Synthetic Organic Chemistry

6 EC

Semester 2, period 4

5254SYOC6Y

Owner Master Chemistry (joint degree)
Coordinator dr. Tati Fernández Ibáñez
Part of Master Chemistry (joint degree), track Molecular Sciences, Master Chemistry (joint degree), track Chemistry of Life, year 1
Links Visible Learning Trajectories

Course manual 2025/2026

Course content

Retrosynthetic analysis; formation of carbon-carbon bonds via ionic, radical and pericyclic mechanisms; rearrangement and fragmentation; heterocyclic chemistry; stereochemistry and asymmetric synthesis.

Study materials

Literature

  • J. Clayden, N. Greeves, S. Warren and P. Wothers, 'Organic Chemistry', 2nd Edition, Oxford University Press, 2012.

Objectives

  • The students are able to identify the type of transformation required to obtain a target organic molecule.
  • The students are able to define the reaction conditions for different types of organic transformations.
  • The students can explain the mechanism of the organic reactions explained during the course as well as similar transformations not covered during the course.
  • The students can apply the organic reactions covered during the course in the synthesis/retrosynthesis of more complex organic molecules.
  • The students are able to identify different type of organic transformations based on the reaction conditions.
  • The students are able to present research articles correctly, clearly and in a comprehensive manner to a broad audience.

Teaching methods

  • Lecture
  • Presentation/symposium
  • Self-study
  • Seminar

Lectures, total synthesis presentations by the students and problem solving sessions.

Learning activities

Activity

Number of hours

Hoorcollege

26

Presentatie

22

Tentamen

3

Vragenuur

2

Werkcollege

26

Zelfstudie

89

Attendance

This programme does not have requirements concerning attendance (TER part B).

Additional requirements for this course:

All students must attend the total synthesis presentations. Exceptions are only possible after personal agreement between student and coordinator.

Assessment

Item and weight Details

Final grade

80%

Tentamen

Everyone wishing to pass the SOC course is required to attend the total synthesis presentations. 

The final grade is based on the exam (80%) and the total synthesis presentation (20%).

A minimum grade of 6.0 is required to pass the course.

Exam: Open book

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

The total synthesis presentations are obligatory for everyone wishing to pass the SOC course (both presentation and presence at presentations by colleagues). Details will be provided separately.

Exam written exam (open book) Wednesday March 25, 2026, 9-12 h, C0.05 Books and notes may be consulted during the exam.

 

Detailed contents of the lectures

Mon Feb 5                   TF                   Retrosynthetic analysis                                       Ch 28

Thu Feb 5                    TF                   Sulfur, silicon and phosphorus                        Ch 27

Mon Feb 9                   ER                   Aromatic heterocycles 1: reactions                Ch 29

Thu Feb 12                  ER                   Aromatic heterocycles 2: synthesis                Ch 30

Mon Feb 16                 ER                   Saturated heterocycles                                        Ch 31

Thu Feb 19                  JvM                 Stereoselectivity in cyclic molecules             Ch 32

Mon Feb 23                 JvM                 Diastereoselectivity                                              Ch 33

Wen Feb 25                 JvM                 Cycloadditions                                                        Ch 34

Mon March 2              JvM                 Sigmatropic and electrocyclic reactions     Ch 35

Mon March 9             TF                   Rearrangement and fragmentation                 Ch 36

Wen March 11          JvM                 Asymmetric synthesis                                          Ch 41

Mon March 16             TF                   Radical Reactions                                                Ch 37

Thu March 19             TF                   Carbenes                                                                  Ch 38

 

 

 

Additional information

Rough-and-ready knowledge of J.P. Clayden, N. Greeves, and S. Warren Organic Chemistry, chapters 1-26;

Further details on the total synthesis presentations

All students wishing to pass the Synthetic Organic Synthesis course must give an oral presentation on the total synthesis of an interesting compound, published in the (recent) literature. The presentation should take about 15 minutes and the audience consists of the other students and the teachers (Fernandez, Van Maarseveen and/or Ruiter).

The schedule of presentations (student name, compound name, publication, date and time) will be provided as soon as possible and can be found on the Canvas site.

Please note that you are not permitted to do the written exam if you have not presented a total synthesis yet.

All students will receive the name of one target compound, the literature reference where the synthesis is described and the date and time they have to give the presentation. They must prepare a Powerpoint presentation (ChemDraw ACS settings), which describes the details of the total synthesis in an attractive way (clear structures and drawings, some colour!).

The presentation must include the following items:

  • Relevance of the target molecule, its biological source or activity 
  • Authors and university (or company), where the research was carried out
  • Retrosynthesis and synthetic strategy • Synthesis in detail, starting from commercially available chemicals
  • Most attention for key steps (mechanism)
  • Pertinent stereochemical issues (racemic or enantiopure, etc.)
  • Overall yield, number of steps, efficiency

The teachers will give a mark for the presentation, which will count as 20% of the final mark of the whole course. The teachers thus should receive both a digital and a paper copy of the presentation. All presentations will be put on theCnvas site.

 

Contact information

Coordinator

  • dr. Tati Fernández Ibáñez