Visualizing Molecular Structure by Computer Graphics

In this PC Lab exercise in the ChemTech PC Lab (Foster Hall 326), you will have an initial taste of the power of advanced computational modeling tools in helping one to visualize the three-dimensional structure of molecules. You will look at several molecules using the software Chem3D, purchased from Cambridge Software by a National Science Foundation grant to the Chem Dept. In doing so, you will try several different types of renderings (styles for displaying the atoms) and will look at molecular dynamics (the motions of molecules). In the VSEPR lab you used small physical models to look at structures that had one central atom, such as methane (CH4). Here, you will look at more complicated molecules, like methanol CH3OH, ethane (CH3CH3), ethanol (CH3CH2OH), and ethylene (CH2CH2).

  1. Launch Chem3D by clicking on START/Programs/Chemistry/Cambridge Software/Chem3D Pro.

  2. Familiarize yourself with the graphical interface of the program. First use the expand button in the upper right hand corner of windows to make use of the entire screen.

  3. Type the formula of the molecule you want to view into the text box near the upper left corner of the window just below the tool buttons. For example, to view methanol, type in CH3OH and return. (Use all upper case.) If the formula is a molecule that Chem3D recognizes in its limited library, the model will appear on the screen with the correct 3D structure. Otherwise, you would need to draw it by hand on the screen by a special procedure not covered in this beginning tutorial.

  4. When a molecule is first built on the screen by the above procedure, all the atoms will start out being "selected" and thus highlighted. To get rid of the this, click on the arrow button in the vertical tool bar, and then click somewhere in the window away from the molecule itself. This deselects all atoms.

  5. Now, some other useful tool buttons need to be accessed. In the very bottom left of the Chem3D window is a button which shrinks the molecule to make it easier to view, and an adjacent one to expand it. If it seems like the molecule is too large on the screen, shrink it for easier viewing.

  6. In the View pull down menu is a Preferences option which brings up an important dialog box. Here you need to adjust the Depth Ratio to a smaller number, such as 30, to get a more realistic 3D view.

  7. It is often easier on the eyes and prettier to see a structure against a black Background instead of a white one, so in the dialog box you may also choose a dark-colored background.

  8. Now go back to look at the molecule window and find the vertical toolbar with the arrow at the top. With the arrow button clicked on, the cursor is an arrow and allows one to select a given atom (by clicking on it) or group of atoms (by dragging). With the rotate button clicked on, the cursor looks like a small hand, which allows the user to rotate the molecule and visualize it from all angles.

  9. Rotate your molecule around and view it from all sides.

  10. Now look at the structure using other types of renderings. In the View pull down menu, choose the Preferences option again and change the Model Type from its default value (Sticks), to Ball and Stick. Put the dialog box away and go back and look at the model and work with it. Then go back to the View/Preferences option and choose a Model Type of Space Filling, and the Atom Fill to Shadowed Colors. Now go back and look at the structure and rotate it in space. The Space Filling Rendering depicts each atom as a ball the size of the electron cloud around that atom.

  11. Finally look at the molecule using the Ball and Stick option again, but this time Select All the atoms, then go to the Object pull down and choose Show Dot Surfaces. This will combine the ball & sticks rendering with a web of dots which show the sizes of the atoms similar to the Space Filling picture.

  12. Write down your impressions of the usefulness of these three different modes of drawing the atoms. Describe below in relative terms their: (a) ease of seeing the connectivity of the atoms, (b) ease of seeing the shape and size of the molecule, (c) ease of seeing the geometry of bonds around each atom, (d) realism, (e) aesthetic beauty, and (f) ease of rotation with the mouse.

 

Ball & Sticks rendering:

 

 

 

 

 

Space Filling rendering

 

 

 

 

Sticks and Dot Surfaces rendering

 

 

 

A. Comparisons about Molecular Structure: Look at each of the four molecules: methanol CH3OH, ethane (CH3CH3), ethanol (CH3CH2OH), and ethylene (CH2CH2) and answer the following questions:

  1. What is the geometry of the bonds around the C atoms in methanol, ethane, and ethanol?

    2.  

  2. What is the geometry of the bonds around the O atom in the two alcohols?

    3.  

  3. What is the similarity between methanol’s structure and that of methane (CH4)?

    4.  

  4. What is the geometry of the bonds around the C atoms in ethylene, which possesses a C=C double bond?

  5. Do all atoms in ethylene lie in the same plane?

 

B. Molecular Motion: With one of your molecules on the screen, preferably in the Ball & Sticks mode, go to the MM2 pull down menu (stands for Molecular Mechanics version 2) and choose the Molecular Dynamics option. What you will see on the screen is a frame-by-frame picture of a movie of the typical motion of this molecule at room temperature. (The pink colored atoms or sticks that somehow got built on the structure are Lone Pairs of nonbonding electrons on the oxygens of the alcohols. These lone pairs are always invoked when using MM2 features.) Note the types of motion in the molecule. Note the range of the motion. To stop the molecular motion, click on the solid button near the lower left of the Chem3D window.

 

 

C. Drug Molecule: Finally, go to the File menu, choose Templates, and open a pre-built model called TAXOL, which is an anticancer drug widely used in chemotherapy today. Look at it in several renderings. Go to the Tools menu and turn on Show H’s and Lp’s (show hydrogens and lone pairs). Turn on the molecular motion. Describe the kinds of motions you see in Taxol.

  1. Is Taxol a rigid molecule, or fairly flexible?

    2.  

  2. Do you see rotations of various groups of atoms in the structure?

  3. Does the overall shape of the molecule change in a fairly lengthy simulation?

  4. How many benzene rings are found in the structure?

  5. What are the geometry types you find around various carbon atoms in the structure? Any tetrahedral? Any trigonal planar?