GAUSSIAN TUTORIAL

AN INTRODUCTION TO COMPUTATIONAL CHEMISTRY USING

G16W AND GAUSSIAN VIEW SOFTWARE

Mu Yuguang

This is a quick tutorial that will help you to make your

way through the first steps of computational chemistry
using Gaussian software (G16). The tutorial is oriented
to beginners and describes in detail the most used
calculations done using G16. However, the theoretical
basis of these calculations will not be covered here. If
you are interested in understading the details, please
refer to textbooks targeting this subject. I found [1] and
[2] very helpful, and strongly recommend to take a look
at these wonderful books.

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1 PROGRAM SPECIFICATIONS
Gaussian 16W (G16) is a computational chemistry program that
runs on any modern Windows 64-bit PC.
VISUALIZATION SOFTWARE: Gaussian View is used for
visualization.
VIDEO TUTORIALS If you prefer watching video tutorials for a
better understanding, please see below:
• Part 1:
• https://www.youtube.com/watch?v=mm-LY_R5JM4
• Part 2:
• https://www.youtube.com/watch?v=dqKWfXsEcWs

1.1 INPUT
The input for G16 can have the following extensions:

• Gaussian Input File: .gjf

• Batch Control File: .bcf

• Avogadro Input File: .com

• Text File: .txt

The input can be done manually or come from Gaussian View.
G16’s input consists of the following parts, shown on Figure 1:

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 Figure 1: G16 input window

This window appears when you click on File→ Open→ ... in the

main G16 window.

• The first line : specifies the path to the file you just loaded.

• Section: specifies the name of the checkpoint file (.Chk)

• Route Section: specifies the basis set, the theoretical model

and the type of job you want to perform

• Title Section: specifies the name of the job (for the user’s ease
only)

• Charge, Multipl.: specifies the charge and spin multiplicity of

the current molecule separated by a space.

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 • Molecule Specification: specifies the atoms and their
coordinates ← this is what we want from the ChemDraw and
Avogadro input, otherwise, we would need to calculate the
coordinates by hand.
More details on each section of the input is available in section
(3.0)
1.2 OUTPUT
To run the G16 job, click on the RUN button, on the right panel of
the Job Entry window (Figure 1). The output has only one
extension: .out. You will be prompt to save the output file before
closing G16 program.
1.3 VISUALIZATION
This tutorial will use Gaussian View software for visualization of the
G09 output. Open the .out file in Gaussian View, your input
molecule should appear on the view screen.
1.4 COMPUTATION MODEL
The mathematical models used to do the computations are called
FEM (Final Element Method) and Symplex method. Using matrices,
this method cuts the N-dimensional space into small sub-systems
that can be described by N linear equations. These equations can
be solved as soon as one of them is solved. Therefore, one must
take a guess of the solution and then, recursively solve all the other
ones. Once all solutions are obtained, the initial guess can be
modified and the calculations repeated. This process is run until the
new solution outputs the same result as in the previous iteration.
This is called convergence.
Because the initial guess can be very far off the real value, many
thousands of iterations are often needed. The basis set selected
influences, among other, the quality of the guesses, while the
theoretical model influences the type of calculations that the
matrices will be subjected to.
The calculation stops as soon as the result converges, however
convergence does not mean that the system reached its minimum.
It is very likely that the minimum outputted is actually only a saddle
point on the potential surface, but the program will not be aware of
this. The user must be careful with this, and always perform a

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check of stability of the system. This is done by perturbing the
"stable" system and re-calculating the minimum. If the output is the
same, one can assume that the energy obtained is the total
minimum. FOR MORE DETAILS ON THE MATH: [3]

2 FIRST LOOK AT A COMPUTATION

This section will describe how to do a simple calculation in G16.
All the parts of this procedure (and more) are explained more in
details in corresponding sections. Let’s take a look.

2.1EXAMPLE 1: SINGLE POINT ENERGY OF WATER

Let’s calculate the Single point energy of water.
For this, we will first open Gaussian View and draw the molecule
(Figure 2).

Figure 2: water molecule in Avogadro

Now, find the Extensions button on the top task bar, and select
"Calculate" and then “Gaussian Calculation Setup…”. A new
window should appear (Figure 3).

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Figure 3: Gaussian Calculation Setup

Now we need to choose several parameters:

 The Job Type “Energy”, means a Single Point energy.
 Method part: can choose DFT, by default, using B3LYP
method,
for Basis Set: 6-31 + (d,p)
charge and Spin
Multiplicity = 2* S +1

If S=0; no net spin; them Mult = 1, Singlet

If S=1/2 ; Mult = 2*1/2+1 = 2, Doublet

S=1/2+1/2=1; Mult = 2*1+1 = 3 , Triplet

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 Figure 4 Method

 Title
type in “water_test”
 Link 0
If your computer has multiple cores, choose Shared
Processors 2 or 3 or 4
Specify the check point file location: Chkpoint File:

 Pop.
Level of output , choose “Full”

Finally can click Preview, show all your inputs for this
calculation.

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 Figure 5 Preview

After all the parameters are set properly, click on the Submit
button. This will begin the calculation after prompting you to save
the final output. Save as water_test.out.
The job is over once the message "Processing Complete" is
shown as on Figure 6. Don’t forget to read the awesome quote at
the end of the output! Now, let’s analyze the results. To see clearer,
you can load the output into the Notepad, by clicking on the
magnifying glass button in the top right corner of the window. For a
detailed overview of the output, see the video tutorials.
Right before the Population analysis you will see the following:
SCF Done: E(RB3LYP) = -76.4337124058 A.U. after 10
cycles

This is the single point energy (similar to free energy of formation)

of water! (units = Hartrees)

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 1 hartree = 27.2107 eV = 627.503 kcal/mol = 2625.5 kJ/mol

Figure 6: Water SP calculation Job successfully

2.2 EXAMPLE 2: OPTIMIZATION OF WATER

Let’s optimize the geometry of a water molecule. Like the
above water, build a water. Choose “Gaussian Calculation
Setup”. In the Job Type, choose “optimization” and save the
Gaussian job file as “water_opt.gjf”.
After the calculation finishes, open the “water_opt.chk” file. You will see
there are 3 frames of water structures Figure 7,.. And Click the left top
green round button, will illustrate the optimization process.

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Figure 7: Optimization of water.

Now we can check the effects of the optimization:

Bond length:

Click the “Modify Bond” button. Then choose two atoms on the molecule
panel. You can find the bond length between the two atoms.

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Bond angle

Similar Click the “Modify Angle” button. Then choose three atoms on the
molecule panel. You can find the bond angle formed by the three atoms

Compare the bond length and bond angle before and after optimization.

2.3 EXAMPLE 3: MOLECULAR ORBITALS VISUALIZATION OF

WATER
Open “water_test.log” file with any plain text editor, such as
Notepad++.
Go to “Population analysis using the SCF Density” section. You
will find “Molecular Orbital Coefficients”.

Figure 8. Molecular orbital coefficients

These numbers (red circle) indicate how importance of each
atomic orbital contributed to each molecular orbital.

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 Here we can find the HOMO/LUMO energy gap, the difference
between HOMO and LUMO eigenvalues, which correspond to
their energies (the blue circles in Figure 8). The HOMO is
designated by the last orbital that is labeled by an "O", while the
LUMO is the first orbital labeled by a "V". In this case, the
HOMO is orbital 5, and the LUMO is orbital 6. Notice, that the
HOMO has a negative eigenvalue, while the LUMO has a
positive value.
THE HOMO/LUMO GAP The difference in the eigenvalues of the
LUMO and the HOMO will give you the HOMO/LUMO gap (units
are Hartrees by default).
NOTE: If you actually need the HOMO/LUMO Gap energy you
shouldn’t take simply the difference between the HOMO and the
LUMO eigenvalues. For these cases, you should compute
electronic transitions.
Now, let’s visualize these orbitals.
Open the file “water_check.chk” using GaussianView. Choose
the “MOs” option in the “Tools” function bar.

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 Click “Visualize” button (red circle), highlight/select the first 6
orbitals ( blue circle), then Click “Update…” (yellow circle).

Then you can see the wavefunction/molecular orbital by click

the small box on the right side.

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2.4 EXAMPLE 4: THE ENERGY OF STEREISOMERS AND
SCALING FACTORS (BUTENE)
Let’s compare the output of a geometry optimization for the cis
and trans isomers of butene. First, draw cis-butene in Avogadro,
optimize its geometry. Generate the G16 input file selecting
Geometry Optimization, using B3LYP model with a 6-31G(d)
basis set. To see how these steps are done in details, refer to
example 1 and 2. Save as cis_butene.com. Repeat the same for
trans-butene. Save as trans_butene.com.

Trans-butene

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 Cis-butene
Run the jobs in G16. Save as their respective names with the .out
extension. You can visualize the molecules in Avogadro, but we will
focus on their SCF energies:
Cis-butene: SCF Done: E(RB3LYP) = -157.224311885
A.U. after 12 cycles

Trans-butene: SCF Done: E(RB3LYP) = -

157.226083227 A.U. after 12 cycles

Our data :

trs: E(RB3LYP) = -157.238521260

cis: E(RB3LYP) = -157.236404776

the energy difference is 0.00211 Hartree = 5.54

kJ/mol

As proved by the energies, the trans configuration is

more stable than the cis one.

3. Using Gaussian validates the paramagnetic state of O 2

molecule.

Hints:

1. Perform 2 calculation by selecting different spins

of O2.

2. Choose optimization.

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 3. Compare the final energies of the two spin state.

4 REFERENCES
1. Young, D. Computational Chemistry: A Practical Guide for
Applying Techniques to Real World Problems; John Wiley &
Sons, inc: USA, 2001.
2. Jensen, F. Introduction to computational Chemistry, 2nd ed.;
John Wiley & Sons, inc: England, 2007.
3. • http://math.nist.gov/mcsd/savg/tutorial/ansys/FEM/

• http://en.wikipedia.org/wiki/Finite_element_method

• http://http://www.britannica.com/EBchecked/topic/430575/
optimization/235508/The-simplex-method
• http://www.math.cornell.edu/~web401/matt.simplex.pdf

4. C.-K. Skylaris, CHEM3023: Spins, Atoms and Molecules,

Lecture 6: Basis Sets.
(http://www.southampton.ac.uk/~compchem/other/CHEM302
3/ chem3023_L6.pdf)
5. C. David Sherrill, Basis Sets in Quantum Chemistry
(http://vergil.chemistry.
gatech.edu/courses/chem6485/pdf/basis-sets.pdf)
6. http://www.gaussian.com/g_tech/g_ur/m_basis_sets.htm
7. http://www.gaussian.com/g_tech/g_ur/g16help.htm
8. Prof. Ephraim Eliav, Computational Chemistry Lab
2011(http://www.tau. ac.il/~ephraim/complab.html)
9. David Lai Gwai Cheung, Structures and Properties of Liquid
Crystals and Related Molecules from Computer Simulation
(http://cmt.dur.ac.uk/ sjc/thesis_dlc/thesis.html)
10. Foresman, J.B.; Frisch, A. Exploring Chemistry with
Electronic Structure Methods, 2nd ed.; Gaussian, Inc:
Pittsburgh, PA, 1996.

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11. Computational Chemistry Comparison and Benchmark
DataBase: Precomputed vibrational scaling factors
(http://cccbdb.nist.gov/vibscalejust.
asp)
12. Joseph W. Ochterski, Ph.D, Vibrational Analysis in Gaussian
(http://www. gaussian.com/g_whitepap/vib/vib.pdf)
13. Joseph W. Ochterski, Ph.D., Thermochemistry in Gaussian
(http://www. gaussian.com/g_whitepap/thermo/thermo.pdf)
14. http://www.gaussian.com/g_tech/g_ur/k_freq.htm
15. http://www.gaussian.com/g_tech/g_ur/k_stable.htm
16. Dr Patricia Hunt, Year 2, Lecture 7: Molecular Orbitals and
Population Analysis
(http://www.huntresearchgroup.org.uk/teaching/teaching_
comp_chem_year4/L7_bonding.pdf)
17. Theoretical Chemistry Institute of the University of Wisconsin,
What Are NBOs (and Other "Natural"-Type Orbitals)?
(http://www.chem.wisc.
edu/~nbo5/web_nbo.htm)
18. Dr. Kalju Kahn, Description of Electronically Excited States
(http://web.
chem.ucsb.edu/~kalju/chem126/public/elspect_theory.html)
19. Chemistry at Sheffield Hallam University, UV-Vis. Absorption
Spectroscopy Theoretical Principles
(http://teaching.shu.ac.uk/hwb/chemistry/
tutorials/molspec/uvvisab1.htm)
20. http://www.gaussian.com/g_tech/g_ur/k_td.htm
21. E. Lewars, "Computational Chemistry", Kluwer, New York,
2003.
22. http://www.gaussian.com/g_tech/g_ur/k_scan.htm
23. http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

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