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Fleischer CH, Holmes ST, Levin K, Veinberg SL, Schurko RW. Characterization of ephedrine HCl and pseudoephedrine HCl using quadrupolar NMR crystallography guided crystal structure prediction. Faraday Discuss 2025; 255:88-118. [PMID: 39308395 DOI: 10.1039/d4fd00089g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
Abstract
Quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) is a nascent protocol for predicting, solving, and refining crystal structures. QNMRX-CSP employs a combination of solid-state NMR data from quadrupolar nuclides (i.e., nuclear spin >1/2), static lattice energies and electric field gradient (EFG) tensors from dispersion-corrected density functional theory (DFT-D2*) calculations, and powder X-ray diffraction (PXRD) data; however, it has so far been applied only to organic HCl salts with small and rigid organic components, using 35Cl EFG tensor data for both structural refinement and validation. Herein, QNMRX-CSP is extended to ephedrine HCl (Eph) and pseudoephedrine HCl (Pse), which are diastereomeric compounds that feature distinct space groups and organic components that are larger and more flexible. A series of benchmarking calculations are used to generate structural models that are validated against experimental data, and to explore the impacts of the: (i) starting structural models (i.e., geometry-optimized fragments based on either a known crystal structure or an isolated gas-phase molecule) and (ii) selection of unit cell parameters and space groups. Finally, we use QNMRX-CSP to predict the structure of Pse in the dosage form Sudafed® using only 35Cl SSNMR data as experimental input. This proof-of-concept work suggests the possibility of employing QNMRX-CSP to solve the structures of organic HCl salts in dosage forms - something which is often beyond the capabilities of conventional, diffraction-based characterization methods.
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Affiliation(s)
- Carl H Fleischer
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Kirill Levin
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Stanislav L Veinberg
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
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2
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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, 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] [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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Beran GJO, Cook CJ, Unzueta PA. Contrasting conformational behaviors of molecules XXXI and XXXII in the seventh blind test of crystal structure prediction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624005043. [PMID: 39405195 PMCID: PMC11789167 DOI: 10.1107/s2052520624005043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/29/2024] [Indexed: 02/05/2025]
Abstract
Accurate modeling of conformational energies is key to the crystal structure prediction of conformational polymorphs. Focusing on molecules XXXI and XXXII from the seventh blind test of crystal structure prediction, this study employs various electronic structure methods up to the level of domain-local pair natural orbital coupled cluster singles and doubles with perturbative triples [DLPNO-CCSD(T1)] to benchmark the conformational energies and to assess their impact on the crystal energy landscapes. Molecule XXXI proves to be a relatively straightforward case, with the conformational energies from generalized gradient approximation (GGA) functional B86bPBE-XDM changing only modestly when using more advanced density functionals such as PBE0-D4, ωB97M-V, and revDSD-PBEP86-D4, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D), or DLPNO-CCSD(T1). In contrast, the conformational energies of molecule XXXII prove difficult to determine reliably, and variations in the computed conformational energies appreciably impact the crystal energy landscape. Even high-level methods such as revDSD-PBEP86-D4 and SCS-MP2D exhibit significant disagreements with the DLPNO-CCSD(T1) benchmarks for molecule XXXII, highlighting the difficulty of predicting conformational energies for complex, drug-like molecules. The best-converged predicted crystal energy landscape obtained here for molecule XXXII disagrees significantly with what has been inferred about the solid-form landscape experimentally. The identified limitations of the calculations are probably insufficient to account for the discrepancies between theory and experiment on molecule XXXII, and further investigation of the experimental solid-form landscape would be valuable. Finally, assessment of several semi-empirical methods finds r2SCAN-3c to be the most promising, with conformational energy accuracy intermediate between the GGA and hybrid functionals and a low computational cost.
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Affiliation(s)
| | - Cameron J. Cook
- Department of ChemistryUniversity of CaliforniaRiversideCA92521USA
| | - Pablo A. Unzueta
- Department of ChemistryUniversity of CaliforniaRiversideCA92521USA
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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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Hunnisett LM, Nyman J, Francia N, Abraham NS, Adjiman CS, Aitipamula S, Alkhidir T, Almehairbi M, Anelli A, Anstine DM, Anthony JE, Arnold JE, Bahrami F, Bellucci MA, Bhardwaj RM, Bier I, Bis JA, Boese AD, Bowskill DH, Bramley J, Brandenburg JG, Braun DE, Butler PWV, Cadden J, Carino S, Chan EJ, Chang C, Cheng B, Clarke SM, Coles SJ, Cooper RI, Couch R, Cuadrado R, Darden T, Day GM, Dietrich H, Ding Y, DiPasquale A, Dhokale B, van Eijck BP, Elsegood MRJ, Firaha D, Fu W, Fukuzawa K, Glover J, Goto H, Greenwell C, Guo R, Harter J, Helfferich J, Hofmann DWM, Hoja J, Hone J, Hong R, Hutchison G, Ikabata Y, Isayev O, Ishaque O, Jain V, Jin Y, Jing A, Johnson ER, Jones I, Jose KVJ, Kabova EA, Keates A, Kelly PF, Khakimov D, Konstantinopoulos S, Kuleshova LN, Li H, Lin X, List A, Liu C, Liu YM, Liu Z, Liu ZP, Lubach JW, Marom N, Maryewski AA, Matsui H, Mattei A, Mayo RA, Melkumov JW, 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, Pantelides CC, Parkin S, Pickard CJ, Pilia L, Pivina T, 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, Salvalaglio M, Sanders de Almada L, Sasikumar K, Sekharan S, Shang C, Shankland K, Shinohara K, Shi B, Shi X, Skillman AG, Song H, Strasser N, van de Streek J, Sugden IJ, Sun G, Szalewicz K, Tan BI, Tan L, Tarczynski F, Taylor CR, Tkatchenko A, Tom R, Tuckerman ME, Utsumi Y, Vogt-Maranto L, Weatherston J, Wilkinson LJ, Willacy RD, Wojtas L, Woollam GR, Yang Z, Yonemochi E, Yue X, Zeng Q, Zhang Y, Zhou T, Zhou Y, Zubatyuk R, Cole JC. The seventh blind test of crystal structure prediction: structure generation methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624007492. [PMID: 39405196 PMCID: PMC11789161 DOI: 10.1107/s2052520624007492] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 02/05/2025]
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.
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Affiliation(s)
- Lily M Hunnisett
- 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
| | - Nicholas Francia
- 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
| | - Claire S Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Srinivasulu Aitipamula
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
| | - Tamador Alkhidir
- Green Chemistry and Materials Modelling Laboratory, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mubarak Almehairbi
- Green Chemistry and Materials Modelling Laboratory, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Andrea Anelli
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dylan M Anstine
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - John E Anthony
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Joseph E Arnold
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Faezeh Bahrami
- Department of Chemistry, Faculty of Science, Science Boulevard, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Rajni M Bhardwaj
- AbbVie Inc., Research & Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | - Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Joanna A Bis
- Catalent Pharma Solutions, 160 Pharma Drive, Morrisville, NC 27560, USA
| | - A Daniel Boese
- University of Graz, Department of Chemistry, Heinrichstrasse 28, Graz, Austria
| | - David H Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - James Bramley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Jan Gerit Brandenburg
- Group Science and Technology Office, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Doris E Braun
- University of Innsbruck, Institute of Pharmacy, Innrain 52c, A-6020 Innsbruck, Austria
| | - Patrick W V Butler
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Joseph Cadden
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
| | - Stephen Carino
- Catalent Pharma Solutions, 160 Pharma Drive, Morrisville, NC 27560, USA
| | - Eric J Chan
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Chao Chang
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - Bingqing Cheng
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Sarah M Clarke
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Dalhousie, Halifax, Canada
| | - Simon J Coles
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Richard I Cooper
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ricky Couch
- Catalent Pharma Solutions, 160 Pharma Drive, Morrisville, NC 27560, USA
| | - Ramon Cuadrado
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Tom Darden
- OpenEye Scientific Software, 9 Bisbee Court, Santa Fe, NM 87508, USA
| | - Graeme M Day
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Hanno Dietrich
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Yiming Ding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | | | - Bhausaheb Dhokale
- 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
| | - Mark R J Elsegood
- Chemistry Department, Loughborough University, Loughborough LE11 3TU, UK
| | - 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
| | - Joseph Glover
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Hitoshi Goto
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, 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
- University of Graz, Department of Chemistry, Heinrichstrasse 28, Graz, Austria
| | - 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
| | - Geoffrey Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
| | - 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 Delaware, Newark, 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 Delaware, Newark, DE 19716, USA
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Dalhousie, Halifax, Canada
| | - 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 C.R. 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 University, Loughborough LE11 3TU, UK
| | - Dmitry Khakimov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninskiy Prospekt 47, Moscow 119991, Russia
| | - Stefanos Konstantinopoulos
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | | | - 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
- University of Graz, Department of Chemistry, Heinrichstrasse 28, Graz, Austria
| | - 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
| | - Zhi Pan Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Key Laboratory of Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Joseph W Lubach
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Alexander A Maryewski
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - 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, Halifax, Canada
| | - John W Melkumov
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Sharmarke Mohamed
- Green Chemistry and Materials Modelling Laboratory, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | | | - Hari S Muddana
- OpenEye Scientific Software, 9 Bisbee Court, Santa Fe, NM 87508, USA
| | - Naofumi Nakayama
- CONFLEX Corporation, Shinagawa Center building 6F, 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, 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 Delaware, Newark, DE 19716, USA
| | - Shigeaki Obata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, 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 Moscow, Russia
| | - 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 Oviedo, Spain
| | - Constantinos C Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Sean Parkin
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Chris J Pickard
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK
| | - Luca Pilia
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, Via Marengo 2, 09123 Cagliari, Italy
| | - Tatyana Pivina
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninskiy Prospekt 47, Moscow 119991, Russia
| | - Rafał Podeszwa
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, 40-006 Katowice, Poland
| | - Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Dalhousie, Halifax, Canada
| | - 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 C.R. Rao Road, Gachibowli, Hyderabad, 500046 Telangana, India
| | - Atta Ur Rehman
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | | | - Jutta Rogal
- Faculty of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, 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, Halifax, Canada
| | - 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 Dhabi, United Arab Emirates
| | - Alireza Salimi
- Department of Chemistry, Faculty of Science, Science Boulevard, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Leticia Sanders de Almada
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Kiran Sasikumar
- Avant-garde Materials Simulation, Alte Strasse 2, 79249 Merzhausen, Germany
| | - Sivakumar Sekharan
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Cheng Shang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Key Laboratory of Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Kenneth Shankland
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Kotaro Shinohara
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa 992-8510, Yamagata, Japan
| | - 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
| | - A Geoffrey Skillman
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Dalhousie, Halifax, Canada
| | - Hongxing Song
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Nina Strasser
- University of Graz, Department of Chemistry, Heinrichstrasse 28, Graz, Austria
| | | | - 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 Delaware, Newark, DE 19716, USA
| | - Benjamin I Tan
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - Lu Tan
- XtalPi Inc., International Biomedical Innovation Park II 3F 2 Hongliu Road, Futian District, Shenzhen, Guangdong, China
| | - 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
| | - Mark E Tuckerman
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, 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 University, Loughborough 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
| | | | - 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
| | - Yizu Zhang
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
| | - 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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Bowskill DH, Tan BI, Keates A, Sugden IJ, Adjiman CS, Pantelides CC. Large-Scale Parameter Estimation for Crystal Structure Prediction. Part 1: Dataset, Methodology, and Implementation. J Chem Theory Comput 2024; 20:10288-10315. [PMID: 39531362 PMCID: PMC11603618 DOI: 10.1021/acs.jctc.4c01091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/04/2024] [Accepted: 10/08/2024] [Indexed: 11/16/2024]
Abstract
Crystal structure prediction (CSP) seeks to identify all thermodynamically accessible solid forms of a given compound and, crucially, to establish the relative thermodynamic stability between different polymorphs. The conventional hierarchical CSP workflow suggests that no single energy model can fulfill the needs of all stages in the workflow, and energy models across a spectrum of fidelities and computational costs are required. Hybrid ab initio/empirical force-field (HAIEFF) models have demonstrated a good balance of these two factors, but the force-field component presents a major bottleneck for model accuracy. Existing parameter estimation tools for fitting this empirical component are inefficient and have severe limitations on the manageable problem size. This, combined with a lack of reliable reference data for parameter fitting, has resulted in development in the force-field component of HAIEFF models having mostly stagnated. In this work, we address these barriers to progress. First, we introduce a curated database of 755 organic crystal structures, obtained using high quality, solid-state DFT-D calculations, which provide a complete set of geometry and energy data. Comparisons to various theoretical and experimental data sources indicate that this database provides suitable diversity for parameter fitting. In tandem, we also put forward a new parameter estimation algorithm implemented as the CrystalEstimator program. Our tests demonstrate that CrystalEstimator is capable of efficiently handling large-scale parameter estimation problems, simultaneously fitting as many as 62 model parameters based on data from 445 structures. This problem size far exceeds any previously reported works related to CSP force-field parametrization. These developments form a strong foundation for all future work involving parameter estimation of transferable or tailor-made force-fields for HAIEFF models. This ultimately opens the way for significant improvements in the accuracy achieved by the HAIEFF models.
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Affiliation(s)
- D. H. Bowskill
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering
and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - B. I. Tan
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering
and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - A. Keates
- Process
Studies Group, Syngenta, Jealott’s
Hill International Research Centre, Bracknell, Berkshire RG42
6EY, U.K.
| | - I. J. Sugden
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering
and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - C. S. Adjiman
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering
and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - C. C. Pantelides
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering
and Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K.
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7
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Galanakis N, Tuckerman ME. Rapid prediction of molecular crystal structures using simple topological and physical descriptors. Nat Commun 2024; 15:9757. [PMID: 39528448 PMCID: PMC11555391 DOI: 10.1038/s41467-024-53596-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/09/2024] [Indexed: 11/16/2024] Open
Abstract
Organic molecular crystals constitute a class of materials of critical importance in numerous industries. Despite the ubiquity of these systems, our ability to predict molecular crystal structures starting only from a two-dimensional diagram of the constituent compound(s) remains a significant challenge. Most structure-prediction protocols require a customized interatomic interaction model on which the quality of the results can depend sensitively. To overcome this problem, we introduce a new topological approach to molecular crystal structure prediction. The approach posits that in a stable structure, molecules are oriented such that principal axes and normal ring plane vectors are aligned with specific crystallographic directions and that heavy atoms occupy positions that correspond to minima of a set of geometric order parameters. By minimizing an objective function that encodes these orientations and atomic positions, and filtering based on the vdW free volume and intermolecular close contact distributions derived from the Cambridge Structural Database, stable structures and polymorphs for a given crystal can be predicted entirely mathematically without reliance on an interaction model.
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Affiliation(s)
| | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, NY, USA.
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai, China.
- Simons Center for Computational Physical Chemistry at New York University, New York, NY, USA.
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8
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Nessler A, Okada O, Kinoshita Y, Nishimura K, Nagata H, Fukuzawa K, Yonemochi E, Schnieders MJ. Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path. CRYSTAL GROWTH & DESIGN 2024; 24:3205-3217. [PMID: 38659664 PMCID: PMC11036363 DOI: 10.1021/acs.cgd.3c01358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 04/26/2024]
Abstract
The formulation of active pharmaceutical ingredients involves discovering stable crystal packing arrangements or polymorphs, each of which has distinct pharmaceutically relevant properties. Traditional experimental screening techniques utilizing various conditions are commonly supplemented with in silico crystal structure prediction (CSP) to inform the crystallization process and mitigate risk. Predictions are often based on advanced classical force fields or quantum mechanical calculations that model the crystal potential energy landscape but do not fully incorporate temperature, pressure, or solution conditions during the search procedure. This study proposes an innovative alchemical path that utilizes an advanced polarizable atomic multipole force field to predict crystal structures based on direct sampling of the NPT ensemble. The use of alchemical (i.e., nonphysical) intermediates, a novel Monte Carlo barostat, and an orthogonal space tempering bias combine to enhance the sampling efficiency of the deposition/sublimation phase transition. The proposed algorithm was applied to 2-((4-(2-(3,4-dichlorophenyl)ethyl)phenyl)amino)benzoic acid (Cambridge Crystallography Database Centre ID: XAFPAY) as a case study to showcase the algorithm. Each experimentally determined polymorph with one molecule in the asymmetric unit was successfully reproduced via approximately 1000 short 1 ns simulations per space group where each simulation was initiated from random rigid body coordinates and unit cell parameters. Utilizing two threads of a recent Intel CPU (a Xeon Gold 6330 CPU at 2.00 GHz), 1 ns of sampling using the polarizable AMOEBA force field can be acquired in 4 h (equating to more than 300 ns/day using all 112 threads/56 cores of a dual CPU node) within the Force Field X software (https://ffx.biochem.uiowa.edu). These results demonstrate a step forward in the rigorous use of the NPT ensemble during the CSP search process and open the door to future algorithms that incorporate solution conditions using continuum solvation methods.
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Affiliation(s)
- Aaron
J. Nessler
- Department
of Biomedical Engineering, University of
Iowa, 103 South Capitol
Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Okimasa Okada
- Sohyaku
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Yuya Kinoshita
- Analytical
Development, Pharmaceutical Sciences, Takeda
Pharmaceutical Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Koki Nishimura
- Analytical
Development, Pharmaceutical Sciences, Takeda
Pharmaceutical Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Hiroomi Nagata
- CMC
Modality Technology Laboratories, Production Technology and Supply
Chain Management Division, Mitsubishi Tanabe
Pharma Corporation, Osaka 541-8505, Japan
| | - Kaori Fukuzawa
- Graduate
School of Pharmaceutical Sciences, Osaka
University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Etsuo Yonemochi
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, 103 South Capitol
Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, 51 Newton Road, 4-403 Bowen Science
Building, Iowa City, Iowa 52242, United States
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9
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Butler PV, Hafizi R, Day GM. Machine-Learned Potentials by Active Learning from Organic Crystal Structure Prediction Landscapes. J Phys Chem A 2024; 128:945-957. [PMID: 38277275 PMCID: PMC10860135 DOI: 10.1021/acs.jpca.3c07129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
A primary challenge in organic molecular crystal structure prediction (CSP) is accurately ranking the energies of potential structures. While high-level solid-state density functional theory (DFT) methods allow for mostly reliable discrimination of the low-energy structures, their high computational cost is problematic because of the need to evaluate tens to hundreds of thousands of trial crystal structures to fully explore typical crystal energy landscapes. Consequently, lower-cost but less accurate empirical force fields are often used, sometimes as the first stage of a hierarchical scheme involving multiple stages of increasingly accurate energy calculations. Machine-learned interatomic potentials (MLIPs), trained to reproduce the results of ab initio methods with computational costs close to those of force fields, can improve the efficiency of the CSP by reducing or eliminating the need for costly DFT calculations. Here, we investigate active learning methods for training MLIPs with CSP datasets. The combination of active learning with the well-developed sampling methods from CSP yields potentials in a highly automated workflow that are relevant over a wide range of the crystal packing space. To demonstrate these potentials, we illustrate efficiently reranking large, diverse crystal structure landscapes to near-DFT accuracy from force field-based CSP, improving the reliability of the final energy ranking. Furthermore, we demonstrate how these potentials can be extended to more accurately model structures far from lattice energy minima through additional on-the-fly training within Monte Carlo simulations.
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Affiliation(s)
| | - Roohollah Hafizi
- School of Chemistry, University
of Southampton, Southampton SO17 1BJ, U.K.
| | - Graeme M. Day
- School of Chemistry, University
of Southampton, Southampton SO17 1BJ, U.K.
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10
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Hoja J, List A, Boese AD. Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties. J Chem Theory Comput 2024; 20:357-367. [PMID: 38109226 PMCID: PMC10782452 DOI: 10.1021/acs.jctc.3c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for the relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which, for instance, the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, the vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.
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Affiliation(s)
- Johannes Hoja
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
| | - Alexander List
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
| | - A. Daniel Boese
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
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11
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Kadan A, Ryczko K, Wildman A, Wang R, Roitberg A, Yamazaki T. Accelerated Organic Crystal Structure Prediction with Genetic Algorithms and Machine Learning. J Chem Theory Comput 2023; 19:9388-9402. [PMID: 38059458 DOI: 10.1021/acs.jctc.3c00853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a high-throughput, end-to-end pipeline for organic crystal structure prediction (CSP)─the problem of identifying the stable crystal structures that will form from a given molecule based only on its molecular composition. Our tool uses neural network potentials to allow for efficient screening and structural relaxation of generated crystal candidates. Our pipeline consists of two distinct stages: random search, whereby crystal candidates are randomly generated and screened, and optimization, where a genetic algorithm (GA) optimizes this screened population. We assess the performance of each stage of our pipeline on 21 molecules taken from the Cambridge Crystallographic Data Centre's CSP blind tests. We show that random search alone yields matches for ≈50% of targets. We then validate the potential of our full pipeline, making use of the GA to optimize the root-mean-square deviation between crystal candidates and the experimentally derived structure. With this approach, we are able to find matches for ≈80% of candidates with 10-100 times smaller initial population sizes than when using random search. Lastly, we run our full pipeline with an ANI model that is trained on a small data set of molecules extracted from crystal structures in the Cambridge Structural Database, generating ≈60% of targets. By leveraging machine learning models trained to predict energies at the density functional theory level, our pipeline has the potential to approach the accuracy of ab initio methods and the efficiency of empirical force fields.
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Affiliation(s)
- Amit Kadan
- Good Chemistry Company, 1285 W Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Kevin Ryczko
- Good Chemistry Company, 1285 W Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Andrew Wildman
- Good Chemistry Company, 1285 W Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Rodrigo Wang
- Good Chemistry Company, 1285 W Pender Street, Vancouver, British Columbia V6E 4B1, Canada
| | - Adrian Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Takeshi Yamazaki
- Good Chemistry Company, 1285 W Pender Street, Vancouver, British Columbia V6E 4B1, Canada
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12
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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: 0] [Impact Index Per Article: 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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13
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Thürlemann M, Riniker S. Hybrid classical/machine-learning force fields for the accurate description of molecular condensed-phase systems. Chem Sci 2023; 14:12661-12675. [PMID: 38020395 PMCID: PMC10646964 DOI: 10.1039/d3sc04317g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are dependent on the quality and quantity of training data. The rise of machine learning (ML) force fields (FFs) exacerbates limitations related to training data even further, especially for condensed-phase systems for which the generation of large and high-quality training datasets is difficult. Here, we propose a hybrid ML/classical FF model that is parametrized exclusively on high-quality ab initio data of dimers and monomers in vacuum but is transferable to condensed-phase systems. The proposed hybrid model combines our previous ML-parametrized classical model with ML corrections for situations where classical approximations break down, thus combining the robustness and efficiency of classical FFs with the flexibility of ML. Extensive validation on benchmarking datasets and experimental condensed-phase data, including organic liquids and small-molecule crystal structures, showcases how the proposed approach may promote FF development and unlock the full potential of classical FFs.
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Affiliation(s)
- Moritz Thürlemann
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 Zürich 8093 Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 Zürich 8093 Switzerland
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14
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Brown M, Skelton JM, Popelier PLA. Application of the FFLUX Force Field to Molecular Crystals: A Study of Formamide. J Chem Theory Comput 2023; 19:7946-7959. [PMID: 37847867 PMCID: PMC10653110 DOI: 10.1021/acs.jctc.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 10/19/2023]
Abstract
In this work, we present the first application of the quantum chemical topology force field FFLUX to the solid state. FFLUX utilizes Gaussian process regression machine learning models trained on data from the interacting quantum atom partitioning scheme to predict atomic energies and flexible multipole moments that change with geometry. Here, the ambient (α) and high-pressure (β) polymorphs of formamide are used as test systems and optimized using FFLUX. Optimizing the structures with increasing multipolar ranks indicates that the lattice parameters of the α phase differ by less than 5% to the experimental structure when multipole moments up to the quadrupole are used. These differences are found to be in line with the dispersion-corrected density functional theory. Lattice dynamics calculations are also found to be possible using FFLUX, yielding harmonic phonon spectra comparable to dispersion-corrected DFT while enabling larger supercells to be considered than is typically possible with first-principles calculations. These promising results indicate that FFLUX can be used to accurately determine properties of molecular solids that are difficult to access using DFT, including the structural dynamics, free energies, and properties at finite temperature.
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Affiliation(s)
- Matthew
L. Brown
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Britain
| | - Jonathan M. Skelton
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Britain
| | - Paul L. A. Popelier
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Britain
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15
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O’Connor D, Bier I, Tom R, Hiszpanski AM, Steele BA, Marom N. Ab Initio Crystal Structure Prediction of the Energetic Materials LLM-105, RDX, and HMX. CRYSTAL GROWTH & DESIGN 2023; 23:6275-6289. [PMID: 38173900 PMCID: PMC10763925 DOI: 10.1021/acs.cgd.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 08/02/2023] [Indexed: 01/05/2024]
Abstract
Crystal structure prediction (CSP) is performed for the energetic materials (EMs) LLM-105 and α-RDX, as well as the α and β conformational polymorphs of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), using the genetic algorithm (GA) code, GAtor, and its associated random structure generator, Genarris. Genarris and GAtor successfully generate the experimental structures of all targets. GAtor's symmetric crossover scheme, where the space group symmetries of parent structures are treated as genes inherited by offspring, is found to be particularly effective. However, conducting several GA runs with different settings is still important for achieving diverse samplings of the potential energy surface. For LLM-105 and α-RDX, the experimental structure is ranked as the most stable, with all of the dispersion-inclusive density functional theory (DFT) methods used here. For HMX, the α form was persistently ranked as more stable than the β form, in contrast to experimental observations, even when correcting for vibrational contributions and thermal expansion. This may be attributed to insufficient accuracy of dispersion-inclusive DFT methods or to kinetic effects not considered here. In general, the ranking of some putative structures is found to be sensitive to the choice of the DFT functional and the dispersion method. For LLM-105, GAtor generates a putative structure with a layered packing motif, which is desirable thanks to its correlation with low sensitivity. Our results demonstrate that CSP is a useful tool for studying the ubiquitous polymorphism of EMs and shows promise of becoming an integral part of the EM development pipeline.
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Affiliation(s)
- Dana O’Connor
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Imanuel Bier
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rithwik Tom
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Anna M. Hiszpanski
- Materials
Science Division, Lawrence Livermore National
Laboratory, Livermore, California 94550, United States
| | - Brad A. Steele
- Materials
Science Division, Lawrence Livermore National
Laboratory, Livermore, California 94550, United States
| | - Noa Marom
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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16
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Price AJA, Otero-de-la-Roza A, Johnson ER. XDM-corrected hybrid DFT with numerical atomic orbitals predicts molecular crystal lattice energies with unprecedented accuracy. Chem Sci 2023; 14:1252-1262. [PMID: 36756332 PMCID: PMC9891363 DOI: 10.1039/d2sc05997e] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Molecular crystals are important for many applications, including energetic materials, organic semiconductors, and the development and commercialization of pharmaceuticals. The exchange-hole dipole moment (XDM) dispersion model has shown good performance in the calculation of relative and absolute lattice energies of molecular crystals, although it has traditionally been applied in combination with plane-wave/pseudopotential approaches. This has limited XDM to use with semilocal functional approximations, which suffer from delocalization error and poor quality conformational energies, and to systems with a few hundreds of atoms at most due to unfavorable scaling. In this work, we combine XDM with numerical atomic orbitals, which enable the efficient use of XDM-corrected hybrid functionals for molecular crystals. We test the new XDM-corrected functionals for their ability to predict the lattice energies of molecular crystals for the X23 set and 13 ice phases, the latter being a particularly stringent test. A composite approach using a XDM-corrected, 25% hybrid functional based on B86bPBE achieves a mean absolute error of 0.48 kcal mol-1 per molecule for the X23 set and 0.19 kcal mol-1 for the total lattice energies of the ice phases, compared to recent diffusion Monte-Carlo data. These results make the new XDM-corrected hybrids not only far more computationally efficient than previous XDM implementations, but also the most accurate density-functional methods for molecular crystal lattice energies to date.
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Affiliation(s)
- Alastair J. A. Price
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo Oviedo 33006 Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
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17
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Xu J, Chen A, Cai T. Polymorphism of Purpurin and Low-level Detection of the Noncentrosymmetric form by Second Harmonic Generation Microscopy. J Pharm Sci 2023; 112:282-289. [PMID: 36257339 DOI: 10.1016/j.xphs.2022.10.011] [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: 07/11/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 12/23/2022]
Abstract
Nonlinear optical imaging based on second harmonic generation (SHG) provides rapid and highly selective detection of polar crystals. Purpurin (PUR) is a natural product with multiple pharmacological activities. Two polymorphs of PUR show distinct crystal packing and structural symmetry, where form I crystallizes in a polar space group and form II crystallizes in a centrosymmetric crystal structure. The two polymorphs are monotropically related, with form I being the thermodynamically stable form, as suggested by slurry experiments, in-situ Raman spectroscopy and crystal structure prediction (CSP). The specificity of SHG to the polar crystals of form I allows rapid polymorphism detection at the limit of individual crystals. SHG is also able to detect low levels of form I in a tablet matrix dominated by amorphous excipients. This study shows that SHG microscopy can achieve the rapid and sensitive detection of noncentrosymmetric crystals in solid dosage forms, which is especially helpful for the early detection of unwanted polymorphic conversion or crystallization of amorphous drugs in formulations and final products.
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Affiliation(s)
- Jia Xu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, 224005, China
| | - An Chen
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ting Cai
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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18
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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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19
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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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20
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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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21
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Xiouras C, Cameli F, Quilló GL, Kavousanakis ME, Vlachos DG, Stefanidis GD. Applications of Artificial Intelligence and Machine Learning Algorithms to Crystallization. Chem Rev 2022; 122:13006-13042. [PMID: 35759465 DOI: 10.1021/acs.chemrev.2c00141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Artificial intelligence and specifically machine learning applications are nowadays used in a variety of scientific applications and cutting-edge technologies, where they have a transformative impact. Such an assembly of statistical and linear algebra methods making use of large data sets is becoming more and more integrated into chemistry and crystallization research workflows. This review aims to present, for the first time, a holistic overview of machine learning and cheminformatics applications as a novel, powerful means to accelerate the discovery of new crystal structures, predict key properties of organic crystalline materials, simulate, understand, and control the dynamics of complex crystallization process systems, as well as contribute to high throughput automation of chemical process development involving crystalline materials. We critically review the advances in these new, rapidly emerging research areas, raising awareness in issues such as the bridging of machine learning models with first-principles mechanistic models, data set size, structure, and quality, as well as the selection of appropriate descriptors. At the same time, we propose future research at the interface of applied mathematics, chemistry, and crystallography. Overall, this review aims to increase the adoption of such methods and tools by chemists and scientists across industry and academia.
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Affiliation(s)
- Christos Xiouras
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Fabio Cameli
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Gustavo Lunardon Quilló
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium.,Chemical and BioProcess Technology and Control, Department of Chemical Engineering, Faculty of Engineering Technology, KU Leuven, Gebroeders de Smetstraat 1, 9000 Ghent, Belgium
| | - Mihail E Kavousanakis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece
| | - Dionisios G Vlachos
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Georgios D Stefanidis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece.,Laboratory for Chemical Technology, Ghent University; Tech Lane Ghent Science Park 125, B-9052 Ghent, Belgium
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22
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Nikhar R, Szalewicz K. Reliable crystal structure predictions from first principles. Nat Commun 2022; 13:3095. [PMID: 35654882 PMCID: PMC9163189 DOI: 10.1038/s41467-022-30692-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
An inexpensive and reliable method for molecular crystal structure predictions (CSPs) has been developed. The new CSP protocol starts from a two-dimensional graph of crystal's monomer(s) and utilizes no experimental information. Using results of quantum mechanical calculations for molecular dimers, an accurate two-body, rigid-monomer ab initio-based force field (aiFF) for the crystal is developed. Since CSPs with aiFFs are essentially as expensive as with empirical FFs, tens of thousands of plausible polymorphs generated by the crystal packing procedures can be optimized. Here we show the robustness of this protocol which found the experimental crystal within the 20 most stable predicted polymorphs for each of the 15 investigated molecules. The ranking was further refined by performing periodic density-functional theory (DFT) plus dispersion correction (pDFT+D) calculations for these 20 top-ranked polymorphs, resulting in the experimental crystal ranked as number one for all the systems studied (and the second polymorph, if known, ranked in the top few). Alternatively, the polymorphs generated can be used to improve aiFFs, which also leads to rank one predictions. The proposed CSP protocol should result in aiFFs replacing empirical FFs in CSP research.
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Affiliation(s)
- Rahul Nikhar
- Department of Physics and Astronomy, University of Delaware, Newark, DE, 19716, USA
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE, 19716, USA.
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23
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Beran GJO, Wright SE, Greenwell C, Cruz-Cabeza AJ. The interplay of intra- and intermolecular errors in modeling conformational polymorphs. J Chem Phys 2022; 156:104112. [DOI: 10.1063/5.0088027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Conformational polymorphs of organic molecular crystals represent a challenging test for quantum chemistry because they require careful balancing of the intra- and intermolecular interactions. This study examines 54 molecular conformations from 20 sets of conformational polymorphs, along with the relative lattice energies and 173 dimer interactions taken from six of the polymorph sets. These systems are studied with a variety of van der Waals-inclusive density functionals theory models; dispersion-corrected spin-component-scaled second-order Møller–Plesset perturbation theory (SCS-MP2D); and domain local pair natural orbital coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. We investigate how delocalization error in conventional density functionals impacts monomer conformational energies, systematic errors in the intermolecular interactions, and the nature of error cancellation that occurs in the overall crystal. The density functionals B86bPBE-XDM, PBE-D4, PBE-MBD, PBE0-D4, and PBE0-MBD are found to exhibit sizable one-body and two-body errors vs DLPNO-CCSD(T) benchmarks, and the level of success in predicting the relative polymorph energies relies heavily on error cancellation between different types of intermolecular interactions or between intra- and intermolecular interactions. The SCS-MP2D and, to a lesser extent, ωB97M-V models exhibit smaller errors and rely less on error cancellation. Implications for crystal structure prediction of flexible compounds are discussed. Finally, the one-body and two-body DLPNO-CCSD(T) energies taken from these conformational polymorphs establish the CP1b and CP2b benchmark datasets that could be useful for testing quantum chemistry models in challenging real-world systems with complex interplay between intra- and intermolecular interactions, a number of which are significantly impacted by delocalization error.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Sarah E. Wright
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Chandler Greenwell
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Aurora J. Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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24
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Cheng P, Chen Q, Liu H, Liu X. Exploration of conjugated π-bridge units in N, N-bis(4-methoxyphenyl)naphthalen-2-amine derivative-based hole transporting materials for perovskite solar cell applications: a DFT and experimental investigation. RSC Adv 2021; 12:1011-1020. [PMID: 35425109 PMCID: PMC8978819 DOI: 10.1039/d1ra08133k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022] Open
Abstract
Organic small molecules as hole-transporting materials (HTMs) are an important part of perovskite solar cells (PSCs). On basis of the arylamine-based HTM (e.g. H101), two N,N-bis(4-methoxyphenyl)naphthalen-2-amine derivative-based HTMs (CP1 and CP2) with different conjugated π-bridge cores of fused aromatic ring are designed. The CP1 and CP2 were investigated by DFT and TD-DFT in combination with Marcus theory. The calculated results indicate that the designed CP1 and CP2 have better properties with good stability and high hole mobility compared with the parent H101. To validate the computational model for the screening of N,N-bis(4-methoxyphenyl)naphthalen-2-amine derivative-based HTMs, the promising CP1 and CP2 were synthesized and applied to PSC devices. The results show that the experimental data used in this paper can reproduce the theoretical results, such as frontier molecular orbital energies, optical properties and hole mobility, very well. Among them, the results show that the power conversion efficiency (PCE) of the H101-based PSC device is 14.78%, while the CP1-based PSC shows a better PCE of 15.91%, due to its high hole mobility and uniform smooth film morphology, which ultimately promoted a higher fill factor. Finally, this work shows that the computational model is a feasible way to obtain potential N,N-bis(4-methoxyphenyl)naphthalen-2-amine derivative-based HTMs.
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Affiliation(s)
- Puhang Cheng
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 P. R. China
| | - Qian Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 P. R. China
| | - Hongyuan Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 P. R. China
| | - Xiaorui Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 P. R. China
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25
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Banerjee A, Jasrasaria D, Niblett SP, Wales DJ. Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization. J Phys Chem A 2021; 125:3776-3784. [PMID: 33881850 PMCID: PMC8279651 DOI: 10.1021/acs.jpca.1c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Indexed: 11/29/2022]
Abstract
Organic molecules can be stable in distinct crystalline forms, known as polymorphs, which have significant consequences for industrial applications. Here, we predict the polymorphs of crystalline benzene computationally for an accurate anisotropic model parametrized to reproduce electronic structure calculations. We adapt the basin-hopping global optimization procedure to the case of crystalline unit cells, simultaneously optimizing the molecular coordinates and unit cell parameters to locate multiple low-energy structures from a variety of crystal space groups. We rapidly locate all the well-established experimental polymorphs of benzene, each of which corresponds to a single local energy minimum of the model. Our results show that basin-hopping can be both an efficient and effective tool for polymorphic crystal structure prediction, requiring no a priori experimental knowledge of cell parameters or symmetry.
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Affiliation(s)
- Atreyee Banerjee
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Max
Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Dipti Jasrasaria
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
| | - Samuel P. Niblett
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94609, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
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26
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Bier I, O'Connor D, Hsieh YT, Wen W, Hiszpanski AM, Han TYJ, Marom N. Crystal structure prediction of energetic materials and a twisted arene with Genarris and GAtor. CrystEngComm 2021. [DOI: 10.1039/d1ce00745a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A molecular crystal structure prediction workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is successfully applied to two energetic materials and a chiral arene.
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Affiliation(s)
- Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Dana O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yun-Ting Hsieh
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Wen Wen
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anna M. Hiszpanski
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - T. Yong-Jin Han
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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27
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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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28
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Tang J, Guo J, Zhang Y, He R, Shen W, Li M. Effects of side-chain of non-fullerene small molecules on the property of electron transport materials in perovskite solar cells. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1858201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Jiwei Tang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
| | - Jiaren Guo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
| | - Yan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
| | - Rongxing He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
| | - Wei Shen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
| | - Ming Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing, People’s Republic of China
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29
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Nguyen D, Macchi P, Volkov A. Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:630-651. [PMID: 33125348 DOI: 10.1107/s2053273320009584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022]
Abstract
The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170-175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536; Nguyen & Volkov (2019). Acta Cryst. A75, 448-464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283-4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10-5 kJ mol-1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28-64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.
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Affiliation(s)
- Daniel Nguyen
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
| | - Anatoliy Volkov
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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30
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McDonagh JL, Swope WC, Anderson RL, Johnston MA, Bray DJ. What can digitisation do for formulated product innovation and development? POLYM INT 2020. [DOI: 10.1002/pi.6056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - David J Bray
- The Hartree Centre STFC Daresbury Laboratory Warrington WA4 4AD UK
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31
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Abstract
Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.
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Affiliation(s)
- Birger Dittrich
- Novartis Campus
- Novartis Pharma AG
- Basel CH-4002
- Switzerland
- Institut für Anorganische Chemie und Strukturchemie
| | - Christoph Sever
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Jens Lübben
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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32
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He X, Xiong Y, Wei X, Zhang C. High throughput scanning of dimer interactions to facilitate confirmation of the molecular stacking mode: a case of 1,3,5-trinitrobenzene and its amino-derivatives. Phys Chem Chem Phys 2019; 21:17868-17879. [PMID: 31380535 DOI: 10.1039/c9cp03503f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Exactly predicting the packing structures of a given molecule is a crucial topic in crystal engineering, while it remains still challenging, as it requires huge calculations, largely above common computation cost and time limitations. However, current progress in high throughput calculations makes the fast screening of structures and properties feasible. In the present work, we exemplify this by considering a special case of ascertainment of the molecular stacking mode and shear properties of energetic materials. Four energetic π-bonded molecules, 1,3,5-trinitrobenzene, 2,4,6-trinitroaniline, 1,3-diamino-2,4,6-trinitrobenzene and 2,4,6-triamino-1,3,5-trinitrobenzene, with a different number of H atoms replaced by amino groups, are adopted as samples to scan the potential energy surfaces (PESs) of dimers through high throughput calculations. It is found that the parallel stacking mode is the most energetically favored, followed by the T-shaped, coplanar and crossing ones. Such an energetically favored stacking mode is observed in all related π-stacked crystal structures at ambient conditions or low temperatures. It shows that the stacking mode can be ascertained through the PES scanning of dimers, and thereby, the stacking structures and properties related to the stacking mode, like mechanical anisotropism, can be quickly screened by means of high throughput calculations.
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Affiliation(s)
- Xudong He
- Institute of Chemical Materials, China Academy of Engineering Physics (CAEP), P. O. Box 919-311, Mianyang, Sichuan 621900, China.
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33
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Liu X, Liu X. Optimizing electron-rich arylamine derivatives in thiophene-fused derivatives as π bridge-based hole transporting materials for perovskite solar cells. RSC Adv 2019; 9:24733-24741. [PMID: 35528681 PMCID: PMC9069755 DOI: 10.1039/c9ra03408k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/25/2019] [Indexed: 11/21/2022] Open
Abstract
Based on the observations of thienothiophene derivatives as π-bridged small molecule hole transporting materials (HTMs), adjusting their electron-rich arylamine derivatives is an effective approach to obtain the alternative HTMs for perovskite solar cells (PSCs). In this work, starting from a new electron-rich arylamine derivative and different π-bridged units of thienothiophene derivatives, a series of arylamine derivative-based HTMs were designed, and their properties were investigated using density functional theory combined with the Marcus charge transfer theory. Compared with the parental Z26 material, the designed H01-H04 exhibit appropriate frontier molecular orbitals, good optical properties, better solubility, good stability and higher hole mobilities. H01-H04 materials with high hole mobility (∼× 10-2) can serve as promising HTMs for improving the efficiency of PSCs. The results confirm that the design strategy of adjusting the electron-rich arylamine derivatives in thienothiophene derivatives as π-bridged HTMs is a reliable approach to obtain the promising HTMs for PSC applications.
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Affiliation(s)
- Xiaorui Liu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 China
| | - Xing Liu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 China
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34
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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35
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Deng J, Hu W, Shen W, Li M, He R. Exploring the electrochemical properties of hole transporting materials from first-principles calculations: an efficient strategy to improve the performance of perovskite solar cells. Phys Chem Chem Phys 2019; 21:1235-1241. [PMID: 30566128 DOI: 10.1039/c8cp06693k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Perovskite solar cells (PSCs) have been achieved with impressively dynamic improvement in power conversion efficiency (PCE), becoming the hottest topic in photovoltaics. One of the hot topics is to develop inexpensive and efficient hole transporting materials (HTMs). In the present work, we systematically investigated the impact of different atoms in the heteromerous structure on the performance of perovskite solar cells. In addition, the influence of the structural modification of the HTM molecular building blocks was also revealed. To further understand the relationship between the charge-transport properties and the structural modification, the electronic properties, reorganization energy, and hole transporting properties of a series of organic hole transporting materials were investigated using first-principles calculations combined with Marcus theory. Moreover, the orientation function μΦ (V, λ, r, θ, γ; Φ) was applied to quantitatively evaluate the overall carrier mobility of HTMs in PSCs. It is revealed that this model predicts the hole mobility of HTMs correctly. The calculated results indicate that hole transporting materials with heteroatoms and larger dimensional structures show higher hole mobility, which may significantly improve the photovoltaic performance of PSCs.
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Affiliation(s)
- Jidong Deng
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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36
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Duarte Ramos Matos G, Mobley DL. Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000Res 2019; 7:686. [PMID: 30109026 PMCID: PMC6069752 DOI: 10.12688/f1000research.14960.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations. We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation. Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.
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Affiliation(s)
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Irvine, California, USA.,Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, Irvine, California, USA
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37
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Dolgonos GA, Hoja J, Boese AD. Revised values for the X23 benchmark set of molecular crystals. Phys Chem Chem Phys 2019; 21:24333-24344. [DOI: 10.1039/c9cp04488d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A revised reference value set for molecular crystals: X23b; new cell volumes and lattice energies including volumetric expansion due to zero-point energy and thermal effects.
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Affiliation(s)
| | - Johannes Hoja
- Institute of Chemistry
- University of Graz
- 8010 Graz
- Austria
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38
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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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39
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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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40
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Kuklin MS, Karttunen AJ. Crystal Structure Prediction of Magnetic Transition-Metal Oxides by Using Evolutionary Algorithm and Hybrid DFT Methods. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:24949-24957. [PMID: 30416641 PMCID: PMC6221369 DOI: 10.1021/acs.jpcc.8b08238] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Although numerous crystal structures have been successfully predicted by using currently available computational techniques, prediction of strongly correlated systems such as transition-metal oxides remains a challenge. To overcome this problem, we have interfaced evolutionary algorithm-based USPEX method with the CRYSTAL code, enabling the use of Gaussian-type localized atomic basis sets and hybrid density functional (DFT) methods for the prediction of crystal structures. We report successful crystal structure predictions of several transition-metal oxides (NiO, CoO, α-Fe2O3, V2O3, and CuO) with correct atomic magnetic moments, spin configurations, and structures by using the USPEX method in combination with the CRYSTAL code and Perdew-Burke-Ernzerhof (PBE0) hybrid functional. Our benchmarking results demonstrate that USPEX + hybrid DFT is a suitable combination to reliably predict the magnetic structures of strongly correlated materials.
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Affiliation(s)
- Mikhail S. Kuklin
- Department of Chemistry and
Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Antti J. Karttunen
- Department of Chemistry and
Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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41
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Abraham NS, Shirts MR. Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion. J Chem Theory Comput 2018; 14:5904-5919. [PMID: 30281302 DOI: 10.1021/acs.jctc.8b00460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel approach to efficiently implement thermal expansion in the quasi-harmonic approximation (QHA) for both isotropic and more importantly, anisotropic expansion. In this approach, we rapidly determine a crystal's equilibrium volume and shape at a given temperature by integrating along the gradient of expansion from 0 Kelvin up to the desired temperature. We compare our approach to previous isotropic methods that rely on a brute-force grid search to determine the free energy minimum, which is infeasible to carry out for anisotropic expansion, as well as quasi-anisotropic approaches that take into account the contributions to anisotropic expansion from the lattice energy. We compare these methods for experimentally known polymorphs of piracetam and resorcinol and show that both isotropic methods agree to within error up to 300 K. Using the Grüneisen parameter causes up to 0.04 kcal/mol deviation in the Gibbs free energy, but for polymorph free energy differences there is a cancellation in error with all isotropic methods within 0.025 kcal/mol at 300 K. Anisotropic expansion allows the crystals to relax into lattice geometries 0.01-0.23 kcal/mol lower in energy at 300 K relative to isotropic expansion. For polymorph free energy differences all QHA methods produced results within 0.02 kcal/mol of each other for resorcinol and 0.12 kcal/mol for piracetam, the two molecules tested here, demonstrating a cancellation of error for isotropic methods. We also find that with expansion in more than a single volume variable, there is a non-negligible rate of failure of the basic approximations of QHA. Specifically, while expanding into new harmonic modes as the box vectors are increased, the system often falls into alternate, structurally distinct harmonic modes unrelated by continuous deformation from the original harmonic mode.
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Affiliation(s)
- Nathan S Abraham
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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42
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Gatsiou CA, Adjiman CS, Pantelides CC. Repulsion-dispersion parameters for the modelling of organic molecular crystals containing N, O, S and Cl. Faraday Discuss 2018; 211:297-323. [PMID: 30094433 DOI: 10.1039/c8fd00064f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In lattice energy models that combine ab initio and empirical components, it is important to ensure consistency between these components so that meaningful quantitative results are obtained. A method for deriving parameters of atom-atom repulsion dispersion potentials for crystals, tailored to different ab initio models, is presented. It is based on minimization of the sum of squared deviations between experimental and calculated structures and energies. The solution algorithm is designed to avoid convergence to local minima in the parameter space by combining a deterministic low-discrepancy sequence for the generation of multiple initial parameter guesses with an efficient local minimization algorithm. The proposed approach is applied to derive transferable exp-6 potential parameters suitable for use in conjunction with a distributed multipole electrostatics model derived from isolated molecule charge densities calculated at the M06/6-31G(d,p) level of theory. Data for hydrocarbons, azahydrocarbons, oxohydrocarbons, organosulphur compounds and chlorohydrocarbons are used for the estimation. A good fit is achieved for the new set of parameters with a mean absolute error in sublimation enthalpies of 4.1 kJ mol-1 and an average rmsd15 of 0.31 Å. The parameters are found to perform well on a separate cross-validation set of 39 compounds.
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Affiliation(s)
- Christina A Gatsiou
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.
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43
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Day GM, Cooper AI. Energy-Structure-Function Maps: Cartography for Materials Discovery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704944. [PMID: 29205536 DOI: 10.1002/adma.201704944] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Some of the most successful approaches to structural design in materials chemistry have exploited strong directional bonds, whose geometric reliability lends predictability to solid-state assembly. For example, metal-organic frameworks are an important design platform in materials chemistry. By contrast, the structure of molecular crystals is defined by a balance of weaker intermolecular forces, and small changes to the molecular building blocks can lead to large changes in crystal packing. Hence, empirical rules are inherently less reliable for engineering the structures of molecular solids. Energy-structure-function (ESF) maps are a new approach for the discovery of functional organic crystals. These maps fuse crystal-structure prediction with the computation of physical properties to allow researchers to choose the most promising molecule for a given application, prior to its synthesis. ESF maps were used recently to discover a highly porous molecular crystal that has a high methane deliverable capacity and the lowest density molecular crystal reported to date (r = 0.41 g cm-3 , SABET = 3425 m2 g-1 ). Progress in this field is reviewed, with emphasis on the future opportunities and challenges for a design strategy based on computed ESF maps.
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Affiliation(s)
- Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew I Cooper
- Department of Chemistry and Materials Innovation Factory, Leverhulme Centre for Functional Materials Design, 51 Oxford Street, Liverpool, L7 3NY, UK
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44
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Bedoya-Martínez N, Giunchi A, Salzillo T, Venuti E, Della Valle RG, Zojer E. Toward a Reliable Description of the Lattice Vibrations in Organic Molecular Crystals: The Impact of van der Waals Interactions. J Chem Theory Comput 2018; 14:4380-4390. [DOI: 10.1021/acs.jctc.8b00484] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalia Bedoya-Martínez
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Andrea Giunchi
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Tommaso Salzillo
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Elisabetta Venuti
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Raffaele Guido Della Valle
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Egbert Zojer
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria
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45
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Li X, Curtis FS, Rose T, Schober C, Vazquez-Mayagoitia A, Reuter K, Oberhofer H, Marom N. Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation. J Chem Phys 2018; 148:241701. [PMID: 29960303 DOI: 10.1063/1.5014038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.
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Affiliation(s)
- Xiayue Li
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Farren S Curtis
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Timothy Rose
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Christoph Schober
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universiät München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | | | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universiät München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universiät München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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46
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Zhao L, Pinon AC, Emsley L, Rossini AJ. DNP-enhanced solid-state NMR spectroscopy of active pharmaceutical ingredients. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:583-609. [PMID: 29193278 DOI: 10.1002/mrc.4688] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/15/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR spectroscopy has become a valuable tool for the characterization of both pure and formulated active pharmaceutical ingredients (APIs). However, NMR generally suffers from poor sensitivity that often restricts NMR experiments to nuclei with favorable properties, concentrated samples, and acquisition of one-dimensional (1D) NMR spectra. Here, we review how dynamic nuclear polarization (DNP) can be applied to routinely enhance the sensitivity of solid-state NMR experiments by one to two orders of magnitude for both pure and formulated APIs. Sample preparation protocols for relayed DNP experiments and experiments on directly doped APIs are detailed. Numerical spin diffusion models illustrate the dependence of relayed DNP enhancements on the relaxation properties and particle size of the solids and can be used for particle size determination when the other factors are known. We then describe the advanced solid-state NMR experiments that have been enabled by DNP and how they provide unique insight into the molecular and macroscopic structure of APIs. For example, with large sensitivity gains provided by DNP, natural isotopic abundance, 13 C-13 C double-quantum single-quantum homonuclear correlation NMR spectra of pure APIs can be routinely acquired. DNP also enables solid-state NMR experiments with unreceptive quadrupolar nuclei such as 2 H, 14 N, and 35 Cl that are commonly found in APIs. Applications of DNP-enhanced solid-state NMR spectroscopy for the molecular level characterization of low API load formulations such as commercial tablets and amorphous solid dispersions are described. Future perspectives for DNP-enhanced solid-state NMR experiments on APIs are briefly discussed.
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Affiliation(s)
- Li Zhao
- Department of Chemistry, Iowa State University, Ames, IA, USA
- US DOE Ames Laboratory, Ames, IA, USA
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Aaron J Rossini
- Department of Chemistry, Iowa State University, Ames, IA, USA
- US DOE Ames Laboratory, Ames, IA, USA
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47
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48
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LeBlanc LM, Otero-de-la-Roza A, Johnson ER. Composite and Low-Cost Approaches for Molecular Crystal Structure Prediction. J Chem Theory Comput 2018; 14:2265-2276. [PMID: 29498837 DOI: 10.1021/acs.jctc.7b01179] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crystal structure prediction (CSP) requires evaluating differences in lattice energy between candidate crystal structures accurately and efficiently. In this work, we explore and compare several low-cost alternatives to dispersion-corrected density-functional theory (DFT) in the plane-waves/pseudopotential approximation, the most accurate and general approach used for CSP at present. Three types of low-cost methods are considered: DFT with a small basis set of finite-support numerical orbitals (the SIESTA method), dispersion-corrected Gaussian small or minimal-basis-set Hartree-Fock and DFT with additional empirical corrections (HF-3c and PBEh-3c), and self-consistent-charge dispersion-corrected density-functional tight binding (SCC-DFTB3-D3). In addition, we study the performance of composite methods that comprise a geometry optimization using a low-cost approach followed by a single-point calculation using the accurate but comparatively expensive B86bPBE-XDM functional. All methods were tested for their abilities to produce absolute lattice energies, relative lattice energies, and crystal geometries. We show that assessing various methods by their ability to produce absolute lattice energies can be misleading and that relative lattice energies are a much better indicator of performance in CSP. The EE14 set of relative solubilities of homochiral and heterochiral chiral crystals is proposed for relative lattice-energy benchmarking. Our results show that PBE-D2 plus a DZP basis set of numerical orbitals coupled with a final B86bPBE-XDM single-point calculation gives excellent performance at a fraction of the cost of a full B86bPBE-XDM calculation, although the results are sensitive to the particular details of the computational protocol. The B86bPBE-XDM//PBE-D2/DZP method was subsequently tested in a practical CSP application from our recent work on the crystal structure of the enantiopure and racemate forms of 1-aza[6]helicene, a chiral organic semiconductor. Our results show that this multilevel method is able to correctly reproduce the energy ranking of both crystal forms.
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Affiliation(s)
- Luc M LeBlanc
- Department of Chemistry , Dalhousie University , 6274 Coburg Road , P.O. Box 15000, Halifax , Nova Scotia , Canada B3H 4R2
| | - Alberto Otero-de-la-Roza
- Department of Chemistry , University of British Columbia, Okanagan , 3247 University Way , Kelowna , British Columbia , Canada V1V 1V7
| | - Erin R Johnson
- Department of Chemistry , Dalhousie University , 6274 Coburg Road , P.O. Box 15000, Halifax , Nova Scotia , Canada B3H 4R2
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49
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Curtis F, Li X, Rose T, Vázquez-Mayagoitia Á, Bhattacharya S, Ghiringhelli LM, Marom N. GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction. J Chem Theory Comput 2018; 14:2246-2264. [PMID: 29481740 DOI: 10.1021/acs.jctc.7b01152] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.
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Affiliation(s)
- Farren Curtis
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Xiayue Li
- Google , Mountain View , California 94030 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Timothy Rose
- Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Álvaro Vázquez-Mayagoitia
- Argonne Leadership Computing Facility , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Saswata Bhattacharya
- Department of Physics , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Luca M Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 , Berlin , Germany
| | - Noa Marom
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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50
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Mohamed S, Alwan AA, Friščić T, Morris AJ, Arhangelskis M. Towards the systematic crystallisation of molecular ionic cocrystals: insights from computed crystal form landscapes. Faraday Discuss 2018; 211:401-424. [DOI: 10.1039/c8fd00036k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The underlying molecular and crystal properties affecting the crystallisation of organic molecular ionic cocrystals (ICCs) are investigated.
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Affiliation(s)
- Sharmarke Mohamed
- Department of Chemistry
- Khalifa University of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Ahmad A. Alwan
- Department of Chemistry
- Khalifa University of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | | | - Andrew J. Morris
- School of Metallurgy and Materials
- University of Birmingham
- Birmingham B15 2TT
- UK
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