Mechanisms of Organic and Biological Reactions


It is intended that students acquire basic knowledge of organic chemistry useful for the understanding of biological processes. Particular emphasis is given to the mechanistic component of chemical reactions and the reactivity of organic compounds.

At the end of the course the student should be able to:

- Understand the three-dimensional molecular architecture identifying the existence of conformers, making a correct representation and analysis in terms of relative stability;

- Master the concepts of reactivity (electrophile, nucleophile, leaving group, alkalinity, acidity, etc.) and know how to write the reaction mechanisms of elimination, substitution and addition; - Obtain knowledge of some reactions of CC bond formation (aldol reaction and acylation);

- Understand the operation of these reactions under catalytic conditions, the role of the catalyst and relate these concepts and corresponding reactions in biological processes.

General characterization





Responsible teacher

Eurico José da Silva Cabrita


Weekly - 4

Total - 57

Teaching language



General knowledge of the chemical bond theory of thermodynamics and reactivity of molecules orgâncias at inical a course of organic chemistry.


Recommended Book:  

Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. “Organic Chemistry”, Oxford University Press, 1st Ed., 2001.

Teaching method

The course will be taught through problem solving (TP)  classes (2 x 1.5 hours per week) and practical sessions (7 sessions of 3 hours per week).

In TP classes by solving oriented problems students are exposed to the theoretical program of UC. When necessary computer programs are used to illustrate three-dimensional molecular modeling concepts of stereochemistry, conformational analysis and reactivity. Students are encouraged to use their own personal computers and to use a number of tools available on the internet.

Practical lessons hours correspond to laboratory classes. Laboratory classes intend to introduce the student to the most commonly used laboratory techniques in organic synthesis, illustrated with the synthesis of various compounds by directly applying the concepts introduced in the TP classes.

Evaluation method

1. Overall assessment of the course

The Course consists of two independent but linked components: problem solving lessons (TP) and practice (P). Only students who obtain a minimum grade of 9.5 in the TP component and 9.5 values in component P can be approved.

The final grade will be the weighted average of the theoretical and practical parts (60%) and practical (40%).

Students who obtain final ranking equal to or greater than 9.5 will be approved in the discipline.

2. Frequencia (Exclusion from Final Exam) 

Students must obtain the Frequencia at both components of the course:

- TP

Students without "frequência" from past years must attend at least two thirds of the classes of the semester.

- Practical (P)

Students mus complete ALL practical sessions and obtain final grade of the practical component equal to or greater than 7.0 values .

A practical grade is valid for the following years.

3. Evaluation of individual components of the course

- TP

The evaluation of the TP part of the course is done through two written tests to be carried out during the semester, each worth 50% of the final TP score.

- Practice

The assessment of the practical component takes into account the following factors:

You need to run ALL Practical Works.
The record of the laboratory work is conducted in a Laboratory Book whose manner of preparation is indicated at the beginning of the semester. Includes a discussion of the results
The frequency in the practical part of UC is calculated as follows: 20% of the preparation work (to be prepared before the practical class), 40% laboratory performance, 40% discussion of the results.
With a final note on the practice < 9.5 the student can not be present at the final examination and is not approved.

Subject matter

1. Revisions: stereochemistry 
1.1. Conformational Analysis

2. Revisions: nucleophilic substitution: solvents and solvent effects efeitos de solvente
2.1. Equilibrio cinética e mecanismos

3. Reacções de eliminação

4.Adição eletrofílica a alcenos

5.Formação e reacções de enóis e enolatos

6.Reacções de aldol

7.Acilação do carbono

8.Catálise e química organometálica

9.Mecanismos em química biológica


Programs where the course is taught: