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Chem350: Thermochemistry using Gaussian.

In this write-up I will quickly go through the features needed to obtain thermochemical
data using gaussview/gaussian09. I will not give you very detailed instructions. You will
have to find your way using the graphical interface, which is quite straightforward to use.
I encourage you to draw some molecules of your own, and see if you can manipulate the
various tools in Gaussview. Below I will give you some instructive examples that
illustrate many of the capabilities of Gaussview/Gaussian09. In lab don't hesitate to ask
questions.

The primary purpose of this section of Chemistry 350 is to show how the formalism we
developed in class directly translates into simple formulas that involve quantities that can
be extracted from routine quantum chemistry calculations: Optimized geometries and
moments of inertia, molecular mass, vibrational frequencies and electronic energies.
Together with this lab I created a Matlab file that requires these quantities as inputs and it
then proceeds to calculate thermodynamical properties. We will check that the results are
exactly the same as in the Gaussian program. Moreover, this gives you explicit access to
the proper formulas and unit conversions.

A. Calculations on a simple example: single point, geometry optimization and
vibrational frequencies of H
2
O.

Let us run through a very simple example first. You can create the water molecule using
the builder (pull down the menu), selecting Oxygen from the atoms menu. Let us first
do a calculation on the guessed structure. Measure the bond angles and distance first
(using inquire, ?). Let us do a Hartree-Fock / 6-31G(d,p) calculation. For this click
Calculate and select Jobtype=Energy, Method=Hartree Fock, Basis is 6-31G, and on
the right hand options select from the between brackets options (d,p), by pulling down
the appropriate menus. This specifies the atomic orbital (AO) basis set. Then Submit the
calculation (see lower-left button). You will have to save your file, for example as h2o.
Follow the directions given by the program. In a little while you get back the result, and
will be asked if you want to see it. Look at results (open the file h2o.log) and look under
summary. Here the main specifics of the calculation are summarized and you can find the
total energy. Next we will optimize the geometry, selecting jobtype=Optimization.
Measure the geometries again. You should find the results as listed in the Table below.


Table I. Results for water

Property / units? Guess geometry HF 6-31G(d,p)
optimized geometry
R(OH) 0.96 0.94319
A(HOH) 109.471 105.921
HF-6-31G(d,p) Energy -76.02255367 -76.02361493
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At the optimized geometry we can now calculate vibrational frequencies. Start from the
geometry in the h2o output file and select frequency under calculate->Jobtype.
After the result returns you can view the vibrational frequencies (select under results).
You can view normal modes and infrared and raman spectra. The frequencies for the
normal modes in water are as follows.

Normal Mode Frequency (cm-1)
Bending 1770(.5)
Symmetric stretch 4145(.87)
Asymmetric stretch 4262(.48)

This same calculation can be done in one shot. Start anew by rebuilding H
2
O from
scratch, and select Opt+Freq under the Jobtype menu. It first does the optimization, and
then calculates the vibrational frequencies. Vibrational frequencies are only meaningful
at the optimized geometry!

You can also look in the output file. The vibrational frequencies are all listed near the end
of the file. This section also lists their symmetry. All of the vibrational motions have a
definite symmetry with respect to planes of symmetry and rotational axes in the
molecule. Normal modes of A1 symmetry preserve the symmetry of the molecule.
Normal modes of other symmetry-type break the symmetry of the molecule. You can
investigate by visualizing normal modes, under summary.

B. Calculations on a slightly more advanced example: trans-butadiene. Some more
options and features in Gaussian.

I will run you through one more example doing similar things. Part of the information is
similar as for water.

Use the gv builder to construct trans butadiene. You only need to build the carbon chain
using the appropriate type of carbon atom. The hydrogens are added automatically. Go to
View to examine different ways to see the structure. In particular switch on Symbols to
see all atom types. Rotate and translate the molecule, using the mouse. If you press the
clean button (broom) in the builder window, you will get a first rough guess for the
structure. It is also useful to click the symmetrize button. It can be useful to use the
pointgroup option under edit. Your molecule should have C
2h
symmetry. Save your
input file, e.g. t_c4h6.


c
1
c
2
c
3
c
4
H
H
H
H
H
H
3

Next optimize the structure and calculate frequencies at the HF/3-21G level of theory. To
this end open the calculate menu and specify options as before.

- Measuring geometrical features.

Click on the inquire button in the builder menu (question mark). This will give you
geometrical information. By clicking two atoms you get the bond distance. By selecting
three atoms you find the angle made by these atoms. Finally by clicking 4 atoms in
sequence you get the dihedral angle (in "4321" format). This is the torsional angle around
atoms 2 and 3. The dihedral angle is measured rotating the fourth atom onto the first atom
along the 3-2 bond axis. Clockwise angles are positive. Now find the C1-C2, C2-C3 and
C3-C4 bond lengths. You clearly see the double bonds in the geometrical structure.
However, also C2-C3 is substantially shorter than typical C-C single bonds (quickly
construct and optimize ethane if you wish to confirm this). Compare terminal and center
CH bond lengths. Also measure various bond angles and comment on your findings.
What is the C1C2C3C4 torsional angle around the C2-C3 bond? Now measure it by
clicking the appropriate atoms. It is of interest to look at the geometry in the original
guessed structure, before optimization. Here you see there is no information on
conjugation. Instead the program guesses standard single and double bonds. Under the
Results menu you will find a number of options that allow you to analyse the output of
your calculation in an easy way.

- Changing geometries.

Let us transform trans-butadiene into cis-butadiene. To this end click on dihedral in the
builder menu, and select four atoms that specify the desired dihedral angle (in '4321'
format). This opens the dihedral smartslide. Change the dihedral from 180 to 0. Save
this new structure as cis-c4h6.com and perform an optimization of the geometry. Now
you can analyse the structure (and energetic and orbitals) of cis-butadiene. You can
similarly change angles and bond distances by clicking the respective buttons in
Gaussview. What is the symmetry of Cis-butadiene?


- Vibrational frequencies and viewing normal modes.

It is very easy to obtain vibrational frequencies in gaussview. Under the jobtype menu
specify OPT+FREQ. Infrared intensities are calculated always, Raman intensities
sometimes by default. Calculate the vibrational spectrum of trans-butadiene. Upon
completion of the calculation you can display by going to Results/Vibrations. This
shows a list of the calculated vibrational frequencies. By clicking any one of the
frequencies and clicking start you can view an animation of the vibrations. Optionally
you can also display the displacement vectors that characterize the normal mode. Set the
Frames/cycle and Displacement scales to your preference. By clicking spectrum you see
the complete vibrational spectrum displayed. Characterize the various vibrations in trans-
butadiene. Where are the CH stretches and how many are there? What is the difference
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between them? Where are the various C-C stretches? Can you clearly distinguish C1-C2
stretch and C2-C3 stretches? Characterize the various bending modes, or rotations around
the various bonds.

- Charges.

For any calculation you can view the charges in the molecule. Trans-butadiene is not
particularly interesting of course. You might create an alcohol or a carbonyl compound to
see something more interesting. Play around with the options to obtain a rendering of the
charges that you prefer. The above gives you an overview of some of the most widely
applicable options in Gaussview/Gaussian09.


C. Investigating Thermochemistry and checking Statmech formulas in Gaussian.

By optimizing a geometry and calculating vibrational frequencies one obtains all of the
information needed to calculate the partition function of a molecule in the gas phase
(ideal gas / rigid rotor / harmonic oscillator approximation). In order to achieve accurate
results that can be compared to experimental values one needs to do accurate electronic
structure calculations. For many practical purposes a Density Functional Calculation
using the B3LYP functional and a cc-PVTZ basis set is sufficiently accurate. For a
molecule that has lone pairs or internal hydrogen bonds a bigger basis set may be
required. We will first do calculations on a linear molecule (CO
2
) and on the water
molecule. I will show you where you can locate the thermochemistry output in the
Gaussian output file. Moreover , we can run a little Matlab program to do the statmech
part of the calculations ourselves. This way we can check what is done in Gaussian, and
if things agree we have a compact representation of all the required formulas and all of
the unit conversions through the Matlab file.

i) Thermochemistry of water (non-linear molecule)

Create the water molecule. Under jobtype select OPT+FREQ, while under Method
select a ground state DFT calculation. Select the B3LYP functional (default) and the
cc-pVTZ basis set under the appropriate menu. Then save the file and submit the
calculation. When you go unuei ResultsSummaiy you will finu the total electionic
eneigy:
E(RB3LYP) -76.45983962 (in Hartree)

This is one piece of infoimation neeueu foi theimochemistiy. If we then click view
file, the output file is openeu. If you scioll the file, neai the enu you finu the
infoimation on the vibiational fiequencies. Foi watei it looks like this:

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Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 A1 B2
Frequencies -- 1638.7752 3803.1701 3903.6257
Red. masses -- 1.0831 1.0447 1.0819
Frc consts -- 1.7139 8.9032 9.7133
IR Inten -- 69.5441 3.2440 40.9209
Atom AN X Y Z X Y Z X Y Z
1 8 0.00 0.00 0.07 0.00 0.00 0.05 0.00 0.07 0.00
2 1 0.00 -0.43 -0.56 0.00 0.59 -0.39 0.00 -0.56 0.43
3 1 0.00 0.43 -0.56 0.00 -0.59 -0.39 0.00 -0.56 -0.43

Foi us the impoitant pait conceins the Fiequencies, which has the haimonic
vibiational fiequencies in wave numbeis.

Frequencies -- 1638.7752 3803.1701 3903.6257

}ust below this section on fiequencies in the output file we finu all the infoimation
on theimochemical quantities. This section of the output file looks like this

-------------------
- Thermochemistry -
-------------------
Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
Atom 1 has atomic number 8 and mass 15.99491
Atom 2 has atomic number 1 and mass 1.00783
Atom 3 has atomic number 1 and mass 1.00783
Molecular mass: 18.01056 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
Eigenvalues -- 2.21189 4.15886 6.37075
X 0.00000 0.00000 1.00000
Y 1.00000 0.00000 0.00000
Z 0.00000 1.00000 0.00000
This molecule is an asymmetric top.
Rotational symmetry number 2.
Rotational temperatures (Kelvin) 39.15821 20.82634 13.59554
Rotational constants (GHZ): 815.92565 433.95112 283.28541
Zero-point vibrational energy 55898.9 (Joules/Mol)
13.36016 (Kcal/Mol)
Vibrational temperatures: 2357.83 5471.91 5616.44
(Kelvin)

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In sequence we find information on the atomic and molecular masses, the moments of
inertia tensor (both the eigenvalues and the eigenvectors), rotational temperatures, and
the symmetry number. Finally, vibrational temperatures for each normal mode. This is all
the information needed to process the data and calculate heat capacities, entropy, Internal
energy, Enthalpy, Gibbs free energy. The Gaussian program does it for you of course,
and the results are listed as follows:

Zero-point correction= 0.021291 (Hartree/Particle)
Thermal correction to Energy= 0.024126
Thermal correction to Enthalpy= 0.025070
Thermal correction to Gibbs Free Energy= 0.003649
Sum of electronic and zero-point Energies= -76.438549
Sum of electronic and thermal Energies= -76.435714
Sum of electronic and thermal Enthalpies= -76.434769
Sum of electronic and thermal Free Energies= -76.456191

E (Thermal) CV S
KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin
Total 15.139 6.007 45.085
Electronic 0.000 0.000 0.000
Translational 0.889 2.981 34.608
Rotational 0.889 2.981 10.470
Vibrational 13.362 0.046 0.007
Q Log10(Q) Ln(Q)
Total Bot 0.209715D-01 -1.678370 -3.864589
Total V=0 0.130223D+09 8.114687 18.684757
Vib (Bot) 0.161103D-09 -9.792897 -22.548979
Vib (V=0) 0.100037D+01 0.000160 0.000368
Electronic 0.100000D+01 0.000000 0.000000
Translational 0.300432D+07 6.477746 14.915562
Rotational 0.433292D+02 1.636781 3.768828


In Chem350 we went through all of the machinery that is involved to do the calculations.
From the chem350 website you can download a Matlab file. In it you find the above data
for the water molecule, and the calculation of thermodynamic properties. Going through
the Matlab file and the Gaussian output file, you will find exact agreement between what
we do in class, and what is implemented in the Gaussian program. These things are used
in actual state-of-the-art calculations! I encourage you to go through the Matlab file and
make sure you understand all the steps in the calculation. Find the corresponding results
in the Gaussian output file.
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ii) CO
2
(linear molecule).

To make sure we get things correctly also for linear molecules, let us do a calculation on
the CO
2
molecule, using the same DFT/B3LYP method using the cc-pVTZ basis set. This
is the output I obtained, and need to set up the corresponding matlab calculation.
From the Summary
E(RB3LYP) -188.66056820
From the output file (view file):
Frequencies -- 671.7935 671.7935 1371.8079
Frequencies -- 2417.0441

Molecular mass: 43.98983 amu.

Principal axes and moments of inertia in atomic units:
1 2 3
Eigenvalues -- 0.00000 153.80801 153.80801
Rotational symmetry number 2.

This is all the information needed to calculate thermodynamical properties. You can feed
it into the Matlab file and calculate properties directly. Then compare with the Gaussian
thermochemistry output section:
Zero-point correction= 0.011693 (Hartree/Particle)
Thermal correction to Energy= 0.014311
Thermal correction to Enthalpy= 0.015255
Thermal correction to Gibbs Free Energy= -0.008999
Sum of electronic and zero-point Energies= -188.648876
Sum of electronic and thermal Energies= -188.646258
Sum of electronic and thermal Enthalpies= -188.645314
Sum of electronic and thermal Free Energies= -188.669567

E (Thermal) CV S
KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin
Total 8.980 6.855 51.046
Electronic 0.000 0.000 0.000
Translational 0.889 2.981 37.270
Rotational 0.592 1.987 13.073
Vibrational 7.499 1.887 0.703
Q Log10(Q) Ln(Q)
Total Bot 0.137819D+05 4.139308 9.531109
Total V=0 0.329230D+10 9.517499 21.914852
Vib (Bot) 0.453971D-05 -5.342972 -12.302648
Vib (V=0) 0.108447D+01 0.035219 0.081095
Electronic 0.100000D+01 0.000000 0.000000
Translational 0.114679D+08 7.059484 16.255062
Rotational 0.264726D+03 2.422797 5.578695
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D. Calculating equilibrium constants from Gibbs free energy calculations.

Consider the reaction
2 2 2 2 4
( ) ( ) ( ) C H g H g C H g + !
To calculate the equilibrium constant at standard temperature and pressure one needs to
calculate the !
r
G
298.15
0
, i.e. the Gibbs free energy for each of the species. Such
calculations are straightforward with what we know now. Create each of the molecular
species in Gaussian and optimize geometries and calculate frequencies at for example the
DFT/B3LYP/cc-pVTZ level. The most critical aspect of the calculation is the electronic
energy. One can try to improve the accuracy in this respect. Since this is not a class on
computational chemistry let us simply proceed at the above level. From the Gaussian
outputs you can obtain the Gibbs free energy for each species, and also Cv and hence Cp
using ideal gas expressions. From the calculated data calculate the equilibrium constant at
298.15 K, 1 atm, and also at 400 K, 1 atm. Also calculate the equilibrium constant using
data in Reid and Engel (or from the web!). Compare the results.


E. Calculation of transition states. Comparing Gaussian output with Matlab
calculation.

As a very simple, standard, example let us consider the hydgron migration reaction in
HCN. You need to provide a guess for the transition state (elongate both CH and CN
bonds a bit, in addition to changing the angle). Then select OPT+FREQ under jobtype,
and select optimize to a transition state (Berny TS), and calculate the force constant
matrix once. Under method select the DFT / B3LYP /cc-pVTZ methodology as usual.
Upon running the calculation we can get the information we need. The first thing to do is
check the Summay/Vibrations. We should find exactly one imaginary frequency
(indicated in Gaussian as a negative frequency). You can look at it, and verify that this
normal mode corresponds to the reaction coordinate. To do the statmech we lift the usual
information from summary and output files:

E(RB3LYP) -93.38546704 a.u.
Frequencies -- -1129.0406 2066.9596 2592.7695
Molecular mass: 27.01090 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
Eigenvalues -- 4.38207 32.45085 36.83292

We can put this information in the Matlab file and run the thermochemistry. Note that the
negative frequency does not enter the equations. Instead we get a factor kT/h in the rate
constant. You can verify that the Gaussian output indeed agrees with our statmech
calculation in Matlab.

To calculate reaction rates and activation barriers we should also calculate the free energy
of reactants (HCN) and products (HNC). This then provides the free energy reaction
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profile, and a first estimate of the rate constant for the elementary reaction. Using these
values the reaction rates can be calculated at any temperature, using the formulas for
Gibbs free energy. You can compare with the traditional thermodynamics way of
calculating the temperature and pressure dependence of the Gibbs free energy and the
Arrhenius law.

F. A case study: Comparing the rate of reaction for cis-trans isomerization in
butadiene to the rate of conformational change in ethane: The effects of
conjugation.

The following calculations are time consuming!! Get them to run but you may wish to
collect results later on. Since you can only run one Gaussian job it is all a bit painful.
Such is life!

Throughout we will use the DFT/B3LYP/cc-PVTZ approach. Optimize the structures of
cis and trans butadiene and calculate vibrational frequencies. It is helpful to impose the
correct pointgroup symmetry. This can be done using the pointgroup option under edit.
Using the correct symmetry speeds up the calculation. If you want to change the structure
and perhaps the symmetry, you have to undo setting the symmetry first. Also locate the
transition state structure, by using an initial guess for the dihedral angel of 90 degrees and
obtain vibrational frequencies. Check that you get one negative (=imaginary) frequency.
Now you can process the free energies and calculate the forward and backward reaction
rates, as well as the equilibrium constant at ambient temperature and pressure. You can
also investigate the various contributions to the thermal properties (rotational, vibrational
etc.). I anticipate the energy barrier to be substantial because the system is conjugated
with its alternating pattern of double bonds. Let us compare to the barrier to rotation in
ethane therefore. You can make the so-called staggered and eclipsed configurations of
ethane, the latter being a transition state. Follow the same recipe and comment on the
differences. See if you can find values for the above quantities in the literature or using
the Web. For example visit the NIST side, which has a wealth of computational and
experimental data.

G. Summary

All gas phase reactions can in principle be studied (given enough computer resources).
We have now discussed all of the underlying theoretical principles in chem254
(thermodynamics), chem350 (kinetics and statmech) and chem356 (Quantum
Mechanics): particle in the box: translational energy; Rigid Rotor model, (using spherical
harmonics): rotational energy contributions; harmonic oscillator models for polyatomics:
vibrational part of the energy. The major component of the reaction enthalpy is the
difference in the electronic energy at the minimum of the potential (the optimized
geometry), for each of the molecules involved in the reaction. Here accurate calculations
are critical, and in prior classes we only scratched the surface regarding electronic energy
calculations. You can obtain more background information on this in classes on
computational chemistry (chem440 / computational), and quantum mechanics in
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chemistry (also chem440 special topics), but it is a rather specialized subject without easy
solutions.