Crystal structure and antimycobacterial evaluation of 2-(cyclohexylmethyl)-7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one

The crystal structure of the title compound features centrosymmetric dimers formed through C—H⋯O weak hydrogen bonds between a C—H group of the electron-deficient benzene ring and the benzothiazolinone carbonyl O atom with an (10) motif.

The title compound, C 15 H 15 F 3 N 2 O 3 S, crystallizes in the monoclinic system, space group I2/a, with Z = 8.As expected, the nine-membered heterobicyclic system is virtually planar and the cyclohexyl group adopts a chair conformation.There is structural evidence for intramolecular N-S� � �O chalcogen bonding between the benzisothiazolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N-S bond [N-S� � �O = 162.7 (1) � ].In the crystal, the molecules form centrosymmetric dimers through C-H� � �O weak hydrogen bonding between a C-H group of the electron-deficient benzene ring and the benzothiazolinone carbonyl O atom with an R 2 2 (10) motif.In contrast to the previously described N-acyl 7-nitro-5-(trifluoromethyl)benzo [d]isothiazol-3(2H)-ones, the title N-cyclohexylmethyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro.

Chemical context
Benzisothiazolinones (BITs) are known to exhibit broadspectrum antimicrobial effects (Gopinath et al., 2017).The unsubstituted BIT and other isothiazolinones are widely used as biocides (Silva et al., 2020).In the course of our quest for new antimycobacterial agents, we recently reported the N-acyl BITs 1a and 1b (Fig. 1).They displayed in vitro activity against Chemical diagrams of previously reported BITs 1a and 1b exhibiting in vitro antimycobacterial activity (Richter et al., 2022) and antitubercular BTZs that have advanced to clinical studies (Makarov & Mikus ˇova ´, 2020).mycobacteria including Mycobacterium tuberculosis (Richter et al., 2022), the major etiological agent of tuberculosis.Together with the corresponding S-oxides, they were originally discovered by chance in an attempt to oxidize benzothiazinones at the S atom (BTZs;Eckhardt et al., 2020).BTZs, in particular 8-NO 2 -BTZs, are a promising class of antituberculosis drug candidates (Seidel et al., 2023), two of which have progressed to clinical studies, viz.BTZ-043 and PBTZ-169 (Fig. 1; Makarov & Mikus ˇova ´, 2020).The pyridine-1carbonyl spiro ketal side chain appended to the N atom in 2position of the BIT scaffold in 1b is inspired by that of BTZ-043.In an attempt to synthesize the analogous BIT 3 bearing the PBTZ-169-inspired piperazin-1-carbonyl side chain from the precursor 2 and cyclohexylmethyl bromide, we unintentionally obtained 4, the title compound (Fig. 2).

Structural commentary
Fig. 3 shows the molecular structure of 4 in the crystal, and Table 1 lists selected bond lengths and angles.The nine-membered heterobicyclic system is virtually planar with a r.m.s.deviation of 0.0294 A ˚.The C-C-C bond angles within the benzene ring alternate in magnitude by ca �2 � , with the larger angles being associated with the C atoms bonded to electron-withdrawing groups, viz.C( O)N, NO 2 and CF 3 .The somewhat long C3-O1 distance of 1.226 (3) A ˚is consistent with the relatively low wavenumber of the carbonyl band at 1630 cm À 1 in the IR spectrum (see supporting information), which is typical of amides.The dihedral angle between the BIT mean plane and the plane defined by the three atoms of the nitro group is 11.4 (3) � .The intramolecular S1� � �O2 distance of 2.603 (2) A ˚and the N2-S1� � �O2 angle of 162.74 (8) � suggest the existence of an intramolecular chalcogen bond on the extension of the covalent N-S bond (Scilabra et al., 2019;Vogel et al., 2019;Pizzi et al., 2023).The orientation of the BIT moiety and the cyclohexylmethyl group to one another renders the molecule axially chiral, although the centrosymmetric crystal structure contains both enantiomeric conformers.The cyclohexyl group adopts a low-energy chair conformation with the C-C-C bond angles being close to the ideal tetrahedral angle (Table 1).

Supramolecular features
The most prominent supramolecular feature of the crystal structure of 4 is weak intermolecular C-H� � �O hydrogen bonding.As shown in Fig. 4, the molecules form centrosymmetric dimers through C-H� � �O hydrogen bonds between the C4-H4 moiety of the benzene ring and the carbonyl O atom of an adjacent symmetry-related molecule.The C4-H4 group is likely activated for weak hydrogen bonding through the electron-withdrawing effect exerted by the C( O)N and CF 3 groups in ortho positions and the NO 2 group in the para position.The graph-set descriptor for the hydrogen-bond motif is R2 2 (10) (Bernstein et al., 1995).Unintentional formation of 4, the title compound, from the 2-(piperazine-1-carbonyl)-BIT 2 and cyclohexylmethyl bromide.

Figure 3
Molecular structure of 4. Displacement ellipsoids are drawn at the 50% probability level.H atoms are represented by small spheres of arbitrary radius.

Table 1
Selected geometric parameters (A ˚, � ).corresponding geometric parameters, which are typical of weak hydrogen bonds (Thakuria et al., 2017).The dominance of the short O� � �H contacts is also revealed by a Hirshfeld surface analysis (Spackman & Jayatilaka, 2009), as shown in Fig. 5.In addition, H� � �H contacts, mostly resulting from close packing of the cyclohexyl groups, as shown in Fig. 6, are evident.The packing index (Kitaigorodskii, 1973) of the crystal structure, as calculated with PLATON (Spek, 2020), is 71.6%.Notably, the crystal structure also features a short intermolecular O� � �N contact (2.87A ˚) between adjacent molecules related by 2 1 screw symmetry.Intermolecular F� � �F contacts between CF 3 groups are not encountered.

Database survey
As of November 2023, a search of the Cambridge Structural Database (CSD; Groom et al., 2016) reveals more than 50 crystal structures containing a BIT scaffold.Specifically, two 7-NO 2 -5-CF 3 -BITs with 2-(piperidine-1-carbonyl) side chains and their benzisothiazol-3-ol constitutional isomers (Richter et al., 2022) as well as the corresponding BIT 1-oxides (Eckhardt et al., 2020) have previously been structurally characterized by us.Of note, the centrosymmetric C-H� � �O weak hydrogenbond-dimer motif encountered in the crystal structure of 4 is not found in the BIT structures contained in the CSD.For a data-mining survey of the CSD for a statistical assessment of the chalcogen bond ability of the sulfur atom in BITs and related compounds, we direct the interested reader to the recent publication by Pizzi et al. (2023).

Antimycobacterial evaluation
Compound 4 was subjected to in vitro testing against Mycobacterium aurum and Mycobacterium smegmatis using the broth microdilution method, as described previously (Richter et al., 2022).The generally considered non-pathogenic mycobacterial species M. aurum (Gupta et al., 2009; Namouchi et    The findings essentially confirm that, similar to antitubercular BTZs (Seidel et al., 2023), the nature of the side chain appended to the N atom in position 2 of the BIT scaffold has a crucial bearing on the antimycobacterial activity (Richter et al., 2022).

Synthesis and crystallization
General: Chemicals were of reagent-grade quality and used as received.7-Nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one was prepared as described previously (Richter et al., 2022).Solvents were distilled prior to use and stored over 4 A ˚molecular sieves.Flash chromatography was performed on an Interchim puriFlash 430 instrument.NMR spectra were recorded on an Agilent Technologies VNMRS 400 MHz or a Varian INOVA 500 MHz NMR spectrometer. 1 H and 13 C chemical shifts are reported relative to the residual solvent signal of CDCl 3 (� H = 7.26 ppm; � C = 77.10ppm) or CD 3 OD (� H = 4.78 ppm).The 19 F chemical shifts are reported relative to the signal of CFCl 3 (� F = 0 ppm) as an external standard.HPLC analysis was conducted with a Shimadzu instrument with a CBM-40 control unit, two LC-40D pumps and an SPD-M40 PDA UV detector, using an Agilent Poroshell 120, EC-C18, 3.0 � 50 mm, 2.7 mm column at a flow rate of 1.2 mL min À 1 , eluting with water/acetonitrile.APCI mass spectrometry was carried out on an Advion Expression compact mass spectrometer using the direct analysis probe method.The ESI mass spectrum was measured on a Thermo Scientific Q Exactive TM Plus Orbitrap mass spectrometer and the EI mass spectrum on a Finnigan MAT 95 mass spectrometer.The IR spectrum was recorded on a Bruker Tensor II Platinum ATR spectrometer at a resolution of 4 cm À 1 , accumulating 16 scans.

Refinement
Crystal data, data collection and structure refinement details are given in Table 3. H atoms were placed in geometrically calculated positions and refined using the appropriate riding model, with C aromatic -H = 0.95 A ˚, C methylene -H = 0.99 A ˚, C methine -H = 1.00A ˚and U iso (H) = 1.2U eq (C).

Special details
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.

Figure 5 (
Figure 5 (a) Hirshfeld surface mapped with d norm (white areas indicate van der Waals contacts, red areas shorter-than and blue areas longer-than van der Waals contacts) and (b) the corresponding two-dimensional fingerprint plot; d i and d e are the respective interior and exterior distances of the nearest atom to the Hirshfeld surface over the range 0.4-2.6A ˚(blue, few points; green, moderate fraction; red, many points).The figure was generated with CrystalExplorer (Spackman et al., 2021).

Figure 6
Figure 6 Packing diagram of 4, viewed along the b-axis direction.H atoms have been omitted for clarity.Colour scheme: C, grey; F, green; N, blue; O, red; S, yellow.

Table 3
Experimental details.