Literature DB >> 18642947

Tailor-made force fields for crystal-structure prediction.

Marcus A Neumann1.   

Abstract

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

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Year:  2008        PMID: 18642947     DOI: 10.1021/jp710575h

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  16 in total

1.  Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine.

Authors:  Albert M Lund; Gabriel I Pagola; Anita M Orendt; Marta B Ferraro; Julio C Facelli
Journal:  Chem Phys Lett       Date:  2015-04-17       Impact factor: 2.328

2.  Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

Authors:  Jacco van de Streek; Marcus A Neumann
Journal:  Acta Crystallogr B       Date:  2010-09-11

3.  Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Authors:  David A Bardwell; Claire S Adjiman; Yelena A Arnautova; Ekaterina Bartashevich; Stephan X M Boerrigter; Doris E Braun; Aurora J Cruz-Cabeza; Graeme M Day; Raffaele G Della Valle; Gautam R Desiraju; Bouke P van Eijck; Julio C Facelli; Marta B Ferraro; Damian Grillo; Matthew Habgood; Detlef W M Hofmann; Fridolin Hofmann; K V Jovan Jose; Panagiotis G Karamertzanis; Andrei V Kazantsev; John Kendrick; Liudmila N Kuleshova; Frank J J Leusen; Andrey V Maleev; Alston J Misquitta; Sharmarke Mohamed; Richard J Needs; Marcus A Neumann; Denis Nikylov; Anita M Orendt; Rumpa Pal; Constantinos C Pantelides; Chris J Pickard; Louise S Price; Sarah L Price; Harold A Scheraga; Jacco van de Streek; Tejender S Thakur; Siddharth Tiwari; Elisabetta Venuti; Ilia K Zhitkov
Journal:  Acta Crystallogr B       Date:  2011-11-17

4.  Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening.

Authors:  M A Neumann; J van de Streek; F P A Fabbiani; P Hidber; O Grassmann
Journal:  Nat Commun       Date:  2015-07-22       Impact factor: 14.919

5.  Report on the sixth blind test of organic crystal structure prediction methods.

Authors:  Anthony M Reilly; Richard I Cooper; Claire S Adjiman; Saswata Bhattacharya; A Daniel Boese; Jan Gerit Brandenburg; Peter J Bygrave; Rita Bylsma; Josh E Campbell; Roberto Car; David H Case; Renu Chadha; Jason C Cole; Katherine Cosburn; Herma M Cuppen; Farren Curtis; Graeme M Day; Robert A DiStasio; Alexander Dzyabchenko; Bouke P van Eijck; Dennis M Elking; Joost A van den Ende; Julio C Facelli; Marta B Ferraro; Laszlo Fusti-Molnar; Christina Anna Gatsiou; Thomas S Gee; René de Gelder; Luca M Ghiringhelli; Hitoshi Goto; Stefan Grimme; Rui Guo; Detlef W M Hofmann; Johannes Hoja; Rebecca K Hylton; Luca Iuzzolino; Wojciech Jankiewicz; Daniël T de Jong; John Kendrick; Niek J J de Klerk; Hsin Yu Ko; Liudmila N Kuleshova; Xiayue Li; Sanjaya Lohani; Frank J J Leusen; Albert M Lund; Jian Lv; Yanming Ma; Noa Marom; Artëm E Masunov; Patrick McCabe; David P McMahon; Hugo Meekes; Michael P Metz; Alston J Misquitta; Sharmarke Mohamed; Bartomeu Monserrat; Richard J Needs; Marcus A Neumann; Jonas Nyman; Shigeaki Obata; Harald Oberhofer; Artem R Oganov; Anita M Orendt; Gabriel I Pagola; Constantinos C Pantelides; Chris J Pickard; Rafal Podeszwa; Louise S Price; Sarah L Price; Angeles Pulido; Murray G Read; Karsten Reuter; Elia Schneider; Christoph Schober; Gregory P Shields; Pawanpreet Singh; Isaac J Sugden; Krzysztof Szalewicz; Christopher R Taylor; Alexandre Tkatchenko; Mark E Tuckerman; Francesca Vacarro; Manolis Vasileiadis; Alvaro Vazquez-Mayagoitia; Leslie Vogt; Yanchao Wang; Rona E Watson; Gilles A de Wijs; Jack Yang; Qiang Zhu; Colin R Groom
Journal:  Acta Crystallogr B Struct Sci Cryst Eng Mater       Date:  2016-08-01

6.  Crystallographic and Dynamic Aspects of Solid-State NMR Calibration Compounds: Towards ab Initio NMR Crystallography.

Authors:  Xiaozhou Li; Lukas Tapmeyer; Michael Bolte; Jacco van de Streek
Journal:  Chemphyschem       Date:  2016-06-08       Impact factor: 3.102

7.  Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

Authors:  Miri Zilka; Dmytro V Dudenko; Colan E Hughes; P Andrew Williams; Simone Sturniolo; W Trent Franks; Chris J Pickard; Jonathan R Yates; Kenneth D M Harris; Steven P Brown
Journal:  Phys Chem Chem Phys       Date:  2017-10-04       Impact factor: 3.676

8.  The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine.

Authors:  Xiaozhou Li; Marcus A Neumann; Jacco van de Streek
Journal:  IUCrJ       Date:  2017-02-15       Impact factor: 4.769

9.  A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

Authors:  Jacco van de Streek; Edith Alig; Simon Parsons; Liana Vella-Zarb
Journal:  IUCrJ       Date:  2019-01-01       Impact factor: 4.769

Review 10.  Can computed crystal energy landscapes help understand pharmaceutical solids?

Authors:  Sarah L Price; Doris E Braun; Susan M Reutzel-Edens
Journal:  Chem Commun (Camb)       Date:  2016-04-12       Impact factor: 6.222

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