Download Molecular Models on a Computer Exp. H-3

Molecular Models on a Computer
Exp. H-3
Name________________________________
Lab Section___________________________
Lab Partner___________________________
In this laboratory activity you will examine three-dimensional models of molecules using the
computer-based molecular viewing program SpartanView. A copy of this program is on the CD
included in the Organic Chemistry Molecular Modeling Workbook, by Hehre, Schusterman, and
Nelson.
Instructions:
If you are using the portable Dell computers in your laboratory disregard the boxed section below.
After starting the computer open WFView, located on the desktop. When WFView is open then go
to file in the menu, go to the Desktop and find the folder H-3 Molecules. Open the file for methane
(CH4). It can be found in the I. VSEPR folder, inside the 4 region sub-folder, under the name
ch4.sxf. (see the Figure at the top of Page 2.)
If you are using a computer in PS241, you will need to insert the disk from the Organic Chemistry
Molecular Modeling Workbook. On the CD open the application called WFView. When WFView is
open then go to file in the menu, go to the Desktop and find the folder H-3 Molecules. Open the file
for methane (CH4). It can be found in the I. VSEPR folder, inside the 4 region sub-folder, under the
name ch4.sxf. (see the Figure at the top of Page 2.)
If you are using your open computer, or a computer in a different computer laboratory: The first step
for doing this lab is to obtain the molecules that you will be using. These can be found at
http://cheminfo.chem.ou.edu/~mra/home.html Click on the highlighted “pc” or “mac” to get the
compacted version of the molecules compatible with your computer. Download this file and
decompress it on your computer. It will be named H-3 Molecules. You will notice that the directory
you unzip/unstuff has several subdirectories. Each subdirectory contains the molecules necessary for
a particular part of the lab. For example, the molecules needed for Part I are included in the folder I.
VSEPR.
Next, open SpartanView. The program works on both PCs and on Macintoshes that can run in the
Classic mode (or with OS9). Put the CD in your computer’s drive, and open the viewer program. On
the PC it is called WFView, whereas on the Mac it is known as SpartanView. You may copy this
program to your hard disk, but it will not work unless the original CD is in the drive.
To open one of the files, go to the place you have decompressed them, and choose which one you
want. As an example, let’s open the file for methane (CH4). It can be found in the I. VSEPR folder,
inside the 4 region sub-folder, under the name ch4.sxf.
PC: In the Spartan program, click on File,
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then Open. Then choose the ch4.sxf file.
MAC: In the Spartan program, click on File, then Open. In the dialogue box on the bottom of the
screen, choose “Spartan Exchange File.” Then click the ch4.sxf file:
If you do not see the files and you are running OSX, use the finder to locate the file, as below:
Then, drag the molecule’s icon to the SpartanView icon on the dock (shown here on the left under
the Finder icon)
The main window should now be showing the CH4 molecule:
You can now interact with the molecule in a number of different ways. To rotate the molecule, click
anywhere in the window and drag your mouse around.
There are a number of different ways of viewing the molecule. To choose between them, click on the
Model window. You will find that “Ball and Spoke” (above) is the easiest to use while manipulating
the molecule, but that “Ball and Wire” is easier to measure some properties with:
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To measure a bond angle, click on the Geometry menu, and then choose Angle. Then click on the
three atoms that form the angle. You must choose these in order; that is the middle atom must be
clicked second. The bond angle will be listed at the bottom of the screen. Click “done” when you are
finished.
To measure a bond length, click on the Geometry menu, and then choose Distance.
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Laboratory:
I. VSEPR
For this part, all of the files will be located in the folder I. VSEPR. Each of the questions asks you to
examine molecules with a certain number of regions of electron density, and these are placed into
separate sub-folders. For example, for part A, all of the files will be in the “2 Regions” subfolder.
It may be helpful for you to refer to the table of geometries in experiment H-1, which is on page 137
of the lab manual.
A. Examine the molecules with two regions of electron density. Draw the molecules and
measure their bond angles.
B. Examine the molecules with three regions of electron density. Draw the molecules and
measure their bond angles. Draw the Lewis structure for each molecule. How do nonbonding
(lone pair - LP) electrons explain the molecular geometry of SO2? Explain any differences
you notice between the theoretical bond angles (see page 349 of your textbook) and your
observed values.
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C. Examine the molecules with four regions of electron density. Draw the molecules and
measure their bond angles. Draw the Lewis structure for each molecule. How do nonbonding
(lone pair - LP) electrons explain the molecular geometries of NH3 and H2O? Explain any
differences you notice between the theoretical bond angles and your observed values.
D. Examine the molecules with five regions of electron density. Draw the molecules and
measure their bond angles. Draw the Lewis structure for each molecule. How do nonbonding
(lone pair - LP) electrons explain the molecular geometry of SF4 and ClF3? Explain any
differences you notice between the theoretical bond angles and your observed values.
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E. Examine the molecules with six regions of electron density. Draw the molecules and measure
their bond angles. Draw the Lewis structure for each molecule. How do nonbonding (lone
pair - LP) electrons explain the molecular geometries of XeF4 and IF5? Explain any
differences you notice between the theoretical bond angles and your observed values.
II. Trends
A. Draw Lewis structures for ONF, ONCl, ONBr, and ONI. Predict their molecular geometries
and bond angles. Record this information in the following space.
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B. Examine these molecules with a molecular viewer. Record the actual bond angles and bond
lengths in the following space. Account for any differences between your predictions in part
A with your findings. Account for any trends you notice in bond angles and bond lengths.
III. Carbon Compounds
A. Bond Types
1. Open the Carbon Compounds file and then the Bond Types file. Measure the carbon-tocarbon bond lengths for single (CH3CH3.sxf), double (CH2CH2.sxf), and triple
(CHCH.sxf) bonds. Make a generalization comparing the lengths of single, double, and
triple bonds.
2. Draw the Lewis structure for benzene - C6H6 - and predict the carbon-tocarbon bond lengths in the molecule. Open the benzene molecule (C6H6.sxf) and
measure the carbon-to-carbon bond lengths. How do you account for
any differences you observe?
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B. Cyclic Compounds
Open the Carbon Compounds file and then the Cyclic compounds file. Compare and contrast
the two six carbon cyclic structures in these files
IV. Molecular Shape and Molecular Polarity
A. Draw Lewis Structures for O2, CO and CO2. Predict their bond polarities (i.e., are the
BONDS in these molecules polar or nonpolar?) Use the table of electronegativities (which is
in your text on page 312) to answer this question.
B. Do you expect these molecules to be polar or nonpolar? Write your predictions below.
Polarity of O2:_______
Polarity of CO:_______
Polarity of CO2:_________
C. SpartanView can be used to examine the overall polarity of the molecules. From the Model
menu, choose “Ball and Wire.” Then, click on the Properties menu and choose “Dipole
Moment”. The modeling program gives you an arrow pointing towards the more negative
end of the molecule, and a value for dipole moment in the debye unit. The higher this
number, the more polar the molecule is.
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D. Draw the arrows indicating the directions of bond polarities and record the overall dipole
moments for the molecules in Part A. Explain the similarities and differences among the
molecules and their bonds. Why do they have these overall dipole moments?
E. Draw Lewis Structures for H2O, NH3, CH4 and CH3Cl. Predict their bond polarities (i.e., are
the BONDS in these molecules polar or nonpolar?) and molecular polarities (i.e., are these
MOLECULES polar or nonpolar?)
F. Examine these molecules with SpartanView. Draw the arrows indicating the directions of
bond polarities and record the overall dipole moments. Explain the similarities and differences
among the molecules and their bonds. Why do they have these overall dipole moments?
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G. Draw Lewis Structures for BF3, NH3 and ClF3. Predict their bond polarities (i.e., are the
BONDS in these molecules polar or nonpolar?) and molecular polarities (i.e., are these
MOLECULES polar or nonpolar?)
H. Examine these molecules with SpartanView. Draw the arrows indicating the directions of
bond polarities and record the overall dipole moments. Explain the similarities and
differences among the molecules and their bonds. Why do they have these overall dipole
moments?
I. Do the overall dipole moments tell you anything about the polarity of the bonds in the
molecule? Why might some molecules be non-polar, but have bonds with a large difference
in electronegativities?
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