1. My first Gaussian input
Application
My first Gaussian input

2. Definition of a molecule
communication

3. Cartesian coordinates5 1 2 4 3 x y z C H H H H
3N coordinates
No symmetry considered

4. No symmetry considered:
Internal coordinates
No symmetry considered:
- Z-matrix
(bond) 5
length
angle
torsion 1 C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1
H 1 B4 3 A3 2 D2 B B B B A A A D D 2 4 3
Symmetry considered: C
H 1 B1
H 1 B1 2 A1
H 1 B1 3 A1 2 D1
H 1 B1 3 A1 2 -D1 B A D
How many coordinates does one need to define a CH4 molecule?

5. Internal coordinates Classification:5
Classification:
Type:
(bond)length (C1-H2)
(bond)angle (C1-H2-H3)
torsion angle (H2-H3-C1-H4)
Measurable properties:
proper (C1-H2)
improper (H2-H5)
The set of coordinates has to be consistent and obvious!!! 1 2 4 3

6. Program independent file formats (.pdb)

7. Ethane.pdb 1 4 3 5 2 7 8 6
COMPND ethane
AUTHOR Created by Dave Woodcock at Okanagan University College
AUTHOR
AUTHOR Date revised: Mon Sep 4 08:23: GENERATED BY BABEL 1.6
HETATM C BEN A C
HETATM H BEN A H
HETATM H BEN A H
HETATM H BEN A H
HETATM C BEN A C
HETATM H BEN A H
HETATM H BEN A H
HETATM H BEN A H
CONECT
CONECT
CONECT
CONECT
CONECT
CONECT
CONECT
CONECT
MASTER
END
type
chain x y z
element No
resname
resID
More detailed:

8. Program dependent file formats (.com /.gjf /.hin)

9. Some examples Gaussian (.inp, .com, .gjf) HyperChem (.hin) Orca (.inp)
Molpro (.inp)
MRCC (.inp)
Dalton (.dal)
Different extensions may mean different information content!
Same extension does not mean that those files are compatible!

10. Gaussian09 www.gaussian.com/ Windows OS, Linux OS, Mac X OS
Methods/Model:
MM,
Semiempirical methods (PM3, AM1)
ab initio (HF, MP2, MP3, MP4, CCSD, CCSD(T), CIS, CIS(D) QCISD, QCISD(T)),
DFT,
composite models (CBS-n, Gn)
We use this

11. Definition of a molecule…
Molecule specification (Cartesian, Z-matrix…)
Net charge
Arrangement of the electrons (Electronic state)
Electron spin: s=½
Net spin quantum number: S
Multiplicity: Ms=2S+1
Examples:
H e (↑) S=½ → S=½ Ms=2 (doublet)
H2 2•1e- (↑↓) S=2•½ =1 → S=0 Ms=1 (singlet)
O2 2•8e- (↑↑) S=1 → S=1 Ms=3 (triplet)
O2 2•8e- (↑↓) S=0 → S=0 Ms=1 (singlet)

12. E Few calculations H 1s1 1e- S=0.5 → Ms=2 H2 2e- S=0 → Ms=1
# B3LYP/6-31G* Opt H
0 2 H
1 Hartree = kJ/mol
Doublet
ΔE=Efinal-Einitial
Hartree
SCF Done: E(UB3LYP) = A.U. after 5 cycles [
-(2× )] ×2625.5
= kJ/mol E
# B3LYP/6-31G* Opt H2
0 1 H H AO AO MO
Singlet
Hartree
SCF Done: E(RB3LYP) = A.U. after 3 cycles

13. Few more calculations C 6e- S=1 → Ms=3 O 8e- S=1 → Ms=3 Triplet
# B3LYP/6-31G* Opt C
0 3 C
Triplet
SCF Done: E(UB3LYP) = A.U. after 9 cycles
# B3LYP/6-31G* Opt O
0 3 O
Triplet
SCF Done: E(UB3LYP) = A.U. after 10 cycles

14. Two more calculations O2 16e- S=1 → Ms=1 O2 16e- S=0 → Ms=3
# B3LYP/6-31G* Opt O2
0 1 O O
excited state
Singlet
SCF Done: E(RB3LYP) = A.U. after 6 cycles
[ –( )]
× = kJ/mol
# ROB3LYP/6-31G* Opt O2
0 3 O O
Triplet
ground state
SCF Done: E(UB3LYP) = A.U. after 7 cycles

15. Calculations of atoms