Acta Crystallographica Section B Structural Science, 2009
We report on the organization and outcome of the fourth blind test of crystal structure predictio... more 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crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee.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...
Solid-state density functional theory calculations including periodic boundary conditions have be... more Solid-state density functional theory calculations including periodic boundary conditions have become well established for calculating the THz spectra of crystalline materials. Here we compare a range of DFT programs and calculation parameters including a number of van der Waals’ dispersive corrections in combination with our post-processing tool, PDielec, to calculate the complex permittivity of a range of powdered crystalline materials.
From an initial crystallographic study of a large family of ring-substituted 2-acetoxybenzoic aci... more From an initial crystallographic study of a large family of ring-substituted 2-acetoxybenzoic acids, only one member - the 5-chloro derivative - showed polymorphism, with two forms (α and β) identified, the former having a marginally higher melting point. The two structures show a close 1-D similarity through a row of carboxylic dimers connected via ClO halogen bonds, which assemble to give an approximate 2-D similarity by the stacking of these rows in a second direction. However, the further packing arrangement of the resulting 2-D stacks is significantly different in the two forms, through different symmetry arrangements and subtle variations in C–HO weak hydrogen bonds. A parallel crystal structure prediction (CSP) calculation identified the two experimental polymorphs in the correct stability order with effective energy rankings of 2 and 3 (lattice energy difference of 0.2 kcal mol−1). The lowest energy crystal structure found during the CSP, as yet not found experimentally, is ...
Acta Crystallographica Section B Structural Science, 2011
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, ... more 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 fi...
Journal of Infrared, Millimeter, and Terahertz Waves
A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ disper... more A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ dispersive corrections have been used to optimize the structure of sodium peroxodisulfate, Na2(SO4)2, and to calculate the infrared, attenuated total reflectance and terahertz absorption spectra of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles of Na2(SO4)2 is also considered using the Mie method. The results of the calculations are compared with expe...
A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ disper... more A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ dispersive corrections have been used to optimize the structure of sodium peroxodisulfate, Na2(SO4)2, and to calculate the infra-red and terahertz absorption spectrum of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles of Na2(SO4)2 is also considered using the Mie method. The results of the calculations are compared with experimental measurements of the...
Acta crystallographica Section B, Structural science, crystal engineering and materials, Aug 1, 2016
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with fi... more 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 s...
Acta Crystallographica Section B Structural Science, 2009
We report on the organization and outcome of the fourth blind test of crystal structure predictio... more 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...
Solid-state density functional theory calculations including periodic boundary conditions have be... more Solid-state density functional theory calculations including periodic boundary conditions have become well established for calculating the THz spectra of crystalline materials. Here we compare a range of DFT programs and calculation parameters including a number of van der Waals’ dispersive corrections in combination with our post-processing tool, PDielec, to calculate the complex permittivity of a range of powdered crystalline materials.
From an initial crystallographic study of a large family of ring-substituted 2-acetoxybenzoic aci... more From an initial crystallographic study of a large family of ring-substituted 2-acetoxybenzoic acids, only one member - the 5-chloro derivative - showed polymorphism, with two forms (α and β) identified, the former having a marginally higher melting point. The two structures show a close 1-D similarity through a row of carboxylic dimers connected via ClO halogen bonds, which assemble to give an approximate 2-D similarity by the stacking of these rows in a second direction. However, the further packing arrangement of the resulting 2-D stacks is significantly different in the two forms, through different symmetry arrangements and subtle variations in C–HO weak hydrogen bonds. A parallel crystal structure prediction (CSP) calculation identified the two experimental polymorphs in the correct stability order with effective energy rankings of 2 and 3 (lattice energy difference of 0.2 kcal mol−1). The lowest energy crystal structure found during the CSP, as yet not found experimentally, is ...
Acta Crystallographica Section B Structural Science, 2011
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, ... more 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 fi...
Journal of Infrared, Millimeter, and Terahertz Waves
A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ disper... more A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ dispersive corrections have been used to optimize the structure of sodium peroxodisulfate, Na2(SO4)2, and to calculate the infrared, attenuated total reflectance and terahertz absorption spectra of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles of Na2(SO4)2 is also considered using the Mie method. The results of the calculations are compared with expe...
A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ disper... more A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ dispersive corrections have been used to optimize the structure of sodium peroxodisulfate, Na2(SO4)2, and to calculate the infra-red and terahertz absorption spectrum of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles of Na2(SO4)2 is also considered using the Mie method. The results of the calculations are compared with experimental measurements of the...
Acta crystallographica Section B, Structural science, crystal engineering and materials, Aug 1, 2016
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with fi... more 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 s...
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