaction pattern. Esters and their chemistry. Hydrolysis: acid catalysed or by dilute alkali. Amides: chemical and physical properties. Thioesters and acyl phosphates: biological carboxylic acid derivatives. Polyamides and polyesters.

Module 3. Molecules of life.

Basicity of amines. Synthesis and reactions of amines. Nitrosamines and their DNA toxicity. Aromaticity of benzene, Huckel rule. Nomenclature of substituted benzenes. Acidity and basicity of benzene derivatives, role of resonance. Polycyclic aromatic hydrocarbons. Aromatic heterocycles and their properties. Definition of stereoisomers, chirality, configuration descriptors (R, S). Assignment of absolute configuration, enantiomers, diastereoisomers, meso forms. Chemico-physical characteristics of enantiomers and diastereoisomers, optical activity. Monosaccharides, aldoses and ketoses. Stereochemistry aspects (D, L), Fisher projection. Cyclic hemiacetals (with formation mechanism), anomers. Drawing carbohydrates: chair conformation, Haworth representation. Disaccharides and polysaccharides. Reducing sugars. Physical properties of fatty acids. Triglycerides, saponification, detergents, micelles. Phospholipids, cell membrane, lipoproteins. Cholesterol and steroid hormones. Amino acids: complete nomenclature, structure, stereochemistry, acid-base and physical properties. Isoelectric point. Peptide bond and peptides. Proteins. Primary structure. Secondary structures: α-helix and β-sheet. Disulphide bonds. Ramachandran plot. Super-secondary structure. Tertiary structure. Quaternary structure. Heterocyclic aromatic bases, nucleoside, nucleotide: complete nomenclature. Structure and role of ADP and ATP. Primary structure of DNA. Secondary structure of DNA, Watson-Crick model. Pairing of nucleobases. Double helix. Tertiary structure. RNA, structure and function. Modified bases. Definition of radical, radical formation, bond dissociation energy, stability and persistency. Radical attack to biological molecules, oxidative stress. Construction and manipulation of 3D models of proteins and nucleic acids by using a specific software, in the informatic laboratory.

Readings/Bibliography

Introduction to Chemistry General, Organic, and Biological v. 1.0. Freely available on: https://2012books.lardbucket.org/pdfs/introduction-to-chemistry-general-organic-and-biological.pdf

Denninston. General, organic and biochemistry. Mc Graw Hill. http://www.mhhe.com/physsci/chemistry/denniston/etext/Denniston.pdf

Brown, Iverson, Anslyn, Foote. Organic Chemistry, 8th edition. Cengage Learning ed. ISBN 9781305580350

Teaching methods

The lectures will involve the use power-point presentations. Problem solving sessions will be carried out for the student to gain acquaintance with the numeric treatment of chemical problems. Some time will be spent in the informatic laboratory to learn the use of specific softwares that allow to build and visulalize in 3D biological macromolecules.

Assessment methods

The final examination comprises a final test made of multiple choice questions and problems, with partial credit for partial answers, lasting 2 hours without the help of notes or books, to ascertain the level of knowledge of the student, as well as an optional colloquium. Access to the optional oral examination requires passing the written test with a vote of at least 17/30. No partial tests will be carried out through the teaching period. The final grade is the average of the written and the optional oral exam.

Teaching tools

Multimedia material will be presented, such as slides, movies, animations and three-dimensional visualization of atoms, molecules and materials. Software that allow to view biological macromolecules in 3D will be used.

The multimedial material utilized during the lectures will be made available for download from the teacher's web site.

Students are asked to report any needs to the teacher via private mail. This will allow the teacher to evaluate which teaching support tools are most adequate to make the course accessible to all students.

Office hours

See the website of Riccardo Amorati

See the website of Francesco Musiani

See the website of Paola Franchi