Organic chemistry has a graphic language of its own. An important part of the course is learning this graphical language. You need to learn how to use this graphic language on you own using paper and pencil, but these days you also need to learn how to use the computer to construct graphical representations of molecules. This is no different than your experience in a Humanaties course. In the classroom for an exam you need to be able to construct an essay in your own handwriting, but for a termpaper you turn to a computer and use a workprocessing program.
How to use MarvinSketch and SMILES
When you first open MarvinSketch you will see the following window appear.
Suppose you want to draw the molecule butane. Select the top button on the left hand menu. The button where you see a single horizontal line. Use your mouse and in the middle of the main window draw three connected lines. The program will automatically add CH3 at each end. This gives you the MarvinSketch representation of butane. Your window should now look like this.
Suppose you now want to extend the chain to make the molecule 1-pentene. To do this you need to change the drawing tool to a double bond. Go back to the same button and choose the double bond from the drop down menu. If you make a mistake you can use the erasure button: .
Extend the chain by one more atom and you should have something that looks like this.
Now look back at the original open window. You should see a second picture of 1-pentene in the graphics box of that window. It should look like this.
Now push the button with the label “Analyze molecule and write SMILES”. You will see some text appear in the box below. The text should be: “CCCC=C”. This text is a SMILES representation of 1-pentene. It is a computer readable representation that you can use to answer a computer based quiz. If the question was:
What is the structure of 1-pentene?
You would draw the molecule in MarvinSketch, push the magic button and then copy and paste the SMILES representation into the quiz answer box.
Let us try an example. Draw the structure of trans-2-pentene. The program should generate the SMILES representation “CC\C=C\C”. Now try drawing cis-2-pentene next to trans-2-pentene so you have both on the screen at the same time.
Push the button and ask for the SMILES representation. You should see: “CC\C=C\C.CC\C=C/C” This is the representation for the two molecules together. A period “.” is used by the program to separate the SMILES of the two different molecules.
Now let us do something more complicated. Let us draw 4-amino-benzaldehyde.
To do this start by selecting the benzene ring
template from the template menu at the bottom of the MarvinSketch window.
This will save you the work of drawing the benzene ring. The use the regular drawing tool to add a single bond at the bottom of the ring and a single and then a double bond at the top. You should have an all carbon representation of the molecule that looks like this.
Now select the oxygen button on the right
and click on the
=CH2 group. It should change to a red oxygen atom. In a similar
manner choose the nitrogen button
and then click on the
CH3 group changing it to a nitrogen atom. Your structure should now
look like this:
Click the SMILES button and you should get the SMILES representation “NC1=CC=C(C=O)C=C1”.
Here is a another nice thing about SMILES. They work in either direction. Copy the text shown below:
NC(=O)\C=C\C1=CC=CC=C1
Delete any text you might already have in the SMILES box and paste this text into the box. Now push the second button, the one that reads “Read SMILES and draw molecule”. You should see the following molecule appear in the MarvinSketch Window.
Sample Problems:
Draw each of the following molecules. You should be able to generate the SMILES given next to each structure. When you make your drawings, do not draw in the hydrogen atoms. Let the program do that for you.
1. acetic acid:
CC(O)=O
2. acetate:
CC([O-])=O
To add the negative charge use the “minus” button found at the bottom of the left hand menu.
3. ethyl acetate:
CCOC(=O)CC
4. triethylamine:
CCN(CC)CC
5. trimethyloxonium ion:
C[O+](C)C
To add the positive charge use the “plus” button found near the bottom of the left hand menu.
6. aspirin:
CC(=O)OC1=C(C=CC=C1)C(O)=O
7. cis-1,2-dimethylcyclohexane
C[C@@H]1CCCC[C@H]1C
Use the “single up” and “single down” option on the bond menu to make the wedges.
8. Draw the two most important resonance structures of N,N-dimethyacetamide:
CN(C)C(C)=O.C\C([O-])=[N+](\C)C
Note: draw both molecules in the same box, then press the SMILES button.
9. aspartame (artificial sweetener):
COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@@H](N)CC(O)=O
10. cholesterol:
CC(C)CCCC(C)[C@H]1CCC2C3CC=C4C[C@@H](O)CC[C@]4(C)C3CC[C@]12C
Note: use the cyclohexane and the cyclopentane templates from the bottom menu.