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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 l.jpg

Materials Simulation Center presents:

Introduction to Gaussian 03

Ping Lin


Course contents l.jpg

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


Overview what is gaussian gaussview l.jpg

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


Capabilities l.jpg

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


Capabilities cont l.jpg

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


Capabilities cont6 l.jpg

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


    Capabilities new and improved features l.jpg

    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


    Course goals l.jpg

    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


    Lesson 1 l.jpg

    Lesson 1

    Preparing Input Files


    Input file structures l.jpg

    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


    Input syntax l.jpg

    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


    Gaussian 03 input section ordering l.jpg

    Gaussian 03 Input Section Ordering

    Introduction to Gaussian 03


    Route section keywords l.jpg

    Route Section: Keywords

    Introduction to Gaussian 03


    Keywords job types l.jpg

    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


    Keywords molecular properties l.jpg

    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


    Keywords algorithms l.jpg

    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


    Available model calculations l.jpg

    Available model calculations

    Introduction to Gaussian 03


    An example keyword nmr l.jpg

    An example: Keyword (NMR)

    Introduction to Gaussian 03


    Keyword basis set l.jpg

    Keyword (Basis set)

    Introduction to Gaussian 03


    Keyword extrabasis and gen l.jpg

    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


    Molecular specification l.jpg

    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


    Molecular specification22 l.jpg

    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


    Molecular specification z matrix l.jpg

    Molecular Specification – Z-matrix

    the Dihedral Angle

    Bond and Angle

    Introduction to Gaussian 03


    Molecular specification 1d system l.jpg

    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


    Molecular specification 2d system l.jpg

    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


    Molecular specification 3d system l.jpg

    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


    Molecular specification oniom l.jpg

    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


    Suggestions for practice l.jpg

    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


    Application example 1 l.jpg

    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


    Example 1 a sample run l.jpg

    Example 1: a Sample Run

    B3LYP/6-31G(d,p) OPT Freq

    B3LYP/6-311G(d,p) OPT Freq

    Introduction to Gaussian 03


    Example 1 orbitals and electron density l.jpg

    Example 1: Orbitals and Electron Density

    HOMO

    LUMO

    Total Electronic Density

    B3LYP/6-31G(d,p) OPT Freq

    Introduction to Gaussian 03


    Application example 2 l.jpg

    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


    Example 2 a sample run l.jpg

    Example 2: a Sample Run

    Introduction to Gaussian 03


    Example 1 l.jpg

    Example 1:

    • Experimental observations:

      • acidity (proton affinity);

      • electron detachment energies (electron affinity);

      • equilibrium ratio between phenoxide and carboxylate (70:30);

    Introduction to Gaussian 03


    Conformation and energies l.jpg

    Conformation and Energies

    Introduction to Gaussian 03


    Example 2 l.jpg

    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


    Vibrational spectra l.jpg

    Vibrational Spectra

    NH3 + OH NH2 + H2O

    Introduction to Gaussian 03


    Potential energy surface l.jpg

    Potential Energy Surface

    • Transition state search, rate constant, etc

    Introduction to Gaussian 03


    Example 3 l.jpg

    Example 3

    Introduction to Gaussian 03


    Structure and electronic properties l.jpg

    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


    Example 4 l.jpg

    Example 4

    Introduction to Gaussian 03


    Slide42 l.jpg

    • 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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