Manual for computational experiments

A6 Ab initio calculation of rotational barrier between eclipsed and staggered conformation

of ethane.
A7 Calculation of potential energy surface (PES) of H2O2 molecule using HF/6-31G(d,p)
A8 Particle in a box: Quantum mechanical calculation of HOMO-LUMO gap in ethene,
1,3-butadiene and 1,3,5-hexatriene

Experiment (A6)

Aim: Ab initio calculation of rotational barrier between eclipsed and staggered conformation of
ethane

Software: GaussView and Gaussian 09W

Theory: Ab initio calculations are computational chemistry calculations based on quantum

chemistry. Ab initio means “from first principles” or “from the beginning”, implying that the
only inputs into an ab initio calculation are physical constants. Ab initio quantum chemistry
methods attempt to solve the electronic Schrodinger equation given the positions of the nuclei
and the number of electrons in order to yield useful information such as electron densities and
other properties of the system.

In computational chemistry, the Hartree - Fock (HF) method is a method of approximation for
the determination of the wave function and the energy of the quantum many-body system in a
stationary state. With the help of variational method, one can derive a set of N-coupled equations
for the N spin orbitals. A solution of these equations yields the Hartree-Fock wave function and
energy of the system.

This method is typically used to solve the time – independent Schrodinger equation for a multi –
electron atom or molecule as described in Born – Oppenheimer approximation. Unlike one
electron systems such as hydrogenic atoms and diatomic hydrogen cation, the analytic solution
for many electron systems is not known. So, the problem is solved numerically. Due to non-
linearities present in the Hartree – Fock approximation, the equations are solved using a non –
linear method such as iteration, which gives rise to the name “self – consistent field method”.
Restricted Hartree – Fock method is applied when the atom or molecule is a closed – shell
system with all orbitals (atomic or molecular) doubly occupied. Open – shell systems, where
some of the electrons are not paired, can be dealt by either the restricted open – shell or
unrestricted Hartree – Fock methods.

In theoretical and computational chemistry, a basis set is a set of functions (called basis
functions) that is used to represent the electronic wave function in the Hartree – Fock method or
density – functional theory. This set turns the partial differential equations suitable for efficient
implementation on the computer.

The smallest basis sets are called minimal basis sets. A minimal basis set is one in which on each
atom in the molecule, a single basis function is used for each orbital in a Hartree – Fock
calculation on the free atom. For ex. each atom in the second period of the periodic system (Li-
Ne) would have a basis set of five functions (two s functions and three p functions).

Procedure:

1. Open Gauss View and click on the Element Fragment (6C) icon to activate the current
fragment. Select the C atom from periodic table. Make sure that the tetravalent atom is
the current fragment.Click once in the view workspace (purple screen). CH4 appears.
Click on one of the H atoms. CH3CH3 in the staggered form appears. Click the clean
icon.
2. Right click on the view workspace and select view. Check the labels option to get
numbers labelled on atoms in the molecule.
3. Click on ‘Edit’ and select Redundant Coordinate Editor to open the dialog window.

4. In the editor click on ‘Add’ (1st across the top). From the top drop down window at the
bottom choose Dihedral and in Coordinates replace the ? with numbers of H-C-C-H atom
numbers that form the 180o dihedral angle. Choose Scan coordinate in the lower drop-
down window at the bottom and type 36 for the number of steps and 5 for the degree
entry. Click OK.
5. Click on Calculate > Gaussian Calculation Setup. Job: Scan, Relaxed (Redundant Coord);
Method: Ground State/ HF/ Default Spin; Basis Set: 3-21G*. Make sure the charge is
zero and Spin is Singlet. Title: ethane rotation (optional); Link 0: Defaults for all tabs.
6. Click Submit. Save the file name as C2H6-3-21G. Click OK. The calculation will take a
few minutes to run.
7. After the calculation is done a screen will appear like

Click Yes twice and open the C2H6-3-21G.chk file. Check on the box that says ‘Read
intermediate geometries’. The last geometry is the structure with minimum energy.
Rotate the molecule to look along the C-C bond. Click the green circle icon at the top of
 the view window and the various conformers will be animated. Clicking the red (X) will
stop the animation. Each individual conformer may be observed by clicking the up/down
arrow at the top.
8. Choose Result > Scan. The graph shows the energy variation with rotation of dihedral
angle in ethane molecule. The rotational barrier is the energy difference between the
energy of highest point in the graph (most unstable conformer) and that of the lowest
point in the graph (most stable conformer). Record the values of energy of both the
conformers in Hartree (from the bottom of the window). Subtract these values and
multiply by 627.5095 value to obtain the barrier energy for rotation of the CH3 group
around a C-C bond in kcal/mol.
9. All the energy values can also be found in the summary at the end of the C2H6-3-21G.log
file which can be opened using a text editor such as WordPad/Notepad.
10. Verify your results from the literature available. Close all windows.

Experiment no. A8

Aim: Particle in a box: Quantum mechanical calculation of HOMO-LUMO gap in ethene, 1,3-
butadiene and 1,3,5-hexatriene.

1. Open Gauss View and click on the Element Fragment (6C) icon to activate the current
fragment. Click the C trivalent atom (4 icon) as the Current Fragment. Click in the View
workspace. Click again at the end of the C= bond. CH2 =CH2 appears. Click the Clean
icon.
2. Click on Calculate > Gaussian Calculation Setup. Job: Optimization; Method: Ground
State/ DFT/ Default Spin/ B3LYP; Basis Set: 3-21G*. Make sure the charge is zero and
Spin is Singlet. Title: Ethene Opt- 3-21G* (optional); Link 0: Defaults for all tabs.
3. Click Submit. Save as C2H4-3-21G. Click OK. The calculation will take a few minutes
to run.
4. After completion of the job, click Yes. Highlight the checkpoint file and check the ‘Read
Intermediate Geometries’ checkbox and then click OK.
5. Select the last structure (most stable, optimized). Choose Edit >MOs. A window
displaying the energy levels of the molecular orbitals of ethene molecule will appear.
 Note down the energy values for HOMO and LUMO energy levels. The energy gap can
be calculated by subtracting HOMO level value from the LUMO value (LUMO –
HOMO). The value so obtained will be in Hartree. Convert the value in kcal/mol by
multiplying it by 627.5095.
6. Extend the ethene fragment to build 1,3-butadiene molecule and 1,3,5-hexatriene. Repeat
steps (2-5) to obtain the HOMO-LUMO gap in kcal/mol.
7. Compare the obtained values with the available literature. Comment on variation in
HOMO-LUMO gap with respect to increasing conjugation.