gOpenmol: Visualization of Electron Density & PES

Example of visualization of electronics properties of a molecule, computed by quantum chemistry program, using gOpenmol program

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

Rangsiman Ketkaew