A Computational Study of SO2, SH2 and S3
Using Gaussian 03 and GaussView
By Louis Scudiero
Washington State University
January 2006
Introduction
Computational chemistry has become an essential tool in many areas of
chemistry. Calculations on molecules based on QM are becoming an important
complement to experiments and are used to explore new chemistry. To expose
undergraduate students to theoretical models we have integrated computational chemistry
into our traditional physical chemistry laboratory and designed three laboratory exercises.
The first computational lab, a study of SO2, SH2 and S3 molecules was written in the
way that guides the student in the use of GaussView 3.09 which is interfaced with
Gaussian 03. During this first lab students will explore the different capabilities of
GaussView by a simple use of the mouse (pointing and clicking on the actions offered by
the menu).
GaussView is a graphical user interface designed to help students to prepare input for
submission to Gaussian and to examine graphically the output that Gaussian produces.
GaussView was design as a front-end/back-end processor to aid in the use of Gaussian.
The software provides three main benefits to Gaussian users.
1) Advanced visualization of very large molecules
2) Makes easy to set up many types of Gaussian calculations
3) Lets you examine the results of Gaussian calculations using a variety of graphical
techniques.
Objectives
The purpose of this lab is to introduce GaussView and Gaussian to undergraduate
students through a simple exercise. Students will get familiar with the software and its
numerous features.
In this first computational lab students would have to sketch the three molecules using the
“Builder” palettes and element table, and then compute the vibrational frequencies using
two different methods (the Mollet-Plesset and the Hartree-Fock methods). Students have
to save the sketched molecules and the IR spectrum for each molecule and assign the
bands. They have to visualize the normal modes and discuss the results produced by the
two computational methods.
In the case of SO2, students will compare computational and experimental data. They
need to discuss the accuracy of the two methods (Mollet-Plesset versus Hartree-Fock).
For instance, which method gives the most accurate results when compare to experiment
values and why?
1
Getting Started
•
•
•
Double click on the X , a batch window will appear
At the prompt sign type ssh –Y [email protected], and the
password. Then type gv (for GaussView)
New windows will then appear as seen below
1 Builder, the molecule fragment is displayed in this area
2 Element table and builder palettes is used to sketch the molecule
3 In this window the partial or entire molecule is viewed. Selection of
atoms for modifications such as angle, bond length, atom deletion,
labeling etc … is done here.
2
1
3
GaussView
with Builder
Element Table
And
Builder palettes
Display
These windows are used to sketch the molecules and to submit jobs to Gaussian 03. The
output of calculations can then be printed, saved or simply displayed.
•
Setting up calculations with GaussView
2
The “Calculation Setup Window” seen below allow students to set up Gaussian 03
jobs in a simple and straightforward manner.
GaussView can graphically display a variety of Gaussian 03 calculation results, including
the following:
a) Molecular orbitals
b) Atomic charges
c) Surfaces from the electron density, electrostatic potential, NMR shielding
density, and other properties. Surfaces may be displayed in solid, translucent
and wire mesh modes.
d) Surfaces can be colored by a separate property
e) Animation of the normal modes corresponding to vibrational frequencies
f) Animation of the steps in geometry optimizations, potential energy surface
scans, intrinsic reaction coordinate (IRC) paths, and molecular dynamics
trajectories from BOMD and ADMP calculations.
3
You can visualize a variety of computed spectra including IR, Raman, NMR, P and U
Depolarization and VCD etc …
Students are encouraged to explore as many of the features as possible if not all and
become familiarized with this software.
Sketching the molecules and computing the IR vibrational frequencies
For this first computational lab
1) Sketch the three different molecules (SO2, SH2 and S3) using the Builder.
2) Submit calculations for vibrational frequencies using the 2nd order MollerPlesset (MP2/3-21G) perturbation theory and the Hartree-Fock (STO-3G)
method. From the menu select “Calculation” and “Gaussian”. The window
“Gaussian Calculation Setup” will appear. In this window, select Job Type
then Frequency. Click then Method and select the method you want to use.
Use 3-31G as Basis Set for this calculation and “Submit”.
3) Use the results from both methods to animate the normal modes (stop the
animation and save the image for each mode using the “save image …” To
animate the normal modes you need to select first from the menu “Results” and
then “Frequency”. The window “G1:M1:V1 Display Vibrations” will appear
with the results. Select a frequency and click on “Start”. This will animate the
normal modes for the selected frequency. To see the vectors associated with the
motion of the atoms click on “show Displacement vectors” and to see the
dipole vector select “show Dipole Derivative Unit Vector” and a brown arrow
will appear which indicates the magnitude and direction of the dipole moment.
4) Visualize the IR spectrum for each molecule and assign the bands. To display
the spectrum simply select “Spectrum”.
5) For SO2 only compare computational results with experimental data. Which
computational method gives the best results and why?
6) If time permits explore and submit more calculations using different methods.
Could you find a method that produces the results that closely match the
experimental measurements?
4