Dancing Molecules
Exploration: Visualize Molecular vibration and View UV and IR spectrum of
atmospheric molecules
Tool:
Webmo Demo website
Skill:
Minimal practice Using Webmo to build molecules
Level:
Physical Science, Chem 1
Objectives:
Visualize Molecular Vibration
Compare IR and UV Spectrums of CO2 and other
atmospheric gases
May be used a teacher demo or by assigning students different atmospheric molecules
(oxygen, ozone (UV), nitrogen, water, methane) in addition to carbon dioxide.
Background: The Infrared Spectrum
The Infrared portion of the electromagnetic spectrum (what we perceive as heat) contains
photons of the correct energy to excite the normal vibrational modes of a molecule. The
precise infrared frequencies absorbed by a molecule will depend on the types of chemical
bonds present. Infrared spectroscospy is a commonly used analytical tool.
This allows the chemist to determine what types of bonds are present in the sample.
In this exercise we will calculate the ultraviolet and infrared spectrums for carbon
dioxide. The software will allow us to animate the various infrared absorptions to see the
corresponding molecular motions.
Do a Google search for Webmo Demo Server
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Login username guest
Password guest
You should now be at Webmo Job Manager.
In the upper left corner click New Job.
To
Build a molecule of carbon dioxide .
Select Open Editor. Select Atoms needed from the Periodic Table.
Select Carbon. Click on notepad. Select Oxygen. You can click and drag Oxygen twice
to add oxygens to carbon. Don’t forget to add your double bonds.
Use Clean-up > Comprehensive – Mechanics.
Close Editor
Choose Mopac as the computational engine. Type in/Choose the following:
Job Name: CO2PM3 (Followed by your initials)
Calculation: Geometry Optimization
Theory: PM3
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Basis Set: Basic: 3-21G (or accept default)
Charge: 0
Multiplicity: Singlet
Click on the blue “continue” arrow in lower right. You should now see your job listed.
When the calculation is finished, open the file by clicking on CO2 formula name.
Click on New Job Using This Geometry, and Type in/Choose the following:
Job name: CO2PM3Vib
Calculation: Vibrational Frequencies
Theory: PM3
Basis Set: Basic: 3-21G (or accept default)
Charge: 0
Multiplicity: Singlet
Click on the blue “continue” arrow. You should now see your job listed. When the
calculation is finished, open the file by clicking on the formula and scroll down to the
Vibrational Modes window (at the bottom)
How many transitions are shown? (count the number of frequencies)____________
Click on the filmstrip next to the first frequency and observe the corresponding
vibrational motion. Use the rotate button in the upper left hand corner to better view the
molecular motion if needed. Try to identify the type of motion for each transition. The
type of motion can be described as stretch (symmetrical or assymetrical), etc.
Record the motion, and calculated vibrational frequencies in the table below.
Due to the approximations in the PM3 method, calculated vibrational frequencies are
often higher than the experimental values. For better comparison with experimental
results, the calculated frequencies are often multiplied by a scaling factor(fudge factor!).
The scaling factor is listed below. Perform the corrections and list the new results in th
appropriate column.
Use the scaling factor (PM3 = 0.9761)
Motion
PM3
Scaled PM3
Exp Val. (cm-1)
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
View the IR Spectrum magnifying glass. Record the intensity and frequency energies of
the absorption peaks.
Go back to Job Manager and select CO2PM3Vib. Select New Job Using This Geometry.
Blue “continue” arrow.
Choose Gaussian, blue “continue” arrow
Job: CO2PM3UV-IR
Calculation: UV-IR Spectrum
Theory: PM3
Basic Set Basic: 3-21 G
Charge: 0
Multiplicity: Singlet
Blue “continue” arrow will send it to Job Manager
Pick up CO2 UV-IR spectrum job
Scroll to bottom. Click on UV-Vis Spectrum magnifying glass.
Why don’t we see absorption peaks?
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright