State University of New York at Oswego

Chemistry Department
Che 331 Laboratory

ChemSketch Tutorial

Fall 2009

Introduction
ChemSketch is a free program for drawing chemical structures. You may download it
from the following address: http://www.acdlabs.com/download/ After drawing a 2D
structure, ChemSketch can convert it to a 3D structure to show you what the molecule
actually looks like. The structures can easily be imported into other documents such as
lab reports done in Word. After opening the program, click OK and the screen shown
below will appear. As an exercise, we will draw the molecule caffeine, whose structure
appears below.
CH3
N

N
N

N
H3C

CH3
O

ChemSketch has two basic modes of operation. In Structure mode, chemical structures
are generated. In Draw mode, things like text, tables, and arrows can be added. We will
move back and forth between these two modes depending upon what we want to do.

Drawing Two-Dimensional Structures with Text

First, click on the Structure icon in the upper left-hand corner. To generate the fused
ring system of caffeine, click on the six-membered ring from the column at the far right.
This will load the arrow with the ring. Click once somewhere near the middle of the
white workspace to place the ring. Now click on the five-membered ring from the right
column. Place the arrow in the middle of the vertical bond on the left-hand side of the
six-membered ring. You will notice that the new ring snaps into place. Click once to
place the ring. If at any point you make a mistake, select Edit>Undo. The structure at
this point should look like this:

To add the nitrogen heteroatoms, click on the N atom from the left-hand vertical column.
When you place the arrow directly over one of the four positions in the ring where the N
atom should be located, notice that a CH2 will appear. This shows what is currently
present at that position. When you click, a nitrogen atom will replace the CH2 group with
a hydrogen atom automatically attached. Add the other three nitrogen atoms in the same
way. To replace the H with a single bond and a CH3 group, click on a C from the lefthand column, place the arrow over one of the three N atoms that should have a CH3
attached to it (refer back to the caffeine structure), click, and drag the bond out. When
you release the mouse, the CH3 will appear singly bonded to the nitrogen atom. Dont
worry about the length or angle of the bond. We will fix that later. Do the same with the
other two nitrogen atoms which should have methyl groups attached to them. At this
point your structure should look similar to the one shown below.
CH3
H
N
N

N
N
CH3

H3C

To add the two carbonyl groups, click on the O from the left-hand menu, place the arrow
over the CH2 where the carbonyl should be located, click and drag out the bond. When
you release the mouse, an OH group bonded to the ring will appear. To turn this into a
carbonyl, place the arrow on the center of the carbon-oxygen single bond and click once.
Add the second carbonyl group in the same way. All that remains is to add the double
bonds in the five and six-membered rings. Place the arrow over the middle of the single
bond where a double bond should be and click once. The structure is now complete. To
clean it up and standardize all the bond lengths and angles, click on Tools and in the drop
down menu choose Clean Structure. Alternatively, you can click on F9. To add text to
the structure, click on the Draw icon in the upper left-hand corner. Then click on the

Text icon, T, the fifth from the bottom on the left. A rectangle will appear. Type the
word caffeine in the box. If you highlight the word by clicking and dragging across it,
you can change the font and size. Click outside the box and a series of small black boxes
will appear around the word. If you move the arrow directly over the letters, you will be
able to click and drag the text any place on the document. To move the structure, click
on the Select/Move/Resize tool (an arrow at the upper left), place the arrow directly over
the structure, click, and drag. Center the text under the structure. The final structure with
text appears below.
CH3
N

N
N

N
H3C

CH3
O

caffeine

Drawing Three-Dimensional Structures

ChemSketch will allow you to change a 2D structure into the corresponding 3D structure.
Make sure you are in Structure mode. Select Tools>3D Structure Optimization or
Ctrl+Shift+3. To open the 3D viewer select ACD/Labs>1 3D Viewer. A new black
screen will appear. Click on the word ChemSketch at the lower left of the screen to
return to ChemSketch. To import the structure into the 3D screen, you must first select
the structure. To do this return to Draw mode. Click on the Select/Move/Resize arrow,
place the arrow over the structure so that a grey box appears around it, and click. A
series of small boxes will appear around the structure. Select Edit>Copy and then click
on Copy to 3D at the bottom left of the screen. The 3D structure will now appear in the
3D viewer. Select the 3D Rotate icon. It is the sixth from the left at the top of the
screen. With this selection you may rotate the molecule by placing the arrow on top of it,
clicking, and dragging. There are several ways to render the molecule. If you click the
Balls and Sticks icon, the molecule will appear as shown below left. Notice that this
rendition does not show the double bonds. Another choice is Wireframe, which is
shown below right. In this representation the double bonds are visible.

To change the backgound and atom colors in the 3D screen, select Options>Colors A
new screen entitled Colors will appear which will allow you to make color changes.

Using Glassware Drawings

A large selection of predrawn glassware items are available in ChemSketch. To access
them you can be either in Structure or Draw mode. Select the Open Template
Window icon from the top row, sixth button from the left. A Template Window will
appear. Select Lab Kit and the following screen will appear:

Click on the Next Page button to toggle through all the pages. In this exercise we will
select the Separation Apparatus on page 2. Select the separatory funnel. Notice that
the template window will dissapear returning you to your working document. Click once
to place the object. Click on the Open Template Window icon again, select the beaker,
and place it below the separatory funnel on your document. It should look like this:

Drawing Chemical Reactions

Organic reactions will require that you draw the structures of the reactants and products
as already discussed in this tutorial. As an example, we will show the reaction for the
conversion of caffeine to caffeine salicylate by reacting caffeine with salicylic acid. The
reaction involves the transfer of the carboxylic acid proton from salicylic acid to the
imine nitrogen atom of caffeine. First, draw the structures of the reactants and product in
ChemSketch. After that, all that remains is to add the names of the compounds, an arrow
between the reactants and products, and a negative charge on the salicylate oxygen atom.
Select Structure mode and click on the Reaction Arrow icon. It is a red arrow pointing
to the upper right in the second row of icons at the top of the page. To add the + sign
between the two reactants, select Draw mode and click on the Text icon as descibed
earlier. To add the negative charge to the carboxylate oxygen atom of caffeine salicylate
select Structure mode, and click on the Decrement (-) Charge icon third from the
bottom, left-hand side. Place the cursor over the oxygen atom that should bear the
negative charge and click. The reaction should look something like the one shown
below.
O

CH3

OH
N

O
O

+
N

N
H3C

salicylic acid

CH3
O

caffeine

CH3

H
+

N
N

N
H3C

CH3
O

caffeine salicylate

To export your structures and drawings to Word, choose Edit>Select All followed by
Edit>Copy. In Word you can then paste the structure or drawing into your document.

Fall 2007