66687 - Organic Chemistry II and Laboratory

Learning outcomes

At the end of the course the student understands the basic reactivity of polyfunctional carbonyl compounds, of aromatic heterocyclic compounds as well as of organic free radicals. The student is able to predict the chemical behaviour of the pericyclic reactions following the symmetry rules of the interacting molecular orbitals; to choose appropriate methodologies for the use of protecting groups; to know oxidation and reduction reactions of organic molecules; various synthetic methods using organometallic compounds; the typical reactions of organic compounds bearing sulfur and phosphorus; the basic chemistry of carbohydrates. The student is able to discuss synthetic pathways, to analyze appropriate synthetic methods as well as to perform the synthesis of organic molecules of average complexity through the use of usual procedures. The student is additionally able to follow the progress of every organic reaction as well as to characterize the outcoming products by means of common analytical techniques including Nuclear Magnetic Resonance (NMR), Mass Spectroscopy (MS) and Gas Chromatography (GLC).

Course contents

Background knowledge

All the learning outcomes of the Organic Chemsitry part 1 course.

In particular, students are expected to know:

• nomenclature, structure, and classification of organic compounds;
• structure and reactivity of the main organic functional groups;
• structural-, regio-, and stereo-isomerism;
• structure and reactivity of the most important reactive intermediates;
• fundamental organic reactions mechanisms (e.g. electrophilic and nucleophilic substitution [both aliphatic and aromatic], additions, eliminations, nucleophilic addition and acyl substitution to carbonyl groups).
• how to work properly and safely in a laboratory of organic chemistry, paying particular attention to safety rules, usage of the most common apparatuses, and standard procedures of preparation, purification, and characterisation of organic compounds.

Theory:

1. Organic reactions and curly arrows.
2. Protecting groups. Oxidations and reduction reactions.
3. Advanced carbonyl chemistry.
4. Conjugated systems and nucleophilic aromatic substitution
5. Organic compounds of lithium, magnesium, copper, zinc and boron.
6. Organic compounds of sulfur, phosphorus and silicon.
7. Heteroaromatic compounds
8. Radicals in organic synthesis.

Laboratory:

The program of the course starts from the knowledge acquired in the course of Laboratory of Organic Chemistry I. It is formed by two parts. The first one concerns basic informations and principles of NMR spectroscopy and mass spectrometry. (GC-MS) applied to the investigations of properties and structure of pre synthesized materials. Several dedicated instruments are available to direct use of students.

The second part of course concerns the practical preparations of several products, in parallel to subjects discussed in the course of Organic Chemistry II.

The proposed experience are as follows:

1. reaction of reduction (by metal hydrides) of a stereogenic carbon in a homochiral molecule;
2. Wittig condensation of an aldehyde with a phosphonium ylide;
3. 1,2-addition of a nucleophile to a conjugated carbonyl compound
4. 1,4-addition of a nucleophile to a conjugated carbonyl compound

Readings/Bibliography

Lectures' handouts will be made available on-line in advance

Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. Organic chemistry 2nd Ed. Oxford, Oxford University Press, 2012.

M. D'Ischia, La Chimica Organica in Laboratorio, Casa Editrice Piccin.

R.M. Silverstein et altri, Identificazione Spettrometrica di Composti Organici, Casa Editrice Ambrosiana.

Teaching methods

Theory: frontal lessons delivered in the classroom with the aid of the blackboard and suitable projection of slides. Classroomsolution of problemsand answers to exercises relevant to the main topics of the course.

Laboratory: Detailed synthesis procedures will be furnished to each student, together with mechanicistic explanation of the considered reactions and NMR spectra of starting materials and final products.

In the laboratory there are working places with suitable equipemments to perform the considered reactions.

Students are expected to summarize the obtained results in dedicated form. The report must be delivered after each lab session. Failing to provide the form in due time will result in a null evaluation for that lab session.

Assessment methods

Learning assessment is achieved through a series of tests distributed during the semester of teaching and a final exam, which is held during one of the six exam calls defined by the teachers in the academic year during exam sessions.

Each test gives rise to a score. The sum of the scores obtained in the various tests constitutes the final score that is between 0 and 100 and is converted to the final grade according to this conversion table:

score/grade conversion table

Points  grade
0         not passed
50       18
55       19
60       20
63       21
65       22
68       23
72       24
75       25
78       26
82       27
85       28
88       29
90       30
95       30 L

Learning of the laboratory part is assessed through six written tests:

1. written NMR/mass exercise
   How: written exercise in which the student must interpret simple spectroscopic data of NMR and mass and be able to assign them to a compound to be selected from a set of eight. The test is carried out approximately in the middle of the semester and before the practical laboratory experiences. The allotted time for this test is 90 min.
   Purpose: Purpose of the test is to assess the student's understanding of the NMR / mass concepts and the ability to apply them to the understanding and solving of simple structural recognition problems. In addition, the test also aims to prepare the student to similar problems of interpretation of NMR and mass spectra that the student will meet during the subsequent laboratory practices.
   Score: The score of this test is between 0 and 14 points Participation: The participation to this test is compulsory; in case of absence, a recovery test with the same features will be planned in the period following the end of the practical experiences in the laboratory. In case of additional absence, the student cannot do the final exam. The recovery test is also open to those students that gave up to the score obtained in the first NMR/MS test. The definitive cancellation should be notified to the teachers in advance, at least one day before. Students rejecting the score obtained in the first NMR/MS test and missing the recovery test, get 0 point for the NMR/MS test but are admitted anyway to the final exam (point 5.).
2. Reports of laboratory practices
   How: The student must participate to four experiences in the laboratory practices, after which they must submit a summary form within the terms established by the teachers. In case of failure to deliver within the time allowed the assessment of that report will be zero points.
   Purpose: The purpose of this test is to assess the degree of understanding of experimental activities and the ability to summarize them scientifically and reproducibly.
   Participation: The participation to practical laboratory experience is compulsory. Only one absence is allowed in the laboratory practical experiences, in which case the student does not have to deliver the form and receives a score of 0 points for that experience. In case of failure to participate to two or more lab experiences, the student is not admitted to the final exam (point 5.).
   Score: The score of each form is between 0 and 2 points for an overall score between 0 and 8 points.
3. Written lab test
   How: In this test students are required to answer to some practical questions about the lab experiences. The duration of the test is 60 minutes
   Purpose: The purpose of this test is to assess the degree of understanding of theoretical and experimental activities performed in the lab.
   When: This test is carried out at the end of the lab session.
   Participation: The participation to this test is compulsory. In case of absence a recovery test with the same features will be planned, concurrently with the recovery of the NMR/MS test (see point 1.). In case of further absence, the student is not admitted to the final exam. The recovery test is also open to those students that gave up to the score obtained in the first written lab test. The definitive cancellation should be notified to the teachers in advance, at least one day before. Students rejecting the score obtained in the first test and missing the recovery test, get 0 point for the written lab test but are admitted anyway to the final exam (point 5.)
   Score: The score of each form is between 0 and 8 points.
   
   Learning of the theory part is assessed through both written and oral tests:
4. Midterm
   How: written test on the topics of the first half of the course theory part. The duration of the test is 60 minutes.
   When: shortly after the middle of the semester.
   Purpose: to evaluate the degree of understanding of the concepts presented during lessons and the ability to apply them to the solution of organic chemistry problems. The test is also a self-assessment opportunity for the students, allowing them to evaluate in advance if their level of study is suitable for passing the examination and, if necessary, to make corrections to their study method in time.
   Score: This test is awarded a score of 0 to 20 points.
   Participation: optional. Students missing this test are admitted anyway to the final exam which, in this case, must be taken in full (both written and oral tests, points 5. and 6. below).
5. final exam - written test
   How: written test on the topics of the entire theory program. The duration of this test is 120 minutes.
   Purpose: to assess the degree of understanding of the course topics and the ability to apply them to the solution of advanced organic chemistry problems.
   Participation: The test is compulsory and can be taken in any of the six calls that take place during exam sessions. Only students who participated to the compulsory lab tests (points 1., 2. and 3. above) are admitted to this test.
   Score: The score of this test is between 0 and 50 points. The test is valid only if a score equal to or greater than 25 points is achieved.
6. Final exam - oral exam
   How: Oral examination on the topics of the entire theory program.
   Purpose: The oral test assesses the students' communication skills and their command of language in the reactional and mechanistic explanation of the steps involved in the transformation of organic molecules of medium complexity.
   Participation: Only students who did not take the midterm (point 4.) or who, despite taking it, gave up to the result obtained. This cancellation is definitive and shall be notified through the institutional email to all teachers of the course, by the day before of this test. To be admitted to this test, students must have obtained a minimum score of 25 points in the final exam written test of the same call (point 5).
   Score: The score of this test is between 0 and 20 points.

Teaching tools

Theory: Typical frontal lessons delivered in the classroom with the aid of the blackboard and suitable projection of slides. materials available on AMS campus. Classroom solution of problems and answers to exercises relevant to the main topics of the course.

Laboratory: Detailed synthesis procedures will be fornished to each student, together with mechanicistic explanation of the considered reactions and NMR spectra of starting materials and final products.

In the laboratory there are working places with suitable equipemments to perform the considered reactions.

Office hours

See the website of Paolo Righi

See the website of Mariafrancesca Fochi

See the website of Letizia Sambri

See the website of Giorgio Bencivenni