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ORGANIC CHEMISTRY

             
Compulsory/Elective Code Semester Lectures Practicals Credits ECTS
Compulsory 13Β003 1st 4 Hrs/Wk 3 Hrs/Wk 6 8.0
Aims:
 
 

The aims of the course are: a) To introduce students to the type of chemical bonds of organic compounds, as a result of hybridized atomic orbitals of carbon. b) To outline how polarization is induced in covalent bonds of carbon due to the difference either in electronegativity or in the bulk of some substituents. c) To introduce students to the acidic and/or basic character of organic compounds and how this is affected by neighboring groups. d) To show the criteria for choosing appropriate reagents, so that the acidic or/and basic character of an organic compound can be revealed. e) To show how to draw the skeleton structures of  organic compounds as well as resonance structures via pattern recognition. f) To introduce students into understanding the three dimensional bond-line structure of organic compounds and how to be able to represent these structures via projections (Newman, Fischer, Haworth). g) To show students how to recognize the different kinds of isomerism, especially stereoisomerism and also how to characterize stereogenic centers using the Cahn-Ingold -Prelog system. h) To prepare students to understand the stereochemistry of the addition reactions to C=C double bond and be able to draw the products. i) To prepare students to understand the terms of regio-selectivity stereoselectivity and stereospecificity for the reactions of nucleophilic aliphatic substitution, elimination and addition to C=C. j) To outline the criteria for the characterization of a compound as aromatic or anti-aromatic. k) To outline the difference in chemical behavior of aromatic compounds (electrophilic aromatic substitution). l) To introduce the students to the chemistry of the most common functional groups (alcohols, carbonylic compounds, carboxylic acids, amines) as well as of biomolecules. m) To help students develop skills in combining  knowledge of chemical reactivity of  different functional groups in order to understand the chemical behavior of biomolecules and also to be able to propose retrosynthetic schemes for the synthesis of new bioactive compounds.

The laboratory course offers knowledge and experience on: a) the basic methods of separation and purification of organic compounds:  distillation, extraction, filtration, recrystallization, sublimation, b) the separation of a mixture of organic compounds using acid-base extraction and use of Thin Layer Chromatography (TLC) to check the efficacy of separation, c) Identification of functional groups: alkenes, alkyl halides, alcohols,  aldehydes, ketones, carboxylic acids, amines, phenols, amides, amino acids, peptides, proteins, carbohydrates, d) structure determination of simple organic compounds using NMR and IR spectroscopy, e) synthesis of an organic compound of pharmacological interest (preparation of acetylsalicylic acid).

 
Objectives:
 
 

At the end of the course students should: a) Know the structure of C atom and the kind of bond it forms, b) Be able to represent the three-dimensional structure of organic compounds using the appropriate projections, c) Be able to draw resonance structures of organic compounds via pattern recognition, d) Be able to characterize the kind of stereoisomers (diastereomers, enantiomers) as well as to identify the stereogenic centers of an organic molecule according to the  Cahn-Ingold-Prelog system, e) Acquire knowledge on the mechanisms of nucleophilic aliphatic substitution (SN1, SN2) and elimination (E1, E2) with emphasis on the stereochemistry of the obtained products (stereoselectivity and stereospecificity of the reactions), f) Acquire knowledge on the chemistry of the functional groups of alcohols, carboxylic acids, amines, carbonyls, g) Acquire knowledge on the chemistry and conformation of biomolecules (nucleotides, amino acids/proteins, lipids, carbohydrates), h) Be able to recognize an aromatic compound, i) Acquire knowledge on the mechanism of the aromatic electrophilic substitution and its application, j) Develop skills to propose retrosynthetic schemes for the synthesis of new bioactive compounds.

Upon completing the laboratory course, students should be able to: a) Recognize, describe and choose methods for the separation and purification of solid and liquid organic compounds, b) Recognize and choose methods for the identification of organic compounds, c) Write chemical equations in order to describe the reactions they performed in the laboratory, d) Calculate the yield of a chemical reaction and the eventual excess of a reagent, e) Distinguish the functional groups of organic compounds and select the suitable reagents to identify them, f) Combine the characteristic chemical reactions in order to distinguish organic compounds, with emphasis on compounds of biological interest, g) Recognize how the basic spectroscopy principles are applied to the determination of the structure of simple organic compounds, h) Recognize the importance of the reaction conditions for a successful synthesis experiment, i) Apply the safety and good laboratory practice rules during a laboratory experiment, j) Organize, compare and evaluate the experimental observations and results, draw conclusions from the experimental data, and present them in post-lab reports, k) Use simple laboratory equipment, l) Handle organic and inorganic reagents, while applying the basic safety and good laboratory practice rules, m) Combination and application of the knowledge/skills obtained, in any similar laboratory environment, n) Cooperation in the lab (common use of instruments and equipment, team reports, team laboratory activities)

 
Lectures:
 
 

Electrons, bonds and molecular properties (2 hrs) - Molecular representations (2 hrs) - Acids and Bases (2 hrs) - Alkanes and cycloalkanes (3 hrs) - Stereoisomerism (6 hrs) - Substitution reactions (3 hrs) - Alkenes: Structure and preparation via elimination reactions (2 hrs) - Addition reactions of alkenes (2 hrs) - Alkynes (1 hr) - Aromatic compounds (3 hrs) - Electrophilic aromatic substitution (2 hrs) -  Alcohols and phenols (3 hrs) - Ethers and epoxides; Thiols and sulfides (1 hr) - Aldehydes and ketones - Reactions of nucleophilic addition (4 hrs) - Carboxylic acids-esters-amides-nitriles - Nucleophilic acyl-substitution (5 hrs) -  Ν-heterocycles (3 hrs) - Carbohydrates, glycosidic bond, nucleic acids (3 hrs) - Amino acids and Proteins (4 hrs) - Lipids (1 hr).

 
Practicals:
 
 

Laboratory experiments: 1. Methods for Separation and Purification of organic compounds: Distillation, Extraction, Filtration, Recrystallization, Sublimation, Separation of a mixture of organic compounds using acid-base extraction and use of Thin Layer Chromatography (TLC) to check the efficacy of separation. 2. Identification of functional groups and analysis of organic compounds: Alkenes, Alkyl halides, Alcohols,  Aldehydes, Ketones, Carboxylic acids, Amines, Phenols, Amides, Amino acids, Peptides, Proteins, Carbohydrates. Introduction to the spectroscopy of organic compounds. 3. Organic Synthesis: Preparation of acetylsalicylic acid.

 
Instructors:
 
  Lectures: P. Moutevelis-Minakakis, Professor of Organic Chemistry (Coordinator) - S. Vassiliou, Assistant Professor of Organic Chemistry
 
  Practicals: G. Kokotos, Professor of Organic Chemistry (Laboratory Experiments Coordinator) - Dr. A. Mores, Laboratory Teaching Staff - Dr. K. Paschalidou, Laboratory Teaching Staff - Dr. E. Sakki, Laboratory Teaching Staff
 
Notes:
 
 

The evaluation procedure takes place in Greek (and in English for Erasmus students) and consists of a final written exam consisting of: a) Long-answer Questions, b) Short-answer Questions, c) Solving exercises/problems. The laboratory grade, obtained after a separate written exam on the practical part, is 30% of the final course grade. The evaluation criteria are described in: https://eclass.uoa.gr/courses/BIOL302/

 
Contact:
 
  If you require more information, please contact the Course Coordinator, Prof. P. Minakakis at: Tel +30 210 727 4484; e-mail: pminakak[at]chem.uoa[dot]gr