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Introduction to Gaussian and GaussView

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### Introduction to Gaussian and GaussView

Shubin Liu, Ph.D.

Renaissance Computing Institute

University of North Carolina at Chapel Hill

Agenda

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

Introduction to Gaussian

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

Introduction to Gaussian

Pre-requisites

- Basic UNIX knowledge
- Introduction to Scientific Computing
- An account on Emerald

Introduction to Gaussian

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

Introduction to Gaussian

About You

- Name, department, group, interest?
- Any experience before with Gaussian or GaussView?
- What do you expect to use them? What kind of systems?

Introduction to Gaussian

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

Introduction to Gaussian

Gaussian

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

Input File – Example 2

%nproc=2 !Link 0 section

%chk=water.chk

#b3lyp/6-311+G(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

r=0.98

a=109.

!Blank line

Introduction to Gaussian

Input File – Link 0 Commands %nproc %rwf %scr

- First “Link 0” options (Examples)
- %chk
- %chk=myjob.chk

- %chk
- %mem
- %mem=12MW

- $nproc=4

- %rwf=1,1999mb,b,1999mb

- %sc=e,1999mb,f,1999mb

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

Input File – Title Specification

- Brief description of calculation – for users benefit
- Terminate with a blank line

Introduction to Gaussian

Input File – Molecular Geometry If parameters used instead of numerical values then variables section follows Again end in blank line

- 1st line charge and multiplicity
- Element label and location
- Cartesian coordinate
- Label x y z

- Cartesian coordinate
- Z-matrix
- Label atoms bond length atom2 angle atm3 dihedral

Introduction to Gaussian

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

Introduction to Gaussian

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)

Introduction to Gaussian

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

Introduction to Gaussian

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)

Introduction to Gaussian

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.

Introduction to Gaussian

GaussView: Build

Introduction to Gaussian

GaussView: Build

Introduction to Gaussian

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.

Introduction to Gaussian

GaussView: Setup

Introduction to Gaussian

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.

Introduction to Gaussian

GuassView: Showing Results

Introduction to Gaussian

Surfaces

Introduction to Gaussian

Reflection-Absorption Infrared Spectrum of AlQ3

Wavenumbers (cm-1)

1473

752

1386

1338

1116

1580

1605

800

1000

1200

1400

1600

Introduction to Gaussian

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).

Introduction to Gaussian

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).

Introduction to Gaussian

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

Introduction to Gaussian

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

- Detailed document available at:

Introduction to Gaussian

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 yatta g03 input.inp

bsub -q idle -R blade g03 input.inp

Introduction to Gaussian

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 example

bsub -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)

Introduction to Gaussian

Default Settings

- Temporary files
- Yatta/cypress: /scr/APPS_SCRDIR
- Emerald: /tmp

- Memory
- Yatta/cypress: 1GB
- Emerald: 512MB

- MAXDISK
- Yatta/cypress: 4GB
- Emerald: 2GB

Introduction to Gaussian

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.

Introduction to Gaussian

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

Introduction to Gaussian

Model Potential Energy Surface

Introduction to Gaussian

Calculating PES in Gaussian/GaussView

- Use the keyword “scan”
- Then change
input file properly

Introduction to Gaussian

Transition State Search

Introduction to Gaussian

Calculating Transition States

Introduction to Gaussian

Locating Transition States

Introduction to Gaussian

TS Search in Gaussian

Introduction to Gaussian

TS Search inGaussian/GaussView

Introduction to Gaussian

Animation of Imaginary Frequency

- Check that the imaginary
frequency corresponds to

the TS you search for.

Introduction to Gaussian

Intrinsic Reaction Coordinate Scans

Introduction to Gaussian

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.

Introduction to Gaussian

IRC Calculation in GaussView

Introduction to Gaussian

Reaction Pathway Graph

Introduction to Gaussian

Thermochemistryfrom ab initio Calculations

Introduction to Gaussian

Thermochemistryfrom ab initio Calculations

Introduction to Gaussian

Thermochemistry from frequency calculation

Introduction to Gaussian

Modeling System in Solution

Introduction to Gaussian

Calculating Solvent Effect

Introduction to Gaussian

Calculating Solvent Effect

Introduction to Gaussian

Solvent Effect: Menshutkin Model Reaction Transition State

Introduction to Gaussian

NMR Shielding Tensors

Introduction to Gaussian

NMR Example Input

%chk=ethynenmr

#p hf/6-311+g(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

R1=1.20756258

R2=1.06759666

R3=1.06759666

A2=180.0

A3=180.0

D3=0.0

Introduction to Gaussian

Comparison of Calculated and Experimental Chemical Shifts

Introduction to Gaussian

QM/MM: ONIOM Model

Introduction to Gaussian

QM/MM: ONIOM Model

From GaussView menu: Edit -> Select Layer

Low Layer

Medium Layer

High Layer

Introduction to Gaussian

QM/MM: ONIOM Setup

Introduction to Gaussian

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

Introduction to Gaussian

NBO Analysis

Introduction to Gaussian

NBO in GaussView

Introduction to Gaussian

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

Introduction to Gaussian

Introduction to Gaussian

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.)

Introduction to Gaussian

Please direct comments/questions about Gaussian/GaussView to

E-mail: [email protected]

Please direct comments/questions pertaining to this presentation to

E-Mail: [email protected]

Introduction to Gaussian

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

Introduction to Gaussian

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

Introduction to Gaussian

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