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Hunnisett LM, Francia N, Nyman J, Abraham NS, Aitipamula S, Alkhidir T, Almehairbi M, Anelli A, Anstine DM, Anthony JE, Arnold JE, Bahrami F, Bellucci MA, Beran GJO, Bhardwaj RM, Bianco R, Bis JA, Boese AD, Bramley J, Braun DE, Butler PWV, Cadden J, Carino S, Červinka C, Chan EJ, Chang C, Clarke SM, Coles SJ, Cook CJ, Cooper RI, Darden T, Day GM, Deng W, Dietrich H, DiPasquale A, Dhokale B, van Eijck BP, Elsegood MRJ, Firaha D, Fu W, Fukuzawa K, Galanakis N, Goto H, Greenwell C, Guo R, Harter J, Helfferich J, Hoja J, Hone J, Hong R, Hušák M, Ikabata Y, Isayev O, Ishaque O, Jain V, Jin Y, Jing A, Johnson ER, Jones I, Jose KVJ, Kabova EA, Keates A, Kelly PF, Klimeš J, Kostková V, Li H, Lin X, List A, Liu C, Liu YM, Liu Z, Lončarić I, Lubach JW, Ludík J, Marom N, Matsui H, Mattei A, Mayo RA, Melkumov JW, Mladineo B, Mohamed S, Momenzadeh Abardeh Z, Muddana HS, Nakayama N, Nayal KS, Neumann MA, Nikhar R, Obata S, O’Connor D, Oganov AR, Okuwaki K, Otero-de-la-Roza A, Parkin S, Parunov A, Podeszwa R, Price AJA, Price LS, Price SL, Probert MR, Pulido A, et alHunnisett LM, Francia N, Nyman J, Abraham NS, Aitipamula S, Alkhidir T, Almehairbi M, Anelli A, Anstine DM, Anthony JE, Arnold JE, Bahrami F, Bellucci MA, Beran GJO, Bhardwaj RM, Bianco R, Bis JA, Boese AD, Bramley J, Braun DE, Butler PWV, Cadden J, Carino S, Červinka C, Chan EJ, Chang C, Clarke SM, Coles SJ, Cook CJ, Cooper RI, Darden T, Day GM, Deng W, Dietrich H, DiPasquale A, Dhokale B, van Eijck BP, Elsegood MRJ, Firaha D, Fu W, Fukuzawa K, Galanakis N, Goto H, Greenwell C, Guo R, Harter J, Helfferich J, Hoja J, Hone J, Hong R, Hušák M, Ikabata Y, Isayev O, Ishaque O, Jain V, Jin Y, Jing A, Johnson ER, Jones I, Jose KVJ, Kabova EA, Keates A, Kelly PF, Klimeš J, Kostková V, Li H, Lin X, List A, Liu C, Liu YM, Liu Z, Lončarić I, Lubach JW, Ludík J, Marom N, Matsui H, Mattei A, Mayo RA, Melkumov JW, Mladineo B, Mohamed S, Momenzadeh Abardeh Z, Muddana HS, Nakayama N, Nayal KS, Neumann MA, Nikhar R, Obata S, O’Connor D, Oganov AR, Okuwaki K, Otero-de-la-Roza A, Parkin S, Parunov A, Podeszwa R, Price AJA, Price LS, Price SL, Probert MR, Pulido A, Ramteke GR, Rehman AU, Reutzel-Edens SM, Rogal J, Ross MJ, Rumson AF, Sadiq G, Saeed ZM, Salimi A, Sasikumar K, Sekharan S, Shankland K, Shi B, Shi X, Shinohara K, Skillman AG, Song H, Strasser N, van de Streek J, Sugden IJ, Sun G, Szalewicz K, Tan L, Tang K, Tarczynski F, Taylor CR, Tkatchenko A, Tom R, Touš P, Tuckerman ME, Unzueta PA, Utsumi Y, Vogt-Maranto L, Weatherston J, Wilkinson LJ, Willacy RD, Wojtas L, Woollam GR, Yang Y, Yang Z, Yonemochi E, Yue X, Zeng Q, Zhou T, Zhou Y, Zubatyuk R, Cole JC. The seventh blind test of crystal structure prediction: structure ranking methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624008679. [PMID: 39418598 PMCID: PMC11789160 DOI: 10.1107/s2052520624008679] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/03/2024] [Indexed: 10/19/2024]
Abstract
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.
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Affiliation(s)
- Lily M. Hunnisett
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Nicholas Francia
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Jonas Nyman
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Nathan S. Abraham
- AbbVie Inc., Research & Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | - Srinivasulu Aitipamula
- Crystallization and Particle Sciences Institute of Chemical and Engineering Sciences 1 Pesek Road Singapore 627833 Singapore
| | - Tamador Alkhidir
- Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
| | - Mubarak Almehairbi
- Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
| | - Andrea Anelli
- Roche Pharma Research and Early Development Therapeutic Modalities Roche Innovation Center Basel F Hoffmann-La Roche Ltd Grenzacherstrasse 124 4070 BaselSwitzerland
| | - Dylan M. Anstine
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - John E. Anthony
- Department of Chemistry University of KentuckyLexington KY 40506 USA
| | - Joseph E. Arnold
- School of Chemistry University of SouthamptonSouthampton SO17 1BJ UK
| | - Faezeh Bahrami
- Department of Chemistry Faculty of Science Ferdowsi University of MashhadMashhadIran
| | | | | | - Rajni M. Bhardwaj
- AbbVie Inc., Research & Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | | | - Joanna A. Bis
- Catalent Pharma Solutions 160 Pharma Drive Morrisville NC 27560 USA
| | - A. Daniel Boese
- Department of Chemistry University of Graz Heinrichstrasse 28 GrazAustria
| | - James Bramley
- School of Chemistry University of SouthamptonSouthampton SO17 1BJ UK
| | - Doris E. Braun
- University of Innsbruck Institute of Pharmacy Innrain 52c A-6020 InnsbruckAustria
| | | | - Joseph Cadden
- Crystallization and Particle Sciences Institute of Chemical and Engineering Sciences 1 Pesek Road Singapore 627833 Singapore
- School of Chemistry University of SouthamptonSouthampton SO17 1BJ UK
| | - Stephen Carino
- Catalent Pharma Solutions 160 Pharma Drive Morrisville NC 27560 USA
| | - Ctirad Červinka
- Department of Physical Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic
| | - Eric J. Chan
- Department of Chemistry New York UniversityNew York NY 10003 USA
| | - Chao Chang
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Sarah M. Clarke
- Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie HalifaxCanada
| | - Simon J. Coles
- School of Chemistry University of SouthamptonSouthampton SO17 1BJ UK
| | - Cameron J. Cook
- Department of Chemistry University of California Riverside CA 92521 USA
| | - Richard I. Cooper
- Department of Chemistry University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Tom Darden
- OpenEye Scientific Software, 9 Bisbee Court, Santa Fe, NM 87508, USA
| | - Graeme M. Day
- School of Chemistry University of SouthamptonSouthampton SO17 1BJ UK
| | - Wenda Deng
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Hanno Dietrich
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | | | - Bhausaheb Dhokale
- Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
- Department of Chemistry University of Wyoming Laramie Wyoming 82071 USA
| | - Bouke P. van Eijck
- University of Utrecht (Retired), Department of Crystal and Structural Chemistry, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Dzmitry Firaha
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Wenbo Fu
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences Osaka University 1-6 Yamadaoka Suita Osaka 656-0871 Japan
- School of Pharmacy and Pharmaceutical Sciences Hoshi University 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | | | - Hitoshi Goto
- Information and Media Center Toyohashi University of Technology 1-1 Hibarigaoka Tempaku-cho Toyohashi Aichi 441-8580 Japan
- CONFLEX Corporation, Shinagawa Center building 6F, 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | | | - Rui Guo
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Jürgen Harter
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Julian Helfferich
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Johannes Hoja
- Department of Chemistry University of Graz Heinrichstrasse 28 GrazAustria
| | - John Hone
- Syngenta Ltd., Jealott’s Hill International Research Station, Berkshire, RG42 6EY, UK
| | - Richard Hong
- AbbVie Inc., Research & Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
- Department of Chemistry New York UniversityNew York NY 10003 USA
| | - Michal Hušák
- Department of Solid State Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic
| | - Yasuhiro Ikabata
- Information and Media Center Toyohashi University of Technology 1-1 Hibarigaoka Tempaku-cho Toyohashi Aichi 441-8580 Japan
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Ommair Ishaque
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Varsha Jain
- OpenEye Scientific Software, 9 Bisbee Court, Santa Fe, NM 87508, USA
| | - Yingdi Jin
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Aling Jing
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Erin R. Johnson
- Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie HalifaxCanada
| | - Ian Jones
- Syngenta Ltd., Jealott’s Hill International Research Station, Berkshire, RG42 6EY, UK
| | - K. V. Jovan Jose
- School of Chemistry University of Hyderabad Professor CR Rao Road Gachibowli Hyderabad 500046 Telangana India
| | - Elena A. Kabova
- School of Pharmacy University of Reading Whiteknights Reading RG6 6AD UK
| | - Adam Keates
- Syngenta Ltd., Jealott’s Hill International Research Station, Berkshire, RG42 6EY, UK
| | - Paul F. Kelly
- Chemistry Department Loughborough UniversityLoughborough LE11 3TU UK
| | - Jiří Klimeš
- Department of Chemical Physics and Optics Faculty of Mathematics and Physics Charles University Ke Karlovu 3 121 16 Prague Czech Republic
| | - Veronika Kostková
- Department of Physical Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic
| | - He Li
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Xiaolu Lin
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Alexander List
- Department of Chemistry University of Graz Heinrichstrasse 28 GrazAustria
| | - Congcong Liu
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Yifei Michelle Liu
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Zenghui Liu
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | | | - Jan Ludík
- Department of Physical Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic
| | - Noa Marom
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Hiroyuki Matsui
- Graduate School of Organic Materials Science Yamagata University 4-3-16 Jonan Yonezawa 992-8510 Yamagata Japan
| | - Alessandra Mattei
- AbbVie Inc., Research & Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | - R. Alex Mayo
- Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie HalifaxCanada
| | - John W. Melkumov
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Bruno Mladineo
- Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Sharmarke Mohamed
- Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
- Center for Catalysis and Separations Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
| | | | - Hari S. Muddana
- OpenEye Scientific Software, 9 Bisbee Court, Santa Fe, NM 87508, USA
| | - Naofumi Nakayama
- Information and Media Center Toyohashi University of Technology 1-1 Hibarigaoka Tempaku-cho Toyohashi Aichi 441-8580 Japan
| | - Kamal Singh Nayal
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Marcus A. Neumann
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Rahul Nikhar
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Shigeaki Obata
- Information and Media Center Toyohashi University of Technology 1-1 Hibarigaoka Tempaku-cho Toyohashi Aichi 441-8580 Japan
- CONFLEX Corporation, Shinagawa Center building 6F, 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Dana O’Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Artem R. Oganov
- Skolkovo Institute of Science and Technology Bolshoy Boulevard 30 121205 MoscowRussia
| | - Koji Okuwaki
- School of Pharmacy and Pharmaceutical Sciences Hoshi University 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | - Alberto Otero-de-la-Roza
- Department of Analytical and Physical Chemistry Faculty of Chemistry University of Oviedo Julián Clavería 8 33006 OviedoSpain
| | - Sean Parkin
- Department of Chemistry University of KentuckyLexington KY 40506 USA
| | - Antonio Parunov
- Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Rafał Podeszwa
- Institute of Chemistry University of Silesia in Katowice Szkolna 9 40-006 KatowicePoland
| | - Alastair J. A. Price
- Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie HalifaxCanada
| | - Louise S. Price
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Sarah L. Price
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Michael R. Probert
- School of Natural and Environmental Sciences Newcastle University Kings Road Newcastle NE1 7RU UK
| | - Angeles Pulido
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Gunjan Rajendra Ramteke
- School of Chemistry University of Hyderabad Professor CR Rao Road Gachibowli Hyderabad 500046 Telangana India
| | - Atta Ur Rehman
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Susan M. Reutzel-Edens
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
- SuRE Pharma Consulting, LLC, 7163 Whitestown Parkway - Suite 305, Zionsville, IN 46077, USA
| | - Jutta Rogal
- Department of Chemistry New York UniversityNew York NY 10003 USA
- Fachbereich Physik, Freie Universität, Berlin, 14195, Germany
| | - Marta J. Ross
- School of Pharmacy University of Reading Whiteknights Reading RG6 6AD UK
| | - Adrian F. Rumson
- Department of Chemistry Dalhousie University 6274 Coburg Road Dalhousie HalifaxCanada
| | - Ghazala Sadiq
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Zeinab M. Saeed
- Green Chemistry and Materials Modelling Laboratory Khalifa University of Science and Technology PO Box 127788 Abu DhabiUnited Arab Emirates
| | - Alireza Salimi
- Department of Chemistry Faculty of Science Ferdowsi University of MashhadMashhadIran
| | - Kiran Sasikumar
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | | | - Kenneth Shankland
- School of Pharmacy University of Reading Whiteknights Reading RG6 6AD UK
| | - Baimei Shi
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Xuekun Shi
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Kotaro Shinohara
- Graduate School of Organic Materials Science Yamagata University 4-3-16 Jonan Yonezawa 992-8510 Yamagata Japan
| | | | - Hongxing Song
- Department of Chemistry New York UniversityNew York NY 10003 USA
| | - Nina Strasser
- Department of Chemistry University of Graz Heinrichstrasse 28 GrazAustria
| | | | - Isaac J. Sugden
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Guangxu Sun
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy University of DelawareNewark DE 19716 USA
| | - Lu Tan
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Kehan Tang
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Frank Tarczynski
- Catalent Pharma Solutions 160 Pharma Drive Morrisville NC 27560 USA
| | | | - Alexandre Tkatchenko
- Department of Physics and Materials Science University of Luxembourg 1511 Luxembourg City Luxembourg
| | - Rithwik Tom
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Petr Touš
- Department of Physical Chemistry University of Chemistry and Technology Technická 5 16628 Prague Czech Republic
| | - Mark E. Tuckerman
- Department of Chemistry New York UniversityNew York NY 10003 USA
- Courant Institute of Mathematical SciencesNew York UniversityNew York NY 10012 USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Pablo A. Unzueta
- Department of Chemistry University of California Riverside CA 92521 USA
| | - Yohei Utsumi
- School of Pharmacy and Pharmaceutical Sciences Hoshi University 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | | | - Jake Weatherston
- School of Natural and Environmental Sciences Newcastle University Kings Road Newcastle NE1 7RU UK
| | - Luke J. Wilkinson
- Chemistry Department Loughborough UniversityLoughborough LE11 3TU UK
| | - Robert D. Willacy
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Lukasz Wojtas
- Department of Chemistry University of South Florida USF Research Park 3720 Spectrum Blvd IDRB 202 Tampa FL 33612 USA
| | | | - Yi Yang
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Zhuocen Yang
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Etsuo Yonemochi
- School of Pharmacy and Pharmaceutical Sciences Hoshi University 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | - Xin Yue
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Qun Zeng
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Tian Zhou
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Yunfei Zhou
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Roman Zubatyuk
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Jason C. Cole
- The Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
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Mayo RA, Price AJA, Otero-de-la-Roza A, Johnson ER. Assessment of the exchange-hole dipole moment dispersion correction for the energy ranking stage of the seventh crystal structure prediction blind test. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624002774. [PMID: 39405194 PMCID: PMC11789164 DOI: 10.1107/s2052520624002774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 02/05/2025]
Abstract
The seventh blind test of crystal structure prediction (CSP) methods substantially increased the level of complexity of the target compounds relative to the previous tests organized by the Cambridge Crystallographic Data Centre. In this work, the performance of density-functional methods is assessed using numerical atomic orbitals and the exchange-hole dipole moment dispersion correction (XDM) for the energy-ranking phase of the seventh blind test. Overall, excellent performance was seen for the two rigid molecules (XXVII, XXVIII) and for the organic salt (XXXIII). However, for the agrochemical (XXXI) and pharmaceutical (XXXII) targets, the experimental polymorphs were ranked fairly high in energy amongst the provided candidate structures and inclusion of thermal free-energy corrections from the lattice vibrations was found to be essential for compound XXXI. Based on these results, it is proposed that the importance of vibrational free-energy corrections increases with the number of rotatable bonds.
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Affiliation(s)
- R. Alex Mayo
- Department of ChemistryDalhousie University6243 Alumni CrescentHalifaxNova ScotiaB3H 4R2Canada
| | - Alastair J. A. Price
- Department of ChemistryDalhousie University6243 Alumni CrescentHalifaxNova ScotiaB3H 4R2Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de QuímicaUniversidad de Oviedo33006OviedoSpain
| | - Erin R. Johnson
- Department of ChemistryDalhousie University6243 Alumni CrescentHalifaxNova ScotiaB3H 4R2Canada
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Wu EJ, Kelly AW, Iuzzolino L, Lee AY, Zhu X. Unprecedented Packing Polymorphism of Oxindole: An Exploration Inspired by Crystal Structure Prediction. Angew Chem Int Ed Engl 2024; 63:e202406214. [PMID: 38825853 DOI: 10.1002/anie.202406214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Crystal polymorphism, characterized by different packing arrangements of the same compound, strongly ties to the physical properties of a molecule. Determining the polymorphic landscape is complex and time-consuming, with the number of experimentally observed polymorphs varying widely from molecule to molecule. Furthermore, disappearing polymorphs, the phenomenon whereby experimentally observed forms cannot be reproduced, pose a significant challenge for the pharmaceutical industry. Herein, we focused on oxindole (OX), a small rigid molecule with four known polymorphs, including a reported disappearing form. Using crystal structure prediction (CSP), we assessed OX solid-state landscape and thermodynamic stability by comparing predicted structures with experimentally known forms. We then performed melt and solution crystallization in bulk and nanoconfinement to validate our predictions. These experiments successfully reproduced the known forms and led to the discovery of four novel polymorphs. Our approach provided insights into reconstructing disappearing polymorphs and building more comprehensive polymorph landscapes. These results also establish a new record of packing polymorphism for rigid molecules.
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Affiliation(s)
- Emily J Wu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Andrew W Kelly
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Luca Iuzzolino
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Alfred Y Lee
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Xiaolong Zhu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
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4
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Pham KN, Modrzejewski M, Klimeš J. Contributions beyond direct random-phase approximation in the binding energy of solid ethane, ethylene, and acetylene. J Chem Phys 2024; 160:224101. [PMID: 38856055 DOI: 10.1063/5.0207090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024] Open
Abstract
The random-phase approximation (RPA) includes a subset of higher than second-order correlation-energy contributions, but stays in the same complexity class as the second-order Møller-Plesset perturbation theory (MP2) in both Gaussian-orbital and plane-wave codes. This makes RPA a promising ab initio electronic structure approach for the binding energies of molecular crystals. Still, some issues stand out in practical applications of RPA. Notably, compact clusters of nonpolar molecules are poorly described, and the interaction energies strongly depend on the reference single-determinant state. Using the many-body expansion of the binding energy of a crystal, we investigate those issues and the effect of beyond-RPA corrections. We find the beneficial effect of quartic-scaling exchange and non-ring coupled-cluster doubles corrections. The nonadditive interactions in compact trimers of molecules are improved by using the self-consistent Hartree-Fock orbitals instead of the usual Kohn-Sham states, but this kind of orbital input also leads to underestimated dimer energies. Overall, a substantial improvement over the RPA with a renormalized singles approach is possible at a modest quartic-scaling cost, which encourages further research into additional RPA corrections.
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Affiliation(s)
- Khanh Ngoc Pham
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
| | - Marcin Modrzejewski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Jiří Klimeš
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
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5
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Dittrich B, Connor LE, Fabbiani FPA, Piechon P. Linking solid-state phenomena via energy differences in `archetype crystal structures'. IUCRJ 2024; 11:347-358. [PMID: 38629168 PMCID: PMC11067740 DOI: 10.1107/s2052252524002641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/20/2024] [Indexed: 05/04/2024]
Abstract
Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.
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Affiliation(s)
- B. Dittrich
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
- Mathematisch Naturwiss. Fakultät, Universität Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | - L. E. Connor
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
| | - F. P. A. Fabbiani
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
| | - P. Piechon
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
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6
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Ye Z, Wang N, Zhou J, Ouyang D. Organic crystal structure prediction via coupled generative adversarial networks and graph convolutional networks. Innovation (N Y) 2024; 5:100562. [PMID: 38379785 PMCID: PMC10878116 DOI: 10.1016/j.xinn.2023.100562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024] Open
Abstract
Organic crystal structures exert a profound impact on the physicochemical properties and biological effects of organic compounds. Quantum mechanics (QM)-based crystal structure predictions (CSPs) have somewhat alleviated the dilemma that experimental crystal structure investigations struggle to conduct complete polymorphism studies, but the high computing cost poses a challenge to its widespread application. The present study aims to construct DeepCSP, a feasible pure machine learning framework for minute-scale rapid organic CSP. Initially, based on 177,746 data entries from the Cambridge Crystal Structure Database, a generative adversarial network was built to conditionally generate trial crystal structures under selected feature constraints for the given molecule. Simultaneously, a graph convolutional attention network was used to predict the density of stable crystal structures for the input molecule. Subsequently, the distances between the predicted density and the definition-based calculated density would be considered to be the crystal structure screening and ranking basis, and finally, the density-based crystal structure ranking would be output. Two such distinct algorithms, performing the generation and ranking functionalities, respectively, collectively constitute the DeepCSP, which has demonstrated compelling performance in marketed drug validations, achieving an accuracy rate exceeding 80% and a hit rate surpassing 85%. Inspiringly, the computing speed of the pure machine learning methodology demonstrates the potential of artificial intelligence in advancing CSP research.
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Affiliation(s)
- Zhuyifan Ye
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Nannan Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
| | - Jiantao Zhou
- State Key Laboratory of Internet of Things for Smart City, University of Macau, Macau 999078, China
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Macau 999078, China
| | - Defang Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau 999078, China
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7
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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8
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Firaha D, Liu YM, van de Streek J, Sasikumar K, Dietrich H, Helfferich J, Aerts L, Braun DE, Broo A, DiPasquale AG, Lee AY, Le Meur S, Nilsson Lill SO, Lunsmann WJ, Mattei A, Muglia P, Putra OD, Raoui M, Reutzel-Edens SM, Rome S, Sheikh AY, Tkatchenko A, Woollam GR, Neumann MA. Predicting crystal form stability under real-world conditions. Nature 2023; 623:324-328. [PMID: 37938708 PMCID: PMC10632141 DOI: 10.1038/s41586-023-06587-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/30/2023] [Indexed: 11/09/2023]
Abstract
The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.
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Affiliation(s)
| | | | | | | | | | - Julian Helfferich
- Avant-garde Materials Simulation, Merzhausen, Germany
- JobRad, Freiburg, Germany
| | - Luc Aerts
- UCB Pharma SA, Chemin du Foriest, Braine-l'Alleud, Belgium
| | - Doris E Braun
- Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Anders Broo
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal, Sweden
| | | | - Alfred Y Lee
- Merck, Analytical Research & Development, Rahway, NJ, USA
| | - Sarah Le Meur
- UCB Pharma SA, Chemin du Foriest, Braine-l'Alleud, Belgium
| | - Sten O Nilsson Lill
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal, Sweden
| | | | - Alessandra Mattei
- Solid State Chemistry, Research & Development, AbbVie, North Chicago, IL, USA
| | | | - Okky Dwichandra Putra
- Early Product Development and Manufacturing, Pharmaceutical Sciences R&D, AstraZeneca Gothenburg, Mölndal, Sweden
| | | | - Susan M Reutzel-Edens
- Cambridge Crystallographic Data Centre, Cambridge, UK
- SuRE Pharma Consulting, Zionsville, IN, USA
| | - Sandrine Rome
- UCB Pharma SA, Chemin du Foriest, Braine-l'Alleud, Belgium
| | - Ahmad Y Sheikh
- Solid State Chemistry, Research & Development, AbbVie, North Chicago, IL, USA
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City, Luxembourg
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9
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Gui Y. Solid Form Screenings in Pharmaceutical Development: a Perspective on Current Practices. Pharm Res 2023; 40:2347-2354. [PMID: 37537423 DOI: 10.1007/s11095-023-03573-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Solid form screening is a crucial step in new drug development because solid forms of a drug substance significantly affect stability, dissolution and manufacturing processes of its drug products. This perspective introduces solid-state science from a practical standpoint, aiming to reduce knowledge gaps and promote communications among scientists with diverse background. This perspective starts with a concise overview that followed by discussion on timeline and goals of solid form screening. Techniques for solid from identification and characterization are then discussed. Subsequently, the perspective presents commonly used methods in solid form screening and introduces criteria and strategies to effectively select a favorable solid form based on screening results. The last section summarizes current practices in pharmaceutical industries and suggests potential opportunities for future research and development.
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Affiliation(s)
- Yue Gui
- China Innovation Center of Roche, Building 5, 371 Lishizhen Road, Shanghai, China.
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10
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Rietveld IB, Barrio M, Ceolin R, Tamarit JL. An unexpected high-pressure stability domain for a lower density polymorph of benzophenone. Sci Rep 2023; 13:11914. [PMID: 37488270 PMCID: PMC10366203 DOI: 10.1038/s41598-023-38985-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
For over a century, it was thought that the crystalline polymorph II of benzophenone does not possess a stable domain in the pressure-temperature phase diagram. With a combination of new experimental results and literature data, this case of crystalline dimorphism has finally been solved and it is shown that form II possesses a stable domain at high pressure and high temperature, even though its density is lower than that of form I, the stable form under ordinary pressure and temperature conditions. The phase diagram of benzophenone is a clear demonstration of the fact that to understand the phase behaviour of a chemical substance both the exchange of heat (due to the change in intermolecular interactions) and work (due to the change of volume at a given pressure) need to be taken into account.
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Affiliation(s)
- I B Rietveld
- SMS Laboratory (UR 3233, Université Rouen-Normandie, Place Émile Blondel, 76821, Mont Saint Aignan, France.
- Faculté de Pharmacie, Université Paris Cité, 4 Avenue de l'observatoire, 75006, Paris, France.
| | - M Barrio
- Grup de Caracterització de Materials, Departament de Física and Barcelona Research Centre in Multiscale Science and Engineering Universitat Politècnica de Catalunya, EEBE, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, 08019, Barcelona, Catalonia, Spain
| | - R Ceolin
- Grup de Caracterització de Materials, Departament de Física and Barcelona Research Centre in Multiscale Science and Engineering Universitat Politècnica de Catalunya, EEBE, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, 08019, Barcelona, Catalonia, Spain
| | - J Ll Tamarit
- Grup de Caracterització de Materials, Departament de Física and Barcelona Research Centre in Multiscale Science and Engineering Universitat Politècnica de Catalunya, EEBE, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, 08019, Barcelona, Catalonia, Spain
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11
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Chew PY, Reinhardt A. Phase diagrams-Why they matter and how to predict them. J Chem Phys 2023; 158:030902. [PMID: 36681642 DOI: 10.1063/5.0131028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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12
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Rana B, Beran GJO, Herbert JM. Correcting π-delocalisation errors in conformational energies using density-corrected DFT, with application to crystal polymorphs. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2138789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | | | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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13
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Tuca E, DiLabio G, Otero-de-la-Roza A. Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction. J Chem Inf Model 2022; 62:4107-4121. [PMID: 35980964 DOI: 10.1021/acs.jcim.2c00656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Crystal structure prediction (CSP), determining the experimentally observable structure of a molecular crystal from the molecular diagram, is an important challenge with technologically relevant applications in materials manufacturing and drug design. For the purpose of screening the randomly generated candidate crystal structures, CSP protocols require energy ranking methods that are fast and can accurately capture the small energy differences between molecular crystals. In addition, a good ranking method should also produce accurate equilibrium geometries, both intramolecular and intermolecular. In this article, we explore the combination of minimal-basis-set Hartree-Fock (HF) with atom-centered potentials (ACPs) as a method for modeling the structure and energetics of molecular crystals. The ACPs are developed for the H, C, N, and O atoms and fitted to a set of reference data at the B86bPBE-XDM level in order to mitigate basis-set incompleteness and missing correlation. In particular, ACPs are developed in combination with two methods: HF-D3/MINIs and HF-3c. The application of ACPs greatly improves the performance of HF-D3/MINIs for lattice energies, crystal energy differences, energy-volume and energy-strain relations, and crystal geometries. In the case of HF-3c, the improvement in the crystal energy differences is much smaller than in HF-D3/MINIs, but lattice energies and particularly crystal geometries are considerably better when ACPs are used. The resulting methods may be useful for CSP but also for quick calculation of molecular crystal lattice energies and geometries.
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Affiliation(s)
- Emilian Tuca
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna V1 V 1 V7, British Columbia, Canada
| | - Gino DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna V1 V 1 V7, British Columbia, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
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14
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Mattei A, Hong RS, Dietrich H, Firaha D, Helfferich J, Liu YM, Sasikumar K, Abraham NS, Miglani Bhardwaj R, Neumann MA, Sheikh AY. Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields. J Chem Theory Comput 2022; 18:5725-5738. [PMID: 35930763 PMCID: PMC9476662 DOI: 10.1021/acs.jctc.2c00451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Crystal structure prediction (CSP) his generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.
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Affiliation(s)
- Alessandra Mattei
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Richard S Hong
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hanno Dietrich
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Dzmitry Firaha
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Julian Helfferich
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Yifei Michelle Liu
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Kiran Sasikumar
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Nathan S Abraham
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marcus A Neumann
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Ahmad Y Sheikh
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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15
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Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
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Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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16
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Habermehl S, Schlesinger C, Schmidt MU. Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross-correlation functions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:195-213. [PMID: 35411858 PMCID: PMC9004021 DOI: 10.1107/s2052520622001500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/08/2022] [Indexed: 06/02/2023]
Abstract
A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II).
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Affiliation(s)
- Stefan Habermehl
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Carina Schlesinger
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin U. Schmidt
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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17
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Beran GJO, Sugden IJ, Greenwell C, Bowskill DH, Pantelides CC, Adjiman CS. How many more polymorphs of ROY remain undiscovered. Chem Sci 2022; 13:1288-1297. [PMID: 35222912 PMCID: PMC8809489 DOI: 10.1039/d1sc06074k] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (a.k.a. ROY) holds the current record for the largest number of fully characterized organic crystal polymorphs. Four of these polymorph structures have been reported since 2019, raising the question of how many more ROY polymorphs await future discovery. Employing crystal structure prediction and accurate energy rankings derived from conformational energy-corrected density functional theory, this study presents the first crystal energy landscape for ROY that agrees well with experiment. The lattice energies suggest that the seven most stable ROY polymorphs (and nine of the twelve lowest-energy forms) on the Z' = 1 landscape have already been discovered experimentally. Discovering any new polymorphs at ambient pressure will likely require specialized crystallization techniques capable of trapping metastable forms. At pressures above 10 GPa, however, a new crystal form is predicted to become enthalpically more stable than all known polymorphs, suggesting that further high-pressure experiments on ROY may be warranted. This work highlights the value of high-accuracy crystal structure prediction for solid-form screening and demonstrates how pragmatic conformational energy corrections can overcome the limitations of conventional density functionals for conformational polymorphs.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - Isaac J Sugden
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Chandler Greenwell
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - David H Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Constantinos C Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Claire S Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
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18
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Sugden IJ, Francia NF, Jensen T, Adjiman CS, Salvalaglio M. Rationalising the difference in crystallisability of two sulflowers using efficient in silico methods. CrystEngComm 2022. [DOI: 10.1039/d2ce00942k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular structures of the first and second generation sulflowers, sulflower and persulfurated coronene (PSC), are remarkably similar: carbon ring structures decorated with sulfur atoms, without any additional moiety.
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Affiliation(s)
- Isaac J. Sugden
- Molecular Systems Engineering Group, Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Nicholas F. Francia
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK
| | - Torsten Jensen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Claire S. Adjiman
- Molecular Systems Engineering Group, Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK
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19
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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20
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Carpenter JE, Grünwald M. Pre-Nucleation Clusters Predict Crystal Structures in Models of Chiral Molecules. J Am Chem Soc 2021; 143:21580-21593. [PMID: 34918909 DOI: 10.1021/jacs.1c09321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kinetics can play an important role in the crystallization of molecules and can give rise to polymorphism, the tendency of molecules to form more than one crystal structure. Current computational methods of crystal structure prediction, however, focus almost exclusively on identifying the thermodynamically stable polymorph. Kinetic factors of nucleation and growth are often neglected because the underlying microscopic processes can be complex and accurate rate calculations are numerically cumbersome. In this work, we use molecular dynamics computer simulations to study simple molecular models that reproduce the crystallization behavior of real chiral molecules, including the formation of enantiopure and racemic crystals, as well as polymorphism. A significant fraction of these molecules forms crystals that do not have the lowest free energy. We demonstrate that at high supersaturation crystal formation can be accurately predicted by considering the similarities between oligomeric species in solution and molecular motifs in the crystal structure. For the case of racemic mixtures, we even find that knowledge of crystal free energies is not necessary and kinetic considerations are sufficient to determine if the system will undergo spontaneous chiral separation. Our results suggest conceptually simple ways of improving current crystal structure prediction methods.
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Affiliation(s)
- John E Carpenter
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Michael Grünwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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21
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Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. J Am Chem Soc 2021; 143:17479-17491. [PMID: 34637297 DOI: 10.1021/jacs.1c06837] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.
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Affiliation(s)
- Ahmad Y Sheikh
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Richard S Hong
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Nathan S Abraham
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gabriela Schneider-Rauber
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenneth M Engstrom
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Moiz Diwan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rodger F Henry
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Yi Gao
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Vivian Juarez
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Erin Jordan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - David A DeGoey
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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22
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Mayo RA, Johnson ER. Improved quantitative crystal-structure comparison using powder diffractograms via anisotropic volume correction. CrystEngComm 2021. [DOI: 10.1039/d1ce01058a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A new anisotropic volume correction improves quantitative crystal structure comparison. Benchmarking against the 6th crystal structure prediction blind test data results in identification of two previously uncredited matching structures.
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Affiliation(s)
- R. Alex Mayo
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
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23
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Li X, Wang N, Yang J, Huang Y, Ji X, Huang X, Wang T, Wang H, Hao H. Molecular conformational evolution mechanism during nucleation of crystals in solution. IUCRJ 2020; 7:542-556. [PMID: 32431837 PMCID: PMC7201291 DOI: 10.1107/s2052252520004959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/07/2020] [Indexed: 05/24/2023]
Abstract
Nucleation of crystals from solution is fundamental to many natural and industrial processes. In this work, the molecular mechanism of conformational polymorphism nucleation and the links between the molecular conformation in solutions and in crystals were investigated in detail by using 5-nitro-furazone as the model compound. Different polymorphs were prepared, and the conformations in solutions obtained by dissolving different polymorphs were analysed and compared. The solutions of 5-nitro-furazone were proven to contain multiple conformers through quantum chemical computation, Raman spectra analysis, 2D nuclear Overhauser effect spectroscopy spectra analysis and molecular dynamics simulation. The conformational evolution and desolvation path was illustrated according to the 1H NMR spectra of solutions with different concentrations. Finally, based on all the above analysis, the molecular conformational evolution path during nucleation of 5-nitro-furazone was illustrated. The results presented in this work shed a new light on the molecular mechanism of conformational polymorphism nucleation in solution.
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Affiliation(s)
- Xin Li
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Na Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Jinyue Yang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Yunhai Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiongtao Ji
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Ting Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Honghai Wang
- School of Chemical Engineering, Hebei University of Technology, Tianjin 300130, People’s Republic of China
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
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24
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Liu Y, Gabriele B, Davey RJ, Cruz-Cabeza AJ. Concerning Elusive Crystal Forms: The Case of Paracetamol. J Am Chem Soc 2020; 142:6682-6689. [DOI: 10.1021/jacs.0c00321] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yumin Liu
- School of Chemical Engineering and Technology, Collaborative Innovation Center of Chemical Science and Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Benjamin Gabriele
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Roger J. Davey
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Aurora J. Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
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25
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Greenwell C, McKinley JL, Zhang P, Zeng Q, Sun G, Li B, Wen S, Beran GJO. Overcoming the difficulties of predicting conformational polymorph energetics in molecular crystals via correlated wavefunction methods. Chem Sci 2020; 11:2200-2214. [PMID: 32190277 PMCID: PMC7059316 DOI: 10.1039/c9sc05689k] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Molecular crystal structure prediction is increasingly being applied to study the solid form landscapes of larger, more flexible pharmaceutical molecules. Despite many successes in crystal structure prediction, van der Waals-inclusive density functional theory (DFT) methods exhibit serious failures predicting the polymorph stabilities for a number of systems exhibiting conformational polymorphism, where changes in intramolecular conformation lead to different intermolecular crystal packings. Here, the stabilities of the conformational polymorphs of o-acetamidobenzamide, ROY, and oxalyl dihydrazide are examined in detail. DFT functionals that have previously been very successful in crystal structure prediction perform poorly in all three systems, due primarily to the poor intramolecular conformational energies, but also due to the intermolecular description in oxalyl dihydrazide. In all three cases, a fragment-based dispersion-corrected second-order Møller-Plesset perturbation theory (MP2D) treatment of the crystals overcomes these difficulties and predicts conformational polymorph stabilities in good agreement with experiment. These results highlight the need for methods which go beyond current-generation DFT functionals to make crystal polymorph stability predictions truly reliable.
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Affiliation(s)
- Chandler Greenwell
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Peiyu Zhang
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Qun Zeng
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Guangxu Sun
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Bochen Li
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Shuhao Wen
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
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26
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The Polymorphism of Drugs: New Approaches to the Synthesis of Nanostructured Polymorphs. Pharmaceutics 2020; 12:pharmaceutics12010034. [PMID: 31906357 PMCID: PMC7022426 DOI: 10.3390/pharmaceutics12010034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/12/2019] [Accepted: 12/25/2019] [Indexed: 11/24/2022] Open
Abstract
Among the significant problems of modern pharmacology are the low solubility and bioavailability of drugs. One way to resolve this problem is to obtain new polymorphic forms of drugs with improved physicochemical properties. Various approaches have been developed with this aim, including the preparation of co-crystals, the use of nanoparticles, or the use of compounds in the form of a salt. A promising direction in pharmacology concerns the production of new stable polymorphic structures. In this mini-review, we consider certain aspects of drug polymorphism, methods for the synthesis of polymorphs, and the stability, size, and transformation of crystalline polymorphs. Moreover, we summarize our results from several studies demonstrating the problems associated with the synthesis of new polymorphous modifications based on inert gases and cryotemperatures. The results indicate that the problems specific to drug polymorphisms have only been partly resolved, are of current interest, and require further development.
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27
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Braun DE. Experimental and computational approaches to rationalise multicomponent supramolecular assemblies: dapsone monosolvates. Phys Chem Chem Phys 2019; 21:17288-17305. [PMID: 31348477 DOI: 10.1039/c9cp02572c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The monosolvate crystal energy landscapes of dapsone (DDS) including the solvents carbon tetrachloride, acetone, cyclohexanone, dimethyl formamide, tetrahydrofuran, methyl ethyl ketone, 1,2-dichloroethane, 1,4-dioxane, dichloromethane and chloroform were established using experimental and computational approaches. To rationalise and understand solvate formation, solvate stability and desolvation reactions a careful control of the experimental crystallisation and storage conditions, a range of thermoanalytical methods and crystal structure prediction were required. Six of the eight DDS monosolvates are reported and characterised for the first time. Structural similarity and diversity of the at ambient conditions unstable monosolvates were apparent from the computed crystal energy landscapes, which had the experimental packings as lowest energy structures. The computed structures were used as input for Rietveld refinements and isostructurality of four of the monosolvates was confirmed. Packing comparisons of the solvate structures and molecular properties of the solvent molecules indicated that both size/shape of the solvent molecule and the possible DDSsolvent interactions are the important factors for DDS solvate formation. Through the combination of experiment and theory solvate stability and structural features have been rationalised.
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Affiliation(s)
- Doris E Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
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28
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Bhardwaj RM, McMahon JA, Nyman J, Price LS, Konar S, Oswald IDH, Pulham CR, Price SL, Reutzel-Edens SM. A Prolific Solvate Former, Galunisertib, under the Pressure of Crystal Structure Prediction, Produces Ten Diverse Polymorphs. J Am Chem Soc 2019; 141:13887-13897. [DOI: 10.1021/jacs.9b06634] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajni M. Bhardwaj
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jennifer A. McMahon
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jonas Nyman
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Sumit Konar
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Iain D. H. Oswald
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow G4 0RE, U.K
| | - Colin R. Pulham
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Susan M. Reutzel-Edens
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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29
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Mortazavi M, Hoja J, Aerts L, Quéré L, van de Streek J, Neumann MA, Tkatchenko A. Computational polymorph screening reveals late-appearing and poorly-soluble form of rotigotine. Commun Chem 2019. [DOI: 10.1038/s42004-019-0171-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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30
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van de Streek J, Alig E, Parsons S, Vella-Zarb L. A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data. IUCRJ 2019; 6:136-144. [PMID: 30713711 PMCID: PMC6327187 DOI: 10.1107/s205225251801686x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase. The anisotropic displacement parameters calculated from the MD simulations readily identified libration as the driving force behind the phase transition. Both the predicted crystal structure and the phase-transition mechanism were verified experimentally using TLS (translation, libration, screw) refinement against X-ray powder diffraction data.
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Affiliation(s)
- Jacco van de Streek
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
- Institute for Inorganic and Analytical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Edith Alig
- Institute for Inorganic and Analytical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Simon Parsons
- School of Chemistry/Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh, UK
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31
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Nyman J, Yu L, Reutzel-Edens SM. Accuracy and reproducibility in crystal structure prediction: the curious case of ROY. CrystEngComm 2019. [DOI: 10.1039/c8ce01902a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Because of excessive electron delocalization, the polymorphs of ROY constitute a surprisingly challenging system for crystal structure prediction.
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Affiliation(s)
- Jonas Nyman
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
- Small Molecule Design & Development
| | - Lian Yu
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
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