RSS-Feed abonnieren
DOI: 10.1055/s-0042-1753141
Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes
![](https://www.thieme-connect.de/media/synlett/202310/lookinside/thumbnails/st-2022-b0335-c_10-1055_s-0042-1753141-1.jpg)
Abstract
We present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning.
1 Introduction
2 The LNCI16 Benchmark Set
3 Computational Details
4 Generation of Reference Values
5 Results and Discussion
6 Conclusions
Key words
non-covalent interaction energies - benchmarking - dispersion - composite methods - semi-empirical methods - force fieldsSupporting Information
- Supporting information for this article is available online at https://doi.org/10.1055/s-0042-1753141.
- Supporting Information
Publikationsverlauf
Eingereicht: 21. Juli 2022
Angenommen nach Revision: 04. Oktober 2022
Artikel online veröffentlicht:
30. November 2022
© 2022. Thieme. All rights reserved
Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany
-
References
- 1 Kolesnichenko IV, Anslyn EV. Chem. Soc. Rev. 2017; 46: 2385
- 2 Bom A, Bradley M, Cameron K, Clark JK, van Egmond J, Feilden H, MacLean EJ, Muir AW, Palin R, Rees DC, Zhang M.-Q. Angew. Chem. Int. Ed. 2002; 41: 265
- 3 Suresh K, López-Mejías V, Roy S, Camacho DF, Matzger AJ. Synlett 2020; 31: 1573
- 4 Kassem S, Leeuwen TV, Lubbe AS, Wilson MR, Feringa BL, Leigh DA. Chem. Soc. Rev. 2017; 46: 2592
- 5 Phipps R. Synlett 2016; 27: 1024
- 6 Renzi P, Bella M. Synlett 2016; 28: 306
- 7 Stone A. The Theory of Intermolecular Forces . Oxford University Press; Oxford: 2013
- 8 Riley KE, Hobza P. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011; 1: 3
- 9 Song Q, Cheng Z, Kariuki M, Hall SC. L, Hill SK, Rho JY, Perrier S. Chem. Rev. 2021; 121: 13936
- 10 Piskorz TK, Martí-Centelles V, Young TA, Lusby PJ, Duarte F. ACS Catal. 2022; 12: 5806
- 11 Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Chem. Rev. 2016; 116: 5105
- 12 Grimme S, Antony J, Ehrlich S, Krieg H. J. Chem. Phys. 2010; 132: 154104
- 13 Grimme S, Ehrlich S, Goerigk L. J. Comput. Chem. 2011; 32: 1456
- 14 Caldeweyher E, Ehlert S, Hansen A, Neugebauer H, Spicher S, Bannwarth C, Grimme S. J. Chem. Phys. 2019; 150: 154122
- 15 Becke AD, Johnson ER. J. Chem. Phys. 2005; 123: 154101
- 16 Becke AD, Johnson ER. J. Chem. Phys. 2005; 122: 154104
- 17 Vydrov OA, Voorhis TV. J. Chem. Phys. 2010; 133: 244103
- 18 Sedlak R, Janowski T, Pitoňák M, Řezáč J, Pulay P, Hobza P. J. Chem. Theory Comput. 2013; 9: 3364
- 19 Sure R, Grimme S. J. Chem. Theory Comput. 2015; 11: 3785
- 20 von Lilienfeld OA, Tkatchenko A. J. Chem. Phys. 2010; 132: 234109
- 21 Muto Y. J. Phys. Math. Soc. Jpn. 1943; 629
- 22 Axilrod BM, Teller E. J. Chem. Phys. 1943; 11: 299
- 23 Tkatchenko A, DiStasio RA, Car R, Scheffler M. Phys. Rev. Lett. 2012; 108: 236402
- 24 DiStasio RA, Gobre VV, Tkatchenko A. J. Phys.: Condens. Matter 2014; 26: 213202
- 25 Risthaus T, Grimme S. J. Chem. Theory Comput. 2013; 9: 1580
- 26 Maurer RJ, Ruiz VG, Tkatchenko A. J. Chem. Phys. 2015; 143: 102808
- 27 Boys S, Bernardi F. Mol. Phys. 1970; 19: 553
- 28 Kruse H, Grimme S. J. Chem. Phys. 2012; 136: 154101
- 29 Witte J, Neaton JB, Head-Gordon M. J. Chem. Phys. 2017; 146: 234105
- 30 Lever G, Cole DJ, Hine ND. M, Haynes PD, Payne MC. J. Phys.: Condens. Matter 2013; 25: 152101
- 31 Christensen AS, Kubař T, Cui Q, Elstner M. Chem. Rev. 2016; 116: 5301
- 32 Bannwarth C, Caldeweyher E, Ehlert S, Hansen A, Pracht P, Seibert J, Spicher S, Grimme S. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2021; 11: e1493
- 33 Bohle F, Grimme S. J. Serb. Chem. Soc. 2019; 84: 837
- 34 Kohn J, Spicher S, Bursch M, Grimme S. Chem. Commun. 2022; 58: 258
- 35 Mackerell AD. J. Comput. Chem. 2004; 25: 1584
- 36 Řezáč J, Hobza P. Chem. Rev. 2016; 116: 5038
- 37 Ni Z, Guo Y, Neese F, Li W, Li S. J. Chem. Theory Comput. 2021; 17: 756
- 38 Wu D, Truhlar DG. J. Chem. Theory Comput. 2021; 17: 3967
- 39 Spicher S, Bursch M, Grimme S. J. Phys. Chem. C 2020; 124: 27529
- 40 Wang Z, Liu YF, Yan H, Tong H, Mei Z. J. Phys. Chem. A 2017; 121: 1833
- 41 Ketchem R, Hu W, Cross T. Science 1993; 261: 1457
- 42 Wang X, Wicher B, Ferrand Y, Huc I. J. Am. Chem. Soc. 2017; 139: 9350
- 43 Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA. Science 1998; 282: 2088
- 44 Ehrlich S, Göller AH, Grimme S. ChemPhysChem 2017; 18: 898
- 45 Raffaini G, Ganazzoli F. J. Appl. Biomater. Biomech. 2010; 8: 135
- 46 Bürckstümmer H, Tulyakova EV, Deppisch M, Lenze MR, Kronenberg NM, Gsänger M, Stolte M, Meerholz K, Würthner F. Angew. Chem. Int. Ed. 2011; 50: 11628
- 47 Bahr J., Höger S., Jester S., Brandenburg J. G., Grimme S.; manuscript in preparation.
- 48 Riley KE, Hobza P. Phys. Chem. Chem. Phys. 2013; 15: 17742
- 49 Kozuch S, Martin JM. L. J. Chem. Theory Comput. 2013; 9: 1918
- 50 Sure R, Grimme S. Chem. Commun. 2016; 52: 9893
- 51 Schweez C, Shushkov P, Grimme S, Höger S. Angew. Chem. Int. Ed. 2016; 553328
- 52 Hollóczki O. Int. J. Quantum Chem. 2021; 121: e26372
- 53 Hollóczki O, Gehrke S. Sci. Rep. 2019; 9: 16013
- 54 Noble RE. Sci. Total Environ. 2000; 262: 1
- 55 Bahl V, Jacob P, Havel C, Schick SF, Talbot P. PLoS ONE 2014; 9: e108258
- 56 Müller M., Hansen A., Grimme S. ωB97X-3c: A composite range-separated hybrid DFT method with a molecule-optimized polarized valence double-ζ basis set J. Chem. Phys., under review.
- 57 Stewart JJ. P. J. Mol. Model. 2007; 13: 1173
- 58 Řezáč J, Hobza P. J. Chem. Theory Comput. 2012; 8: 141
- 59 Řezáč J, Hobza P. Chem. Phys. Lett. 2011; 506: 286
- 60 Stewart JJ. P. J. Mol. Model. 2013; 19: 1
- 61 Molecular Orbital PACkage (Version 19.179L); https://github.com/openmopac/mopac
- 62 Bannwarth C, Ehlert S, Grimme S. J. Chem. Theory Comput. 2019; 15: 1652
- 63 Grimme S, Bannwarth C, Shushkov P. J. Chem. Theory Comput. 2017; 13: 1989
- 64 Pracht P, Caldeweyher E, Ehlert S, Grimme SA. ChemRxiv 2019; preprint; DOI: 10.26434/chemrxiv.8326202.v1.
- 65 Spicher S, Grimme S. Angew. Chem. Int. Ed. 2020; 59: 15665
- 66 Semiempirical Extended Tight-Binding Program Package, xtb; https://github.com/grimme-lab/xtb
- 67 Grimme S, Bannwarth C, Caldeweyher E, Pisarek J, Hansen A. J. Chem. Phys. 2017; 147: 161708
- 68 General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations (Version 1.1); https://github.com/grimme-lab/xtbiff
- 69 Reimplementation of the DFT-D3 program; https://github.com/dftd3/simple-dftd3/releases/tag/v0.5.0
- 70 Caldeweyher E, Bannwarth C, Grimme S. J. Chem. Phys. 2017; 147: 034112
- 71 Generally Applicable Atomic-Charge Dependent London Dispersion Correction (Version 3.4.0); https://github.com/dftd4/dftd4/releases/tag/v3.4.0
- 72 Rüger R, Yakovlev A, Philipsen P, Borini S, Melix P, Oliveira A, Franchini M, van Vuren T, Soini T, de Reus M, Ghorbani Asl M, Teodoro TQ, McCormack D, Patchkovskii S, Heine T. AMS DFTB 2022.1, SCM, Theoretical Chemistry . Vrije Universiteit; Amsterdam: https://www.scm.com/product/dftb/
- 73 Wahiduzzaman M, Oliveira AF, Philipsen P, Zhechkov L, van Lenthe E, Witek HA, Heine T. J. Chem. Theory Comput. 2013; 9: 4006
- 74 Oliveira AF, Philipsen P, Heine T. J. Chem. Theory Comput. 2015; 11: 5209
- 75 Rüger R, Franchini M, Trnka T, Yakovlev A, van Lenthe E, Philipsen P, van Vuren T, Klumpers B, Soini T. AMS 2022.1, SCM, Theoretical Chemistry . Vrije Universiteit; Amsterdam: http://www.scm.com
- 76 Rappe AK, Casewit CJ, Colwell KS, Goddard WA, Skiff WM. J. Am. Chem. Soc. 1992; 114: 10024
- 77 O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. J. Cheminf. 2011; 3: 33
- 78 Open Babel: The Open Source Chemistry Toolbox (Version 2.4.0); https://github.com/openbabel/openbabel/releases/tag/ openbabel-2-4-0
- 79 Halgren TA. J. Comput. Chem. 1996; 17: 490
- 80 Halgren TA. J. Comput. Chem. 1996; 17: 520
- 81 Hassinen T, Peräkylä M. J. Comput. Chem. 2001; 22: 1229
- 82 Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. J. Comput. Chem. 2004; 25: 1157
- 83 Gasteiger J, Marsili M. Tetrahedron 1980; 36: 3219
- 84 TURBOMOLE Version 7.5.1 (2021), A development of the University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007; TURBOMOLE GmbH: Karlsruhe, 2021; https://www.turbomole.org
- 85 Grimme S, Hansen A, Ehlert S, Mewes J.-M. J. Chem. Phys. 2021; 154: 064103
- 86 Sure R, Grimme S. J. Comput. Chem. 2013; 34: 1672
- 87 Brandenburg JG, Bannwarth C, Hansen A, Grimme S. J. Chem. Phys. 2018; 148: 064104
- 88 Grimme S, Brandenburg JG, Bannwarth C, Hansen A. J. Chem. Phys. 2015; 143: 054107
- 89 Neese F, Wennmohs F, Becker U, Riplinger C. J. Chem. Phys. 2020; 152: 224108
- 90 Neese F. ORCA – An ab initio, density functional and semiempirical program package, Version 5.0.1. Max-Planck-Institut für Kohlenforschung; Germany: 2021
- 91 Mardirossian N, Head-Gordon M. J. Chem. Phys. 2015; 142: 074111
- 92 Weigend F, Ahlrichs R. Phys. Chem. Chem. Phys. 2005; 7: 3297
- 93 Rappoport D, Furche F. J. Chem. Phys. 2010; 133: 134105
- 94 Epifanovsky E, Gilbert AT. B, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You Z.-Q, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HG. A, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang P.-T, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MW. D, Harbach PH. P, Hauser A, Herbst MF, Vera MH, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li Y.-P, Liang J, Liebenthal M, Lin H.-H, Lin Y.-S, LiuF F, Liu K.-Y, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao S.-P, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MF. S. J, Mewes J.-M, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su Y.-C, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai J.-D, Coriani S, Cramer CJ, Cserey G, DePrince AE. III, DiStasio RA. Jr, Dreuw A, Dunietz BD, Furlani TR, Goddard WA. III, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu C.-P, Jagau T.-C, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy W, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJ. W, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA., Whaley KB, Woodcock HL. III, Zimmerman PM, Faraji S, Gill PM. W, Head-Gordon M, Herbert JM, Krylov AI. J. Chem. Phys. 2021; 155: 084801
- 95 Villot C, Ballesteros F, Wang D, Lao KU. J. Phys. Chem. A 2022; 126: 4326
- 96 Mardirossian N, Head-Gordon M. Phys. Chem. Chem. Phys. 2014; 16: 9904
- 97 Becke AD. J. Chem. Phys. 1993; 98: 5648
- 98 Lee C, Yang W, Parr RG. Phys. Rev. B 1988; 37: 785
- 99 Spicher S, Caldeweyher E, Hansen A, Grimme S. Phys. Chem. Chem. Phys. 2021; 23: 11635
- 100 Al-Hamdani YS, Nagy PR, Zen A, Barton D, Kállay M, Brandenburg JG, Tkatchenko A. Nat. Commun. 2021; 12: 3927
- 101 Řezáč J, Riley KE, Hobza P. J. Chem. Theory Comput. 2011; 7: 2427
- 102 Miriyala VM, Řezáč J. J. Phys. Chem. A 2018; 122: 2801
- 103 Řezáč J. J. Chem. Theory Comput. 2020; 16: 2355
- 104 Teale A, Helgaker T, Savin A, Adamo C, Aradi B, Arbuznikov A, Ayers P, Baerends EJ, Barone V, Calaminici P, Cancès E, Carter EA, Chattaraj PK, Chermette H, Ciofini I, Crawford TD, De Proft F, Dobson JF, Draxl C, Frauenheim T, Fromager E, Fuentealba P, Gagliardi L, Galli G, Gao J, Geerlings P, Gidopoulos N, Gill PM. W, Gori-Giorgi P, Görling A, Gould T, Grimme S, Gritsenko O, Jensen HJ. A, Johnson ER, Jones RO, Kaupp M, Köster AM, Kronik L, Krylov AI, Kvaal S, Laestadius A, Levy M, Lewin M, Liu S, Loos P, Maitra NT, Neese F, Perdew JP, Pernal K, Pernot P, Piecuch PE., Rebolini E, Reining L, Romaniello P, Ruzsinszky A, Salahub DR, Scheffler M, Schwerdtfeger P, Staroverov VN, Sun J, Tellgren E, Tozer DJ, Trickey SB, Ullrich CA, Vela A, Vignale G, Wesolowski TA, Xu X, Yang W. Phys. Chem. Phys. Chem. 2022; 24: Advance Article
- 105 Bursch M, Caldeweyher E, Hansen A, Neugebauer H, Ehlert S, Grimme S. Acc. Chem. Res. 2019; 52: 258
- 106 Grimme S. Chem. Eur. J. 2012; 18: 9955
- 107 Thiel W. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014; 4: 145
- 108 Ehlert S, Grimme S, Hansen A. J. Phys. Chem. A 2022; 126: 3521
- 109 Hostaš J, Řezáč J, Hobza P. Chem. Phys. Lett. 2013; 568-569: 161
- 110 Grimme S. J. Comput. Chem. 2006; 27: 1787
- 111 Tsuzuki S, Uchimaru T. Phys. Chem. Chem. Phys. 2020; 22: 22508
- 112 Kolář M, Hobza P. J. Chem. Theory Comput. 2012; 8: 1325