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1.  Report on the sixth blind test of organic crystal structure prediction methods 
Reilly, Anthony M. | Cooper, Richard I. | Adjiman, Claire S. | Bhattacharya, Saswata | Boese, A. Daniel | Brandenburg, Jan Gerit | Bygrave, Peter J. | Bylsma, Rita | Campbell, Josh E. | Car, Roberto | Case, David H. | Chadha, Renu | Cole, Jason C. | Cosburn, Katherine | Cuppen, Herma M. | Curtis, Farren | Day, Graeme M. | DiStasio Jr, Robert A. | Dzyabchenko, Alexander | van Eijck, Bouke P. | Elking, Dennis M. | van den Ende, Joost A. | Facelli, Julio C. | Ferraro, Marta B. | Fusti-Molnar, Laszlo | Gatsiou, Christina-Anna | Gee, Thomas S. | de Gelder, René | Ghiringhelli, Luca M. | Goto, Hitoshi | Grimme, Stefan | Guo, Rui | Hofmann, Detlef W. M. | Hoja, Johannes | Hylton, Rebecca K. | Iuzzolino, Luca | Jankiewicz, Wojciech | de Jong, Daniël T. | Kendrick, John | de Klerk, Niek J. J. | Ko, Hsin-Yu | Kuleshova, Liudmila N. | Li, Xiayue | Lohani, Sanjaya | Leusen, Frank J. J. | Lund, Albert M. | Lv, Jian | Ma, Yanming | Marom, Noa | Masunov, Artëm E. | McCabe, Patrick | McMahon, David P. | Meekes, Hugo | Metz, Michael P. | Misquitta, Alston J. | Mohamed, Sharmarke | Monserrat, Bartomeu | Needs, Richard J. | Neumann, Marcus A. | Nyman, Jonas | Obata, Shigeaki | Oberhofer, Harald | Oganov, Artem R. | Orendt, Anita M. | Pagola, Gabriel I. | Pantelides, Constantinos C. | Pickard, Chris J. | Podeszwa, Rafal | Price, Louise S. | Price, Sarah L. | Pulido, Angeles | Read, Murray G. | Reuter, Karsten | Schneider, Elia | Schober, Christoph | Shields, Gregory P. | Singh, Pawanpreet | Sugden, Isaac J. | Szalewicz, Krzysztof | Taylor, Christopher R. | Tkatchenko, Alexandre | Tuckerman, Mark E. | Vacarro, Francesca | Vasileiadis, Manolis | Vazquez-Mayagoitia, Alvaro | Vogt, Leslie | Wang, Yanchao | Watson, Rona E. | de Wijs, Gilles A. | Yang, Jack | Zhu, Qiang | Groom, Colin R.
The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.
doi:10.1107/S2052520616007447
PMCID: PMC4971545  PMID: 27484368
crystal structure prediction; polymorphism; lattice energies; Cambridge Structural Database
2.  Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine 
Chemical physics letters  2015;626:20-24.
Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.
doi:10.1016/j.cplett.2015.03.015
PMCID: PMC4379511  PMID: 25843964
Crystal Structure Prediction; DFT-D; polymorphs; glycine
3.  Transition from exo- to endo- Cu absorption in CuSin clusters: A Genetic Algorithms Density Functional Theory (DFT) Study 
Molecular simulation  2011;37(8):678-688.
The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors have postulated that there is a transition between exo to endo absorption of Cu in Sin clusters and showed that for n larger than 9 it is possible to find endohedral clusters. Unfortunately, no global searchers have confirmed this observation, which is based on local optimizations of plausible structures. Here we use parallel Genetic Algorithms (GA), as implemented in our MGAC software, directly coupled with DFT energy calculations to show that the global search of CuSin cluster structures does not find endohedral clusters for n < 8 but finds them for n ≥ 10.
doi:10.1080/08927020903583830
PMCID: PMC3139224  PMID: 21785526
copper-silicon clusters; genetic algorithms; global optimization
4.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test 
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
doi:10.1107/S0108768111042868
PMCID: PMC3222142  PMID: 22101543
5.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test 
The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
doi:10.1107/S0108768111042868
PMCID: PMC3222142  PMID: 22101543
prediction; blind test; polymorph; crystal structure prediction
6.  Crystal Structure Prediction (CSP) of Flexible Molecules using Parallel Genetic Algorithms with a Standard Force Field 
Journal of computational chemistry  2009;30(13):1973-1985.
This paper describes the application of our distributed computing framework for crystal structure prediction (CSP), Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC) to predict the crystal structure of flexible molecules using the General Amber Force Field (GAFF) and the CHARMM program. The MGAC distributed computing framework which includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling crystal structures using a distributed parallel genetic algorithm, local energy minimization of the structures followed by the classifying, sorting and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.
doi:10.1002/jcc.21189
PMCID: PMC2720422  PMID: 19130496

Results 1-6 (6)