Tutorial 1: Basic Substructure Search

 

Objectives

 

•	To draw a chemical fragment (substructure).

•	To search the CSD for entries which contain the fragment.

•	To obtain a list of journal references for the hit entries.

•	Transfer the results to Mercury.

 

Steps Required

 

•	Draw the fragment in the substructure drawing window.

•	Start the search.

•	Decide which hit entries to keep.

•	Write out the journal references.

 

The Example

 

•	The tutorial explains how to search for the following fragment:

 

where 7A = F, Cl, Br or I.

 

Menu Commands Required

 

1.	Start ConQuest and hit the Draw button to open the Draw window.

 

2.	Draw a chain of atoms.

•

Move the cursor into the white drawing area, press the left-hand mouse button, and move the mouse while keeping the button depressed. Release the mouse button and you should have drawn a C-C bond. Keep the cursor where it is, i.e. on one of the carbon atoms. Press the left-hand button again and draw a second bond, and then a third to produce:

 

If you make a mistake (here, or elsewhere in the drawing area), click on Edit
(in the top-level menu) and then Undo.

 

3.	Add the carbonyl group.

•	Select O from the list of common elements at the bottom of the Draw window.

•	Click on the button next to the word Bond at the bottom of the Draw window and change the bond type from Single to Double.

•	Move the cursor back into the white area and draw a bond to the second carbon in the chain. Since the current atom type is O and the current bond type is double, this creates an O=C bond:

4.	Create an acetoxy group.

•	O is the current element, so click on the first carbon in the chain to change it to an oxygen:

 

5.	Create a halogen substituent.

•	Click with the right-hand mouse button on the carbon at the other end of the chain. Select Element from the pull-down menu, followed by More from the next menu, then Any Halogen.

•	The terminal carbon should now have changed to 7A (the symbol used in ConQuest to denote the halogen group of elements).

 

6.	The fragment is now drawn. Do the search.

•	Hit the Search button in the bottom right-hand corner of the drawing window. This produces a pop-up window telling you which version of the CSD you are going to search.

•	This window allows you to specify some filters. Click on 3D coordinates determined to ensure that you will only find CSD entries for which 3D atomic positions are available.

•	Hit Start Search.

 

7.	Look at the results.

•	As soon as you start the search, the ConQuest interface moves to the View Results pane. After a few moments, the refcodes of hit structures start to appear in the list on the right-hand side. Click on any structure to see its chemical diagram.

•	Click on the Detach Diagram button, this allows the 2D diagram to be shown in its own window enabling the 2D diagram and any other results panes to be viewed simultaneously. Now use the tabs (Author/Journal, Chemical, etc.) to see other types of information.

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Rather than allowing the search to go to completion, you can stop it by hitting the Stop Search button in the bottom right-hand corner. The blue progress bar indicates how much of the CSD has been searched so far. A pop-up menu asks if you really wish to stop the search as it cannot be resumed once stopped.

 

8.	View structures in 3D.

•	Click on the 3D Visualiser tab to see the currently selected structure in 3D.

•	Rotate the structure by moving the cursor in the 3D-display area while pressing on the left-hand mouse button.

•	Change the display style by clicking anywhere in the 3D-display area with the right-hand mouse button. Select Display Style from the pull-down menu, then select a display style.

 

9.	Suppress unwanted hits.

•	Suppose you don’t want to keep the first hit. Suppress it by clicking on the green tick next to the refcode. The tick turns into a red cross. This structure will not be written out in any files you export.

 

10.	Writing out a file containing journal references.

•	Click on File in the top-level menu and select Export Entries as... from the pull-down menu.

•	Click on the file type bar and select TXT: Text representation from the pull-down menu.

•	Turn the output off for everything except Bibliographic information (i.e. click in the check-boxes so that only the one next to Bibliographic is coloured red).

•	Hit Save to save the file of journal references.

 

11.	Transferring the hits to Mercury.

•	Mercury is an advanced crystal structure visualiser. To view the hits from this search in Mercury hit Analyse Hitlist and select View in Mercury from the pull-down menu,

 

This ends the tutorial.