《分子电子结构》研究生课程教学资源（Electronic Structure of Molecules）ESM-1-Intro2Gaussview

Intro toGaussian&GaussView2022

Intro to Gaussian & GaussView 2022

FiletypesofGaussianfilefunctionextensionSpecify resources for computation,.gijf (windows)Inputfilecomputation type, method, information.com (linux)aboutthe molecule...Variouscomputationresults,e.g.structureof.out(windows)geometricoptimization,populationanalysis,Outputfile.log (linux)Mo energy, density matrix, excitationenergy....chkMolecular structure,orbital coefficients,Checkpointfile.fchkforce constant ..All information,including electronintegrals.rwfRead-write filederivatives.Big.Automatically deleted afternormaltermination..inp.de2.int.sce.gInformationduring calculation and will beOtherfilesXXautomaticallyremovedafterthejobisdone

File types of Gaussian file extension function Input file .gjf (windows) .com (linux) Specify resources for computation, computation type, method, information about the molecule. Output file .out(windows) .log (linux) Various computation results, e.g. structure of geometric optimization, population analysis, MO energy, density matrix, excitation energy. Checkpoint file .chk .fchk Molecular structure, orbital coefficients, force constant . Read-write file .rwf All information, including electron integrals, derivatives. Big. Automatically deleted after normal termination. Other files .inp .de2 .int .sce .g xx Information during calculation and will be automatically removed after the job is done

GaussView5and6X口&GaussView5.0.9Filee Edit View Calculate Results Windows HelpPRCarbon Tetrahedral-智一栏XG际Carbon TetrahedralBuilder Fragment:Build newmoleculeHighlightedwindow,.shortcutatom isthekey:ctrl+NconnectingatomCommonshortcutkeysa, select allctrl+l, print screen;alt+ left/right button, rotate an isolated molecular moiety;alt+shift+left button, translate an isolated molecular moiety

GaussView 5 and 6 Highlighted atom is the connecting atom Build new molecule window, shortcut key: ctrl+N Common shortcut keys a, select all ctrl+I, print screen; alt+ left/right button, rotate an isolated molecular moiety; alt+shift+left button, translate an isolated molecular moiety;

GaussviewHelp/The BuilderpaletteCenterRebondNewXBuildermoleculebrgroupChooseO-RfragmentClean (byhelpSelect aForce field)fragment9Set bond lengthangle and dihedralDe-select-HX-Select allAdd or remove valency (key n) symmetrize(key a)厦XAtomselectionAAtom listeditorRedundantcoordinateReditorMO editor

Gaussview Help/The Builder palette Choose fragment Select a fragment Set bond length, angle and dihedral Add or remove valency Atom selection New molecule group Center Rebond Clean (by Force field) De-select (key n) Select all (key a) symmetrize help Atom list editor Redundant coordinate editor MO editor

Notice the linking atomElementFragments+Ring FragmentsMDHeHOBeNeAlSiDCNaMsArCrFeCoNiCuZhScTiVMnGaGeBSSeBrKr82OZrNbMoIcRuRhPdCdInSnSbRbSYAgTeTXHfOsIrHg11PbBiTaWRePtAuPoBaLaoSRMtAcRfDbSgBhHsFrRaCeHoPrNdEuGdTbDyErPmSmImYbLuThBkEsCCfFmMdDaTTNpPuAmNotrans-cis-DecalinDecalinSelect Carbon Fragment:1C60AtomR-GroupFragments-R大CHHCHCHECHCHC-CHCHHBiologicalFragments+?Amino AcidType:NHAlanineCentral FragmentCloseHelpOTSOMSH-CO

Notice the linking atom

Custom fragmentsBuild a structure,then in the Custom fragmentswindow, right click, select New Fragment FromActive Molecule, current fragment will be addedas a new fragment template and can be reloadedin the future.&CustomFragmentsXMLibrary:C:/Users/lccmiki/DesktopGroupDescriptionFragment白FragmentAFragment A2OkHelp

Custom fragments Build a structure, then in the Custom fragments window, right click, select New Fragment From Active Molecule, current fragment will be added as a new fragment template and can be reloaded in the future

Customize the view(rightclick/View)口XG1:M1:V1-NewBuilderFileEditViewAddViewLCalculateCenterOResultsBuilderWindowsHydrogensVHelpDummiesLabelsSymbolsBondsSynchronizeCartesian AxesStereochemistryPositioning ToolsDisplayFormat...Ctrl+DBuild Select Placement4 atoms, 16 electrons, neutral, singlet

Customize the view (right click/View)

(right click/View/Display Format or Ctrl+D)G1:M1:V1-Display FormatXXG1:M1:V1-DisplayFormatMoleculeSurfaceGeneralTextSurfaceGeneralMoleculeTextTubeHigh Layer:Format:TransparentVyMeshBall&StickTransparent OptionsMedium Layer:SolidBall &Bond TypeLow Layer:TransparentOpaqueTubeTransparentwireframeUse van derFade mapped surface valuesNone Use BondAnimation Delay (msec):LCScale Radii by76IsoValues:BothVHide BacksideZ-Clip: (min)(max)z-Clip: (min)(max)OkDefaultHelpOkDefaultCancelCancelHelp

(right click/View/Display Format or Ctrl+D)

Calculation setup(calculate/Gaussiancalculation setup/ctrl+G)XG1:M1:V1-Gaussian Calculation SetupTitle:Check chargeand spinKeywords:hf/3-21ggeon=connectivityCharge/Mult.acumultiplicity!Job TypeAdd.InpMethodTitleLink0GeneralJobtypeEnersyEnersyOptimizationFrequencyOpt+FreqIRCScanStabilityHMRAdditional Keywords:UpdateScheme:(Default Scheme)CancelDefaultsHelpSubmit...QuickLaunchEdit...Retain

Calculation setup (calculate/Gaussian calculation setup/ctrl+G) Check charge and spin multiplicity! Job type

MethodsXG1:M1:V1-Gaussian Calculation SetupTitle:hf/3-21g geon=connectivityKeywords01Charge/Mult.:MethodTitleGeneralPBCJob TypeLink 0GuessKBOSolvationAdd.InpMultilayer ONIoM ModelMethod:Ground StateHartree-FockVDefault SpinMMechanics.3-21GBasis Set:Semi-empirical.0SinglCharge:Spin:Hartree-FockDFTJP2Select Custom..., thenIP4CCSDtype key words inBDCASSCFAdditionalKeywordsCompound.External job..Custom.Additional Keywords:Update(Default Scheme)SchemeCancelEdit...DefaultsHelpSubmit.Quick LaunchRetain

Select Custom., then type key words in Additional Keywords Methods