o-Nitro­aniline, C6H6N2O3, is known to be polymorphic. The α-form is probably amorphous, while the β- and γ-forms are crystalline. Difficulties with the unit-cell determination of the γ-form were reported as a consequence of twinning. In this paper, newly recorded diffraction data of the γ-form of o-nitro­aniline are described that were processed taking into account the two twin lattices. Data were partly deconvoluted and much better agreement was obtained in terms of R1 values and C—C bond precision. The availability of raw data and proper reprocessing using twin lattices is by far superior to efforts to de-twin processed structure factors

Kroon-Batenburg, Loes

Lutz, Martin

Utrecht University Repository

raw data lettersIUCrData (2022). 7, x221059 https://doi.org/10.1107/S2414314622010598 1 of 4ISSN 2414-3146Received 5 July 2022Accepted 3 November 2022Edited by S. J. Coles, University of Southampton,United KingdomKeywords: twinning; scattering; twin interface;raw data.CCDC reference: 2217206Structural data: full structural data are availablefrom iucrdata.iucr.orgPublished under a CC BY 4.0 licenceAccurate intensity integration in the twinned c-formof o-nitroanilineMartin Lutz and Loes Kroon-Batenburg*Department of Chemistry, Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, UtrechtUniversity, Utrecht, The Netherlands. *Correspondence e-mail: l.m.j.kroon-batenburg@uu.nlo-Nitroaniline, C6H6N2O3, is known to be polymorphic. The �-form is probablyamorphous, while the �- and �-forms are crystalline. Difficulties with the unit-cell determination of the �-form were reported as a consequence of twinning. Inthis paper, newly recorded diffraction data of the �-form of o-nitroaniline aredescribed that were processed taking into account the two twin lattices. Datawere partly deconvoluted and much better agreement was obtained in terms ofR1 values and C—C bond precision. The availability of raw data and properreprocessing using twin lattices is by far superior to efforts to de-twin processedstructure factors.Bruker SMART data files and CBF files: https://doi.org/10.5281/zenodo.7193538Metadata imgCIF file: https://doi.org/10.1107/S2414314622010598/ii4001img.cifIntroductiono-Nitroaniline is known to be polymorphic (Aakeröy et al., 1998a,b). The �-form isprobably amorphous, while the �- and �-forms are crystalline. Difficulties with the unit-cell determination of the �-form were reported as a consequence of twinning. The unitcell appears to be C-centered orthorhombic, but was determined to be a pseudo-mero-hedral monoclinic twin by Herbstein (1965), who also observed diffuse streaks along a*.Pseudo-orthorhombic twinning together with unusual extinctions was discussed byDunitz (1964). While he assumed a twin obliquity of 0�, we here show an example wherethis is not exactly the case, i.e. the twin obliquity is 0.743�. The structure was determinedbefore, supposedly from data of untwinned crystals, but the R1 values of 10.9, 7.01 and7.98% remain large (Dhaneshwar et al., 1978; Nieger, 2007; Zych et al., 2007). In thispaper we describe newly recorded diffraction data of the �-form of o-nitroaniline (I) andprocess these by taking into account the two twin lattices. Weshow that the availability of raw data and proper reprocessingusing twin lattices is by far superior to efforts to de-twinprocessed structure factors.Data processing and refinementData were processed in two ways: by using a single lattice,ignoring the second lattice completely, and by using two twinlattices. EVAL software (Schreurs et al., 2010) was used forboth, followed by SADABS/TWINABS (Krause et al., 2015;Sevvana et al., 2019) for scaling. Splitting of the radiation inK�1 and K�2 in a 2:1 ratio is taken into account in the EVALmodel profiles for either lattice. The statistics for the twoapproaches are given in Table 1. Several indicators in thesingle-crystal data processing show that the crystal is not asingle crystal. The first real sign of an alarm occurs when itcomes to the space-group determination: the most likely spaceraw data letters2 of 4 Lutz and Kroon-Batenburg � Twinned �-form of o-nitroaniline IUCrData (2022). 7, x221059Table 1Experimental details.Raw dataDOI https://doi.org/10.5281/zenodo.7193538Data archive ZenodoData format CBFData collectionDiffractometer Bruker Kappa APEXIITemperature (K) 150Detector type APEXII CCDRadiation type Mo K�Wavelength (Å) 0.71073Beam center (mm)   30.401,   30.637Detector axis   ZDetector distance (mm) 41Swing angle (�)   21.52Pixel size (mm) 0.12 � 0.12No. of pixels 512 � 512No. of scans 7Exposure time per frame (s) 10Scan axis Start angle, increment per frame (�) Scan range (�) No. of frames�,   X (! = 164.659�, � = 46.226�) 74.659,   0.300   360 1200!,   X (� =   73.760�, � = 10.746�)   169.393,   0.300   118.2 394!,   X (� =   73.760�, � =   91.253�)   169.393,   0.300   118.2 394!,   X (� = 88.307�, � = 160.033�)   157.189,   0.300   82.2 274!,   X (� = 88.307�, � = 58.033�)   157.189,   0.300   82.2 274!,   X (� =   73.760�, � =   40.253�)   169.393,   0.300   118.2 394!,   X (� =   73.760�, � = 166.747�)   169.393,   0.300   118.2 394Crystal dataChemical formula C6H6N2O2Mr 138.13Crystal system, space group Monoclinic, P21/aa, b, c (Å) 15.2066 (5), 10.0938 (4), 8.3580 (2)� (�) 106.693 (3)V (Å3) 1228.82 (7)Z 8� (mm  1) 0.12Crystal size (mm) 0.37 � 0.30 � 0.16Data processingTwin Single latticeAbsorption correction Multi-scan Multi-scan(TWINABS2012/1; Sevvana et al., 2019) (SADABS; Krause et al., 2015)Tmin, Tmax 0.683, 0.746 0.628, 0.746No. of measured, independent andobserved [I > 2�(I)] reflections26077, 2864, 26292145 overlapping and 842 single reflections and 123systematic absences24760, 2816, 2547Rint 0.028 0.034(sin �/�)max (Å  1) 0.655 0.655RefinementNo. of reflections 2864 2816No. of parameters 198 197H-atom treatment N—H refined freely; C—H refined witha riding modelN—H refined freely; C—H refined witha riding modelR[F2 > 2�(F2)], wR(F2), S 0.0314, 0.0860, 1.085 0.0787, 0.2545, 1.154Twin fraction BASF 0.2003 (10)Weighting scheme a = 0.0449, b = 0.2210 a = 0.0702, b = 6.2812��max, ��min (e Å  3) 0.23,   0.22 0.35,   0.36Bond precision C—C (Å) 0.0017 0.0062group is P21/a but systematic absences for the a-glide plane areclearly violated (reflection condition h0l; h = 2n). Structurerefinement with SHELXL (Sheldrick, 2015) converges at highresiduals R1[I > 2�(I)] = 0.0787 and wR2(all refl.) = 0.2545 andthe proposed weighting scheme is rather unusual. The twotwin lattices are related by a twofold rotation about c,resulting in the twin matrix (  1 0   1 / 0   1 0 / 0 0 1) (seebelow). With only single-crystal structure factors it is stillpossible to use the knowledge of the twin matrix. Inclusion ofthis matrix in the SHELXL refinement assumes that thelattices overlap exactly and the obliquity would be 0�. Inreality, not all reflections overlap and thus the refinementresults improve only slightly {R1[I > 2�(I)] = 0.0678 andwR2(all refl.) = 0.2390}. As a last resort, one can de-twin themerged data with TWINROTMAT in PLATON (Spek, 2020).This produces an HKLF5-type file for refinement in SHELXLin which each reflection is either overlapped or single (935reflections are overlapping). The structure refinementimproved to R1[I > 2�(I)] = 0.0465 and wR2(all refl.) = 0.1332.As we will see below, it is a poor approach for resolving thetwinning issue with processed data, clearly raw diffraction dataare needed to reprocess with two lattices.To show the advantage of proper processing we used twomatrices. One twin component was clearly the largest and weprocessed the data with this lattice while including the secondlattice as interfering in EVAL. Reflections are deconvolutedwhen the covariance of the overlapping intensities is below agiven threshold. This led to 2145 overlapping and 842 singlereflections and 123 systematic absences (Table 1). The agree-ment factors of the SHELXL refinement are much improvedto R1[I > 2�(I)] = 0.0314 and wR2(all refl.) = 0.0860 (Table 1)and the displacement ellipsoids of the two independentmolecules are perfectly reasonable (Fig. 1).The crystal structure has P21/a symmetry with two inde-pendent molecules, which are shown in Fig. 1. The moleculesare connected by hydrogen bonds, forming two-dimensionallayers in the bc plane (Fig. 2).Data descriptionData were collected on our in-house APEXII diffractometerwith Mo K� radiation, with multiple scans (Table 1). In total3324 images were recorded. The unit cell was determined withDIRAX (Duisenberg, 1992) and two lattices were found thatcould be transformed into each other with a nearly twofoldrotation. Pseudo-orthorhombic twinning is characterized by abase-centered orthorhombic twin lattice derived from amonoclinic-P crystal lattice (Dunitz, 1964). The monoclinic Pcell of (I) can be transformed to a near orthorhombic B lattice[the non-standard setting of the space group P21/a was chosenfor compatibility with earlier literature (Herbstein, 1965);base-centered B-orthorhombic was chosen so as to leave b andc unchanged] with the following operation:a0b0c00@1A ¼2 0 10 1 00 0 10@1Aabc0@1Agiving cell parameters a0 = 29.1340 (10), b0 = 10.0938 (4), c0 =8.3580 (2), Å, �0 = 90, �0 = 90.743 (3), � 0 = 90�. The c axis waschosen as the twofold twin rotation axis. Clearly we find a twinobliquity of 0.743 (3)� and a non-merohedral twin. As aconsequence, the orthorhombic B lattices of the individualtwin components do not exactly overlap. If one overlooks thetwinning and indexes the spots as B-centered orthorhombic inspace group B2212, the reflection conditions appear to be:hkl; h + l = 2n, 0k0; k = 2n, which is usual for the space group,raw data lettersIUCrData (2022). 7, x221059 Lutz and Kroon-Batenburg � Twinned �-form of o-nitroaniline 3 of 4Figure 2Hydrogen-bonded layers in the monoclinic structure.Figure 1Molecular structure of the two independent molecules of (I) in thecrystal. Displacement ellipsoids are drawn at the 50% probability level.Hydrogen atoms are drawn as small spheres of arbitrary radii. Themolecules are related by a non-crystallographic twofold axis approxi-mately along a*.and h00; h = 4n, 00 l; l = 4n. The latter two are non-space-group extinctions and exactly such observations are consid-ered as a signal for pseudo-orthorhombic twinning of anunderlying monoclinic lattice (Dunitz, 1964). Processing thedata as single-component orthorhombic does not result in astructure solution, notably because the a glide plane is absentin B2212.The twin rotation about the c-axis results in stacking faultsof the hydrogen-bonded layers. In Fig. 3, the two domains andthe twinning interface is shown. The second lattice wasgenerated by 180� rotation around c followed by a translationover 1/2a, by which the two independent molecules areinterchanged in the position. In fact, the two molecules canalmost be transformed into each other by a twofold rotationalong a0, the long orthorhombic axis, showing that this axis is anear orthorhombic twofold axis. The twinning and stackingfaults follow the OD theory as proposed by Dornberger-Schiff(1966) for similar systems.As a consequence of the twin obliquity ! = 0.743 (3)�,reflections are split in reciprocal space. This can be seen insimulated precession photographs that were generated withthe program PRECESSION in the EVAL package. In the 0thlayers, this mainly affects layer h0l (Fig. 4). In the layers, hk0and 0kl reflections remain nearly unaffected.ReferencesAakeröy, C. B., Nieuwenhuyzen, M. & Price, S. L. (1998a). J. Am.Chem. Soc. 120, 8986–8993.Aakeröy, C. B., Beatty, A. M., Nieuwenhuyzen, M. & Zou, M.(1998b). J. Mater. Chem. 8, 1385–1389.Dhaneshwar, N. N., Tavale, S. S. & Pant, L. M. (1978). Acta Cryst. B34,2507–2509.Dornberger-Schiff, K. (1966). Acta Cryst. 21, 311–322.Duisenberg, A. J. M. (1992). J. Appl. Cryst. 25, 92–96.Dunitz, J. D. (1964). Acta Cryst. 17, 1299–1304.Herbstein, F. H. (1965). Acta Cryst. 19, 590–595.Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J.Appl. Cryst. 48, 3–10.Nieger, M. (2007). CSD Communication (CCDC No. 655336). CCDC,Cambridge, England.Schreurs, A. M. M., Xian, X. & Kroon-Batenburg, L. M. J. (2010). J.Appl. Cryst. 43, 70–82.Sevvana, M., Ruf, M., Usón, I., Sheldrick, G. M. & Herbst-Irmer, R.(2019). Acta Cryst. D75, 1040–1050.Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8.Spek, A. L. (2020). Acta Cryst. E76, 1–11.Zych, T., Misiaszek, T. & Szostak, M. M. (2007). Chem. Phys. 340,260–272.raw data letters4 of 4 Lutz and Kroon-Batenburg � Twinned �-form of o-nitroaniline IUCrData (2022). 7, x221059Figure 3Twin domains viewed down the monoclinic b-axis, with alternate layerscolored in white, blue, green and magenta. The layers have a width of twohydrogen-bonded molecules (see Fig. 2) and have hydrophobic faces. Thesecond lattice (left) has a row of molecules in the blue layer in commonwith that of the white layer in the first lattice (right). The second domainis generated by a twofold rotation around c and a shift over 1/2a. Thepseudo-orthorhombic unit cell is shown in red. The hydrophobic inter-actions between the layers are almost completely conserved across thetwin interface.Figure 4Left: simulated precession photograph in the h0l plane of (I) up to aresolution of 0.9 (Å). The reconstruction is based on seven scans with atotal of 3324 raw images. Right: zoomed image, is from the yellow squarein the left image. White circles are the predicted impacts for the first twincomponent, blue circles for the second.

Accurate intensity integration in the twinned γ-form of o-nitro­aniline

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Accurate intensity integration in the twinned γ-form of o-nitroaniline

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Accurate intensity integration in the twinned γ-form of o-nitro­aniline

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Accurate intensity integration in the twinned γ-form of o-nitroaniline