Drawing Molecules in ChemSketch
This exercise is to show you how to use ChemSketch to draw molecules, and to look at the
molecules in the 3D viewer.
Drawing METHANE
Open ChemSketch, make sure you are in structure mode
Click on the C (for Carbon) in the left hand column, then
Click somewhere in the blank workspace.
You will see CH4 appear in the workspace.
ChemSketch automatically adds the hydrogens to carbons,
but you can change this if you need to.
To make it look like a molecule
Click on the H (for Hydrogen in the left hand column)
Click on the C in the workspace, and drag away from
the C about one centimeter to draw the hydrogen bond.
Repeat for the other 3 hydrogen bonds
Select the methane molecule by
clicking on the selection button.
Then click on the square selection button
(The other option is a lasso selection
can be used for irregular shapes)
, which
Then drag the mouse over the molecule
Selection handles should appear, as in the picture.
Now the molecule is selected, you need to get it
Ready to view in the 3D viewer.
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Click on the 3D optimization button
at the far right end of that row of buttons
A pop-up will appear asking to remove hydrogens.
Click No.
The molecule on the screen should now look like this,
If you click the mouse on the page, the selection marks
will disappear, and you can see that the molecule looks a
bit 3D already, but not very exciting.
To see the molecule in the 3D viewer, click on the button
above the 3D optimization button.
The screen will now switch to the 3D window, which by
default has a black background. The model usually appears
as a stick model, but you can change this to a different kind
of model, eg ball and stick or space fill, using the buttons.
Stick Model
Ball and Stick
The models can be rotated, with the mouse, so you can look at them from any
angle.
To measure the distance between 2 atoms, click
. . Then click the mouse on the first atom,
then on the second. The distance between the 2 atoms will be shown on the status bar at the
bottom
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To measure bond angles, click
,then on the 3 atoms with the angle atom in the middle, and
the angle between them is shown on the status bar at the bottom
What are the bond angles in methane?
Save the molecule, the molecule will be saved as a 3D file.
Close the 3D window by clicking in the top right hand cross.
This will take you back to the normal ChemSketch window.
You can also switch between 3D and ChemSketch using
the tabs at the bottom left of the screen.
If you want to save the drawing of the methane molecule, you will need to save it again from the
Chemsketch window, it will save as a file with an .SK2 extension.
Close the methane file (File-Close). Now try following exactly the same procedure, and draw a
molecule of Ammonia. Instead of starting with C as the first atom, start with N, and add 3
Hydrogens.
What are the bond angles in Ammonia?
Draw and measure the bond angles in SO2, H2O and CCl4, filling in the worksheet as you go
along.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Shapes of Molecules Worksheet
Using the attached guide, learn how to draw structures in ChemSketch and view them in 3D.
Draw and look at each of the molecules below using ChemSketch.
Copy to the 3D viewer. For each one measure the bond angles, draw the shape on the worksheet,
and decide the geometry of the molecule. The first one is done for you.
Molecule
Drawing
Methane
CH4
Bond Angles
All 109.5
H
0
Shape of Molecule
Tetrahedral
o
109.5
C
H
H
H
Ammonia
NH3
Sulfur Dioxide
SO2
Carbon
Tetrachloride
CCl4
Your choice
http://excellence.qia.org.uk/page.aspx?o=140401 original document source
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright