Example: TS and IRC for Claisen reaction¶
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 $AMSBIN/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
Model SCC-DFTB
ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor
AMS_JOBNAME=IRC_molecule $AMSBIN/ams << eor
Task IRC
IRC
MaxIterations 1000
InitialHessian
Type FromFile
File TS_molecule.results
End
end
LoadSystem
File TS_molecule.results/ams.rkf
End
Engine DFTB
Model SCC-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 $AMSBIN/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
Model SCC-DFTB
ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor
AMS_JOBNAME=IRC_polymer $AMSBIN/ams << eor
Task IRC
IRC
MaxIterations 1000
InitialHessian
Type FromFile
File TS_polymer.results
End
Direction Forward
end
LoadSystem
File TS_polymer.results/ams.rkf
End
Engine DFTB
Model SCC-DFTB
ResourcesDir DFTB.org/3ob-3-1
EndEngine
eor