Exercises "Werkcollege" 4: UV/VIS, IR, Raman
This werkcollege deals with electronic excitations, Infrared absorption, and
Raman spectroscopy. The objective of this werkcollege is to learn how to
compute IR/Raman Spectra of molecules and to visualize the normal modes,
which give rise to the specific peaks of these spectra. Furthermore, we will
compute excitation energies, which can be used to construct a UV-Vis spectrum
of a molecule. Lastly, we will learn how to compute the geometry of the first
excited state, which is useful to calculate the fluorescence frequency of a
molecule.
At the end of this werkcollege we ask you to write a small report (max 2 pages)
in English answering the supplied questions. Please hand in the report before
Friday June 5th (23:59), either during the werkcollege as a paper version or as a
digital file sent to F.M.F.deGroot@uu.nl and J.M.Boereboom@uu.nl. If you
choose to send in a file by email, please make sure that in the subject of the email
at least the acronym TDFT is placed so that we can archive these emails
appropriately.
1. Infrared absorption of greenhouse gasses
In this exercise we will calculate the absorption (IR) spectra of different
greenhouse gasses. In order to assess the greenhouse potential of a molecule it is
important to look for absorption in the so-called IR atmospheric window
(between 800 cm-1 and 1400 cm-1), where there is no absorption from water or
carbon dioxide. From benchmarks it is known that the simple LDA functional
reproduces the IR frequencies and intensities of a reference calculation (MP2)
quite well. Therefore, we will take this functional and a TZP basis set in this
exercise.
a. Create a water molecule and optimize the geometry with the LDA functional
and a TZP basis set. After optimization, perform a frequencies analysis by
selecting Preset: Frequencies. Start ADFSpectra and tabulate the
absorption maxima and their intensity.
b. Repeat the calculation for carbon dioxide, again tabulating the absorption
maxima and their intensity. You should find one absorption in the IR
atmospheric window, but with zero intensity. Looking at the normal mode of
this vibration explain why it has zero intensity.
c. For carbon dioxide we will also perform a Raman calculation. Which modes
do you expect to have intensity in a Raman spectrum? Explain this with the
selection rules of IR and Raman spectroscopy. In order to perform Raman
calculations select Preset: Frequencies, go to the Properties tab
and select Raman, VROA then select Calculate: Raman Full. Do the
results from the calculations agree with your theory?
d. Now consider nitrous oxide (N2O) and methane, gases that are known to be
potent greenhouse gases. Do you indeed observe significant absorptions in
the calculated IR atmospheric window?
e.
Other important greenhouse gases are chlorofluorocarbons. Find out what is
meant by CFC11, CFC21, CFC12, etc. and choose one such molecule to
calculate its IR absorption spectra. Describe the normal modes that give rise
to the most intense absorptions in the IR atmospheric window.
2. Electronic excitations
Being able to calculate excitation energies is important for the study of various
photochemical processes. The easiest and most common of TD-DFT is to
calculate vertical excitation energies at an optimized structure. This corresponds
reasonably well with the absorption maxima measured in UV-Vis spectra if you
take care to chose an appropriate basis (often also diffuse functions are needed,
which are in augmented basis sets) and functional. More advanced is the
optimization of the structure of the molecule in its (first) excited state. This will
provide you with information about the fluorescence frequency.
In order to keep the calculations not too time-demanding we choose here just a
TZP basis set and the BP functional.
a. Draw trans-1,3-butadiene, and optimize the geometry. Tabulate the carboncarbon bond lengths, do these indeed reflect the C-C and C=C bond lengths
character you have drawn?
b. In order to calculate the excitation energy, do a Single Point calculation
selecting Excitations, CD under the Properties tab. Specify Type
of Excitations: SingletOnly and choose Number of
excitations: 4. If you go the Spectra module you can see a simulated
UV-Vis spectra, note that the transitions are artificially broadened by
convolution of a Gaussian function. Click on the axis to change the units of
the excitation on the x-axis. The maximum absorbance of this molecule is
around 217 nm, how does your calculation agree with experiment? What are
the orbitals involved in the first excitation (tip: if you point your mouse to on
the transitions you can visualize the orbitals by clicking on the orbital
transition with the largest percentage in the green field that appears when
hovering over the excitation)?
c. Now, optimize the geometry of the first excited state to get an estimate of the
fluorescence frequency. First we need to find out what the symmetry is of
the lowest excitation (this can be found in the output file of b). Set Preset:
Geometry optimization and go to Excited State and
Geometry under the Properties tab. Fill the symmetry you just found in
under Excitation:________. If you start from the previous input, please
make sure that you reduce the number of excitations to 1.
What is the Stokes shift? What happened to the C-C and C=C bond lengths
and is this what you expected on the basis of the nature of the excitation?
At the end of this werkcollege we ask you to write a small report (max 2 pages)
in English answering the supplied questions.
Please hand in the report before Friday June 5th (23:59), either during the
werkcollege as a paper version or as a digital file sent to F.M.F.deGroot@uu.nl
and J.M.Boereboom@uu.nl. If you choose to send a file by email, please make
sure that in the subject of the email at least the acronym TDFT is placed so that
we can archive these emails appropriately.