Introduction to Gaussian and GaussViewShubin Liu, Ph.D.Renaissance Computing InstituteUniversity of North Carolina at Chapel Hill

Introduction to Gaussian

AgendaIntroductionCapabilitiesInput File PreparationGaussian GUI GaussViewRun G03 Jobs @ UNC-CHSome Advanced TopicsHands-on Experiments

Introduction to Gaussian

Course GoalWhat Gaussian/GaussView packages areHow to prepare input files via GaussView How to run G03 jobs on UNC-CH serversHow to view G03 resultsLearn selected advanced topicsHands-on experiments

Introduction to Gaussian

Pre-requisitesBasic UNIX knowledgeIntroduction to Scientific ComputingAn account on Emerald

Introduction to Gaussian

About MyselfPh.D. from Chemistry, UNC-CHCurrently Senior Computational Scientist @ UNC ITS Research Computing DivisionResponsibilities:Support Comp Chem/Phys/Material Science software, Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.Engagement projects with faculty members on campusConduct own research on Comp ChemDFT theory and conceptSystems in biological and material science

Introduction to Gaussian

About YouName, 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 & GaussViewGaussian 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.Vendors website: http://www.gaussian.com

Introduction to Gaussian

Gaussian

Introduction to Gaussian

Gaussian 98/03 FunctionalityEnergiesMM: AMBER, Dreiding, UFF force fieldSemiempirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3HF: closed-shell, restricted/unrestricted open-shellDFT: many local/nonlocal functionals to chooseMP: 2nd-5th order; direct and semi-direct methodsCI: single and doubleCC: single, double, triples contributionHigh accuracy methods: G1, G2, CBS, etc.MCSCF: including CASSCFGVB

Introduction to Gaussian

Gaussian 98/03 FunctionalityGradients/Geometry optimizationsFrequencies (IR/Raman, NMR, etc.)Other propertiesPopulations analysesElectrostatic potentialsNMR tensorsSeveral solvation models (PCM, COSMOS)Two and three layer ONIOM E, grad, freqTransition state searchIRC for reaction path

Introduction to Gaussian

New in Gaussian 03Molecular DynamicsBOMD Born-Oppenheimer MDADMP Atom-Centered Density Matrix PropagationPeriodic Boundary Conditions (PBC) HF and DFT energies and gradientsProperties with ONIOM modelsSpin-spin coupling and other additions to spectroscopic propertiesAlso 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 insensitiveSpaces, commas, tabs, forward slash as delimiters between keywords! as comment line/sectionDivided into sections (in order)Link 0 commands (%)Route section what calculation is to doTitleMolecular specificationOptional additional sections

Introduction to Gaussian

Input File Example 1# HF/6-31G(d)!Route section !Blank linewater energy !Title section !Blank line0 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

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 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

Introduction to Gaussian

Input File Link 0 CommandsFirst 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

Introduction to Gaussian

Input File Keyword SpecificationKeyword line(s) specify calculation type and other job optionsStart with # symbolCan be multiple linesTerminate with a blank lineFormatkeyword=optionkeyword(option)keyword(option1,option2,)keyword=(option1,option2,)Users guide provides list of keywords, options, and basis set notionhttp://www.gaussian.com/g_ur/keywords.htm

Introduction to Gaussian

Introduction to Gaussian

Basis SetMinimal 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

Introduction to Gaussian

Input File Title SpecificationBrief description of calculation for users benefitTerminate with a blank line

Introduction to Gaussian

Input File Molecular Geometry1st line charge and multiplicityElement label and locationCartesian coordinateLabel x y zZ-matrixLabel atoms bond length atom2 angle atm3 dihedralIf parameters used instead of numerical values then variables section followsAgain end in blank line

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 Utilitiesformchk formats checkpoint file so it can be used by other programscubgen generate cube file to look at MOs, densities, gradients, NMR in GaussViewfreqchk retrieves frequency/thermochemsitry data from chk filenewzmat 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: BuildBuild 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 structuresConstrain 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: SetupMolecule 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.

Introduction to Gaussian

GaussView: Setup

Introduction to Gaussian

GuassView: Showing ResultsShow 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

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Surfaces

Introduction to Gaussian

Reflection-Absorption Infrared Spectrum of AlQ37521116133813861473158016051600140012008001000Wavenumbers (cm-1)

Introduction to Gaussian

GaussView: VCD (Vibrational Circular Dichroism) SpectraGaussView 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. sterle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).

Introduction to Gaussian

GaussView: ONIOMBacteriorhodopsin, 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 @ UNCInstalled in AFS ISIS package space /afs/isis/pkg/gaussianPackage name: gaussianVersions: 03C02, 03D02 (default version)Type ipm add gaussian to subscribe the serviceAvailabilitySGI Altix 3700, cedar/cypress IBM P690, happy/yattaLINUX cluster, emerald.isis.unc.eduLINUX Cluster, topsail.unc.edu (available upon request)Package information available at: http://help.unc.edu/6082

Introduction to Gaussian

Access GaussViewFrom UNIX workstationType xhost + emerald.isis.unc.edu or xhost + happy.isis.unc.eduLogin to emerald or happySet display to your local hostInvoke gaussview or gview via LSF interactive queueFrom PC desktop via X-Win32 or SecureCRTDetailed document available at:http://www.unc.edu/atn/hpc/applications/science/gaussian/access_gv/g03_gv_instructions.htm

Introduction to Gaussian

Submit G03 Jobs to ServersTo 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

Introduction to Gaussian

Submit G03 Jobs to ServersTo 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)

Introduction to Gaussian

Default SettingsTemporary filesYatta/cypress: /scr/APPS_SCRDIREmerald:/tmpMemory Yatta/cypress: 1GBEmerald: 512MBMAXDISKYatta/cypress: 4GBEmerald: 2GB

Introduction to Gaussian

Advanced TopicsPotential energy surfacesTransition state optimizationThermochemistryNMR, VCD, IR/Raman spectraNBO analysisExcited states (UV/visible spectra)Solvent effectPBCONIOM modelABMD, BOMD, etc.

Introduction to Gaussian

Potential Energy SurfacesMany 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 geometryEnergy is plotted on the vertical axis, geometric coordinates (e.g bond lengths, valence angles, etc.) are plotted on the horizontal axesA PES can be thought of it as a hilly landscape, with valleys, mountain passes and peaksReal 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/GaussViewUse 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

Introduction to Gaussian

Animation of Imaginary FrequencyCheck that the imaginaryfrequency corresponds tothe TS you search for.

Introduction to Gaussian

Intrinsic Reaction Coordinate Scans

Introduction to Gaussian

Input for IRC CalculationStepSize=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

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 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

Introduction to Gaussian

Introduction to Gaussian

Introduction to Gaussian

Comparison of Calculated and Experimental Chemical Shifts

Introduction to Gaussian

QM/MM: ONIOM Model

Introduction to Gaussian

QM/MM: ONIOM ModelFrom GaussView menu: Edit -> Select LayerLow LayerMedium LayerHigh Layer

Introduction to Gaussian

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

Introduction to Gaussian

QM/MM: ONIOM SetupFor the medium and low layers:

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 BondC-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 0.4209060.000111 H-1.188060 -1.1611350.000063 N-1.084526 -0.1573150.000032 C0.163001 0.386691-0.000154 O1.196265 -0.2463720.000051 H0.140159 1.4922690.000126

Introduction to Gaussian

NPA Output Sample

Introduction to Gaussian

Further ReadingsComputational 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

QUESTIONS & COMMENTS?Please direct comments/questions about Gaussian/GaussView toE-mail: research@unc.eduPlease direct comments/questions pertaining to this presentation toE-Mail: shubin@email.unc.edu

Introduction to Gaussian

Hands-on: Part IAccess GaussView to Emerald cluster from PC desktopIf not done so before, type ipm add gaussianCheck if Gaussian is subscribed by typing ipm qGet to know GaussView GUIBuild a simple molecular modelGenerate an input file for G03 called, for example, input.comView and modify the G03 input fileSubmit 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 IICalculate/View Molecular Orbitals with GaussView http://educ.gaussian.com/visual/Orbs/html/OrbsGaussView.htmCalculate/View Electrostatic Potential with GaussView http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htmCalculate/View Vibrational Frequencies in GaussViewhttp://educ.gaussian.com/visual/Vibs/html/VibsGaussview.htmCalculate/View NMR Tensors with GaussView http://educ.gaussian.com/visual/NMR/html/NMRGausview.htmCalculate/View a Reaction Path with GaussView http://educ.gaussian.com/visual/RPath/html/RPathGaussView.htm

Introduction to Gaussian

Research Computing, ITS, UNC-CHIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CHIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CHIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CH- begining to look at some organic semiconductors- very good agreement with ALQ3 - an electron transport material- so many bands that intensities are essential for identifying peaksIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CHIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CHPass around copies of the textsWe can get the book store to order some if there is enough demandMost will need to buy Exploring Chemistry we need to order that directly from GaussianIntroduction to Gaussian & GaussViewResearch Computing, ITS, UNC-CHIntroduction to Gaussian & GaussView