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In combinatorial chemistry, hundreds of thousands of reactions are run in parallel, on beads, or simultaneously in solution. A careful planning of these reactions is therefore of paramount importance in order to influence the products obtained in these experiments.

If the synthesis of an individual organic compound or a combinatorial library is planned the most important questions for an organic chemist are:
  • Which suitable starting materials are (commercially) available for the synthesis of the target compound?
  • What is the most convenient and efficient synthesis towards the target compound?
  • Which structural manifoldness of my starting materials is available if a the synthesis of combinatorial library is planned ?
  • Are there any suitable and powerful synthesis reactions?


The program system WODCA (Workbench for the Organization of Data for Chemical Applications) has been developed to assist in the planning of the synthesis of individual target compounds. Work of recent years now also enables its use in designing entire libraries of compounds.

Starting Materials
To search for available starting materials, similarity searches, substructure searches, and some classical retrieval methods such as full structure search, name search, empirical formula search, etc. have been integrated into the system. All searches can be applied to a number of catalogs of available fine chemicals (e.g. Fluka). In addition, compound libraries such as in-house catalogs can easily be integrated.

Generating Precursors

Only in simple synthesis problems one can expect that a search for suitable starting materials already succeeds with the target compound. In most cases, the synthesis problem has to be simplified by first generating synthesis precursors. Therefore, methods for the search and evaluation of strategic bonds have been implemented in WODCA.


In order to make WODCA more capable for use in designing the synthesis of libraries of compounds, substructure search methods have been included in the system. These, in conjunction with the search for strategic bonds can provide a series of representatives of certain classes of compounds that can act as precursors for the synthesis of an entire library.

In order to verify a retrosynthetic step suggested by WODCA a direct connection to reaction databases (e.g. Theilheimer, ChemInform) has been established in the most recent version of WODCA. Reaction databases are containing a wealth of reactions performed in the laboratory and published in the literature.

Gasteiger, J.; Engel, T.; Editors "Chemoinformatics - a Textbook"
Wiley-VCH, Weinheim 2003.

Gasteiger, J.; Editor "Handbook of Chemoinformatics"
Wiley-VCH, Weinheim 2003.

Gasteiger, J.; Pförtner, M.; Sitzmann, M.; Höllering, R.; Sacher, O.; Kostka, T.; Karg, N.  "Computer-assisted synthesis and reaction planning in combinatorial chemistry" Perspectives in Drug Discovery and Design 2000, 20, 245-264.

Ihlenfeldt, W. D.; Gasteiger, J. "Computer-assisted planning of organic syntheses: the second generation of programs" Angewandte Chemie, International Edition in English 1996, 34, 2613-2633.
Ihlenfeldt, W. D.; Gasteiger, J. "Computergestützte Planung organisch-chemischer Synthesen: Die zweite Programmgeneration" Angewandte Chemie 1995 , 107, 2807-2829.

Gasteiger, J.; Ihlenfeldt, W. D.; Fick, R.; Rose, J. R. "Similarity concepts for the planning of organic reactions and syntheses" Journal of Chemical Information and Computer Sciences 1992, 32, 700-712.

Fick, R.; Ihlenfeldt, W. D.; Gasteiger, J. "Computer-assisted design of synthesis for heterocyclic compounds" Heterocycles 1995, 40, 993-1007.

Markus Sitzmann 2003