Introduction To Computational Chemistry

Last updated 20 th September 2002 

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Objective

The goal of this experiment is:

• to examine the bond lengths and angles of some simple organic and inorganic molecules by using molecular modeling software programs to perform complex calculations using quantum mechanics.

Grading

You will be assessed on:

• answers to the pre-lab questions.
• completion of the report form.
• TA evaluation of lab procedure.

The pre-lab assignment must be completed and handed in to your TA at the beginning of lab. You will not be allowed to begin the lab until this assignment is complete.

The Report Form is to be filled out and turned in at the end of this lab period.

 Introduction  

In addition to having more sophisticated lab equipment available to perform experiments, modern chemists now increasingly take advantage of molecular modeling software programs to perform complex calculations on molecules using quantum mechanics. While the theory behind the computation is beyond the scope of this course, we can take advantage of the software to explore many aspects of molecular structure and bonding that are related to lecture. The importance of these techniques was recently recognized when the 1998 Nobel Prize in Chemistry was bestowed upon two scientists who contributed to the development of molecular modeling.

In this exercise, you will use a software package called PCSpartan Plus to examine the bond lengths and angles of some simple organic and inorganic molecules. In next week’s lab, you will be introduced to the computational power of the program to determine various parameters such as enthalpy of formation and dipole moment.

Note that the bond lengths and angles, while reported to 5 significant figures, are only accurate to about 3 digits. So the difference between a bond length of 1.1015 and one of 1.1031 is probably not significant whereas the difference between 1.1015 and 1.0559 is significant.

General Procedures for Using PCSpartan Plus

1. Open the program by going to the Start menu and navigating through the folders in the following order: Programs/Graphics Programs/PCSpartan Plus.
2. Construct the molecule you wish to examine by using the Builder. (Instructions follow.)
3. Optimize the geometry of the molecule by choosing Minimize.
4. To begin examining the molecule, exit the Builder and enter the Viewer by either clicking on the "V" button at the top of the screen or by choosing Build/View from the drop-down menus. NOTE: You will switch back and forth frequently between the Builder and the Viewer.

Using the Builder

To build a molecule go to the File menu and choose New.

The palette of tools appears on the right side of the screen on top of the entry builder.

The basic idea is to pick up a tool from the palette by clicking on it with the mouse, then use the tool by clicking in the entry builder window.

You can add objects to the item you just created by clicking on the dangling bonds or open valences.

If you leave the molecule as is, the program will insert hydrogen atoms at all open valences.

Part 1 Simple Hydrocarbons

Methane

Practice by building methane, CH₄.

• Pick up the sp³-hybridized C tool (a C atom with four lines sticking out from it) and click once in the entry builder window to place the molecule there.
• The program will adjust the bond lengths and bond angles of the molecule to the values expected from theory with the command Minimize found in the palette. Do this now. When the minimization is finished, click Done on the toolbar at the top of the screen and enter the Viewer.

Exploring Features of Spartan

Representations

View different representations of methane by choosing from among the options in the Model menu.

• Sketch at least three different representations in your Report Form.

Manipulation

Practice manipulating the molecule around the screen. To see a list of commands for rotating, translating, and sizing molecules in the window, choose Use of the Mouse from the Help menu in the upper right corner of the menu. Take a few minutes to become familiar with these commands.

As you move the molecule around, answer the following questions on your Lab Report Form:

• Is this molecule planar, that is, do all the atoms appear to lie in the same plane?
• How might you describe the shape of this molecule?

Structural Information

Spartan can report structural information such as bond lengths and bond angles.

• Select Distance from the Geometry menu and then click on the C atom and one H atom OR on the bond between them. The distance between them in this molecule will be displayed in the dialog box at the top of the screen. When you are finished click Done to remove the box.
• Select Angle from the Geometry menu and select three atoms OR two bonds to find the angle between them.

Comparative Structural Analysis

Alkanes

In organic chemistry, hydrocarbons with the general formula C_nH_2n+2 are known as alkanes. You have already examined the simplest alkane, methane.

Use Spartan to build the next two alkanes in the homologous series: ethane, C₂H₆, and propane, C₃H₈.

• Using the Builder, first put one sp³ hybridized carbon group in the window. To make a C-C single bond, click again on any open valence of the molecule in the window. This attaches another sp³ hybridized carbon group to the first one to form ethane. Clicking again will form propane. Build and minimize both structures then enter the Viewer.

NOTE: you can show both molecules in the same window but only work with one at a time. Select the molecule of interest by clicking on it to make it "active". The other molecule will still be visible, but not active.
 

• Find the H-C-H bond angle in each molecule. Compare these values to each other and to the value in methane. Does the presence of another group on the carbon atom affect the bond angle? Is this what we expect from VSEPR theory? Explain your results.
• Compare the H-C-C bond angle in both ethane and propane.

It is possible with ethane (and propane) to find the dihedral angle as a test of planarity. [Dihedral angles of 0 and 180° indicate a planar structure.)

• For ethane only, select Dihedral Angle from the Geometry menu and select H-C-C-H atoms to find the angles between them.

Go back into Build mode and rotate the molecule so you are looking along the C-C bond. You should be able to see all 6 H atoms in what is known as the staggered conformation.

• Rotate along the C-C bond length (Alt+left mouse) until the H atoms on each C atom line up with one another in the eclipsed conformation. (You will need to rotate the molecule between different views until you get it right.)

   

• Minimize the molecule again and note what happens to the structure. What does this suggest about the preferred conformation of ethane? Can you suggest a reason why this is true?

Multiple C-C bonds

Non-cyclic hydrocarbons with a C-C double bond have the general formula C_nH_2n and are called alkenes; those with a C-C triple bond have the general formula C_nH_2n-2 and are called alkynes.

Use Spartan to build the simplest alkene, ethylene (C₂H₄) and the simplest alkyne, acetylene (C₂H₂). [Ethylene’s systematic name is ethene and acetylene’s systematic name is ethyne.] These require the use of the sp² and sp hybridized carbon tools, respectively, and may require you to rotate the molecule prior to adding the second group. Build and minimize each structure then enter the Viewer.

For ethylene, find the

• H-C-H and H-C-C bond angles
• C-C bond length
• H-C-C-H dihedral angles

How might you describe the shape of this molecule? Is it planar?

For acetylene, find the

• C-C bond length
• H-C-C bond angle
• H-C-C-H dihedral angle

How would you describe the shape of this molecule? Is it planar?

Compare the bond lengths and angles of ethane, ethylene, and acetylene. Discuss any general trends you observe and relate these to the structures predicted by VSEPR theory.

C-X triple bonds

Compare the C-X bond lengths in HCN, CO, and acetylene, discuss your findings, and propose an explanation.

To make CO, you must use the Expert set of tools on the palette.

• Click on the () button, then on the C atom in the periodic table. When you click in the builder screen, you should see a C atom with only one bond attached.
• Now click on O in the periodic table and place an O at the free valence of C in the Builder.
• Choose the triple bond tool and click on the bond between C and O until a triple bond is formed.
• Minimize and enter the Viewer.

Part 2 Structures with Rings

Benzene

Benzene, C₆H₆, is an extremely important molecule in organic chemistry. It can be easily built and derivatized in Spartan.

• In the entry builder choose Rings/Phenyl (phenyl is another name given to a benzene ring) and place a benzene in the builder screen. Minimize and enter the Viewer.
• Find the bond lengths and angles for the molecule. What do they tell you about the structure of benzene?
• Compare the way the bonds are depicted on the screen vs. how they represented on the tool palette. Which do you think is a more accurate representation of electron distribution in the molecule? What structural information led you to your conclusion?

Furfural
Practice your molecule building skills with furfural, shown below.
(Instructions for this section were adapted from the MacSpartan Plus Tutorial and User’s Guide, Wavefunction, Inc.)

Furfural can be constructed using a combination of both rings and functional groups.

• Start with the Cyclopentyl shape from the Rings pop-up menu.
• Replace one of the C atoms with O by selecting the -O- atomic fragment and double-clicking on one of the C atoms on the ring.
• Make double bonds by clicking on Make Bond on the palette. Click on one of the unfilled valences of a carbon bonded to the oxygen atom, then click on one of the unfilled valences of the adjacent carbon. A double bond appears between the two carbon atoms. Create a second double bond in the same way. Click on Done, then Minimize.
• Add the C=O group to the ring by first clicking on the Groups button, then selecting Carbonyl from the pop-up menu. Click on the appropriate free valence on the molecule to add the C=O group. If the C=O group is pointing in the wrong direction, use the mouse to rotate around the C-C bond. Minimize and enter the Viewer.

Compare

• the C=C bond length in the ring with that of ethylene.
• the C-C bond length in the ring with that of the straight-chain alkanes.
• If there are significant differences, propose explanations for the differences.

To do the next section, you will also need the C-O bond length and the H-C=O bond angle.
 

Part 3

Carbon-Oxygen bonds

Compare the C-O bond lengths in methanol (CH₃OH), formaldehyde (H₂CO), and carbon monoxide (CO). On your Lab Report Form, draw Lewis structures of the molecules which reflect the geometry represented by the software.

• Record the H-C=O bond angle in formaldehyde. Compare this bond angle with the H-C=O bond angle in furfural.
• Compare the C-O bond length of methanol and formaldehyde with that in the furfural ring.
• Explain your findings.