AFIRサンプル

Multi-component algorithm (MC-AFIR)

Multi-component algorithm (MC-AFIR)

A stochastic search for AFIR paths starting from random mutual orientations and positions is performed when the MC-AFIR keyword is designated. An example for the Aldol reaction is shown below:

MC-AFIR/B3LYP/6-31G
 
0 1
C        0.000000    0.000000   -0.542432   1
O        0.000000    0.000000    0.689131   1
H        0.000000    0.933503   -1.129226   1
H        0.000000   -0.933503   -1.129226   1
C        0.000000    0.449088    0.000000   2
C        1.229479   -0.074689    0.000000   2
O       -1.202903   -0.246241    0.000000   2
H       -0.199138    1.513645    0.000000   2
H        1.411363   -1.146198    0.000000   2
H        2.098519    0.571041    0.000000   2
H       -1.064389   -1.214959    0.000000   2
Options
NFault = 50
Add Interaction
Fragm.1 = 1,2
Fragm.2 = 5-7,11
1 2
GAMMA = 200
END
 

The last integer in each Cartesian coordinate is for random distribution of each molecule; in this case, HCHO is part #1 and H2C=CHOH is part #2 (see Part designation for random structure generation).

The NFault = 50 keyword provides a stopping criterion, where the stochastic search will be terminated when the last 50 AFIR paths give no new product. In a MC-AFIR calculation, you need to specify a stopping criterion by using NFault = n or NSample = n keyword.

There are four lines between the Add Interaction … END keywords:
(1) Fragm.1 = 1,2 specifies that atoms 1 and 2 belong to fragment #1 (atoms belonging to the fragment A of the AFIR function),
(2) Fragm.2 = 5-7,11 specifies that atoms 5–7 and 11 belong to fragment #2 (atoms belonging to the fragment B of the AFIR function),
(3) the artificial force is applied between the fragments #1 and #2,
(4) the initial γ value is set to 200s kJ/mol and is gradually increased to 200 kJ/mol, where s is the random number between 0 and 1.

The history of AFIR minimizations and corresponding AFIR path profiles appear in xxx_EQn.log files. For example, this AFIR minimization gives the aldol addition product (3-hydroxypropanal, CHOCH2CH2OH) from HCHO and H2C=CHOH.

# Geometry optimization starting from a random structure
 
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
 
# ITR. 0
C         -0.540936514510          0.642893723683          0.666366212385
O          0.026751246314          0.125252441047          1.628928174905
H         -0.105004419262          1.492775128740          0.115530615210
H         -1.517832851012          0.286285985996          0.299951804105
C          0.568973384233         -0.053494217478         -0.791852842498
C         -0.262880591377          0.673833504707         -1.543500569145
O          0.268899839016         -1.228357438722         -0.113538516775
H          1.607310832988          0.204482332750         -0.623802280651
H         -1.302735396999          0.400164089027         -1.701678825180
H          0.086155801452          1.577613934590         -2.026773044611
H         -0.663847278893         -1.495343702957         -0.241217177722
           Item                    Value                Threshold
           ENERGY       -268.019793471042
           Spin(**2)       0.000000000000
           LAMDA          -0.352906091272
           TRUST RADII     0.100000000000
           STEP RADII      0.099999989666
  Maximum  Force           0.210290244955          0.000060000000
  RMS      Force           0.060599825781          0.000040000000
  Maximum  Displacement    0.020532281193          0.000300000000
  RMS      Displacement    0.009137884037          0.000200000000
NORMAL MODE EIGENVALUE : N_MODE = 27
 -0.014681504  -0.008511168  -0.000178336   0.011266906   0.017799578
  0.027561925   0.032817954   0.049674405   0.059800244   0.095898853
  0.122765847   0.129883647   0.137069574   0.162066311   0.173561445
  0.189233172   0.205047624   0.261867122   0.323541243   0.396700830
  0.593958115   0.790149481   0.819969212   0.961279874   1.069551765
  1.449123479   1.536917879
 
# ITR. 1
 

 
# ITR. 121
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
           Item                    Value                Threshold
           ENERGY       -268.147165081138
           Spin(**2)       0.000000000000
           LAMDA           0.000000047011
           TRUST RADII     0.010000000000
           STEP RADII      0.000038327528
  Maximum  Force           0.000007800063          0.000060000000
  RMS      Force           0.000002700314          0.000040000000
  Maximum  Displacement    0.000016894323          0.002307673758
  RMS      Displacement    0.000006184179          0.001538449172
NORMAL MODE EIGENVALUE : N_MODE = 27
  0.002948307   0.003514348   0.011132064   0.017382588   0.028646131
  0.042045668   0.047591209   0.056494074   0.070584220   0.077213762
  0.099431003   0.105421624   0.144396599   0.178250796   0.195439892
  0.230543169   0.266132098   0.277794184   0.432649094   0.562201985
  0.693605925   0.783379895   0.814074876   0.883169566   0.916859801
  1.018291727   1.504266977
 
=========================================================================
Optimized structure, SYMMETRY = C1  
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
ENERGY    = -268.147165081138 (-268.266268520120 :    0.000000000000)
Spin(**2) =    0.000000000000
GRADIENT VECTOR
   0.000001792320
  -0.000000951514

  -0.000004418902
 
Stationary point was found
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
 
---Profile of AFIR path
   Itr.       Length (ang)          Energy (real)            Energy (fit)
      0     0.000000000000       -268.091781022859       -268.091843039207         -0.79
      1     0.052493147309       -268.106691683549       -268.106635647314         -0.82
      2     0.153933590264       -268.130250034996       -268.130176731684         -0.84
      ︙
    121     7.376087521129       -268.266268520120       -268.266221739599         -1.00
 
---Approximate TS geometry (between 53 and 54)
C         -0.769043350099          0.836174754828          0.553666033676
O         -0.946931216613         -0.363105624661          1.069183231473
H          0.081022489940          1.436287874035          0.914124669930
H         -1.652266963961          1.448484153975          0.333105701673
C          0.797124542080         -0.256455727715         -1.107244840230
C         -0.326367647985          0.553591793619         -1.306893151361
O          0.713078562496         -1.378208111551         -0.412787655918
H          1.808089199114          0.082216129416         -1.330941548075
H         -1.278879764100          0.062283179364         -1.488712985732
H         -0.184297425384          1.470276554491         -1.875647339676
H         -0.076674373533         -1.265439194417          0.320561434271
ENERGY    = -268.211573137597
 
---Approximate EQ geometry (121)
C         -0.786968582858          0.757425948976          0.321251614371
O         -1.270570428742         -0.501447730380          0.878342487417
H         -0.021078167273          1.192492267741          0.981359179036
H         -1.651398924495          1.425474886429          0.344920923743
C          0.936913938706         -0.285129777403         -1.184527664387
C         -0.273258397260          0.613550446855         -1.042373355847
O          1.390920127639         -0.987430927167         -0.268372420966
H          1.413620884046         -0.300743880949         -2.180683453084
H         -1.049536329939          0.202185768103         -1.709407370810
H         -0.012032370467          1.591764473351         -1.477911262354
H         -0.511757697409         -1.082035694189          1.005814872905
ENERGY    = -268.266221739599

The approximate product and TS structures will be listed in xxx_EQ_list.log and xxx_TS_list.log files, respectively. These approximate structures may be optimized either manually one by one (by using MIN, SADDLE or LUP keyword), or automatically using the RePATH keyword.

Frequently used options
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Updated At:Feb. 13, 2018, 6:18 p.m.

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