Example 2: VCD and ECD Spectra Simulation
In this example, we simulate the Vibrational Circular Dichroism (VCD) and the Electronic Circular Dichroism (ECD) spectra of a chiral molecule and automatically fit it against an experimental reference file (vcd_ref.dat, ecd_ref.dat).
ensemble_analyzer -e ensemble.xyz -p protocol_vcd.json -cpu 44
{
"0": {
"functional": "B97-3c",
"basis": "def2-mTZVP"
},
"1": {
"functional": "r2SCAN-3c",
"basis": "def2-mTZVPP",
"opt": true,
"freq": true
},
"2": {
"functional": "wB97X-D4rev",
"basis": "def2-QZVPP"
},
"3": {
"functional": "B3LYP D4",
"basis": "def2-QZVPPD",
"freq": true
}
}
27
-55.76954216
C 1.3226789038 0.0637124090 -0.3767052001
H 1.5110023818 -0.1525730016 -1.4344441507
C 1.9646062804 1.4202123147 -0.1076228998
C -0.1733223631 0.1164400550 -0.1441928771
C 2.0118998742 -1.0036260326 0.4790554967
C -0.7035717298 0.3741387095 1.1174817065
C -2.0675285144 0.4048973372 1.3076234656
C -2.9397177769 0.1731022014 0.2413939157
C -2.4126258354 -0.0856926506 -1.0196016137
C -1.0409764896 -0.1098838975 -1.2016615889
F 3.2586086704 1.4451902893 -0.4876144795
F 1.3591983527 2.4106780726 -0.7757715296
F 1.9626095543 1.7739826867 1.1871064866
N 1.6279506265 -2.3590196430 0.0411569053
O 1.3501071582 -2.5285939346 -1.1215100551
O 1.6409759025 -3.2251092601 0.8835970015
O -4.2654676362 0.2216668773 0.5392872812
C -5.2059584317 -0.0043993122 -0.4938395682
H 3.1004019070 -0.9336306134 0.3705529988
H 1.7577758219 -0.9148047548 1.5371305900
H -0.0563749761 0.5640371414 1.9596443989
H -2.4878799247 0.6061150338 2.2799772607
H -3.0547773061 -0.2698483785 -1.8650091638
H -0.6468681135 -0.3185876985 -2.1846794432
H -5.1146813996 0.7465348140 -1.2832912341
H -5.0946718509 -1.0058281792 -0.9183511680
H -6.1815417999 0.0831563958 -0.0192955899
27
-55.76937955
C 1.3446089644 0.0569149006 -0.3805890075
H 1.6283956591 -0.1586594094 -1.4170235503
C 1.9368374623 1.4251208038 -0.0610308231
C -0.1667322243 0.0856027167 -0.2786372678
C 1.9770776572 -0.9973908871 0.5346689321
C -0.8081281463 0.3227898844 0.9289075825
C -2.1897069978 0.3357173385 1.0110948254
C -2.9565908581 0.1043662882 -0.1262971451
C -2.3124130562 -0.1351861136 -1.3423409671
C -0.9370557104 -0.1422713436 -1.4148304098
F 3.2607743023 1.4702814312 -0.3127515100
F 1.3827057851 2.4017374515 -0.7909519117
F 1.8022818018 1.7856671315 1.2253672215
N 1.6476494436 -2.3566191021 0.0648571569
O 1.5939119622 -2.5494050317 -1.1258067022
O 1.4757316358 -3.2001480292 0.9124249554
O -4.3156158680 0.0893285824 -0.1615166189
C -5.0325965012 0.3215486165 1.0364364985
H 3.0692310296 -0.9095675289 0.5112190341
H 1.6331648235 -0.9114610326 1.5669908689
H -0.2391460743 0.5128993099 1.8261249969
H -2.6526344872 0.5256272938 1.9654423523
H -2.9166726909 -0.3140342525 -2.2172065964
H -0.4564115794 -0.3346517871 -2.3617161621
H -4.8194728221 1.3154880285 1.4392039043
H -6.0833822468 0.2590000402 0.7597998392
H -4.8067842260 -0.4406637025 1.7872192008
27
-55.76915033
C 0.9148830500 -0.3355160634 -0.3332819679
H 1.0786531668 -0.5807066791 -1.3895929605
C 1.7168404421 0.9366951247 -0.0666858030
C -0.5568342321 -0.0601334525 -0.1050658185
C 1.4556770480 -1.4804519065 0.5243847222
C -1.4003481606 0.1209740086 -1.1905272023
C -2.7462207906 0.3914556270 -1.0136679269
C -3.2701192485 0.4894680996 0.2713468923
C -2.4211003300 0.3104803060 1.3662445985
C -1.0827353522 0.0417210686 1.1801593070
F 3.0352284019 0.7682579857 -0.2937652062
F 1.3273122638 1.9565540005 -0.8435640915
F 1.6202697698 1.3648228483 1.2033486224
N 2.6416736332 -2.1253794685 -0.0810974978
O 2.7447755432 -2.1219088360 -1.2845845556
O 3.4209215255 -2.6458964368 0.6811190084
O -4.5713508273 0.7499113779 0.5665550230
C -5.4848494524 0.9539721762 -0.4949807901
H 1.7377082614 -1.1625728066 1.5302734253
H 0.6874764750 -2.2559026440 0.6052455661
H -1.0079948462 0.0521039602 -2.1939959100
H -3.3705351149 0.5254277072 -1.8815959983
H -2.8383782778 0.3919919105 2.3570876006
H -0.4481929687 -0.0801467581 2.0432531786
H -5.5666158641 0.0632146041 -1.1237765485
H -6.4426995701 1.1508160344 -0.0170973113
H -5.1974107815 1.8146842908 -1.1048697512
27
-55.76904634
C 0.9379822481 -0.3734726002 -0.3244318977
H 1.2172506775 -0.7057805385 -1.3313976251
C 1.7188279599 0.9150383325 -0.0742968033
C -0.5474085840 -0.0794630757 -0.2888705987
C 1.3632950939 -1.4452875284 0.6804844376
C -1.2056978666 0.1681911186 0.9071855836
C -2.5596968208 0.4555436656 0.9282822593
C -3.2802405502 0.5013488408 -0.2610274826
C -2.6185040987 0.2519613177 -1.4657385278
C -1.2705804544 -0.0317466949 -1.4766952267
F 1.4247652459 1.8701324870 -0.9663976545
F 1.4907822834 1.4437682020 1.1404367677
F 3.0522181374 0.7278191828 -0.1426538767
N 2.6161283640 -2.1243590655 0.2825451112
O 2.8658576701 -2.2221951254 -0.8950388668
O 3.2969657334 -2.5678864630 1.1764876013
O -4.6084270589 0.7739834503 -0.3593637984
C -5.3385012947 1.0498808089 0.8212741120
H 1.5143235329 -1.0496905262 1.6869792209
H 0.5896040128 -2.2184143011 0.7197410609
H -0.6674687151 0.1488387687 1.8416777193
H -3.0372863534 0.6444165152 1.8755498024
H -3.1869051236 0.2906696291 -2.3811082908
H -0.7750097411 -0.2169339977 -2.4173612291
H -5.3282296583 0.1945742301 1.5023178175
H -4.9484228880 1.9354942671 1.3302079573
H -6.3583058537 1.2398715956 0.4917983491
27
-55.76596431
C 1.1622663567 0.3615418082 -0.9732869526
H 1.2470270404 0.9045515715 -1.9219171922
C 1.9868165213 1.1825565836 0.0137497466
C -0.3022994146 0.2749773356 -0.6038079272
C 1.8105293994 -1.0219115506 -1.2077511973
C -0.7509524354 0.1941014261 0.7063271827
C -2.1018119944 0.0885073787 0.9908530457
C -3.0324311738 0.0523441388 -0.0409128216
C -2.5839139598 0.1337433801 -1.3621041632
C -1.2403739359 0.2447248137 -1.6345343894
F 2.2027482832 0.5956420648 1.2001160129
F 3.2097754727 1.4525838119 -0.4865887296
F 1.4222879242 2.3714889723 0.2748095919
N 1.6906441421 -1.8970925126 -0.0315739978
O 2.7042899288 -2.1633107125 0.5747070903
O 0.5849829827 -2.2983637014 0.2531440971
O -4.3770452985 -0.0544823389 0.1227626766
C -4.8996922536 -0.1556704441 1.4339940370
H 1.2759942094 -1.5027884695 -2.0293064752
H 2.8726552362 -0.9119259665 -1.4384526515
H -0.0604223324 0.2121385894 1.5348100952
H -2.4094669871 0.0286375810 2.0216321310
H -3.3143318173 0.1079790769 -2.1548886524
H -0.9131659176 0.3078994674 -2.6612705471
H -4.5166041271 -1.0429567736 1.9450730705
H -4.6715417984 0.7381444130 2.0210579642
H -5.9773324591 -0.2437627641 1.3087721712
27
-55.76537555
C 1.1436554086 0.4462192497 -0.8748234703
H 1.1773825081 1.0985076066 -1.7554088776
C 2.0340755846 1.1428688022 0.1501252868
C -0.2967003283 0.3233533530 -0.4276641223
C 1.7628275020 -0.9008936492 -1.3116408094
C -1.2957096869 0.4335224004 -1.3864568124
C -2.6307948036 0.3061282387 -1.0530234817
C -2.9932363980 0.0664961936 0.2693490877
C -1.9927220238 -0.0404807107 1.2364880006
C -0.6637227845 0.0804557194 0.8930175111
F 2.3159994401 0.4211441732 1.2437979599
F 3.2272200733 1.4666057728 -0.3901199555
F 1.4979495592 2.2952536234 0.5803481759
N 1.6797440242 -1.9190305898 -0.2529929598
O 0.5836923524 -2.3612443186 0.0065473216
O 2.7105449816 -2.2524271628 0.2869429549
O -4.2690596864 -0.0720599386 0.7156779574
C -5.3311734886 0.0120145067 -0.2162690164
H 1.1883729194 -1.2689904078 -2.1638531036
H 2.8156147283 -0.7696650827 -1.5720364225
H -1.0320587747 0.6227935651 -2.4163898598
H -3.3752223034 0.3961352769 -1.8269747144
H -2.2829170850 -0.2277410968 2.2577640241
H 0.0770588449 -0.0171527889 1.6706467472
H -6.2383402420 -0.1335879001 0.3672166638
H -5.3597570929 0.9937913321 -0.6966859161
H -5.2548065766 -0.7719363094 -0.9745339988
27
-55.76361739
C 1.2161539335 0.3198557219 -0.8957982992
H 1.3165078542 0.7866339544 -1.8845140466
C 2.0002495448 1.2552000272 0.0197873113
C -0.2649706691 0.2301649453 -0.5777731191
C 1.8951332335 -1.0535787530 -1.0062814186
C -1.1195895659 -0.1986254477 -1.5920209537
C -2.4724786082 -0.3190175188 -1.3702512174
C -3.0130493659 -0.0059627360 -0.1206864827
C -2.1652269023 0.4297000785 0.8906419705
C -0.8039507256 0.5415143258 0.6597950099
F 2.2221409685 0.8184758905 1.2642672110
F 3.2310242766 1.4839761794 -0.4981415806
F 1.4233542480 2.4611218365 0.1297149128
N 1.6266108256 -1.9899006042 0.1024689928
O 1.0697613405 -1.5955769125 1.0956849889
O 2.0016857460 -3.1280586425 -0.0770501320
O -4.3600400467 -0.1576283044 -0.0022890687
C -4.9727055365 0.1410516287 1.2376707824
H 1.5622157766 -1.5592196243 -1.9159473329
H 2.9829310470 -0.9414544461 -1.0672953908
H -0.7236763540 -0.4368581960 -2.5676458941
H -3.1385001426 -0.6525051378 -2.1499903165
H -2.5455310138 0.6805685597 1.8669497718
H -0.1749359425 0.8656421824 1.4727507162
H -4.5867399584 -0.5002573875 2.0346975736
H -4.8314907052 1.1916340125 1.5058290275
H -6.0326293091 -0.0582781251 1.0908379912
27
-55.76299204
C 1.1654655228 0.3423248435 -0.8946074697
H 1.1748699742 0.8172466028 -1.8843983020
C 2.0564695762 1.2545619924 -0.0563911108
C -0.2766153042 0.2790555045 -0.4265853378
C 1.8006564631 -1.0444550016 -1.0839954784
C -1.2412833632 -0.0995768385 -1.3513708579
C -2.5753412451 -0.1977433027 -1.0008718961
C -2.9699640618 0.0932564466 0.3012425885
C -2.0033078151 0.4795719625 1.2307243495
C -0.6745860606 0.5681721013 0.8737959394
F 2.4017986610 0.8011533618 1.1526519013
F 3.2295303103 1.4702825748 -0.7001562699
F 1.5136350614 2.4677095207 0.1236749683
N 1.5770859272 -2.0002871074 0.0179011729
O 1.2020115836 -1.5958105690 1.0891618078
O 1.8020874376 -3.1614379276 -0.2459796699
O -4.2490241759 0.0351619780 0.7611695144
C -5.2766384320 -0.3570786788 -0.1292199208
H 1.4021545400 -1.5192023126 -1.9834321805
H 2.8855051750 -0.9540983669 -1.2064485434
H -0.9549751654 -0.3204703155 -2.3689002494
H -3.2924314303 -0.4971111326 -1.7475505093
H -2.3188803216 0.7020520159 2.2373150244
H 0.0438148837 0.8535039869 1.6243568739
H -5.3622416948 0.3402767388 -0.9670685240
H -5.1106053942 -1.3709227515 -0.5036933542
H -6.1920387557 -0.3325723766 0.4590312087
27
-55.76220237
C 1.1597437632 0.1045348460 -0.9837315590
H 1.2880629572 0.5107272567 -1.9953446278
C 1.9094684122 1.0981112385 -0.0772563362
C -0.3221093738 0.1444223877 -0.6508044587
C 1.7973661828 -1.2860070246 -1.0162817190
C -1.0023525245 -0.9053997790 -0.0564019542
C -2.3505321726 -0.8040280383 0.2486037216
C -3.0452907161 0.3657127470 -0.0333835463
C -2.3658181348 1.4236799292 -0.6426188557
C -1.0287246155 1.3102623545 -0.9470072076
F 3.2181218736 0.8129140662 0.0414161330
F 1.8671581221 2.3414569143 -0.6053872511
F 1.4131971998 1.2189438231 1.1555123689
N 1.8808274263 -1.9909557496 0.2757894438
O 1.8253574618 -3.2004678873 0.2307493237
O 2.0387560805 -1.3447928944 1.2831521828
O -4.3619129272 0.5770012960 0.2304130931
C -5.1039866550 -0.4489568434 0.8626768250
H 1.2442910904 -1.9278162152 -1.7051060026
H 2.8308870311 -1.2011442822 -1.3715448400
H -0.5122176464 -1.8350213392 0.1827797950
H -2.8402719662 -1.6455338151 0.7103601147
H -2.9123976115 2.3258566788 -0.8656945435
H -0.5245400772 2.1406662972 -1.4175686589
H -6.1080324283 -0.0464030473 0.9826384396
H -5.1426140777 -1.3488723196 0.2428312689
H -4.6876966135 -0.6911538910 1.8442008057
27
-55.76216496
C 1.1775690535 0.4194358039 -0.8794159517
H 1.3137522505 1.1338340241 -1.7019208464
C 1.9451549644 1.0438985337 0.3021060452
C -0.3059052893 0.3609045294 -0.5525761625
C 1.7988914970 -0.8913655183 -1.3631834206
C -0.9691355447 1.5604740176 -0.2923153024
C -2.3078849151 1.5751189245 0.0250459014
C -3.0342638522 0.3832324653 0.0854554726
C -2.3834449804 -0.8127278406 -0.1904866238
C -1.0329835602 -0.8168963977 -0.5029360023
F 1.4123249246 0.8188010141 1.5039261447
F 3.2301682266 0.6499744297 0.3556454503
F 1.9973948365 2.3890151215 0.1768393464
N 1.8121431785 -1.9863797795 -0.3758825581
O 1.8476106100 -1.7100903769 0.7985232651
O 1.8224715330 -3.1116151631 -0.8242792624
O -4.3493032077 0.5027923889 0.4086515203
C -5.1398233565 -0.6679669907 0.4946124834
H 1.2700876201 -1.2497981476 -2.2485275156
H 2.8474798789 -0.7226211205 -1.6337566419
H -0.4311553069 2.4951976557 -0.3359886442
H -2.8198637170 2.5011163258 0.2319413750
H -2.9099678049 -1.7525863339 -0.1629160315
H -0.5806183822 -1.7728468344 -0.7114370439
H -6.1341002934 -0.3243990497 0.7737790842
H -5.1884448068 -1.1842739331 -0.4680590100
H -4.7593756593 -1.3475675183 1.2619421373
27
-55.76214086
C 1.2030904956 0.3223118947 -0.8460521518
H 1.3472548469 1.0108770837 -1.6891362207
C 1.8829310024 1.0263366794 0.3448269958
C -0.2908831363 0.2018311342 -0.5899168325
C 1.9084720365 -0.9739669752 -1.2447053856
C -1.0154921966 1.3667641308 -0.3657202642
C -2.3745567987 1.3359945102 -0.1138513153
C -3.0469796515 0.1182290494 -0.0898437887
C -2.3278182234 -1.0518040784 -0.3335754371
C -0.9706623128 -1.0105673387 -0.5770244315
F 1.9018022149 2.3658288063 0.1569635636
F 1.2906524524 0.8425461531 1.5254854919
F 3.1739510044 0.6782560255 0.4890919292
N 1.9139868386 -2.0274062395 -0.2129948864
O 2.0479815102 -3.1637892901 -0.6093846269
O 1.8216279673 -1.7050373804 0.9465170716
O -4.3765831258 -0.0375240323 0.1477457245
C -5.1589500992 1.1096647487 0.4216417990
H 1.4469353098 -1.3897958233 -2.1424762334
H 2.9619172020 -0.7683495831 -1.4662809214
H -0.5162276622 2.3240279067 -0.3837516716
H -2.8935349620 2.2639776477 0.0608887549
H -2.8563994822 -1.9916149073 -0.3221717296
H -0.4694447298 -1.9466875994 -0.7608313516
H -5.1630306312 1.7981768212 -0.4277785650
H -6.1670423694 0.7365623061 0.5923937488
H -4.8038501128 1.6261511488 1.3174807579
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--- Andrea Pellegrini ---
MIT license
v. 1.0.0
GitHub: https://github.com/andre-cloud/Ensemble_Analyser.git
======================================================================
Calculation Input
======================================================================
Ensemble: 11 confromer(s)
Protocols: 5
Temperature: 298.15 K
CPU cores: 44
Protocol Steps:
000. → b97-3c/def2-mTZVP | SP
thrG : 0.25 kcal/mol
thrB : 1e-05 cm-1
thrGMAX : 6 kcal/mol
001. → r2scan-3c/def2-mTZVPP | OPT+FREQ
thrG : 0.5 kcal/mol
thrB : 5e-05 cm-1
thrGMAX : 3.5 kcal/mol
002. → wb97x-d4rev/def2-qzvpp | SP
thrG : 0.25 kcal/mol
thrB : 1e-05 cm-1
thrGMAX : 6 kcal/mol
003. → B3LYP D4/def2-QZVPPD | FREQ
thrG : 0.5 kcal/mol
thrB : 5e-05 cm-1
thrGMAX : 3.75 kcal/mol
======================================================================
======================================================================
PROTOCOL 0 - SP
======================================================================
Level: b97-3c/def2-mTZVP
Active conformers: 11
======================================================================
001. → CONF 001 | Protocol 0
⊗ No previous thermochemical data found for conformer 1: setting G, H, S, ZPVE to NaN.
✓ E = -966.56656184 Eh | Time: 8.5s
002. → CONF 002 | Protocol 0
⊗ No previous thermochemical data found for conformer 2: setting G, H, S, ZPVE to NaN.
✓ E = -966.56656638 Eh | Time: 8.6s
003. → CONF 003 | Protocol 0
⊗ No previous thermochemical data found for conformer 3: setting G, H, S, ZPVE to NaN.
✓ E = -966.56491529 Eh | Time: 8.5s
[...]
Total elapsed time for protocol 0: 0:01:34.561081
**********************************************************************
Summary Before Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ---------- -------- ---------- --------------- --------- ------------------ -----------
1 -966.566561842759 nan nan 0.02506 nan nan 8.49
2 -966.566566375643 nan nan 0.02484 nan nan 8.57
3 -966.564915292485 nan nan 0.03329 nan nan 8.50
4 -966.564812715069 nan nan 0.03286 nan nan 8.54
5 -966.558330812902 nan nan 0.03059 nan nan 8.66
6 -966.558040083384 nan nan 0.03159 nan nan 8.77
7 -966.555719126123 nan nan 0.02826 nan nan 8.64
8 -966.555710703914 nan nan 0.02880 nan nan 8.52
9 -966.553968233567 nan nan 0.02886 nan nan 8.38
10 -966.553591870827 nan nan 0.02893 nan nan 8.77
11 -966.553131368091 nan nan 0.02954 nan nan 8.62
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pruning sequence
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Filtering conformers above 6 kcal/mol energy window
******************************
Conformers over energy window
******************************
∆E [kcal/mol]
------- ---------------
Conf 7 6.81
Conf 8 6.81
Conf 9 7.91
Conf 10 8.14
Conf 11 8.43
✓ Deactivated 5 conformer(s)
No conformers deactivated by similarity check
✓ Pruning completed in 0.0008s
Initial: 11 → Final: 6 (54.5% retained)
Deactivated: 5
**********************************************************************
Summary After Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ---------- -------- ---------- --------------- --------- ------------------ -----------
2 -966.566566375643 nan nan 0.02484 0.00 43.01 8.57
1 -966.566561842759 nan nan 0.02506 0.00 42.80 8.49
3 -966.564915292485 nan nan 0.03329 1.04 7.48 8.50
4 -966.564812715069 nan nan 0.03286 1.10 6.71 8.54
5 -966.558330812902 nan nan 0.03059 5.17 0.01 8.66
6 -966.558040083384 nan nan 0.03159 5.35 0.01 8.77
**************************************************
Energetic Summary of the active conformers
**************************************************
Conformer ∆E [Eh] Boltzamnn Pop. on ∆E ∆(E+ZPVE) [Eh] Boltzamnn Pop. on ∆(E+ZPVE) ∆H [Eh] Boltzamnn Pop. on ∆H ∆G [Eh] Boltzamnn Pop. on ∆G
----------- ----------------- ---------------------- ---------------- ----------------------------- --------- ---------------------- --------- ----------------------
Conf 2 -966.566566375643 43.01 nan nan nan nan nan nan
Conf 1 -966.566561842759 42.80 nan nan nan nan nan nan
Conf 3 -966.564915292485 7.48 nan nan nan nan nan nan
Conf 4 -966.564812715069 6.71 nan nan nan nan nan nan
Conf 5 -966.558330812902 0.01 nan nan nan nan nan nan
Conf 6 -966.558040083384 0.01 nan nan nan nan nan nan
**************************************************
Ensemble Average Energies
**************************************************
T [K] E_av [Eh] E+ZPVE_av [Eh] H_av [Eh] G_av [Eh]
------- ------------------ ---------------- ----------- -----------
298.15 -966.5663223637399 nan nan nan
----------------------------------------
Spectra convolution
----------------------------------------
⊗ No calculation of IR graphs. Skipping
⊗ No calculation of VCD graphs. Skipping
⊗ No calculation of UV graphs. Skipping
⊗ No calculation of ECD graphs. Skipping
✓ Sprectra convolution completed in 0.0868s
Protocol 0 completed in 0:01:34.653447
Active: 6 | Deactivated: 5
======================================================================
END PROTOCOL 0
======================================================================
======================================================================
PROTOCOL 1 - OPT+FREQ
======================================================================
Level: r2scan-3c/def2-mTZVPP
Active conformers: 6
======================================================================
001. → CONF 001 | Protocol 1
✓ E = -966.84402123 Eh | Time: 264.3s | Imag. Freq 0
002. → CONF 002 | Protocol 1
✓ E = -966.84389866 Eh | Time: 269.0s | Imag. Freq 0
003. → CONF 003 | Protocol 1
✓ E = -966.84246714 Eh | Time: 246.9s | Imag. Freq 0
004. → CONF 004 | Protocol 1
✓ E = -966.84235384 Eh | Time: 247.5s | Imag. Freq 0
005. → CONF 005 | Protocol 1
✓ E = -966.83779221 Eh | Time: 332.8s | Imag. Freq 0
006. → CONF 006 | Protocol 1
✓ E = -966.83749484 Eh | Time: 377.3s | Imag. Freq 0
Total elapsed time for protocol 1: 0:28:57.857529
**********************************************************************
Summary Before Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -966.844021228332 0.15232760155754477 -966.6916936267745 0.02507 nan nan 264.32
2 -966.843898659037 0.1522861155232249 -966.6916125435138 0.02489 nan nan 269.02
3 -966.842467139309 0.15246332050605815 -966.6900038188029 0.03328 nan nan 246.87
4 -966.842353837097 0.1524124171172616 -966.6899414199797 0.03273 nan nan 247.46
5 -966.837792205694 0.15284063051728936 -966.6849515751767 0.02852 nan nan 332.79
6 -966.837494837675 0.15297786457563234 -966.6845169730993 0.02930 nan nan 377.27
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pruning sequence
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Filtering conformers above 3.5 kcal/mol energy window
******************************
Conformers over energy window
******************************
∆E [kcal/mol]
------ ---------------
Conf 5 4.23
Conf 6 4.50
✓ Deactivated 2 conformer(s)
No conformers deactivated by similarity check
✓ Pruning completed in 0.0005s
Initial: 6 → Final: 4 (66.7% retained)
Deactivated: 2
**********************************************************************
Summary After Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -966.844021228332 0.15232760155754477 -966.6916936267745 0.02507 0.00 44.63 264.32
2 -966.843898659037 0.1522861155232249 -966.6916125435138 0.02489 0.05 40.95 269.02
3 -966.842467139309 0.15246332050605815 -966.6900038188029 0.03328 1.06 7.45 246.87
4 -966.842353837097 0.1524124171172616 -966.6899414199797 0.03273 1.10 6.97 247.46
**************************************************
Energetic Summary of the active conformers
**************************************************
Conformer ∆E [Eh] Boltzamnn Pop. on ∆E ∆(E+ZPVE) [Eh] Boltzamnn Pop. on ∆(E+ZPVE) ∆H [Eh] Boltzamnn Pop. on ∆H ∆G [Eh] Boltzamnn Pop. on ∆G
----------- ----------------- ---------------------- ------------------ ----------------------------- ------------------ ---------------------- ------------------ ----------------------
Conf 1 -966.844021228332 44.61 -966.6475910088928 43.37 -966.6329710092479 43.27 -966.6916936267745 44.63
Conf 2 -966.843898659037 39.17 -966.6474988075722 39.33 -966.6328919343662 39.79 -966.6916125435138 40.95
Conf 3 -966.842467139309 8.59 -966.6461090466568 9.02 -966.6314654954111 8.78 -966.6900038188029 7.45
Conf 4 -966.842353837097 7.62 -966.6460278893901 8.28 -966.631397549066 8.17 -966.6899414199797 6.97
**************************************************
Ensemble Average Energies
**************************************************
T [K] E_av [Eh] E+ZPVE_av [Eh] H_av [Eh] G_av [Eh]
------- ------------------ ------------------ ------------------ ------------------
298.15 -966.8437125430996 -966.6472916936933 -966.6326789037934 -966.6914124412149
----------------------------------------
Spectra convolution
----------------------------------------
-----------------------------------
IR Spectra convolution
-----------------------------------
Spectra convolution results:
Shift: 0.85 FWHM: 5.74 Similarity: 99.64 Similarity Unweighted: 84.64 Time: 0:00:00.873867 Cycle: 90
-----------------------------------
VCD Spectra convolution
-----------------------------------
Spectra convolution results:
Shift: 0.85 FWHM: 4.00 Similarity: 99.60 Similarity Unweighted: 94.27 Time: 0:00:00.235392 Cycle: 60
⊗ No calculation of UV graphs. Skipping
⊗ No calculation of ECD graphs. Skipping
✓ Sprectra convolution completed in 1.2539s
Protocol 1 completed in 0:28:59.115012
Active: 4 | Deactivated: 2
======================================================================
END PROTOCOL 1
======================================================================
======================================================================
PROTOCOL 2 - SP
======================================================================
Level: wb97x-d4rev/def2-qzvpp
Active conformers: 4
======================================================================
001. → CONF 001 | Protocol 2
✓ E = -967.64598650 Eh | Time: 107.8s
002. → CONF 002 | Protocol 2
✓ E = -967.64585185 Eh | Time: 107.8s
003. → CONF 003 | Protocol 2
✓ E = -967.64454925 Eh | Time: 106.6s
004. → CONF 004 | Protocol 2
✓ E = -967.64442652 Eh | Time: 105.8s
Total elapsed time for protocol 2: 0:07:08.054879
**********************************************************************
Summary Before Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -967.645986503336 0.15232760155754477 -967.4936589017784 0.02507 nan nan 107.78
2 -967.64585185224 0.1522861155232249 -967.4935657367167 0.02489 nan nan 107.79
3 -967.64454925377 0.15246332050605815 -967.492085933264 0.03328 nan nan 106.63
4 -967.644426518304 0.1524124171172616 -967.4920141011868 0.03273 nan nan 105.80
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pruning sequence
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Filtering conformers above 6 kcal/mol energy window
✓ No conformers above threshold
No conformers deactivated by similarity check
✓ Pruning completed in 0.0004s
Initial: 4 → Final: 4 (100.0% retained)
Deactivated: 0
**********************************************************************
Summary After Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -967.645986503336 0.15232760155754477 -967.4936589017784 0.02507 0.00 44.06 107.78
2 -967.64585185224 0.1522861155232249 -967.4935657367167 0.02489 0.06 39.91 107.79
3 -967.64454925377 0.15246332050605815 -967.492085933264 0.03328 0.99 8.32 106.63
4 -967.644426518304 0.1524124171172616 -967.4920141011868 0.03273 1.03 7.71 105.80
**************************************************
Energetic Summary of the active conformers
**************************************************
Conformer ∆E [Eh] Boltzamnn Pop. on ∆E ∆(E+ZPVE) [Eh] Boltzamnn Pop. on ∆(E+ZPVE) ∆H [Eh] Boltzamnn Pop. on ∆H ∆G [Eh] Boltzamnn Pop. on ∆G
----------- ----------------- ---------------------- ------------------ ----------------------------- ------------------ ---------------------- ------------------ ----------------------
Conf 1 -967.645986503336 43.93 -967.4495562838968 42.65 -967.4349362842518 42.57 -967.4936589017784 44.06
Conf 2 -967.64585185224 38.08 -967.4494520007752 38.19 -967.4348451275691 38.65 -967.4935657367167 39.91
Conf 3 -967.64454925377 9.58 -967.4481911611178 10.04 -967.4335476098722 9.77 -967.492085933264 8.32
Conf 4 -967.644426518304 8.41 -967.4481005705971 9.12 -967.4334702302731 9.00 -967.4920141011868 7.71
**************************************************
Ensemble Average Energies
**************************************************
T [K] E_av [Eh] E+ZPVE_av [Eh] H_av [Eh] G_av [Eh]
------- ------------------ ------------------ ------------------ ------------------
298.15 -967.6456663442161 -967.4492466362248 -967.4346333172836 -967.4933640186741
----------------------------------------
Spectra convolution
----------------------------------------
⊗ No calculation of IR graphs. Skipping
⊗ No calculation of VCD graphs. Skipping
⊗ No calculation of UV graphs. Skipping
⊗ No calculation of ECD graphs. Skipping
✓ Sprectra convolution completed in 0.0836s
Protocol 2 completed in 0:07:08.142737
Active: 4 | Deactivated: 0
======================================================================
END PROTOCOL 2
======================================================================
======================================================================
PROTOCOL 3 - FREQ
======================================================================
Level: B3LYP D4/def2-QZVPPD
Active conformers: 4
======================================================================
001. → CONF 001 | Protocol 3
✓ E = -966.97590791 Eh | Time: 2762.3s | Imag. Freq 0
002. → CONF 002 | Protocol 3
✓ E = -966.97570334 Eh | Time: 2772.1s | Imag. Freq 0
003. → CONF 003 | Protocol 3
✓ E = -966.97435313 Eh | Time: 2624.2s | Imag. Freq 0
004. → CONF 004 | Protocol 3
✓ E = -966.97425101 Eh | Time: 2677.4s | Imag. Freq 0
Total elapsed time for protocol 3: 3:00:36.049882
**********************************************************************
Summary Before Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -966.975907908181 0.15391147995580923 -966.8219964282251 0.02507 nan nan 2762.27
2 -966.975703341707 0.153760678978756 -966.8219426627282 0.02489 nan nan 2772.08
3 -966.974353133434 0.15395328740760306 -966.8203998460264 0.03328 nan nan 2624.20
4 -966.974251010288 0.15377425386816412 -966.8204767564198 0.03273 nan nan 2677.41
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pruning sequence
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Filtering conformers above 3.75 kcal/mol energy window
✓ No conformers above threshold
No conformers deactivated by similarity check
✓ Pruning completed in 0.0004s
Initial: 4 → Final: 4 (100.0% retained)
Deactivated: 0
**********************************************************************
Summary After Pruning
**********************************************************************
Conformers E [Eh] G-E [Eh] G [Eh] B [cm-1] ∆G [kcal/mol] Pop [%] Elap. time [sec] # Cluster
------------ ----------------- ------------------- ------------------ ---------- --------------- --------- ------------------ -----------
1 -966.975907908181 0.15391147995580923 -966.8219964282251 0.02507 0.00 42.94 2762.27
2 -966.975703341707 0.153760678978756 -966.8219426627282 0.02489 0.03 40.57 2772.08
4 -966.974251010288 0.15377425386816412 -966.8204767564198 0.03273 0.95 8.58 2677.41
3 -966.974353133434 0.15395328740760306 -966.8203998460264 0.03328 1.00 7.91 2624.20
**************************************************
Energetic Summary of the active conformers
**************************************************
Conformer ∆E [Eh] Boltzamnn Pop. on ∆E ∆(E+ZPVE) [Eh] Boltzamnn Pop. on ∆(E+ZPVE) ∆H [Eh] Boltzamnn Pop. on ∆H ∆G [Eh] Boltzamnn Pop. on ∆G
----------- ----------------- ---------------------- ------------------ ----------------------------- ------------------ ---------------------- ------------------ ----------------------
Conf 1 -966.975907908181 46.07 -966.7792323300883 43.59 -966.7645929669437 43.64 -966.8219964282251 42.94
Conf 2 -966.975703341707 37.09 -966.7791211912688 38.75 -966.764492762362 39.25 -966.8219426627282 40.57
Conf 4 -966.974251010288 7.96 -966.7777296185803 8.87 -966.7630687028312 8.68 -966.8204767564198 8.58
Conf 3 -966.974353133434 8.87 -966.7777222302085 8.80 -966.7630409179617 8.43 -966.8203998460264 7.91
**************************************************
Ensemble Average Energies
**************************************************
T [K] E_av [Eh] E+ZPVE_av [Eh] H_av [Eh] G_av [Eh]
------- ------------------ ----------------- ------------------ ------------------
298.15 -966.9755621982915 -966.778923132367 -966.7642905433372 -966.8217179202562
----------------------------------------
Spectra convolution
----------------------------------------
-----------------------------------
IR Spectra convolution
-----------------------------------
Spectra convolution results:
Shift: 0.86 FWHM: 4.00 Similarity: 99.64 Similarity Unweighted: 85.21 Time: 0:00:00.425557 Cycle: 96
-----------------------------------
VCD Spectra convolution
-----------------------------------
Spectra convolution results:
Shift: 0.97 FWHM: 4.00 Similarity: 99.60 Similarity Unweighted: 94.61 Time: 0:00:00.284486 Cycle: 69
⊗ No calculation of UV graphs. Skipping
⊗ No calculation of ECD graphs. Skipping
✓ Sprectra convolution completed in 0.8724s
Protocol 3 completed in 3:00:36.926409
Active: 4 | Deactivated: 0
======================================================================
END PROTOCOL 3
======================================================================
Saved IR_comparison.png
Saved VCD_comparison.png
======================================================================
Calculation COMPLETED
======================================================================
Total elapsed time: 3:38:18.837605
Final conformers: 4
======================================================================
**********************************************************************
CALCULATIONS COMPLETED SUCCESSFULLY
**********************************************************************
At the end of the calculation, two files per spectra will be stored: one .pickle file and one .png file. If you want to modify the automatically generated spectra, it is possible to use the terminal interface of the enan_graph_editor module, to customize the spectra.
To refine the interested area and the multiplier, it is possible to change the values stored in the setting.json file and use the CLI command enan_regraph to recompute the various spectra, without the need of relaunching the calculation.
The same workflow has been used to simulate the ECD spectra, but with the following ensemble and following protocol
{
"0": {
"functional": "r2SCAN-3c",
"basis": "def2-mTZVPP",
"opt": true,
"freq": true,
"solvent":{
"solvent": "acetonitrile",
"smd": true
}},
"1":{
"functional": "wb97X-D4",
"basis": "def2-TZVPP",
"solvent": {
"solvent": "acetonitrile",
"smd": true
},
"add_input":"%tddft nroots 40 TDA FALSE end"
},
"2":{
"functional": "CAM-B3LYP D4",
"basis": "def2-TZVPP",
"solvent": {
"solvent": "acetonitrile",
"smd": true
},
"add_input":"%tddft nroots 40 TDA false end",
"read_orbitals": "1"
}
}
27
-55.76954216
C 1.3226789038 0.0637124090 -0.3767052001
H 1.5110023818 -0.1525730016 -1.4344441507
C 1.9646062804 1.4202123147 -0.1076228998
C -0.1733223631 0.1164400550 -0.1441928771
C 2.0118998742 -1.0036260326 0.4790554967
C -0.7035717298 0.3741387095 1.1174817065
C -2.0675285144 0.4048973372 1.3076234656
C -2.9397177769 0.1731022014 0.2413939157
C -2.4126258354 -0.0856926506 -1.0196016137
C -1.0409764896 -0.1098838975 -1.2016615889
F 3.2586086704 1.4451902893 -0.4876144795
F 1.3591983527 2.4106780726 -0.7757715296
F 1.9626095543 1.7739826867 1.1871064866
N 1.6279506265 -2.3590196430 0.0411569053
O 1.3501071582 -2.5285939346 -1.1215100551
O 1.6409759025 -3.2251092601 0.8835970015
O -4.2654676362 0.2216668773 0.5392872812
C -5.2059584317 -0.0043993122 -0.4938395682
H 3.1004019070 -0.9336306134 0.3705529988
H 1.7577758219 -0.9148047548 1.5371305900
H -0.0563749761 0.5640371414 1.9596443989
H -2.4878799247 0.6061150338 2.2799772607
H -3.0547773061 -0.2698483785 -1.8650091638
H -0.6468681135 -0.3185876985 -2.1846794432
H -5.1146813996 0.7465348140 -1.2832912341
H -5.0946718509 -1.0058281792 -0.9183511680
H -6.1815417999 0.0831563958 -0.0192955899
27
-55.76937955
C 1.3446089644 0.0569149006 -0.3805890075
H 1.6283956591 -0.1586594094 -1.4170235503
C 1.9368374623 1.4251208038 -0.0610308231
C -0.1667322243 0.0856027167 -0.2786372678
C 1.9770776572 -0.9973908871 0.5346689321
C -0.8081281463 0.3227898844 0.9289075825
C -2.1897069978 0.3357173385 1.0110948254
C -2.9565908581 0.1043662882 -0.1262971451
C -2.3124130562 -0.1351861136 -1.3423409671
C -0.9370557104 -0.1422713436 -1.4148304098
F 3.2607743023 1.4702814312 -0.3127515100
F 1.3827057851 2.4017374515 -0.7909519117
F 1.8022818018 1.7856671315 1.2253672215
N 1.6476494436 -2.3566191021 0.0648571569
O 1.5939119622 -2.5494050317 -1.1258067022
O 1.4757316358 -3.2001480292 0.9124249554
O -4.3156158680 0.0893285824 -0.1615166189
C -5.0325965012 0.3215486165 1.0364364985
H 3.0692310296 -0.9095675289 0.5112190341
H 1.6331648235 -0.9114610326 1.5669908689
H -0.2391460743 0.5128993099 1.8261249969
H -2.6526344872 0.5256272938 1.9654423523
H -2.9166726909 -0.3140342525 -2.2172065964
H -0.4564115794 -0.3346517871 -2.3617161621
H -4.8194728221 1.3154880285 1.4392039043
H -6.0833822468 0.2590000402 0.7597998392
H -4.8067842260 -0.4406637025 1.7872192008
27
-55.76915033
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27
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27
-55.76220237
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H 1.2880629572 0.5107272567 -1.9953446278
C 1.9094684122 1.0981112385 -0.0772563362
C -0.3221093738 0.1444223877 -0.6508044587
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C -2.3505321726 -0.8040280383 0.2486037216
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27
-55.76216496
C 1.1775690535 0.4194358039 -0.8794159517
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O 1.8476106100 -1.7100903769 0.7985232651
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C -5.1398233565 -0.6679669907 0.4946124834
H 1.2700876201 -1.2497981476 -2.2485275156
H 2.8474798789 -0.7226211205 -1.6337566419
H -0.4311553069 2.4951976557 -0.3359886442
H -2.8198637170 2.5011163258 0.2319413750
H -2.9099678049 -1.7525863339 -0.1629160315
H -0.5806183822 -1.7728468344 -0.7114370439
H -6.1341002934 -0.3243990497 0.7737790842
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H -4.7593756593 -1.3475675183 1.2619421373
27
-55.76214086
C 1.2030904956 0.3223118947 -0.8460521518
H 1.3472548469 1.0108770837 -1.6891362207
C 1.8829310024 1.0263366794 0.3448269958
C -0.2908831363 0.2018311342 -0.5899168325
C 1.9084720365 -0.9739669752 -1.2447053856
C -1.0154921966 1.3667641308 -0.3657202642
C -2.3745567987 1.3359945102 -0.1138513153
C -3.0469796515 0.1182290494 -0.0898437887
C -2.3278182234 -1.0518040784 -0.3335754371
C -0.9706623128 -1.0105673387 -0.5770244315
F 1.9018022149 2.3658288063 0.1569635636
F 1.2906524524 0.8425461531 1.5254854919
F 3.1739510044 0.6782560255 0.4890919292
N 1.9139868386 -2.0274062395 -0.2129948864
O 2.0479815102 -3.1637892901 -0.6093846269
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O -4.3765831258 -0.0375240323 0.1477457245
C -5.1589500992 1.1096647487 0.4216417990
H 1.4469353098 -1.3897958233 -2.1424762334
H 2.9619172020 -0.7683495831 -1.4662809214
H -0.5162276622 2.3240279067 -0.3837516716
H -2.8935349620 2.2639776477 0.0608887549
H -2.8563994822 -1.9916149073 -0.3221717296
H -0.4694447298 -1.9466875994 -0.7608313516
H -5.1630306312 1.7981768212 -0.4277785650
H -6.1670423694 0.7365623061 0.5923937488
H -4.8038501128 1.6261511488 1.3174807579
At the end of the calculations, the final ECD comparison figure is saved (both as a .pickle and a .png).
