Gaussian4beginners

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If you want to learn how to use Gaussian, please take the files below and follow the instructions. The documents were prepared for the Master on Computational Chemistry and are a guide to develop some simple calculations.

File:General.pdf <- In this document you will find the general instructions to follow.

File:Guions 0809.pdf <- In this document you will find the systems to study.

Search reactants and products:

0.- You may want to make a look at Linux & Unix

1.- Read the general instruction on File:General.pdf and chose some of the reactions to study from the file attached File:Guions 0809.pdf.
2.- Draw the reactant or product of the reaction with GaussView (call it from kimik as gview; Gauss View)
3.- After drawing them, go to "Calculate" menu and chose "Gaussian". In the menu, chose "Opt+Freq" (Optimization and Frequencies calculations), 
then the "semiempirical" method "AM1"& Press on "Retain".
4.- Save the files as input files, namefile.in. (The GaussView default is namefile.com, save it as namefile.in in GaussView or with a 
"mv namefile.com namefile.in" in kimik. Edit it in kimik (vi namefile.in) and try to understand the commands that appear on it.
5.- Send them to the queue; "qs 1 s g03 namefile.in"; more information about queues on KIMIK:
6.- Once finished,open the namefile.out with gview or molden check if the geometries correspond to the Reactant and products you wanted.
7.- Now, open namefile.out with vi and to get the energies type the command '?Energy= ' (with the blanck space), find the highlighted line and save the Energies in an Spreadsheet. Compute the difference in energy between reactant and 
products (be carefull outputs give energies in hartree)
8.- Run single point calculations "b3lyp/6-31g" on the AM1 geometries you obtained before. Open the optimized geometries, wich you can find in the output file with the command '?Standart orientation'. Copy the number below XYZ line, 
and use them as input for new calculation. Don't forget to remove the first column. Open your new input file vith Gview, chose in the "Calculate" & "Gaussian" menu: "Energies" & "DFT" & "b3lyp" & "6-31G".
9.- Open your new output file with vi, the energies can be found with the 'Done' command (first highlighted line, near ' E(RB+HF-LYP)').
10.- Copy theese Energies on the spreadsheet and compare this energies with the ones obtained with AM1.

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Run reaction coordinate searches between reactants and products of the chosen reactions:

1.- That is take the geometry of your reactant or product, thing which is the geometrical parameter that changes the most along the reaction.
2.- Measure this parameter in the reactants and products.
3.- Run optimization calculations freezing this parameter at different values (ranging from the value in reactants to the value in products, 
or viceversa). To do so, use the command "opt=(modredundant)" in the command line and add what you want to freeze after the coordinates      
(http://www.gaussian.com/g_ur/k_opt.htm look for Modredundant), and send them to kimik as before "qs 1 s g03 namefile.in"
4.- Plot the energies you obtain for the optimizations with the frozen parameter versus the value of this parameter. 
Include the values of the reactant and product. You should obtain something similar to a Gaussian.
5.- The top of this curve is an structure likely to be close to the transition state between reactants and products 
(more likely if you chose an appropiate parameter)

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Find the Transition states between reactant and products:

1.- Take the geometry of the maximum of the coordinate (the optimized geometry). An send it to optimize as a Transition State 
"opt=(ts,noeigentest,calcfc) freq"
2.- Run a single point calculation on the Transition state at b3lyp/6-31g level, as explained above.