Drawing Molecules

Double-click on the Draw icon.

A periodic table appears. Click on the element you wish to include. Make sure "Allow Ions" is checked and "Explicit Hydrogens" is not checked. For this tutorial, choose carbon.

Close the periodic table by clicking on the top right "x" button.

Click on the Draw icon again. Click anywhere on the black screen to insert a carbon atom.

Add three more carbons as shown:

Chose another element and click anywhere to add it

To connect atoms together, place the mouse on the first carbon atom, hold the left mouse button down, and drag to the second carbon atom. Release the button. Connect the other atoms together as shown.

If you make a mistake and want to erase a bond, right-click on the bond.

To create multiple bonds, simply left-click on the bond once. Click on the second bond created. Click on the double bond to create a triple bond.

Finally, on the top menu choose Build, then Add H & Model Build.

This command adds hydrogens and presents a more realistic view of the molecule's conformation.

Viewing Molecules

Choose the 3 Dimensional Rotation tool.

Left click the mouse and keep the button depressed. Move the mouse around to make the molecule rotate in space.

You can also rotate the molecule in a plane by clicking on the rotate in-plane button.

Or you can translate the molecule in the plane of the screen by choosing the translate button.

Changing How the Molecule is Displayed

Choose Display, then Rendering

You'll see the following options. Make sure the "Rendering Methods" tab is selected.

The default rendering method is sticks. Choose "Balls and Cylinders" to see another common view.

When finished return the rendering view to "Sticks"

Molecular Information

Hyperchem can also compute chemical information about the molecule it is displaying. For example, the program can compute the bond length and bond angle.

Center the molecule on the screen. (Press the space bar)

Under Setup, make sure Semi-empirical is checked

Click on Semi-Empirical. Select AM1.

Next press Compute, Geometry Optimization

Make sure Polak_Ribiere optimization is selected, then press OK.

Hyperchem begins its computation. The bottom of the screen shows the progress of the computation. When the process is complete, the line will read Conv = yes.

You can only obtain information about the molecule after the computation is completed.

Finding the bond length

Click on the select tool:

You use the select tool to select which atoms you want to extract information from.

Select one of the end carbon atoms by clicking on it. The atom will become highlighted in green. Move to the next carbon atom and select it as well. A green line connects the two atoms. The information line on the bottom of the screen tells you the bond length.

Finding the bond angle

Select a third consecutive carbon atom. The information line now shows the bond length. You can always right click on an atom to deselect it.

Obtaining additional information

Hyperchem can also give you information regarding a molecules heat of formation, dipole moment, and many other items. In order to see this you need to record a log of hyperchem's calculations as it minimizes your molecule.

Start a log

Select File, Start Log… from the top menu.

After you click Start Log, you get the following dialogue box:

The default name for the log file is chem.log. There may also be a previous version of the chem.log file present in the directory - as is the case shown above. You can change the name of the log file by typing a new name. But here we will keep the default name. Press the "OK" button. A prompt will ask you if you want to replace the existing chem.log file. Choose "Yes".

Repeat the minimization computation for our molecule. Choose Compute, Geometry Optimizations…, and click on the OK button. When the computation is complete, go back to the file menu and choose stop log.

Here's a trick to view the log file quickly. Normally you would have to open up the Notepad program and find the chem.log file to open it. An easier way to do this is to go to File, Start Log again. You will see the same screen you saw before when you initially starting the log. Now find the filename of the log we just created. Right-click on this file and choose open. The Notepad program will open up the file for you to view.

When you are done viewing the log file, close the notepad program by clicking on its close icon.

Saving your work

To save the molecule so that you can work on it later choose File, Save from the menu:

Choose a name for your molecule. Type this name under File name as shown below. Then choose "Save".

You can now close the Hyperchem program.

Retrieving a program that has been saved

Run the Hyperchem program. Choose File, Open from the menu. Look for the filename you saved and double click on it.