Learning to use Chemical Drawing Software by Dr. C. Bender

Endemic to the discussion of chemistry is the discussion of structure. The structure of molecules, ions, crystals, etc. may well dictate what chemistry will happen or even if any chemistry will happen. Knowing how to draw chemical structures with chemical drawing software is the emphasis of this assignment.

The web is rife with chemical drawing software, and thankfully, many of those programs are freeware. Here is a recommended website with free drawing software to complete this assignment.

The download button is near the bottom of the page—you will have to create an account, but the software should be free. If it isn’t, see me! There is also a commercial version that costs money.

The only way to learn new software adequately is to play around with it for a while. When you download the ACD Lab ChemSketch program, you will also download some other programs and files that you can see under StartProgramsACDLABS 12.0. If you follow the tabs under “GUIDES”, you will see both a ChemSketch Reference Manual as well as a ChemSketch Tutorial (both are pdf files) that may also be helpful

This program has some features that most drawing software has:

  • Templates—these are located on the right side of the screen
  • Atom labels that can be changed—common atom labels are listed on the left side and the top icon in that list opens a periodic table that allows you to choose any atom

Under the Tools menu, you can

  • show all of the “hidden” (implied) hydrogens (the top figure to the right has them hidden, while the bottom figure has them explicitly shown)
  • Calculate the molecular formula, molecular weight, or even the percent composition (and many other things such as density, refractive index, molar volume, etc.)—note that molecular formula and molecular weight are also found at the bottom of the page.
  • Generate the name of the chemical

A neat feature of this program is that you can clean up your drawing with clicking one button–—in the toolbar at the top of the page. This means a structure goes from

this

to this

in one easy step.

Another interesting feature of this software is to view a 3D version of your structures. By clicking on this icon, , you can view your drawing with a 3D perspective. Clicking on this icon, , will put the molecule in a whole new window for additional modification and viewing modes.

To get you started, here are a few of the important symbols:

  • The “lasso” allows you to select structures by circling them (another option is a square (box))—this may allow you to move a structure from one place to another on the screen, or you can select just a part of a structure, then delete it or move just that part of the structure.
  • The pencil with one line is the basic drawing unit.
  • The pencil with two lines is the “draw continuous” icon.
  • The pencil with the zig-zag lines is the “draw chains”icon and allows you to draw carbon chains as you click the mouse and extend the line. Try this last option to make the following in a fraction of a second (chain length 11 is indicated as you draw).

If you want to modify the structure with a double bond, simply click on the basic drawing unit and click on the bond that you want to modify. If you want a triple bond, click that bond again.

If you want to draw a branched chain off of one of the carbons, click on the carbon of interest and draw in a new bond

One trick you can use is to make a skeleton of the entire structure out of carbons, then go back and modify if you need heteroatoms. So you can quickly make this

and turn it into this

by clicking on the atom labels to the left of the screen and modifying as appropriate.

So how do you get to see all of the hydrogens in the molecule?

Go to the menu tabs at the top of the page and click on “Tools” You will see these options:

Explore these options like “Add Explicit Hydrogens” or “Show Aromaticity” (to make cicles inside benzene rings, instead of alternating single and double bonds).

Under “Generate” (third item from the bottom), you can have the program give you the systematic name of your compound.

Under “Calculate” (last item) you can have the program find the value of many properties (though if the structure is too complex, it can’t estimate the value), as well as percent composition, molecular weight, molecular formula, etc.

Another handy tool is the “Template” menu. Click on that and you get a list of chemical structures already built in and ready to be modified (Template Window). The “Template Organizer” has additional structures, such as crown ethers, certain fullerenes, and selected vitamins.

To get smaller items as templates (like 5- or 6-membered rings), look at the tool bar on the right side of the screen.

You can click on these and other common functional groups (like a carboxylic acid, nitro, sulfonic acid, etc.) to quickly and easily add them to your already existing structure or to use it as a staring point for your structure.

Your assignment is to use ACD Lab ChemSketch and create structures for the following molecules. You will cut and paste them all into a single word document to be turned in on Wednesday March 23rd at the start of class.

  1. Heptane
  2. Heptane with hydrogens explicitly drawn
  3. 2,4-octadiene (draw two isomers, one of which must have a trans (Z) double bond)
  4. p-xylene
  5. p-xylene with aromaticity indicated
  6. TNT
  7. Diethyl ether
  8. MTBE
  9. Vitamin E, but change all branched methyl groups into ethyl groups (may want to clean up the structure afterward)
  1. Draw this fused ring structure:
  1. Get the 30-crown-10 from the template menu (under Template Organizer, select “Crown ethers” then click “Open document”. Modify it (anywhere you want) with one extra fluoride, two extra methyl groups, three extra phenyl groups, and a bromide on one of the phenyls (be sure that Br is coming off the carbon, not in place of it!).
  1. Draw this random structure and also paste in the percent composition as determined by the program.