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Introduction to Gaussian 03

Materials Simulation Center presents:. Introduction to Gaussian 03. Ping Lin. Course contents. Overview : What is Gaussian / GaussView Lesson 1: Preparing input file Lesson 2: Running Gaussian 03 Lesson 3: Viewing outputs Lesson 4: Some examples.

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Introduction to Gaussian 03

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  1. Materials Simulation Center presents: Introduction to Gaussian 03 Ping Lin

  2. Course contents • Overview: What is Gaussian/GaussView • Lesson 1: Preparing input file • Lesson 2: Running Gaussian 03 • Lesson 3: Viewing outputs • Lesson 4: Some examples Each lesson includes hand-on excises. Introduction to Gaussian 03

  3. Overview: What is Gaussian/GaussView Gaussian 03is the latest in the Gaussian series of electronic structure programs. Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions, including both stable species and unstable or non-observable such as short-lived intermediates and transition structures. GaussView is a full-featured graphical user interface for Gaussian. (to construct molecular systems; to set up and run Gaussian calculations; to visualize results.) http://www.gaussian.com Introduction to Gaussian 03

  4. Capabilities • Energies • Molecular mechanics: AMBER, DREIDING, UFF force field • Semi-empirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3 • Hartree-Fock: closed-shell (RHF), restricted/unrestricted open-shell (ROHF/UHF) • Møller-Plesset perturbation theory: MP2, MP3, … • Configuration interaction: double (CID) or all single and double excitations (CISD) • Coupled cluster theory: CCD, CCSD, QCISD, BD • Density functional theory: including general, user-configurable hybrid methods • Automated, high accuracy energy methods: G1, G2, G2(MP2), G3, CBS, … • General MCSCF (CASSCF, CASMP2, RASSCF) and Generalized Valence Bond(GVB) • Excited State: CIS, TD-DFT, SAC-CI Introduction to Gaussian 03

  5. Capabilities – cont. • Gradients and Geometry Optimizations • Automated geometry optimization to either minima or saddle points, transition state searching; Reaction path following(IRC); Conical intersection optimization • Born Oppenheimer molecular dynamics (BOMD); Atom Centered Density Matrix Propagation molecular dynamics • Frequencies and Second Derivatives • Harmonic vibrational analysis and thermochemistry analysis • IR and Raman intensities • Harmonic and anharmonic vibration and vibration-rotation coupling Introduction to Gaussian 03

  6. Capabilities – cont. • Molecular Properties • Evaluation of various one-electron properties, i.e. electrostatic potentials • Polarizabilities and hyperpolarizabilities • NMR shielding tensors and molecular susceptibilities • Electron affinities and ionization potentials • etc. • Solvation Models • Onsager model • Polarized Continuum model (PCM) Introduction to Gaussian 03

  7. Capabilities – new and improved features • Enhanced ONIOM Method • able to model large molecules by defining two or three layers within the structure that are treated at different levels of accuracy; • applicable in many other areas, including enzyme reactions, cluster models of surfaces and surface reactions, photochemical processes, substituent effects and reactivity of organic and organometallic compounds, and homogeneous catalysis. • Periodic Boundary Conditions • PBC calculations for studying periodic systems: e.g., polymers, surfaces and crystals • predict the equilibrium geometries and transition structures of polymers; study polymer reactivity, reaction energetics, and so on. Introduction to Gaussian 03

  8. Course goals • Learn to prepare Gaussian input files • Learn to run Gaussian job in HPC clusters • Learn to view and analyze the Gaussian output Introduction to Gaussian 03

  9. Lesson 1 Preparing Input Files

  10. Input File Structures Link 0 Commands (% lines): System specific parameter Routesection (#lines): Specify calculation type, model chemistry and other options Titlesection: Brief description of the calculation Moleculespecification: Specify molecular system to be studied Optionaladditionalsections: Additional input needed for specific job types Link 0 section (#of processors for SMP) (amount of memory) (checkpoint file name and location) Route section Title section Molecule Specification section (charge, multiplicity) Structure representation in Z-matrix format %NProcShared=2 %MEM=64MW %chk=h2o_opt.chk # RHF/6-31g** OPT H2O RHF/6-31g** optimization 0 1 O H 1 r1 H 1 r1 2 tha1 r1 1.000 tha1 105.0 Introduction to Gaussian 03

  11. Input Syntax • Free-format and case-insensitive. • Spaces, tabs, commas, or forward slashes can be used to separate items. • Options to keywords may be specified as followed: •          keyword = option •          keyword(option) •          keyword=(option1, option2, ...) •         keyword(option1, option2, ...) • In case the options also take values, the option is followed by an equals sign and value: for example, CBSExtrap(NMin=6). • All keywords and options may be shortened to their shortest unique abbreviation. • The contents of an external file may be included within input file using the following syntax: @filename. • Comments may appear anywhere on a line beginning with (!) Introduction to Gaussian 03

  12. Gaussian 03 Input Section Ordering Introduction to Gaussian 03

  13. Route Section: Keywords Introduction to Gaussian 03

  14. Keywords (Job types) • SP     Single point energy. • Opt     Geometry optimization. • Freq     Frequency and thermochemical analysis. • IRC     Reaction path following. • IRCMax     Find the maximum energy along a specific reaction path. • Scan     Potential energy surface scan. • PolarPolarizabilities and hyperpolarizabilities. • ADMP and BOMD     Direct dynamics trajectory calculation. • Force     Compute forces on the nuclei. • Stable     Test wavefunction stability. • Volume     Compute molecular volume. • Density=CheckpointRecompute population analysis only. • Guess=Only     Print initial guess only; recompute population analysis. • ReArchive     Extract archive entry from checkpoint file only. Introduction to Gaussian 03

  15. Keywords (Molecular properties) • Atomic charges, Dipole moment, Multipole moments : Pop • Electron affinities and Ionization potentials via propagator methods: OVGF • Electron density: cubegen • Electronic circular dichroism: TD • Electrostatic potential: cubegen, Prop • Electrostatic-potential derived charges: Pop=Chelp, ChelpG or MK • Frequency-dependent polarizabilities/hyperpolarizabilities: PolarCPHF=RdFreq • High accuracy energies: CBS-QB3, G2, G3, W1U • Hyperfine coupling constants (anisotropic): Prop • Hyperfine spectra tensors (incl. g tensors): Freq=(VCD, VibRot[, Anharmonic]) • Hyperpolarizabilities: Freq, Polar • IR and Raman spectra: Freq • Molecular orbitals: Pop=Regular • NMR shielding and chemical shifts: NMR • NMR spin-spin coupling constants: NMR=SpinSpin • Optical rotations: Polar=OptRot CPHF=RdFreq • Polarizabilities: Freq, Polar • Thermochemical analysis: Freq • UV/Visible spectra: CIS, Zindo, TD • Vibration-rotation coupling: Freq=VibRot • Vibrational circular dichroism: Freq=VCD Introduction to Gaussian 03

  16. Keywords (Algorithms) • Self-Consistent Field: SCF • Complex molecular orbital: Complex • Coupled-perturbed Hartree–Fock: CPHF • Using an external program: External • Fast multipole method: FMM • Controls the initial guess: Guess • Controls two-electron integrals and their derivatives: Integral • Density Fitting Basis Sets: Auto, DGA1, DGA2 • …… Introduction to Gaussian 03

  17. Available model calculations Introduction to Gaussian 03

  18. An example: Keyword (NMR) Introduction to Gaussian 03

  19. Keyword (Basis set) Introduction to Gaussian 03

  20. Keyword (ExtraBasis and Gen) H 0 ! Applies to all hydrogen atoms. S 3 1.00 0.1873113696D+02 0.3349460434D-01 0.2825394365D+01 0.2347269535D+00 0.6401216923D+00 0.8137573262D+00 S 1 1.00 0.1612777588D+00 0.1000000000D+01 **** C 0 ! Applies to all carbons. S 6 1.00 ! 6-31G functions. 0.3047524880D+04 0.1834737130D-02 0.4573695180D+03 0.1403732280D-01 0.1039486850D+03 0.6884262220D-01 0.2921015530D+02 0.2321844430D+00 0.9286662960D+01 0.4679413480D+00 0.3163926960D+01 0.3623119850D+00 SP 3 1.00 0.7868272350D+01 -0.1193324200D+00 0.6899906660D-01 0.1881288540D+01 -0.1608541520D+00 0.3164239610D+00 0.5442492580D+00 0.1143456440D+01 0.7443082910D+00 SP 1 1.00 0.1687144782D+00 0.1000000000D+01 0.1000000000D+01 D 1 1.00 ! Polarization function. 0.8000000000D+00 0.1000000000D+01 **** C 0 ! Applies to all carbons. SP 1 1.00 ! Diffuse function. 0.4380000000D-01 0.1000000000D+01 0.1000000000D+01 **** Gen and ExtraBasis can be used for customized Basis Set input: i.e. # Becke3LYP/Gen Opt and # HF/6-31G(d,p) ExtraBasis Example 1 Example 2 C O 0 6-31G(d) **** @/home/gwtrucks/basis/chrome.gbs/N Similar keywords exist for Density Fitting Basis and ECP: i.e. # RBLYP/Gen/Gen GenECP 6D Introduction to Gaussian 03

  21. Molecular Specification Molecules can be specified by Z-matrix or Cartesian coordinate. The Z-matrix is a way to represent a system built of atoms. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates. Molecular builders Some softwares provide sketcher and fragment library to build molecules with ease, i.e. GaussView, Accerlys’s Discovery Studio, Materials Studio, Java Molecular Editor, HyperChem, Gabedit, etc. Some softwares provide interface to write out z-matrix or Cartesian coordinates, i.e. Molden Introduction to Gaussian 03

  22. B1 1.08999986 B2 1.09000014 B3 1.51000001 B4 1.34000054 B5 1.40090802 B6 1.09000019 B7 1.42999936 B8 1.31000041 B9 1.39999909 B10 1.01000007 B11 1.40000057 B12 1.40999487 B13 1.08999912 B14 1.09000026 B15 1.35000035 B16 1.09000000 B17 1.09000021 B18 1.43000000 B19 0.96000000 A1 109.44241338 A2 106.62395021 A3 127.00002734 A4 127.53691525 A5 119.99998192 A6 107.00000552 A7 109.00000126 A8 129.46331494 A9 125.50000034 A10 127.99998355 A11 117.00038525 A12 122.99974026 A13 119.99996777 A14 121.99985314 A15 118.00014897 A16 119.00001322 A17 114.99999736 A18 109.50000006 D1 -114.96173497 D2 58.42552990 D3 -180.00000000 D4 0.00000000 D5 -180.00000000 D6 0.00000000 D7 0.00000000 D8 -180.00000000 D9 -180.00000000 D10 -180.00000000 D11 -0.00000000 D12 -0.00000000 D13 -0.00000000 D14 180.00000000 D15 -180.00000000 D16 180.00000000 D17 180.00000000 Molecular Specification • %chk=test0004.chk • %mem=64MW • # hf/6-31g(d,p) • Test Molecular Stucture Sepcification • 0 1 • C • H 1 B1 • H 1 B2 2 A1 • C 1 B3 2 A2 3 D1 • C 4 B4 1 A3 2 D2 • C 4 B5 1 A4 5 D3 • H 5 B6 4 A5 1 D4 • N 5 B7 4 A6 1 D5 • C 8 B8 5 A7 4 D6 • C 6 B9 4 A8 1 D7 • H 8 B10 5 A9 4 D8 • C 9 B11 8 A10 5 D9 • C 10 B12 6 A11 4 D10 • H 10 B13 6 A12 4 D11 • H 12 B14 9 A13 8 D12 • C 13 B15 10 A14 6 D13 • H 13 B16 10 A15 6 D14 • H 16 B17 13 A16 10 D15 • O 1 B18 4 A17 5 D16 • H 19 B19 1 A18 4 D17 • B1 1.08999986 • B2 1.09000014 Introduction to Gaussian 03

  23. Molecular Specification – Z-matrix the Dihedral Angle Bond and Angle Introduction to Gaussian 03

  24. Molecular Specification – 1D system One dimension periodic system specification: # PBEPBE/6-31g(d,p)/Auto SCF=Tight neoprene, [-CH2-CH=C(Cl)-CH2-] optimized geometry 0 1 C,-1.9267226529,0.4060180273,0.0316702826 H,-2.3523143977,0.9206168644,0.9131400756 H,-1.8372739404,1.1548899113,-0.770750797 C,-0.5737182157,-0.1434584477,0.3762843235 H,-0.5015912465,-0.7653394047,1.2791284293 C,0.5790889876,0.0220081655,-0.3005160849 C,1.9237098673,-0.5258773194,0.0966261209 H,1.772234452,-1.2511397907,0.915962512 H,2.3627869487,-1.0792380182,-0.752511583 Cl,0.6209825739,0.9860944599,-1.7876398696 TV,4.8477468928,0.1714181332,0.5112729831 Introduction to Gaussian 03

  25. Molecular Specification – 2D system Two-dimension periodic system specification: # PBEPBE/6-31g(d,p)/Auto SCF=Tight BN optimized geometry 0,1 5 0 -0.635463 0.000000 0.733871 7 0 -0.635463 0.000000 -0.733871 7 0 0.635463 0.000000 1.467642 5 0 0.635463 0.000000 -1.467642 TV 0 0.000000 0.000000 4.403026 TV 0 2.541855 0.000000 0.000000 Introduction to Gaussian 03

  26. Molecular Specification – 3D system Three-dimension periodic system specification: # PBEPBE/6-31g(d,p)/Auto SCF=Tight GaAs optimized geometry 0 1 Ga 0.000000 0.000000 0.000000 Ga 0.000000 2.825000 2.825000 Ga 2.825000 0.000000 2.825000 Ga 2.825000 2.825000 0.000000 As 1.412500 1.412500 1.412500 As 1.412500 4.237500 4.237500 As 4.237500 1.412500 4.237500 As 4.237500 4.237500 1.412500 TV 5.650000 0.000000 0.000000 TV 0.000000 5.650000 0.000000 TV 0.000000 0.000000 5.650000 Introduction to Gaussian 03

  27. Molecular Specification – ONIOM # oniom(blyp/3-21g/dga1:amber) geom=connectivity opt=loose blyp/3-21g:amber with density fitting from Luecke 3 1 1 1 N-N3-0.181200 22.076181 24.563316 -13.077047 L C-CT-0.003400 20.736756 24.514869 -13.699982 L C-C-0.616300 20.734957 25.313129 -14.988472 L O-O--0.572200 20.731825 24.680955 -16.030293 L …… C-CT--0.043900 19.775830 32.473200 7.920456 L C-CT--0.015800 18.776883 33.512258 7.403331 L H-HC 0 0. 0. C-CT--0.082400 17.966350 32.942557 6.232525 H C-CT-0.377886 16.928731 33.900731 5.689445 H N-N2--0.693824 17.521649 35.160530 5.191031 H N-N--0.415700 22.301376 31.316157 8.955475 L …… H-HW-0.417000 10.154733 46.125705 25.662719 L H-HW-0.417000 11.339041 47.039598 25.433539 L H-H-0.274700 21.866560 34.137178 7.953109 L H-H-0.377886 17.847763 35.188083 4.238902 H H-H-0.341200 18.066775 49.503351 -1.731201 L H-HO-0.474700 15.931300 31.668829 17.328019 L 1 2 1.0 1770 1.0 1771 1.0 1772 1.0 2 3 1.0 5 1.0 1769 1.0 3 4 2.0 8 2.0 4 5 6 1.0 7 1.0 1764 1.0 6 1768 1.0 Two-Layer ONIOM specification # oniom(blyp/3-21g:amber) geom=connectivity # ONIOM(mp2/6-311g**:b3lyp/6-31g*:hf/3-21g) 3-layer ONIOM 0 1 0 1 0 1 0 1 0 1 0 1 0 1 C -0.006049274275 0.000000000000 0.066754956170 H O 0.011403425950 0.000000000000 1.308239478983 H H 0.944762558657 0.000000000000 -0.507359536461 H C -1.307562483867 0.000000000000 -0.766510748030 M H 1 0.723886 0.723886 0.723886 C -1.047480751885 0.000000000000 -2.301387120377 L H 4 0.723886 0.723886 0.723886 H -1.903669606697 -0.885256630266 -0.468844831106 M H -1.903669606697 0.885256630266 -0.468844831106 M H -1.988817319373 0.000000000000 -2.842389774687 L H -0.482972255230 0.881286097766 -2.591806824941 L H -0.482972255230 -0.881286097766 -2.591806824941 L Three-Layer ONIOM specification # ONIOM(mp2/6-311g**:b3lyp/6-31g*:hf/3-21g) Introduction to Gaussian 03

  28. Suggestions for practice • Use GaussView to generate Gaussian input • Introduction to the GaussView menu • Builder; File; Molecule; Coordinate; View; Windows toolbars • Use Mouse to sketch and manipulate molecules; use Atom List to make change to atoms; clean the system • Theoretical model Gaussian input selection • Save generated input file or run directly Introduction to Gaussian 03

  29. Application Example 1: • Infrared Spectroscopy of the tert-Butyl Cation in the Gas Phase (J. Am. Chem. Soc. ASAP) • Sketch C4H9+ at three different conformation • Select a theoretical model; perform geometry optimization • Calculate frequency and Infrared spectrum • Compare with the reference. • 1Eh = 4.35974394×10−18 J = 2625.5 kJ/mol Introduction to Gaussian 03

  30. Example 1: a Sample Run B3LYP/6-31G(d,p) OPT Freq B3LYP/6-311G(d,p) OPT Freq Introduction to Gaussian 03

  31. Example 1: Orbitals and Electron Density HOMO LUMO Total Electronic Density B3LYP/6-31G(d,p) OPT Freq Introduction to Gaussian 03

  32. Application Example 2: • SiC Nanotubes: A Novel Material for Hydrogen Storage (Nano Lett., 6 (8), 1581 -1583, 2006) • Sketch SiCnanotube cluster • Select a theoretical model; perform geometry optimization • Calculate potential energy curve • Compare with the reference. Introduction to Gaussian 03

  33. Example 2: a Sample Run Introduction to Gaussian 03

  34. Example 1: • Experimental observations: • acidity (proton affinity); • electron detachment energies (electron affinity); • equilibrium ratio between phenoxide and carboxylate (70:30); Introduction to Gaussian 03

  35. Conformation and Energies Introduction to Gaussian 03

  36. Example 2 • For the first time the water amidogen radical complex (H2O-NH2) was identified using matrix isolation FT-IR spectroscopy. • Gas-phase oxidation of ammonia (NH3) by a hydroxyl radical (OH) is considered important for atmospheric oxidation of NH3, the combustion of fossil fuels, and the production and elimination of atmospheric NOx Introduction to Gaussian 03

  37. Vibrational Spectra NH3 + OH NH2 + H2O Introduction to Gaussian 03

  38. Potential Energy Surface • Transition state search, rate constant, etc Introduction to Gaussian 03

  39. Example 3 Introduction to Gaussian 03

  40. Structure and Electronic properties • B3LYP vertical detachment energy estimated for this anion is 1.93 eV. MP2-corrected geometry yields a VDE of 2.12 eV. the maximum of the PES feature is observed at ∼2.1 eV Introduction to Gaussian 03

  41. Example 4 Introduction to Gaussian 03

  42. Ab initio calculation is able to predict both vibrational spectra and NMR spectra, as well as accurate heat of formation. Introduction to Gaussian 03

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