The corse describes the structure and use of some chemical databases, principally referring to organic chemistry; in addition, it considers the description of the fundamental aspects of chemical models applied to: organic reactivity, organic synthesis, structure-activity relationships. Besides, it will give some hints to the structure of a computational program.
Expected learning outcomes
The student will achieve the competence of using a database and to get data in agreement with her/his research. She/he will be able to rationalize and evaluate the results of a modelling program and to understand its basics from its goal description and the structure of its operations.
Lesson period: Second semester
(In case of multiple editions, please check the period, as it may vary)
Course content Aim and scope of chemical database use. Types of databases. Searching for and refining chemical information from databases. Search by subject and by structure; search of chemical reactions. Factual and bibliographic databases (e.g. Scifinder, Reaxys, Protein Data Bank). Use of selected databases. Empirical and theoretical models in organic chemistry: statistical approaches; expert systems. Data representation (molecular structures and descriptors) and algorithm development. Similarity in organic chemistry: similar structures; similar reactions; similar synthetic paths. Similarity coefficients. Molecular diversity. Hints on application of models to: chemical reactivity prediction, organic synthesis planning, chemical property prediction, study of chemical-biological interactions. Reactivity models: electronic interactions; geometrical interactions; product preparation and their evaluation, reaction conditions. Synthesis planning: target description, transformation strategy, single step product preparation, alternative syntheses evaluation. Chemical-biological interactions: experimental reference data, compound description and biological activity description, QSAR (Quantitative Structure Activity Relationship), model validation. An example: toxicity prediction - applicability domain, mode of action.
Reference material - Some chapters of the following textbook: A.R. Leach, V.J. Gillet "An Introduction to Chemoinformatics" ed. Kluwer Academic Publisher, 2003. - Available course items.
Prerequisites Organic chemistry fundamentals
Assessment method Spoken: The assessment is based on two parts. In the first, the competence in using a chemical database will be assessed; in the second, the understanding of models in organic chemistry will be checked.