A Quick Introduction to Gaussian &

GaussView

SCH 207: Introduction to Computational Chemistry

Lucy Kiruri, Ph.D.

Chemistry Department
Kenyatta University
 Agenda

 Introduction
 Capabilities
 Input File Preparation
 Gaussian GUI – GaussView
 Run G03/G09 Jobs
 Hands-on Experiments
 Course Goal

 What Gaussian/GaussView packages are

 How to prepare input files via GaussView
 How to run G09 jobs on local desktop
 How to view G09 results
 Learn selected advanced topics
 Hands-on experiments
 Gaussian & GaussView

Gaussian is a general purpose

electronic structure package for use in
computational chemistry. For SCH
207, Gaussian 09 will be used.

Most widely used computational

chemistry package. The latest release
is Gaussian 16 B02.
 GaussView

GaussView is a graphical user interface (GUI)

designed to be used with Gaussian to make
calculation preparation and output analysis
easier, quicker and more efficient. The version
installed is 6.0.16.
Creae New Job
 Gaussian 03/09/16 Functionality
 Gradients/Geometry optimizations
 Frequencies (IR/Raman, NMR, etc.)
 Other properties
 Populations analyses
 Electrostatic potentials
 NMR tensors
 Several solvation models (PCM, COSMOS)
 Two and three layer ONIOM – E, grad, freq
 Transition state search
 IRC for reaction path
 Gaussian Input File Structure
.com or .gjf (Windows version)
Free format, case insensitive
Spaces, commas, tabs, forward slash as delimiters between
keywords
! as comment line/section
Input file divided into sections
(in the order)
 Link 0 commands (%)
 Route section – what calculation is to do
 Title
 Molecular specification
 Optional additional sections
Input File – Cartesian coordinates

%chk=F:\sch207\water.chk !checkpoint file

# hf/3-21g geom=connectivity !Route section
!Blank line
Water optimization !Title section
!Blank line
01 !Charge & multiplicity
O 0.00000000 0.00000000 0.00000000 !Geometry in
H 0.00000000 0.00000000 0.96000000 Cartesian
H 0.90493583 0.00000000 -0.32045459 coordinates
!Blank line
1 2 1.0 3 1.0
!Geom-connectivity
2
3
Input File – z-matrix

%chk=F\sch207\water1.chk !checkpoint file

# hf/3-21g geom=connectivity !Route section
!Blank line
Water energy !Title section
!Blank line
01 !Charge & multiplicity
O
H 1 B1 !Geometry z-matrix (atom
H 1 B2 2 A1 connectivity)
!Blank line
B1 0.96000000 !Geometry z-matrix
B2 0.96000000 (variables)
A1 109.50000032
!Blank line
1 2 1.0 3 1.0
2 !Geom-connectivity
3
 Basis Set

Why are basis sets required: MO-LCAO!

Basis sets are atomic orbitals (AOs).

Examples:
Minimal basis set (e.g., STO-3G)
Double zeta basis set (DZ)
Split valence basis Set (e.g., 6-31G)
Polarization and diffuse functions (6-31+G*)
Correlation-consistent basis functions (e.g., aug-cc-pvTZ)
Pseudopotentials, effective core potentials
 GaussView
GaussView 6.0 makes the use of Gaussian 09 to be
simple and straightforward:

Sketch in molecules using its advanced 3D Structure

Builder, or load in molecules from standard files.

Set up and submit Gaussian 03 jobs right from the

interface, and monitor their progress as they run.

Examine calculation results graphically via state-of-the-art

visualization features: display molecular orbitals and
other surfaces, view spectra, animate normal modes,
geometry optimizations and reaction paths.
GaussView: Build
 GaussView: Setup

• Molecule specification input is set up automatically.

• Specify the input for any Gaussian 09 calculation
type.

1. Select the job from a pop-up menu. Related options

automatically appear in the dialog.
2. Select any method and basis set from pop-up menus.
3. Set up calculations for systems in solution. Select the
desired solvent from a pop-up menu.

 Start and monitor local Gaussian jobs.

 Start remote jobs via a custom script.
GaussView: Setup
 GaussView: Showing Results
Show calculation results summary.
Examine atomic changes: display numerical values or color atoms by charge (optionally
selecting custom colors).
Create surfaces for molecular orbitals, electron density, electrostatic potential, spin density, or
NMR shielding density from Gaussian job results.
Display as solid, translucent or wire mesh.
Color surfaces by a separate property.
Load and display any cube created by Gaussian 03.
Animate normal modes associated with vibrational frequencies (or indicate the motion with
vectors).
Display spectra: IR, Raman, NMR, VCD.
Display absolute NMR results or results with respect to an available reference compound.
Animate geometry optimizations, IRC reaction path following, potential energy surface scans,
and BOMD and ADMP trajectories.
Produce web graphics and publication quality graphics files and printouts.
Save/print images at arbitrary size and resolution.
Create TIFF, JPEG, PNG, BMP and vector graphics EPS files.
Customize element, surface, charge and background colors, or select high quality gray
scale output.
Surfaces
 Reflection-Absorption Infrared Spectrum of AlQ3

N O

O Al N

N O

752
Wavenumbers (cm-1) 1473
1386
1116 1338 1580 1605

800 1000 1200 1400 1600

 GaussView: VCD
(Vibrational Circular Dichroism) Spectra

GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the
VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin,
P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
 Advanced Topics

• Potential energy surfaces

• Transition state optimization
• Thermochemistry
• NMR, VCD, IR/Raman spectra
• NBO analysis
• Excited states (UV/visible spectra)
• Solvent effect
• PBC
• ONIOM model
• ABMD, BOMD, etc.
 Potential Energy Surfaces
A PES displays the energy of a molecule as a
function of its geometry

Energy is plotted on the vertical axis, geometric

coordinates (e.g bond lengths, valence angles,
etc.) are plotted on the horizontal axes

A PES can be thought of as a hilly landscape,

with valleys, mountain passes and peaks

Real PES have many dimensions, but key feature

can be presented by a 3 dimensional PES
Model Potential Energy Surface
 Calculating PES in
Gaussian/GaussView

Use the keyword “scan”

Then change
input file properly
Transition State Search
TS Search in Gaussian
 TS Search in
Gaussian/GaussView
 Animation of Imaginary Frequency

Check that the imaginary

frequency corresponds to
the TS you search for.
Intrinsic Reaction Coordinate Scans
 Input for IRC Calculation

StepSize=N
Step size along the reaction path, in units of 0.01 amu-1/2-Bohr. The default is 10.

RCFC
Specifies that the computed force constants in Cartesian coordinates from a
frequency calculation are to be read from the checkpoint file. ReadCartesianFC
is a synonym for RCFC.
IRC Calculation in GaussView
Reaction Pathway Graph
 Thermochemistry
from ab initio Calculations
 Thermochemistry
from ab initio Calculations
Thermochemistry from frequency
calculation
Calculating Solvent Effect
Calculating Solvent Effect