ADF-中间体过渡态.docx

四 几何结构优化和频率计算几何结构优化是个非常普遍的问题，ADF可以研究多种复杂条件的几何结构优化，过渡态搜索，IRC等问题，主要使用Geometry和GeoVar关键，下面介绍这类问题解决办法。4.1 H2O的几何结构优化1、离域坐标格式$ADFBIN/adf eorTitle WATER Geometry Optimization with Delocalized CoordinatesAtoms O 0.000000 0.000000 0.000000 H 0.000000 -0.689440 -0.578509 H 0.000000 0.689440 -0.578509End Basis Type TZP Core SmallEndGeometry Optim Deloc Converge 0.0000001EndEnd InputEor2、直角坐标格式$ADFBIN/adf eorTitle WATER Geometry Optimization in Cartesians with new optimizerAtoms O 0.000000 0.000000 0.000000 H 0.000000 -0.689440 -0.578509 H 0.000000 0.689440 -0.578509End Basis Type TZP Core SmallEndGeometry Optim Cartesian Branch New Converge 0.0000001EndEnd Inputeor3、内坐标（Z-矩阵）格式$ADFBIN/adf eorTitle WATER Geometry Optimization with Internal CoordinatesAtoms Z-Matrix 1. O 0 0 0 2. H 1 0 0 rOH 3. H 1 2 0 rOH thetaEnd Basis Type TZP Core SmallEndGeoVar rOH=0.9 theta=100End Geometry Converge 0.0000001EndEnd Inputeor4.2 用Restraint关键字做限制性结构优化1、对键长进行限制$ADFBIN/adf eortitle WATER Geometry Optimization with bond length restraintATOMS 1.O 0.001356 0.000999 0.000000 2.H 0.994442 -0.037855 0.000000 3.H -0.298554 0.948531 0.000000ENDBASIS Type DZPENDINTEGRATION 4 4RESTRAINT DIST 1 2 1.03 DIST 1 3 1.03ENDGEOMETRYENDendinputeor2、对键角进行限制$ADFBIN/adf eortitle WATER geometry optimization with angle restraintATOMS 1.O 0.001356 0.000999 0.000000 2.H 0.994442 -0.037855 0.000000 3.H -0.298554 0.948531 0.000000ENDBASIS Type DZPENDINTEGRATION 4 4RESTRAINT ANGLE 3 1 2 125.0ENDGEOMETRYENDendinputeor3、对二面角进行限制$ADFBIN/adf eorTitle Restraining dihedral of ethaneSYMMETRY NOSYMATOMS 1.C -0.004115 -0.000021 0.000023 2.C 1.535711 0.000022 0.000008 3.H -0.399693 1.027812 -0.000082 4.H -0.399745 -0.513934 0.890139 5.H -0.399612 -0.513952 -0.890156 6.H 1.931188 0.514066 0.890140 7.H 1.931432 0.513819 -0.890121 8.H 1.931281 -1.027824 0.000244ENDINTEGRATION 4 4RESTRAINT DIHED 6 2 1 3 20.00ENDBASIS type DZPENDGEOMETRYENDendinputeor4.4 用Constraint关键字线性组合结构优化的限制条件1、对键长进行限制$ADFBIN/adf eortitle WATER Geometry Optimization with bond length constraintATOMS 1.O 0.001356 0.000999 0.000000 2.H 0.994442 -0.037855 0.000000 3.H -0.298554 0.948531 0.000000ENDBASIS Type DZPENDINTEGRATION 4 4CONSTRAINTS DIST 1 2 1.03 DIST 1 3 1.03ENDGEOMETRY OPTIM CARTESIAN BRANCH NEWENDendinputeor2、对键角进行限制$ADFBIN/adf eortitle WATER geometry optimization with angle constraintATOMS 1.O 0.001356 0.000999 0.000000 2.H 0.994442 -0.037855 0.000000 3.H -0.298554 0.948531 0.000000ENDBASIS Type DZPENDINTEGRATION 4 4CONSTRAINTS ANGLE 3 1 2 125.0ENDGEOMETRY OPTIM DELOCALENDendinputeor3、冻结原子的三维坐标$ADFBIN/adf eortitle WATER geometry optimization with fixed-atom constraintATOMS 1.O 0.001356 0.000999 0.000000 2.H 0.994442 -0.037855 0.000000 3.H -0.298554 0.948531 0.000000ENDBASIS Type DZPENDINTEGRATION 4 4SYMMETRY NOSYMCONSTRAINTS ATOM 1 0.0 0.0 0.0 ATOM 2 1.0 0.0 0.0ENDGEOMETRY OPTIM CARTESIAN BRANCH NEWENDendinputeor4、对两个基团之间的二面角加以限制$ADFBIN/adf eorTitle Block constraints (with a dihedral constraint)SYMMETRY NOSYMATOMS 1.C -0.004115 -0.000021 0.000023 b=b1 2.C 1.535711 0.000022 0.000008 b=b2 3.H -0.399693 1.027812 -0.000082 b=b1 4.H -0.399745 -0.513934 0.890139 b=b1 5.H -0.399612 -0.513952 -0.890156 b=b1 6.H 1.931188 0.514066 0.890140 b=b2 7.H 1.931432 0.513819 -0.890121 b=b2 8.H 1.931281 -1.027824 0.000244 b=b2ENDINTEGRATION 4 4CONSTRAINTS DIHED 6 2 1 3 20.00 BLOCK b1 BLOCK b2ENDBASIS type DZPENDGEOMETRY OPTIM DELOCALENDendinputeor五 过渡态搜索、频率分析和内反应坐标过渡态优化、频率计算和跟踪内反应坐标等都是很常见的量化计算任务，ADF中也提供这些计算，和几何结构优化一样，都使用Geometry关键字，并且在几何结构优化中的很多关键字在这类计算中同样适用。下面是一组例子，分别使用了这4类计算，可以看做是研究反应机理类问题的一个过程。计算中使用了很多Geometry关键字中的字段。5.1 线性过渡计算$ADFBIN/adf eorTitle HCN Linear Transit, first partNoPrint SFO, Frag, Functions, Computation Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.3 0 0 3 H 1 2 0 1.0 th 0EndBasis Type DZPEndSymmetry NOSYMIntegration 6.0 6.0Geometry Branch Old LinearTransit 10 Iterations 30 4 Converge Grad=3e-2, Rad=3e-2, Angle=2ENDGeovar th 180 0EndEnd Inputeormv TAPE21 t21.LTrm logfile$ADFBIN/adf eorTitle HCN Linear TransitNoPrint SFO,Frag,Functions,ComputationRestart t21.LTFragments N t21.N C t21.C H t21.HEnd Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.3 0 0 3 H 1 2 0 1.0 th 0Endsymmetry NOSYMIntegration 6.0 6.0Geometry Branch Old LinearTransit 10 Converge Grad=3e-2, Rad=3e-2, Angle=2ENDGeovar th 180 0EndEnd Inputeorrm logfilemv TAPE21 HCN_LT.t215.2 频率计算$ADFBIN/adf eorTitle HCN Frequencies in LT max (approx), moderate precisionNoPrint SFO,Frag,Functions,ComputationIntegration 6.0 6.0Fragments N t21.N C t21.C H t21.HEndAtoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.186 0 0 3 H 1 2 0 1.223 70 0EndGeometry FrequenciesEndEnd Inputeormv TAPE21 HCN_Freq.t215.3 过渡态搜索1、利用初始猜测的Hessian矩阵进行过渡态搜索$ADFBIN/adf eorTitle HCN Transition State, automatic initial HessianNoPrint SFO,Frag,Functions,ComputationIntegration 6.0 6.0Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.186 0 0 3 H 1 2 0 1.223 70 0EndFragments N t21.N C t21.C H t21.HEndGeometry TransitionState Converge Grad=0.0001EndEnd Inputeorrm TAPE21 logfile2、利用频率分析的结果进行过渡态搜索$ADFBIN/adf eorTitle HCN Transition State, initial Hessian from Freq runNoPrint SFO,Frag,Functions,ComputationRestart HCN_Freq.t21Save TAPE13Integration 5.0 5.0Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.186 0 0 3 H 1 2 0 1.223 70 0EndFragments N t21.N C t21.C H t21.HEndGeometry TransitionStateEndEnd Inputeormv TAPE13 t13.TSrm logfilemv TAPE21 HCN_TS.t213、在过渡态搜索过程设置限制条件$ADFBIN/adf eorTitle HCN constrained TS searchNoPrint SFO,Frag,Functions,ComputationRestart HCN_Freq.t21Integration 5.0 5.0Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 rNC 0 0 3 H 1 2 0 1.223 70 0EndGeoVar rNC=1.186 FEndFragments N t21.N C t21.C H t21.HEndGeometry TransitionState Converge Grad=0.0001EndEnd Inputeorrm TAPE21 logfile5.4 IRC方法跟踪反应路径1、从过渡态到反应物$ADFBIN/adf eorTitle HCN IRC partial path (forward)NoPrint SFO,Frag,Functions, ComputationIntegration 6.0 6.0Restart t13.TSSave TAPE13Atoms Internal 1 C 0 0 0 0 0 0 2 N 1 0 0 1.186 0 0 3 H 1 2 0 1.223 70 0EndFragments N t21.N C t21.C H t21.HEndGeometry IRC Points=5 Converge Grad=0.0005EndSCF Converge 0.00000001EndEnd Inputeormv TAPE13 t13.IRC_1rm TAPE21 logfile2、从过渡态到产物$ADFBIN/adf eorTitle HCN IRC partial part