research papers\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296

Can we trust the experiment? Anisotropic dis­placement parameters in 1-(halometh­yl)-3-nitro­benzene (halogen = Cl or Br)

aInstitute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany, bInstitute of Molecular Science, Shanxi University, 030006 Taiyuan, Shanxi, People's Republic of China, cJülich-Aachen Research Alliance (JARA-HPC), Forschungszentrum Jülich, 52056 Aachem, Germany, and dHoffmann Institute of Advanced Materials, Shenzhen, Liuxian 7098, People's Republic of China
*Correspondence e-mail: ullrich.englert@ac.rwth-aachen.de, drons@HAL9000.ac.rwth-aachen.de

Edited by A. L. Spek, Utrecht University, The Netherlands (Received 2 April 2020; accepted 7 May 2020; online 20 May 2020)

1-(Chloro­meth­yl)-3-nitro­benzene, C7H6NClO2, and 1-(bromo­meth­yl)-3-nitro­benzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In-house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in-house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.

1. Introduction

Careful diffraction experiments on crystals of reasonable quality provide reliable intensity data from which atomic positions and anisotropic displacement parameters (ADPs) can be derived almost routinely. The alternative route towards ADPs, namely, their calculation from first principles, has made good progress (George et al., 2015a[George, J., Deringer, V. L. & Dronskowski, R. (2015a). Inorg. Chem. 54, 956-962.],b[George, J., Wang, A., Deringer, V. L., Wang, R., Dronskowski, R. & Englert, U. (2015b). CrystEngComm, 17, 7414-7422.], 2016[George, J., Deringer, V. L., Wang, A., Müller, P., Englert, U. & Dronskowski, R. (2016). J. Chem. Phys. 145, 234512.], 2017[George, J., Wang, R., Englert, U. & Dronskowski, R. (2017). J. Chem. Phys. 147, 074112.]; Deringer et al., 2014[Deringer, V. L., Stoffel, R. P., Togo, A., Eck, B., Meven, M. & Dronskowski, R. (2014). CrystEngComm, 16, 10907-10915.], 2016[Deringer, V. L., Wang, A., George, J., Dronskowski, R. & Englert, U. (2016). Dalton Trans. 45, 13680-13685.], 2017[Deringer, V. L., George, J., Dronskowski, R. & Englert, U. (2017). Acc. Chem. Res. 50, 1231-1239.]; Baima et al., 2016[Baima, J., Zelferino, A., Olivero, P., Erba, A. & Dovesi, R. (2016). Phys. Chem. Chem. Phys. 18, 1961-1968.]; Lane et al., 2012[Lane, N. J., Vogel, S. C., Hug, G., Togo, A., Chaput, L., Hultman, L. & Barsoum, M. W. (2012). Phys. Rev. B, 86, 214301.]; Madsen et al., 2013[Madsen, A. Ø., Civalleri, B., Ferrabone, M., Pascale, F. & Erba, A. (2013). Acta Cryst. A69, 309-321.]; Pozzi et al., 2013[Pozzi, C. G., Fantoni, A. C., Goeta, A. E., de Matos Gomes, E., McIntyre, G. J. & Punte, G. (2013). Chem. Phys. 423, 85-91.]; Dittrich et al., 2012[Dittrich, B., Pfitzenreuter, S. & Hübschle, C. B. (2012). Acta Cryst. A68, 110-116.]).

This progress has been benchmarked by comparison with the results from single-crystal X-ray or neutron diffraction. In this context, a `heavy atom problem' with ADPs from theory was suspected (Deringer et al., 2016[Deringer, V. L., Wang, A., George, J., Dronskowski, R. & Englert, U. (2016). Dalton Trans. 45, 13680-13685.]) but not conclusively proven. We therefore decided to calculate the ADPs in two iso­morphous (Authier & Chapuis, 2014[Authier, A. & Chapuis, G. (2014). Editors. A Little Dictionary of Crystallography. Chester, UK: IUCr.]; IUCr Online Dic­tionary of Crystallography, 2017[Online Dictionary of Crystallography (2017). Isomorphous Crystals. https://dictionary.iucr.org/Isomorphous_crystals.]) organic crystals and com­pare the results from theory to their experimental counterparts. The nitro­aromatic compounds 1-(chloro­meth­yl)-3-nitro­ben­zene, 1, and 1-(bromo­meth­yl)-3-nitro­benzene, 2 (Fig. 1[link]), were identified as suitable test candidates: they share the same crystal chemistry but differ significantly with respect to the mass and electron count of the heavy atom involved, i.e. Cl versus Br.

[Figure 1]
Figure 1
Chemical diagram (left) for 1-(chloro­meth­yl)-3-nitro­benzene (1) and 1-(bromo­meth­yl)-3-nitro­benzene (2), and the unit cell (right) of 1 at 100 K based on an in-house single-crystal X-ray diffraction experiment (data set 1a).

The crystal structures of both compounds have been reported previously: a single-crystal diffraction experiment at standard resolution and room temperature was conducted on 1 [Cambridge Structural Database (CSD; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) refcode PUJSUJ (Abbasi et al., 2010[Abbasi, M. A., Jahangir, M., Akkurt, M., Aziz-ur-Rehman, Khan, I. U. & Sharif, S. (2010). Acta Cryst. E66, o608.])]. More relevant in the context of this work is the previous report on 2 (CSD refcode INEFIS; Maris, 2016[Maris, T. (2016). Private communication (deposition number 1476711). CCDC, Cambridge, England.]) because it was based on diffraction data collected at 100 K, the same temperature as in our case; we will come back to this CSD communication in more detail below.

2. Experimental

Compounds 1 and 2 were obtained from Sigma–Aldrich and recrystallized from methanol by slow evaporation at room tem­perature. The elevated vapour pressure of these com­pounds does not permit their storage for periods longer than a few weeks. An Oxford Cryostream device was used to maintain a constant data-collection temperature of 100 K.

Synchrotron data were collected at the DESY Hamburg, beamline P24 for Chemical Crystallography at PETRA-III on the κ diffractometer (station EH1) at a photon energy of 20 keV (λ = 0.61992 Å). A Dectris CdTe 1M area detector was used and the exposure time per frame was 5 s. Data were processed with XDS (Kabsch et al., 2010[Kabsch, W. (2010). Acta Cryst. D66, 125-132.]) and corrected for absorption with SADABS (Bruker, 2015[Bruker (2015). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]).

H atoms were introduced in calculated positions and treated as riding, with C—H distances of 0.95 (aromatic) or 0.99 Å (methyl­ene) and with Uiso(H) = 1.2Ueq(C). Crystal data, data collection parameters and key quality indicators have been compiled in Table 1[link].

Table 1
Experimental details

For all structures: monoclinic, P21/c, Z = 4. Experiments were carried out at 100 K. H-atom parameters were constrained.

  1 2
  1a 1b 2a 2b
Crystal data
Chemical formula C7H6ClNO2 C7H6BrNO2
Mr 171.58 216.04
a, b, c (Å) 11.7867 (11), 4.4744 (4), 15.0453 (14) 11.785 (4), 4.4690 (9), 15.004 (4) 12.1412 (5), 4.4763 (2), 15.0876 (6) 12.152 (9), 4.470 (3), 15.070 (11)
β (°) 112.464 (7) 112.537 (6) 112.626 (3) 112.56 (2)
V3) 733.26 (12) 729.9 (3) 756.87 (6) 756.0 (9)
Radiation type Mo Kα Synchrotron, λ = 0.61992 Å Mo Kα Synchrotron, λ = 0.61992 Å
μ (mm−1) 0.46 0.32 5.37 3.76
Crystal size (mm) 0.28 × 0.17 × 0.04 0.12 × 0.10 × 0.04 0.23 × 0.22 × 0.04 0.10 × 0.06 × 0.04
 
Data collection
Diffractometer Stoe STADIVARI with a DECTRIS Pilatus 200K detector Kappa diffractometer (EH1) with Dectris CdTe area detector Stoe STADIVARI with a DECTRIS Pilatus 200K detector Kappa diffractometer (EH1) with Dectris CdTe area detector
Absorption correction Multi-scan [LANA (Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]; Koziskova et al., 2016[Koziskova, J., Hahn, F., Richter, J. & Kožíšek, J. (2016). Acta Chim. Slov. 9, 136-140.]) in X-AREA (Stoe & Cie, 2017[Stoe & Cie (2017). X-AREA. Stoe & Cie GmbH, Darmstadt, Germany.])] Multi-scan (SADABS; Bruker, 2015[Bruker (2015). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan [LANA (Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]; Koziskova et al., 2016[Koziskova, J., Hahn, F., Richter, J. & Kožíšek, J. (2016). Acta Chim. Slov. 9, 136-140.]) in X-AREA (Stoe & Cie, 2017[Stoe & Cie (2017). X-AREA. Stoe & Cie GmbH, Darmstadt, Germany.])] Multi-scan (SADABS; Bruker, 2015[Bruker (2015). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.545, 1.000 0.728, 0.863 0.302, 1.000 0.604, 0.747
No. of measured, independent and observed [I > 2σ(I)] reflections 34338, 3231, 2604 19608, 3194, 2947 37127, 3332, 2062 18687, 3233, 3018
Rint 0.035 0.110 0.165 0.056
(sin θ/λ)max−1) 0.807 0.807 0.807 0.806
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.085, 1.06 0.043, 0.122, 1.07 0.037, 0.075, 1.09 0.033, 0.090, 1.10
No. of reflections 3231 3194 3332 3233
No. of parameters 100 101 101 101
Δρmax, Δρmin (e Å−3) 0.52, −0.23 0.63, −0.48 0.93, −0.60 0.91, −1.29
Computer programs: PILATUS, RECIPE, INTEGRATE and LANA in X-AREA (Stoe & Cie, 2017[Stoe & Cie (2017). X-AREA. Stoe & Cie GmbH, Darmstadt, Germany.]), XDS (Kabsch et al., 2010[Kabsch, W. (2010). Acta Cryst. D66, 125-132.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and SHELXL2018 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]).

Electronic-structure calculations based on density-functional theory (DFT) were performed using the Vienna ab initio simulation package (Version 5.4.4) (Kresse & Hafner, 1993[Kresse, G. & Hafner, J. (1993). Phys. Rev. B, 47, 558-561.], 1994[Kresse, G. & Hafner, J. (1994). Phys. Rev. B, 49, 14251-14269.]; Kresse & Furthmüller, 1996a[Kresse, G. & Furthmüller, J. (1996a). Comput. Mater. Sci. 6, 15-50.],b[Kresse, G. & Furthmüller, J. (1996b). Phys. Rev. B, 54, 11169-11186.]). The PBE functional (Perdew et al., 1996[Perdew, J. P., Burke, K. & Ernzerhof, M. (1996). Phys. Rev. Lett. 77, 3865-3868.]), in conjunction with the projector-augmented wave method (Kresse & Joubert, 1999[Kresse, G. & Joubert, D. (1999). Phys. Rev. B, 59, 1758-1775.]; Blöchl, 1994[Blöchl, P. E. (1994). Phys. Rev. B, 50, 17953-17979.]), were utilized. Additionally, the D3 dispersion correction of Grimme and co-workers in combination with Becke–Johnson damping was used to account for van der Waals inter­actions (Grimme et al., 2010[Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. (2010). J. Chem. Phys. 132, 154104.], 2011[Grimme, S., Ehrlich, S. & Goerigk, L. (2011). J. Comput. Chem. 32, 1456-1465.]). The kinetic energy cutoff of the plane wave expansion was limited to 500 eV.

The structures under investigation were optimized with respect to the energy, using a convergence criterion of 10−6 eV with regard to the structural optimization and 10−8 eV for the electronic steps. After checking the k-point convergence in the calculations, supercells were created based on the optimized structures with Phonopy (Togo et al., 2008[Togo, A., Oba, F. & Tanaka, I. (2008). Phys. Rev. B, 78, 134106.]; Togo & Tanaka, 2015[Togo, A. & Tanaka, I. (2015). Scr. Mater. 108, 1-5.]). All supercells had a length of at least about 15 Å in each direction. The subsequent phonon calculations were performed with 27 × 62 × 22 q-points for both structures, concerning the phononic DOS (density of phonon states, DPS) and thermal displacements, as implemented in Phonopy, while using a frequency cutoff of 0.1 THz. A finite displacement (Parlinski et al., 1997[Parlinski, K., Li, Z. Q. & Kawazoe, Y. (1997). Phys. Rev. Lett. 78, 4063-4066.]) of 0.01 Å was used for the calculations, as mentioned above. However, it should be noted that the supercell calculations were only performed at the Γ point. The conversion of the crystallographic coordinates to Cartesian coordinates (Grosse-Kunstleve & Adams, 2002[Grosse-Kunstleve, R. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 477-480.]) was per­formed by a custom-made program, namely, the Mol­ecular Toolbox (George, 2016[George, J. (2016). Molecular Toolbox, This code is freely available via the Internet at http://www.ellipsoids.de, together with additional information regarding ADP computation.]), written in MATLAB (MATLAB, 2016[MATLAB (2016). The MathWorks Inc., Natick, Massachusetts, USA. https://www.mathworks.com/.]). Moreover, this program was used to calculate the root-mean-square of the Cartesian deviations (RMS) (George et al., 2014[George, J., Deringer, V. L. & Dronskowski, R. (2014). Inorg. Chem. 54, 956-962.]).

The quasiharmonic approximation (Stoffel et al., 2010[Stoffel, R. P., Wessel, C., Lumey, M. W. & Dronskowski, R. (2010). Angew. Chem. Int. Ed. 49, 5242-5266.]) was also used by optimizing the initial structure for various compression and expansion factors of the unit-cell volume. This procedure was carried out in steps of 0.01 in the range from 0.96 to 1.04. The subsequent phonon calculations were performed as described above. After calculating the thermal properties and energies, the Vinet equation of state (Vinet et al., 1987[Vinet, P., Smith, J. R., Ferrante, J. & Rose, J. H. (1987). Phys. Rev. B, 35, 1945-1953.]), as implemented in Phonopy, was used to predict the thermal expansion of the system at 100 K. The following steps were performed as described above for the harmonic case, but with a unit cell relaxed under the estimated thermal expansion.

3. Results and discussion

Our initial diffraction experiments were conducted with in-house equipment at 100 K. Mo Kα radiation from a microfocus tube was used, and data collections extended to a resolution of 0.62 Å (λmax = 35°). We will refer to these data sets as 1a and 2a. A first comparison between the experimental and energy-minimized crystal structures in terms of lattice parameters and overall residuals of mean Cartesian displacements (RMS) is provided in Table 2[link] and documents a good match.

Table 2
Experimental (exp) and theoretically (theo) predicted lattice parameters, monoclinic angle, volume of the unit cell and root-mean-square (RMS) values of Cartesian deviations

  1 2
  Exp* Theo Exp* Theo
a (Å) 11.7867 (11) 11.9202 12.152 (9) 12.2703
b (Å) 4.4744 (4) 4.3898 4.470 (3) 4.3909
c (Å) 15.0453 (14) 15.0807 15.070 (11) 15.1254
β (°) 112.464 (7) 112.584 112.56 (2) 112.621
RMS 0.0920 0.0943
V3) 733.26 (12) 728.63 756.0 (9) 752.23
(*) Experimental values for compound 1 are based on in-house intensities (1a) and those for compound 2 stem from synchrotron intensities (2b).

Lattice parameters of the minimum energy structures match those observed experimentally equally well for 1 and 2, but a different picture is obtained when displacement parameters are considered. At low temperatures, such as 100 or 150 K, theoretical ADPs from first principles based on the harmonic approximation can be expected to match experiments reasonably well (George et al., 2015a[George, J., Deringer, V. L. & Dronskowski, R. (2015a). Inorg. Chem. 54, 956-962.],b[George, J., Wang, A., Deringer, V. L., Wang, R., Dronskowski, R. & Englert, U. (2015b). CrystEngComm, 17, 7414-7422.]; Deringer et al., 2016[Deringer, V. L., Wang, A., George, J., Dronskowski, R. & Englert, U. (2016). Dalton Trans. 45, 13680-13685.]; Mroz et al., 2019[Mroz, D., George, J., Kremer, M., Wang, R., Englert, U. & Dronskowski, R. (2019). CrytEngComm, 21, 6396-6404.]).

Fig. 2[link] shows that this is only true for the home-lab data associated with chloro derivative 1 because the slope (0.944) is close to unity; for heavy-atom structure 2, the apparent underestimation by theory versus data set 2a (slope = 0.863) is more pronounced than expected. This trend can alternatively be visualized when the experimental ADPs for both isomorphous compounds are correlated with each other (Fig. 3[link]). The lower slope of 0.788 in this figure indicates that the experimental ADPs derived from 1a, designated as Ux(1a), stay smaller than those obtained from 2a, given as Ux(2a), throughout. If we trust in the home-lab data collected on the diffractometer and the same (low) temperature of 100 K, the ADPs for 2 are significantly larger than for the lighter congener 1. Despite their very close structural relationship, these compounds represent two solids with different composition: one may not reasonably expect `the same' displacement for both! Experimental differences as large as those indicated by Figs. 2[link] and 3[link](a), however, must necessarily raise suspicion. Inter­estingly enough, theory predicts (Fig. 3[link]b) more similar displacements (slope = 0.848) for both isomorphous com­pounds, especially for the less peripheral C atoms, depicted as red data points, which lie close to the diagonal of this subfigure. It should be noted that the threefold standard uncertainties of the experimental values are too small to be visible.

[Figure 2]
Figure 2
Scatter plots of the theoretical and experimental main-axis components Ux (x = 1, 2 or 3) with linear fits and coefficients of determination (CODs) for 100 K in the harmonic approximation. The superscript notation `exp' denotes experimental values and `theo' stands for theoretical values. (a) Plot for compound 1, data set 1a. (b) Plot for compound 2, data set 2a.
[Figure 3]
Figure 3
(a) Scatter plot of the experimental main-axis components derived from data set 1a versus the experimental main-axis components derived from data set 2a. (b) Analogous to the scatter plot in part (a), but now correlating theoretical results for 1 with those for 2. The main axes components of the C atoms are highlighted in red. All other atoms are portrayed in blue.

In addition to this semiqu­anti­tative tool of comparison, the quasiharmonic approximation was tested for compound 2; the results are shown in Fig. S1 (see supporting information). Here, one finds the expected result that the quasiharmonic approximation improves on the amplitude of the ADPs by incorporating temperature effects, thereby leading to larger values. However, in this case, the approach results in a clear overestimation (slope = 1.185), as also frequently seen (George et al., 2017[George, J., Wang, R., Englert, U. & Dronskowski, R. (2017). J. Chem. Phys. 147, 074112.]).

In view of the marked discrepancy between the ADPs derived from data sets 1a and 2a, the question arises whether our experimental data are sufficiently reliable to benchmark our theoretical results and diagnose a potential `heavy atom' problem. They might also be affected by systematic errors, in particular when the high absorption of the atom type Br in 2 for Mo Kα radiation (data set 2a) is taken into account.

Two potentially relevant aspects of absorption may be addressed at the same time when home-lab Mo Kα radiation is replaced by a shorter wavelength at a synchrotron; the shorter wavelength will lead to a lower linear absorption coefficient for 2, and the high flux of the synchrotron will allow the use of significantly smaller crystals. Our experiments were conducted at beamline P24 of the DESY; we will refer to the resulting intensity data as 1b and 2b. The synchrotron facility eliminated another possible systematic error with the experimental data: modern radiation sources, such as microfocus and metal jet sources, typically produce beams of a small diameter at the sample position, whereas P24 optics ensure that even large crystals of 0.2 mm are completely illuminated. We will come back to this aspect below. Fig. 4[link] compiles displacement ellipsoid plots for 2 and 1 based on experimental diffraction data. Clearly, the too-large ADPs of 2 as given by the laboratory data 2a using Mo Kα radiation (Fig. 4a[link]) become significantly smaller using synchrotron radiation (2b; Fig. 4b[link]), and then they resemble those of 1 based on data set 1a obtained with Mo Kα radiation (Fig. 4c[link]).

[Figure 4]
Figure 4
Displacement ellipsoid plots (50% probability for the complete mol­ecules and 90% probability for the magnification at the bottom showing atoms C4, C5 and C6) based on experimental diffraction data. (a) ADPs for 2, based on data set 2a, Mo Kα radiation; (b) ADPs for 2, based on data set 2b, synchrotron radiation (λ = 0.61992 Å); (c) ADPs for 1, based on data set 1a, Mo Kα radiation.

In more general terms, Fig. 5[link] evidences that ADPs based on intensity data collected at the synchrotron compare much more favourably to theory in terms of absolute numbers (mirrored from the slopes). Additionally, the correlation between the two experimental data sets stemming from synchrotron measurements is also more satisfying.

[Figure 5]
Figure 5
(a) Scatter plot of experimental main-axis components derived from data set 1b versus the experimental main-axis components derived from data set 2b. The main axes components of the C atoms are highlighted in red. All other atoms are portrayed in blue. (b) Correlation of the theoretical results for 2 with the synchrotron data 2b.

As an additional test, the diffraction experiment on 1 was repeated at the synchrotron; both home lab (1a) and synchrotron data (1b) are almost superimposable. The corresponding correlation is shown in the supporting information (Fig. S2). Moreover, the supporting information contain more details of further theoretical results.

It is important to note that the results of both diffraction experiments on 2, at the usual Mo Kα home source and at the synchrotron, result in ADPs which comply with Hirshfeld's rigid bond test (Hirshfeld, 1976[Hirshfeld, F. L. (1976). Acta Cryst. A32, 239-244.]), a well-established requirement for mol­ecular crystals. Even better, the ADPs derived from both data collections agree with respect to the essential message about the main directions of mol­ecular motion, whereas their disagreement largely corresponds to the amplitudes. We have recently suggested (Mroz et al., 2019[Mroz, D., George, J., Kremer, M., Wang, R., Englert, U. & Dronskowski, R. (2019). CrytEngComm, 21, 6396-6404.]) that the directionality of sufficiently prolate ADPs provides a simple way to visually compare the main modes of thermal movement suggested by theory and experiment. The corresponding synoptic picture for the alternative diffraction data on 2 is provided in Fig. 6[link]. The analogous analysis of ADP directionality for 1 has been compiled in the supporting information.

[Figure 6]
Figure 6
Comparison between sufficiently anisotropic displacement ellipsoids (Umax/Umin > 1.8) and the resulting angles between the largest theoretical (blue) and experimental (red) main-axes components for data set 2b at 100 K. ADPs are derived from intensity data collected at the synchrotron. The structure is drawn in the theoretically predicted coordinate system.

Fig. 6[link] shows that the agreement between the theoretical ADPs for 2 and the experimental ones derived from synchrotron experiments (data set 2b) is satisfying. The only qualitative exception occurs for one O atom where the resulting angle is slightly larger than usual but still in a reasonable range, and such a deviation is not too surprising. The corresponding picture for the data set based on Mo Kα radiation is shown in the supporting information. They essentially differ with respect to size, with a ratio Ueq(Mo Kα):Ueq(sync) = 1.22 (2), whereas the correspondence of the directions is qualitatively the same. The results of an earlier diffraction experiment on 2 are available as a private communication (CSD refcode INEFIS; Maris, 2016[Maris, T. (2016). Private communication (deposition number 1476711). CCDC, Cambridge, England.]). This diffraction experiment was performed with Ga Kα radiation from a metal jet source at 100 K, i.e. at the same temperature as our data collections. Both unit-cell volume and geometry confirm this published data-collection temperature. Similar ADPs might therefore be expected, but the displacement parameters from INEFIS are about twice as large as ours. We are not in a position to give a reliable inter­pretation of the apparent trend Ueq(sync) < Ueq(Mo Kα) << Ueq(Ga Kα), but it is tempting to speculate about possible reasons. When the linear absorption coefficients (μ) for the different wavelengths and the sample sizes (r) in all three experiments are taken into account, we find μr(sync) < μr(Mo Kα) < μr(Ga Kα). Moreover, one might expect different illumination for the three samples, with the largest beam diameter at the present setup of synchrotron beamline P24 and the smallest one for the metal jet. Hence, the very large ADPs seen in INEFIS might be an artefact going back to strong absorption and insufficient illumination, but this hypothesis needs independent experimental verification. Multi-scan absorption corrections, such as those employed here, have become the de facto standard for diffraction data collected with area detectors. As these techniques rely on the comparison between symmetry-equivalent intensities, they necessarily require an elevated redundancy; this journal suggests at least a fourfold multiplicity of observations for multi-scan corrections. As symmetry-equivalent reflections necessarily share the same diffraction angle, a second quasi-spherical correction has to account for the 2θ dependence of absorption. Both corrections together, i.e. for very high redundancies and with a perfectly chosen quasi-radius for the spherical correction, should ideally correspond to the classical analytical absorption correction (de Meulenaer & Tompa, 1965[Meulenaer, J. de & Tompa, H. (1965). Acta Cryst. 19, 1014-1018.]) based on indexed crystal faces. The latter approach only corrects for absorption and requires complete illumination of the crystal; additional corrections, e.g. for crystal decay, may be performed independently. In contrast, multi-scan corrections can to a certain extent even handle variable illumination or crystal decay via a (restrained) incident beam scale factor (Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.]). If one wants to establish to what extent either absorption or variable illumination are responsible for apparent ADP problems, diffraction data on the same crystal should be collected as a function of beam size and wavelength, and multi-scan corrections should be tested as a function of multiplicity of observations. If the aim are benchmark ADPs, absorption and incomplete illumination should be avoided.

4. Conclusions

We set out to benchmark ADPs based on dispersion-corrected DFT calculations on the harmonic approximation, and it turned out that our in-house experiment, despite elevated redundancy and resolution, was not really able to do so. An alternative experiment at a synchrotron beamline at the same temperature but on a smaller crystal and with a short wavelength gave results in better agreement with theory. We do not dwell on compiling all possible sources of error but rather draw three optimistic conclusions: (i) the quality of theoretically calculated ADPs may challenge that of standard experiments, (ii) the directionality of the ADPs based on the intensity data of our in-house diffractometer match that obtained at the synchrotron beamline even if the amplitudes do not agree and (iii) for the (many!) crystal structures with minor absorption effects only, ADPs from good in-house data match those obtained at the synchrotron beamline; compound 1, with its unexceptional absorption properties, provides a good example for that statement. In our future work, we will attempt to gain insight into the various sources of experimental error. The calculation of absorption-affected data by analytical methods, followed by their treatment with a multi-scan correction program might be a suitable approach.

Supporting information


Computing details top

Data collection: PILATUS in X-AREA (Stoe & Cie, 2017) for (1a); PLATINUS in X-AREA (Stoe & Cie, 2017) for (2a). Cell refinement: RECIPE in X-AREA (Stoe & Cie, 2017) for (1a), (2a); XDS (Kabsch et al., 2010) for (1b), (2b). Data reduction: INTEGRATE and LANA in X-AREA (Stoe & Cie, 2017) for (1a), (2a); XDS (Kabsch et al., 2010) for (1b), (2b). Program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) for (1a), (2a). For all structures, program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015). Software used to prepare material for publication: SHELXL2018 (Sheldrick, 2015) for (1a), (2a).

1-(Chloromethyl)-3-nitrobenzene (1a) top
Crystal data top
C7H6ClNO2F(000) = 352
Mr = 171.58Dx = 1.554 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 11.7867 (11) ÅCell parameters from 8126 reflections
b = 4.4744 (4) Åθ = 2.8–34.5°
c = 15.0453 (14) ŵ = 0.46 mm1
β = 112.464 (7)°T = 100 K
V = 733.26 (12) Å3Plate, colourless
Z = 40.28 × 0.17 × 0.04 mm
Data collection top
Stoe STADIVARI
diffractometer
3231 independent reflections
Radiation source: Genix Mo, microsource2604 reflections with I > 2σ(I)
Graded multilayer mirror monochromatorRint = 0.035
Detector resolution: 5.81 pixels mm-1θmax = 35.0°, θmin = 2.8°
rotation method, ω scansh = 1919
Absorption correction: multi-scan
[LANA (Blessing, 1995; Koziskova et al., 2016) in X-AREA (Stoe & Cie, 2017)]
k = 67
Tmin = 0.545, Tmax = 1.000l = 1224
34338 measured reflections
Refinement top
Refinement on F2Primary atom site location: other
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.085 w = 1/[σ2(Fo2) + (0.0462P)2 + 0.0937P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
3231 reflectionsΔρmax = 0.52 e Å3
100 parametersΔρmin = 0.22 e Å3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.04686 (2)0.10408 (5)0.09846 (2)0.02394 (7)
O10.41468 (7)0.24541 (18)0.51475 (5)0.02842 (16)
O20.28441 (7)0.11388 (18)0.49312 (5)0.02906 (16)
N10.34038 (7)0.06427 (18)0.46314 (5)0.01928 (14)
C10.09689 (8)0.3057 (2)0.13419 (7)0.02167 (16)
H1A0.1140380.3564090.0764900.026*
H1B0.0907580.4944500.1663940.026*
C20.19980 (7)0.11937 (18)0.20144 (6)0.01618 (14)
C30.22183 (7)0.11330 (18)0.29929 (6)0.01717 (14)
H30.1723090.2265870.3240510.021*
C40.31730 (7)0.06106 (18)0.35977 (5)0.01577 (14)
C50.39211 (7)0.23188 (19)0.32737 (6)0.01700 (14)
H50.4566610.3502820.3704210.020*
C60.36905 (7)0.2233 (2)0.22928 (6)0.01816 (15)
H60.4187400.3369910.2047900.022*
C70.27375 (7)0.04942 (19)0.16695 (6)0.01725 (14)
H70.2590150.0457950.1003100.021*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01484 (9)0.02877 (12)0.02674 (11)0.00110 (7)0.00630 (7)0.00470 (8)
O10.0322 (4)0.0348 (4)0.0187 (3)0.0037 (3)0.0102 (3)0.0073 (3)
O20.0320 (4)0.0363 (4)0.0214 (3)0.0008 (3)0.0131 (3)0.0092 (3)
N10.0193 (3)0.0238 (4)0.0159 (3)0.0054 (3)0.0080 (2)0.0026 (2)
C10.0187 (3)0.0185 (4)0.0257 (4)0.0004 (3)0.0061 (3)0.0044 (3)
C20.0143 (3)0.0150 (3)0.0187 (3)0.0016 (3)0.0058 (2)0.0011 (3)
C30.0165 (3)0.0165 (3)0.0199 (3)0.0006 (3)0.0085 (3)0.0023 (3)
C40.0162 (3)0.0181 (3)0.0138 (3)0.0032 (3)0.0067 (2)0.0016 (3)
C50.0152 (3)0.0190 (4)0.0168 (3)0.0002 (3)0.0061 (2)0.0006 (3)
C60.0173 (3)0.0212 (4)0.0177 (3)0.0011 (3)0.0086 (3)0.0005 (3)
C70.0171 (3)0.0194 (4)0.0160 (3)0.0019 (3)0.0072 (3)0.0002 (3)
Geometric parameters (Å, º) top
Cl1—C11.8104 (9)C3—C41.3858 (12)
O1—N11.2277 (11)C3—H30.9500
O2—N11.2253 (10)C4—C51.3885 (11)
N1—C41.4730 (10)C5—C61.3952 (11)
C1—C21.5007 (12)C5—H50.9500
C1—H1A0.9900C6—C71.3934 (12)
C1—H1B0.9900C6—H60.9500
C2—C71.3947 (11)C7—H70.9500
C2—C31.3941 (12)
O2—N1—O1123.43 (8)C2—C3—H3120.6
O2—N1—C4118.31 (7)C3—C4—C5123.00 (7)
O1—N1—C4118.26 (7)C3—C4—N1118.34 (7)
C2—C1—Cl1110.31 (6)C5—C4—N1118.65 (7)
C2—C1—H1A109.6C4—C5—C6117.58 (7)
Cl1—C1—H1A109.6C4—C5—H5121.2
C2—C1—H1B109.6C6—C5—H5121.2
Cl1—C1—H1B109.6C7—C6—C5120.56 (7)
H1A—C1—H1B108.1C7—C6—H6119.7
C7—C2—C3119.45 (7)C5—C6—H6119.7
C7—C2—C1120.60 (8)C6—C7—C2120.64 (7)
C3—C2—C1119.95 (8)C6—C7—H7119.7
C4—C3—C2118.76 (7)C2—C7—H7119.7
C4—C3—H3120.6
Cl1—C1—C2—C796.41 (8)O2—N1—C4—C5171.16 (8)
Cl1—C1—C2—C383.37 (9)O1—N1—C4—C58.86 (11)
C7—C2—C3—C40.10 (12)C3—C4—C5—C60.35 (12)
C1—C2—C3—C4179.88 (7)N1—C4—C5—C6179.50 (7)
C2—C3—C4—C50.29 (12)C4—C5—C6—C70.24 (12)
C2—C3—C4—N1179.57 (7)C5—C6—C7—C20.06 (13)
O2—N1—C4—C38.71 (11)C3—C2—C7—C60.01 (12)
O1—N1—C4—C3171.27 (8)C1—C2—C7—C6179.77 (8)
1-(Chloromethyl)-3-nitrobenzene (1b) top
Crystal data top
C7H6ClNO2F(000) = 352
Mr = 171.58Dx = 1.561 Mg m3
Monoclinic, P21/cSynchrotron radiation, λ = 0.61992 Å
a = 11.785 (4) ÅCell parameters from 2924 reflections
b = 4.4690 (9) Åθ = 1.6–24.2°
c = 15.004 (4) ŵ = 0.32 mm1
β = 112.537 (6)°T = 100 K
V = 729.9 (3) Å3Platelet, colourless
Z = 40.12 × 0.10 × 0.04 mm
Data collection top
Kappa
diffractometer (EH1) with Dectris CdTe area detector
2947 reflections with I > 2σ(I)
Radiation source: beamline P24 at PETRA-IIIRint = 0.110
ω scansθmax = 30.0°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2015)
h = 1819
Tmin = 0.728, Tmax = 0.863k = 77
19608 measured reflectionsl = 2424
3194 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.043 w = 1/[σ2(Fo2) + (0.0532P)2 + 0.2792P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.122(Δ/σ)max < 0.001
S = 1.07Δρmax = 0.63 e Å3
3194 reflectionsΔρmin = 0.48 e Å3
101 parametersExtinction correction: SHELXL2018 (Sheldrick 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.033 (6)
Primary atom site location: other
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.04663 (2)0.10411 (6)0.09861 (2)0.02329 (9)
O10.41472 (9)0.2455 (2)0.51470 (6)0.02824 (19)
O20.28438 (9)0.1135 (2)0.49323 (6)0.0290 (2)
N10.34036 (8)0.0642 (2)0.46314 (6)0.01869 (17)
C10.09687 (10)0.3056 (2)0.13435 (8)0.02094 (19)
H1A0.1137710.3568930.0764290.025*
H1B0.0908310.4943880.1667920.025*
C20.19973 (9)0.1197 (2)0.20140 (7)0.01517 (16)
C30.22194 (9)0.1134 (2)0.29940 (7)0.01622 (17)
H30.1725150.2267260.3243100.019*
C40.31746 (9)0.0613 (2)0.35991 (6)0.01466 (16)
C50.39201 (9)0.2314 (2)0.32727 (6)0.01598 (16)
H50.4566460.3500580.3704300.019*
C60.36906 (9)0.2227 (2)0.22927 (6)0.01705 (17)
H60.4187770.3363140.2047080.020*
C70.27378 (9)0.0488 (2)0.16692 (6)0.01618 (16)
H70.2590270.0447980.1000800.019*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01498 (13)0.02849 (16)0.02457 (13)0.00112 (8)0.00552 (9)0.00488 (8)
O10.0335 (5)0.0352 (5)0.0159 (3)0.0034 (4)0.0094 (3)0.0072 (3)
O20.0330 (5)0.0371 (5)0.0191 (3)0.0014 (4)0.0126 (3)0.0096 (3)
N10.0202 (4)0.0232 (4)0.0134 (3)0.0054 (3)0.0073 (3)0.0027 (3)
C10.0185 (4)0.0175 (4)0.0239 (4)0.0007 (3)0.0049 (3)0.0051 (3)
C20.0154 (4)0.0140 (4)0.0156 (3)0.0013 (3)0.0055 (3)0.0010 (3)
C30.0168 (4)0.0160 (4)0.0169 (3)0.0006 (3)0.0075 (3)0.0019 (3)
C40.0165 (4)0.0167 (4)0.0114 (3)0.0029 (3)0.0060 (3)0.0014 (2)
C50.0155 (4)0.0187 (4)0.0139 (3)0.0004 (3)0.0058 (3)0.0006 (3)
C60.0174 (4)0.0208 (4)0.0143 (3)0.0013 (3)0.0075 (3)0.0001 (3)
C70.0174 (4)0.0184 (4)0.0131 (3)0.0016 (3)0.0063 (3)0.0006 (3)
Geometric parameters (Å, º) top
Cl1—C11.8065 (12)C3—C41.3848 (14)
O1—N11.2261 (13)C3—H30.9500
O2—N11.2237 (12)C4—C51.3854 (13)
N1—C41.4668 (12)C5—C61.3900 (13)
C1—C21.4956 (14)C5—H50.9500
C1—H1A0.9900C6—C71.3910 (14)
C1—H1B0.9900C6—H60.9500
C2—C31.3915 (14)C7—H70.9500
C2—C71.3937 (14)
O2—N1—O1123.51 (9)C2—C3—H3120.6
O2—N1—C4118.47 (9)C3—C4—C5122.95 (8)
O1—N1—C4118.02 (9)C3—C4—N1118.14 (8)
C2—C1—Cl1110.36 (7)C5—C4—N1118.91 (8)
C2—C1—H1A109.6C4—C5—C6117.77 (9)
Cl1—C1—H1A109.6C4—C5—H5121.1
C2—C1—H1B109.6C6—C5—H5121.1
Cl1—C1—H1B109.6C5—C6—C7120.45 (9)
H1A—C1—H1B108.1C5—C6—H6119.8
C3—C2—C7119.36 (9)C7—C6—H6119.8
C3—C2—C1119.85 (9)C6—C7—C2120.74 (8)
C7—C2—C1120.79 (9)C6—C7—H7119.6
C4—C3—C2118.73 (8)C2—C7—H7119.6
C4—C3—H3120.6
Cl1—C1—C2—C383.36 (10)O2—N1—C4—C5171.20 (10)
Cl1—C1—C2—C796.46 (10)O1—N1—C4—C58.90 (14)
C7—C2—C3—C40.03 (14)C3—C4—C5—C60.33 (14)
C1—C2—C3—C4179.78 (9)N1—C4—C5—C6179.44 (9)
C2—C3—C4—C50.20 (14)C4—C5—C6—C70.24 (15)
C2—C3—C4—N1179.57 (8)C5—C6—C7—C20.02 (15)
O2—N1—C4—C38.58 (13)C3—C2—C7—C60.11 (14)
O1—N1—C4—C3171.32 (9)C1—C2—C7—C6179.70 (9)
1-(Bromomethyl)-3-nitrobenzene (2a) top
Crystal data top
C7H6BrNO2F(000) = 424
Mr = 216.04Dx = 1.896 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 12.1412 (5) ÅCell parameters from 3178 reflections
b = 4.4763 (2) Åθ = 1.8–38.1°
c = 15.0876 (6) ŵ = 5.37 mm1
β = 112.626 (3)°T = 100 K
V = 756.87 (6) Å3Plate, colourless
Z = 40.23 × 0.22 × 0.04 mm
Data collection top
Stoe STADIVARI
diffractometer
3332 independent reflections
Radiation source: Genix Mo2062 reflections with I > 2σ(I)
Graded multilayer mirror monochromatorRint = 0.165
Detector resolution: 5.81 pixels mm-1θmax = 35.0°, θmin = 1.8°
rotation method, ω scansh = 1917
Absorption correction: multi-scan
[LANA (Blessing, 1995; Koziskova et al., 2016) in X-AREA (Stoe & Cie, 2017)]
k = 77
Tmin = 0.302, Tmax = 1.000l = 1324
37127 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.037 w = 1/[σ2(Fo2) + (0.020P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.075(Δ/σ)max < 0.001
S = 1.09Δρmax = 0.93 e Å3
3332 reflectionsΔρmin = 0.60 e Å3
101 parametersExtinction correction: SHELXL2018 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0022 (6)
Primary atom site location: other
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.04496 (2)0.11089 (6)0.10366 (2)0.02885 (8)
O10.41819 (18)0.2481 (5)0.51406 (13)0.0338 (5)
O20.29226 (18)0.1116 (5)0.49388 (13)0.0357 (4)
N10.3460 (2)0.0654 (5)0.46357 (15)0.0261 (5)
C10.1097 (2)0.3165 (6)0.1373 (2)0.0290 (6)
H1A0.1237220.3593210.0780990.035*
H1B0.1079710.5090420.1690320.035*
C20.2085 (2)0.1268 (6)0.20295 (16)0.0215 (4)
C30.2311 (2)0.1160 (6)0.30100 (16)0.0235 (4)
H30.1835240.2276370.3264880.028*
C40.3232 (2)0.0588 (5)0.35992 (17)0.0208 (5)
C50.3949 (2)0.2282 (5)0.32711 (17)0.0227 (5)
H50.4572440.3488180.3696360.027*
C60.3725 (2)0.2158 (6)0.22947 (17)0.0225 (5)
H60.4207840.3273350.2046780.027*
C70.2798 (2)0.0412 (5)0.16797 (17)0.0220 (5)
H70.2648220.0363480.1013860.026*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.02157 (11)0.03043 (12)0.03340 (13)0.00172 (14)0.00931 (9)0.00551 (14)
O10.0393 (12)0.0367 (11)0.0260 (9)0.0033 (9)0.0132 (9)0.0068 (8)
O20.0391 (11)0.0439 (11)0.0282 (9)0.0018 (11)0.0175 (8)0.0125 (10)
N10.0258 (11)0.0289 (12)0.0243 (10)0.0076 (9)0.0104 (9)0.0045 (8)
C10.0251 (13)0.0220 (12)0.0366 (14)0.0017 (9)0.0084 (11)0.0055 (10)
C20.0217 (10)0.0158 (9)0.0269 (11)0.0032 (10)0.0092 (9)0.0009 (9)
C30.0245 (11)0.0182 (9)0.0300 (11)0.0030 (10)0.0130 (9)0.0041 (10)
C40.0231 (11)0.0201 (12)0.0202 (10)0.0048 (8)0.0096 (9)0.0022 (8)
C50.0233 (12)0.0194 (11)0.0247 (12)0.0002 (9)0.0086 (10)0.0007 (9)
C60.0224 (12)0.0230 (11)0.0249 (12)0.0001 (9)0.0119 (10)0.0006 (9)
C70.0219 (12)0.0217 (12)0.0225 (11)0.0020 (8)0.0086 (10)0.0009 (8)
Geometric parameters (Å, º) top
Br1—C11.974 (3)C3—C41.374 (3)
O1—N11.226 (3)C3—H30.9500
O2—N11.222 (3)C4—C51.381 (3)
N1—C41.480 (3)C5—C61.392 (3)
C1—C21.493 (3)C5—H50.9500
C1—H1A0.9900C6—C71.391 (3)
C1—H1B0.9900C6—H60.9500
C2—C71.394 (3)C7—H70.9500
C2—C31.398 (3)
O2—N1—O1123.8 (2)C2—C3—H3120.5
O2—N1—C4118.2 (2)C3—C4—C5123.3 (2)
O1—N1—C4117.9 (2)C3—C4—N1118.0 (2)
C2—C1—Br1110.34 (17)C5—C4—N1118.7 (2)
C2—C1—H1A109.6C4—C5—C6117.6 (2)
Br1—C1—H1A109.6C4—C5—H5121.2
C2—C1—H1B109.6C6—C5—H5121.2
Br1—C1—H1B109.6C7—C6—C5120.5 (2)
H1A—C1—H1B108.1C7—C6—H6119.8
C7—C2—C3119.0 (2)C5—C6—H6119.8
C7—C2—C1120.9 (2)C6—C7—C2120.7 (2)
C3—C2—C1120.2 (2)C6—C7—H7119.6
C4—C3—C2118.9 (2)C2—C7—H7119.6
C4—C3—H3120.5
Br1—C1—C2—C7100.0 (2)O2—N1—C4—C5171.2 (2)
Br1—C1—C2—C380.1 (3)O1—N1—C4—C58.5 (3)
C7—C2—C3—C40.3 (4)C3—C4—C5—C60.8 (4)
C1—C2—C3—C4179.5 (2)N1—C4—C5—C6179.3 (2)
C2—C3—C4—C50.6 (4)C4—C5—C6—C70.9 (4)
C2—C3—C4—N1179.6 (2)C5—C6—C7—C20.7 (4)
O2—N1—C4—C38.9 (3)C3—C2—C7—C60.4 (4)
O1—N1—C4—C3171.3 (2)C1—C2—C7—C6179.4 (2)
1-(Bromomethyl)-3-nitrobenzene (2b) top
Crystal data top
C7H6BrNO2F(000) = 424
Mr = 216.04Dx = 1.898 Mg m3
Monoclinic, P21/cSynchrotron radiation, λ = 0.61992 Å
a = 12.152 (9) ÅCell parameters from 2817 reflections
b = 4.470 (3) Åθ = 1.6–24.2°
c = 15.070 (11) ŵ = 3.76 mm1
β = 112.56 (2)°T = 100 K
V = 756.0 (9) Å3Block-shaped fragment, colourless
Z = 40.10 × 0.06 × 0.04 mm
Data collection top
Kappa
diffractometer (EH1) with Dectris CdTe area detector
3018 reflections with I > 2σ(I)
Radiation source: beamline P24 at PETRA-IIIRint = 0.056
ω scansθmax = 30.0°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2015)
h = 1919
Tmin = 0.604, Tmax = 0.747k = 77
18687 measured reflectionsl = 2424
3233 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.033 w = 1/[σ2(Fo2) + (0.0493P)2 + 0.4467P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.090(Δ/σ)max < 0.001
S = 1.10Δρmax = 0.91 e Å3
3233 reflectionsΔρmin = 1.29 e Å3
101 parametersExtinction correction: SHELXL2018 (Sheldrick 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.024 (3)
Primary atom site location: other
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.04475 (2)0.11083 (4)0.10376 (2)0.02382 (7)
O10.41763 (14)0.2474 (3)0.51400 (9)0.0308 (3)
O20.29170 (15)0.1110 (3)0.49409 (11)0.0325 (3)
N10.34579 (12)0.0644 (3)0.46340 (9)0.0210 (2)
C10.10956 (14)0.3161 (3)0.13734 (13)0.0232 (3)
H1A0.1234850.3593260.0780540.028*
H1B0.1078390.5087420.1691910.028*
C20.20836 (13)0.1269 (3)0.20274 (11)0.0170 (2)
C30.23076 (14)0.1172 (3)0.30098 (11)0.0181 (2)
H30.1831260.2291710.3263940.022*
C40.32338 (12)0.0583 (3)0.36039 (10)0.0159 (2)
C50.39545 (13)0.2277 (3)0.32699 (10)0.0173 (2)
H50.4582970.3470290.3694910.021*
C60.37246 (13)0.2166 (3)0.22934 (10)0.0181 (2)
H60.4202560.3296530.2043350.022*
C70.27992 (13)0.0412 (3)0.16784 (10)0.0173 (2)
H70.2652830.0358670.1012410.021*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.01557 (9)0.02765 (10)0.02685 (10)0.00195 (4)0.00658 (6)0.00578 (5)
O10.0375 (7)0.0375 (7)0.0180 (5)0.0017 (6)0.0113 (5)0.0065 (5)
O20.0348 (7)0.0436 (8)0.0220 (6)0.0019 (5)0.0139 (5)0.0137 (5)
N10.0220 (6)0.0269 (5)0.0152 (5)0.0075 (4)0.0084 (4)0.0047 (4)
C10.0201 (6)0.0180 (5)0.0286 (7)0.0009 (5)0.0062 (5)0.0059 (5)
C20.0165 (5)0.0145 (5)0.0197 (6)0.0010 (4)0.0066 (4)0.0013 (4)
C30.0184 (6)0.0177 (5)0.0197 (6)0.0009 (4)0.0090 (5)0.0026 (4)
C40.0173 (5)0.0178 (5)0.0134 (5)0.0032 (4)0.0067 (4)0.0019 (4)
C50.0168 (5)0.0201 (5)0.0148 (5)0.0002 (4)0.0059 (4)0.0000 (4)
C60.0188 (5)0.0208 (5)0.0158 (5)0.0016 (4)0.0077 (4)0.0002 (4)
C70.0180 (5)0.0198 (5)0.0147 (5)0.0010 (4)0.0068 (4)0.0013 (4)
Geometric parameters (Å, º) top
Br1—C11.971 (2)C3—C41.382 (2)
O1—N11.226 (2)C3—H30.9500
O2—N11.222 (2)C4—C51.390 (2)
N1—C41.470 (2)C5—C61.390 (2)
C1—C21.490 (2)C5—H50.9500
C1—H1A0.9900C6—C71.392 (2)
C1—H1B0.9900C6—H60.9500
C2—C71.396 (2)C7—H70.9500
C2—C31.399 (2)
O2—N1—O1123.43 (15)C2—C3—H3120.6
O2—N1—C4118.63 (15)C3—C4—C5122.98 (13)
O1—N1—C4117.94 (13)C3—C4—N1117.99 (13)
C2—C1—Br1110.57 (11)C5—C4—N1119.03 (13)
C2—C1—H1A109.5C6—C5—C4117.74 (13)
Br1—C1—H1A109.5C6—C5—H5121.1
C2—C1—H1B109.5C4—C5—H5121.1
Br1—C1—H1B109.5C5—C6—C7120.53 (13)
H1A—C1—H1B108.1C5—C6—H6119.7
C7—C2—C3119.04 (13)C7—C6—H6119.7
C7—C2—C1121.11 (15)C6—C7—C2120.88 (14)
C3—C2—C1119.86 (14)C6—C7—H7119.6
C4—C3—C2118.84 (13)C2—C7—H7119.6
C4—C3—H3120.6
Br1—C1—C2—C7100.04 (15)O2—N1—C4—C5171.48 (14)
Br1—C1—C2—C380.20 (15)O1—N1—C4—C58.9 (2)
C7—C2—C3—C40.2 (2)C3—C4—C5—C60.3 (2)
C1—C2—C3—C4179.58 (13)N1—C4—C5—C6179.75 (13)
C2—C3—C4—C50.3 (2)C4—C5—C6—C70.1 (2)
C2—C3—C4—N1179.71 (12)C5—C6—C7—C20.0 (2)
O2—N1—C4—C38.6 (2)C3—C2—C7—C60.0 (2)
O1—N1—C4—C3171.03 (14)C1—C2—C7—C6179.73 (14)
Experimental and theoretically predicted lattice parameters, monoclinic angle, volume of the unit cell and root-mean-square (RMS) values of Cartesian deviations top
12
Exp*TheorExp*Theor
a (Å)11.7867 (11)11.920212.152 (9)12.2703
b (Å)4.4744 (4)4.38984.470 (3)4.3909
c (Å)15.0453 (14)15.080715.070 (11)15.1254
β (°)112.464 (7)112.584112.56 (2)112.621
RMS0.09200.0943
V3)733.26 (12)728.63756.0 (9)752.23
(*) Experimental values for compound 1 are based on in-house intensities (1a) and those for compound 2 stem from synchrotron intensities (2b).
 

Acknowledgements

We thank Irmgard Kalf for crystallizing the target compounds and Dr Carsten Paulmann for help with the synchrotron data collections. We acknowledge support from the One Hundred-Talent Program of Shanxi Province. We are grateful to JARA–HPC for providing additional computing time within the JARA project jara0069 and DESY for travel support.

Funding information

Funding for this research was provided by: Deutsche Forschungsgemeinschaft (DFG) within projects EN 309/10-1 and DR 342/35-1 (`Density-functional Calculation of Anisotropic Displacement Parameters and its Use for Improving Experimental X-ray and Neutron Diffraction').

References

First citationAbbasi, M. A., Jahangir, M., Akkurt, M., Aziz-ur-Rehman, Khan, I. U. & Sharif, S. (2010). Acta Cryst. E66, o608.  CSD CrossRef IUCr Journals Google Scholar
First citationAuthier, A. & Chapuis, G. (2014). Editors. A Little Dictionary of Crystallography. Chester, UK: IUCr.  Google Scholar
First citationBaima, J., Zelferino, A., Olivero, P., Erba, A. & Dovesi, R. (2016). Phys. Chem. Chem. Phys. 18, 1961–1968.  CrossRef CAS PubMed Google Scholar
First citationBlessing, R. H. (1995). Acta Cryst. A51, 33–38.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationBlöchl, P. E. (1994). Phys. Rev. B, 50, 17953–17979.  CrossRef Web of Science Google Scholar
First citationBruker (2015). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationDeringer, V. L., George, J., Dronskowski, R. & Englert, U. (2017). Acc. Chem. Res. 50, 1231–1239.  Web of Science CrossRef CAS PubMed Google Scholar
First citationDeringer, V. L., Stoffel, R. P., Togo, A., Eck, B., Meven, M. & Dronskowski, R. (2014). CrystEngComm, 16, 10907–10915.  Web of Science CrossRef CAS Google Scholar
First citationDeringer, V. L., Wang, A., George, J., Dronskowski, R. & Englert, U. (2016). Dalton Trans. 45, 13680–13685.  CSD CrossRef CAS PubMed Google Scholar
First citationDittrich, B., Pfitzenreuter, S. & Hübschle, C. B. (2012). Acta Cryst. A68, 110–116.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationGeorge, J., Deringer, V. L. & Dronskowski, R. (2014). Inorg. Chem. 54, 956–962.  CrossRef ICSD PubMed Google Scholar
First citationGeorge, J. (2016). Molecular Toolbox, This code is freely available via the Internet at http://www.ellipsoids.de, together with additional information regarding ADP computation.  Google Scholar
First citationGeorge, J., Deringer, V. L. & Dronskowski, R. (2015a). Inorg. Chem. 54, 956–962.  CrossRef ICSD CAS PubMed Google Scholar
First citationGeorge, J., Deringer, V. L., Wang, A., Müller, P., Englert, U. & Dronskowski, R. (2016). J. Chem. Phys. 145, 234512.  CrossRef PubMed Google Scholar
First citationGeorge, J., Wang, A., Deringer, V. L., Wang, R., Dronskowski, R. & Englert, U. (2015b). CrystEngComm, 17, 7414–7422.  CSD CrossRef CAS Google Scholar
First citationGeorge, J., Wang, R., Englert, U. & Dronskowski, R. (2017). J. Chem. Phys. 147, 074112.  Web of Science CSD CrossRef PubMed Google Scholar
First citationGrimme, S., Antony, J., Ehrlich, S. & Krieg, H. (2010). J. Chem. Phys. 132, 154104.  Web of Science CrossRef PubMed Google Scholar
First citationGrimme, S., Ehrlich, S. & Goerigk, L. (2011). J. Comput. Chem. 32, 1456–1465.  Web of Science CrossRef CAS PubMed Google Scholar
First citationGroom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179.  Web of Science CrossRef IUCr Journals Google Scholar
First citationGrosse-Kunstleve, R. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 477–480.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationHirshfeld, F. L. (1976). Acta Cryst. A32, 239–244.  CrossRef IUCr Journals Web of Science Google Scholar
First citationKabsch, W. (2010). Acta Cryst. D66, 125–132.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKoziskova, J., Hahn, F., Richter, J. & Kožíšek, J. (2016). Acta Chim. Slov. 9, 136–140.  Web of Science CrossRef CAS Google Scholar
First citationKrause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10.  Web of Science CSD CrossRef ICSD CAS IUCr Journals Google Scholar
First citationKresse, G. & Furthmüller, J. (1996a). Comput. Mater. Sci. 6, 15–50.  CrossRef CAS Web of Science Google Scholar
First citationKresse, G. & Furthmüller, J. (1996b). Phys. Rev. B, 54, 11169–11186.  CrossRef CAS Web of Science Google Scholar
First citationKresse, G. & Hafner, J. (1993). Phys. Rev. B, 47, 558–561.  CrossRef CAS Web of Science Google Scholar
First citationKresse, G. & Hafner, J. (1994). Phys. Rev. B, 49, 14251–14269.  CrossRef CAS Web of Science Google Scholar
First citationKresse, G. & Joubert, D. (1999). Phys. Rev. B, 59, 1758–1775.  Web of Science CrossRef CAS Google Scholar
First citationLane, N. J., Vogel, S. C., Hug, G., Togo, A., Chaput, L., Hultman, L. & Barsoum, M. W. (2012). Phys. Rev. B, 86, 214301.  Web of Science CrossRef Google Scholar
First citationMadsen, A. Ø., Civalleri, B., Ferrabone, M., Pascale, F. & Erba, A. (2013). Acta Cryst. A69, 309–321.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMaris, T. (2016). Private communication (deposition number 1476711). CCDC, Cambridge, England.  Google Scholar
First citationMATLAB (2016). The MathWorks Inc., Natick, Massachusetts, USA. https://www.mathworks.com/Google Scholar
First citationMeulenaer, J. de & Tompa, H. (1965). Acta Cryst. 19, 1014–1018.  CrossRef IUCr Journals Web of Science Google Scholar
First citationMroz, D., George, J., Kremer, M., Wang, R., Englert, U. & Dronskowski, R. (2019). CrytEngComm, 21, 6396-6404.  CSD CrossRef CAS Google Scholar
First citationOnline Dictionary of Crystallography (2017). Isomorphous Crystals. https://dictionary.iucr.org/Isomorphous_crystalsGoogle Scholar
First citationParlinski, K., Li, Z. Q. & Kawazoe, Y. (1997). Phys. Rev. Lett. 78, 4063–4066.  CrossRef CAS Web of Science Google Scholar
First citationPerdew, J. P., Burke, K. & Ernzerhof, M. (1996). Phys. Rev. Lett. 77, 3865–3868.  CrossRef PubMed CAS Web of Science Google Scholar
First citationPozzi, C. G., Fantoni, A. C., Goeta, A. E., de Matos Gomes, E., McIntyre, G. J. & Punte, G. (2013). Chem. Phys. 423, 85–91.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationStoe & Cie (2017). X-AREA. Stoe & Cie GmbH, Darmstadt, Germany.  Google Scholar
First citationStoffel, R. P., Wessel, C., Lumey, M. W. & Dronskowski, R. (2010). Angew. Chem. Int. Ed. 49, 5242–5266.  CrossRef CAS Google Scholar
First citationTogo, A., Oba, F. & Tanaka, I. (2008). Phys. Rev. B, 78, 134106.  Web of Science CrossRef Google Scholar
First citationTogo, A. & Tanaka, I. (2015). Scr. Mater. 108, 1–5.  Web of Science CrossRef CAS Google Scholar
First citationVinet, P., Smith, J. R., Ferrante, J. & Rose, J. H. (1987). Phys. Rev. B, 35, 1945–1953.  CrossRef CAS Web of Science Google Scholar

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