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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

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My first Gaussian input

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  1. Application Myfirst Gaussian input http://www.kollewin.com/blog/density-functional-theory/

  2. Definition of a molecule communication

  3. Cartesiancoordinates 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 symmetryconsidered

  4. Internalcoordinates No symmetryconsidered: - 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 Symmetryconsidered: 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 Howmanycoordinates doesoneneedtodefine a CH4 molecule?

  5. Internalcoordinates 5 • Classification: • Type: • (bond)length (C1-H2) • (bond)angle (C1-H2-H3) • torsion angle (H2-H3-C1-H4) • Measurableproperties: • 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. 7 4 8 1 5 3 2 6 Ethane.pdb 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 chain x y type z element resname resID No More detailed: http://www.wwpdb.org/documentation/Format_v32_A4.pdf

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

  9. Someexamples • Gaussian (.inp, .com, .gjf) • HyperChem (.hin) • Orca (.inp) • Molpro (.inp) • MRCC (.inp) • Dalton (.dal) Differentextensionsmaymeandifferentinformationcontent! Sameextensiondoesnotmeanthatthosefilesarecompatible!

  10. Gaussian09 • www.gaussian.com/ • Windows OS, Linux OS, Mac X OS • Methods/Model: • MM, • Semiempiricalmethods (PM3, AM1) • ab initio (HF, MP2, MP3, MP4, CCSD, CCSD(T), CIS, CIS(D) QCISD, QCISD(T)), • DFT, • compositemodels (CBS-n, Gn) • Weusethis

  11. Definition of a molecule… • Moleculespecification (Cartesian, Z-matrix…) • Net charge • Arrangement of theelectrons (Electronicstate) • Electron spin: s=½ • Net spin quantumnumber: S • Multiplicity: Ms=2S+1 • Examples: H 1e- (↑) S=½ → S=½Ms=2 (doublet) H2 2•1e- (↑↓) S=2•½ =1 → S=0Ms=1 (singlet) O2 2•8e- (↑↑) S=1 → S=1Ms=3 (triplet) O2 2•8e- (↑↓) S=0 → S=0Ms=1 (singlet)

  12. E Fewcalculations H 1s1 1e-S=0.5 → Ms=2 H2 2e-S=0 → Ms=1 # B3LYP/6-31G*Opt H 0 2 H 0.00.0 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 H0.740.0 0.0 AO AO MO Singlet Hartree SCF Done: E(RB3LYP) = -1.17548238441 A.U. after 3 cycles

  13. Few more calculations C 6e-S=1 → Ms=3 O 8e-S=1 → Ms=3 # B3LYP/6-31G* Opt C 0 3 C 0.00.0 0.0 Triplet SCF Done: E(UB3LYP) = -37.8462804085 A.U. after 9 cycles # B3LYP/6-31G* Opt O 0 3 O 0.00.0 0.0 Triplet SCF Done: E(UB3LYP) = -75.0606231181 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-1.11118534 1.97770357 0.01134399 O -2.27278534 1.97770357 0.01134399 excitedstate 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 groundstate SCF Done: E(UB3LYP) = -150.320042076 A.U. after 7 cycles

  15. Calculations of atoms

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