Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole

Poulain, Agnieszka; Wenger, Emmanuel; Durand, Pierrick; Jarzembska, Katarzyna N.; Kamiński, Radosław; Fertey, Pierre; Kubicki, Maciej; Lecomte, Claude

doi:10.1107/s2052252514002838

Cited by 13 publications

(15 citation statements)

References 41 publications

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“…Additionally, the refined anharmonic parameters appeared to be rather weakly correlated with multipolar parameters (the average correlation coefficient was equal to $ 0.5, the maximal was equal to 0.79 for the C 111 and Z -oriented dipole). These results are among many recent literature reports on this matter (Poulain et al, 2014;Herbst-Irmer et al, 2013;Zhurov et al, 2011;Scheins et al, 2010), where high-quality data allow for clear deconvolution of electron density and thermal motion features.…”

Section: Structure Solution and Refinementsupporting

confidence: 66%

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First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate

Jarzembska

Kamiński

Cyrański

2014

Acta Crystallogr Sect B

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The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 Å(-1) with high completeness (89.1%; Rmrg = 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat and almost featureless. It was possible to derive reliable information on intermolecular interactions to model the anharmonic motion of a water molecule, and also to observe the fine details of the charge density distribution, such as polarization on O and H atoms involved in the strongest hydrogen bonds. When compared with our previous statistical study on oxalic acid data collected with the aid of CCD cameras, the complementary metal-oxide semiconductor (CMOS) detector can certainly be classified as a promising alternative in advanced X-ray diffraction studies.

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Section: Structure Solution and Refinementsupporting

confidence: 66%

“…As illustrated in Fig. 4(a), before the modelling a characteristic alternated residual density pattern (Herbst-Irmer et al, 2013;Poulain et al, 2014) at high-order data is clearly seen. Using only the third-order Gram-Charlier (GC) expansion parameters (Table 3), the anharmonic motion of the O atom was successfully modelled (Fig.…”

Section: Figurementioning

confidence: 85%

First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate

Jarzembska

Kamiński

Cyrański

2014

Acta Crystallogr Sect B

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“…With the help of the fractal dimension plot and artificial data it was shown that neglect of third-order anharmonic motion leads to a characteristic (shashlik-like) pattern in the residual density . This imprint was also found in experimental data HerbstIrmer et al, 2013) and confirmed by other scientists [see, for example, Paul et al (2011) and Poulain et al (2014)]. …”

Section: Introductionsupporting

confidence: 82%

“…This data set corresponds to an anharmonic motion model refinement of the explosive RDX at 20 K (Zhurov et al, 2011). With increasing data quality, anharmonic motion models become more and more important in charge-density studies (see, for example, Meindl et al, 2010;Paul et al, 2011;Herbst-Irmer et al, 2013;Poulain et al, 2014;Jarzembska et al, 2014;Pinkerton et al, 2014, and many more).…”

Section: A Refinement With Few Systematic Errorsmentioning

confidence: 98%

Statistical tests against systematic errors in data sets based on the equality of residual means and variances from control samples: theory and applications

Henn¹,

Meindl

2015

Acta Cryst Sect A

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Statistical tests are applied for the detection of systematic errors in data sets from least-squares refinements or other residual-based reconstruction processes. Samples of the residuals of the data are tested against the hypothesis that they belong to the same distribution. For this it is necessary that they show the same mean values and variances within the limits given by statistical fluctuations. When the samples differ significantly from each other, they are not from the same distribution within the limits set by the significance level. Therefore they cannot originate from a single Gaussian function in this case. It is shown that a significance cutoff results in exactly this case. Significance cutoffs are still frequently used in charge-density studies. The tests are applied to artificial data with and without systematic errors and to experimental data from the literature.

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“…A thorough study on the explosive 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) provided a good example in this respect [21], and it demonstrated the importance of anharmonic atomic displacement parameters (ADPs) for the determination of an accurate molecular electron density distribution (EDD) ρ(r). 2 Other more recent examples where anharmonicity was reported include the free radical p-(methylthio) phenyl nitronyl nitroxide [22], 1-(20-aminophenyl)-2-methyl-4-nitroimidazole [23] and the non-linear optical material 2-methyl-4-nitroaniline (MNA) [24].…”

Section: Introductionmentioning

confidence: 99%

On avoiding negative electron density in Gram-Charlier refinements of anharmonic motion: the example of glutathione

Hübschle

Ruhmlieb

Burkhardt

et al. 2018

Zeitschrift Für Kristallographie - Crystalline Materials

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The structure of glutathione, γ-l-Glutamyl-l-cysteinyl-glycine (C10H17N3O6S), was studied by multi-temperature single-crystal X-ray diffraction. Residual density maps from conventional independent atom model refinement gave indication of anharmonic motion in the molecule. This was further investigated by invariom refinement with anisotropic displacement parameters for all atoms, which described asphericity due to chemical bonding and lone pairs; afterwards only the residual-density signal of anharmonic motion remained. Treating anharmonicity with third-order Gram-Charlier displacement parameters led to regions with unphysical negative electron density. In contrast, a maximum entropy method (MEM) determination of the electron density successfully takes the features into account. Respective difference electron density plots (MEM minus prior and [Invariom+GC] minus invariom) agree well with each other. Challenges in treating and understanding the phenomenon are discussed. A procedure is proposed how unphysical negative electron density can be avoided. It is closely related to the free lunch algorithm.

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Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole

Cited by 13 publications

References 41 publications

First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate

First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate

Statistical tests against systematic errors in data sets based on the equality of residual means and variances from control samples: theory and applications

On avoiding negative electron density in Gram-Charlier refinements of anharmonic motion: the example of glutathione

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