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Global reaction route mapping by ADDF (ADDF)

Global reaction route mapping by ADDF (ADDF)

An input file for formaldehyde is:

ADDF/B3LYP/D95V(d)
 
0 1
C         -0.000000000711          0.000000000452         -0.533622543616
O          0.000000000233          0.000000000201          0.679217381431
H          0.000000000239          0.942015259527         -1.124391918573
H          0.000000000239         -0.942015260180         -1.124391919242
 

The initial structure should be a tightly optimized equilibrium structure (EQ). Only five lowest energy EQs are printed in xxx.log file. Many other intermediate (.rrm) and output (.log) files are created. Structures and energies of obtained EQs and transition structures (TSs) are listed in xxx_EQ_list.log and xxx_TS_list.log files, respectively. Structures, energies, spin expectation values, ZPVE values, and normal mode eigenvalues of each EQ are listed in the xxx_EQ_list.log file as:

List of Equilibrium Structures
 
# Geometry of EQ 0, SYMMETRY = C2v
C         -0.000000000711          0.000000000452         -0.533622543616
O          0.000000000233          0.000000000201          0.679217381431
H          0.000000000239          0.942015259527         -1.124391918573
H          0.000000000239         -0.942015260180         -1.124391919242
Energy    = -114.523864895551
Spin(**2) =    0.000000000000
ZPVE      =    0.026781405457
Normal mode eigenvalues : nmode = 6
  0.054381882   0.061068479   0.089972737   0.125646043   0.324888966
  0.338899385
 
# Geometry of EQ 1, SYMMETRY = Cs
C          0.000017816605          0.085845090558         -0.674964095891

Structures, energies, spin expectation values, ZPVE values, normal mode eigenvalues, and connections of each TS are listed in xxx_TS_list.log file as:

List of Transition Structures
 
# Geometry of TS 0, SYMMETRY = Cs
C         -0.000046636612          0.047463176643         -0.614956667154
O         -0.000010868853         -0.036612594364          0.694077532502
H         -0.000042816335          1.092948196786         -1.011273921072
H         -0.000043257975         -1.024478709164          0.050321046042
Energy    = -114.382131557803
Spin(**2) =    0.000000000000
ZPVE      =    0.020549889138
Normal mode eigenvalues : nmode = 6
 -0.169524733   0.021339591   0.065453655   0.078877823   0.256428524
  0.319912796
CONNECTION : 1 - 0
 
# Geometry of TS 1, SYMMETRY = Cs
C          0.000000347948          0.203303451832         -0.440128790222
O         -0.000000512953          0.024619965442          0.723680190983
H          0.000001528644          0.039127648981         -1.527043580004
H          0.000002756701         -1.234232329090         -1.285621345410
Energy    = -114.379676433735
Spin(**2) =    0.000000000000
ZPVE      =    0.018559403880
Normal mode eigenvalues : nmode = 6
 -0.142565838   0.025285360   0.030235391   0.070032351   0.136811298
  0.381165199
CONNECTION : 0 - DC
 
# Geometry of TS 2, SYMMETRY = C1
C          0.140064731097          0.170588364840         -0.720640475828

Here, CONNECTION : 1 - 0 indicates that this TS is a transition state between EQ1 and EQ0, and CONNECTION : 0 - DC indicates that this TS is a transition state for a dissociation channel (DC) from EQ0. Results of IRC calculation starting from TSn are printed in xxx_TSn.log file, and a product of DC can be identified from a structure of one end of the IRC path.

In addition to lists for EQs and TSs, xxx_DC_list.log file will be created. Structures, energies, spin expectation values, ZPVE values, normal mode eigenvalues, and connections of each DC are listed in xxx_DC_list.log file as:

List of Dissociated Structures
 
# Geometry of DC 0, SYMMETRY = Cs
C         -0.000000000582         -0.093385182469         -0.475913107336
O          0.000000000179         -0.005895400177          0.693772489764
H          0.000000000467          2.188910262049         -2.021692192760
H         -0.000000000656         -0.983424605885         -1.145228147891
Energy    = -114.351428838885
Spin(**2) =    0.000000000000
ZPVE      =    0.016819248762
Normal mode eigenvalues : nmode = 5
  0.007826154   0.014382926   0.055375561   0.175053671   0.329587967
CONNECTION : 0 - DC
 
# Geometry of DC 1, SYMMETRY = C2v
C         -0.000000010482          0.000009848372         -1.411500913220

This file shows end-points of ADDF paths that reached a dissociation limit without passing through any barrier, e.g., a radical dissociation channel with single bond dissociation. Here, CONNECTION : 0 - DC indicates that the meta-IRC (mass-weighted steepest descent path starting from a non-stationary point) starting from this DC structure reaches EQ0. Results of meta-IRC calculations starting from DCn are printed in xxx_DCn.log file. Structures in xxx_DC_list.log by ADDF are not stationary points, and it is recommended to reoptimize these structures by MIN with Opt = Fragment, RePATH, or ReStruct before using them in discussions. Their ZPVE and normal mode eigenvalues are based on a normal mode analysis using the Hessian matrix from which the force projection is eliminated.

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

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