《分子电子结构》研究生课程教学资源（Electronic Structure of Molecules）10-CubeFile
Cubefilesandcontour/density/electrostaticpotential plots2022
Cube files and contour/density/electrostatic potential plots 2022
Cubefilegeneratedfromchkfile1.Open a normally terminated chkfile,Results->Surfaces/contours-cube ActionsNew cubeType.The default is Molecular Orbital.Select the orbital number and its grid density (Coarse is the default).G1:M1:V1-SurfacesandContoursXCubes Available:Cube ActionsSurface ActionsySurfaces kvailable:XG1:M1:V1-Generate CubesOrbitalMolecular OrbitalType:[Isovaluel fOrbitals:NumberHOMOAlpha8ContoursAons26Virt80cGrid:Coarse2PointsAddviewsOkCancelHelpCloseHelp
1. Open a normally terminated chk file, Results→ Surfaces/Contours→ cube Actions→ New cube→ Type. The default is Molecular Orbital. Select the orbital number and its grid density (Coarse is the default). Orbital Number Cube file generated from chk file
2.For the cubefile,Surfaces actions New surfaceto generatethe MOG1:M1:V1-SurfacesandContoursXCubes kvailable:Cube ActionsMD(mo=8:npts=42,40,40：res(A)=0.176392,0.176392,0.176392)Chooseto showSurface ActionsySurfaces kvailableorhideMO（(MD=8)：isoval=0.02）(Showing）an orbital[Isovalue|for new surfaces:MO=Density--0.0200000.000400ContourskvailableContour ActionsAdd views fornew surfaoes/contoursCloseHelpa3. Save cube file.ln Cubes Available section,choose a MO CubeActions →SaveCube
2. For the cube file, Surfaces actions→ New surface to generate the MO Choose to show or hide an orbital 3. Save cube file. In Cubes Available section, choose a MO → Cube Actions → Save Cube
Plot IsosurfaceOpenchkfile,Results→Surfaces/Contours→CubeActionsNewCubeG1:M1:V1-Generate CubesXTotal DensityVType:SCEforHFandDETcalculations;MP2forSCFDensity Matrix:MP2calculationsUse full density matrixIncludingcontribution fromGrid:MediunPoints.coreelectronsOkCancelHelpClick OK,grid data are generated, select Surface Actions NewG1:M1:V1-SurfacesandContoursXsurfacesCubes Available?Cube AotionsElectron densityfromTotal SCFDensity(npts84,79,79:res(A)>Surfaces AvailableSurface ActionsElectron densityfrom Total SCFDensity(isoval=0.0004)(Showing)|Isovaluefornewsurfaces:MO0.020000Density0.000400
Open chk file, Results → Surfaces/Contours → Cube Actions → New Cube SCF for HF and DFT calculations; MP2 for MP2 calculations Including contribution from core electrons Click OK, grid data are generated, select Surface Actions → New surfaces Plot Isosurface
XG1:M1:V1-SurfacesandContoursSpin densityCubes Available:Cube ActionsOnlyforopen-shell systemsXG1:M1:V1-GenerateCubesMolecular OrbitalType:SurMethyl radicalMolecular OrbitalOrbitals:# opt freq b3lyp/6-31g(d)Total DensityHOMD5VAlpha DensityAlphaBeta Density5OcoAlpha300016 Virt BetaTitle Card RequiredI:Spin DensityESPGridCoarseConCurrent Density02Shielding Densityc-0.511049140.233649260.00000000OkSubtraot Two CubesH-0.15439471-0.775160740.00000000AddTwo CubesScale a CubeH0.87365150-0.154376300.73804745Square a CubeAddviewsfor new surfaH0.00000000-1.581049140.23366245CloseHelpG2:M1:V1-SurfacesandContoursxCubes Available:Cube ActionsElectron densityfrom Spin SCFDensity (npts=40,40,40 :res (A)=0<>Surfaces kvailable:Surface ActionsElectron density from Spin SCF Density(isoval -0.05)(Showing)[Isovalue|for new surfaces:MODensity0.0200000.050000
Only for open-shell systems Methyl radical # opt freq b3lyp/6-31g(d) Title Card Required 0 2 C -0.51104914 0.23364926 0.00000000 H -0.15439471 -0.77516074 0.00000000 H -0.15437630 0.73804745 0.87365150 H -1.58104914 0.23366245 0.00000000 Spin density
ElectrostaticpotentialClick OK, then SurfaceActions-> NewMappedResults> Surfaces/Contours,Surfaceclick CubeActionsNew CubeG1:M1:V1-SurfaceMappingXG1:M1:V1-GenerateCubesXUsean existing cubeType:Total DensityGenerate values only at surface pointsoSCFDensity Matrix:Type:ESPVUse full density matrixSCFDensity Matrix:Grid:MediunPointsOkHelpCancelOkCancelHelpG1:M1:V1-Efectron density from Total SCFDensit.G1:M1:V1 -Electron density from Total SCF Densit..OL.157e4.157-2157.-2-4.157.-Adjust displayformat (rightclick),surfacesettingSurface MapValoe0.0253456InquireSeleetAtonl4stoss,16laetrons, neutral,singletInquire Soleet Aton 1
Results→ Surfaces/Contours, click Cube Actions→New Cube Click OK, then Surface Actions→ New Mapped Surface Adjust display format (right click), surface setting Electrostatic potential
Contourplot,e.g.total densityContourActionsNewContourG1:M1:V1-SurfacesandContoursXCubes Available:Cube Actions-G1:M1:V1-GenerateContoursXBydefault,projected2-D Grid:Plane:AngstromsNormal1.0G1:M1:V1-GenerateCubesXtotheXYplane1f-5.05.0Origin0.0Iype:Total DensitySurfaceL1Aotionsy5.05.0Define Plane.ResolutionSCFDensity Matrix:Cube:IsoValues:Use full density matrixOUse an existing cube[Isovalu0004000.001OGeneratevalues fortheplanar grid0.002PointsGrid:CoarseContour:ActionstElectron density from Total SCF Density (npts420.0040.008OkCancelHelp0.020.040.08Addviews for newsurfaces/contours0.20.40.8OkCancelHelpResultsofreducedthe isovalues
Contour Actions→ New Contour Results of reduced the isovalues By default, projected to the XY plane Contour plot, e.g. total density
Contourplot,e.g.molecularorbitalG1:M1:V1-GenerateContoursX2-D Grid:Plane:AngstromsNormalVeotor=05.05.0Origin Point=V"5.05.0DefinePlane.Resolution1IsoValues:Cube:0.001OUse an existing cube0.001Generatevalues for theplanar grid0.002MO(mo=8：npts=42,40,40：res(A)=0.176392,0.0040.0080.020.040.080.20.40.8OkHelpCancelBy default
By default Contour plot, e.g. molecular orbital
Project MO to the plane vertical to the C=O residing planeclickdefineplaneG1:M1:V1-GenerateContours-DefinePlaneMethod:Nornal VectorVAtom(s)Origin point O::n000n00nn.000000000000000Atom(s)Nornal point 000000Translate plane long ONby0.00000000nstron:Hel,01ancaNormal Vector:O,o,1Normal Vector:1,o,Normal Vector:1,o,0Origin Point: O,o,0Origin Point: 2,0,0Origin Point:O,o,0Default
Project MO to the plane vertical to the C=O residing plane, click define plane Normal Vector：0,0,1 Origin Point：0,0,0 Default Normal Vector：1,0,0 Origin Point：0,0,0 Normal Vector：1,0,0 Origin Point：2,0,0
XG1:M1:V1-GenerateContours2-D Grid:Plane:AngstromsHormalVector=1I=-5.05.0Origin Point=0V5.05.1Define Plane..Resolution1IsoValues.Cube:0.001O Use an existing cube0.001OGeneratevalues forthe planargrid0. 002ChoosetheproperMO（mo=8:npts=42,40,40:res(A)0.176392,0.004Electron density from Total SCF Density (npts =42)0.008cubefile0. 020.040.080.20.40.8OkCancelHelp
Choose the proper cube file
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