Jaguar 1

Jaguar
Exercises
Per-Ola Norrby, 2011
Introduction

Molecules for Jaguar are built using Maestro, which you’ve already learned how to use. For the exercises
here, we’ll stick with simple molecules, to allow the calculations to finish in seconds or minutes.
Exercise 1 Build a water molecule and optimize it using MMFF in the gas phase (as you learned earlier,
under Applications>MacroModel>Minimization). With the MMFF-minimized water molecule on
screen, select Applications>Jaguar>Singel Point Energy which brings up a separate window with
several tabs, each many options. For most tasks here, accept the values that are already filled in; only
change what is listed here, or whatever you wish if you really know what you’re doing. However, you
should always check that the listing of charge and multiplicity is correct under the Molecule tab (a
normal, closed shell neutral molecule has charge 0, multiplicity 1; a radical has multiplicity 2). If you
don’t change any other settings, you’ll use quick SCF (not fully converged) at the B3LYP/6-31G** level
of theory. Run this job for H2O with the Start button, then create an entry name when asked. NOTE:
this will run the job on the local computer! Only do this for very small jobs, not much more than a dozen
atoms. You can run jobs with over 100 atoms, but you should then Write the job and start it on a faster
machine, and be prepared to wait for a while. Final energies will mostly be reported in Hartree (atomic
units, au), but sometimes in kcal/mol. 1 au = 627.5 kcal/mol = 2625.5 kJ/mol; 1kcal/mol = 4.18 kJ/mol.
Note the final total energy for the water structure (this is the B3LYP/6-31G**//MMFF energy; the
double-slash denotes that the geometry is taken from another level of theory). Now select the HF
(Hartree-Fock) method under Theory:Level of theory, change the Basis Set under the Molecule tab to 6-
31G*, then run again. Note the HF/6-31G*//MMFF energy.
You can optimize the structure at any level of theory. Select Applications>Jaguar>Optimization. The
program uses a Hessian update method, so it starts out with an approximate Hessian (Schlegel’s guess),
which gets better as the calculation progresses. Run the calculation, which will now give you the HF/6-
31G* energy. Compare it to the previously calculated HF/6-31G*//MMFF energy, calculate the
difference in kJ/mol. Which is lower? How much? By doing a separate calculation, you can also do the
same type of comparison between B3LYP/6-31G** and B3LYP/6-31G**//MMFF. What is MMFF most
similar to, HF or B3LYP?
If you lose contact with the job, you can still see the optimized structure in Maestro later. In any Jaguar
window, you can use the Read button and select the appropriate Jaguar file. The starting structure will be
named jobname.in, and the result can be found in jobname.01.in. You may need to change directory in
the Read window. Jaguar also produces text information that can be found in the jobname.out file. All
these files can be read using Project>Import Structures… and selecting the appropriate file format.
Jaguar 2
Exercise 2 We will now look at the energy of the water molecule as a function of the H–O–H angle.
With the water molecule on screen, open Applications>Jaguar>Relaxed Coordinate Scan. Under the
Molecule tab, check the charge and multiplicity (0 and 1), and select the 6-31G* basis set. Under
Theory, select DFT level of theory and the hybrid B3LYP Functional. Under SCF, set the Accuracy
level to Accurate. Don’t change anything under Optimization, but under Scan, select Type: Angle, then
pick the atoms in the order H-O-H. Set the Starting value to 90, Final value to 160, and Increment to 10
(which will give you an 8-step calculation). Now select Start and give it an appropriate name, then take
a coffee break,1 it will take a minute. The program will lock the angle to 90°, optimize all other
coordinates, then lock it at 100° and so on, until it reaches 160°.
When the job has finished, select Tools>1D Plot…, then open the file jobname.grd
For how large deviations will a harmonic function be a good approximation for this curve?
Exercise 3 Use the procedure from exercise 2, but now instead drive the dihedral angle of HOOH from
0° to 180° in steps of 30°. You can also do this in MacroModel using the MMFF or MM3* force fields.
How do the energy curves compare to each other?

Acid-base equilibria

Exercise 4 Build H2O, H3O+, NH3, and NH4+, optimize each using the B3LYP/6-31G** level of theory.
Note the energy of each of them. Calculate the following equilibrium energy by adding the energies on
the left, subtracting those on the right.
K
NH3 + H3O NH4 + H2O

You can now calculate the equilibrium constant using the Boltzmann equation or, alternatively assuming
that each 6 kJ/mol gives one pKa unit in difference. How good are the values? Recalculate all values
using solvent. Under Applications>Jaguar>Optimization, the Solvation tab, you select Water. Did
the values improve?
If you try to compare neutral to cationic acids, the results can be disastrous in the gas phase, but may be
quite good when solvent is used. Try to calculate the pKa of formic acid, and convince yourself that the
value lies just between H3O+ and NH4+ (in water, not in gas phase).

1
If you don’t drink coffee, your future as a computational chemist is in severe danger.
Jaguar 3
Surfaces

Exercise 5 We will now look at some surfaces of unsaturated molecules at the B3LYP/6-31G*/MMFF
level of theory. Start by building ethene, minimize the energy using MMFF, then select the B3LYP/6-
31G* level under Applications>Jaguar>Single Point Energy as before. Turn off any solvation, then
select the Properties tab. Now, select “Surfaces (MO, density, potential”, making sure that the line is
selected (yellow shaded) and the check box is crossed. Of the available surfaces, select “Electrostatic
potential”, “Electron density”, and “Molecular Orbitals” (the latter defaults to HOMO and LUMO, don’t
change the numbers at this point). Now Start the job as before. The potential surface should appear
when the job is finished. In the project table (Project>Show Table), you will notice that the “Surf”
column has appeared, with an S button for your entry. Click this to bring up the surface table (can also be
found under Display>Surfaces>Surface Table). Look at MO_8 (the HOMO) and MO_9 (the LUMO),
they should look like what you’ve seen for π-systems in previous courses. Now bring up the “density”
surface, which should at this point be uniform in color (it encloses all points with a high electron density,
you can change the size of the volume by manipulating the isodensity value). Now select Display
Options..., bringing up a window which allows you to manipulate the density surface. Under “Color
scheme”, the Property option will allow you to map a lot of molecular mechanics features onto this
surface, but to use QM data, instead select Map values from volume data. Select the “Color Ramp:”
Red_White_Blue, then in turn select MO_8, MO_9, and potential, then click Apply. This will show you
how much of the HOMO, LUMO, and electrostatic potential is actually visible on the surface of the
molecule, a very essential feature for reactivity and for docking.

Exercise 6 Repeat exercise 5 with formaldehyde, but when you specify the orbitals, also change the
number after HOMO- to “2”, to display the two orbitals below HOMO in energy. The HOMO is still
MO_8 and the LUMO is MO_9. Which orbital corresponds to the π-system, and which are lone pairs on
oxygen? Had you expected the results? Can you draw some conclusions about possible UV absorptions?

Homolytic cleavage

Exercise 7 We will look at homolytic bond cleavage for the H2 molecule. Due to the high symmetry, we
must use some tricks to ensure a correct diradical state in the broken molecule. Build H2, then go into
Applications>Jaguar>Rigid Coordinate Scan. First, to test an improper method, set up a normal HF/6-
31G** calculation, then under scan, select the H–H distance, start at 3.0 Å and go to 0.5 Å in steps of 0.1
Å (you must start at the longer distance). Run this calculation and plot the energy as a function of
distance. Now do the same, but under the Molecule tab, turn off “Symmetry”. Under the Theory tab,
select the Spin-unrestricted option. Finally using the Edit... button, bring up the “Edit Job” window.
Here, insert a new line directly after “&gen” (the first line), and write “ioss=1” (without the citation
marks), exactly, with no spaces anywhere. This allows Jaguar to create an initial guess where the α and β
electron can be in different places. Save the change by clicking OK, then start the job normally. Again,
plot the energy as a function of distance, and note the change at long distances where the behavior is
supposed to be biradical-like. Details can be seen in the jobname.out file, can be shown in the Monitor.