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Essentials: Making a First Try on WODCA


WODCA is intended to be used by organic chemists and process chemists that work in the laboratory. We therefore have aimed to make it as easy to use as possible. On the other hand, WODCA offers many tools for planning a synthesis and gives the user great flexibility in switching from one tool to another. This has required us to provide WODCA with many windows, menu entries, buttons, options, etc. somehow frightening the novice.
We therefore give a brief introduction that should allow a novel user to make a first study with WODCA within a few hours of learning. A synthesis study for a simple target structure is presented in the first Tutorial of the next chapter.

Starting WODCA

Launch WODCA by calling the WODCA start script from a UNIX shell. After a few seconds the main window of WODCA appears.

The Main Window of WODCA

Figure 1: The most important window elements of WODCA's main window

Input of the Target

The target structure can be graphically input by a molecule editor. Click with the right mouse button on the structure display in WODCA's main window and select the entry Define New Target ... from the context menu appearing. Now, the molecule editor is started and opens a window that allows the drawing of the structure of the target compound just with the mouse. The use of this molecule editor should be self-explanatory. For further information see the CACTVS molecule editor manual. Once the target structure has been drawn it has to be transferred into the structure display of WODCA's main window. In order to achieve this click on the File entry in the menu bar of the molecule editor, pull it down and click on Export. The chemical compound is now automatically transferred into WODCA.

Figure 2: Defining a targt structure with the CACTVS Molecule Editor

Searches in Catalogs of Available Compounds

WODCA aims to find as quickly as possible promising available starting materials for the synthesis of the target structure. Thus, searches in catalogs of chemical suppliers play an important role. In order to learn how such searches have to be performed we will first check whether the desired target compound is contained in a chemical supplier catalog.
In WODCA's main window you can see which catalog is loaded on the left-most icon of the information area. This icon gives the name of the catalog and the number of compounds this catalog contains. To switch the catalog of chemicals just click on the catalog icon and select another one.
You are now set to perform a search with your target as query in the selected catalog. First, we will check whether your target is already contained in the loaded catalog. For this purpose click on the Searches menu and select the entry Identical Structure. Now, WODCA performs an identity search. The result of this identity search will be indicated in the alphanumeric output of the console and in the central icon Match List of the information area. If the target compound is contained in the catalog, the Match List icon will indicate this by giving the number of matching structures. In most cases, your target compound will not be commercially available, and therefore an empty match list will be indicated.
In order to make you familiar with similarity searches - and give you a feeling of success - we will first present a few similarity criteria you should try with your own target compound. If you have defined an acyclic target compound, you could use the similarity criterion Carbon Skeleton. In case of cyclic target compounds the criterion Ring Substitution Positions would be a good choice and if an aromatic ring system is contained in your target structure, the criterion Aromatic System + Alpha Atoms seems to be the right one to start with.
To perform a similarity search, click on the Searches menu and select the entry Similar Compounds ... . A new dialog box with a series of similarity criteria appears. Select one similarity criterion from the list box on the right side of the window and click on the Search button as shown in Figure 3.

Figure 3: Performing a similarity search

Quite often, a very general similarity criterion like Carbon Skeleton will provide you with many hits, most of them not really promising starting materials for the synthesis of your target structure. You may therefore try other, more specific similarity criteria like Carbon Skeleton + Alpha Atoms. To show the match list of suitable starting materials just click on the Match List icon in WODCA's main window. After a few seconds the hits will be displayed in a browser window.
In fact, these similarity searches can give you quite new stimulations and ideas for the synthesis of your target structure. For more information see the chapter Similarity Searches in the WODCA manual. However, in this very brief introduction to WODCA we want to acquaint you with a second, powerful tool for planning a synthesis: the search for strategic bonds.

Search for Strategic Bonds

For any somehow more complex target compound similarity searches will not give enough specific hits to plan an entire synthesis. In this situation the complexity of the target structure, has to be simplified. This can be achieved by searching for strategic bonds, breaking those bonds to provide synthons, and then convert these synthons to synthesis precursors.
In order to search for strategic bonds click on the Disconnection entry in WODCA's menu bar and select Strategic Bonds ... . A set of four different types of disconnection strategies are offered. Depending on your target structure it will probably be quite clear to you which one of the four types of strategic bonds should be selected.

Figure 4: The evaluation of strategic bonds

The disconnection of strategic bonds directly leads to synthesis precursors, since WODCA automatically adds suitable atoms to the open valences obtained on heterolysis of a bond. In a first try we have decided to cut the strategic bond with the maximum rating of "100" by pressing the Cut Bond button.


Having done all this as described in this short introduction will probably not have solved your synthesis problem. However, it should have given you a flavor what can be done with WODCA and should have shown you what to expect behind the doors of WODCA and, thus, prepare you to embark on a journey through the complete WODCA manual. You probably should initially not read the manual from the beginning to the end but dig into certain parts with a target structure of your interest. Again, the most important tools are similarity searches and searches for strategic bonds. Try them both to fully understand, one at a time, starting with similarity searches. A simple example is more fully explored in the Tutorial.

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Last change: 2000-06-28