Example: TS and IRC for Claisen reactionΒΆ

Download TS_and_IRC_Claisen.run

#! /bin/sh

# Transition State Search (TS search) followed by Intrinsic Reaction 
# Coordinates (IRC) for two similar Claisen rearrangement reactions.


# ============================================================
# Claisen rearrangement from C=CCC1C=CC=CC1=O to C=CCOc1ccccc1 
# ============================================================

AMS_JOBNAME=TS_molecule $ADFBIN/ams << eor

Task TransitionStateSearch

System
   Atoms
      C  -1.6622561642524  -1.4933421191817   0.6484353677288        
      C  -2.6070283916282  -1.7718977641902  -0.3933564306530 
      C  -2.7546368861548  -3.0534770331072  -0.8757259422474 
      C  -1.9443405437492  -4.1131780924428  -0.3870796280948 
      C  -1.0139402388630  -3.8827189276564   0.5979937257975 
      C  -0.7543606665660  -2.5518266272325   1.0788971265869
      H  -3.2590342954832  -0.9734836183880  -0.7410179986476 
      H  -3.5074724102535  -3.2690301027846  -1.6324229738243
      H  -2.1044351565280  -5.1220091436618  -0.7615296311573 
      H  -0.4323033724363  -4.7107876462166   1.0021729248699
      H  -0.3533176373037  -2.4841001370767   2.0927436180830
      O  -1.5058234397159  -0.2844936546832   1.1029538316409
      C   0.1375150486634   0.3928947854321   0.4626789880484 
      C   1.0578648498087  -0.6180364119671   0.7737587143345 
      C   0.8861173890663  -1.8991002496105   0.2125497351161 
      H   0.5725481135101  -1.9591100578644  -0.8292382400922 
      H  -0.2171264706145   0.4859594211539  -0.5641152540806 
      H   0.1902646842718   1.3359879065177   1.0025369222419
      H   1.5779002347488  -0.5540482019233   1.7307360489935
      H   1.6031168776346  -2.6724262749099   0.4842127285858 
   End
End

Properties NormalModes=Yes

GeometryOptimization
    InitialHessian Type=Calculate
End

Engine DFTB
    ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor


AMS_JOBNAME=IRC_molecule $ADFBIN/ams << eor

Task IRC

IRC
   MaxIterations 1000
   InitialHessian 
      Type FromFile 
      File TS_molecule.results/dftb.rkf
   End
end

LoadSystem 
    File TS_molecule.results/ams.rkf
End

Engine DFTB
    ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor


# ===========================================================================
# Claisen rearrangement for a (periodic) polymer containing the same aromatic 
# ring of the previous calculation (from C=CCC1C=CC=CC1=O to C=CCOc1ccccc1)
# ===========================================================================

AMS_JOBNAME=TS_polymer $ADFBIN/ams << eor

Task TransitionStateSearch

System
   Atoms
      C  9.4367476128766   1.6156795441351   0.8542644025030
      C  8.6813349262903   0.7302865575002   0.0170374963868
      C  9.3238583586638  -0.1438417574104  -0.8314773024306
      C  10.741095802442  -0.1538813927018  -0.9297572682512
      C  11.499909556383   0.6929842950328  -0.1576524435776
      C  10.884234857485   1.6861365363275   0.6817028097694
      C  7.1928255650616   0.6847044785103   0.0090333093191
      H  8.7472521390038  -0.8479982636647  -1.4293934603813
      H  11.224348014063  -0.8771406786637  -1.5831686891584
      C  12.930798908912   0.8113031163622  -0.1971191730819
      H  11.474366091679   2.0120169601893   1.5412690799783
      O  8.8401614254340   2.4539245100299   1.6503819438045
      C  9.0152184164720   4.1939147755043   0.9354292967913
      C  10.386800460742   4.3070474573655   0.6675488559614
      C  10.983233806221   3.4166811386158  -0.2473786535066
      H  10.425317882010   3.1661173633779  -1.1491528320010
      H  8.3301833043316   4.0024301166114   0.1091130317749
      H  8.5863952766270   4.7863410214548   1.7409077918798
      H  11.023307058306   4.7274400682699   1.4475913648158
      H  12.053474297431   3.5124067242738  -0.4244212846926
      C  13.897191373368  -0.0308805104165  -0.7206407708622
      C  15.267346128343   0.2274543686942  -0.4348415320624
      C  16.387786908031  -0.4341710477973  -0.8962646879782
      C  6.2048264493065  -0.0924013581064  -0.6266734325417
      C  4.8694123304551   0.1638639419185  -0.3442585289372
      C  3.7074226634814  -0.4584344973285  -0.8689206409329
      C  2.4653410147781   0.0102007864139  -0.4848760767909
      H  16.298210512111  -1.2787892169088  -1.5797017846452
      H  3.7984002771976  -1.2806821291979  -1.5787594353897
      H  6.8240750625775   1.4435007199212   0.7047818340481
      H  13.314194383001   1.6434188966421   0.3984353613768
      H  13.626424975736  -0.8770823766787  -1.3528414377622
      H  15.451469431625   1.0743039058568   0.2322503424471
      H  2.4641684561885   0.8477050600186   0.2182734314177
      H  6.4819803798672  -0.8741436365939  -1.3339335062636
      H  4.6807561767470   0.9698264886906   0.3703766590249
   End
   Lattice
      15.210 0.0 0.0
   End
End

Properties
    NormalModes Yes
End

GeometryOptimization
    Method Quasi-Newton
    InitialHessian Type=Calculate
End

Engine DFTB
    ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor


AMS_JOBNAME=IRC_polymer $ADFBIN/ams << eor

Task IRC

IRC
   MaxIterations 1000
   InitialHessian 
      Type FromFile 
      File TS_polymer.results/dftb.rkf
   End
   Direction Forward
end

LoadSystem 
    File TS_polymer.results/ams.rkf
End

Engine DFTB
    ResourcesDir DFTB.org/3ob-3-1
EndEngine
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