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Introduction%20to%20Gaussian%20

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Title: Introduction%20to%20Gaussian%20


1
Introduction to Gaussian GaussView
  • Shubin Liu, Ph.D.
  • Research Computing Center, ITS
  • University of North Carolina at Chapel Hill

2
Agenda
  • Introduction
  • Capabilities
  • Input File Preparation
  • Gaussian GUI GaussView
  • Run G03 Jobs _at_ UNC-CH
  • Some Advanced Topics
  • Hands-on Experiments next hour

The PDF format of this presentation is available
here http//www.unc.edu/shubin/Courses/Gaussian_
GaussView.pdf
3
Course Goal
  • What Gaussian/GaussView packages are
  • How to prepare input files via GaussView
  • How to run G03 jobs on UNC-CH servers
  • How to view G03 results
  • Learn selected advanced topics
  • Hands-on experiments

4
Pre-requisites
  • Basic UNIX knowledge
  • Introduction to Scientific Computing
  • An account on Emerald

5
About Us
  • ITS Information Technology Services
  • http//its.unc.edu
  • http//help.unc.edu
  • Physical locations
  • 401 West Franklin St.
  • 211 Manning Drive
  • 10 Divisions/Departments
  • Information Security IT Infrastructure and
    Operations
  • Research Computing Center Teaching and Learning
  • User Support and Engagement Office of the CIO
  • Communication Technologies Communications
  • Enterprise Applications Finance and
    Administration

6
Research Computing Center
  • Where and who are we and what do we do?
  • ITS Manning 211 Manning Drive
  • Website
  • http//its.unc.edu/research-computing.html
  • Groups
  • Infrastructure -- Hardware
  • User Support -- Software
  • Engagement -- Collaboration

7
About Myself
  • Ph.D. from Chemistry, UNC-CH
  • Currently Senior Computational Scientist _at_
    Research Computing Center, UNC-CH
  • Responsibilities
  • Support Computational Chemistry/Physics/Material
    Science software
  • Support Programming (FORTRAN/C/C) tools, code
    porting, parallel computing, etc.
  • Training, Workshops/Short Courses currently 4,
    one more to come soon
  • Conduct research and engagement projects in
    Computational Chemistry
  • Development of DFT theory and concept tools
  • Applications in biological and material science
    systems

8
Gaussian GaussView
  • Gaussian is a general purpose electronic
    structure package for use in computational
    chemistry. Current version 03 E01.
  • GaussView is a graphical user interface (GUI)
    designed to be used with Gaussian to make
    calculation preparation and output analysis
    easier, quicker and more efficient. Current
    version 4.1.2.
  • Vendors website http//www.gaussian.com

9
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10
Gaussian 98/03 Functionality
  • Energies
  • MM AMBER, Dreiding, UFF force field
  • Semiempirical CNDO, INDO, MINDO/3, MNDO, AM1,
    PM3
  • HF closed-shell, restricted/unrestricted
    open-shell
  • DFT many local/nonlocal functionals to choose
  • MP 2nd-5th order direct and semi-direct methods
  • CI single and double
  • CC single, double, triples contribution
  • High accuracy methods G1, G2, CBS, etc.
  • MCSCF including CASSCF
  • GVB

11
Gaussian 98/03 Functionality
  • Gradients/Geometry optimizations
  • Frequencies (IR/Raman, NMR, etc.)
  • Other properties
  • Populations analyses
  • Electrostatic potentials
  • NMR tensors
  • Several solvation models (PCM, COSMOS)
  • Two and three layer ONIOM E, grad, freq
  • Transition state search
  • IRC for reaction path

12
New in Gaussian 03
  • Molecular Dynamics
  • BOMD Born-Oppenheimer MD
  • ADMP Atom-Centered Density Matrix Propagation
  • Periodic Boundary Conditions (PBC) HF and DFT
    energies and gradients
  • Properties with ONIOM models
  • Spin-spin coupling and other additions to
    spectroscopic properties
  • Also improved algorithms for initial guesses in
    DFT and faster SCF convergence

13
Gaussian Input File Structure
  • .com,.inp, or .gjf (Windows version)
  • Free format, case insensitive
  • Spaces, commas, tabs, forward slash as delimiters
    between keywords
  • ! as comment line/section
  • Divided into sections (in order)
  • Link 0 commands ()
  • Route section what calculation is to do
  • Title
  • Molecular specification
  • Optional additional sections

14
Input File Example 1
  • HF/6-31G(d) !Route section
  • !Blank line
  • water energy !Title section
  • !Blank line
  • 0 1 !Charge multiplicity
  • O -0.464 0.177 0.0 !Geometry in Cartesian
    Coordinate
  • H -0.464 1.137 0.0
  • H 0.441 -0.143 0.0
  • !Blank line

15
Input File Example 2
  • nproc2 !Link 0 section
  • chkwater.chk
  • b3lyp/6-311G(3df,2p) opt freq !Route/Keywords
    !Blank line
  • Calcn Title test !Title
  • !Ban line
  • 0 1 !Charge multiplicity
  • O !Geometry in Z-matrix
  • h 1 r
  • h 1 r 2 a
  • variables
  • r0.98
  • a109.
  • !Blank line

16
Input File Link 0 Commands
  • First Link 0 options (Examples)
  • chk
  • chkmyjob.chk
  • mem
  • mem12MW
  • nproc
  • nproc4
  • rwf
  • rwf1,1999mb,b,1999mb
  • scr
  • sce,1999mb,f,1999mb

17
Input File Keyword Specification
  • Keyword line(s) specify calculation type and
    other job options
  • Start with symbol
  • Can be multiple lines
  • Terminate with a blank line
  • Format
  • keywordoption
  • keyword(option)
  • keyword(option1,option2,)
  • keyword(option1,option2,)
  • Users guide provides list of keywords, options,
    and basis set notion
  • http//www.gaussian.com/g_ur/keywords.htm

18
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19
Basis Set
  • Minimal basis set (e.g., STO-3G)
  • Double zeta basis set (DZ)
  • Split valence basis Set (e.g., 6-31G)
  • Polarization and diffuse functions (6-31G)
  • Correlation-consistent basis functions (e.g.,
    aug-cc-pvTZ)
  • Pseudopotentials, effective core potentials

20
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21
Input File Title Specification
  • Brief description of calculation for users
    benefit
  • Terminate with a blank line

22
Input File Molecular Geometry
  • 1st line charge and multiplicity
  • Element label and location
  • Cartesian coordinate
  • Label x y z
  • Z-matrix
  • Label atoms bond length atom2 angle atm3 dihedral
  • If parameters used instead of numerical values
    then variables section follows
  • Again end in blank line

23
A More Complicated Example
chk/scr/APPS_SCRDIR/f33em5p77c.chk mem4096MB
NProc4 B3LYP/6-31G opt geomCheckpoint
Guessread nosymm scftight Geometry
optimization of a sample molecule 1 1
--Link1-- chk/scr/APPS_SCRDIR/f33em5p77c.chk m
em4096MB NProc2 B3LYP/6-311G sp popnbo
nosymm guessread geomcheckpoint Single Point
Energy for the "reference state" of molecule with
one more electron. 0 2
24
Other Gaussian Utilities
  • formchk formats checkpoint file so it can be
    used by other programs
  • cubgen generate cube file to look at MOs,
    densities, gradients, NMR in GaussView
  • freqchk retrieves frequency/thermochemsitry
    data from chk file
  • newzmat converting molecular specs between
    formats (zmat, cart, chk, cache, frac coord,
    MOPAC, pdb, and others)

25
GaussView
  • GaussView 4.1.2 makes using Gaussian 03 simple
    and straightforward
  • Sketch in molecules using its advanced 3D
    Structure Builder, or load in molecules from
    standard files.
  • Set up and submit Gaussian 03 jobs right from the
    interface, and monitor their progress as they
    run.
  • Examine calculation results graphically via
    state-of-the-art visualization features display
    molecular orbitals and other surfaces, view
    spectra, animate normal modes, geometry
    optimizations and reaction paths.
  • Online help http//www.gaussian.com/g_gv/gvtop.ht
    m

26
GaussView Availability
  • Support platforms
  • IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
  • LINUX 32-bit OS (Emeraldtest)
  • LINUX 64-bit OS (Emerald, Topsail,
    Cedar/Cypress)

27
GaussView Build
  • Build structures by atom, functional group, ring,
    amino acid (central fragment, amino-terminated
    and carboxyl-terminated forms) or nucleoside
    (central fragment, C3-terminated, C5-terminated
    and free nucleoside forms).
  • Show or hide as many builder panels as desired.
  • Define custom fragment libraries.
  • Open PDB files and other standard molecule file
    formats.
  • Optionally add hydrogen atoms to structures
    automatically, with excellent accuracy.
  • Graphically examine modify all structural
    parameters.
  • Rotate even large molecules in 3 dimension
    translation, 3D rotation and zooming are all
    accomplished via simple mouse operations.
  • Move multiple molecules in the same window
    individually or as a group.
  • Adjust the orientation of any molecule display.
  • View molecules in several display modes wire
    frame, tubes, ball and stick or space fill style.
  • Display multiple views of the same structure.
  • Customize element colors and window backgrounds.
  • Use the advanced Clean function to rationalize
    sketched-in structures
  • Constrain molecular structure to a specific
    symmetry (point group).
  • Recompute bonding on demand.
  • Build unit cells for 1, 2 and 3 dimensional
    periodic boundary conditions calculations
    (including constraining to a specific space group
    symmetry).
  • Specify ONIOM layer assignments in several
    simple, intuitive ways by clicking on the
    desired atoms, by bond attachment proximity to a
    specified atom, by absolute distance from a
    specified atom, and by PDB file residue.

28
GaussView Build
29
GaussView Build
30
GuassView Setup
  • Molecule specification input is set up
    automatically.
  • Specify additional redundant internal coordinates
    by clicking on the appropriate atoms and
    optionally setting the value.
  • Specify the input for any Gaussian 03 calculation
    type.
  • Select the job from a pop-up menu. Related
    options automatically appear in the dialog.
  • Select any method and basis set from pop-up
    menus.
  • Set up calculations for systems in solution.
    Select the desired solvent from a pop-up menu.
  • Set up calculations for solids using the periodic
    boundary conditions method. GaussView specifies
    the translation vectors automatically.
  • Set up molecule specifications for QST2 and QST3
    transition state searches using the Builders
    molecule group feature to transform one structure
    into the reactants, products and/or transition
    state guess.
  • Select orbitals for CASSCF calculations using a
    graphical MO editor, rearranging the order and
    occupations with the mouse.
  • Start and monitor local Gaussian jobs.
  • Start remote jobs via a custom script.

31
GaussView Setup
32
GuassView Showing Results
  • Show calculation results summary.
  • Examine atomic changes display numerical values
    or color atoms by charge (optionally selecting
    custom colors).
  • Create surfaces for molecular orbitals, electron
    density, electrostatic potential, spin density,
    or NMR shielding density from Gaussian job
    results.
  • Display as solid, translucent or wire mesh.
  • Color surfaces by a separate property.
  • Load and display any cube created by Gaussian 03.
  • Animate normal modes associated with vibrational
    frequencies (or indicate the motion with
    vectors).
  • Display spectra IR, Raman, NMR, VCD.
  • Display absolute NMR results or results with
    respect to an available reference compound.
  • Animate geometry optimizations, IRC reaction path
    following, potential energy surface scans, and
    BOMD and ADMP trajectories.
  • Produce web graphics and publication quality
    graphics files and printouts.
  • Save/print images at arbitrary size and
    resolution.
  • Create TIFF, JPEG, PNG, BMP and vector graphics
    EPS files.
  • Customize element, surface, charge and background
    colors, or select high quality gray scale output.

33
GuassView Showing Results
34
Surfaces
35
Reflection-Absorption Infrared Spectrum of AlQ3
Wavenumbers (cm-1)
1473
752
1386
1338
1116
1580
1605
1600
1400
1200
800
1000
36
GaussView VCD (Vibrational Circular Dichroism)
Spectra
GaussView can display a variety of computed
spectra, including IR, Raman, NMR and VCD. Here
we see the VCD spectra for two conformations of
spiropentyl acetate, a chiral derivative of
spiropentane. See F. J. Devlin, P. J. Stephens,
C. Österle, K. B. Wiberg, J. R. Cheeseman, and M.
J. Frisch, J. Org. Chem. 67, 8090 (2002).
37
GaussView ONIOM
Bacteriorhodopsin, set up for an ONIOM
calculation (stylized). See T. Vreven and K.
Morokuma, Investigation of the S0-gtS1 excitation
in bacteriorhodopsin with the ONIOM(MOMM) hybrid
method, Theor. Chem. Acc. (2003).
38
Gaussian/GaussView _at_ UNC
  • Installed in AFS ISIS package space
    /afs/isis/pkg/gaussian
  • Package name gaussian
  • Versions 03D02, 03E01 (default version)
  • Type ipm add gaussian to subscribe the service
  • Availability
  • SGI Altix 3700, cedar/cypress
  • IBM P690, happy/yatta
  • LINUX cluster, emerald.isis.unc.edu
  • LINUX Cluster, topsail.unc.edu (available upon
    request)
  • Package information available at
  • http//help.unc.edu/6082

39
Access GaussView
  • From UNIX workstation
  • Type xhost emerald.isis.unc.edu or xhost
    happy.isis.unc.edu
  • Login to emerald, cedar, topsail, or happy
  • Set display to your local host
  • Invoke gaussview or gview via LSF interactive
    queue
  • From PC desktop via X-Win32 or SecureCRT
  • Detailed document available at
  • http//www.unc.edu/atn/hpc/applications/science/ga
    ussian/access_gv/g03_gv_instructions.htm

40
Submit G03 Jobs to Servers
  • To submit single-CPU G03 jobs to computing
    servers via LSF
  • bsub -q qname -m mname g03 input.inp
  • where qname stands for a queue name, e.g.,
    week, month, etc., mname represents a machine
    name, e.g., cypress, yatta, etc., and input.inp
    denotes the input file prepared manually or via
    GaussView.
  • For example
  • bsub -q week -m cypress g03 input.inp
  • bsub -q month -m p575-n02 g03 input.inp
  • bsub -q idle -R blade g03 input.inp

41
Submit G03 Jobs to Servers
  • To submit multiple-CPU G03 jobs via LSF
  • -- G03 is parallelized via OpenMP
  • bsub -q qname -n ncpu -m mname g03 input.inp
  • where qname stands for a queue name, e.g.,
    week, idle, etc., ncpu is the number of CPUs
    requested, e.g., 2 or 4 or 8, mname represents
    a machine name, e.g., yatta, cypress, etc., and
    input.inp denotes the input file prepared
    manually or via GaussView.
  • For example
  • bsub -q week -n 4 -m cypress g03 input.inp
  • To submit multiple CPU g03 jobs on Emerald, make
    sure only all CPUs are from the same node because
    G03 is parallelized via OpenMP (for share-memory
    SMP machines)
  • bsub -q week -n 4 R blade spanptile4 g03
    input.inp

42
Default Settings
  • Temporary files
  • P575/Yatta/cypress /scr/APPS_SCRDIR
  • Emerald /tmp
  • Memory
  • P575/Yatta/cypress 1GB
  • Emerald 512MB
  • MAXDISK
  • P575/Yatta/cypress 4GB
  • Emerald 2GB

43
Advanced Topics
  • Potential energy surfaces
  • Transition state optimization
  • Thermochemistry
  • NMR, VCD, IR/Raman spectra
  • NBO analysis
  • Excited states (UV/visible spectra)
  • Solvent effect
  • PBC
  • ONIOM model
  • ABMD, BOMD, etc.

44
Potential Energy Surfaces
  • Many aspects of chemistry can be reduced to
    questions about potential energy surfaces (PES)
  • A PES displays the energy of a molecule as a
    function of its geometry
  • Energy is plotted on the vertical axis, geometric
    coordinates (e.g bond lengths, valence angles,
    etc.) are plotted on the horizontal axes
  • A PES can be thought of it as a hilly landscape,
    with valleys, mountain passes and peaks
  • Real PES have many dimensions, but key feature
    can be represented by a 3 dimensional PES

45
Model Potential Energy Surface
46
Calculating PES in Gaussian/GaussView
  • Use the keyword scan
  • Then change
  • input file properly

47
Transition State Search
48
Calculating Transition States
49
Locating Transition States
50
TS Search in Gaussian
51
TS Search inGaussian/GaussView
52
TS Search inGaussian/GaussView
53
Animation of Imaginary Frequency
  • Check that the imaginary
  • frequency corresponds to
  • the TS you search for.

54
Intrinsic Reaction Coordinate Scans
55
Input for IRC Calculation
StepSizeN Step size along the reaction path, in
units of 0.01 amu-1/2-Bohr. The default is 10.
RCFC Specifies that the computed force
constants in Cartesian coordinates from a
frequency calculation are to be read from the
checkpoint file. ReadCartesianFC is a synonym for
RCFC.
56
IRC Calculation in GaussView
57
Reaction Pathway Graph
58
Thermochemistryfrom ab initio Calculations
59
Thermochemistryfrom ab initio Calculations
60
Thermochemistry from frequency calculation
61
Modeling System in Solution
62
Calculating Solvent Effect
63
Calculating Solvent Effect
64
Solvent Effect Menshutkin Model Reaction
Transition State
65
Solvent Effect Menshutkin Model Reaction
Transition State
66
NMR Shielding Tensors
67
NMR Example Input
chkethynenmr p hf/6-311g(2d,p) nmr nmr
ethyne 0 1 C C,1,r1 H,1,r2,2,a2 H,2,r3,1,a3,3,d3,
0 Variables R11.20756258 R21.06759666 R31.0
6759666 A2180.0 A3180.0 D30.0
68
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69
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70
Comparison of Calculated and Experimental
Chemical Shifts
71
QM/MM ONIOM Model
72
QM/MM ONIOM Model
  • From GaussView menu Edit -gt Select Layer

Low Layer
Medium Layer
High Layer
73
QM/MM ONIOM Setup
  • From GaussView menu Calculate -gtGaussian-gtMethod

74
QM/MM ONIOM Setup
  • For the medium and low layers

75
QM/MM ONIOM Setup
76
What Is NBO?
  • Natural Bond Orbitals (NBOs) are localized
    few-center orbitals ("few" meaning typically 1 or
    2, but occasionally more) that describe the
    Lewis-like molecular bonding pattern of electron
    pairs (or of individual electrons in the
    open-shell case) in optimally compact form. More
    precisely, NBOs are an orthonormal set of
    localized "maximum occupancy" orbitals whose
    leading N/2 members (or N members in the
    open-shell case) give the most accurate possible
    Lewis-like description of the total N-electron
    density.

C-C Bond
C-H Bond
77
NBO Analysis
78
NBO in GaussView
79
Natural Population Analysis
  • rhf/3-21g popnbo RHF/3-21G for formamide
    (H2NCHO) 0 1   H  -1.908544     
    0.420906     0.000111   H  -1.188060    
    -1.161135     0.000063   N  -1.084526    
    -0.157315     0.000032   C   0.163001     
    0.386691    -0.000154   O   1.196265    
    -0.246372     0.000051   H   0.140159     
    1.492269     0.000126

80
NPA Output Sample
81
Further Readings
  • Computational Chemistry (Oxford Chemistry Primer)
    G. H. Grant and W. G. Richards (Oxford University
    Press)
  • Molecular Modeling Principles and Applications,
    A. R. Leach (Addison Wesley Longman)
  • Introduction to Computational Chemistry, F.
    Jensen (Wiley)
  • Essentials of Computational Chemistry Theories
    and Models, C. J. Cramer (Wiley)
  • Exploring Chemistry with Electronic Structure
    Methods, J. B. Foresman and A. Frisch (Gaussian
    Inc.)

82
Hands-on Part I
  • Access GaussView to Emerald cluster from PC
    desktop
  • If not done so before, type ipm add gaussian
  • Check if Gaussian is subscribed by typing ipm q
  • Get to know GaussView GUI
  • Build a simple molecular model
  • Generate an input file for G03 called, for
    example, input.com
  • View and modify the G03 input file
  • Submit G03 job to emerald compute nodes using the
    week or now queue
  • bsub R blade q now g03 input.com

83
Hands-on Part II
  • Calculate/View Molecular Orbitals with GaussView
  • http//educ.gaussian.com/visual/Orbs/html/OrbsGaus
    sView.htm
  • Calculate/View Electrostatic Potential with
    GaussView
  • http//educ.gaussian.com/visual/ESP/html/ESPGaussV
    iew.htm
  • Calculate/View Vibrational Frequencies in
    GaussView
  • http//educ.gaussian.com/visual/Vibs/html/VibsGaus
    sview.htm
  • Calculate/View NMR Tensors with GaussView
  • http//educ.gaussian.com/visual/NMR/html/NMRGausvi
    ew.htm
  • Calculate/View a Reaction Path with GaussView
  • http//educ.gaussian.com/visual/RPath/html/RPathGa
    ussView.htm

84
Comments Questions???
Please direct comments/questions about
Gaussian/GaussView to E-mail research_at_unc.edu Ple
ase direct comments/questions pertaining to this
presentation to E-Mail shubin_at_email.unc.edu
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