gOpenmol: Visualization of Electron Density & PES
Example of visualization of electronics properties of a molecule, computed by quantum chemistry program, using gOpenmol program
Download gOpenmol --> https://research.csc.fi/-/gopenmol_download
Step 1: Calculate electronic structure of Naphthalene molecule using following Gaussian input file
%chk=napthalene.chk
%mem=2GB
%nprocs=2
#p Opt B3LYP/6-31g(d) GFInput iop(6/7=3) pop=full
Opt of Napthalene using B3LYP/6-31g(d) for ESP visualization
0 1
C 0.7236038 2.506637 -8.140115E-12
C 1.432963 1.277991 -8.140115E-12
C 0.7236038 0.04934528 1.435729E-12
C -0.6951143 0.04934528 1.101157E-11
C -1.404473 1.277991 2.058742E-11
C -0.6951143 2.506637 2.058742E-11
C -1.404473 -1.179301 1.101157E-11
C -0.6951143 -2.407947 1.435729E-12
C 0.7236038 -2.407947 -1.771596E-11
C 1.432963 -1.179301 -2.72918E-11
H 1.260564 3.43668 -8.140115E-12
H 2.506883 1.277991 -1.53887E-11
H -2.478394 1.277991 2.7836E-11
H -1.232075 3.43668 2.7836E-11
H -2.478394 -1.179301 1.826016E-11
H -1.232075 -3.337989 8.684312E-12
H 1.260564 -3.337989 -2.496454E-11
H 2.506883 -1.179301 -4.178897E-11
Gaussian output files include
1. napthalene.log
2. napthalene.chk
Step 2: Convert napthalene.chk to *.fchk and *.cube files using following commands
1. napthalene.fchk (generated from napthalene.chk by command $ formchk napthalene.chk)
2. napthalene.cube (generated from napthalene.fchk by command $ cubegen 0 mo=6 napthalene.fchk napthalene.cube 40 h)
The procedure of creating a Contour plot and Cusplane for the Naphthalene molecule
Step 3: Create a surface
Click File --> Import --> Coords:
Select "Gaussian"
Browse to formatted checkpoint file, such as Browse --> select "napth.FChk"
Open the file and click Apply
Click Run --> gCube2plt
Select Input file --> Browse --> select "napth.data"
Select Output file --> select "napth.plt"
Click Apply
Select Plot --> Contour --> File name:
Click Browse --> select "napth.plt"
Click Open and Import
Click Plot --> Cutplane
Choose "XZ-plane" and apply
Choose "YZ-plane" and apply
Define the value of position of YZ-plane --> เลือก set coord เป็น "1.21"
Choose Plot --> Contour Scale:
Set Max = "0.3"
Click display to "on"
Click Apply
Clicl Plot --> Cutplane
Set Min = "0" for XZ and YZ, and click Apply
Set Max = "0" for XZ and YZ, and click Apply
Rangsiman Ketkaew