LABORATORY SCHEDULE

Professor Charles E. McKenna
Department of Chemistry
Last updated March 22, 2002

All labs are in SGM 121

Back to page 1

The following is designed as a very brief introduction to the program ISIS draw. This program is designed to quickly draw 2-d chemical structures more accurately and quickly than drawing them by hand. The drawings can then be cut and pasted into a word processor such as MS Word or Wordperfect.ISIS Draw can also calculate molecular mass and percent compositions, . This diagram of the drug RU-486 was created in ISIS draw.

The program available on all of the Macs and PCs in: SGM121, ou can download ISIS draw from the web at http://www.mdli.com/ (Follow the "download center" button )for both the MAC and PC

As an example we're going to use ISIS draw today to draw the structure of LSD, then paste that structure into a Microsoft Word document.

The screen is divided up into three main parts: the toolbox on the left, the drawing area, and some predefined structures (cycles) on the top. 

From left to right, we have:

• The Chem inspector (Check the chemical structure)

• Open the last template page used

• Draw previous template

• The other buttons correspond to the different rings you can draw

From top to bottom: The Select tool:  Allow to select bonds, atoms, part or whole molecule, allow to move selection 2D rotate: Allow to rotate the selection in 2-dimensions Eraser Atom tool: Allow to write atom labels as (ex: CH3, OH, N .) bond tool: Allow to create single double or triple bonds ( Select the bond type by clicking and holding the mouse down) Down wedge: Give some perspective to a bond (Several options are available) Chain: Allow to create hydrocarbon chains Add a + sign into a reaction ( 2H2 + O2 --- 2H2O) Arrows for writing chemical reactions Atom-Atom Map Sequence Brackets Text Draw lines Draw shapes

We'll start drawing the structure of LSD now.

LSD, Lysergic Acid Diethylamide, is a potent hallucinogen and has the structure to the right. To start drawing, click on the six-membered, non-aromatic ring icon in the top panel (). 

Move anywhere into the main drawing area and click the mouse button: you've just drawn your first ring. Don't worry that the bonds are incorrect- you'll fix that later.

Now move the mouse button over one of the two right-hand-side carbons in the ring. The cursor will change to a small box. This means that when you click here, whatever you have selected in the toolbox (Currently the six-membered ring tool.) will be attached at this point. Go ahead and click here.

Whoops- not quite what you wanted! If you simply click once, you'll "sprout" a new ring, rather than joining it. It's OK to make a mistake like this, however. Simply go to the Edit menu and click Undo. This will return you to just having a single six membered ring.

Instead, move back over one of the side (bond) until you see a rectangle covering the bong and click. Now you'll see another six membered ring appear fused to the first one by the selected bond.  Alternativelly you can obtain the same result by clicking and holding the mouse on one of the carbon atoms and rotating the new ring to the correct place

Now go back to the toolbox and click on one of the six-membered aromatic rings: (The one with three double bonds). Attach it to the upper right of the second six-membered ring the same way you attached the second ring to the first. Go back to the toolbox and choose the five membered ring with the point facing up. Click at the point where the aromatic and non-aromatic rings join and fuse the five membered ring to both of them. You've now completed the skeleton of LSD. You can save your work at any time: just go to the File menu and pick Save. Now is probably a good time.

Now we'll add the nitrogens to the skeleton. Click on the Atom (Label) tool. Move to the bottom point of the first ring until the cursor turns into the little box again and click. Type the letter N for nitrogen or select it from the list: the ring will rearrange to fit the letter. Move to the right side of the five membered ring and click, then type NH.

We can also use the label tool to add groups away from the ring. Move back to the first N you added- the cursor will turn into a box over the N. Click and drag down. This will create a bond pointing away from the structure. Type in CH3. Note that the 3 becomes a subscript automatically.

The label tool (or the bond tool) can also be used to change a bond from single to double to triple and back. Move the cursor to the middle of the upper right hand bond of the first ring. The cursor again changes to a box. Click once and the bond changes to a double bond. Click again and it's a triple, once more and it's back to a single. Note that it doesn't work very well for bonds inside rings- they are too long and don't look right, as shown in the picture on the left. To put multiple bonds into a ring, use the ring-multiple bond tool, which looks like two lines, one shorter than the other. Put the double bond into the five membered ring as well.

Now go ahead and add the large group to the upper left. The trick here is that there is a chiral center at this point, and you should mark the correct form. To place bonds that go "in" or "out" of a page, you use the wedge and dashed line tools. The only other tool you should need is the label tool. To create the wedge, click on the wedge tool and drag like you did with the label tool (or bond rool). When you are done, use the label tool to click on the end of the wedge and enter whatever atoms you need. Then use the dashed like tool to enter in the hydrogen, and the label tool to finish off the rest of the big group. 

A problems that you will encounter are: how to have the single carbon showing its label

To be able to view a single carbon with its label rather than a point or an edge, you have to explicitly tell the program to do so. The default for the program is to hide carbon and hydrogen atoms click on the select tool and double click on the carbon you would like the label to show up. the window shown on the right will appear. Go to the Symbol menu Select C(show) and click OK.

In a similar way if you double click on a bond, you can customize the bond itself.

To determine the molecular weight, formula and composition of your structure: Select the whole structure, go to the "chemistry" menu and select "calculate Mol values" and "calculate". You can paste the results into your drawing

Hopefully, this will get you enough information to start using these programs to draw complex structures. This program and competetors like ChemDraw are used by virtually all professional chemists in preparing slides and papers.

Back to page 1

(C) CE McKenna, Ph.D. USC, Chemistry Dept., 2002