S C H 207: Introduction to Computational Chemistry

Lab Introduction

L . Kiruri

Chem-Dept@KU

Sem-II, 2023

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 Computational Workflow
No matter what the project you're working on is, everyone follows
the same workflow. We'll consider each step in turn:
This is the hardest part, but
think of a computation unfortunately, there's no room to
that you want to run talk much about this.

You have to tell Gaussian, a

create a Gaussian
input file (*.gjf) quantum chemistry software
package what you want it to do.

submit job Computing resources.

retrieve results (*.log) Output comes back in a text file,

but you can use GaussView to
look at the results graphically.

analyze results This is where you have to use

your chemical intuition.
Creating a Molecule of NH 3

The following are detailed instructions on how to set up a

calculation, it is important you take the time to read the
instructions and follow them precisely.
Create a folder where you will save all your files
Then Launch/ or open gaussview
Two palettes or windows will appear one with buttons, which
has all the controls in it and one that is blank, which will have
your molecule in it

On the controls palette click on the button that has a grey

periodic table (or element fragment) on it:

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 When the periodic table comes up choose N for nitrogen (1.), then
when the nitrogen options appear along the bottom of this window
choose the pyramidal fragment (2.):

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 now move the mouse to the molecule window and click once inside
this window, a molecule of NH 3 will appear:

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 Options for labelling and manipulating your molecule.
Now put the mouse on one of the atoms and move it across the screen,
the molecule will rotate. Spend a few minutes getting comfortable with
manipulating your molecule. Make sure you can:

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Manipulating the Molecule
Rotate the molecule
Magnify and shrink the molecule
Translate the molecule
I took this image from the gaussview help menu. If at any point you
want to find out more about manipulating molecules in gaussview the
help section should be your first port of call.

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 you should also look at the options in the view menu, for example
you can put the letters for each atom on the ball-and-stick diagram

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Controlling bond distance parameters

Along the top of the controls palette the next three buttons allow
you to change the b o nd distances, angles and torsion angles
of a molecule

Return to your window with NH 3 , click on the bond distance

Then click on the N-atom and one H-atom, they should now be
highlighted and a new window will appear

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 Refer to slide 10..
When we set the new bond distance, we don’t want the N to
move, only the H, so set the N atom to be F i x e d (1.), this will be
either atom 1 or atom 2 depending on whether you clicked on the
N atom first (atom 1) or second (atom 2)
Then we want to make the bond longer, enter 1.3 in the text box
(2.), you will see the chosen bond elongate (3.) Then press the
O K button, if you don’t press ok the change will not be effected.

Set all three N-H bonds to 1.3 angstrom.

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Bond Length

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 The angle and torsion angle controls work similarly, try them
out and explore how these controls the molecule.
Check the symmetry of your molecule
We need to ensure your molecule has the right symmetry. The
model builder does not always get this right, and so for each
molecule you need to manually check it. In the edit menu choose
Po i nt group

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Point group

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Point group
A new window will open, as shown in the image below
First select the enable point group option (1.)
Then select C3v (2.) and click O K

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 The point group names a structure according to a set of rules
which define how a molecule transforms onto itself. For example if
you look down on the molecule (with the N in the center and the
3 H-atoms spread out away from you) you can see that if the
molecule is rotated 120 degrees it maps back onto itself. We say
that the molecule has 3-fold rotational symmetry and a C 3 axis.
This is where the 3 in the point group name comes from.

You have now created and manipulated your first molecule!

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Quiz

Draw and manipulate the following molecules:

H 2 O, C H 4 , C O 2

Exercise:
Add labels
Assign bond lengths
Assign Angles
Write the respective Point groups

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Understanding the Optimization Process

Next you are going to optimize your NH 3 molecule, but first I want to
explain what the computer is doing for you and then we will set the job
running.

Let us start by considering the energy E of a molecule. When we solve

the Schrdinger equation Eφ=Hφ under the Born-Oppenheimer
approximation we assume the nuclei are fixed, and we solve for the
electrons (the wavefunction φ) and energy ( E ) .

The dissociation curve of a diatomic represents a potential energy

curve E ( R ) , that is, E dependent on R (the distance between the two
atoms), see the figure below.

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As the nuclei get close together, they repel each other (two positive
charges repel) and the energy goes up. As the nuclei become stretched
and the electrons no longer form a bond, the electron-nuclear
attraction decreases, the energy goes up and the molecule dissociates.

Somewhere in the middle the electrons and nuclei are able to arrange
themselves so that they are stable, we say that the system is in
equilibrium.

When something is in equilibrium we say there are no net forces on the

atoms within a molecule (nothing pushing on them to make them want
to move).

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 When carrying out calculations, the first thing we do is choose the
position of the nuclei, this is the information you have provided in
building your molecule. Rather than specify each position
independently I’m going to define R as a collective coordinate
which represents all the atomic positions.
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We then solve the Schrdinger equation for the fixed nuclear positions,
and obtain an energy E and wavefunction φwhich are dependent on
the frozen position of the nuclei, we write this as: E ( R ) and φ(R1).
This process is called a self consistent field ( S C F ) calculation.
During the S C F calculation we are finding the electronic wavefunction
(φ) that gives the lowest energy (for the fixed nuclei).

The nuclear positions chosen when building the molecule are unlikely
to be the correct ones, and so one must optimize the structure to find
the position of the nuclei that gives the lowest energy E(R o p t ). That is
we need to find the equilibrium or lowest energy geometry (represented
by R opt ) as shown on the figure above.

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First the nuclear positions (R1) are set and an S C F cycle is run to find
the energy E ( R 1 ) and wavefuntion φ(R1). Then we move the nuclei a
small amount to positions represented by R 2 and the S C F cycle gives
us E ( R 2 ) and φ(R2). Then we choose the positions, R 1 or R 2 that give
us the lowest energy, thus if E ( R 2 ) < E ( R 1 ) we choose R2.

As the system moves there will be a sequence of different energies all

dependent on the changing coordinates of the nuclei and electrons. We
are traversing a Potential Energy Surface ( P E S ) , the potential energy
surface E ( R ) for a diatomic has already been shown above. The
process of optimization is shown in the figure below.

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 When the nuclei and electrons are in equilibrium, they experience
no forces trying to shift them one way or another.

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 At equilibrium the slope of the graph is zero, see the figure below.
When the system is not in equilibrium the slope of the E ( R ) graph
is not zero. Thus we now have a criteria for searching for the
structure of a molecule, the structure we want is the one at which
the first derivative of the P E S is zero.

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Optimising a Molecule of NH 3

Bring the window with your NH 3 molecule to the front.

now we are ready to set up the commands that tell the program
how to do the calculation, we tell it
the method: B 3 LY P
the basis set: 6-31G(d,p) and what type of calculation to do:
optimize and frequency analysis)
In carrying out an optimization we are determining the optimum
position of the nuclei for a given electronic configuration, this is
the first step for any quantum chemical calculation.

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Optimization step
From the main menu along the top of the screen (in gaussview) choose
C a l c u l at i o n and then choose G a u s s i a n C a l c u l at i o n Setup...:

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 a new palette will appear (calculation palette). It opens with the
job type tab open. Use the pull down menu under energy to
choose o p t + f r e q (ignore the other stuff that appears)

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then click on the m ethod tab to open it,
use the pull down menu under H a r t re e - Fo c k to pick D F T
find the pull-down menu and choose B 3 L Y P
in basis set choose 6-31G in the first button
type into the additional keywords section: pop=(full,nbo)
don’t change anything else!
pop stands for population analysis, and these extra keywords turn on
some options for examining the electronic structure

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 you should also add a title for your job, so under the ”title” tab
type in something descriptive about the job I used ”nh3
optimization”.
Now you are ready to go! Press submit (button is in the bottom
left of the palette)
a new window will pop-up and telling you that you must save the
file first, press ”save”
a new window will then pop-up and ask you for a file name,
navigate to the folder (2ndyearlab) you created at the beginning
and save your input file. It is important to give your file a
descriptive name otherwise after running a few jobs you will forget
which one is which.

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Draw and manipulate the following molecules:
new window will then pop-up and ask you if you want to submit
the job, press submit!
close the molecule window, this is important as the finished
molecule will look very similar to your starting one and you may
accidentally take the wrong molecule in subsequent sections!
after a small amount of time a window should pop-up saying the
job is completed, you want to open the *.log file.
Note: This time will vary depending on how efficient your computer
resources are...

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 the output (*.out) file contains information that is directly human
readable, the checkpoint file (*.chk) contains information in binary
that is only computer readable. Gausview reads these files and
then graphically represents the information in them.
When using gaussview it can matter which one you look at, use
the *.out file normally, but when you want to visualize molecular
orbitals use the *.chk file.

This is your optimized NH 3 molecule!

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Viewing and Understanding your Optimised NH 3 output

Open your *.out file by choosing F i l e and open in gaussview.

Navigate to your 2ndyearlab folder and open your output file.
Find out some geometric information on the commands palette
click on the button with a question-mark in front of a ruler. This
is the i n q u i ry button and will tell you bond distances if you click
on two atoms, and bond angles if you click on three atoms use the
inquiry button to determine the optimized N -H bond distance and
the optimized H-N-H bond angle, record this information for your
mini-report.
To obtain general information about the job click on the results
tab at the top and choose Summary. This will open a window that
lists important information about your calculation.

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Summary

For every molecule you study, the following key information should be
in your mini-report...
What is the molecule?
What is the calculation method?
What is the basis set?
What is the final energy E ( R B 3 LY P ) in atomic units (au)?
What is the R M S gradient?
What is the point group of your molecule?

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Summary

some important conceptual things to know about how the various

programs integrate.
Gaussian r u n s the jobs (i.e. does all the number crunching)
Gaussview is a separate program which is used to create and edit
files used by Gaussian.
When you submit a job you or Gaussview makes a *.gjf file and
when you look at the output you or Gaussview is looking at a
*.out file
Gaussian also makes a third file, where it stores information in a
machine only readable format these are called checkpoint files
and have the file extension *.chk file. Sometimes we will also use
Gaussview to process information in the *.chk file for us to view
graphically, like the molecular orbitals

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Potential Energy Surfaces

Born-Oppenheimer approx. allows us to separate electronic and

nuclear motion
when nuclei move, the electrons re-adjust quickly
energy of molecule is a function of the positions of the nuclei
potential energy surface describes energy of a molecule in terms of
its structure

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Coordinates for Potential Energy Surfaces

In the absence of fields, a molecules potential energy doesnt change if it

is translated or rotated in space. Thus the potential energy only
depends on a molecules internal coordinates . There are 3N total
coordinates for a molecule (x, y, z for each atom), minus three
translations and three rotations which dont matter (only two rotations
for linear molecules). The internal coordinates may be represented by
simple stretch, bend, torsion coordinates, or symmetry-adapted linear
combinations, or redundant coordinates, or normal modes coordinates,
etc

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Characterizing Potential Energy Surfaces

The most interesting points on P E S s are the stationary points, where

the gradients with respect to all internal coordinates are zero.
M i n i m a : correspond to stable or quasi-stable species; i.e.,
reactants, products, intermediates
T r a n s itio n states: addle points which are minima in all
dimensions but one; a maximum in that dimension
H i g h e r - o r d e r saddle points: minimum in all dimensions but n,
where n > 1; maximum in the other n dimensions.

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Hessian Index

The Hessian index is the number of negative eigenvalues of the force

constant matrix. For a stationary point, this corresponds to the
number of internal degrees of freedom along which that point is a
potential energy maximum. The Hessian index is 0 for minima, 1 for
transition states, > 1 for higher-order saddle points. The Hessian index
also corresponds to the number of imaginary vibrational frequencies

A geometry optimization, when run to completion, will provide a

stationary point geometry. Typically, this is a potential energy
minimum. However, the optimization might get stuck on a saddle
point. A vibrational analysis can verify the nature of the stationary
point via the Hessian index.

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