Metal-Organic Materials
To demonstrate possible applications of xtb, we want to start with metal-organic frameworks (MOFs, 3D) and cages (MOCs, 0D). Due to their diverse elemental composition, consisting of organic linkers and complexed metal atoms, and their usually large size of hundreds of atoms, they can be challenging to treat computationally. The broad parameterization of all elements up to at least Z=86 combined with the computational costs that are much cheaper than usual DFT or WFT methods make the GFN methods a valuable tool for treating such systems. In the following, we present an excerpt from a workflow-like compilation of experiments with the HUMJIL MOC (CCDC nomenclature).
Geometry Optimization
Perform a geometry optimization for humjil.xyz in the gas phase and with THF as a solvent (via an implicit solvation model, ALPB - Analytically Linearized Poisson Boltzmann Model) at the GFN2-xTB and GFN-FF levels of theory.
Compare the 4 geometries by visually overlaying within e.g. Chimera or with a (commandline) RMSD tool.
xtb humjil.xyz --opt --gfn 2 --alpb thf > opt.out &xtb humjil.xyz --opt --gff --alpb thf > opt.out &xtb humjil.xyz --opt --gfn 2 > opt.out &xtb humjil.xyz --opt --gff > opt.out &
270
Energy =
Pd 0.0000000 -0.0000000 -9.3798511
N -1.3354224 -0.5674368 -7.8625033
C -1.2764300 -1.7910299 -7.3066982
H -0.5696081 -2.4832666 -7.7376007
C -2.0841670 -2.1621617 -6.2461927
H -2.0012811 -3.1569726 -5.8406101
C -2.9976205 -1.2508124 -5.7156836
C -3.8300020 -1.5896796 -4.5281567
N -4.6170320 -0.6330408 -4.0213480
C -5.3146620 -0.9673456 -2.9289736
C -6.1665561 0.0786934 -2.2984962
C -6.9112742 -0.1849734 -1.1484659
H -6.9315650 -1.1735558 -0.7202096
C -7.6384137 0.8293590 -0.5503892
H -8.2294635 0.6447898 0.3335154
N -7.6601257 2.0830703 -1.0381398
C -6.9783362 2.3389052 -2.1692700
H -7.0502987 3.3423151 -2.5598749
Pd -8.6656352 3.6201240 -0.0228356
N -9.7389978 5.0783740 0.8896466
C -9.2788257 5.9114056 1.8347371
H -8.2515049 5.7930855 2.1323057
C -10.0783495 6.8816614 2.4080625
H -9.6689237 7.5312355 3.1660863
C -11.3963152 6.9997045 1.9943720
H -12.0468695 7.7480618 2.4227445
C -11.8711153 6.1394692 1.0181582
H -12.8941718 6.2213890 0.6882777
C -11.0328811 5.1784913 0.4698386
C -11.4264608 4.2281294 -0.5549908
C -12.6924008 4.1571177 -1.1199336
H -13.4678358 4.8366298 -0.8047396
C -12.9662894 3.2109716 -2.0935812
H -13.9506150 3.1541725 -2.5348556
C -11.9586056 2.3442347 -2.4876506
C -10.7129958 2.4501151 -1.8989897
H -9.9088703 1.7935085 -2.1823282
H -12.1299920 1.5926167 -3.2425626
N -6.8738894 3.9822651 1.0085774
C -6.5994280 3.3459561 2.1617906
H -7.3776777 2.7143489 2.5616291
C -5.3909927 3.4946365 2.8195921
H -5.2232193 2.9663498 3.7436702
C -4.4073466 4.3280932 2.2862148
C -3.0685241 4.4559181 2.9255083
N -2.1733114 5.2675612 2.3497260
C -0.9711032 5.3213206 2.9355092
C 0.0749749 6.1730150 2.3050245
C -0.1895719 6.9198634 1.1566198
H -1.1788191 6.9424831 0.7300211
C 0.8250569 7.6458117 0.5577917
H 0.6405173 8.2380863 -0.3252551
N 2.0796000 7.6645599 1.0435061
C 2.3362599 6.9812641 2.1735583
H 3.3404300 7.0510823 2.5625613
Pd 3.6152242 8.6664942 0.0241441
N 3.3615457 10.4523390 0.9512402
C 4.2226793 11.4295410 0.5458256
C 4.1510129 12.6979107 1.1053085
C 3.2047536 12.9754995 2.0779332
C 2.3384396 11.9690555 2.4763261
H 1.5866689 12.1432771 3.2303716
H 3.1476985 13.9615659 2.5152620
H 4.8300800 13.4724937 0.7869000
C 5.1730734 11.0319911 -0.4777617
C 6.1341972 11.8678789 -1.0294255
H 6.2168904 12.8919583 -0.7030208
C 6.9940783 11.3894738 -2.0042581
C 6.8754788 10.0701263 -2.4133624
H 7.5245408 9.6578250 -3.1702471
C 5.9051647 9.2729696 -1.8368538
H 5.7866105 8.2446265 -2.1307425
H 7.7427438 12.0382143 -2.4349336
C 2.4447857 10.7209432 1.8928576
H 1.7882839 9.9179410 2.1796554
N 3.9757621 6.8713412 -1.0029936
C 4.8140842 5.9464257 -0.5013019
H 5.3438074 6.2132013 0.4002682
C 5.0081670 4.7172035 -1.1064086
H 5.6942850 4.0128578 -0.6658077
C 4.3202863 4.4033585 -2.2789230
C 4.4484021 3.0644926 -2.9183365
N 5.2601788 2.1693359 -2.3426616
C 5.3146620 0.9673456 -2.9289736
C 6.1665561 -0.0786934 -2.2984962
C 6.2308167 -1.3720128 -2.8177975
C 6.9783362 -2.3389052 -2.1692700
H 7.0502987 -3.3423151 -2.5598749
N 7.6601257 -2.0830703 -1.0381398
C 7.6384137 -0.8293590 -0.5503892
H 8.2294635 -0.6447898 0.3335154
Pd 8.6656352 -3.6201240 -0.0228356
N 9.7389978 -5.0783740 0.8896466
C 9.2788257 -5.9114056 1.8347371
H 8.2515049 -5.7930855 2.1323057
C 10.0783495 -6.8816614 2.4080625
H 9.6689237 -7.5312355 3.1660863
C 11.3963152 -6.9997045 1.9943720
H 12.0468695 -7.7480618 2.4227445
C 11.8711153 -6.1394692 1.0181582
H 12.8941718 -6.2213890 0.6882777
C 11.0328811 -5.1784913 0.4698386
C 11.4264608 -4.2281294 -0.5549908
C 12.6924008 -4.1571177 -1.1199336
H 13.4678358 -4.8366298 -0.8047396
C 12.9662894 -3.2109716 -2.0935812
H 13.9506150 -3.1541725 -2.5348556
C 11.9586056 -2.3442347 -2.4876506
C 10.7129958 -2.4501151 -1.8989897
H 9.9088703 -1.7935085 -2.1823282
H 12.1299920 -1.5926167 -3.2425626
N 6.8738894 -3.9822651 1.0085774
C 6.5994280 -3.3459561 2.1617906
H 7.3776777 -2.7143489 2.5616291
C 5.3909927 -3.4946365 2.8195921
H 5.2232193 -2.9663498 3.7436702
C 4.4073466 -4.3280932 2.2862148
C 3.0685241 -4.4559181 2.9255083
N 2.1733114 -5.2675612 2.3497260
C 0.9711032 -5.3213206 2.9355092
C -0.0749749 -6.1730150 2.3050245
C 0.1895719 -6.9198634 1.1566198
C -0.8250569 -7.6458117 0.5577917
H -0.6405173 -8.2380863 -0.3252551
N -2.0796000 -7.6645599 1.0435061
C -2.3362599 -6.9812641 2.1735583
H -3.3404300 -7.0510823 2.5625613
Pd -3.6152242 -8.6664942 0.0241441
N -3.3615457 -10.4523390 0.9512402
C -2.4447857 -10.7209432 1.8928576
H -1.7882839 -9.9179410 2.1796554
C -2.3384396 -11.9690555 2.4763261
H -1.5866689 -12.1432771 3.2303716
C -3.2047536 -12.9754995 2.0779332
H -3.1476985 -13.9615659 2.5152620
C -4.1510129 -12.6979107 1.1053085
H -4.8300800 -13.4724937 0.7869000
C -4.2226793 -11.4295410 0.5458256
C -5.1730734 -11.0319911 -0.4777617
C -6.1341972 -11.8678789 -1.0294255
H -6.2168904 -12.8919583 -0.7030208
C -6.9940783 -11.3894738 -2.0042581
H -7.7427438 -12.0382143 -2.4349336
C -6.8754788 -10.0701263 -2.4133624
C -5.9051647 -9.2729696 -1.8368538
H -5.7866105 -8.2446265 -2.1307425
H -7.5245408 -9.6578250 -3.1702471
N -5.0725592 -9.7366665 -0.8930907
N -3.9757621 -6.8713412 -1.0029936
C -4.8140842 -5.9464257 -0.5013019
H -5.3438074 -6.2132013 0.4002682
C -5.0081670 -4.7172035 -1.1064086
H -5.6942850 -4.0128578 -0.6658077
C -4.3202863 -4.4033585 -2.2789230
C -4.4484021 -3.0644926 -2.9183365
C -3.4860022 -5.3865083 -2.8119413
H -2.9564644 -5.2177099 -3.7350489
C -3.3380182 -6.5955279 -2.1551077
H -2.7056723 -7.3732675 -2.5549008
H 1.1788191 -6.9424831 0.7300211
C -1.3691318 -6.2344812 2.8225426
H -1.6255439 -5.7080812 3.7270802
N 0.6364106 -4.6228885 4.0271963
C 1.5930887 -3.8360611 4.5340651
C 1.2535958 -3.0024172 5.7203347
C 0.0019851 -3.0828416 6.3315166
C -0.3037111 -2.2445696 7.3892863
H -1.2612698 -2.2985820 7.8840285
N 0.5684861 -1.3360543 7.8630959
C 1.7923601 -1.2777475 7.3078634
H 2.4840975 -0.5697951 7.7376313
Pd -0.0000000 0.0000000 9.3790567
N 0.5430832 -1.1894033 10.9288782
C 0.3070136 -0.6577260 12.1624934
C 0.6523556 -1.3661518 13.3050255
H 0.4691120 -0.9471030 14.2813657
C 1.2376001 -2.6166789 13.1960775
H 1.5079827 -3.1694234 14.0837333
C 1.4694338 -3.1401658 11.9334328
H 1.9238786 -4.1101228 11.8043495
C -0.3070136 0.6577260 12.1624934
C -0.6523556 1.3661518 13.3050255
H -0.4691120 0.9471030 14.2813657
C -1.2376001 2.6166789 13.1960775
H -1.5079827 3.1694234 14.0837333
C -1.4694338 3.1401658 11.9334328
H -1.9238786 4.1101228 11.8043495
C -1.1103515 2.4002125 10.8230239
H -1.2775969 2.7762196 9.8288037
C 1.1103515 -2.4002125 10.8230239
H 1.2775969 -2.7762196 9.8288037
N -0.5430832 1.1894033 10.9288782
N -0.5684861 1.3360543 7.8630959
C -1.7923601 1.2777475 7.3078634
H -2.4840975 0.5697951 7.7376313
C -2.1642924 2.0874592 6.2492125
H -3.1591016 2.0048759 5.8435728
C -1.2535958 3.0024172 5.7203347
C -0.0019851 3.0828416 6.3315166
H 0.7316469 3.7957848 5.9929975
C -1.5930887 3.8360611 4.5340651
C 0.3037111 2.2445696 7.3892863
H 1.2612698 2.2985820 7.8840285
H -0.7316469 -3.7957848 5.9929975
C 2.1642924 -2.0874592 6.2492125
H 3.1591016 -2.0048759 5.8435728
N 2.8213392 -3.7187883 4.0151154
C 4.7203104 -5.0152270 1.1130627
H 4.0156767 -5.7011808 0.6725395
C 5.9488811 -4.8205665 0.5070309
H 6.2151987 -5.3495556 -0.3950890
N 10.4479301 -3.3666895 -0.9563373
H 5.7064551 -1.6279445 -3.7236404
C 6.9112742 0.1849734 -1.1484659
H 6.9315650 1.1735558 -0.7202096
N 4.6170320 0.6330408 -4.0213480
C 3.8300020 1.5896796 -4.5281567
C 2.9976205 1.2508124 -5.7156836
C 2.0841670 2.1621617 -6.2461927
H 2.0012811 3.1569726 -5.8406101
C 1.2764300 1.7910299 -7.3066982
H 0.5696081 2.4832666 -7.7376007
C 3.0782890 -0.0007394 -6.3269784
H 3.7899449 -0.7349724 -5.9870696
C 2.2423030 -0.3054806 -7.3868810
H 2.2971622 -1.2627864 -7.8820269
N 3.7118021 2.8174997 -4.0083532
C 3.4860022 5.3865083 -2.8119413
H 2.9564644 5.2177099 -3.7350489
C 3.3380182 6.5955279 -2.1551077
H 2.7056723 7.3732675 -2.5549008
N 5.0725592 9.7366665 -0.8930907
C 1.3691318 6.2344812 2.8225426
H 1.6255439 5.7080812 3.7270802
N -0.6364106 4.6228885 4.0271963
N -2.8213392 3.7187883 4.0151154
C -4.7203104 5.0152270 1.1130627
H -4.0156767 5.7011808 0.6725395
C -5.9488811 4.8205665 0.5070309
H -6.2151987 5.3495556 -0.3950890
N -10.4479301 3.3666895 -0.9563373
C -6.2308167 1.3720128 -2.8177975
H -5.7064551 1.6279445 -3.7236404
N -5.2601788 -2.1693359 -2.3426616
N -3.7118021 -2.8174997 -4.0083532
C -3.0782890 0.0007394 -6.3269784
H -3.7899449 0.7349724 -5.9870696
C -2.2423030 0.3054806 -7.3868810
H -2.2971622 1.2627864 -7.8820269
N 1.3354224 0.5674368 -7.8625033
N 1.1902163 0.5416441 -10.9298751
C 2.4018344 1.1073285 -10.8241635
H 2.7780627 1.2745780 -9.8299210
C 3.1424714 1.4648923 -11.9345913
H 4.1130954 1.9180941 -11.8056847
C 2.6188939 1.2331385 -13.1972060
H 3.1721798 1.5023782 -14.0849403
C 1.3675233 0.6497181 -13.3060998
H 0.9484020 0.4668439 -14.2824633
C 0.6582706 0.3059091 -12.1635150
C -0.6582706 -0.3059091 -12.1635150
C -1.3675233 -0.6497181 -13.3060998
C -2.6188939 -1.2331385 -13.1972060
C -3.1424714 -1.4648923 -11.9345913
C -2.4018344 -1.1073285 -10.8241635
H -2.7780627 -1.2745780 -9.8299210
H -4.1130954 -1.9180941 -11.8056847
H -3.1721798 -1.5023782 -14.0849403
H -0.9484020 -0.4668439 -14.2824633
N -1.1902163 -0.5416441 -10.9298751
Perform GFN2-xTB single-point gas-phase calculations on both structures optimized with GFN2-xTB and check their energy difference.
Note: To perform single-point calculations, replace –opt by –sp. The total energies are given in Hartree. To have more meaningful values, convert them to kcal/mol with 1 Eh = 627.5 kcal/mol.
Docking
Use the optimized structure from the previous exercise at the GFN2-xTB (gas) level of theory and perform a docking with a CO2 molecule at the same level of theory. The aISS docking module can be called as follows:
xtb dock humjil_opt.xyz co2.xyz --gfn 2 --nfinal 2 > aiss.out &
3
C 0.00765 0.03540 0.00000
O -1.17431 -0.14918 0.00000
O 1.18955 0.22040 0.00000
The energetically best structure can be found in the best.xyz file.
For the docking, most flags possible for a geometry optimization can also be used. For example, implicit solvation can also be employed by providing the –alpb flag.
Note: To save computational time for this workshop, the number of final structures optimized with GFN2-xTB was limited to 2 with the –nfinal flag. Per default, 15 structures are produced.
Molecular Dynamics
Use the docked structure from the previous exercise to perform a molecular dynamics (MD) simulation at the GFN-FF (gas) level of theory. You’ll need a second input file md.inp besides the coordinate file:
xtb docked_coord.xyz --md --gfnff -I md.inp > md.out &
$md
temp=298 # temperature in K
time=20.0 # duration in ps
dump=300.0 # coordinate dump interval in fs
step=2.0 # stepsize in fs
velo=false # scale velocities
nvt=true # uses NVT ensemble
hmass=4 # increased hydrogen mass for FF stability
shake=2 # constrain all bonds from breaking
sccacc=2.0 # SCC accuracy
$end
Note: This calculation can take about 10 minutes. To speed up this exercise you may reduce the length of the MD by modifying the
time keyword in md.inp.Before you list any content of this directory when the calculation has finished, remove all scoord files:
rm scoord*
Have a look at the simulation by opening the xtb.trj file with, e. g., Molden.
You can do this already during the calculation.
Note: If the MD takes too long, you might cancel it. The trajectory up to this point will still be available in the
xtb.trj file. Alternatively, you can start a shorter MD by adjusting the time keyword of the md.inp file as mentioned before.Optional
xtb can also be helpful in generating structures relevant to reaction mechanism exploration. For example, the Buchwald Hartwig amination of bromobenzene and (S)-3-amino-2-methylpropan-1-ol with a Pd(BINAP) catalyst involves the complexation of the intermediate catalyst by the amine. Try to generate this complex with the following input
xtb dock amine.xyz cat.xyz --alpb dmso --fast > aiss.out &
17
C -3.83142 2.84076 -0.12858
C -2.71271 3.80734 0.30971
H -3.71462 1.86884 0.40191
H -3.75622 2.64976 -1.22212
N -5.15092 3.38956 0.17246
C -1.33694 3.16769 0.04220
H -1.25577 2.18168 0.55506
O -0.29754 4.00686 0.46991
H -1.20946 2.97517 -1.04499
C -2.83420 5.15491 -0.42082
H -2.80779 3.98502 1.40408
H -3.81369 5.63034 -0.20316
H -2.74149 5.01454 -1.51927
H -2.04024 5.85352 -0.08200
H -0.26205 3.93413 1.45941
H -5.25016 3.49470 1.20852
H -5.87559 2.70758 -0.14876
91
C 1.93043500098766 1.88705038720360 1.27636508509218
C 1.97459955939123 0.74829779266863 0.44541875684329
C 1.02990478561238 -0.25192813715073 0.61271403691281
C 0.01601735664743 -0.12897843953165 1.59684329718372
C 0.00486602136491 1.01110036222777 2.44153841945833
C 0.97835673662409 2.01174361389064 2.24665778060226
C -0.97905754314325 1.11228749020351 3.44591237208907
C -1.91732132645756 0.13258429215518 3.60623449046156
C -1.91580023210662 -0.98853603691249 2.76273320705236
C -0.97388551841309 -1.11865256011331 1.78244381763454
H 2.65978989329656 2.67284509679964 1.13525202046656
P 3.40713569692185 0.45063598133824 -0.66730537531161
H 0.96019342902486 2.88618786841156 2.88182270064755
H -0.97520803758161 1.98254339068831 4.08664095236231
H -2.66738870368542 0.21483103956499 4.37886209692111
H -2.66684386400195 -1.75316672163424 2.89574895976153
H -0.97655866734491 -1.98426023003818 1.13659299566919
C 0.14526976821989 -1.59943917510233 -1.31351060703041
C 1.07251821082195 -1.45287954419223 -0.25056729192353
C 2.01675163349715 -2.43347387046616 -0.00496289247722
P 3.16338763564251 -2.18383389437502 1.40106621266299
C 2.09382972162840 -3.55943079098827 -0.84871958824212
H 2.83641281317833 -4.31953291581165 -0.65217511543419
C 1.24280991573976 -3.69290879737754 -1.90717437340130
H 1.31553262831252 -4.55229356826996 -2.55820916660748
C -0.87091005687256 -0.65166269717626 -1.56151193975196
H -0.95748963139948 0.20553325193108 -0.91031863064544
C -1.73979297136593 -0.81645211711138 -2.60279427063404
H -2.51734053271247 -0.08796162352007 -2.77956466580218
C -1.62876259469206 -1.92603748517661 -3.45412086454612
H -2.31889204202597 -2.03459993938128 -4.27768220744122
C -0.65665910714600 -2.86135403786885 -3.23917435001203
H -0.56554282455158 -3.72146199672846 -3.88685605699420
C 0.24636505357355 -2.72958028321865 -2.16482109262523
H 5.04053258549462 1.95308963427405 1.04874130293099
C 4.89299905597580 2.58285906489136 0.16680216541704
C 4.10488718080303 2.11753771222348 -0.88819970805292
C 3.97295738904971 2.88967645799337 -2.03513257239657
H 3.39723484500199 2.52608137901539 -2.87409316269410
C 4.59842473761614 4.12259113716083 -2.10916621820447
H 4.49632983073021 4.71832348999157 -3.00459307720805
C 5.36052464719349 4.58801603121167 -1.05134179967215
H 5.85161053486878 5.54723300913738 -1.12057939847728
C 5.51132642475435 3.81457877063409 0.08906544598702
H 6.12430221283919 4.16423408293853 0.90645144171876
H 4.02235854811705 -1.50514117966998 -2.62568631546343
C 3.17171560446993 -0.95856763004698 -3.01734431858295
C 2.63287562149439 0.08153169594252 -2.26955458530146
C 1.54867283380819 0.80195882229825 -2.75892383744741
H 1.12910258822322 1.60673248403452 -2.16984850528478
C 1.01257926858250 0.47853247540941 -3.99057124693866
H 0.17235393384064 1.03814430156328 -4.37523265288449
C 1.54560532773241 -0.56581734842844 -4.72987768534842
H 1.11691409607470 -0.81711771999023 -5.68872690644839
C 2.62541313998850 -1.28431754891050 -4.24489077872467
H 3.04105424986400 -2.09553801038726 -4.82408759676300
H 1.33583677784850 -0.82873466427346 5.74959205741078
C 1.26250407321549 -1.53427439323018 4.93563022334869
C 0.29685622096144 -2.52577568384178 4.96085114639427
H -0.38313849657341 -2.59518745232414 5.79689008875041
C 0.19668480503760 -3.42844758612526 3.91363117399716
H -0.55933008558367 -4.19984014517295 3.93572836724455
C 1.05679203332485 -3.33904298939608 2.83622868708840
H 0.97445240569863 -4.03019593470187 2.00770835752968
C 2.03445785679514 -2.34902776756531 2.81406458864911
C 2.13344773754576 -1.44693938519777 3.86489629972164
H 2.89614915297169 -0.67987095722238 3.83313387572892
H 3.25921334801924 -4.71335584827297 3.07226012100153
C 4.00261823026728 -4.76527466002177 2.28923954719084
C 4.13222360890273 -3.72488308629829 1.37980089608449
C 5.12501838704103 -3.78362597909007 0.39615117544011
H 5.25174418682844 -2.94381011451806 -0.29798750601985
C 5.94979789753754 -4.88747721429718 0.30547426182948
H 6.71495850178344 -4.92841143016068 -0.45555496637095
C 5.80628422003005 -5.93092016593784 1.20919590786652
H 6.45742194745829 -6.79014207166281 1.14714340803080
C 4.84174527360330 -5.86441400163025 2.19959273526782
H 4.74234127515449 -6.67004520297639 2.91238124196596
Pd 4.78192197941655 -0.66933638538210 0.85762028033921
Br 6.90486545126967 -0.17867263571098 -0.18326172511155
H 7.37446354631147 -1.04019934049166 6.04329576704061
C 6.91663995455383 -1.04349587877704 5.06457569303456
C 6.05508853955129 -0.02279064401079 4.70077220142163
H 5.83860591747490 0.78008768332450 5.39255355348365
C 5.47218706806705 -0.03062310789953 3.44297757635991
H 4.79334920330727 0.78885028511248 3.17067260451879
C 5.74792721423441 -1.05736492435150 2.54875260346842
C 6.62248653363798 -2.06747078693591 2.90806661030017
H 6.87538232643100 -2.85581054435732 2.20921648721850
C 7.20078991262123 -2.05881341616422 4.16869328286306
H 7.88469613172747 -2.84885038665529 4.44540467384734
The outcome shows a structure in which the amine functional group does not coordinates to the metal center, but rather a hydrogen bond is formed between the bromine and the OH group. However, this is not the desired complex required for the reaction. For such cases, the program can be told to search for an amine coordination by defining a preferred interaction site by providing an input file that specifies the atom numbers relevant for complexation:
xtb dock amine.xyz cat.xyz --alpb dmso --fast -I xtb.inp > aiss.out &
$directed
scaling factor= 1.0
atoms: 5,16,17
$end