An ISIS/Draw Tutorial                                                                                                                             September, 2002

This exercise is designed to introduce you to the basics of how to create organic structures using ISIS/Draw 2.4. As with any drawing program, there are many alternative ways to accomplish the same thing, and as you use the program you will find many shortcuts and useful features. Here we are hoping to just get you started.

Obtaining the Program

The program is available free from MDL Information, Inc. for academic users and for individual personal users. You can download a copy onto your own computer. Alternatively you will find it on the computers in Sc 271, and it will eventually be on the SOU network.

To download your own copy go to www.mdli.com/download/isisdraw.html. Choose either the Windows or the Macintosh version, and be sure to select the English version unless you are fluent in Japanese. Download two files: ISIS/Draw 2.4 is the program, and ISIS/Draw 2.4 Help is the very useful set of instructions of how to use it. Make note of the directory you are downloading to, and when complete you can install both the program and the help files by going to Start, then Run, then Browse. Select one of the programs Draw23.exe or help23.exe, click on Open and OK. The programs will then be installed onto your hard drive.

Drawing a Simple Structural Formula

First lets draw the structure of 2-butanol, CH₃CH(OH)CH₂CH₃. You want to produce something which looks like this:

Each icon in the program can be identified by moving the cursor over it and waiting a moment; an identifying label will then appear. Expand the window to full screen so all icons are visible.

1. On the vertical toolbar, select the single bond icon (5^th from the top), and click on the page. This will create a line which represents two carbon atoms connected by a single bond.

2. Move the cursor to one end of the line and click again; this will produce a second single bond connected to the first.

3. Click again on the same carbon atom to create a third, branching bond, and one more time on one of the end carbons to produce the complete skeletal structure containing four single bonds. If you don't like the direction the bonds are pointing, use the eraser icon (3^rd one down) to eliminate what you don't like, and then click and drag a bond pointing in the direction you want.

4. Now let's show the atoms explicitly. Let's do the oxygen atoms first. Select the atom icon (4^th from the top), and click on the end of the bond where the oxygen atom should be. This will open up a window into which you can type text. You can also select the atom from the drop-down menu. Either type or select an "O."

5. The remaining four atoms are all carbons by default, but the symbols are not shown. Also, none of the hydrogen atoms are visible. To see all of the atoms choose the lasso select icon (the top one), and click and drag a circle around your drawing to select the entire molecule. On the menu bar select Object, and Edit Molecule (or just double-click the selected molecule) to open an editing box. Click the Atom tab, and under the Hydrogens drop-down list choose Auto Position. Click OK, and all of the atom symbols will appear.

6. You may not like the look of the CH₂ group, which probably has the H's below the C. It would be nice to put those H's to the right of the C. Click the cursor in some empty space to clear the molecule selection, and then click on the CH₂ to select that carbon atom only. On the menu bar choose Object and Edit Atom (or double click on the atom) to open the editing box again. Click the Atom tab, and under the Hydrogens drop-down list choose Right, and then OK.

7. The formula could also be improved by using a smaller font so it doesn't look so crowded. Select the entire molecule again as you did above, go to the Edit Molecule box, click the Font tab, and change it to 10 point or 8 point.

Now let's make a molecule which has a ring, some double bonds and a charge in it:

8. Select the icon on the top which represents the benzene ring and click in an empty space.

9. Add the other bonds to the ring using the single bond tool. To produce the double bond, first create a single bond, and then click the center of the bond to change it to double.

10. Use the atom tool to add the nitrogen and two oxygen atoms. Also edit the carbon atom of the carbon-oxygen double bond so that the symbol is C(show) rather than C(hide).

11. To show the hydrogens on the nitrogen and oxygen without also showing those on the ring, use the lasso select to tool to select those two atoms (hold the shift key down to select more than one at a time). Go to Object/Edit Atom (or double click) and change the Hydrogens selection to Autoposition.

12. Since the nitrogen is supposed to be the positive conjugate acid, select the nitrogen and double click to edit the atom. Change the charge from zero to 1; the number of hydrogens will be properly adjusted automatically.

We want to write a chemical equation showing a reaction between the two compounds we have drawn, producing something like the following.

13. Select the butanol structure, and drag it to the left of the page.

14. Select the + tool on the left to add a plus sign.

15. Select the benzene compound you made and move it to an appropriate location.

16. Select the arrow tool on the left. If you hold down the button you get a choice of different kinds of arrows. Make your choice and then click where you want the arrow to be.

Now we will put in the reaction products. Often the easiest approach is to copy and modify the reactants. The products are shown below.

17. First select the benzene compound you drew as a reactant, and under the Edit menu select Duplicate. This will produce a second copy. Click on it and drag it over to the right side of the arrow.

18. Use the single bond tool to add the four carbon piece to the oxygen atom. Notice that the hydrogen automatically disappears when you hook another carbon to the oxygen.

19. Select the new carbon atoms, and edit them to show the hydrogen atoms.

20. Use the plus tool to put a plus sign in the correct spot.

21. Select the atom tool, and click where you want to put the water molecule. Put in an oxygen atom, and then edit it so the Hydrogens are shown on the left.

It is common to show catalysts, solvent, temperatures, etc over and under the reaction arrow, as shown below.

22. Select the Text tool on the left side, and under the Text menu select Formula. Now click over the arrow and type in the formula of sulfuric acid.

23. Again, using the Text tool, type in the temperature below the arrow. Use the Superscript choice under the Text menu to produce the degree sign.

24. When you have the text elements where you want them, select both of them along with the arrow itself, and select Group under the Object menu. This will let you move it around as a single object.

25. To finish your equation, select everything, and under the Object menu select Align. Choose Horizontal Top/Bottom Centers, and this will get everything looking nice. You should finish with something like the following:

26. Now that you have finished your drawing, you can select it, copy it and paste it into your word processing document. Also, don't forget to save it!

You assignment due next week is to draw the chemical equation for the synthesis of acetaminophen, shown on page 109 of your text. In addition to turning in a copy of it, save it for use in a future report.