Ch121a Problem Set 1

Due: April 11 2014 @ 2:00PM

Part 0:
A note on notation: Things in italics will be literal commands that you type into the terminal.
These will usually be preceded by a percent sign to indicate this is a terminal. DO NOT TYPE IN
THE PERCENT SIGNS. Angle brackets denote general variables that you should replace with the
correct value. DO NOT INCLUDE THE ANGLE BRACKETS. For instance, <username> for me
would mean cescott. So,
% ssh <username>@atom.wag.caltech.edu
means I should type in ssh cescott@atom.wag.caltech.edu into a terminal.
If you use Windows and have not already done so, you'll need to install Cygwin and PuTTy. A good
tutorial for setting this up is:
http://www.cs.dartmouth.edu/~campbell/cs50/putty-cygwin-tutorial.pdf
In this problem set we will use a quantum mechanics code called Jaguar to optimize the structure and
compute vibrational frequencies and MOs of butadiene.
Part 1:
1. For Windows user, start X-win and log into dell1, dell3, or dell12.wag.caltech.edu using PuTTy.
Make sure to enable X-forwarding. If you use a Mac or other Posix operating system, you should be
able to simply open a terminal and type
% ssh -Y <username>@<hostname>
I recommend creating a new directory for each problem set via
% mkdir HW1
and entering that directory via
% cd HW1
Start maestro (it takes a while to start up).
% maestro
2. Build a butadiene molecule.
3. Go to Applications Jaguar Optimization. We will use the chemist's darling DFT: B3LYP with
the 6-31G** basis set. Choose these in the Molecule and Theory tabs. In the Properties tab, select
Vibrational Frequencies. Click on Write... and choose a filename <fname>.
4. Check to make sure you have <fname>.in in your HW1 directory:
% ls
We'll run the jobs on our cluster atom. You can either open a new PuTTy session (Windows) or ssh in
a new terminal (Mac), or simply ssh from whichever dell you're using to atom.

% ssh -Y atom.wag.caltech.edu
Now submit the job to the cluster
% ~jmendoza/bin/qsubjaguar.py <fname>.in
You can check on your job status and get the PID with % qstat -u <username>.
You kill a job by % qdel <PID>.
5. After optimization, you should see three more files: <fname>.out, <fname>.log and <fname>.01.in at
the same directory. We can visualize the optimization process by converting the .out file to .xyz file to
see how it converges to the stable structure. Use the script
% jaguar babel -ijagout <fname>.out -oxyz <fname>.xyz
to get the xyz file. Then type
% /source/molden/linux/molden4.2.linux <fname>.xyz
to view the trajectory of optimization. Click movie to show the trajectory, click the skull button to
quit.
6. Use the script
% /ul/wgliu/bin/jaguar/molfreq.py <fname>.out > <fname>.freq.molf
MAKE SURE TO INCLUDE THE HIGHLIGHTED ANGLE BRACKET.
To generate frequency files for molden, and you can use molden:
% /source/molden/linux/molden4.2.linux
to visualize all vibrational modes. Click the Norm. Mode box to show the modes.
Part 2:
7. Open <fname>.01.in, which contains the geometry of the optimized molecule and the wavefunction.
Now we want to plot MOs of this molecule. To generate new orbital files from optimized structures, we
calculate single point energy, check the surface box in Properties, and select MO from HOMO-1 to
LUMO +1 (MO 14-17 in the molecular orbital list). Also check the Mulliken populations box. After the
job is done, you should see four .vis file in the same directory. Go to Display->surfaces->import to
load .vis file. Choose entry from all and check the geometry we want to put MOs on. You need to
look into the output file and find the mulliken charges. Refer to the next step for how to use text editor
vi.
8. With the same <fname>.01.in, we are now going to investigate the energetics of rotating butadiene
about the C2 C3 bond in C1 = C2 C3 = C4 (the C atoms may be indexed by other numbers). Ensure
that the optimized butadiene molecule is selected and from the Jaguar menu option, select Relaxed
Coordinate Scan. The new window should be familiar, as its exactly the same as the Optimization
window with one important change: there is now a Scan tab. Click on this tab and select Dihedral as the
type of constraint in the add new coordinate box. You will now select the atoms involved in the
dihedral that you want to rotate about, so sequentially select the 4 carbon atoms in the following order
C1 C2 C3 C4 and the dihedral angle will show up in the defined coordinates list. In the Selected
coordinate box, enter 180 as the starting value, 360 as the final value and 20 as the increment. This
should give you 10 scan points. Write out the input file (you may want to change the input file name to
<fname>_scan.in) and submit to atom using
% ~jmendoza/bin/qsubjaguar.py <fname>_scan.in

Once finished, search for the keyword scan, and you will get the energies of each increment of the
angle. Note: You can use text editors like vi, emacs or gedit to view the input and output files. Take vi
for example, use vi text_<fname> to view the file, use j, k, h, l, PgUp, PgDn or the arrow keys to
move the icon. Type :q to quit. For more: http://www.imss.caltech.edu/node/324#f_editors
Use the following command to search for the lines that contains energy information in your output file:
grep in scan.*energy butadiene_scan.out
For more about searching through files: http://www.imss.caltech.edu/node/324#f_searching
To see what the scan looks like, we can convert the .out file to .xyz file by using jaguar babel. You can
also get the .xyz file for the overall potential surface by
% perl ~wgliu/bin/stepin2xyz.perl
You should be prompted to enter <fname>.steps.in, and you will get the converted <fname>.xyz file.
Open the .xyz file in molden, click movie to show the scan, click the hourglass button to slow down
the movie. Click Geom. conv. to show the potential energy curve.
Write-up:
1. Report the geometries (bond length and bond angle), Mulliken charges and energy of the ground
state of butadiene (cis or trans?). Report the vibrational frequencies and identify the characteristic
vibrational frequencies by C-H and C-C. Look up experimental data (geometry and vibrational
frequencies) from NIST database: http://webbook.nist.gov/cgi/cbook.cgi?ID=C106990 and make a
comparison.
Note: In maestro, use tools->measurement to get the bond lengths and angles. You may need to explore
the above link to get the experimental data.
2. Report the rotational barrier and energies in kcal/mol. Is the geometry at dihedral angle 0 a local
minimum? Explain your result.
3. Plot HOMO-1, HOMO, LUMO and LUMO+1 of the ground state of butadiene (in maestro, use
maestro --> save image).
Either email the write-up to cescott@caltech.edu or turn it in before class .