a First Try
- 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
- Launch WODCA by calling the WODCA start script
from a UNIX shell. After a few seconds the main window of WODCA
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
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.
- Last change: 2000-06-28