Quantum Chemistry

Computer Exercise IV
Autumn 2015

Ionization of the H2O molecule

Quantum Chemistry
Computer Exercise IV
Autumn 2015

Introduction

Ionization, i.e. the loss of electrons, can occur from different molecular orbitals
(MO's) of a molecule. In this exercise you will calculate the binding energies
(BEs) for the water molecule with respect to different MO's. From the electronic
structure of the neutral water molecule it will be possible to explain the
geometric effects of ionization from different MO's. You will use both Hartree-
Fock and DFT (B3LYP). Electrostatic solvent effects on the BEs will be calculated
by using a continuum model of the solvent.

1. Binding energy

The binding energy is defined as:

BE=E(H2O)-E(H2O+)

First, optimize the geometry of the neutral H 2O molecule at the HF/6-31G(d,p)

level of theory. Then do the same for the ion H 2O+. By changing the charge in the
input file from 0 to +1, Gaussian will automatically remove one electron from the
highest occupied molecular orbital (HOMO) of the H2O molecule, i.e. MO no 5.

Next, switch the two highest MO's in the H2O+ ion and optimize the geometry at
the same level of theory using the wave function from the first calculation of
neutral H2O. The wave function is stored in the checkpoint file (.chk) so you just
make a copy of the .chk file and tell Gaussian to read it on the command line in
the input file. Also add the keywords scf=qc and nosymm to your list of
keywords. In this calculation Gaussian will interchange MO's no 4 and 5, and the
electron will consequently be removed from MO no 4. When this is done, switch
MO's no 5 and 3, and optimize the geometry of the ion. How to switch orbitals
and to read an old .chk file is shown in the input file example below.

When you have done all the above calculations at the HF/6-31G(d,p) level of
theory, compute the BE from MO no 5 and 4 at the B3LYP/6-31G(d,p) level of
theory.

Questions to answer and values to report:

a) What are the different BEs?

(1 au = 27.21 eV = 627.51 kcal/mol)

b) How good is the agreement with Koopmans theorem?

(look at the MO eigenvalues in the .log file and see page 64 in Jensen)

c) Report the structural parameters for all optimized geometries.

Quantum Chemistry
Computer Exercise IV
Autumn 2015

(OH distance, HOH angle)

d) Report the electronic parameters for all ions and the neutral molecule.
(charge and spin population on all atoms, dipole moments)

e) Report the point group symmetry for all ions and the molecule.

f) Compare your computed values with the following experimental data for
the H2O molecule. Make a comment on the accuracy of the methods.

rOH=0.957
HOH=104.52
=1.854 Debye
BE=12.6 eV

g) Make some comments on the differences between the results obtained

by Hartree-Fock and B3LYP.

2. Rationalization of results

Now perform a single-point calculation (i.e. no geometry optimization) on the

optimized geometry of the neutral H 2O molecule at the HF/STO-3G level of
theory. The STO-3G basis set is a so called minimal basis set which uses only one
basis function for each MO. This basis set is not good enough to predict energies
like the BEs computed above, but for the purpose of this calculation it will do
fine. Adding the keywords gfinput and IOP(6/7=3) and gfoldprint on the
command line (see example below) will make it possible to look at the MOs in
Molden.

Open the file in Molden, go to Density Mode. In order to visualize the MO's,
choose Space and give the value 0.05. Now you click on Orbital and choose
which MO you want to see, HOMO is the default. To save a picture of an MO as a
postscript file, press Postcript and give the file a name.

To print the file you first need to copy it to the local computer in the computer
room. Instructions on how to do that are found in general_lab_instr.pdf.

To print the file, open it with any graphics program or insert it into a word-
document, and use the menu.

Print all the MO's and attach them in your report. Now take a closer look at the
MO's that you have ionized the H2O molecule with respect to, i.e. HOMO, HOMO-
1 and HOMO-2, and answer the questions given below.
Quantum Chemistry
Computer Exercise IV
Autumn 2015

h) Thinking of these molecular orbitals (MO) as linear combinations of

atomic orbitals (AO), which AO does each MO consist of?
(either you use your knowledge about the spatial atomic orbitals or you look for orbital
coefficients in the Gaussian .log file)

i) Considering the spatial distribution (shape) of each MO, how does it

influence the geometry of the molecule?
(this is best done using concepts such as bonding- and antibonding orbitals and electron
density)

j) The geometry of the H2O+ ion depends on from which MO the electron
was removed (see your own results). These geometric changes could have
been predicted qualitatively from the shape of the MO's in the neutral
H2O molecule? Do that!
(if you are not used to MO's, useful discussions can be found in for example: Levine
Quantum Chemistry or Volatron An Introduction to Molecular Orbitals)

3. Solvent effects

So far, in this exercise, everything has been calculated in gas phase. However,
chemical reactions taking place in solution can be influenced by the solvent. The
simplest method for evaluation of solvent effects is to model the solvent as a
homogeneous and polarizable continuum, characterized by a dielectric constant
() which is specific for the solvent in question.
(The molecule to be solvated is placed in a cavity in the continuum, which is then polarized by the
molecule. The dielectric field created in the continuum is represented by point charges on the
cavity surface. These charges polarizes the molecule, giving it a new, slightly different wave
function and charge distribution. The new charge distribution once again polarizes the
continuum and the process is repeated in an iterative fashion until convergence is achieved. This
process is called the self-consistent reaction field method.)

In this exercise two different values of will be used, =80 and =4,
corresponding to liquid water and protein interior respectively.

Perform single-point calculations (i.e. no opt) on the already optimized

geometries of H2O and H2O+ (only the lowest ion, i.e. where the electron is taken
from the HOMO and only with HF) using the .chk files from these calculations.
Do this for both dielectric constants in order to evaluate the dielectric effects of
both water and protein. Use the keyword scrf=(cpcm, solvent=1, read) to do
this (see the example input given below). The scrf keyword tells Gaussian to
perform a self-consistent reactant field calculation (described in parenthesis
above) using a continuum representation of the solvent (cpcm). The keyword
solvent=1 uses parameters for the water molecule to create the cavity about the
solute and read tells Gaussian to read a specified value for . When you have
Quantum Chemistry
Computer Exercise IV
Autumn 2015

done these calculations, answer the question given below.

k) How did the dielectric effects change the BEs? Report and explain your
new solution phase values.

4. Gaussian inputs

Example of Gaussian input for interchanging orbitals, visualization of orbitals

and for using the wave function and coordinates from an old checkpoint file:
%chk=my-old-checkpoint-file.chk
# HF/6-31G(d,p) opt geom=check guess=check guess=alter gfinput IOP(6/7=3) gfoldprint
scf=qc nosymm

101022: lab4 H2O+ change MO 5 and 4

12
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45
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Example of Gaussian input for solvent effects:

%chk=my-old-checkpoint-file.chk
# HF/6-31G(d,p) scrf=(cpcm, solvent=1, read) geom=check guess=check

101022: lab4 H2O solvent effects protein

01
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eps=4.0
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5. Your report

Your report should include...

1) Introduction to the problem.

2) Short description of the methods used.
3) Your results summarized in figures (MO's) and tables.
4) Discussion that (at least) answers all the questions given above.
5) Conclusions.

...and be handed in before the next exercise!

Good luck!