Molecular Modelling: class 1

GETTING STARTED WITH AMS

1. Geometry optimization of the ethanol molecule.

You should follow a tutorial to perform a geometry optimization of the ethanol molecule
(CH3CH2OH) at the B3LYP-D3(BJ)/TZ2P level of theory and visualize the results of the AMS
calculation.

The slides will guide you through the following steps:

 build the ethanol molecule

 view the molecule from all sides and save a picture
 set up your AMS calculation
 perform the actual AMS calculation
 visualize some results: geometric parameters, energy levels, orbitals, electron density,
molecular electrostatic potential, …

More detailed information can be found in the following link:

https://www.scm.com/doc/Tutorials/GettingStarted/GeometryOptimizationOfEthanol.html

2. Molecular orbital diagram of diatomic molecules.

The objective of this exercise is to compare the chemical bond parameters and Molecular
Orbital (MO) diagrams of diatomic molecules, with a focus on F 2 and N2.

First, you should perform the geometry optimization of the molecules with the BP86 (GGA)
functional and the TZP (no frozen core) basis set, with no relativity. Use the option Good for the
accuracy of the numerical integration. Press the Frequencies tab to verify the nature of the
stationary point.

Note: For all calculations, you should adjust the geometry convergence criteria (cf. Details tab
in the ADFinput): Energy convergence: 1e -4 hartree, Gradient convergence: 1e -4 hartree/Å; Step
convergence: 1e-3 Å.

2.a. Once the calculation has finished, visualize the results of the optimization using
SCM→Movie. Check also the vibrational frequency via SCM→Spectra. For the optimized
geometries, you can extract the bond length (Re in pm) and the bond energy (Ebond in kcal mol-1)
for F2 and N2. Which of the two molecules exhibits the strongest bond?
2.b. Compute the bond dissociation energy (De in kcal mol-1), which is defined as the energy
required to separate the atoms to infinity [X 2(g) → 2X(g)]. You need to compute the energy of the
isolated atoms at the BP86/TZP level of theory with no frozen core, with the proper electronic
configuration (F: 2s2 2p5 and N: 2s2 2p3). Note, that most single atoms exhibit a multiplet ground
state, so unrestricted calculations need to be performed at the same level of theory. When
performing an unrestricted calculation, we need to specify the spin polarization, which is the
number of spin-a electrons in excess of spin-b electrons, i.e. the number of unpaired electrons.
The De can then be computed as:

De = 2 E [X (g)] – E [X2 (g)]

Besides computing the bond dissociation energy De, estimate the vibrationally corrected zero-
point value D0. The differences between De and D0 can be graphically visualized in the scheme
above.

D0 should be computed taking into account the energy of the first vibrational state (v=0) which
is different from 0. This value is listed in the frequency .out file as a zero-point energy in
hartrees.

What is the difference between the bond energy provided in the calculation of the diatomic
molecules and D0 and De?

2.c. Use a qualitative molecular orbital (MO) energy-level diagram to predict the electron
configuration and the bond order of F2 and N2. Just consider the valence atomic orbitals 2s and
2p. The bond order (b) is given by:

b = ½ (n-n*)

where n is the number of electrons in bonding molecular orbitals and n* is the number of
electrons in antibonding molecular orbitals.

What is the bond order in F2 and N2? Do they have unpaired electrons?
2.d. Visualize the molecular orbital diagram of the energy levels of F 2 and N2 using ADFlevels.
In the diagram, you can see from which atomic orbitals the molecular levels are built. You can
zoom the diagram by selecting a suitable energy range to visualize just the MO derived from the
2s and 2p atomic orbitals (e.g. for F2, the energy range can be set up between -1.3 and -0.2
Hartree, while for N2 the energy range can be set up between -1.3 and 0.2 Hartree ). You can
move the mouse above different levels, and balloons will pop up with information about the
level (energy, occupancy and the orbital labels). You can easily identify the bonding and
antibonding sigma and pi orbitals.

In addition, you should visualize the different orbitals, by clicking and holding on the desired
level. If the option “Orbitals in one window” in the View menu is selected, all the orbitals will
be displayed in the same window. Use an isosurface value of 0.03 to display the molecular
orbitals. You can check the contribution of each atomic orbital to the molecular orbital by
clicking on the red lines. Similarly the energy of each orbital is displayed when the mouse is on
top of this particular orbital.

Compare the N2 and F2 diagrams; which differences do you observe? What is the
contribution from the AOs to the 2s and 3s orbitals? Check the energy difference
between the 2s and 2p atomic orbitals in N and F fragments.

2.e. Visualize and obtain the energies of the Highest Occupied Molecular Orbital (HOMO) and
the energy of the Lowest Unoccupied Molecular Orbital (LUMO). Estimate the HOMO-LUMO
GAP (in eV), also known as optical gap, from the energy difference between the LUMO and
HOMO orbitals.

What is the optical GAP (in eV) of F 2 and N2? What is the symmetry of the HOMO
orbitals in both diatomic molecules?