My first Gaussian input Application My first Gaussian input http://www.kollewin.com/blog/density-functional-theory/

Definition of a molecule communication

Cartesian coordinates 5 1 2 4 3 x y z C 0.000000 0.000000 0.000000 H 1.070000 0.000000 0.000000 H -0.356662 1.008807 0.000000 H -0.356670 -0.504398 -0.873652 H -0.356670 -0.504398 0.873652 3N coordinates No symmetry considered

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 B1 1.070 B2 1.070 B3 1.070 B4 1.070 A1 109.471 A2 109.471 A3 109.471 D1 -120.000 D2 120.000 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 B1 1.070 A1 109.471 D1 -120.000 How many coordinates does one need to define a CH4 molecule?

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

Program independent file formats (.pdb)

Ethane.pdb 1 4 3 5 2 7 8 6 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 COMPND ethane AUTHOR Created by Dave Woodcock at Okanagan University College AUTHOR email:djw_bcca@yahoo.ca AUTHOR Date revised: Mon Sep 4 08:23:32 2000 GENERATED BY BABEL 1.6 HETATM 1 C BEN A 1 0.000 0.000 0.000 1.00 0.00 C HETATM 2 H BEN A 1 -0.360 -0.514 -0.891 1.00 0.00 H HETATM 3 H BEN A 1 -0.360 1.029 0.000 1.00 0.00 H HETATM 4 H BEN A 1 -0.360 -0.514 0.891 1.00 0.00 H HETATM 5 C BEN A 1 1.533 0.000 0.000 1.00 0.00 C HETATM 8 H BEN A 1 1.893 0.514 -0.891 1.00 0.00 H HETATM 7 H BEN A 1 1.893 0.514 0.891 1.00 0.00 H HETATM 6 H BEN A 1 1.893 -1.029 0.000 1.00 0.00 H CONECT 1 2 3 4 5 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 6 7 8 CONECT 6 2 CONECT 7 2 CONECT 8 2 MASTER 0 0 0 0 0 0 0 0 8 0 8 0 END type chain x y z element No resname resID More detailed: http://www.wwpdb.org/documentation/Format_v32_A4.pdf

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

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!

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

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 1e- (↑) 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)

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 0.0 0.0 0.0 1 Hartree = 2625.5 kJ/mol Doublet ΔE=Efinal-Einitial Hartree SCF Done: E(UB3LYP) = -0.500272784191 A.U. after 5 cycles [-1.17548238441 -(2×-0.500272784191)] ×2625.5 =-459.3 kJ/mol E # B3LYP/6-31G* Opt H2 0 1 H 0.0 0.0 0.0 H 0.74 0.0 0.0 AO AO MO Singlet Hartree SCF Done: E(RB3LYP) = -1.17548238441 A.U. after 3 cycles

Few more calculations C 6e- S=1 → Ms=3 O 8e- S=1 → Ms=3 Triplet # B3LYP/6-31G* Opt C 0 3 C 0.0 0.0 0.0 Triplet SCF Done: E(UB3LYP) = -37.8462804085 A.U. after 9 cycles # B3LYP/6-31G* Opt O 0 3 O 0.0 0.0 0.0 Triplet SCF Done: E(UB3LYP) = -75.0606231181 A.U. after 10 cycles

Two more calculations O2 16e- S=1 → Ms=1 O2 16e- S=0 → Ms=3 # B3LYP/6-31G* Opt O2 0 1 O -1.11118534 1.97770357 0.01134399 O -2.27278534 1.97770357 0.01134399 excited state Singlet SCF Done: E(RB3LYP) = -150.257426636 A.U. after 6 cycles [-150.257426636 –(-150.320042076)] ×2625.5 = 164.4 kJ/mol # ROB3LYP/6-31G* Opt O2 0 3 O -1.11118534 1.97770357 0.01134399 O -2.27278534 1.97770357 0.01134399 Triplet ground state SCF Done: E(UB3LYP) = -150.320042076 A.U. after 7 cycles

Calculations of atoms