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Spectroscopy - Computational FTIR

The document explains the fundamentals of FTIR spectroscopy, detailing how infrared light interacts with molecular vibrations to provide structural information. It outlines a step-by-step procedure for using WebMO to calculate vibrational frequencies of water, including creating a water molecule and configuring job options for analysis. The document emphasizes the interpretation of peaks in the FTIR spectrum and the effects of broadening on overlapping peaks.

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8 views2 pages

Spectroscopy - Computational FTIR

The document explains the fundamentals of FTIR spectroscopy, detailing how infrared light interacts with molecular vibrations to provide structural information. It outlines a step-by-step procedure for using WebMO to calculate vibrational frequencies of water, including creating a water molecule and configuring job options for analysis. The document emphasizes the interpretation of peaks in the FTIR spectrum and the effects of broadening on overlapping peaks.

Uploaded by

natelink2003
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Peak Assignment in FTIR Spectroscopy

In order to understand what the peaks in our Fourier transform infrared (FTIR) spectrum mean, it is first
important to give a brief overview of infrared spectroscopy. Like the electronic orbital states described
in general chemistry, molecules also have vibrational energy levels. If infrared light is resonant with a
vibrational transition, that frequency of light is absorbed by the sample. When this happens, that
particular vibration is excited. In other words, FTIR spectroscopy offers us a powerful way to gain
structural information by probing molecular movement with IR light.

Once we have collected our FTIR spectrum, then next step is to interpret what each of the peaks mean.
One way to do this is to use computational chemistry. Consider the FTIR transmittance spectrum of
water:

It is easy to see two large peaks, where IR light is being absorbed by this sample: ~1630/cm and
3270/cm. To assign these peaks, we will use WebMO to calculate the vibrational frequencies of our
molecule.

1. Go to https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi. Sign in with the username:


guest, and the password: guest.

2. In the upper left corner, click the “New Job” dropdown menu, and select “Create New Job” from the
list. The application may take a few seconds to load.

3. Click the small periodic table button in the left column. Choose oxygen (O). Click in the main building
area on the screen to place an oxygen atom.

4. Go back to the periodic table menu and select hydrogen. Click on the oxygen atom and drag to form a
bond with hydrogen. Add another hydrogen to the oxygen to construct a water molecule. Do not worry
about the bond lengths and angles; the program will correct these.
5. Click on the broom icon (Comprehensive Cleanup) on the left. This will clean up your structure and
give it the approximate bond angles and bond lengths.

6. Next, click the right arrow at the bottom of the screen to advance.

7. Now, select the NWChem software engine from the list, and click the right arrow at the bottom again
to advance.

8. On the “Configure NWChem Job Options” page, change options to match those listed in the table:

Setting Selected Option What it means


Job Name H2O [Your Name] simulation/molecule name and your Name
Calculation Optimize + Vib Freq. Calculates the optimized geometry and vibrational modes
Theory HF Describes that we are using Hartree-Fock Theory for calculations
Basis Set Routine:6-31G(d) Describes how many functions/orbitals used in the calculation
Charge 0 Overall charge on our molecule. (Zero means not an ion)
Multiplicity Singlet All electrons are paired

9. Click the arrow at the bottom to advance. Your calculation will be added to the Queue and will
become green and say “Complete” when finished.

10. Once completed, click the blue H2O [Your Name] link or the magnifying glass next to your job to
open your data. This may take a few seconds to load.

11. Scroll to the bottom of the page to the Calculated Quantities section. Here, you will find a lot of
useful molecular properties. At the bottom of this section, there will be a Vibrational Modes section
with three modes at different frequencies. If you click the magnifying glass next to “IR Spectrum” it will
pull up the simulated infrared spectrum for the molecule.

12. Next, click the filmstrip under “Actions” next to peak 1. You should now see a movie of the
vibrational mode at the first frequency. Record your observations for each peak in the table below.
Water has a bending mode, symmetric stretch, and an asymmetric stretch.

Frequency (cm-1) Type of Vibrational Mode


Peak 1

Peak 2

Peak 3

Notice that two of the peaks in the output are close together. They overlap in the experimental
spectrum due to broadening effects and are affected by factors such as pressure or molecular collisions.
Although these broadening effects are not calculated in our quick calculations, these simulations offer a
fast and simple way to visualize and interpret each of our frequencies in an IR spectrum.

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