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CHEMISTRY II (A-L)
MARIO ORENA

Seat Scienze
A.A. 2016/2017
Credits 8
Hours 64
Period 1^ semestre
Language ENG
U-gov code ST01 3S011

Prerequisites

Knowledge of some chemistry topics including either molecular structure and types of chemical bonds. Chemical thermodynamics and kinetics arguments will be also useful.

Development of the course

Lectures are planned (8 credits, 64 hours) during which questions are presented with a guided solution, concerning the most significant reaction mechanisms of organic chemistry. The lectures’ educational activity is supported in e-learning mode disclosing all slides discussed in class and audio files of lectures; the final examinations texts with solutions  are also given, thus allowing students to assess their level of preparation.

Learning outcomes

Knowledge:
The course enables students to acquire the basic knowledge about the transformations and interactions mechanisms of organic compounds present in biological systems, in order to understand their action in living organisms.

Ability to apply the knowledge:
The student should acquire the ability to define the reaction mechanisms underlying biological processes, so that he can apply this knowledge within other courses, in particular those dealing with biological chemistry and molecular biology.

Soft skills:
The solution of selected problems, with single and group work, can improve the student insight together with the ability to communicate stemming from teamwork.

Program

Topics (Lectures, 8 CFU, 64 hours):
1.Introduction to the structure of organic molecules. Atomic orbitals and electronic configuration. The chemical bond. The rendering of an organic structure. Functionalities and nomenclature of organic compounds. The theory of the valence bond. 
2. The theory of molecular orbital. Resonance structures. Non-covalent interactions. Relationship between non-covalent interactions and physical properties of organic compounds. 
3.Conformational equilibria and static stereochemistry. Conformations of molecules with linear chain. Conformations of cyclic molecules: cyclopentane, cyclohexane and glucose.   Confurations and stereochemistry: chirality and chirality centres. Compounds displaying one chirality centre: the enantiomers. Compounds dispolaying more chirality centre: the diastereomers. Stereochemistry and reactivity. Prochirality in biological molecules. 
4.Introduction to reaction mechanisms. Thermodynamics and kinetis of organic reactions. Energy graphics and reaction plots. Electrophiles and nucleophiles versus Lewis acids and bases.
5.The acid-base processes. Structure effects on acidity and basicity. Mesomeric effect. Hyperconjugative effect. Inductive effect. Acidity of phenols an basicity of nitrogen-containing compounds. The resonance on pyridine, pyrrole and imidazole. Carbon acids an enolate anions. 
6.The nucleophilic substitutio to sp3 carbons. Associative nucleophilic substitution: SN2 mechanism. Dissociative nucleophilic substitution: SN1 mechanism. Steric and electronic effects acting on electrophilicity. Leaving groups and their properties. The SN1 o SN2 mechanism can be easily provided starting from structural considerations. The nucleophilic substitution of epoxides. Nucleophilic substitution in biological systems: the SAM (S-adenosylmethionine). 
7.Elimination reactions leading to double bonds. E1 and E2 mechanisms. Steric and thermodynamic effects leading to formation of double bonds. 
8.The π moieties as bases and nucleophiles. The electrophilic addition process. Cations as reaction intermediates and 1,2-shift. Intermediate cations stabilized by mesomeric or hyperconiugative effect. Regioselectivity and stereoselectivity of addition processes. Enantiotopic and diastereotopic re and  si faces of cationic intermediates. Kinetic and/or thermodynamic control in addition to dienes. Cationic intermediates within isomerization reactions. Cationic intermediates within alkylation of aromatic substrates.   
9.Transfer of phosphate groups. The cleavage of phospate esters: inter and intramolecular processes. Behaviour of molecules significant for biological systems: ATP, PEP, DHP, G6P e F6P.
10.Addition of nucleophiles to the carbonyl group. Keto-enolic tautomerism. Steric and electronic effects within the addition process. The addition process occurs as an equilibrium reaction. Kinds of nucleophiles. Nucleophiles at hydrogen, nucleophiles at nitrogen, nucleophiles at oxygen. Stereoselectivity of the addition process. Intramolecular addition in glucose leading to the anomers formation.  Nucleophiles at carbon: cyanide anion and enolate anions. Enolate anions can arise under kinetic or thermodynamic control. Aldol reaction, retroaldol reaction and aldol condensation. Requirements for the E1cB reaction mechanism. 
11.Addition of nucleophiles to the carbonyl group followed by removal of a leaving group. Nucleophiles at hydrogen, nucleophiles at nitrogen, nucleophiles at oxygen.  Nucleophiles at carbon leading to β-dicarbonyl compounds. The reactivity of β-ketoacyl-SCoAs.Comparison between esters and thioesters reactivity. 
12.Addition of nucleophiles to αβ-unsaturated systems. Processes occurring under kinetic and/or thermodynamic control. The conversion of fumarate into (S)-malate.
13.Redox reactions in organic chemistry.

Development of the examination

Methods for assessing learning outcomes:
he exam consists of a written test and oral examination with commentary of the written test results and discussion of one or more slides presented in class. In the task there are six issues concerning the reaction mechanisms. For each response is given a score between zero and five. In order to overrun the written test, the student must attain a score not less than half of the available points. The exam is passed when after the oral test final vote is greater than or equal to 18.

Criteria for assessing learning outcomes:
In the written test, the student must demonstrate knowledge of the major organic chemical reaction mechanisms and to have acquired basic knowledge about the reactivity of the most common types of organic compounds.

Criteria for measuring learning outcomes:
The final mark is awarded out of thirty. The exam is passed when the grade is greater than or equal to 18. It is expected to be awarded the highest marks with honors (30 cum laude).

Criteria for conferring final mark:
The final grade is given by adding to the written score the evaluation of the oral interview, up to a maximum of five points. Praise is attributed when the score obtained from the previous sum exceeds the value 30, while the student has demonstrated full mastery of the subject.

Recommended reading

1. Lecture notes
2. Soderberg, Organic Chemistry with a Biological Emphasis, Lulu, 2016
3. Klein, Fondamenti di Chimica Organica, Pearson, 2016
4. Vollhardt & Smith, Chimica Organica, Zanichelli, 2016

Courses

• Scienze biologiche