scholarly journals Sixth blind test of organic crystal-structure prediction methods

2014 ◽  
Vol 70 (4) ◽  
pp. 776-777 ◽  
Author(s):  
Colin R. Groom ◽  
Anthony M. Reilly
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Organic Molecules ◽  
Prediction Methods ◽  
Crystal Structure Prediction ◽  
Cambridge Crystallographic Data Centre ◽  
Blind Test ◽  
Small Organic Molecules ◽  
Data Centre ◽  
The Past

Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.

scholarly journals Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test

2009 ◽  
Vol 65 (2) ◽  
pp. 107-125 ◽  
Author(s):  
Graeme M. Day ◽  
Timothy G. Cooper ◽  
Aurora J. Cruz-Cabeza ◽  
Katarzyna E. Hejczyk ◽  
Herman L. Ammon ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Organic Molecules ◽  
Dramatic Improvement ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Collaborative Project ◽  
Small Organic Molecules ◽  
Modelling Methods

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.

scholarly journals Report on the sixth blind test of organic crystal structure prediction methods

2016 ◽  
Vol 72 (4) ◽  
pp. 439-459 ◽  
Author(s):  
Anthony M. Reilly ◽  
Richard I. Cooper ◽  
Claire S. Adjiman ◽  
Saswata Bhattacharya ◽  
A. Daniel Boese ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Density Functional ◽  
Organic Crystal ◽  
Drug Candidate ◽  
Prediction Methods ◽  
Chloride Salt ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Flexible Molecules

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 disorderedZ′ = 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.

A test of crystal structure prediction of small organic molecules

2000 ◽  
Vol 56 (4) ◽  
pp. 697-714 ◽  
Author(s):  
Jos P. M. Lommerse ◽  
W. D. Sam Motherwell ◽  
Herman L. Ammon ◽  
Jack D. Dunitz ◽  
Angelo Gavezzotti ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Compound A ◽  
Small Organic Molecules ◽  
Wide Range ◽  
Field Methodology ◽  
Selection Of

A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were close to an experimental one and were classified as `correct'. One compound occurred in two polymorphs, but only one form was predicted correctly among the calculated structures. The basic problem with lattice energy based methods of crystal structure prediction is that many structures are found within a few kJ mol−1 of the global minimum. The fine detail of the force-field methodology and parametrization influences the energy ranking within each method. Nevertheless, present methods may be useful in providing a set of structures as possible polymorphs for a given molecular structure.

Crystal structure prediction of small organic molecules: a second blind test

2002 ◽  
Vol 58 (4) ◽  
pp. 647-661 ◽  
Author(s):  
W. D. Sam Motherwell ◽  
Herman L. Ammon ◽  
Jack D. Dunitz ◽  
Alexander Dzyabchenko ◽  
Peter Erk ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Organic Molecules ◽  
Molecular Model ◽  
Objective Measure ◽  
Lattice Energy ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Space Groups ◽  
Common Space

The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.

scholarly journals Blind crystal structure prediction of a novel second polymorph of 1-hydroxy-7-azabenzotriazole

2006 ◽  
Vol 62 (4) ◽  
pp. 642-650 ◽  
Author(s):  
Harriott Nowell ◽  
Christopher S. Frampton ◽  
Julie Waite ◽  
Sarah L. Price
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Structure Refinement ◽  
Lattice Energy ◽  
Polymorphic Form ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Coupling Reagent ◽  
Energy Penalty ◽  
Alcohol Solvents

The commercially available peptide coupling reagent 1-hydroxy-7-azabenzotriazole has been shown to crystallize in two polymorphic forms. The two polymorphs differ in their hydrogen-bonding motif, with form I having an R_2^2(10) dimer motif and form II having a C(5) chain motif. The previously unreported form II was used as an informal blind test of computational crystal structure prediction for flexible molecules. The crystal structure of form II has been successfully predicted blind from lattice-energy minimization calculations following a series of searches using a large number of rigid conformers. The structure for form II was the third lowest in energy with form I found as the global minimum, with the energy calculated as the sum of the ab initio intramolecular energy penalty for conformational distortion and the intermolecular lattice energy which is calculated from a distributed multipole representation of the charge density. The predicted structure was sufficiently close to the experimental structure that it could be used as a starting model for crystal structure refinement. A subsequent limited polymorph screen failed to yield a third polymorphic form, but demonstrated that alcohol solvents are implicated in the formation of the form I dimer structure.

scholarly journals Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

2011 ◽  
Vol 67 (6) ◽  
pp. 535-551 ◽  
Author(s):  
David A. Bardwell ◽  
Claire S. Adjiman ◽  
Yelena A. Arnautova ◽  
Ekaterina Bartashevich ◽  
Stephan X. M. Boerrigter ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Density Functional ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Functional Theory ◽  
Flexible Molecule ◽  
Successful Prediction ◽  
The Many ◽  
Complex Organic

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.

scholarly journals Comparing hypothetical structures generated in the third Cambridge blind test of crystal structure prediction

2005 ◽  
Vol 61 (5) ◽  
pp. 528-535 ◽  
Author(s):  
Bouke P. van Eijck
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Good Correspondence ◽  
The Third ◽  
New Energy ◽  
Order Of Magnitude ◽  
True Energy

In the third Cambridge blind test of crystal structure prediction, participants submitted extended lists of up to 100 hypothetical structures. In this paper these lists are analyzed for the two small semi-rigid molecules, hydantoin and azetidine, by performing a new energy minimization using an accurate force field, and grouping these newly minimized structures into clusters of equivalent structures. Many participants found the same low-energy structures, but no list appeared to be complete even for the structures with one independent molecule in the asymmetric unit. This may well be due to the fact that a cutoff at even 100 structures cannot ensure the presence of a structure that has a relatively high ranking in another force field. Moreover, some structures should have possibly been discarded because they correspond to transition states rather than true energy minima. The r.m.s. deviation between energies in corresponding clusters was calculated to compare the reported relative crystal energies for each pair of participants. Some groups of force fields show a reasonably good correspondence, yet the order of magnitude of their discrepancies is comparable to the energy differences between, say, the first ten structures of lowest energy. Therefore, even if we assume that energy is a sufficient criterion, it is not surprising that crystal structure predictions are still inconsistent and unreliable.

scholarly journals Phase relations, and mechanical and electronic properties of nickel borides, carbides, and nitrides from ab initio calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (53) ◽  
pp. 33781-33787
Author(s):  
Nursultan E. Sagatov ◽  
Aisulu U. Abuova ◽  
Dinara N. Sagatova ◽  
Pavel N. Gavryushkin ◽  
Fatima U. Abuova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Ab Initio Calculations ◽  
Structure Prediction ◽  
Density Functional ◽  
Pressure Range ◽  
Prediction Methods ◽  
Crystal Structure Prediction ◽  
Functional Theory ◽  
C And N

Based on density functional theory and the crystal structure prediction methods, USPEX and AIRSS, stable intermediate compounds in the Ni–X (X = B, C, and N) systems and their structures were determined in the pressure range of 0–400 GPa.

scholarly journals First-year experience with fully automated crystal structure prediction

2014 ◽  
Vol 70 (a1) ◽  
pp. C1618-C1618
Author(s):  
Marcus Neumann ◽  
Bernd Doser
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Density Functional ◽  
Method Development ◽  
Force Fields ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Structure Generation ◽  
Statistical Correlations ◽  
Pharmaceutical Molecules

With improving hardware and software performance, usability has become one of the main obstacles to a more widespread use of Crystal Structure Prediction (CSP) with the GRACE program. In terms of method development, important milestones had already been passed by the time of the 5th blind test [1] in 2010, including the parameterization of dispersion-corrected Density Functional Theory (DFT-D) [2], the generation of tailor-made force fields from ab-initio reference data [3], a Monte-Carlo parallel tempering crystal structure generation engine and a DFT-d reranking procedure exploiting statistical correlations. These components have now been incorporated in automated data flow processes that remove the burden of scores of expert decisions from the user. Summarizing the results of CSP studies performed with the new Force Field Factory and CSP Factory modules throughout a year, the current performance of CSP is critically assessed and further method development needs are pinpointed. Studied compounds include 20 small molecules with competing hydrogen bonds motifs, 4 mono-hydrates of non-ionic molecules and the hydrates and chloride salts of several amino acids. The ability to handle flexible pharmaceutical molecules is demonstrated by a validation study on aripiprazole with one and two molecules per asymmetric unit. Salient features of the energy landscapes of other pharmaceutical molecules are discussed. Statistics are presented for the accuracy of tailor-made force fields, and the energy ranking performance of several DFT-d flavors is compared.

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