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

Lily M. Hunnisett, Jonas Nyman, Nicholas Francia, Nathan S. Abraham, Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, Mubarak Almehairbi, Andrea Anelli, Dylan M. Anstine, John E. Anthony, Joseph E. Arnold, Faezeh Bahrami, Michael A. Bellucci, Rajni M. Bhardwaj, Imanuel Bier, Joanna A. Bis, A. Daniel Boese, David H. Bowskill, James BramleyJan Gerit Brandenburg, Doris E. Braun, Patrick W.V. Butler, Joseph Cadden, Stephen Carino, Eric J. Chan, Chao Chang, Bingqing Cheng, Sarah M. Clarke, Simon J. Coles, Richard I. Cooper, Ricky Couch, Ramon Cuadrado, Tom Darden, Graeme M. Day, Hanno Dietrich, Yiming Ding, Antonio DiPasquale, Bhausaheb Dhokale, Bouke P. van Eijck, Mark R.J. Elsegood, Dzmitry Firaha, Wenbo Fu, Kaori Fukuzawa, Joseph Glover, Hitoshi Goto, Chandler Greenwell, Rui Guo, Jürgen Harter, Julian Helfferich, Detlef W.M. Hofmann, Johannes Hoja, John Hone, Richard Hong, Geoffrey Hutchison, Yasuhiro Ikabata, Olexandr Isayev, Ommair Ishaque, Varsha Jain, Yingdi Jin, Aling Jing, Erin R. Johnson, Ian Jones, K. V.Jovan Jose, Elena A. Kabova, Adam Keates, Paul F. Kelly, Dmitry Khakimov, Stefanos Konstantinopoulos, Liudmila N. Kuleshova, He Li, Xiaolu Lin, Alexander List, Congcong Liu, Yifei Michelle Liu, Zenghui Liu, Zhi Pan Liu, Joseph W. Lubach, Noa Marom, Alexander A. Maryewski, Hiroyuki Matsui, Alessandra Mattei, R. Alex Mayo, John W. Melkumov, Sharmarke Mohamed, Zahrasadat Momenzadeh Abardeh, Hari S. Muddana, Naofumi Nakayama, Kamal Singh Nayal, Marcus A. Neumann, Rahul Nikhar, Shigeaki Obata, Dana O’Connor, Artem R. Oganov, Koji Okuwaki, Alberto Otero-De-la-Roza, Constantinos C. Pantelides, Sean Parkin, Chris J. Pickard, Luca Pilia, Tatyana Pivina, Rafał Podeszwa, Alastair J.A. Price, Louise S. Price, Sarah L. Price, Michael R. Probert, Angeles Pulido, Gunjan Rajendra Ramteke, Atta Ur Rehman, Susan M. Reutzel-Edens, Jutta Rogal, Marta J. Ross, Adrian F. Rumson, Ghazala Sadiq, Zeinab M. Saeed, Alireza Salimi, Matteo Salvalaglio, Leticia Sanders de Almada, Kiran Sasikumar, Sivakumar Sekharan, Cheng Shang, Kenneth Shankland, Kotaro Shinohara, Baimei Shi, Xuekun Shi, A. Geoffrey Skillman, Hongxing Song, Nina Strasser, Jacco van de Streek, Isaac J. Sugden, Guangxu Sun, Krzysztof Szalewicz, Benjamin I. Tan, Lu Tan, Frank Tarczynski, Christopher R. Taylor, Alexandre Tkatchenko, Rithwik Tom, Mark E. Tuckerman, Yohei Utsumi, Leslie Vogt-Maranto, Jake Weatherston, Luke J. Wilkinson, Robert D. Willacy, Lukasz Wojtas, Grahame R. Woollam, Zhuocen Yang, Etsuo Yonemochi, Xin Yue, Qun Zeng, Yizu Zhang, Tian Zhou, Yunfei Zhou, Roman Zubatyuk, Jason C. Cole

Research output: Contribution to journalArticlepeer-review

55 Scopus citations

Abstract

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Original languageEnglish
Pages (from-to)517-547
Number of pages31
JournalActa Crystallographica Section B: Structural Science, Crystal Engineering and Materials
Volume80
DOIs
StatePublished - Dec 1 2024

Bibliographical note

Publisher Copyright:
© 2024 International Union of Crystallography. All rights reserved.

Funding

Group 1. Funding for this research was provided by: EngineeringandPhysicalSciencesResearchCouncil(grant Nos .EP/J014958/1,EP/J003840/1,EP/P022561/1,EP/P020194, andEP/T51780X/1),EliLillyandCompanyandSyngenta.W e wouldliketoacknowledgetheImperialCollegeResearch ComputingService ,DOI:10.14469/hpc/2232,theCirrusUK NationalT ier -2 HPCServiceatEPCC(https://www .cirrus .ac. uk)fundedbytheUniversityofEdinburghandEPSRC(EP/ P020267/1),andtheUKMaterialsandMolecularModelling Hubforcomputationalresources ,whichispartiallyfundedby EPSRC(EP/P020194/1andEP/T022213/1). The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett, J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge numerous CCDC colleagues for their helpful feedback and suggestions on the manuscript (P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python knowledge (A. Moldovan), providing and maintaining internal compute resources (K. Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind test meeting (E. Clarke), and improvements to the Crystal Packing Similarity tool (M. Read). Data analysis was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/ T022159/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). N. Francia thanks M. Salvalaglio for advice on the metadynamics simulations and the University College London for providing access to the Kathleen High Performance Computing Facility (Kathleen@UCL) on which simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson for counselling on crystal structure similarity. I. Sugden and N. Francia participated in the blind test as members of Groups 1 and 24, respectively. They were involved in the analysis of the results and in writing this paper only after all results were made available to participants. Group 1. Funding for this research was provided by: Engineering and Physical Sciences Research Council (grant Nos. EP/J014958/1, EP/J003840/1, EP/P022561/1, EP/P020194, and EP/T51780X/1), Eli Lilly and Company and Syngenta. We would like to acknowledge the Imperial College Research Computing Service, DOI: 10.14469/hpc/2232, the Cirrus UK National Tier-2 HPC Service at EPCC (https://www.cirrus.ac. uk) funded by the University of Edinburgh and EPSRC (EP/ P020267/1), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1 and EP/T022213/1). (XSEDE) award CHE200122, which is supported by NSF grant number ACI-1053575. This research is part of the Frontera computing project at the Texas Advanced Computing Center. Frontera is made possible by the National Science Foundation award OAC-1818253. This research in part was done using resources provided by the Open Science Grid, which is supported by the award 1148698, and the US DOE Office of Science. The Marom group acknowledges support from National Science Foundation (NSF) through grant DMR-2131944. This research used resources of Argonne Leadership Computing Facility (ALCF), which is a DOE Office of Science User Facility supported under Contract DEAC02-06CH11357. We also acknowledge the Extreme Science and Engineering Discovery Environment (XSEDE) award MAT210006, which supported 3 million central processing unit (CPU) core hours. Group 22. Group 22 acknowledges support from the Russian Science Foundation (grant 19-72-30043). Competing interests: the USPEX code is free for academic researchers, but is distributed at a fee to companies. Group5.W ethanktheUniversityofSouthamptonfora UniversityofSouthamptonPresidentialScholarship(Patrick W .V .Butler),J ohnson Mattheyforfunding(J ames Bramley), theAirF orce OfficeofScientificResearchforfundingunder award No . F A8655-20-1-700 0 (J oseph E. Arnold) and the EuropeanResearchCouncilundertheEuropeanUnion’s Horizon2020researchandinnovationprogram(grant agreement No . 856405) (Christopher T aylor, Ramon Cuadrado,J oseph Glover,GraemeM.Day).W eacknowledge theuseoftheIRIDISHigh-PerformanceComputingF acility andassociatedsupportservicesattheUniversityofSouth-ampton.V ia ourmembershipoftheUK’sHECMaterials ChemistryConsortium,whichisfundedbytheEPSRC(EP/ R029431),thisworkusedtheUKMaterialsandMolecular ModellingHubforcomputationalresources ,theMMMHub , whichispartiallyfundedbytheEPSRC(EP/P020194/1and EP/T022213/1). Groups26and27.T he workattheUniversityofDelaware wassupportedbytheUSArmyResearchLaboratoryand ArmyResearchOfficeundergrantW911NF-19-0117and National Science F oundation under grants CHE-1900551, CHE-2154908,andCHE-2313826.JRacknowledgesfinancial supportfromtheDeutscheF orschungsge meinschaft(DFG) throughtheHeisenbergProgrammeproject428315600.JR andMETacknowledgefundingfromtheNationalScience F oundation grantDMR-2118890.METacknowledgessupport from the National Science F oundation, grant No . CHE-1955381.

FundersFunder number
EngineeringandPhysicalSciencesResearchCouncil
Heriot-Watt University, Edinburgh
Eli Lilly and Company
EuropeanResearchCouncilundertheEuropeanUnion’s Horizon2020researchandinnovationprogram
Texas Advanced Computing Center
Association for Library Service to Children
NSF Extreme Science and Engineering Discovery Environment
Imperial College Research Computing Service
UK Medical Research Council, Engineering and Physical Sciences Research CouncilEP/P020194/1, EP/T022213/1, CHE200122, EP/J014958/1, EP/ T022159/1, ACI-1053575, EP/ P020267/1
National Science F oundationCHE-1955381
Russian Science Foundation19-72-30043
Office of Science ProgramsDMR-2131944, DEAC02-06CH11357
National Science Foundation Arctic Social Science ProgramOAC-1818253, 1148698
Science and Technology Facilities CouncilEP/P022561/1, EP/T51780X/1, EP/J003840/1, EP/P020194
XSEDEMAT210006

    Keywords

    • Cambridge Structural Database
    • blind test
    • crystal structure prediction
    • lattice energy
    • polymorphism

    ASJC Scopus subject areas

    • Electronic, Optical and Magnetic Materials
    • Atomic and Molecular Physics, and Optics
    • Metals and Alloys
    • Materials Chemistry

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