Mod:gaussview
See also: Laptop use, Windows mode, Linux mode, Programs, Module 1, Module 2, Module 3,Writing up
About Gaussian and GaussView
Gaussian is a set of programs for carrying out electronic structure calculations. Many different methods for carrying out total energy calculations of molecules are implemented, including molecular mechanics (or force field) methods, but mainly semi-empirical and ab initio molecular orbital-based methods. In addition, energy derivatives as a function of inter-nuclear coordinates can be calculated, making it possible to optimise and characterise minima and transition structures on molecular potential energy surfaces.
For more information, see:
D. A. McQuarrie: Quantum Chemistry (University Science Books, 2008)
F. Jensen: Introduction to Computational Chemistry (Wiley, 2007)
C. J. Cramer: Essentials of Computational Chemistry (Wiley, 2006)
Learning to use GaussView
Before you can run calculations on the various molecules you will be looking at, you will need to know how to submit them as "jobs" to Gaussian. The easiest way to do so is to use GaussView to create the molecule and tell Gaussian what to calculate and how.
Basics
Everything you need to make your molecular structure is available on the GaussView menu bar and it works primarily on a click and drag system. The first set of 11 icons from the left are what you need to create the desired structure.
They are:
Element Fragment - Brings up a periodic table for you to select an element and then it's structure and bonding.
Ring Fragment - This allows you to quickly create common compound rings.
R-Group Fragment - Gives easy access to common side chains.
Biological Fragment - Gives a selection of Amino Acids and Nucleosides to add to your molecule.
Custom Fragment - This allows you to save and load custom built structures.
Modify Bond - Clicking on two atoms to create bonds of varing types and set the distance between atoms.
Modify Angle - Clicking on three atoms allows you to specify the angle between them.
Modify Dihedral - Clicking on four atoms allows you to specify the dihedral angle between them.
Inquire - clicking two atoms shows you the distance between them, clicking three shows you the angle formed and clicking four shows you the dihedral angle formed.
Add Valence - Adds a Hydrogen bond to the selected atom.
Delete Atom - Deletes the selected atom.
Three sets of tutorial exercises are available:
Click here for the BH3 Introduction Module
Work through as much as you need to - you may find you need to revisit the tutorials after attempting some of the exercises.
See also: Laptop use, Windows mode, Linux mode, Programs, Module 1, Module 2, Module 3,Writing up
