Some errors from the crystallographic literature, some amplifications and a questionable result

Herbstein, F. H.; Hu, Sheng-Zhi; Kapon, Moshe

doi:10.1107/s0108768102010261

Cited by 24 publications

(16 citation statements)

References 31 publications

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“…In view of the importance of the dibenzylidene cyclohexanone series, the present paper reports the crystal structure of the title compound. Its metrical parameters (Table 1) are similar to those observed in other related cyclohexanone derivatives (Ompraba et al, 2003;Yu et al, 2000;Higham et al, 2004;Jia et al, 1989;Quail, Doroudi et al, 2005;Biradha et al, 1997;Kawamata et al, 1998;Yakimanski et al, 1997;Herbstein et al, 2002;Mannan & Rahaman, 1972;Du et View of the molecular structure of (I) with displacement ellipsoids drawn at the 20% probability level.…”

Section: Commentsupporting

confidence: 70%

2,6-Bis(4-methoxybenzylidene)cyclohexanone

Butcher

Yathirajan

Sarojini³

et al. 2006

Acta Cryst E

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Section: Commentsupporting

confidence: 70%

2,6-Bis(4-methoxybenzylidene)cyclohexanone

Butcher

Yathirajan

Sarojini³

et al. 2006

Acta Cryst E

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“…However, crystal twinning commonly occurs and results in diffraction spots of different domains being partially or wholly coincident in the reciprocal space, which in turn makes the analysis of reflection intensities of 'Bijvoet pairs' invalid. Consequently, the space groups of many compounds reported in the literature are doubtful or ambiguous (Baur & Kassner, 1992;Herbstein et al, 2002;Clemente & Marzotto, 2004;Henling & Marsh, 2014;Hu & Ng, 2014). For example, Clemente & Marzotto noted that 'approximately 800 structures' with space groups of 'unnecessarily low symmetry' had been revised and 'nearly 7000 incorrect structures' might be included among the structures reported in the Cambridge Structural Database (CSD; Groom & Allen, 2014; Clemente & Marzotto, 2004).…”

Section: Introductionmentioning

confidence: 99%

Polymorphism of NaVO₂F₂: aP2₁/csuperstructure with pseudosymmetry ofP2₁/min the subcell

Wang

Huang

et al. 2015

Acta Crystallogr C

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The ADDSYM routine in the program PLATON [Spek (2015). Acta Cryst. C71, 9-18] has helped researchers to avoid structures of (metal-)organic compounds being reported in an unnecessarily low symmetry space group. However, determination of the correct space group may get more complicated in cases of pseudosymmetric inorganic compounds. One example is NaVO2F2, which was reported [Crosnier-Lopez et al. (1994). Eur. J. Solid State Inorg. Chem. 31, 957-965] in the acentric space group P2₁ based on properties but flagged by ADDSYM as (pseudo)centrosymmetric P2₁/m within default distance tolerances. Herein a systematic investigation reveals that NaVO2F2 exists in at least four polymorphs: P2₁, (I), P2₁/m, (II), P2₁/c, (III), and one or more low-temperature ones. The new centrosymmetric modification, (III), with the space group P2₁/c has a similar atomic packing geometry to phase (I), except for having a doubled c axis. The double-cell of phase (III) arises from atomic shifts from the glide plane c at (x, ¼, z). With increasing temperature, the number of observed reflections decreases. The odd l reflections gradually become weaker and, correspondingly, all atoms shift towards the glide plane, resulting in a gradual second-order transformation of (III) into high-temperature phase (II) (P2₁/m) at below 493 K. At least one first-order enantiotropic phase transition was observed below 139 K from both the single-crystal X-ray diffraction and the differential scanning calorimetry analyses. Periodic first-principles calculations within density functional theory show that both P2₁/c superstructure (III) and P2₁ substructure (I) are more stable than P2₁/m structure (II), and that P2₁/c superstructure (III) is more stable that P2₁ substructure (I).

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“…The literature was searched for review papers on missed space-group symmetry. These papers (Clemente, 2003;Clemente & Marzotto, 2003;Marsh & Clemente, 2007;Marsh, 1997Marsh, , 1999Marsh, , 2002Marsh, , 2005Herbstein & Marsh, 1998;Marsh & Spek, 2001;Herbstein et al, 2002;Marsh et al, 2002;Henling & Marsh, 2014) describe crystal structures which were originally published with too low symmetry, or where the space group was questionable. In order to investigate if DFT-D is able to find additional symmetry, the original structures were minimized.…”

Section: Optimization Of 200 Structures With Reported Missed Symmetrymentioning

confidence: 99%

“…Therefore, in the current paper we wish to validate the extent to which DFT-D energy minimizations can be employed to assign correct space-group symmetries by adding 200 more energy-minimized crystal structures to our validation set, bringing the total to 640 molecular crystal structures. Famous in this connection are of course the hundreds of cases of missed symmetry in SX structures uncovered by crystallographers such as Baur (Baur & Tillmanns, 1986;Baur & Kassner, 1992), Marsh or Herbstein (Marsh & Herbstein, 1983,1988Marsh, 1997Marsh, , 1999Marsh, , 2002Marsh, , 2005Herbstein & Marsh, 1998;Marsh & Spek, 2001; Herbstein et al, 2002;Marsh et al, 2002;Henling & Marsh, 2014), Clemente (Clemente, 2003, ISSN 2052 # 2017 International Union of Crystallography 2005; Clemente & Marzotto, 2003;Marsh & Clemente, 2007) and others. Software and algorithms for the detection of missed symmetry, operating on the atomic coordinates of experimental crystal structures, can be found in the literature (Le Page, 1988;Herbst-Irmer, 1990;Marsh & Spek, 2001).…”

Section: Introductionmentioning

confidence: 99%

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

Hempler

Schmidt

Streek

2017

Acta Crystallogr B Struct Sci Cryst Eng Mater

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More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å. For 98.5% of 200 molecular crystal structures published with missed symmetry, the correct space group is identified; there are no false positives. Very small, very symmetrical molecules can end up in artificially high space groups upon energy minimization, although this is easily detected through visual inspection. If the space group of a crystal structure determined from powder diffraction data is ambiguous, energy minimization with DFT-D provides a fast and reliable method to select the correct space group.

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Some errors from the crystallographic literature, some amplifications and a questionable result

Cited by 24 publications

References 31 publications

2,6-Bis(4-methoxybenzylidene)cyclohexanone

2,6-Bis(4-methoxybenzylidene)cyclohexanone

Polymorphism of NaVO₂F₂: aP2₁/csuperstructure with pseudosymmetry ofP2₁/min the subcell

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

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Some errors from the crystallographic literature, some amplifications and a questionable result

Cited by 24 publications

References 31 publications

2,6-Bis(4-methoxybenzylidene)cyclohexanone

2,6-Bis(4-methoxybenzylidene)cyclohexanone

Polymorphism of NaVO2F2: aP21/csuperstructure with pseudosymmetry ofP21/min the subcell

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

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Polymorphism of NaVO₂F₂: aP2₁/csuperstructure with pseudosymmetry ofP2₁/min the subcell