The seventh blind test of crystal structure prediction: structure ranking methods

. 2024 Dec 01 ; 80 (Pt 6) : 548-74. [epub] 20241201

Status Publisher Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid39418598

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol-1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

AbbVie Inc Research and Development 1 N Waukegan Road North Chicago IL 60064 USA

Avant garde Materials Simulation Alte Strasse 2 79249 Merzhausen Germany

Catalent Pharma Solutions 160 Pharma Drive Morrisville NC 27560 USA

Chemistry Department Loughborough University Loughborough LE11 3TU UK

Crystallization and Particle Sciences Institute of Chemical and Engineering Sciences 1 Pesek Road Singapore 627833 Singapore

Department of Analytical and Physical Chemistry Faculty of Chemistry University of Oviedo Julián Clavería 8 33006 Oviedo Spain

Department of Chemical Physics and Optics Faculty of Mathematics and Physics Charles University Ke Karlovu 3 121 16 Prague Czech Republic

Department of Chemistry Carnegie Mellon University 4400 5th Avenue Pittsburgh PA 15213 USA

Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie Halifax Canada

Department of Chemistry Faculty of Science Science Boulevard Ferdowsi University of Mashhad Mashhad Iran

Department of Chemistry New York University New York NY 10003 USA

Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK

Department of Chemistry University of California Riverside CA 92521 USA

Department of Chemistry University of Graz Heinrichstrasse 28 Graz Austria

Department of Chemistry University of Kentucky Lexington KY 40506 USA

Department of Chemistry University of Oxford 12 Mansfield Road Oxford OX1 3TA UK

Department of Chemistry University of South Florida USF Research Park 3720 Spectrum Blvd IDRB 202 Tampa FL 33612 USA

Department of Materials Science and Engineering Carnegie Mellon University 5000 Forbes Avenue Pittsburgh PA 15213 USA

Department of Physical Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic

Department of Physics and Astronomy University of Delaware Newark DE 19716 USA

Department of Physics and Materials Science University of Luxembourg 1511 Luxembourg City Luxembourg

Department of Solid State Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic

Genentech Inc 1 DNA Way South San Francisco CA 94080 USA

Graduate School of Organic Materials Science Yamagata University 4 3 16 Jonan Yonezawa 992 8510 Yamagata Japan

Graduate School of Pharmaceutical Sciences Osaka University 1 6 Yamadaoka Suita Osaka 656 0871 Japan

Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu Dhabi United Arab Emirates

Information and Media Center Toyohashi University of Technology 1 1 Hibarigaoka Tempaku cho Toyohashi Aichi 441 8580 Japan

Institute of Chemistry University of Silesia in Katowice Szkolna 9 40 006 Katowice Poland

Novartis Pharma AG Basel 4002 Switzerland

OpenEye Scientific Software 9 Bisbee Court Santa Fe NM 87508 USA

Roche Pharma Research and Early Development Therapeutic Modalities Roche Innovation Center Basel F Hoffmann La Roche Ltd Grenzacherstrasse 124 4070 Basel Switzerland

Ruđer Bošković Institute Bijenička cesta 54 Zagreb CroatiaCroatia

School of Chemistry University of Hyderabad Professor C R Rao Road Gachibowli Hyderabad 500046 Telangana India

School of Chemistry University of Southampton Southampton SO17 1BJ UK

School of Natural and Environmental Sciences Newcastle University Kings Road Newcastle NE1 7RU UK

School of Pharmacy and Pharmaceutical Sciences Hoshi University 2 4 41 Ebara Shinagawa ku Tokyo 142 8501 Japan

School of Pharmacy University of Reading Whiteknights Reading RG6 6AD UK

Skolkovo Institute of Science and Technology Bolshoy Boulevard 30 121205 Moscow Russia

Syngenta Ltd Jealott's Hill International Research Station Berkshire RG42 6EY UK

The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK

University of Innsbruck Institute of Pharmacy Innrain 52c A 6020 Innsbruck Austria

University of Utrecht Department of Crystal and Structural Chemistry Padualaan 8 3584 CH Utrecht The Netherlands

XtalPi Inc 245 Main Street Cambridge MA 02142 USA

XtalPi Inc International Biomedical Innovation Park 2 3F 2 Hongliu Road Futian District Shenzhen Guangdong China

Zobrazit více v PubMed

Abramov, Y. A., Li, B., Chang, C., Zeng, Q., Sun, G. & Gobbo, G. (2021). Cryst. Growth Des.21, 5496–5502.

Adamo, C. & Barone, V. (1999). J. Chem. Phys.110, 6158–6170.

Addicoat, M., Adjiman, C. S., Arhangelskis, M., Beran, G. J. O., Bowskill, D., Brandenburg, J. G., Braun, D. E., Burger, V., Cole, J., Cruz-Cabeza, A. J., Day, G. M., Deringer, V. L., Guo, R., Hare, A., Helfferich, J., Hoja, J., Iuzzolino, L., Jobbins, S., Marom, N., McKay, D., Mitchell, J. B. O., Mohamed, S., Neumann, M., Nilsson Lill, S., Nyman, J., Oganov, A. R., Piaggi, P., Price, S. L., Reutzel-Edens, S., Rietveld, I., Ruggiero, M., Ryder, M. R., Sastre, G., Schön, J. C., Taylor, C., Tkatchenko, A., Tsuzuki, S., van den Ende, J., Woodley, S. M., Woollam, G. & Zhu, Q. (2018). Faraday Discuss.211, 325–381. PubMed

Anstine, D., Zubatyuk, R. & Isayev, O. (2023). ChemRxiv, 10.26434/chemrxiv-2023-296ch.

Anstine, D. M. & Isayev, O. (2023). J. Phys. Chem. A, 127, 2417–2431. PubMed PMC

Apostolakis, J., Hofmann, D. W. M. & Lengauer, T. (2001). Acta Cryst. A57, 442–450. PubMed

Asmadi, A., Neumann, M. A., Kendrick, J., Girard, P., Perrin, M.-A. & Leusen, F. J. J. (2009). J. Phys. Chem. B, 113, 16303–16313. PubMed

Bannwarth, C., Ehlert, S. & Grimme, S. (2019). J. Chem. Theory Comput.15, 1652–1671. PubMed

Bardwell, D. A., Adjiman, C. S., Arnautova, Y. A., Bartashevich, E., Boerrigter, S. X. M., Braun, D. E., Cruz-Cabeza, A. J., Day, G. M., Della Valle, R. G., Desiraju, G. R., van Eijck, B. P., Facelli, J. C., Ferraro, M. B., Grillo, D., Habgood, M., Hofmann, D. W. M., Hofmann, F., Jose, K. V. J., Karamertzanis, P. G., Kazantsev, A. V., Kendrick, J., Kuleshova, L. N., Leusen, F. J. J., Maleev, A. V., Misquitta, A. J., Mohamed, S., Needs, R. J., Neumann, M. A., Nikylov, D., Orendt, A. M., Pal, R., Pantelides, C. C., Pickard, C. J., Price, L. S., Price, S. L., Scheraga, H. A., van de Streek, J., Thakur, T. S., Tiwari, S., Venuti, E. & Zhitkov, I. K. (2011). Acta Cryst. B67, 535–551.

Bartók, A. P., Kondor, R. & Csányi, G. (2013). Phys. Rev. B, 87, 184115.

Bartók, A. P. & Yates, J. R. (2019). J. Chem. Phys.150, 161101.

Bauer, J., Spanton, S., Henry, R., Quick, J., Dziki, W., Porter, W. & Morris, J. (2001). Pharm. Res.18, 859–866. PubMed

Becke, A. (1986). J. Chem. Phys.85, 7184–7187.

Becke, A. D. (1993). J. Chem. Phys.98, 5648–5652.

Beran, G. J. O., Wright, S. E., Greenwell, C. & Cruz-Cabeza, A. J. (2022). J. Chem. Phys.156, 104112. PubMed

Bitzek, E., Koskinen, P., Gähler, F., Moseler, M. & Gumbsch, P. (2006). Phys. Rev. Lett.97, 170201. PubMed

Boerrigter, S. X. M., Josten, G. P. H., van de Streek, J., Hollander, F. F. A., Los, J., Cuppen, H. M., Bennema, P. & Meekes, H. (2004). J. Phys. Chem. A, 108, 5894–5902.

Brandenburg, J., Bates, J., Sun, J. & Perdew, J. (2016). Phys. Rev. B, 94, 115144.

Brandenburg, J. G. & Grimme, S. (2014a). J. Phys. Chem. Lett.5, 1785–1789. PubMed

Brandenburg, J. G. & Grimme, S. (2014b). In Prediction and Calculation of Crystal Structures, edited by S. Atahan-Evrenk & A. Aspuru-Guzik, vol. 345 of Topics in Current Chemistry, pp. 1–23. Springer International Publishing.

Braun, D. E., McMahon, J. A., Bhardwaj, R. M., Nyman, J., Neumann, M. A., van de Streek, J. & Reutzel-Edens, S. M. (2019). Cryst. Growth Des.19, 2947–2962.

Broyden, C. G. (1967). Math. C, 21, 368–381.

Bučko, T., Hafner, J. & Ángyán, J. G. (2005). J. Chem. Phys.122, 124508. PubMed

Caldeweyher, E., Bannwarth, C. & Grimme, S. (2017). J. Chem. Phys.147, 034112. PubMed

Caldeweyher, E., Mewes, J.-M., Ehlert, S. & Grimme, S. (2020). Phys. Chem. Chem. Phys.22, 8499–8512. PubMed

Červinka, C. & Beran, G. J. (2018). Chem. Sci.9, 4622–4629. PubMed PMC

Červinka, C. & Fulem, M. (2017). J. Chem. Theory Comput.13, 2840–2850. PubMed

Červinka, C. & Fulem, M. (2018). Cryst. Growth Des.19, 808–820.

Červinka, C., Fulem, M., Stoffel, R. P. & Dronskowski, R. (2016). J. Phys. Chem. A, 120, 2022–2034. PubMed

Červinka, C., Klajmon, M. & Štejfa, V. (2019). J. Chem. Theory Comput.15, 5563–5578. PubMed

Chakraborty, D., Berland, K. & Thonhauser, T. (2020). J. Chem. Theory Comput.16, 5893–5911. PubMed

Chisholm, J. A. & Motherwell, S. (2005). J. Appl. Cryst.38, 228–231.

Cohen, A. J., Mori-Sánchez, P. & Yang, W. (2012). Chem. Rev.112, 289–320. PubMed

Cole, J. C., Groom, C. R., Korb, O., McCabe, P. & Shields, G. P. (2016). J. Chem. Inf. Model.56, 652–661. PubMed

Coombes, D. S., Price, S. L., Willock, D. J. & Leslie, M. (1996). J. Phys. Chem.100, 7352–7360.

Cruz-Cabeza, A. J., Reutzel-Edens, S. M. & Bernstein, J. (2015). Chem. Soc. Rev.44, 8619–8635. PubMed

Cutini, M., Civalleri, B., Corno, M., Orlando, R., Brandenburg, J. G., Maschio, L. & Ugliengo, P. (2016). J. Chem. Theory Comput.12, 3340–3352. PubMed

Day, G. M., Cooper, T. G., Cruz-Cabeza, A. J., Hejczyk, K. E., Ammon, H. L., Boerrigter, S. X. M., Tan, J. S., Della Valle, R. G., Venuti, E., Jose, J., Gadre, S. R., Desiraju, G. R., Thakur, T. S., van Eijck, B. P., Facelli, J. C., Bazterra, V. E., Ferraro, M. B., Hofmann, D. W. M., Neumann, M. A., Leusen, F. J. J., Kendrick, J., Price, S. L., Misquitta, A. J., Karamertzanis, P. G., Welch, G. W. A., Scheraga, H. A., Arnautova, Y. A., Schmidt, M. U., van de Streek, J., Wolf, A. K. & Schweizer, B. (2009). Acta Cryst. B65, 107–125.

Day, G. M., Motherwell, W. D. S., Ammon, H. L., Boerrigter, S. X. M., Della Valle, R. G., Venuti, E., Dzyabchenko, A., Dunitz, J. D., Schweizer, B., van Eijck, B. P., Erk, P., Facelli, J. C., Bazterra, V. E., Ferraro, M. B., Hofmann, D. W. M., Leusen, F. J. J., Liang, C., Pantelides, C. C., Karamertzanis, P. G., Price, S. L., Lewis, T. C., Nowell, H., Torrisi, A., Scheraga, H. A., Arnautova, Y. A., Schmidt, M. U. & Verwer, P. (2005). Acta Cryst. B61, 511–527. PubMed

Day, G. M., Motherwell, W. D. S. & Jones, W. (2005). Cryst. Growth Des.5, 1023–1033.

Day, G. M. & Price, S. L. (2003). J. Am. Chem. Soc.125, 16434–16443. PubMed

Day, G. M., Price, S. L. & Leslie, M. (2003). J. Phys. Chem. B, 107, 10919–10933.

Deij, M. A., ter Horst, J. H., Meekes, H., Jansens, P. & Vlieg, E. (2007). J. Phys. Chem. B, 111, 1523–1530. PubMed

Deringer, V. L., Bartók, A. P., Bernstein, N., Wilkins, D. M., Ceriotti, M. & Csányi, G. (2021). Chem. Rev.121, 10073–10141. PubMed PMC

Devereux, C., Smith, J. S., Huddleston, K. K., Barros, K., Zubatyuk, R., Isayev, O. & Roitberg, A. E. (2020). J. Chem. Theory Comput.16, 4192–4202. PubMed

Dolgonos, G. A., Hoja, J. & Boese, A. D. (2019). Phys. Chem. Chem. Phys.21, 24333–24344. PubMed

Ehlert, S., Huniar, U., Ning, J., Furness, J. W., Sun, J., Kaplan, A. D., Perdew, J. P. & Brandenburg, J. G. (2021). J. Chem. Phys.154, 061101. PubMed

van Eijck, B. P. (2001). J. Comput. Chem.22, 816–826.

van Eijck, B. P. & Kroon, J. (1997). J. Phys. Chem. B, 101, 1096–1100.

Eike, D. M., Brennecke, J. F. & Maginn, E. J. (2005). J. Chem. Phys.122, 014115. PubMed

Ewald, P. P. (1921). Ann. Phys.369, 253–287.

Firaha, D., Liu, Y. M., van de Streek, J., Sasikumar, K., Dietrich, H., Helfferich, J., Aerts, L., Braun, D. E., Broo, A., DiPasquale, A. G., Lee, A. Y., Le Meur, S., Nilsson Lill, S. O., Lunsmann, W. J., Mattei, A., Muglia, P., Putra, O. D., Raoui, M., Reutzel-Edens, S. M., Rome, S., Sheikh, A. Y., Tkatchenko, A., Woollam, G. R. & Neumann, M. A. (2023). Nature, 623, 324–328. PubMed PMC

Frenkel, D. & Ladd, A. J. (1984). J. Chem. Phys.81, 3188–3193.

Frenkel, D. & Smit, B. (2001). Understanding Molecular Simulation: from Algorithms to Applications. Elsevier.

Fulem, M., Růžička, K., Červinka, C., Bazyleva, A. & Della Gatta, G. (2014). Fluid Phase Equilib.371, 93–105.

Fultz, B. (2010). Prog. Mater. Sci.55, 247–352.

Gale, J. D. & Rohl, A. L. (2003). Mol. Simul.29, 291–341.

Gao, X., Ramezanghorbani, F., Isayev, O., Smith, J. S. & Roitberg, A. E. (2020). J. Chem. Inf. Model.60, 3408–3415. PubMed

Gasteiger, J. & Marsili, M. (1978). Tetrahedron Lett.19, 3181–3184.

Gaus, M., Goez, A. & Elstner, M. (2013). J. Chem. Theory Comput.9, 338–354. PubMed

Gavezzotti, A. (2002). J. Phys. Chem. B, 106, 4145–4154.

Gavezzotti, A. (2005). Z. Kristallogr. Cryst. Mater.220, 499–510.

Gavezzotti, A. & Filippini, G. (1995). J. Am. Chem. Soc.117, 12299–12305.

Gelder, R. de, Wehrens, R. & Hageman, J. A. (2001). J. Comput. Chem.22, 273–289.

Gilat, G. & Alder, B. J. (1976). Editors. Methods in Computational Physics: Vibrational Properties of Solids of Advances in Research and Applications. Academic Press.

Grau-Crespo, R. & Hamad, S. (2015). In Proceedings of MOL2NET, International Conference on Multidisciplinary Sciences. MDPI. https://dx.doi.org/10.3390/MOL2NET-1-c002.

Gray, A. E., Day, G. M., Leslie, M. & Price, S. L. (2004). Mol. Phys.102, 1067–1083.

Greenwell, C. & Beran, G. J. (2020). Cryst. Growth Des.20, 4875–4881.

Greenwell, C., Řezáč, J. & Beran, G. J. (2022). Phys. Chem. Chem. Phys.24, 3695–3712. PubMed

Grimme, S. (2006). J. Comput. Chem.27, 1787–1799. PubMed

Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. (2010). J. Chem. Phys.132, 154104. PubMed

Grimme, S., Ehrlich, S. & Goerigk, L. (2011). J. Comput. Chem.32, 1456–1465. PubMed

Grisafi, A. & Ceriotti, M. (2019). J. Chem. Phys.151, 204105. PubMed

Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. PubMed PMC

Habgood, M., Grau-Crespo, R. & Price, S. L. (2011). Phys. Chem. Chem. Phys.13, 9590. PubMed

Head, J. D. & Zerner, M. C. (1985). Chem. Phys. Lett.122, 264–270.

Heit, Y. N. & Beran, G. J. O. (2016). Acta Cryst. B72, 514–529. PubMed

Heit, Y. N., Nanda, K. D. & Beran, G. J. O. (2016). Chem. Sci.7, 246–255. PubMed PMC

Herbert, J. M. (2019). J. Chem. Phys.151, 170901.

Hjorth Larsen, A., Jørgen Mortensen, J., Blomqvist, J., Castelli, I. E., Christensen, R., Dułak, M., Friis, J., Groves, M. N., Hammer, B., Hargus, C., Hermes, E. D., Jennings, P. C., Bjerre Jensen, P., Kermode, J., Kitchin, J. R., Leonhard Kolsbjerg, E., Kubal, J., Kaasbjerg, K., Lysgaard, S., Bergmann Maronsson, J., Maxson, T., Olsen, T., Pastewka, L., Peterson, A., Rostgaard, C., Schiøtz, J., Schütt, O., Strange, M., Thygesen, K. S., Vegge, T., Vilhelmsen, L., Walter, M., Zeng, Z. & Jacobsen, K. W. (2017). J. Phys. Condens. Matter, 29, 273002. PubMed

Hofmann, D. W. M. & Apostolakis, J. (2003). J. Mol. Struct.647, 17–39.

Hoja, J., Ko, H.-Y., Neumann, M. A., Car, R., DiStasio, R. A. Jr & Tkatchenko, A. (2019). Sci. Adv.5, eaau3338. PubMed PMC

Hoja, J., List, A. & Boese, A. D. (2024). J. Chem. Theory Comput.20, 357–367. PubMed PMC

Hoja, J., Reilly, A. M. & Tkatchenko, A. (2017). Wiley Interdiscip. Rev. Comput. Mol. Sci.7, e1294.

Hoja, J. & Tkatchenko, A. (2018). Faraday Discuss.211, 253–274. PubMed

Hourahine, B., Aradi, B., Blum, V., Bonafé, F., Buccheri, A., Camacho, C., Cevallos, C., Deshaye, M. Y., Dumitrică, T., Dominguez, A., Ehlert, S., Elstner, M., van der Heide, T., Hermann, J., Irle, S., Kranz, J. J., Köhler, C., Kowalczyk, T., Kubař, T., Lee, I. S., Lutsker, V., Maurer, R. J., Min, S. K., Mitchell, I., Negre, C., Niehaus, T. A., Niklasson, A. M. N., Page, A. J., Pecchia, A., Penazzi, G., Persson, M. P., Řezáč, J., Sánchez, C. G., Sternberg, M., Stöhr, M., Stuckenberg, F., Tkatchenko, A., Yu, V. W.-Z. & Frauenheim, T. (2020). J. Chem. Phys. 152, 124101. PubMed

Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S., Aitipamula, S., Alkhidir, T., Almehairbi, M., Anelli, A., Anstine, D. M., Anthony, J. E., Arnold, J. E., Bahrami, F., Bellucci, M. A., Bhardwaj, R. M., Bier, I., Bis, J. A., Boese, A. D., Bowskill, D. H., Bramley, J., Brandenburg, J. G., Braun, D. E., Butler, P. W. V., Cadden, J., Carino, S., Chan, E. J., Chang, C., Cheng, B., Clarke, S. M., Coles, S. J., Cooper, R. I., Couch, R., Cuadrado, R., Darden, T., Day, G. M., Dietrich, H., Ding, Y., DiPasquale, A., Dhokale, B., van Eijck, B. P., Elsegood, M. R. J., Firaha, D., Fu, W., Fukuzawa, K., Glover, J., Goto, H., Greenwell, C., Guo, R., Harter, J., Helfferich, J., Hofmann, D. W. M., Hoja, J., Hone, J., Hong, R., Hutchison, G., Ikabata, Y., Isayev, O., Ishaque, O., Jain, V., Jin, Y., Jing, A., Johnson, E. R., Jones, I., Jose, K. V. J., Kabova, E. A., Keates, A., Kelly, P. F., Khakimov, D., Konstantinopoulos, S., Kuleshova, L. N., Li, H., Lin, X., List, A., Liu, C., Liu, Y. M., Liu, Z., Liu, Z.-P., Lubach, J. W., Marom, N., Maryewski, A. A., Matsui, H., Mattei, A., Mayo, R. A., Melkumov, J. W., Mohamed, S., Momenzadeh Abardeh, Z., Muddana, H. S., Nakayama, N., Nayal, K. S., Neumann, M. A., Nikhar, R., Obata, S., O’Connor, D., Oganov, A. R., Okuwaki, K., Otero-de-la-Roza, A., Pantelides, C. C., Parkin, S., Pickard, C. J., Pilia, L., Pivina, T., Podeszwa, R., Price, A. J. A., Price, L. S., Price, S. L., Probert, M. R., Pulido, A., Ramteke, G. R., Rehman, A. U., Reutzel-Edens, S. M., Rogal, J., Ross, M. J., Rumson, A. F., Sadiq, G., Saeed, Z. M., Salimi, A., Salvalaglio, M., Sanders de Almada, L., Sasikumar, K., Sekharan, S., Shang, C., Shankland, K., Shinohara, K., Shi, B., Shi, X., Skillman, A. G., Song, H., Strasser, N., van de Streek, J., Sugden, I. J., Sun, G., Szalewicz, K., Tan, B. I., Tan, L., Tarczynski, F., Taylor, C. R., Tkatchenko, A., Tom, R., Tuckerman, M. E., Utsumi, Y., Vogt-Maranto, L., Weatherston, J., Wilkinson, L. J., Willacy, R. D., Wojtas, L., Woollam, G. R., Yang, Z., Yonemochi, E., Yue, X., Zeng, Q., Zhang, Y., Zhou, T., Zhou, Y., Zubatyuk, R. & Cole, J. C. (2024). Acta Cryst. B80, 517–547.

Iuzzolino, L., McCabe, P., Price, S. L. & Brandenburg, J. G. (2018). Faraday Discuss.211, 275–296. PubMed

Jorgensen, W. L. S. M. D., Maxwell, D. S. & Tirado-Rives, J. (1996). J. Am. Chem. Soc.118, 11225–11236.

Kamencek, T., Wieser, S., Kojima, H., Bedoya-Martínez, N., Dürholt, J. P., Schmid, R. & Zojer, E. (2020). J. Chem. Theory Comput.16, 2716–2735. PubMed PMC

Kazantsev, A., Karamertzanis, P., Pantelides, C. & Adjiman, C. (2010). Process Systems Engineering, Vol. 6: Molecular Systems Engineering, pp. 1–42.

Kazantsev, A. V., Karamertzanis, P. G., Adjiman, C. S., Pantelides, C. C., Price, S. L., Galek, P. T. A., Day, G. M. & Cruz-Cabeza, A. J. (2011). Int. J. Pharm.418, 168–178. PubMed

Kendrick, J., Leusen, F. J. J., Neumann, M. A. & van de Streek, J. (2011). Chem. A Eur. J.17, 10736–10744. PubMed

Kitaura, K., Ikeo, E., Asada, T., Nakano, T. & Uebayasi, M. (1999). Chem. Phys. Lett.313, 701–706.

Klimeš, J., Bowler, D. R. & Michaelides, A. (2009). J. Phys. Condens. Matter, 22, 022201. PubMed

Ko, T. W., Finkler, J. A., Goedecker, S. & Behler, J. (2021). Nat. Commun.12, 398. PubMed PMC

Kresse, G. & Joubert, D. (1999). Phys. Rev. B, 59, 1758–1775.

LeBlanc, L. M., Dale, S. G., Taylor, C. R., Becke, A. D., Day, G. M. & Johnson, E. R. (2018). Angew. Chem.130, 15122–15126. PubMed

Liu, D. C. & Nocedal, J. (1989). Math. Program.45, 503–528.

Loboda, O. A., Dolgonos, G. A. & Boese, A. D. (2018). J. Chem. Phys.149, 124104. PubMed

Lommerse, J. P. M., Motherwell, W. D. S., Ammon, H. L., Dunitz, J. D., Gavezzotti, A., Hofmann, D. W. M., Leusen, F. J. J., Mooij, W. T. M., Price, S. L., Schweizer, B., Schmidt, M. U., van Eijck, B. P., Verwer, P. & Williams, D. E. (2000). Acta Cryst. B56, 697–714. PubMed

Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst.53, 226–235. PubMed PMC

Mattei, A., Hong, R. S., Dietrich, H., Firaha, D., Helfferich, J., Liu, Y. M., Sasikumar, K., Abraham, N. S., Miglani Bhardwaj, R., Neumann, M. A. & Sheikh, A. Y. (2022). J. Chem. Theory Comput.18, 5725–5738. PubMed PMC

Mayo, R. A. & Johnson, E. R. (2021). CrystEngComm, 23, 7118–7131.

Mayo, R. A., Otero-de-la-Roza, A. & Johnson, E. R. (2022). CrystEngComm,24, 8326–8338.

Mayo, S. L., Olafson, B. D. & Goddard, W. A. (1990). J. Phys. Chem.94, 8897–8909.

Mejía-Rodríguez, D. & Trickey, S. B. (2019). J. Chem. Phys.151, 207101. PubMed

Mennucci, B., Tomasi, J., Cammi, R., Cheeseman, J. R., Frisch, M. J., Devlin, F. J., Gabriel, S. & Stephens, P. J. (2002). J. Phys. Chem. A, 106, 6102–6113.

Metz, M. P., Piszczatowski, K. & Szalewicz, K. (2016). J. Chem. Theory Comput.12, 5895–5919. PubMed

Misquitta, A. J., Podeszwa, R., Jeziorski, B. & Szalewicz, K. (2005). J. Chem. Phys.123, 214103. PubMed

Mochizuki, Y., Koikegami, S., Nakano, T., Amari, S. & Kitaura, K. (2004a). Chem. Phys. Lett.396, 473–479.

Mochizuki, Y., Nakano, T., Koikegami, S., Tanimori, S., Abe, Y., Nagashima, U. & Kitaura, K. (2004b). Theor. Chem. Acc.112, 442–452.

Moellmann, J. & Grimme, S. (2014). J. Phys. Chem. C, 118, 7615–7621.

Momenzadeh Abardeh, Z., Salimi, A. & Oganov, A. R. (2022). CrystEngComm, 24, 6066–6075.

Monacelli, L., Bianco, R., Cherubini, M., Calandra, M., Errea, I. & Mauri, F. (2021). J. Phys. Condens. Matter, 33, 363001. PubMed

Mooij, W. T. M. & Leusen, F. J. J. (2001). Phys. Chem. Chem. Phys.3, 5063–5066.

Mortazavi, M., Brandenburg, J. G., Maurer, R. J. & Tkatchenko, A. (2018). J. Phys. Chem. Lett.9, 399–405. PubMed

Motherwell, W. D. S., Ammon, H. L., Dunitz, J. D., Dzyabchenko, A., Erk, P., Gavezzotti, A., Hofmann, D. W. M., Leusen, F. J. J., Lommerse, J. P. M., Mooij, W. T. M., Price, S. L., Scheraga, H., Schweizer, B., Schmidt, M. U., van Eijck, B. P., Verwer, P. & Williams, D. E. (2002). Acta Cryst. B58, 647–661. PubMed

Musil, F., De, S., Yang, J., Campbell, J. E., Day, G. M. & Ceriotti, M. (2018). Chem. Sci.9, 1289–1300. PubMed PMC

Nakano, T., Kaminuma, T., Sato, T., Fukuzawa, K., Akiyama, Y., Uebayasi, M. & Kitaura, K. (2002). Chem. Phys. Lett.351, 475–480.

Neumann, M. A. (2008). J. Phys. Chem. B, 112, 9810–9829. PubMed

Neumann, M. A., Leusen, F. J. J. & Kendrick, J. (2008). Angew. Chem. Int. Ed.47, 2427–2430. PubMed

Neumann, M. A. & Perrin, M.-A. (2005). J. Phys. Chem. B, 109, 15531–15541. PubMed

Neumann, M. & van de Streek, J. (2018). Faraday Discuss.211, 441–458. PubMed

Nikhar, R. & Szalewicz, K. (2022). Nat. Commun.13, 3095. PubMed PMC

Nyman, J. & Day, G. M. (2015). CrystEngComm, 17, 5154–5165.

Nyman, J., Pundyke, O. S. & Day, G. M. (2016). Phys. Chem. Chem. Phys.18, 15828–15837. PubMed

Nyman, J. & Reutzel-Edens, S. M. (2018). Faraday Discuss.211, 459–476. PubMed

Nyman, J., Yu, L. & Reutzel-Edens, S. M. (2019). CrystEngComm, 21, 2080–2088.

O’Connor, D., Bier, I., Hsieh, Y.-T. & Marom, N. (2022). J. Chem. Theory Comput.18, 4456–4471. PubMed

O’Connor, D., Bier, I., Tom, R., Hiszpanski, A. M., Steele, B. A. & Marom, N. (2023). Cryst. Growth Des.23, 6275–6289. PubMed PMC

Otero-de-la-Roza, A. & Johnson, E. R. (2012). J. Chem. Phys.137, 054103. PubMed

Otero-de-la-Roza, A. & Johnson, E. R. (2013). J. Chem. Phys.138, 054103. PubMed

Otero-de-la-Roza, A., LeBlanc, L. M. & Johnson, E. R. (2019). J. Chem. Theory Comput.15, 4933–4944. PubMed

Packwood, D., Kermode, J., Mones, L., Bernstein, N., Woolley, J., Gould, N., Ortner, C. & Csányi, G. (2016). J. Chem. Phys.144, 164109. PubMed

Perdew, J. P. & Schmidt, K. (2001). AIP Conf. Proc.577, 1–20.

Perdew, J. P., Burke, K. & Ernzerhof, M. (1996a). Phys. Rev. Lett.77, 3865–3868. PubMed

Perdew, J. P., Ernzerhof, M. & Burke, K. (1996b). J. Chem. Phys.105, 9982–9985.

Perdew, J. P. & Zunger, A. (1981). Phys. Rev. B, 23, 5048–5079.

Pokorný, V., Touš, P., Štejfa, V., Růžička, K., Rohlíček, J., Czernek, J., Brus, J. & Červinka, C. (2022). Phys. Chem. Chem. Phys.24, 25904–25917. PubMed

Price, A. J. A., Mayo, R. A., Otero-de-la-Roza, A. & Johnson, E. R. (2023b). CrystEngComm, 25, 953–960.

Price, A. J., Otero-de-la-Roza, A. & Johnson, E. R. (2023a). Chem. Sci.14, 1252–1262. PubMed PMC

Price, S. L. (2013). Acta Cryst. B69, 313–328. PubMed

Price, S. L., Leslie, M., Welch, G. W. A., Habgood, M., Price, L. S., Karamertzanis, P. G. & Day, G. M. (2010). Phys. Chem. Chem. Phys.12, 8478. PubMed

Pyzer-Knapp, E. O., Thompson, H. P. G. & Day, G. M. (2016). Acta Cryst. B72, 477–487. PubMed PMC

Rana, B., Beran, G. J. O. & Herbert, J. M. (2022). Mol. Phys.121, e2138789.

Reilly, A. M. & Tkatchenko, A. (2013). J. Chem. Phys.139, 024705. PubMed

Reilly, A. M. & Tkatchenko, A. (2015). Chem. Sci.6, 3289–3301. PubMed PMC

Reilly, A. M., Cooper, R. I., Adjiman, C. S., Bhattacharya, S., Boese, A. D., Brandenburg, J. G., Bygrave, P. J., Bylsma, R., Campbell, J. E., Car, R., Case, D. H., Chadha, R., Cole, J. C., Cosburn, K., Cuppen, H. M., Curtis, F., Day, G. M., DiStasio, R. A. Jr, Dzyabchenko, A., van Eijck, B. P., Elking, D. M., van den Ende, J. A., Facelli, J. C., Ferraro, M. B., Fusti-Molnar, L., Gatsiou, C.-A., Gee, T. S., de Gelder, R., Ghiringhelli, L. M., Goto, H., Grimme, S., Guo, R., Hofmann, D. W. M., Hoja, J., Hylton, R. K., Iuzzolino, L., Jankiewicz, W., de Jong, D. T., Kendrick, J., de Klerk, N. J. J., Ko, H.-Y., Kuleshova, L. N., Li, X., Lohani, S., Leusen, F. J. J., Lund, A. M., Lv, J., Ma, Y., Marom, N., Masunov, A. E., McCabe, P., McMahon, D. P., Meekes, H., Metz, M. P., Misquitta, A. J., Mohamed, S., Monserrat, B., Needs, R. J., Neumann, M. A., Nyman, J., Obata, S., Oberhofer, H., Oganov, A. R., Orendt, A. M., Pagola, G. I., Pantelides, C. C., Pickard, C. J., Podeszwa, R., Price, L. S., Price, S. L., Pulido, A., Read, M. G., Reuter, K., Schneider, E., Schober, C., Shields, G. P., Singh, P., Sugden, I. J., Szalewicz, K., Taylor, C. R., Tkatchenko, A., Tuckerman, M. E., Vacarro, F., Vasileiadis, M., Vazquez-Mayagoitia, A., Vogt, L., Wang, Y., Watson, R. E., de Wijs, G. A., Yang, J., Zhu, Q. & Groom, C. R. (2016). Acta Cryst. B72, 439–459.

Řezáč, J. (2017). J. Chem. Theory Comput.13, 4804–4817. PubMed

Řezáč, J. (2019). J. Comput. Chem.40, 1633–1642. PubMed

Rossi, M., Gasparotto, P. & Ceriotti, M. (2016). Phys. Rev. Lett.117, 115702. PubMed

Sacchi, P., Lusi, M., Cruz-Cabeza, A. J., Nauha, E. & Bernstein, J. (2020). CrystEngComm, 22, 7170–7185.

Sarma, J. & Desiraju, G. R. (2002). Cryst. Growth Des.2, 93–100.

Schröder, E., Cooper, V. R., Berland, K., Lundqvist, B. I., Hyldgaard, P. & Thonhauser, T. (2017). In Non-Covalent Interactions in Quantum Chemistry and Physics, edited by A. Otero-de-la-Roza & G. A. DiLabio, pp. 241–274. Elsevier.

Spath, H. (1980). Cluster Analysis Algorithms for Data Reduction and Classification of Objects. Chichester: Ellis Horwood.

Stone, A. J. (1981). Chem. Phys. Lett.83, 233–239.

Stone, A. J. & Price, S. L. (1988). J. Phys. Chem.92, 3325–3335.

Sun, H. (1998). J. Phys. Chem. B, 102, 7338–7364.

Sun, J., Ruzsinszky, A. & Perdew, J. P. (2015). Phys. Rev. Lett.115, 036402. PubMed

Tao, J., Perdew, J. P., Staroverov, V. N. & Scuseria, G. E. (2003). Phys. Rev. Lett.91, 146401. PubMed

Tkatchenko, A., DiStasio, R. A., Car, R. & Scheffler, M. (2012). Phys. Rev. Lett.108, 236402. PubMed

Tom, R., Gao, S., Yang, Y., Zhao, K., Bier, I., Buchanan, E. A., Zaykov, A., Havlas, Z., Michl, J. & Marom, N. (2023). Chem. Mater.35, 1373–1386. PubMed PMC

Touš, P. & Červinka, C. (2023). Cryst. Growth Des.23, 4082–4097.

Tu, N. T. P., Rezajooei, N., Johnson, E. R. & Rowley, C. N. (2023). Digit. Discov.2, 718–727.

Tuckerman, M. & Galanakis, N. (2023).Topological Crystal Structure Prediction, https://doi.org/10.21203/rs.3.rs-3361974/v1.

Vydrov, O. A. & van Voorhis, T. (2010). J. Chem. Phys.33, 244103. PubMed

Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. (2004). J. Comput. Chem.25, 1157–1174. PubMed

Welch, G. W. A., Karamertzanis, P. G., Misquitta, A. J., Stone, A. J. & Price, S. L. (2008). J. Chem. Theory Comput.4, 522–532. PubMed

Wen, S. & Beran, G. J. O. (2011). J. Chem. Theory Comput.7, 3733–3742. PubMed

Whittleton, S. R., Otero-de-la-Roza, A. & Johnson, E. R. (2016). J. Chem. Theory Comput.13, 441–450. PubMed

Widdowson, D., Mosca, M. M., Pulido, A., Cooper, A. I. & Kurlin, V. (2022). Match, 87, 529–559.

Williams, D. E. (2001a). J. Comput. Chem.22, 1–20.

Williams, D. E. (2001b). J. Comput. Chem.22, 1154–1166.

Woollam, G. R., Neumann, M. A., Wagner, T. & Davey, R. J. (2018). Faraday Discuss.211, 209–234. PubMed

Yang, M., Dybeck, E., Sun, G., Peng, C., Samas, B., Burger, V. M., Zeng, Q., Jin, Y., Bellucci, M. A., Liu, Y., Zhang, P., Ma, J., Jiang, Y. A., Hancock, B. C., Wen, S. & Wood, G. P. F. (2020). Cryst. Growth Des.20, 5211–5224.

Yu, L. (1995). J. Pharm. Sci.84, 966–974. PubMed

Yu, L., Huang, J. & Jones, K. J. (2005). J. Phys. Chem. B, 109, 19915–19922. PubMed

Yue, S., Muniz, M. C., Calegari Andrade, M. F., Zhang, L., Car, R. & Panagiotopoulos, A. Z. (2021). J. Chem. Phys.154, 034111. PubMed

Zhang, L., Wang, H., Muniz, M. C., Panagiotopoulos, A. Z., Car, R. & E, W. (2022). J. Chem. Phys.156, 124107. PubMed

Zhang, P., Wood, G. P., Ma, J., Yang, M., Liu, Y., Sun, G., Jiang, Y. A., Hancock, B. C. & Wen, S. (2018). Cryst. Growth Des.18, 6891–6900.

Zubatyuk, R., Smith, J. S., Nebgen, B. T., Tretiak, S. & Isayev, O. (2021). Nat. Commun.12, 4870. PubMed PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...