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1.  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
2.  Stacking faults and superstructures in a layered brownmillerite 
Stacking faults in Ca4Fe2Mn0.5Ti0.5O9 have been examined using X-ray diffraction and high-resolution transmission electron microscopy. Electron diffraction revealed two superstructures with ordered stacking sequences.
Single crystals of Ca4Fe2Mn0.5Ti0.5O9 have been synthesized using a flux method. The structural characterization using single-crystal X-ray diffraction revealed the space group Amma and unit-cell dimensions of a = 5.3510 (6), b = 26.669 (3), c = 5.4914 (6) Å. The structure is isotypic with Sr3NdFe3O9 [Barrier et al. (2005 ▸). Chem. Mater. 17, 6619–6623] and exhibits separated brownmillerite-type layers. One-dimensional diffuse scattering shows that the unit cell is doubled along c by alternating the intra-layer order of tetrahedral chains, causing stacking faults along the b direction. A computer simulation was performed, proving that the observed intensity variations along the diffuse scattering rods originates from two different local structures depending on the configuration of the tetrahedral chains. Selected-area electron diffraction experiments exhibit well ordered regions characterized by satellite reflections corresponding to two different superstructures. Both superstructures can be described using the superspace group A21/m(0βγ)0s, with γ = 0.5 and β ≃ 0.27 or β = 0.
doi:10.1107/S0108768111042005
PMCID: PMC3222140  PMID: 22101537
layered brownmillerite; diffuse scattering; stacking faults; modulated structure
3.  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
4.  Determining the structure of a benzene7.2-silicalite-1 zeolite using a single-crystal X-ray method 
An orthorhombic benzene-silicalite-1 single crystal was obtained from a monoclinic twin crystal, and the structure was determined by a single-crystal method for the first time.
A simple method for preparing orthorhombic single crystals of benzene-silicalite-1 was developed. A silicalite-1 crystal was pressed with a weight of 2 g along the +c and −c crystallographic axes while the temperature was increased to 473 K. The temperature was then slowly reduced to 313 K, and these heating and cooling steps were repeated three times. After the orthorhombic single crystals adsorbed benzene, the crystal structure of the resulting benzene-silicalite-1 was determined. There were two kinds of benzene molecules in the asymmetric unit. One was located at the intersection of the straight channels and the sinusoidal channels with the benzene ring parallel to the ac plane. The other benzene was located in the middle of the straight channel.
doi:10.1107/S0108768111038560
PMCID: PMC3222141  PMID: 22101540
ZSM-5; MFI; silicalite-1; benzene-silicalite-1
5.  Deducing chemical structure from crystallographically determined atomic coordinates 
An improved algorithm has been written for assigning chemical structures to incoming entries to the Cambridge Structural Database.
An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures.
doi:10.1107/S0108768111024608
PMCID: PMC3143025  PMID: 21775812
Cambridge Structural Database; structure assignment; catena structure; disorder resolution; Bayesian statistics
6.  Modulated anharmonic ADPs are intrinsic to aperiodic crystals: a case study on incommensurate Rb2ZnCl4  
The superspace maximum entropy method (MEM) density in combination with structure refinements has been used to uncover the modulation in incommensurate Rb2ZnCl4 close to the lock-in transition. Modulated atomic displacement parameters (ADPs) and modulated anharmonic ADPs are found to form an intrinsic part of the modulation. Refined values for the displacement modulation function depend on the presence or absence of modulated ADPs in the model.
A combination of structure refinements, analysis of the superspace MEM density and interpretation of difference-Fourier maps has been used to characterize the incommensurate modulation of rubidium tetrachlorozincate, Rb2ZnCl4, at a temperature of T = 196 K, close to the lock-in transition at T lock-in = 192 K. The modulation is found to consist of a combination of displacement modulation functions, modulated atomic displacement parameters (ADPs) and modulated third-order anharmonic ADPs. Up to fifth-order Fourier coefficients could be refined against diffraction data containing up to fifth-order satellite reflections. The center-of-charge of the atomic basins of the MEM density and the displacive modulation functions of the structure model provide equivalent descriptions of the displacive modulation. Modulations of the ADPs and anharmonic ADPs are visible in the MEM density, but extracting quantitative information about these modulations appears to be difficult. In the structure refinements the modulation parameters of the ADPs form a dependent set, and ad hoc restrictions had to be introduced in the refinements. It is suggested that modulated harmonic ADPs and modulated third-order anharmonic ADPs form an intrinsic part, however small, of incommensurately modulated structures in general. Refinements of alternate models with and without parameters for modulated ADPs lead to significant differences between the parameters of the displacement modulation in these two types of models, thus showing the modulation of ADPs to be important for a correct description of the displacive modulation. The resulting functions do not provide evidence for an interpretation of the modulation by a soliton model.
doi:10.1107/S0108768111013814
PMCID: PMC3098556  PMID: 21586828
aperiodic crystals; incommensurate modulated structures; MEM density; ADPs

Results 1-6 (6)