《分子电子结构》研究生课程教学资源（Electronic Structure of Molecules）7-scan
Scanning PES2022
Scanning PES 2022
Scanangleof waterAtomList Editormolecule(rigidscan)StdLAR1.Choose Z-matrix and Optimzation flags2.Choosethe corresponding opt of theinterestedbond/angle/dihedraltoRxn/ScanG1:M1:V1-AtomListEditorFile Edit ViewRows ColumnsGo To4MZ-matrixOpt7RowHighlightDTagNANBNCBondOpt1*nlaySymoolAngleDihedralShow02Show2Yes0.900083H23Show0.9600000Yes109.300092AddShow1.271921748.7722845Yes180.000000NoYesActiveSublistFilters:NoneRxn/ScanAngleOpt2*DihedralOpt1YesYes109.5000001Rxn/Scan
1. Choose Z-matrix and Optimzation flags. 2. Choose the corresponding opt of the interested bond/angle/dihedral to Rxn/Scan . Scan angle of water molecule (rigid scan) Atom List Editor Z-matrix Opt
Scan angle ofwaterTitleJob TypeMethodLinkmolecule(rigidscan)ScanRelaxed(Redundant Coord)RigidRelaxed (Z-matrix)Relaxed(Redundant Coord)1.Calculation setup/Jobtype/Scan;2. Choose RigidG1:M1:V1-GaussianCalculationSetupTitle:Keywords:#scanhf/3-21g geom=connectivityCharge/Mult.:01Job TypeTitleLink 0GeneralPBCSolvationMethodGuessPop.ScanRigid scan coordinate setupRigidAdditional Keywords:Scan CoordinateScanCoordinate2Type:AngleAtoms:3,1,2Scheme:(Unnamed Scheme)Current Value:109.5DegreesAdd scan coordinate using Redundant# of Steps:10Step Size:-10End Value:Start Value:109.59.5QuickSubmit
1. Calculation setup/Job type/Scan; 2. Choose Rigid Scan angle of water molecule (rigid scan) Rigid scan coordinate setup
Results-Scan)G1:M1:V1-H20.out(D:/doctor/mywork/undergrad..Xof171口G1:M6:V1-ScanPlotPlotsScan of Total EnergyScan of Total Energy76.420X-Axis:Scan Coordinate()-76.425Y-Axis:Total Energy (Hartree)X-76.43080.0000000000-76.443438924476.43585.0000000000-76.449898018190.0000000000-76.454730196676.44095.0000000000-76.458050066076.445100.0000000000-76.459971790276.450105.0000000000-76.46060810131100000000000-76.460070236676.455115.0000000000-76.458471300476.460120.0000000000-76.455932191476.465125.0000000000-76.4525873432T130.0000000000-76.44858784968090100110120130140150160135.0000000000-76.4441013641Scan Coordinate140.0000000000-76.4393105832145.0000000000-76.4344109699？Scan Coordinate=105,Total Energy (Hartree)=-76.4606150.0000000000-76.4296065700Right click->savedata->savedatatotxtfile155.0000000000-76.4251027144160.0000000000-76.4210968409forlateranalysisand plotting
Results-Scan Right click -> save data -> save data to txt file for later analysis and plotting
Scanthe dihedral angleoEdit-RedundantCoordinates-ofethane(relaxedscan)XM1-RedundantCoordinateEditor[1]5XStatCoordinatDihedral (5,1,2,8):Scan 10 step(s)of size 12degrees(4]81[2]1[3]2Click add, Select the new line and directlychoosetheatomsinvolvedinscan#p opt=modredundantb3lyp/6-31g(d)nosymm2DihedralF2rdinate3Scan CoordinateTake10Step(s)of size12degrees.VD5128S1012.0000000Current valuedegrees0Don't Setdihedral todegrees.G2:M1:V1-GaussianCalculation SetupApplyifgreaterthanodegreesTitle:Scan dihedral of C2H6Applyifless than0degreesKeywords:b3lyp/6-31g(a)tp optaodredundantValidStatus:Charge/Mult.01OkCancelHelpJob TypeMethodTitleLink 0GeneralGuesNotice:positiveorSean-AutomaticallychangesjobtypenegativedegreesRelaxed (Redundant cafterdesignating the redundant coordinate
Edit-Redundant Coordinates #p opt=modredundant b3lyp/6-31g(d) nosymm . . D 5 1 2 8 S 10 12.000000 Click add, Select the new line and directly choose the atoms involved in scan 1 2 3 Notice: positive or negative degrees Scan the dihedral angle of ethane (relaxed scan) Automatically changes job type after designating the redundant coordinate
Results-scan口XG1:M1:V1-ScanPlotPlotsScan of Total Energya-79.8255)-79.8260a79.8265-79.827079.8275-79.828079.8285-79.8290-79.8295bb-79.830079.8305FUTTUTUTTUTTTTTTTTTTTTUTTTTUTTTUTUTTTTUUUTT020406080100120Scan CoordinateC
a a b b c c Results-scan
Exercises:1.Drawa small organicmolecule,optimizeit andcomputeitsIRspectrum.Modelchemistry:B3LYP/6-31g(d).Frequencycorrectionfactoris0.9614(keywordscale=0.9614)2.Scan Ar-Ar distance (rigid scan). Model chemistry: MP2/aug-cc-pVTZ, from 2.3 to 6.3 A. Step size is 0.2 A. Hint: Use non-Cartesiancoordinate, edit the saved gjf by adding the scan variables: 2.30 200.2.3.Using PM6, to relaxed scan the dihedral angle of butane,from0XG2:M1-Redundant Coordinate Editorto 360°, step size 20°.文中鸟Statu CoordinateDihedral (5,1,2,8):Scan10 step(s)of size12degrees[4]C[1]CClick add,Selectthe new lineand directlychoosetheatomsinvolvedinscan[3]c[2]CDihedraloordinate:Scan CoordinateTake10Step(s)ofsize12degrees
Exercises：1. Draw a small organic molecule, optimize it and compute its IR spectrum. Model chemistry: B3LYP/6-31g(d). Frequency correction factor is 0.9614 (keyword scale=0.9614). 2. Scan Ar-Ar distance (rigid scan). Model chemistry: MP2/aug-ccpVTZ, from 2.3 to 6.3 Å. Step size is 0.2 Å. Hint: Use non-Cartesian coordinate, edit the saved gjf by adding the scan variables: 2.30 20 0.2. 3. Using PM6, to relaxed scan the dihedral angle of butane, from 0 to 360o , step size 20o . Click add, Select the new line and directly choose the atoms involved in scan
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