SUPPLEMENTARY MATERIAL: DETERMINING THE PREFERRED INTERNAL BOND ANGLE IN CYCLOHEXANE USING THE FULL CSD

 

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

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Draw a cyclohexane substructure (hint: this can be done quickly by selecting the appropriate ring template from the bottom left-hand corner of the Draw window and then clicking in the white drawing area). Since we also want to retrieve substituted cyclohexanes don’t include any hydrogen atoms when sketching your search substructure.

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For each hit structure retrieved by the search we need to record the average of the six internal bond angles in the cyclohexane fragment. To define the required geometric parameters click on the Add 3D button. This will open the Geometric Parameters window. Click on the All Parameters... button, then in the resultant dialogue box select Define all: Valence Angles from the drop down menu. Choose to tabulate the average of these angles by enabling the tick-box next to the word Average.

 

•	Hit OK, to define the selected parameters and then Done to close the Geometric Parameters window.

•	Hit Search, then in the Search Setup window set the filters R factor <= 0.1, Not disordered and No errors, and then hit Start Search.

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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 will start to appear in the list on the right-hand side. Click on any structures refcode to see its chemical diagram, the cyclohexane substructure will be highlighted and the average value of the internal valence angles will also be displayed.

•	The blue progress bar indicates how much of the CSD has been searched so far. There is no need to allow the search to go to completion, you can stop it after about 20% by hitting the Stop Search button in the bottom right-hand corner.

•	Geometric parameters retrieved from a ConQuest search can be exported to Vista for statistical analysis. Select File from the top-level menu followed by View in Vista..., then in the resulting window click on the View in Vista button. The main Vista TABLE SPREADSHEET window should appear:

 

•	To determine the mean value of the average internal angle across all hit structures select the parameter AVG1 by clicking on the grey numbered button at the top of the relevant column, then select Histogram from the Data Visualization options on the right hand side of the window.

•	The resulting histogram shows the distribution of the average internal cyclohexane valence angle across a large number of crystal structures.

 

•	The mean value is given on the right hand side of the plot. Calculate the angle strain by subtracting this value from 109.5 (the ideal sp3 angle). The angle strain should be close to zero.