Dispersion correction

sahar · February 23, 2025, 7:19am

Hello!
I am trying to do geometry optimization of a BQR molecule with DFT-D3 dispersion correction. But using this parameter curves the molecules into a C shape instead of the linear shape that we think it should be in.
Here I have posted the commands of the input file as a reference. $rem method b3lyp jobtype opt dft_d d3 basis 6-31G(d,p) geom_opt_max_cycles 130 max_scf_cycles 100 mem_static 8000 mem_total 60000 scf_algorithm gdm scf_convergence 8 $end
Optimizing the molecule without the dispersion correction gives a linear molecule. Is there any additional command needed in this file?
Any help would be greatly appreciated
Thank you

jherbert · February 23, 2025, 11:17pm

This looks like the correct input. You could try D4 dispersion.

sahar · February 23, 2025, 11:50pm

Thank you for your response
My QChem version 5.2 doesn’t have a D4 dispersion correction… Should I update to a newer version.
I want to know if it is a problem with the dispersion correction or the version of QChem installed.
The same input also curves Y6 molecule, which should be a planer molecule as well.
Any input would be appreciated.

jherbert · February 24, 2025, 12:03am

D4 was just a suggestion to help you get a 2nd opinion. There are some alternative damping functions that are available with D3, which you could try. Alternatively, try wB97X-D, which has a slightly different dispersion correction, or a functional such as wB97X-V that doesn’t need one. Just try to figure out if this is something unique to the particular combination you were trying or not.

sahar · February 24, 2025, 12:16am

I have already tried wB97XD. It does not curve the molecule.
I will try the other suggestions that you gave.

sahar · February 25, 2025, 1:08am

I checked different functionals and dispersion parameters.
So, with

just B3LYP (No dispersion correction)= No curve in the structure, molecule seems quite linear
B3LYP+D3= Curved in a C shape
MO6L (No dispersion correction)= Close to linear molecule, again no curve
wB97XD (No dispersion correction)= No curve
wB97XD3 = Curved into a C shape
B3LYP+empirical grimme= slightly bend on edge but molecule is quite linear
B3LYP+D3_BJ = Curved into a C shape
B3LYP+D2= No curve, close to planer
wB97XV= not a curve but molecule is not even close to linear, seems like a wave
B3LYP+D3_zero= wave like structure.
Could you help me it? Should I sent the input file for one of them, so that maybe, if possible, you can check if it is a problem with this version of QChem (5.2.2) that I am using or not?
Thank you

jherbert · February 25, 2025, 11:11am

what is the vibrational frequency associated with the curvature? It sounds like the potential surface may be very close to flat, in which case small differences in the level of theory might lead to a curved or uncurved geometry.

sahar · February 27, 2025, 12:05am

I ran the calculations for frequency. All of them gave the same error. ERROR** Hessian Appears to have all zero or negative eigenvalues

Q-Chem fatal error occurred in module 0, line 9:

OPTIMIZE fatal error

I am not an expert in QChem so I don’t know if just the following commands were enough to restart the already optimized file and do a frequency calculation.
$molecule
read
$end

$rem
jobtype freq
method b3lyp
basis 6-31G(d,p)
max_scf_cycles 100
mem_static 8000
mem_total 60000
scf_convergence 8
scf_algorithm gdm
scf_guess read
max_scf_cycles 100
thresh 12
$end
~

sahar · February 27, 2025, 12:25am

these are coordinates of one of the optimized geometries

C 1.52471284 1.75429766 -0.21176357
C 1.12405706 2.78555632 0.68744952
C -0.21729241 3.13274057 0.89612075
C -1.18488258 2.41027446 0.15049368
C -0.76749414 1.38702412 -0.74742239
C 0.56399588 1.03071175 -0.95055177
C 2.93377096 1.56685784 -0.23406288
C 3.62229716 2.37852113 0.62474551
S 2.53423429 3.46980447 1.50604218
C -2.61828587 2.54498114 0.15713558
C -3.26290460 1.65279894 -0.65810570
S -2.13716155 0.58513260 -1.50300362
C 0.88242919 -0.08243346 -1.86195977
C -0.62982106 4.18526228 1.83349148
C 0.50871906 -0.22042606 -3.17448365
C 0.83637547 -1.48495606 -3.75782927
C 1.47049933 -2.32080247 -2.86947071
S 1.65375025 -1.55718799 -1.30888213
C -0.23331912 5.49523388 1.86713923
C -0.88605243 6.28869868 2.86663743
C -1.77866325 5.55606563 3.61231008
S -1.82149044 3.88699457 3.08860166
C 1.93877130 -3.73099381 -3.08197523
C 0.47700415 -1.84738176 -5.17591261
C -2.66217899 5.98265805 4.74709717
C -0.60758524 7.76013424 3.01064100
C -4.67459235 1.45775534 -0.91051525
C 5.05080749 2.34314161 0.82594691
C 5.92587252 3.25445437 1.37742311
C 7.29416934 2.86147944 1.33162779
C 7.46588498 1.62248119 0.72792952
S 5.91815570 0.92630614 0.27874060
C -5.24012142 0.90060448 -2.03700055
C -6.64987905 0.76151418 -1.99782961
C -7.18792951 1.21969693 -0.80113101
S -5.91945786 1.81311828 0.26790958
C 8.64479274 0.85865277 0.39096461
C -8.56256885 1.23103572 -0.35128473
C 8.71006205 -0.14301981 -0.55792904
C 9.95696103 -0.79576248 -0.67230432
C 10.90150493 -0.28339452 0.21190756
S 10.20203600 1.01613047 1.17900163
C -9.14030724 1.99171358 0.64932242
C -10.51469211 1.72657442 0.88811589
C -11.01151395 0.73584176 0.05112581
S -9.75673085 0.12635151 -1.01087187
C 12.28034533 -0.65091223 0.41554663
C -12.34253002 0.18978927 -0.09517088
S 13.17541308 -1.59874589 -0.75581702
C 14.63933717 -1.55382325 0.21891725
C 14.42933826 -0.81831953 1.38426739
C 13.10698132 -0.32282023 1.47615331
S -13.49864104 0.09319816 1.21843850
C -14.69431983 -0.71139444 0.20466177
C -14.20041458 -0.88604705 -1.08615842
C -12.88562648 -0.38298844 -1.22949969
C 15.79499391 -2.26071521 -0.26668782
C -15.96696416 -1.06661691 0.77936330
C 15.86022493 -3.09925104 -1.37754801
C 17.13247400 -3.63599348 -1.61107656
C 18.09471609 -3.23575484 -0.69184980
S 17.37382703 -2.15148426 0.48954741
C -16.33611439 -0.99931108 2.12075235
C -17.65424403 -1.40638246 2.37059716
C -18.34972011 -1.80357662 1.23385389
S -17.31884602 -1.65345717 -0.18112794
C 19.45602345 -3.65116244 -0.69607793
C -19.69391134 -2.27500715 1.21712146
C -20.48396342 -2.69548570 0.19251647
C 20.47700716 -3.35224652 0.15103223
C -7.42625935 0.19493802 -3.15926074
C -11.33567304 2.47845387 1.90058827
C -14.94503150 -1.50942318 -2.23770281
C 8.41059315 3.72086878 1.85439660
C 10.15977252 -1.91452721 -1.66061503
C 15.45110245 -0.57535753 2.45854066
S -20.12997416 -2.80923382 -1.53504427
C -21.75858453 -3.43353649 -1.89591481
N -22.48982583 -3.53187439 -0.74244630
C -21.86288860 -3.14446147 0.46346029
S 20.47809304 -2.32226088 1.58544831
C 22.20402891 -2.63967889 1.89209490
N 22.70335104 -3.48097576 0.93402276
C 21.81613305 -3.92566454 -0.07053520
C 24.09684504 -3.91530706 0.93130119
S 23.02640102 -1.98532403 3.16212664
O 22.14709533 -4.67623951 -0.97348933
C -23.86682058 -4.01676710 -0.74150674
S -22.25585646 -3.82186474 -3.41963199
O -22.41646746 -3.18964091 1.54921957
H 3.40737464 0.84535091 -0.88794545
H -3.15326231 3.29193986 0.72747229
H 0.00419343 0.56853238 -3.72149019
H 0.48226675 5.89914572 1.15923982
H 2.13401942 -3.91505152 -4.14230502
H 1.18664670 -4.45965424 -2.75553919
H 2.86144752 -3.94131611 -2.53252627
H 0.49649673 -0.96592833 -5.82376675
H -0.53246469 -2.27319965 -5.23442868
H 1.16352616 -2.58591503 -5.59971682
H -2.59516103 7.06078594 4.90591275
H -2.38127740 5.48962941 5.68479122
H -3.71268071 5.73990223 4.55151136
H -0.82005243 8.28692092 2.07311906
H 0.44669162 7.93786689 3.25024103
H -1.20902571 8.22449105 3.79450190
H 5.59866965 4.20752052 1.77863975
H -4.65218529 0.61295420 -2.90162244
H 7.86370836 -0.40452755 -1.18343098
H -8.59115496 2.75479581 1.18963475
H 12.75865298 0.25372458 2.32581354
H -12.35188092 -0.41976437 -2.17258567
H 14.99752872 -3.32162115 -1.99468849
H 17.36147729 -4.31306996 -2.42642646
H -15.65532085 -0.67175976 2.89702062
H -18.10728270 -1.42457011 3.35536607
H 19.73316557 -4.32243491 -1.50782775
H -20.18485815 -2.30900046 2.18852870
H -6.80065450 0.16356114 -4.05529590
H -8.31406666 0.79232715 -3.38967094
H -7.76716106 -0.82833775 -2.96296259
H -10.83268729 3.40240905 2.19560863
H -11.50024666 1.88516844 2.80776854
H -12.32105572 2.73905801 1.50166250
H -15.30028266 -2.51767827 -1.99937065
H -14.29928012 -1.58258205 -3.11617001
H -15.82238922 -0.91724248 -2.52281571
H 8.05384692 4.73326270 2.05860155
H 9.23501538 3.78710001 1.13747091
H 8.82182394 3.31859858 2.78775833
H 9.19655571 -2.23396427 -2.06785395
H 10.63508553 -2.78639002 -1.20114017
H 10.78627958 -1.60650024 -2.50555642
H 15.86492173 -1.51419546 2.84148478
H 15.00196165 -0.03822559 3.29691655
H 16.29012737 0.02457167 2.08879660
H 24.32029341 -4.44914085 1.85738840
H 24.75424431 -3.04647648 0.86042088
H 24.22624551 -4.56858365 0.06929401
H -23.90266033 -5.02671675 -1.15569521
H -24.48965953 -3.36532030 -1.35866478
H -24.20978430 -4.01067401 0.29218947

jherbert · February 27, 2025, 12:43am

I have not seen that error message before, suggests that something is seriously wrong with the frequency calculation but I’m not convinced it’s not just something with reading in the old calculation. I suggest that you set up an optimization job followed by a frequency calculation. If the geometry is already optimized it won’t need more than 1 step, but then you’ll be certain that the subsequent frequency calculation has everything that it needs. Something like this:

$molecule
[coords]
$end

$rem
jobtype = opt
...etc...
$end

@@@

$molecule
READ
$end

$rem
jobtype = freq
scf_guess = read
...etc...
$end

sahar · February 27, 2025, 12:46am

Yes. I have already started such a calculation. Will post what the results are after it runs through. Just for a test I am also running a frequency calculation on the ‘‘un-optimized’’ geometry that I initially got from literature.

jherbert · February 27, 2025, 5:22pm

I took a look at your molecule and I am quite certain that the energy barrier to make the pi-system planar vs. curved will be tiny. (You can easily check and quantify this.) That means that whether or not the molecule exhibits a curved geometry will be incredibly sensitive to the level of theory, and may not be answerable with quantum chemistry. In fact, at some level this answer is “it doesn’t matter” if the energy barrier is sufficiently low, because both geometries will be sampled.