Step 4A: Validate the Transition State using the Intrinsic Reaction Coordinate (IRC) Method¶
Tip
Download the template folder for this step by clicking the button below and work on the files in the template folder as you read through this tutorial.
To perform the IRC method, we want to include the following in the orca.inp file:
We also want to include the following options for the IRC method:
%IRC
MaxIter 2000
InitHess calc_numfreq
Direction both
TolMAXG 2.e-3 # Max gradient (a.u.). Currently set to values equivalent to LooseOpt.
TolRMSG 5.e-4 # RMS gradient (a.u.). Currently set to values equivalent to LooseOpt.
PrintLevel 1
END
Notes about the TolMAXG and TolRMSG keywords
- The
TightOPTkeyword (and other geometric convergence likeNormalOPTandLooseOPT) does not work withIRC. Instead, we include theTolMAXGandTolRMSGkeywords in theorca.inpfile. - It is recommended to set
TolMAXGandTolRMSGto values equivalent to theLooseOPTkeyword. This is because IRC can take a very long time to run to you use tighter convergence criteria. We will check the outputs from the IRC method with theTightOPTkeyword in Step 4B. -
While we are using the default setting
TolMAXGandTolRMSG(set to that ofLooseOPT), you can change this. If you want to tighten the geometric convergence criteria for the IRC method, see the following below. However, for this procedure it is recommended to keep theLooseOPTsettings forTolMAXGandTolRMSG, and use tighter convergence settings in Step 4B.# TolMAXG and TolRMSG settings for: LooseOpt TolMAXG 2.e-3 # Max gradient (a.u.). Currently set to values equivalent to LooseOpt. TolRMSG 5.e-4 # RMS gradient (a.u.). Currently set to values equivalent to LooseOpt. NormalOpt TolMAXG 3.e-4 # Max gradient (a.u.). Currently set to values equivalent to NormalOpt. TolRMSG 1.e-4 # RMS gradient (a.u.). Currently set to values equivalent to NormalOpt. TightOPT TolMAXG 1.e-4 # Max gradient (a.u.). Currently set to values equivalent to TightOPT. TolRMSG 3.e-5 # RMS gradient (a.u.). Currently set to values equivalent to TightOPT.
An example of the complete orca.inp file for running a IRC calculation in ORCA is given below (also located here):
Example of a ORCA input file for a IRC calculation
!B3LYP DEF2-TZVP D3BJ
!IRC TightSCF defgrid2
%SCF
MaxIter 2000 # Here setting MaxIter to a very high number. Intended for systems that require sometimes 1000 iterations before converging (very rare).
DIISMaxEq 5 # Default value is 5. A value of 15-40 necessary for difficult systems.
directresetfreq 15 # Default value is 15. A value of 1 (very expensive) is sometimes required. A value between 1 and 15 may be more cost-effective.
END
%CPCM EPSILON 6.02 REFRAC 1.3723 END
%PAL NPROCS 32 END
%maxcore 2000
%IRC
MaxIter 2000
InitHess calc_numfreq
Direction both
TolMAXG 2.e-3 # Max gradient (a.u.). Currently set to values equivalent to LooseOpt.
TolRMSG 5.e-4 # RMS gradient (a.u.). Currently set to values equivalent to LooseOpt.
PrintLevel 1
END
* xyzfile 1 1 TS.xyz
Outputs from ORCA¶
ORCA will create a number of files. These are the important ones to looks at for the IRC method:
output.out: We will want to look at this file to make sure the IRC method has not run into any problems.orca_IRC_F_trj.xyz: This is the geometric optimisation steps performed for the forward steporca_IRC_B_trj.xyz: This is the geometric optimisation steps performed for the backwards steporca_IRC_Full_trj.xyz: This is the geometric optimisation steps performed for the full IRC method. This include the steps from theorca_IRC_B_trj.xyzandorca_IRC_F_trj.xyzfiles.
Note
You will find that the output from the Forward step maybe either the reactant or the product. So don't worry if the Forward step gives you your reactant. This only means that in that case your Backward step should be your product.
Once ORCA has finished, you want to do the following checks:
Check 1: Make sure the output.out file indicates the calculation finished successfully¶
Look at the end of the output.out file and makes sure there is some sort of message that says that ORCA finished successfully, like that below:
Successful ORCA calculation message expected at the end of the ORCA output file
****ORCA TERMINATED NORMALLY****
Also, make sure you see the following HURRAY messages for the forward and reverse components of the calculation
Example of HURRAY message indicating the IRC calculation completed successfully
***********************HURRAY********************
*** THE IRC HAS CONVERGED ***
*************************************************
See an example of this below:
Example of IRC optimisation calculation text from the ORCA output file
*************************************************************
* FORWARD IRC *
*************************************************************
Iteration E(Eh) dE(kcal/mol) max(|G|) RMS(G)
Convergence thresholds 0.002000 0.000500
0 -1967.123694 -0.987880 0.009347 0.001949
1 -1967.125262 -1.971692 0.010633 0.002266
2 -1967.125852 -2.342362 0.009561 0.002027
3 -1967.126824 -2.951750 0.009004 0.001925
4 -1967.127879 -3.613810 0.009124 0.001951
5 -1967.128956 -4.289687 0.009018 0.001951
6 -1967.130017 -4.955706 0.008720 0.001916
7 -1967.131043 -5.599642 0.008250 0.001895
8 -1967.132027 -6.216796 0.007772 0.001775
9 -1967.132967 -6.806843 0.007140 0.001741
10 -1967.133844 -7.356805 0.006597 0.001594
11 -1967.134673 -7.877617 0.005964 0.001505
12 -1967.135396 -8.330929 0.005465 0.001403
13 -1967.136183 -8.824805 0.005304 0.001313
14 -1967.136867 -9.254130 0.005093 0.001211
15 -1967.137494 -9.647347 0.004860 0.001251
16 -1967.138020 -9.977561 0.004589 0.001172
17 -1967.138244 -10.118093 0.004476 0.001128
18 -1967.138493 -10.274561 0.004343 0.000969
19 -1967.138760 -10.441927 0.004194 0.000937
20 -1967.138998 -10.591222 0.004041 0.000929
21 -1967.139225 -10.734009 0.003895 0.000876
22 -1967.139452 -10.875971 0.003749 0.000835
23 -1967.139718 -11.043042 0.003608 0.000801
24 -1967.139845 -11.122736 0.003467 0.000761
25 -1967.140080 -11.270521 0.003330 0.000731
26 -1967.140277 -11.393680 0.003197 0.000702
27 -1967.140464 -11.511368 0.003070 0.000674
28 -1967.140637 -11.619494 0.002943 0.000741
29 -1967.140715 -11.668661 0.002891 0.000664
30 -1967.140798 -11.720524 0.002835 0.000631
31 -1967.140860 -11.759730 0.002776 0.000609
32 -1967.140961 -11.823302 0.002717 0.000597
33 -1967.141042 -11.873813 0.002660 0.000598
34 -1967.141120 -11.922679 0.002603 0.000572
35 -1967.141197 -11.971354 0.002547 0.000604
36 -1967.141268 -12.015933 0.002493 0.000551
37 -1967.141345 -12.064045 0.002437 0.000559
38 -1967.141415 -12.107775 0.002382 0.000528
39 -1967.141487 -12.152988 0.002325 0.000535
40 -1967.141553 -12.194724 0.002273 0.000507
41 -1967.141623 -12.238554 0.002219 0.000504
42 -1967.141688 -12.279047 0.002162 0.000485
43 -1967.141757 -12.322336 0.002107 0.000474
44 -1967.141804 -12.352192 0.002052 0.000620
45 -1967.141837 -12.372873 0.002037 0.000479
46 -1967.141883 -12.401622 0.002011 0.000491
47 -1967.141897 -12.410438 0.001987 0.000502
48 -1967.141921 -12.425304 0.001963 0.000447
***********************HURRAY********************
*** THE IRC HAS CONVERGED ***
*************************************************
*************************************************************
* BACKWARD IRC *
*************************************************************
Iteration E(Eh) dE(kcal/mol) max(|G|) RMS(G)
Convergence thresholds 0.002000 0.000500
0 -1967.124432 -1.450797 0.013548 0.003054
1 -1967.128179 -3.802362 0.019874 0.004412
2 -1967.133463 -7.118203 0.025990 0.005520
3 -1967.139815 -11.103897 0.028442 0.006038
4 -1967.146176 -15.095469 0.025081 0.005721
5 -1967.151785 -18.615266 0.021519 0.004885
6 -1967.156345 -21.476904 0.019615 0.004011
7 -1967.160267 -23.937845 0.017255 0.003408
8 -1967.163664 -26.069666 0.014997 0.002976
9 -1967.166694 -27.970753 0.013013 0.002697
10 -1967.169479 -29.718182 0.011530 0.002474
11 -1967.172077 -31.348800 0.010293 0.002306
12 -1967.174459 -32.843560 0.009384 0.002123
13 -1967.176652 -34.219491 0.008341 0.001943
14 -1967.178609 -35.447602 0.007524 0.001794
15 -1967.180284 -36.498332 0.006505 0.001811
16 -1967.180799 -36.822042 0.006206 0.001874
17 -1967.181037 -36.970895 0.006081 0.001495
18 -1967.181400 -37.198822 0.005876 0.001356
19 -1967.181750 -37.418312 0.005669 0.001312
20 -1967.182089 -37.631256 0.005467 0.001242
21 -1967.182416 -37.836382 0.005276 0.001192
22 -1967.182752 -38.047361 0.005091 0.001133
23 -1967.183039 -38.227080 0.004909 0.001083
24 -1967.183346 -38.420263 0.004729 0.001053
25 -1967.183594 -38.575570 0.004544 0.000989
26 -1967.183880 -38.755051 0.004352 0.000934
27 -1967.184122 -38.907028 0.004147 0.000882
28 -1967.184278 -39.004650 0.005538 0.001872
29 -1967.184371 -39.063508 0.003907 0.001106
30 -1967.184429 -39.099643 0.003868 0.001106
31 -1967.184437 -39.104382 0.003827 0.001095
32 -1967.184495 -39.141192 0.003788 0.000806
33 -1967.184532 -39.164363 0.003735 0.000827
34 -1967.184582 -39.195809 0.003710 0.000779
35 -1967.184629 -39.225129 0.003657 0.000811
36 -1967.184679 -39.256314 0.003605 0.000771
37 -1967.184730 -39.288669 0.003550 0.000749
38 -1967.184792 -39.327326 0.003497 0.000767
39 -1967.184820 -39.344886 0.003443 0.000736
40 -1967.184882 -39.383827 0.003390 0.000791
41 -1967.184915 -39.404885 0.003338 0.000696
42 -1967.184964 -39.435277 0.003282 0.000702
43 -1967.184881 -39.383478 0.003257 0.000682
44 -1967.185025 -39.473599 0.003205 0.000675
45 -1967.185078 -39.507012 0.003149 0.000757
46 -1967.185116 -39.530892 0.003102 0.000636
47 -1967.185162 -39.559376 0.003055 0.000664
48 -1967.185193 -39.579049 0.003004 0.000683
49 -1967.185217 -39.594308 0.002952 0.000614
50 -1967.185167 -39.562848 0.002896 0.000602
51 -1967.185294 -39.642716 0.002843 0.000594
52 -1967.185245 -39.611372 0.002787 0.000572
53 -1967.185371 -39.690597 0.002733 0.000555
54 -1967.185407 -39.713298 0.002680 0.000583
55 -1967.185427 -39.725635 0.002628 0.000550
56 -1967.185455 -39.743316 0.002605 0.000686
57 -1967.185485 -39.762253 0.002559 0.000607
58 -1967.185523 -39.786160 0.002515 0.000571
59 -1967.185524 -39.786625 0.002463 0.000683
60 -1967.185589 -39.827267 0.002427 0.000794
61 -1967.185606 -39.838302 0.002392 0.000664
62 -1967.185624 -39.849721 0.002353 0.000478
63 -1967.185637 -39.857889 0.002302 0.000504
64 -1967.185667 -39.876769 0.002253 0.000504
65 -1967.185727 -39.914169 0.002210 0.000641
66 -1967.185718 -39.908741 0.002189 0.000446
67 -1967.185747 -39.926823 0.002141 0.000523
68 -1967.185769 -39.940362 0.002100 0.000528
69 -1967.185789 -39.952710 0.002061 0.000608
70 -1967.185870 -40.003626 0.002035 0.000817
71 -1967.185828 -39.977567 0.002012 0.000472
72 -1967.185827 -39.977023 0.001971 0.000413
***********************HURRAY********************
*** THE IRC HAS CONVERGED ***
*************************************************
Check 2: Make sure that the energies of each geometric optimisation step is less than the transition step from the output.out file¶
We want to make sure that the energy of our transition state is in fact lower than all points along the energy profile. This is because:
- The IRC method works by initially pushing the molecule down the saddle of the potential energy surface towards the reactant and product minima, so the energy should have decreased from transition state in the forward and backwards directions.
To do this, you want to look at the IRC PATH SUMMARY in your output file and make sure your transition state (TS) is the highest energy step in the IRC path.
The transition state should be the number of the final Convergence Iteration from the backwards step, plus 2. In this example, our BACKWARD IRC process required 72 geometry optimisation steps, so we expect our transition state to be at step 74 in the IRC PATH SUMMARY table.
Below show an example of this from Examples/Step4_Validate_TS/Step4A_IRC/output.log. You can see that the transition step occurs at step 74, as expected. We also see that the energy of the transition state is the largest for all steps.
Example of IRC PATH SUMMARY text from the ORCA output file
---------------------------------------------------------------
IRC PATH SUMMARY
---------------------------------------------------------------
All gradients are in Eh/Bohr.
Step E(Eh) dE(kcal/mol) max(|G|) RMS(G)
1 -1967.185827 -39.977023 0.001971 0.000413
2 -1967.185828 -39.977567 0.002012 0.000472
3 -1967.185870 -40.003626 0.002035 0.000817
4 -1967.185789 -39.952710 0.002061 0.000608
5 -1967.185769 -39.940362 0.002100 0.000528
6 -1967.185747 -39.926823 0.002141 0.000523
7 -1967.185718 -39.908741 0.002189 0.000446
8 -1967.185727 -39.914169 0.002210 0.000641
9 -1967.185667 -39.876769 0.002253 0.000504
10 -1967.185637 -39.857889 0.002302 0.000504
11 -1967.185624 -39.849721 0.002353 0.000478
12 -1967.185606 -39.838302 0.002392 0.000664
13 -1967.185589 -39.827267 0.002427 0.000794
14 -1967.185524 -39.786625 0.002463 0.000683
15 -1967.185523 -39.786160 0.002515 0.000571
16 -1967.185485 -39.762253 0.002559 0.000607
17 -1967.185455 -39.743316 0.002605 0.000686
18 -1967.185427 -39.725635 0.002628 0.000550
19 -1967.185407 -39.713298 0.002680 0.000583
20 -1967.185371 -39.690597 0.002733 0.000555
21 -1967.185245 -39.611372 0.002787 0.000572
22 -1967.185294 -39.642716 0.002843 0.000594
23 -1967.185167 -39.562848 0.002896 0.000602
24 -1967.185217 -39.594308 0.002952 0.000614
25 -1967.185193 -39.579049 0.003004 0.000683
26 -1967.185162 -39.559376 0.003055 0.000664
27 -1967.185116 -39.530892 0.003102 0.000636
28 -1967.185078 -39.507012 0.003149 0.000757
29 -1967.185025 -39.473599 0.003205 0.000675
30 -1967.184881 -39.383478 0.003257 0.000682
31 -1967.184964 -39.435277 0.003282 0.000702
32 -1967.184915 -39.404885 0.003338 0.000696
33 -1967.184882 -39.383827 0.003390 0.000791
34 -1967.184820 -39.344886 0.003443 0.000736
35 -1967.184792 -39.327326 0.003497 0.000767
36 -1967.184730 -39.288669 0.003550 0.000749
37 -1967.184679 -39.256314 0.003605 0.000771
38 -1967.184629 -39.225129 0.003657 0.000811
39 -1967.184582 -39.195809 0.003710 0.000779
40 -1967.184532 -39.164363 0.003735 0.000827
41 -1967.184495 -39.141192 0.003788 0.000806
42 -1967.184437 -39.104382 0.003827 0.001095
43 -1967.184429 -39.099643 0.003868 0.001106
44 -1967.184371 -39.063508 0.003907 0.001106
45 -1967.184278 -39.004650 0.005538 0.001872
46 -1967.184122 -38.907028 0.004147 0.000882
47 -1967.183880 -38.755051 0.004352 0.000934
48 -1967.183594 -38.575570 0.004544 0.000989
49 -1967.183346 -38.420263 0.004729 0.001053
50 -1967.183039 -38.227080 0.004909 0.001083
51 -1967.182752 -38.047361 0.005091 0.001133
52 -1967.182416 -37.836382 0.005276 0.001192
53 -1967.182089 -37.631256 0.005467 0.001242
54 -1967.181750 -37.418312 0.005669 0.001312
55 -1967.181400 -37.198822 0.005876 0.001356
56 -1967.181037 -36.970895 0.006081 0.001495
57 -1967.180799 -36.822042 0.006206 0.001874
58 -1967.180284 -36.498332 0.006505 0.001811
59 -1967.178609 -35.447602 0.007524 0.001794
60 -1967.176652 -34.219491 0.008341 0.001943
61 -1967.174459 -32.843560 0.009384 0.002123
62 -1967.172077 -31.348800 0.010293 0.002306
63 -1967.169479 -29.718182 0.011530 0.002474
64 -1967.166694 -27.970753 0.013013 0.002697
65 -1967.163664 -26.069666 0.014997 0.002976
66 -1967.160267 -23.937845 0.017255 0.003408
67 -1967.156345 -21.476904 0.019615 0.004011
68 -1967.151785 -18.615266 0.021519 0.004885
69 -1967.146176 -15.095469 0.025081 0.005721
70 -1967.139815 -11.103897 0.028442 0.006038
71 -1967.133463 -7.118203 0.025990 0.005520
72 -1967.128179 -3.802362 0.019874 0.004412
73 -1967.124432 -1.450797 0.013548 0.003054
74 -1967.122120 0.000000 0.000008 0.000004 <= TS
75 -1967.123694 -0.987880 0.009347 0.001949
76 -1967.125262 -1.971692 0.010633 0.002266
77 -1967.125852 -2.342362 0.009561 0.002027
78 -1967.126824 -2.951750 0.009004 0.001925
79 -1967.127879 -3.613810 0.009124 0.001951
80 -1967.128956 -4.289687 0.009018 0.001951
81 -1967.130017 -4.955706 0.008720 0.001916
82 -1967.131043 -5.599642 0.008250 0.001895
83 -1967.132027 -6.216796 0.007772 0.001775
84 -1967.132967 -6.806843 0.007140 0.001741
85 -1967.133844 -7.356805 0.006597 0.001594
86 -1967.134673 -7.877617 0.005964 0.001505
87 -1967.135396 -8.330929 0.005465 0.001403
88 -1967.136183 -8.824805 0.005304 0.001313
89 -1967.136867 -9.254130 0.005093 0.001211
90 -1967.137494 -9.647347 0.004860 0.001251
91 -1967.138020 -9.977561 0.004589 0.001172
92 -1967.138244 -10.118093 0.004476 0.001128
93 -1967.138493 -10.274561 0.004343 0.000969
94 -1967.138760 -10.441927 0.004194 0.000937
95 -1967.138998 -10.591222 0.004041 0.000929
96 -1967.139225 -10.734009 0.003895 0.000876
97 -1967.139452 -10.875971 0.003749 0.000835
98 -1967.139718 -11.043042 0.003608 0.000801
99 -1967.139845 -11.122736 0.003467 0.000761
100 -1967.140080 -11.270521 0.003330 0.000731
101 -1967.140277 -11.393680 0.003197 0.000702
102 -1967.140464 -11.511368 0.003070 0.000674
103 -1967.140637 -11.619494 0.002943 0.000741
104 -1967.140715 -11.668661 0.002891 0.000664
105 -1967.140798 -11.720524 0.002835 0.000631
106 -1967.140860 -11.759730 0.002776 0.000609
107 -1967.140961 -11.823302 0.002717 0.000597
108 -1967.141042 -11.873813 0.002660 0.000598
109 -1967.141120 -11.922679 0.002603 0.000572
110 -1967.141197 -11.971354 0.002547 0.000604
111 -1967.141268 -12.015933 0.002493 0.000551
112 -1967.141345 -12.064045 0.002437 0.000559
113 -1967.141415 -12.107775 0.002382 0.000528
114 -1967.141487 -12.152988 0.002325 0.000535
115 -1967.141553 -12.194724 0.002273 0.000507
116 -1967.141623 -12.238554 0.002219 0.000504
117 -1967.141688 -12.279047 0.002162 0.000485
118 -1967.141757 -12.322336 0.002107 0.000474
119 -1967.141804 -12.352192 0.002052 0.000620
120 -1967.141837 -12.372873 0.002037 0.000479
121 -1967.141883 -12.401622 0.002011 0.000491
122 -1967.141897 -12.410438 0.001987 0.000502
123 -1967.141921 -12.425304 0.001963 0.000447
Check 3 (Optional): Make sure that the energies of each geometric optimisation step is less than the transition step using the viewORCA irc program¶
We can also repeat Check 2 by looking at the energy profile from the orca_IRC_Full_trj.xyz file so that we can see how the IRC ran visually. This is a good idea as an extra check.
To do this, we want to use the viewORCA irc program by performing the following steps:
- Open a terminal.
cdinto the folder with theorca_IRC_Full_trj.xyzfile.- Run the
viewORCA ircprogram in the terminal.
For example:
# cd into the folder with the ``orca_IRC_Full_trj.xyz`` file
cd ORCA_Mechanism_Procedure/Examples/Step4_Validate_TS/Step4A_IRC
# Run the ``viewORCA irc`` program in the terminal
viewORCA irc
Note
viewORCA irc will also create a xyz file called IRC_images.xyz that you can copy and view on your own computer.
- If you just want to create the
IRC_images.xyzfile, type into the terminalviewORCA irc --view False(which will create theIRC_images.xyzfile without creating aase guiwindow).
You will get a GUI that shows you the following IRC pathway:
The energy profile for this example is given below:
If you put the cursor over the energy profile, you will see in this example that the maximum peak occurs at x=36. Because ASE starts at 0 rather than 1, x=73 here means step 74, so we are happy.
Troubleshooting Intrinsic Reaction Coordinate (IRC) calculations¶
Here are some troubleshooting tips for performing IRC calculations
No troubleshooting issues have been found yet.
Info
If you have any issues about this step, raise a New issue at the Issues section by clicking here.