I came across a weird situation where I am getting huge interaction energies (BSSE corrected) when I modeled Fe3+/Al3+ complexes with aliphatic and aromatic alcohols. In all cases metal was interacting with the O atom/s. This was not the case for a benzene monomer or dimer interaction with the metal cation. I am using wB97x-D/def2-SVPD to compute BSSE corrected interaction energies. Has someone come across such situation or does anybody have any idea on what is really going on here?
Thank you
Hello dlsenal94w,
Could you post the input file? If the system is confidential, you may build a representitive model system.
Thanks
Hello kyliu,
I have attached two different calculations of cellulose and hemicellulose with Fe3+. I couldn’t find anyway to attach *.out files. Because of this I will quote the final answer for each input along with this. As you would see Fe3+ bound system computed using def2-SVPD have interaction energies well above typical values.
Thanks in advance!
> --------------------------------------------------------------
> User input:
> --------------------------------------------------------------
> $comment
> BSSE_W_FE
> $end
> $molecule
> 3 6
> -- Fragment_w_Fe
> 3 6
> 6 -0.3851502204 2.086900661 -2.0614174479
> 6 0.42828536064 2.5102486451 -3.2738015568
> 1 1.4930024548 2.2806517311 -3.0857862539
> 6 0.28497058143 4.0314028672 -3.4461659867
> 1 -0.763164231 4.2522515417 -3.7285214537
> 6 0.58047737551 4.7488692065 -2.1155201264
> 1 1.6403198549 4.5809421368 -1.8415274953
> 6 0.34852593075 6.2550710313 -2.1785186618
> 1 -0.67396850803 6.4505532895 -2.5622726746
> 1 0.4086052343 6.6512291827 -1.1513809198
> 8 -0.2209290731 0.71177706361 -1.75956983
> 8 -0.053388351169 1.7751586505 -4.3725905387
> 8 1.1658727304 4.541768226 -4.4183282984
> 8 1.3327589992 6.8948363269 -2.9467664543
> 1 -0.46996072101 0.13215268983 -2.5309842485
> 1 0.68691906212 1.5042193676 -4.9338227975
> 1 1.4536512502 6.3607321335 -3.7520587449
> 6 0.96927170167 -5.5200841212 3.3390056856
> 6 0.044498094702 2.8904775793 -0.84676847436
> 6 -0.034054470154 4.8486508462 3.0939236379
> 6 0.038820050275 4.3095453857 1.6701281404
> 1 -0.61071330197 4.9443977727 1.0440668241
> 6 -0.47240772036 2.8735494748 1.6003321008
> 1 0.28798326423 2.2205297631 2.0648926048
> 6 -1.8246978731 2.7266727887 2.3331780328
> 1 -2.5926390263 3.2401228895 1.7221742702
> 6 -2.2511312899 1.2866632462 2.6128802724
> 1 -1.5014913685 0.8143118065 3.2667746694
> 1 -3.2155735217 1.2998751349 3.1382969308
> 8 0.33036783918 6.2007754355 3.02989895
> 8 1.3620901453 4.3287020023 1.200109001
> 8 -0.70315648553 2.4031257792 0.24669610259
> 8 -2.3731323068 0.49027990011 1.432685076
> 1 0.36585646527 6.54862309 3.9340082911
> 1 1.6224631216 5.2532705275 1.0708453876
> 1 -3.2965736633 0.26183362925 1.2360046033
> 8 -1.7460950473 3.2814702732 3.6184164829
> 8 -0.26093342608 4.2163675257 -1.1086169536
> 1 -1.4540704045 2.2933370929 -2.2475765721
> 6 0.65810404411 4.5984998246 -5.736947153
> 1 -0.24304171149 5.2386674189 -5.7833625504
> 1 0.40571933899 3.5949327013 -6.1163698424
> 1 1.4479657202 5.0384103207 -6.3635436251
> 1 1.1228049327 2.7714954024 -0.63618107942
> 1 0.65729695821 4.2701063517 3.7375830031
> 6 -1.4380276233 4.6600215084 3.647651662
> 1 -2.1757645183 5.2103053679 3.0227183415
> 8 -1.46513708 5.1001607034 4.9447745585
> 6 -2.7544210872 5.2367504155 5.5062351254
> 1 -3.3891442108 5.8905353053 4.8786893583
> 1 -2.6263719765 5.6967810297 6.4968404503
> 1 -3.2480059779 4.255842224 5.6199264418
> 26 -0.81440545007 0.20537940594 0.14134764838
> -- Fragment_wout_Fe
> 0 1
> 6 -0.42698337263 -2.3586512642 -1.4521096282
> 6 -0.93967614218 -2.5270113476 -2.8755544893
> 1 -1.9550971887 -2.9580828454 -2.8848605217
> 6 -0.0025096484565 -3.4670971023 -3.6842190189
> 1 1.0086633165 -3.0423581779 -3.7966789896
> 6 0.13799040082 -4.812029039 -2.7189426282
> 1 -0.9059771298 -5.1394405689 -2.5572695455
> 6 0.93999196667 -5.8686987299 -3.4648536363
> 1 1.9190793174 -5.4740616362 -3.7850029746
> 1 1.1168482658 -6.6613220114 -2.7081078095
> 8 -1.3524769509 -1.6231399435 -0.66792565844
> 8 -0.91195074393 -1.2577065554 -3.4606191384
> 8 -0.57406657572 -3.8241184474 -4.8400745183
> 8 0.17011729564 -6.3542195799 -4.5107708429
> 1 -2.2145169224 -2.0711926239 -0.57438971539
> 1 -1.5186516396 -1.1878740047 -4.2173126046
> 1 0.70561151109 -6.4568787918 -5.3131551971
> 6 1.0651793231 -5.1205485701 1.8730488128
> 1 2.138333152 -5.0275384849 1.611594364
> 6 0.40990130795 -3.7663710811 1.6454965884
> 1 -0.68392217896 -3.8747522003 1.758340239
> 6 0.90963473568 -2.7206746826 2.6524345123
> 1 1.9798987071 -2.5134044519 2.443102183
> 6 0.13331169756 -1.4042933968 2.6239268696
> 1 -0.9479464329 -1.5871669332 2.5383785985
> 1 0.33245867646 -0.86374532186 3.561887876
> 8 1.7147878675 -6.6955581603 3.5064790929
> 8 0.42920032453 -6.0513445218 1.0352414571
> 8 0.71485724167 -3.2637683435 0.35954006076
> 8 0.48197375531 -0.55588101564 1.5206630763
> 1 1.6114683933 -6.9913381272 4.4242668044
> 1 0.88693048413 -6.9007428963 1.1247274509
> 1 1.4111017981 -0.26566793223 1.5663056416
> 8 0.76440042178 -4.4141245812 -1.588258745
> 1 0.49151951579 -1.7531483926 -1.4967293298
> 6 -0.041114321118 -3.6388863492 -0.70979717347
> 8 0.74897774709 -3.210797696 3.958666017
> 1 -0.93158622928 -4.2272215383 -0.42188750447
> 6 0.158981872 -3.6705033062 -6.0533479587
> 1 1.2082152996 -3.9779098652 -5.9144762329
> 1 0.11557536112 -2.6028935139 -6.3307641657
> 1 -0.34522971678 -4.2884654925 -6.8058535673
> 1 -0.096798885714 -5.6754162936 3.5958000722
> 6 1.4877913578 -4.3882903582 4.2207794948
> 1 2.5607471271 -4.1959807855 3.996919069
> 8 1.3149665687 -4.7440983556 5.5331338874
> 6 2.0354119539 -3.9648188586 6.4652988846
> 1 3.12100547 -4.0130007477 6.2595282213
> 1 1.8356463374 -4.3864324482 7.4609569486
> 1 1.708845644 -2.9104831816 6.4447614579
> $end
>
> $rem
> JOBTYPE BSSE
> METHOD WB97X-D
> BASIS DEF2-SVPD
> MAXSCF 5000
> MEM_TOTAL 24000
> $end
---------------------------------------------------------------------
* Fragment's binding energy *
---------------------------------------------------------------------
Fragment E(TOTAL) E(CP-CORR) DE(BSSE)
---------------------------------------------------------------------
1 -2675.7533605473 -2679.7145283284 3.9611677811
2 -1336.8373204342 -1339.1964570513 2.3591366171
Complex -4013.1227347589
---------------------------------------------------------------------
DE, kJ/mol -1396.9237705959 15197.2323579761
---------------------------------------------------------------------
--------------------------------------------------------------
User input:
--------------------------------------------------------------
$comment
BSSE_W_FE
$end
$molecule
3 6
-- Fragment_w_Fe
3 6
1 -3.0731693517 -6.410857818 7.7112406874
6 -2.9414970178 -6.1877916255 6.6421189427
1 -3.4070409149 -5.2096720525 6.4142701694
1 -3.4417099868 -6.9698816546 6.0438757233
8 -1.5544965285 -6.1506549428 6.3933111894
6 -1.2133294739 -5.7767444047 5.1175866324
1 -1.7964022088 -4.8852284971 4.7983983292
8 -1.4965897419 -6.8515563028 4.2453157074
6 -1.2324581847 -6.5867799625 2.8909664377
1 -1.5293909241 -7.4779854768 2.3188724584
1 -1.8168805564 -5.719627478 2.528560294
6 0.25803217256 -6.3109371867 2.7060971154
1 0.82587126287 -7.2134667588 2.9900698573
8 0.48477393412 -6.0055022908 1.3383153773
6 0.68553622833 -5.1548535267 3.6113700494
1 1.7781392166 -5.0208819755 3.5499456585
6 0.27910366048 -5.4554058415 5.0637475191
1 0.81555344375 -6.3616139067 5.4039155714
8 0.5286440057 -4.3643460028 5.9108441875
1 1.4851480643 -4.2756257189 6.0365997232
8 0.025979729571 -3.9934777557 3.155427137
6 0.76380325434 -2.8066571661 3.1661399587
1 1.1165678268 -2.5656133207 4.1797709373
6 -0.12551034908 -1.715538722 2.5540217609
1 -1.1548808841 -2.1029482142 2.4502115933
6 0.5007881646 -1.5087994587 1.1639087301
1 1.1037219699 -0.59544206734 1.2672306701
6 1.4848069515 -2.6595892975 1.0047029835
1 0.97913373929 -3.5443916278 0.57994639294
6 2.7084658729 -2.3193959316 0.17620112683
1 2.3965555482 -2.0438064041 -0.84273060303
1 3.3710998622 -3.2000480691 0.11539547487
8 3.4203303683 -1.2178770454 0.71003891069
1 3.6080541288 -1.4119033175 1.6442865177
8 1.8968324606 -2.9079751168 2.3409403531
8 -0.38075626563 -1.4188007849 0.083270723925
1 -0.80842616537 -0.54520597612 0.16221032284
8 -0.083870316961 -0.55009055434 3.3383670015
1 -0.34143059272 0.19555323443 2.7632126487
6 1.5410087985 -6.5885208699 0.72778012923
1 1.6974895616 -7.6387473732 1.0415137019
8 2.7351866252 -5.8535916787 1.0571701202
6 3.8785895245 -6.3614457955 0.60185360584
1 4.7365578505 -5.7739608117 0.95445194736
1 3.9720797562 -7.458670128 0.67449906077
6 3.873998848 -6.1573053215 -1.1104470118
1 3.8006118009 -5.0671124549 -1.2596879034
6 2.6256608243 -6.9376922598 -1.5416368783
1 2.4950531271 -6.6861927146 -2.6142104715
8 2.7632920356 -8.3077284924 -1.3483109033
1 3.371569016 -8.6895102632 -2.0015432746
6 1.3568952081 -6.5041496907 -0.80626937227
1 1.1309332763 -5.4543161041 -1.050776199
8 0.27585471365 -7.2838472283 -1.201773824
1 0.57887017967 -8.2083088302 -1.2431919825
8 4.9944777072 -6.7052419798 -1.5694082581
6 6.1330744919 -5.8683376686 -1.766505012
1 6.9031175853 -6.49901764 -2.2265578445
1 6.4854926381 -5.4885152676 -0.79263967722
1 5.8646417212 -5.0292687463 -2.4277606447
26 -0.010258731851 5.1028714203 -1.8778887177
-- Fragment_wout_Fe
0 1
1 -3.2746706106 3.961942816 4.1206680775
6 -4.2881653888 4.1298144077 3.7105246665
1 -4.5339085481 5.203345636 3.7798292101
1 -5.0172417983 3.5514553403 4.2957356009
8 -4.3757811429 3.6676281984 2.3783652821
6 -3.4501896328 4.1901206477 1.5198878719
1 -2.4226791187 4.1299760621 1.9443876217
8 -3.7668376258 5.5433212073 1.267206153
6 -2.8477635278 6.2052733286 0.44538007549
1 -3.1537680302 7.2585873287 0.37711202374
1 -1.822028913 6.158012109 0.860913893
6 -2.8786736875 5.5715919574 -0.94537279103
1 -3.8406287484 5.7801427114 -1.4332432131
8 -1.817817725 6.16762311 -1.7092839478
6 -2.6490347458 4.060069425 -0.87108429006
1 -2.8303819239 3.5809986027 -1.848635408
6 -3.5285637819 3.4150259042 0.20316750287
1 -4.5749565237 3.4711994218 -0.14118993269
8 -3.1480929345 2.0831457537 0.42979388951
1 -3.5151692271 1.4996395894 -0.25423354631
8 -1.2502283399 3.9213265953 -0.54281509632
6 -0.54738871473 2.7292830347 -0.79549402308
1 -1.1454388305 2.0271336936 -1.3964659989
6 0.10685631671 2.1057176863 0.42634129818
1 0.40901289646 2.9253605602 1.1042457301
6 1.368519831 1.4738144458 -0.17052371085
1 1.0647922823 0.51145183383 -0.61628435695
6 1.7801473418 2.4289710613 -1.308860104
1 2.5462421236 3.1316876192 -0.95119166274
6 2.2048234425 1.7480065955 -2.5970495935
1 3.1579599401 1.2239294779 -2.3990687541
1 2.3930344186 2.521235221 -3.3606158595
8 1.2076409637 0.88934085471 -3.0865152266
1 1.3650997362 -0.0135989358 -2.7747698554
8 0.56333059115 3.213165488 -1.568522419
8 2.3824565222 1.3074498536 0.76466357291
1 2.789093532 0.41276309545 0.66997316875
8 -0.71078645589 1.1767184693 1.0780440163
1 -1.636493809 1.5172720433 1.098454598
6 -1.9687058439 6.4691232288 -3.0826214736
1 -2.7816845946 5.8803752069 -3.5347290805
8 -0.69731403468 6.013006922 -3.5537803101
6 -0.37697495528 6.2663693465 -4.9408131896
1 0.65604008285 5.9246574376 -5.0799418206
1 -1.0618425768 5.6707254734 -5.5626171451
6 -0.52890578045 7.7555087518 -5.2350299342
1 0.25854988333 8.317765016 -4.6985269402
6 -1.9154504102 8.2569876303 -4.791882934
1 -1.9695281548 9.3529824455 -4.9329490556
8 -2.9154445973 7.5993091713 -5.5270310825
1 -2.6489703377 7.6280372596 -6.4617354814
6 -2.1256110433 7.9631482821 -3.3132155822
1 -1.3256762034 8.46987672 -2.744914193
8 -3.3998910233 8.359437192 -2.8934649695
1 -3.3559524422 8.6720130794 -1.9772601604
8 -0.39051741087 7.875455926 -6.6231586004
6 0.1246080883 9.1096223299 -7.0718886458
1 -0.51424168496 9.9590608457 -6.7660447091
1 0.15224966647 9.0659595743 -8.1706822734
1 1.1496440479 9.2706669872 -6.6878220076
$end
$rem
JOBTYPE BSSE
METHOD WB97X-D
BASIS DEF2-SVPD
MAXSCF 5000
MEM_TOTAL 24000
$end
---------------------------------------------------------------------
* Fragment's binding energy *
---------------------------------------------------------------------
Fragment E(TOTAL) E(CP-CORR) DE(BSSE)
---------------------------------------------------------------------
1 -2904.7220419692 -2913.8550124595 9.1329704904
2 -1643.6311259425 -1645.8433338315 2.2122078890
Complex -4546.9000381613
---------------------------------------------------------------------
DE, kJ/mol 3815.2374370359 33602.3567703211
---------------------------------------------------------------------
I am running this myself to see if anything looks out of place, but my intuitive guess is to wonder if somehow it’s an artifact of the use of fragments. What if you compute the interaction energy in the old-fashioned way, as three individual calculations? If you want the counterpoise-corrected result, use @ symbols for the ghost atoms in the $molecule section (e.g., @C instead of C). Also, in fragment jobs (including but not limited to JOBTYPE=BSSE), you can use SCF_PRINT_FRGM=TRUE in $rem to monitor the progress and check the energies of individual fragment calculations. That’s often useful for troubleshooting.
I did compute single point energies for complex and each fragment, and the values are still excessively high. Furthermore, I had recently computed BSSE corrected energies using wB97x-D/def2-SVP and the energies seem okay. However, for the system without Fe3+ still there is an inconsistent nature. (Hemicellulose without Fe: -91 kJ/mol, Cellulose without Fe: -1700 kJ/mol). So basically again there is a huge difference between the computed values.
Do you intend to be computing the high-spin state? Fe(3+) is 3d^5, therefore the low-spin state is a doublet.
Yes, I already did a preliminary calculation for both the states and it seem high-spin state is evidently stable. So, all my remaining calculations were done using the high-spin state.
I was concerned about linear dependencies in this calculation, and in fact you may notice a warning message
Overlap eigenvalue is smaller than square root of threshold
Use THRESH >= 12 to get rid of this warning
Running the job with THRESH=14, I obtain the following:
---------------------------------------------------------------------
* Fragment's binding energy *
---------------------------------------------------------------------
Fragment E(TOTAL) E(CP-CORR) DE(BSSE)
---------------------------------------------------------------------
1 -2904.4859960275 -2904.5021521184 0.0161560909
2 -1642.0768730725 -1642.0815776366 0.0047045640
Complex -4546.8582305743
---------------------------------------------------------------------
DE, kJ/mol -775.4807537996 -720.7104542915
---------------------------------------------------------------------
The interaction energies are still quite large, however the 9 Hartree of BSSE that was present in your calculation is gone and the magnitude of the counterpoise corrections looks reasonable in my case.
Thanks jherbert.
I redid my wB97x-D/def2-SVPD calculations with tighter threshold and I was able to obtain acceptable values. However, there is still a concern to me which did not resolve regardless of the basis sets I have used. I have attached the interaction energies for both the systems where I have removed the metal cation. Also, in these calculations I have omitted dimer relaxation due to removal of cation. My concern is while values for cellulose lies in the range of -1700 kJ/mol, hemicellulose lies around -91 kJ/mol. So, again there is a huge difference between these two systems although structurally they are mostly similar. I would have expected a value up to 200 kJ/mol for cellulose given its -OH network.
---------------------------------------------------------------------
* Fragment's binding energy *
---------------------------------------------------------------------
Fragment E(TOTAL) E(CP-CORR) DE(BSSE)
---------------------------------------------------------------------
1 -1412.9258721916 -1412.9340581360 0.0081859445
2 -1336.7645867704 -1336.7696850076 0.0050982372
Complex -2750.3772744846
---------------------------------------------------------------------
DE, kJ/mol -1803.2555548710 -1768.3775220202
---------------------------------------------------------------------
---------------------------------------------------------------------
* Fragment's binding energy *
---------------------------------------------------------------------
Fragment E(TOTAL) E(CP-CORR) DE(BSSE)
---------------------------------------------------------------------
1 -1642.0857116178 -1642.0887404583 0.0030288405
2 -1642.0768591482 -1642.0800447700 0.0031856218
Complex -3284.2038190085
---------------------------------------------------------------------
DE, kJ/mol -108.2985457376 -91.9822814080
---------------------------------------------------------------------
I appreciate if you could share some thoughts on this as well.
Thanks again
I agree that ~1700 kJ/mol raises eyebrows for this system (seems too large). Have you tried to do this calculation in the “usual” (old-fashioned) way, as three separate single points with ghost atoms for the two monomers? The reason it occurred to me to tighten the thresholds, other than the fact that this is my response to most signs of trouble, is that the fragment code has not always dealt well with linear dependencies.
Hey jherbert,
Thank you for your support throughout!
I did try the old fashioned ghost atom approach. However, it doesn’t really do much difference compared to what I had already computed through BSSE algorithm. However, I do feel a concern about the linear dependency issue I originally got at default threshold. I was under the impression that Q-Chem is capable of handling linear dependencies perfectly well in most cases. So, this led me to believe that there is something complicated going on with my structures. What do you think about this?
Updated Sept 3, 2022:
Note that your first input given above (with default THRESH) generates the following warning:
Overlap eigenvalue is smaller than square root of threshold
Use THRESH >= 12 to get rid of this warning
In general I think you should take this seriously. My opinion is that default thresholds in Q-Chem are too loose for large molecules. (They were increased slightly in the v. 6.0 release.) For large molecules, my group usually runs THRESH=12 as our local default. Ironically, this is sometimes faster than the default thresholds because the SCF converges in fewer cycles, even if the cycles are (very slightly) more expensive.
That said, using Q-Chem 6.0.1, the difference between default THRESH and THRESH=14 is miniscule:
DE, kJ/mol -1803.5354500318 -1768.7441148718 (default)
DE, kJ/mol -1803.8924920436 -1768.3793142564 (THRESH=14)
However, the reason for the anomalously large interaction energy in this case appears to be a bad definition of the fragments. I think that you have inadvertently placed one or more atoms that should be in fragment #1 into fragment #2. Please visualize the fragment geometries (e.g., using IQmol) to see what I mean.