Computational Chemistry Lab Activity

Calculating the bonding of Lithium hydride (LiH)

You need to obtain a copy of a computational chemistry software package called "GAMESS: General and Atomic Molecular Electronic Structure System". It is a free software package and is available for both Macs and PCs. You can download the software from:

http://www.msg.ameslab.gov/GAMESS/GAMESS.html
How you install and run GAMESS will be a little different for the two different machines (Macs or PCs). Contact Bob Gotwals (gotwals@unc.edu) if you need some help with installation or running the code.
For the LiH project, you need this input file. You can cut and paste this text into a text editor (SimpleText or TextEdit for Macs, NotePad for Windows machines), or you can download the file in text format.
```
 $CONTRL SCFTYP=RHF $END
 $BASIS GBASIS=STO NGAUSS=6 $END
 $DATA
LiH for plot. . . 
CNV 4

LITHIUM 3.0 0.0 0.0 -1.00
HYDROGEN 1.0 0.0 0.0 1.00
 $END
 $GUESS GUESS=MINGUESS $END
 $ELDENS IEDEN=1 WHERE=GRID OUTPUT=PUNCH MORB=2 $END
 $GRID ORIGIN(1)=0,-2,-2 XVEC(1)=0,-2,2 YVEC(1)=0,2,-2 SIZE=0.1
 $END
```
Pay attention to the spacing. Note that there is a space in front of each of the lines that start with a "$" sign.
What the students do is to simply change the coordinate of the Z-axis. In this example input file, the bond length is 2.0 angstroms (-1 for lithium, 1 for hydrogen). Nothing else in the input file needs to be changed.
Once you run the input file with GAMESS, you get two new files: a LOG file, and a DAT (data) file. It is the data file that contains your electron density data. This is the file that was used in the December workshop. Open this file with Excel, do the filtering of the data (starting on line 33, the dataset below where the datafile says "ELECTRON DENSITY, IPOINT,X,Y,Z,EDENS". Don't forget to delete out the last two lines of the datafile that have some extraneous data.

Use Gnuplot to do the visualization. It is helpful to put the datafile in the Gnuplot folder, so that Gnuplot can easily find the data. The instruction set that we used (with a few additions) in the December workshop were:

gnuplot> splot "lih_dat.txt"
gnuplot> set view 90,90
gnuplot> replot
gnuplot> set view 60,60
gnuplot> replot
gnuplot> set dgrid3d 50,50,5
gnuplot> set contour base
gnuplot> set cntrparam levels 50
gnuplot> set nokey
gnuplot> set title "LiH Visualization of Electron Densities"
gnuplot> set cntrparam bspline
gnuplot> replot
gnuplot> exit

Depending on your classroom situation, what I have done with this lab is to have several groups of students construct visualizations at different bond lengths. Then all of the students can display their visualizations, and the entire class can see how the orbitals are changing as the atoms get closer.