Learning objectives
Knowledge and understanding:
The course aims to teach students the scientific methodology that is the basis of organic chemistry and related disciplines; The course has the purpose of providing the basic concepts to understand, and also predict, the reactivity of the functional groups present in simple and complex organic molecules.The course also provides students with the basic language relating to the rationalization and interpretation of the main reaction mechanisms in correlation with the different mono and poly functional groups that are the subject of the course.
Applied knowledge and understanding :
The student will acquire the expertise to know the reactivity of functional groups present in organic molecules and to understand the reactivity of organic compounds according to the main reaction mechanisms.
Knowledge and understanding
The aim of the course is to provide the students: a) the basic theoretical knowledge for the structural determination of simple organic compounds by using several spectroscopic techniques and b) the theoretical and practical aspects of the synthetic methodologies learnt during the course of organic chemistry II. This will enable the student to acquire the ability to understand the relationship between structure and physical and chemical properties of the principal classes of organic compounds. Applying knowledge and understanding The student will be able to realize autonomously the preparation and purification of an organic compound by applying common and simple synthetic methodologies and to identify its structure through the interpretation of the corresponding MS, UV, IR and NMR (1H and 13C)
spectra.
Prerequisites
Knowledge of the contents of the General and Inorganic Chemistry course and of the Organic Chemistry and Laboratory I course.
Course unit content
1: Heteroaromaticity - Aromaticity and Huckel rule for heteroaromatic systems; - 5 and 6 atom heterocycles, reactivity: orientation in the electrophilic aromatic substitution reactions; - Orientation in the electrophilic aromatic substitution of naphthalene ring. 2: Aldehydes and ketones – Reactivity: nucleophilic addition and protonation-addition reactions; - Reactions of hydration, formation of hemiacetals and acetals, formation of imines and enamines, Wittig reactions, reactions with carbon nucleophiles; - Nucleophilic Addition to conjugated α, β unsaturated systems, kinetic and thermodynamic control. Michael addition. Aldehydes and ketones as electrophiles in SEAR. 3: Carboxylic acids and derivatives - Acidity of carboxylic acids, influence of the substituents; - Discussion of nucleophilic acyl substitutions; - Derivatives of carboxylic acids, synthesis and reactivity; - Electrophilic rearrangements towards C, N and O electron deficient atoms; - Thioesters and symmetrical and mixed anhydrides. 4: Substitution reactions in alpha to the carbonyl group - keto-enol tautomerism, reactions of α substitution, halogenations; - Alkylation of enolates, malonic and acetacetic synthesis, direct alkylation; - Condensation reactions of carbonyl compounds, aldol condensation and dehydration, Koevenagel condensation, Claisen condensation, condensation of importance in biological components. 5: Amines - Basicity of amines - Synthesis and reactivity of amines - Quaternary ammonium salts. 6: Carbohydrates - Classification of carbohydrates, monosaccharides, disaccharides, polysaccharides – Five and six-atom cyclic structures - Stereochemistry, formulas of Fisher and Haworth, anomers and epimers; - Mutarotation, acetals and hemiacetals; - Glycosidic bond: formation and stereochemistry of this bond; - Cellulose, starch and glycogen. 7: Amino acids, peptides, proteins - Amino acids: structure and acidity, isoelectric points, the synthesis of amino acids – peptides: peptide bond, introduction to the synthesis of peptides; - Introduction to proteins. 8: Lipids - Lipids, waxes, fats and oils; - Triglycerides, phospholipids, sphingolipids, soaps; - Terpenes and steroids. 9: Nucleic Acids - Structure of nucleic acids, nucleosides and nucleotides; - Purine and pyrimidine bases.
Some synthesis of mono-and polyfunctional molecules will be discussed according to the retrosynthetic approach.
The safety in the organic chemistry lab. IR Spectroscopy: principles and investigation of different classes of organic molecules. NMR Spectroscopy: review of the main concepts studied in the previous laboratory course, 13C spectroscopy, advanced aspects of spin-spin coupling; dynamic NMR. Mass Spectrometry: principles and features of the main ionization techniques. Use of the fragmentation processes occurring in the electron impact mass spectrometry for the determination of the molecular structure. Determination of organic molecular structures from 1H-NMR, IR, UV-vis and MS data. Primary and secondary bibliographic chemistry resources. Databases and software used for bibliographic researches for the synthesis of organic compounds.
Laboratory Experiences
• Reduction of a ketone with sodium borohydride and purification of the product by high vacuum distillation.
• Aldol condensation and characterisation of the product by gaschromatography/mass spectrometry.
• 1,4-Addition reaction to an alfa,beta-unsaturated compound.
• Synthesis of a deuterated compound through Knoevenagel condensation.
• Protection reaction of D-mannose with acetone.
• Protection reaction of an amino acid with CBz protecting group
• Synthesis of a dipetide.
Full programme
1: Heteroaromaticity - Aromaticity and Huckel rule for heteroaromatic systems; - 5 and 6 atom heterocycles, reactivity: orientation in the electrophilic aromatic substitution reactions; - Orientation in the electrophilic aromatic substitution of naphthalene ring. 2: Aldehydes and ketones – Reactivity: nucleophilic addition and protonation-addition reactions; - Reactions of hydration, formation of hemiacetals and acetals, formation of imines and enamines, Wittig reactions, reactions with carbon nucleophiles; - Nucleophilic Addition to conjugated α, β unsaturated systems, kinetic and thermodynamic control. Michael addition. Aldehydes and ketones as electrophiles in SEAR. 3: Carboxylic acids and derivatives - Acidity of carboxylic acids, influence of the substituents; - Discussion of nucleophilic acyl substitutions; - Derivatives of carboxylic acids, synthesis and reactivity; - Electrophilic rearrangements towards C, N and O electron deficient atoms; - Thioesters and symmetrical and mixed anhydrides. 4: Substitution reactions in alpha to the carbonyl group - keto-enol tautomerism, reactions of α substitution, halogenations; - Alkylation of enolates, malonic and acetacetic synthesis, direct alkylation; - Condensation reactions of carbonyl compounds, aldol condensation and dehydration, Koevenagel condensation, Claisen condensation, condensation of importance in biological components. 5: Amines - Basicity of amines - Synthesis and reactivity of amines - Quaternary ammonium salts. 6: Carbohydrates - Classification of carbohydrates, monosaccharides, disaccharides, polysaccharides – Five and six-atom cyclic structures - Stereochemistry, formulas of Fisher and Haworth, anomers and epimers; - Mutarotation, acetals and hemiacetals; - Glycosidic bond: formation and stereochemistry of this bond; - Cellulose, starch and glycogen. 7: Amino acids, peptides, proteins - Amino acids: structure and acidity, isoelectric points, the synthesis of amino acids – peptides: peptide bond, introduction to the synthesis of peptides; - Introduction to proteins. 8: Lipids - Lipids, waxes, fats and oils; - Triglycerides, phospholipids, sphingolipids, soaps; - Terpenes and steroids. 9: Nucleic Acids - Structure of nucleic acids, nucleosides and nucleotides; - Purine and pyrimidine bases.
Some synthesis of mono-and polyfunctional molecules will be discussed according to the retrosynthetic approach.
The safety in the organic chemistry lab. IR Spectroscopy: principles and investigation of different classes of organic molecules. NMR Spectroscopy: review of the main concepts studied in the previous laboratory course, 13C spectroscopy, advanced aspects of spin-spin coupling; dynamic NMR. Mass Spectrometry: principles and features of the main ionization techniques. Use of the fragmentation processes occurring in the electron impact mass spectrometry for the determination of the molecular structure. Determination of organic molecular structures from 1H-NMR, IR, UV-vis and MS data. Primary and secondary bibliographic chemistry resources. Databases and software used for bibliographic researches for the synthesis of organic compounds.
Laboratory Experiences
• Reduction of a ketone with sodium borohydride and purification of the product by high vacuum distillation.
• Aldol condensation and characterisation of the product by gaschromatography/mass spectrometry.
• 1,4-Addition reaction to an alfa,beta-unsaturated compound.
• Synthesis of a deuterated compound through Knoevenagel condensation.
• Protection reaction of D-mannose with acetone.
• Protection reaction of an amino acid with CBz protecting group
• Synthesis of a dipetide.
Bibliography
- V. H. Brown, C. Foote: Chimica Organica, Casa Ed. Edises, Napoli
- Morrison-Boyd: Chimica Organica, Casa Ed. Ambrosiana, Milano.
- P. Volhardt, N. Schore: Chimica Organica, Casa Ed. Zanichelli, Bologna.
- J. McMurry: Chimica Organica, Casa Ed. Piccin, Padova
Spectroscopy
M. Hesse, H. Meier, B. Zeeh, "Metodi spettroscopici in chimica Organica", 2^ edizione, EdiSES, 2010.
R. M. Silverstein, F. X. Webster, D. J. Kiemle, “Identificazione spettrometrica di composti organici, 2^ edizione, Casa Editrice Ambrosiana (MI), 2006.
G. M. Lampman, D. L. Pavia, G. S. Kriz, J. R. Vyvyan, "Spectroscopy", 4th ed (international edition), Brooks/Cole - CENGAGE learning, 2010.
Laboratory
M. D'Ischia: "La Chimica Organica in Laboratorio." Piccin (Padova) 2002.
R. M. Roberts, J. C. Gilbert, S. F. Martin: "Chimica Organica Sperimentale". Zanichelli Editore (BO), prima edizione 1999.
J. R. Mohrig et al. "Techniques in Organic Chemistry", 2nd ed., W.H. Freeman and Company, NY, 2006.
K. L. Williamson, K. M. Masters, "Organic Experiments: macroscale and microscale", 6th ed (international edition), Brooks/Cole – CENGAGE learning, 2011.
Teaching methods
Teaching materials available to students. The lectures are supplemented by tutoring activities in the classroom.
Classroom activities: basic theoretical aspects of IR and NMR spectroscopy and mass spectrometry (electron impact); exercises for the interpretation of 1H and 13C NMR, IR, UV and MS spectra for the
determination of the structure of simple organic molecules. Laboratory activities: seven lab experiences of synthesis and characterization of organic substances.
Assessment methods and criteria
The acquisition of a formally correct language will be checked, as well as the ability to express the content in a clear way and to connect the knowledge acquired in different parts of the course; it will be evaluated the ability to apply the fundamental concepts of organic chemistry in the rationalization and prediction of the reactivity of an organic compound (also complex).
In particular, the evaluation will be done through a written and oral exam, and will be based on the following parameters: a) knowledge and understanding of the methods and language of the discipline (6 points), b) understanding and ability to apply the knowledge acquired (15 points); c) independence of judgment in dealing with problems relating to the topics of the course (3 points); d) ability to express their knowledge and skills both in writing and verbally, using a chemical language appropriately (5 points).
The final examination of the Laboratory will include a written part in which the students have to determine the structure of a unknown organic compounds using NMR (1H and 13C), UV-vis, IR and MS data. In the following oral part, the student will be enquired on the theoretical topics discussed during the first part of the course. Editing of a personal lab booknote is also requested.
Other information
The teacher is available to students for explanations of the topics covered during the course, by appointment.
regarding the Laboratory, the format of the class will be lectures of one or two hours each spread over two mornings per week. The laboratory training will be articulated in 7 experiences of four hours each held weekly.
