Constraints and restraints in crystal structure analysis

Immirzi, A.

doi:10.1107/s0021889808044142

Cited by 5 publications

(3 citation statements)

References 13 publications

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“…As powder diffraction methods of molecular materials of moderate complexity do not have the same “resolving power” of conventional single crystal analyses, the structural models which can be refined need to rely on known, or easily assessable, preconceived units; additionally, mathematical restraints limiting the number of free parameters and providing a stable convergence to the least-squares (Rietveld-like) refinement are also typically added . Accordingly, a single isotropic thermal factor was employed for all atoms (disregarding the differential connectivities) and, above all, fixing intramolecular distances and angles (much stiffer than torsions) to known values (see Experimental Section).…”

Section: Resultsmentioning

confidence: 99%

Disclosing the Rich Crystal Chemistry of Lesinurad by ab Initio Laboratory X-ray Powder Diffraction Methods

Terruzzi

Bellomi²,

Marras³

et al. 2018

Crystal Growth & Design

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Lesinurad, a uric acid reabsorption inhibitor that received Food and Drug Administration approval in 2015, is known to crystallize in three unsolvated crystal forms and in a few solvated phases. The structures of the former have been determined by state-of-the-art powder diffraction methods, highlighting significant conformational as well as supramolecular differences, resulting in hydrogen bonded centrosymmetric dimers (Form 1) or helical chains (Form 2). In the complex crystal packing in Form 3, additional one-dimensional (1D) ribbons held together by unexpected CO···Br interactions of the halogen-bond type are found. Thermal analyses and variable-temperature powder diffraction measurements (including high-temperature synchrotron X-ray diffraction experiments) provided evidence for the reversible formation of a new phase, Form 2hT, obtained upon heating above 100 °C powders of Form 2. Structure solution and refinement of the high-temperature phase made it possible to attribute the structural change to a 60° rotation of the cyclopropyl residue, leaving unaffected the conformation of the (longer) polar branch and the supramolecular 1D helical chain arrangement found in the RT phase.

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Section: Resultsmentioning

confidence: 99%

Disclosing the Rich Crystal Chemistry of Lesinurad by ab Initio Laboratory X-ray Powder Diffraction Methods

Terruzzi

Bellomi²,

Marras³

et al. 2018

Crystal Growth & Design

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“…This applies in particular for the refinement of target molecules along with only weakly interacting disordered solvents. However, when the interest lies in the disordered part of a structure, there is always the question about what additional information is obtained beyond what is already known or included explicitly; see also Immirzi (2009) and Spek (2018).…”

Section: Constraints and Restraintsmentioning

confidence: 99%

checkCIF validation ALERTS: what they mean and how to respond

Spek

2020

Acta Crystallogr E Cryst Commun

956

948

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Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of interest and their interpretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with interesting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and interpretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, interoperable, and reusable) initiative [Helliwell (2019). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and interpretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.

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“…The modelling algorithm discussed above, though unfit for structure discovery, could well be adopted for structural refinement, allowing only the torsion angle adjustment. The advantage over the most commonly used procedures (based on atomic coordinates and substantial use of restraints; see Ten Eyck & Watenpaugh, 2001) is a marked reduction in the number of variables employed (Immirzi, 2009).…”

Section: Cyclo-mentioning

confidence: 99%

Finding crystal structures of peptides by random search and evolutionary algorithms

2009

Self Cite

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Structures of crystalline peptides can be established using a special computer program, PTRY, which needs only limited diffraction data, the lattice constants, space group and primary structure. Crystal structures can be found by doing a random search in the internal‐coordinate space and `combinations' among the plausible solutions found according to the genetic rules (crossover and mutation). PTRY, which also performs structural refinement, is simple and user friendly. Because only limited diffraction data are needed, data from powder diffraction spectra could be used, as well as single‐crystal data.

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Constraints and restraints in crystal structure analysis

Abstract: The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed.

Cited by 5 publications

References 13 publications

Disclosing the Rich Crystal Chemistry of Lesinurad by ab Initio Laboratory X-ray Powder Diffraction Methods

Disclosing the Rich Crystal Chemistry of Lesinurad by ab Initio Laboratory X-ray Powder Diffraction Methods

checkCIF validation ALERTS: what they mean and how to respond

Finding crystal structures of peptides by random search and evolutionary algorithms

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