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BY 4.0 license Open Access Published by De Gruyter (O) July 30, 2021

Redetermination of the crystal structure of 3-bromonitrobenzene at 200 K, C6H4BrNO2 – temperature effects on cell constants

Pholani Manana, Eric C. Hosten ORCID logo and Richard Betz ORCID logo

Abstract

C6H4BrNO2, orthorhombic, Pna21 (no. 33), a = 21.3992(17) Å, b = 5.9311(4) Å, c = 5.2923(4) Å, V = 671.70(9) Å3, Z = 4, R gt (F) = 0.0284, wR ref (F 2) = 0.0708, T = 200(2) K.

CCDC no.: 2097351

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colorless rod
Size: 0.50 × 0.26 × 0.14 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 6.05 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θ max, completeness: 28.3°, >99%
N(hkl)measured, N(hkl)unique, R int: 3459, 1595, 0.024
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 1364
N(param)refined: 91
Programs: Bruker [1, 2], SHELX [3], WinGX/ORTEP [4], Mercury [5], PLATON [6]

Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y Z U iso*/U eq
Br1 0.26427 (2) 0.54725 (8) 0.08920 (17) 0.03670 (16)
O1 0.41907 (19) 0.3645 (6) 0.8493 (7) 0.0377 (9)
O2 0.48054 (18) 0.6513 (6) 0.9122 (6) 0.0361 (8)
N1 0.4384 (2) 0.5550 (6) 0.7983 (7) 0.0260 (9)
C1 0.3322 (2) 0.6846 (7) 0.2633 (9) 0.0265 (10)
C2 0.3589 (2) 0.5715 (7) 0.4644 (9) 0.0251 (10)
H2 0.343943 0.428412 0.517733 0.030*
C3 0.40832 (18) 0.6756 (6) 0.5840 (12) 0.0236 (7)
C4 0.4313 (2) 0.8848 (8) 0.5151 (9) 0.0281 (10)
H4 0.465486 0.951069 0.602372 0.034*
C5 0.4026 (3) 0.9953 (8) 0.3131 (10) 0.0295 (11)
H5 0.417025 1.139877 0.262316 0.035*
C6 0.3530 (2) 0.8950 (8) 0.1857 (9) 0.0284 (10)
H6 0.333674 0.969520 0.047468 0.034*

Source of material

The compound was obtained commercially (Sigma–Aldrich). Crystals suitable for the diffraction study were taken directly from the provided product.

Experimental details

Carbon-bound H atoms were placed in calculated positions (C–H 0.95 Å) and were included in the refinement in the riding model approximation, with U(H) set to 1.2U eq(C).

Comment

Benzene is among the most important synthons in chemistry. Via electrophilic substitution reactions a vast variety of functionalized derivatives is readily available. The interplay between activating and deactivating substituents as well as the competition and synergism between inductive and mesomeric effects allows for the seemingly endless functionalization of the respective archetype hydrocarbon scaffold. The later gives rise to a large toolbox of new synthons that can be applied for the production of dyes, medications, catalysts and ligands for novel coordination compounds. Several simple and fundamental derivatives of benzene are powerful and versatile reagents themselves and have entered the preparative chemist's toolbox decades ago. One notable example for the latter statement is meta-bromo nitrobenzene which is readily available upon bromination of nitrobenzene and offers a wealth of follow up reactions. During the preparation of a number of functionalized derivatives of boronic and borinic acids the title compound – which is commercially available – was used as a starting material. To prevent accidentally characterizing the title compound instead of the sought-after ligands by means of diffraction studies based on single crystals and in continuation of our own studies into the structural aspects of core-halogenated derivatives of benzene [7], [8], [9], [10], [11], [12] the crystallographic data for the substrate was sought. The molecular and crystal structure of the title compound has been reported earlier [13], however, the hydrogen atoms were not included in the refinement. A later structure determination conducted at room temperature (295 K) took the latter atoms into account [14]. Furthermore, the molecular and crystal structures of several other multi-halogenated and nitrated derivatives of benzene have been reported earlier [15, 16].

The structure solution shows the title compound to be a derivative of nitrobenzene bearing a bromo substituent in meta position to the nitro group. The C–Br bond length was measured at 1.904(5) Å while the C–N bond length was found at 1.488(7) Å. N–O resonance is indicated by the pertaining bond lengths determined to be almost identical with values of 1.226(5) and 1.233(5) Å, respectively. The latter values are in good agreement with pertaining values for comparable compounds whose metrical parameters have been deposited with the Cambridge Structural Database [17]. C–C–C angles cover a range of 117.0(4)–123.6(5)° with the smallest angle found on the carbon atom in between the two functionalized ring atoms while the largest value is located on the carbon atom bearing the nitro group. In comparison to the corresponding metrical parameters apparent for the structure at room temperature [14] a slight increase to longer bond distances at 200 K is observed. The molecule is essentially planar with the least-squares plane engulfing all non-hydrogen atoms featuring one of the two oxygen atoms deviating most with a value of only 0.046(4) Å. The extension of mesomeric effects to the pnicogen-based substituent is further corroborated by the angle of only 3.0(5)° enclosed by the least-squares planes as defined by the carbon atoms of the phenyl ring on the one hand and the nitrogen and oxygen atoms of the NO2 group on the other hand.

In the crystal, C–H⃛O contacts are observed whose range falls by more than 0.1 Å below the sum of van-der-Waals radii of the atoms participating in them. These contacts are supported by the hydrogen atom in two-fold meta-orientation to both substituents as donor and one of the two oxygen atoms of the nitro group as acceptor and connect the molecules to chains along [0 1 1]. In terms of graph-set analysis [18, 19], these contacts require a C 11(6) descriptor on the unary level. Furthermore, a C–Br⃛π interaction can be observed which precludes the formation of π stacking with the shortest distance in between two centers of gravity measured at 5.292(3) Å. Although the qualitative mode of packing in this low-temperature study is in agreement with the picture obtained at room temperature [14], an interesting increase for the distance between two centers of gravity is apparent that was measured at 5.342(2) Å in the latter case. While this trend of an increase in bond distance is in contrast to the otherwise invariably smaller/shorter values found at room temperature (see above), this finding might explain why the a and c axes reported for the compound's unit cell at 295 K show a marked lengthening. The latter would reflect the more “lofty” packing of the molecules.


Corresponding author: Dr. Richard Betz, Department of Chemistry, Nelson Mandela University, Summerstrand Campus (South), University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa, E-mail:

Funding source: National Research Foundationdoi.org/10.13039/501100001321

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This research was financially supported by National Research Foundation.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Bruker AXS Inc. APEX2; Bruker AXS Inc.: Madison, Wisconsin, USA, 2012.Search in Google Scholar

2. Bruker AXS Inc. SADABS; Bruker AXS Inc.: Madison, Wisconsin, USA, 2008.Search in Google Scholar

3. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. 2008, A64, 112–122; https://doi.org/10.1107/s0108767307043930.Search in Google Scholar

4. Farrugia, L. J. WinGX and ORTEP for Windows: an update. J. Appl. Crystallogr. 2012, 45, 849–854; https://doi.org/10.1107/s0021889812029111.Search in Google Scholar

5. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J., Wood, P. A. Mercury CSD 2.0 - new features for the visualization and investigation of crystal structures. J. Appl. Crystallogr. 2008, 41, 466–470; https://doi.org/10.1107/s0021889807067908.Search in Google Scholar

6. Spek, A. L. Structure validation in chemical crystallography. Acta Crystallogr. 2009, D65, 148–155; https://doi.org/10.1107/s090744490804362x.Search in Google Scholar

7. Betz, R., McCleland, C., Glover, S. 2-(4-Iodophenoxy)acetamide. Acta Crystallogr. 2011, E67, o1928; https://doi.org/10.1107/s1600536811025840.Search in Google Scholar

8. Betz, R., Klüfers, P. 1-Bromomethyl-2-iodobenzene. Acta Crystallogr. 2007, E63, o4753; https://doi.org/10.1107/s1600536807058151.Search in Google Scholar

9. Betz, R., Klüfers, P. 2-Iodobenzaldehyde. Acta Crystallogr. 2007, E63, o4879; https://doi.org/10.1107/s1600536807061272.Search in Google Scholar

10. Betz, R., Betzler, F., Klüfers, P. 2-Bromobenzaldehyde cyanohydrin. Acta Crystallogr. 2008, E64, o55; https://doi.org/10.1107/s1600536807049604.Search in Google Scholar

11. Nogororabanga, J., Mama, N., Hosten, E. C., Betz, R. Crystal structure of 3-iodo-4,6-dimethoxy-benzaldehyde, C9H9IO3. Z. Kristallogr. - N. Cryst. Struct. 2015, 230, 91–92; https://doi.org/10.1515/ncrs-2014-9006.Search in Google Scholar

12. Hosten, E. C., Betz, R. Redetermination of the crystal structure of p-bromophenacyl bromide at 200 K – Localization of hydrogen atoms, C8H6Br2O. Z. Kristallogr. - N. Cryst. Struct. 2015, 230, 59–60; https://doi.org/10.1515/ncrs-2014-9027.Search in Google Scholar

13. Charlton, T. L., Trotter, J. The structure of m-bromonitrobenzene. Acta Crystallogr. 1963, 16, 313; https://doi.org/10.1107/s0365110x63000803.Search in Google Scholar

14. Gutierrez, K. R., Bond, M. R. CSD Communication. CCDC 1970344: Experimental crystal structure determination. 2019. https://doi.org/10.5517/ccdc.csd.cc2449h3.Search in Google Scholar

15. Romero, J. A., Aguirre Hernandez, G., Bernes, S. Anomalous halogen bonds in the crystal structures of 1,2,3-tribromo-5-nitro- benzene and 1,3-dibromo-2-iodo-5-nitrobenzene. Acta Crystallogr. 2015, E71, 960–964; https://doi.org/10.1107/s2056989015013377.Search in Google Scholar

16. Thallapally, P. K., Basavoju, S., Desiraju, G. R., Bagieu-Beucher, M., Masse, R., Nicoud, J.-F. Square networks based on the Br⃛NO2 supramolecular synthon. Curr. Sci. 2003, 85, 995–1001.Search in Google Scholar

17. Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. 2002, B58, 380–388; https://doi.org/10.1107/s0108768102003890.Search in Google Scholar

18. Bernstein, J., Davis, R. E., Shimoni, L., Chang, N.-L. Patterns in hydrogen bonding: functionality and graph set analysis in crystals. Angew. Chem. Int. Ed. 1995, 34, 1555–1573; https://doi.org/10.1002/anie.199515551.Search in Google Scholar

19. Etter, M. C., MacDonald, J. C., Bernstein, J. Graph-set analysis of hydrogen-bond patterns in organic crystals. Acta Crystallogr. 1990, B46, 256–262; https://doi.org/10.1107/s0108768189012929.Search in Google Scholar

Received: 2021-06-03
Accepted: 2021-07-19
Published Online: 2021-07-30
Published in Print: 2021-12-20

© 2021 Pholani Manana et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.