Introduction to Gaussian Introduction to Gaussian and GaussViewand GaussView

Shubin Liu, Ph.D.Renaissance Computing Institute

University of North Carolina at Chapel Hill

11/6/2006 Introduction to Gaussian 2

Agenda

• Introduction• Capabilities• Input File Preparation• Gaussian GUI – GaussView• Run G03 Jobs @ UNC-CH• Some Advanced Topics• Hands-on Experiments

11/6/2006 Introduction to Gaussian 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

11/6/2006 Introduction to Gaussian 4

Pre-requisites

• Basic UNIX knowledge

• Introduction to Scientific Computing

• An account on Emerald

11/6/2006 Introduction to Gaussian 5

About Myself• Ph.D. from Chemistry, UNC-CH• Currently Senior Computational Scientist @ UNC ITS Research Computing Division• Responsibilities:

– Support Comp Chem/Phys/Material Science software, Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.

– Engagement projects with faculty members on campus– Conduct own research on Comp Chem

• DFT theory and concept• Systems in biological and material science

11/6/2006 Introduction to Gaussian 6

About You

• Name, department, group, interest?• Any experience before with Gaussian or

GaussView?• What do you expect to use them? What

kind of systems?

11/6/2006 Introduction to Gaussian 7

Gaussian & GaussView

• Gaussian is a general purpose electronic structure package for use in computational chemistry. Current version 03 D02.

• 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 3.0.9.

• Vendor’s website: http://www.gaussian.com

11/6/2006 Introduction to Gaussian 8

Gaussian

11/6/2006 Introduction to Gaussian 9

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

11/6/2006 Introduction to Gaussian 10

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

11/6/2006 Introduction to Gaussian 11

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

11/6/2006 Introduction to Gaussian 12

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

11/6/2006 Introduction to Gaussian 13

Input File – Example 1

# HF/6-31G(d) !Route section !Blank line

water energy !Title section !Blank line

0 1 !Charge & multiplicityO -0.464 0.177 0.0 !Geometry in Cartesian

CoordinateH -0.464 1.137 0.0 H 0.441 -0.143 0.0

!Blank line

11/6/2006 Introduction to Gaussian 14

Input File – Example 2%nproc=2 !Link 0 section%chk=water.chk #b3lyp/6-311+G(3df,2p) opt freq !Route/Keywords

!Blank lineCalcn Title: test !Title

!Ban line0 1 !Charge &

multiplicityO !Geometry in Z-matrixh 1 r h 1 r 2 a variablesr=0.98 a=109.

!Blank line

11/6/2006 Introduction to Gaussian 15

Input File – Link 0 Commands

• First “Link 0” options (Examples)– %chk

– %chk=myjob.chk– %mem

– %mem=12MW– %nproc

– $nproc=4– %rwf

– %rwf=1,1999mb,b,1999mb– %scr

– %sc=e,1999mb,f,1999mb

11/6/2006 Introduction to Gaussian 16

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

– keyword=option– keyword(option)– keyword(option1,option2,…)– keyword=(option1,option2,…)

• User’s guide provides list of keywords, options, and basis set notion

http://www.gaussian.com/g_ur/keywords.htm

11/6/2006 Introduction to Gaussian 17

11/6/2006 Introduction to Gaussian 18

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 (6-31+G*)• Correlation-consistent basis functions (e.g., aug-cc-

pvTZ)• Pseudopotentials, effective core potentials

11/6/2006 Introduction to Gaussian 19

11/6/2006 Introduction to Gaussian 20

Input File – Title Specification

• Brief description of calculation – for users benefit

• Terminate with a blank line

11/6/2006 Introduction to Gaussian 21

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

11/6/2006 Introduction to Gaussian 22

A More Complicated Example

%chk=/scr/APPS_SCRDIR/f33em5p77c.chk%mem=4096MB%NProc=4#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight

Geometry optimization of a sample molecule

1 1 --Link1--%chk=/scr/APPS_SCRDIR/f33em5p77c.chk%mem=4096MB%NProc=2# B3LYP/6-311++G** sp pop=nbo nosymm guess=read geom=checkpoint

Single Point Energy for the "reference state" of molecule with one more electron.

0 2

11/6/2006 Introduction to Gaussian 23

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)

11/6/2006 Introduction to Gaussian 24

GaussView

GaussView 3.0.9 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.htm

11/6/2006 Introduction to Gaussian 25

GaussView Availability

• Support platforms:– IBM RS6000 (AIX 5.1)– SGI (IRIX 6.5.3)– Intel Pentium II, III, IV/Athlon (IA32) Linux (RedHat 8.0, 9.0; SuSE 8.2, 9.0, 9.1)

11/6/2006 Introduction to Gaussian 26

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.

11/6/2006 Introduction to Gaussian 27

GaussView: Build

11/6/2006 Introduction to Gaussian 28

GaussView: Build

11/6/2006 Introduction to Gaussian 29

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 Builder’s 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.

11/6/2006 Introduction to Gaussian 30

GaussView: Setup

11/6/2006 Introduction to Gaussian 31

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.

11/6/2006 Introduction to Gaussian 32

GuassView: Showing Results

11/6/2006 Introduction to Gaussian 33

Surfaces

11/6/2006 Introduction to Gaussian 34

Reflection-Absorption Infrared Spectrum of AlQ3

ON

AlO

ON

N

752

1116 1338

13861473

1580 1605

160014001200800 1000

Wavenumbers (cm-1)

11/6/2006 Introduction to Gaussian 35

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).

11/6/2006 Introduction to Gaussian 36

GaussView: ONIOM

Bacteriorhodopsin, set up for an ONIOM calculation (stylized). See T. Vreven and K. Morokuma, “Investigation of the S0->S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method,” Theor. Chem. Acc. (2003).

11/6/2006 Introduction to Gaussian 37

Gaussian/GaussView @ UNC• Installed in AFS ISIS package space /afs/isis/pkg/gaussian

– Package name: gaussian– Versions: 03C02, 03D02 (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

11/6/2006 Introduction to Gaussian 38

Access GaussView• From UNIX workstation

– Type “xhost + emerald.isis.unc.edu” or “xhost + happy.isis.unc.edu”

– Login to emerald 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/gaussian/access_gv/g03_gv_instructions.htm

11/6/2006 Introduction to Gaussian 39

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.inpbsub -q month -m yatta g03 input.inpbsub -q idle -R blade g03 input.inp

11/6/2006 Introduction to Gaussian 40

Submit G03 Jobs to Servers• To submit multiple-CPU G03 jobs via LSF:

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., “mname” represents a machine name, e.g., yatta, cypress, etc., and “input.inp” denotes the input file prepared manually or via GaussView.

For examplebsub -q week -n 4 -m cypress g03 input.inp

On Emerald, only serial G03 is available because G03 is parallelized via OpenMP (for share-memory SMP machines)

11/6/2006 Introduction to Gaussian 41

Default Settings

• Temporary files– Yatta/cypress: /scr/APPS_SCRDIR– Emerald: /tmp

• Memory – Yatta/cypress: 1GB– Emerald: 512MB

• MAXDISK– Yatta/cypress: 4GB– Emerald: 2GB

11/6/2006 Introduction to Gaussian 42

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.

11/6/2006 Introduction to Gaussian 43

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

11/6/2006 Introduction to Gaussian 44

Model Potential Energy Surface

11/6/2006 Introduction to Gaussian 45

Calculating PES in Gaussian/GaussView

• Use the keyword “scan”

• Then change input file properly

11/6/2006 Introduction to Gaussian 46

Transition State Search

11/6/2006 Introduction to Gaussian 47

Calculating Transition States

11/6/2006 Introduction to Gaussian 48

Locating Transition States

11/6/2006 Introduction to Gaussian 49

TS Search in Gaussian

11/6/2006 Introduction to Gaussian 50

TS Search inGaussian/GaussView

11/6/2006 Introduction to Gaussian 51

11/6/2006 Introduction to Gaussian 52

Animation of Imaginary Frequency

• Check that the imaginary

frequency corresponds to

the TS you search for.

11/6/2006 Introduction to Gaussian 53

Intrinsic Reaction Coordinate Scans

11/6/2006 Introduction to Gaussian 54

Input for IRC Calculation

StepSize=N 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.

11/6/2006 Introduction to Gaussian 55

IRC Calculation in GaussView

11/6/2006 Introduction to Gaussian 56

Reaction Pathway Graph

11/6/2006 Introduction to Gaussian 57

Thermochemistryfrom ab initio Calculations

11/6/2006 Introduction to Gaussian 58

Thermochemistryfrom ab initio Calculations

11/6/2006 Introduction to Gaussian 59

Thermochemistry from frequency calculation

11/6/2006 Introduction to Gaussian 60

Modeling System in Solution

11/6/2006 Introduction to Gaussian 61

Calculating Solvent Effect

11/6/2006 Introduction to Gaussian 62

Calculating Solvent Effect

11/6/2006 Introduction to Gaussian 63

Solvent Effect: Menshutkin Model Reaction Transition State

11/6/2006 Introduction to Gaussian 64

11/6/2006 Introduction to Gaussian 65

NMR Shielding Tensors

11/6/2006 Introduction to Gaussian 66

NMR Example Input

%chk=ethynenmr#p hf/6-311+g(2d,p) nmr

nmr ethyne

0 1CC,1,r1H,1,r2,2,a2H,2,r3,1,a3,3,d3,0 VariablesR1=1.20756258R2=1.06759666R3=1.06759666A2=180.0A3=180.0D3=0.0

11/6/2006 Introduction to Gaussian 67

11/6/2006 Introduction to Gaussian 68

11/6/2006 Introduction to Gaussian 69

Comparison of Calculated and Experimental Chemical Shifts

11/6/2006 Introduction to Gaussian 70

QM/MM: ONIOM Model

11/6/2006 Introduction to Gaussian 71

QM/MM: ONIOM Model

From GaussView menu: Edit -> Select Layer

Low Layer Medium Layer High Layer

11/6/2006 Introduction to Gaussian 72

QM/MM: ONIOM SetupFrom GaussView menu: Calculate ->Gaussian->Method

11/6/2006 Introduction to Gaussian 73

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

11/6/2006 Introduction to Gaussian 74

QM/MM: ONIOM Setup

11/6/2006 Introduction to Gaussian 75

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 BondC-C Bond C-H BondC-H Bond

11/6/2006 Introduction to Gaussian 76

NBO Analysis

11/6/2006 Introduction to Gaussian 77

NBO in GaussView

11/6/2006 Introduction to Gaussian 78

Natural Population Analysis

#rhf/3-21g pop=nbo

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

11/6/2006 Introduction to Gaussian 79

NPA Output

Sample

11/6/2006 Introduction to Gaussian 80

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.)

11/6/2006 Introduction to Gaussian 81

QUESTIONS & COMMENTS?

Please direct comments/questions about Gaussian/GaussView to

E-mail: research@unc.edu

Please direct comments/questions pertaining to this presentation to

E-Mail: shubin@email.unc.edu

Please direct comments/questions about Gaussian/GaussView to

E-mail: research@unc.edu

Please direct comments/questions pertaining to this presentation to

E-Mail: shubin@email.unc.edu

11/6/2006 Introduction to Gaussian 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

11/6/2006 Introduction to Gaussian 83

Hands-on: Part II• Calculate/View Molecular Orbitals with GaussView

– http://educ.gaussian.com/visual/Orbs/html/OrbsGaussView.htm• Calculate/View Electrostatic Potential with GaussView

– http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm• Calculate/View Vibrational Frequencies in GaussView

– http://educ.gaussian.com/visual/Vibs/html/VibsGaussview.htm• Calculate/View NMR Tensors with GaussView

– http://educ.gaussian.com/visual/NMR/html/NMRGausview.htm• Calculate/View a Reaction Path with GaussView

– http://educ.gaussian.com/visual/RPath/html/RPathGaussView.htm