[2-Chloro-3-nitro-5-(tri­fluoro­meth­yl)phen­yl](piperidin-1-yl)methanone: structural characterization of a side product in benzo­thia­zinone synthesis

The crystal and mol­ecular structure of [2-chloro-3-nitro-5-(tri­fluoro­meth­yl)phen­yl](piperidin-1-yl)methanone, a side product in the synthesis of an 8-nitro-1,3-benzo­thia­zin-4-one, which belongs to a class of new anti-tuberculosis drug candidates, is reported.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.003 Å
• Disorder in main residue
• R factor = 0.043
• wR factor = 0.115
• Data-to-parameter ratio = 13.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT717_ALERT_1_C D...A   Unknown or Inconsistent Label ..........    CGC1-C6 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          3 Report

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          8 Note
PLAT171_ALERT_4_G The CIF-Embedded .res File Contains EADP Records          3 Report
PLAT176_ALERT_4_G The CIF-Embedded .res File Contains SADI Records          3 Report
PLAT230_ALERT_2_G Hirshfeld Test Diff for    F3'      --C7       .        7.6 s.u.
PLAT242_ALERT_2_G Low    'MainMol' Ueq as Compared to Neighbors of         C7 Check
PLAT301_ALERT_3_G Main Residue  Disorder ..............(Resd  1  )        14% Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............         45 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          1 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          4 Note
PLAT913_ALERT_3_G Missing # of Very Strong Reflections in FCF ....          2 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          3 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  11 ALERT level G = General information/check it is not something unexpected

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check


checkCIF publication errors

Alert level A
PUBL024_ALERT_1_A The number of authors is greater than 5.
              Please specify the role of each of the co-authors
              for your paper.

   1 ALERT level A = Data missing that is essential or data in wrong format
   0 ALERT level G = General alerts. Data that may be required is missing

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Computing details

Data collection: APEX3 (Bruker, 2017); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXT2014/4 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg, 2018); software used to prepare material for publication: enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).

[2-Chloro-3-nitro-5-(trifluoromethyl)phenyl](piperidin-1-yl)methanone

Crystal data

C13H12ClF3N2O3	Dx = 1.581 Mg m^−3
Mr = 336.70	Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, Pbca	Cell parameters from 9968 reflections
a = 18.0904 (7) Å	θ = 4.9–71.6°
b = 7.8971 (3) Å	µ = 2.88 mm^−1
c = 19.8043 (8) Å	T = 100 K
V = 2829.28 (19) Å^3	Block, colourless
Z = 8	0.59 × 0.50 × 0.44 mm
F(000) = 1376

Data collection

Bruker Kappa Mach3 APEXII diffractometer	2784 independent reflections
Radiation source: 0.2 × 2 mm^2 focus rotating anode	2699 reflections with I > 2σ(I)
MONTEL graded multilayer optics monochromator	Rint = 0.041
Detector resolution: 66.67 pixels mm^-1	θmax = 72.2°, θmin = 4.9°
φ– and ω–scans	h = −21→22
Absorption correction: gaussian (SADABS; Krause et al., 2015)	k = −9→9
Tmin = 0.297, Tmax = 0.586	l = −24→24
49954 measured reflections

Refinement

Refinement on F^2	Primary atom site location: dual
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.115	H-atom parameters constrained
S = 1.15	w = 1/[σ^2(Fo^2) + (0.0508P)^2 + 2.7994P] where P = (Fo^2 + 2Fc^2)/3
2784 reflections	(Δ/σ)max < 0.001
209 parameters	Δρmax = 0.32 e Å^−3
45 restraints	Δρmin = −0.32 e Å^−3

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	0.41556 (10)	0.3250 (3)	0.23581 (10)	0.0230 (4)
C2	0.38370 (10)	0.1651 (3)	0.23833 (10)	0.0224 (4)
C3	0.35007 (10)	0.1004 (3)	0.18023 (10)	0.0227 (4)
C4	0.34763 (10)	0.1927 (3)	0.12111 (10)	0.0243 (4)
H4	0.325215	0.146458	0.081847	0.029*
C5	0.37831 (10)	0.3541 (3)	0.11961 (10)	0.0242 (4)
C6	0.41190 (11)	0.4206 (3)	0.17666 (10)	0.0250 (4)
H6	0.432417	0.531321	0.175487	0.030*
C7	0.37425 (12)	0.4549 (3)	0.05572 (11)	0.0298 (5)
C8	0.45848 (10)	0.3906 (2)	0.29575 (10)	0.0232 (4)
C9	0.34929 (13)	0.5683 (3)	0.32422 (11)	0.0327 (5)
H9A	0.325497	0.503425	0.287381	0.039*
H9B	0.351745	0.688568	0.310277	0.039*
C10	0.30335 (12)	0.5528 (3)	0.38813 (13)	0.0404 (6)
H10A	0.296350	0.431647	0.399304	0.048*
H10B	0.254021	0.603627	0.380559	0.048*
C11	0.34134 (13)	0.6421 (3)	0.44689 (11)	0.0373 (5)
H11A	0.344826	0.764952	0.437412	0.045*
H11B	0.311898	0.626777	0.488581	0.045*
C12	0.41843 (12)	0.5691 (3)	0.45695 (10)	0.0294 (5)
H12A	0.443955	0.632047	0.493365	0.035*
H12B	0.414464	0.449164	0.470978	0.035*
C13	0.46343 (11)	0.5807 (3)	0.39245 (10)	0.0277 (4)
H13A	0.473754	0.701122	0.382205	0.033*
H13B	0.511333	0.522352	0.398982	0.033*
N1	0.31581 (9)	−0.0681 (2)	0.17845 (9)	0.0253 (4)
N2	0.42423 (9)	0.5038 (2)	0.33544 (8)	0.0249 (4)
O1	0.28104 (8)	−0.1161 (2)	0.22819 (8)	0.0324 (4)
O2	0.32229 (8)	−0.1493 (2)	0.12611 (8)	0.0341 (4)
O3	0.52198 (7)	0.33806 (19)	0.30471 (7)	0.0288 (3)
F1	0.38438 (14)	0.3603 (2)	0.00122 (7)	0.0711 (7)	0.972 (2)
F2	0.30831 (8)	0.52847 (19)	0.04797 (8)	0.0418 (4)	0.972 (2)
F3	0.42321 (8)	0.5801 (2)	0.05379 (8)	0.0470 (4)	0.972 (2)
F1'	0.352 (3)	0.612 (3)	0.0688 (18)	0.0711 (7)	0.028 (2)
F2'	0.4387 (11)	0.472 (6)	0.0269 (18)	0.0418 (4)	0.028 (2)
F3'	0.325 (2)	0.397 (5)	0.0129 (15)	0.0470 (4)	0.028 (2)
Cl1	0.38924 (3)	0.05417 (6)	0.31320 (2)	0.02635 (16)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0194 (9)	0.0250 (9)	0.0246 (9)	0.0021 (7)	0.0012 (7)	−0.0019 (8)
C2	0.0186 (8)	0.0246 (9)	0.0239 (9)	0.0021 (7)	0.0011 (7)	0.0002 (8)
C3	0.0166 (8)	0.0219 (9)	0.0296 (10)	0.0011 (7)	0.0009 (7)	−0.0021 (8)
C4	0.0202 (9)	0.0288 (10)	0.0239 (9)	0.0050 (8)	−0.0004 (7)	−0.0031 (8)
C5	0.0219 (9)	0.0261 (10)	0.0247 (10)	0.0056 (8)	0.0021 (7)	0.0011 (8)
C6	0.0248 (10)	0.0226 (9)	0.0277 (10)	0.0006 (8)	0.0004 (8)	0.0002 (8)
C7	0.0350 (11)	0.0292 (11)	0.0251 (10)	0.0056 (9)	0.0005 (8)	−0.0002 (8)
C8	0.0225 (9)	0.0226 (9)	0.0245 (9)	−0.0035 (8)	−0.0003 (7)	0.0033 (8)
C9	0.0335 (11)	0.0298 (11)	0.0347 (11)	0.0094 (9)	−0.0117 (9)	−0.0088 (9)
C10	0.0200 (10)	0.0517 (15)	0.0495 (14)	0.0058 (9)	−0.0038 (9)	−0.0188 (11)
C11	0.0324 (11)	0.0474 (14)	0.0322 (11)	0.0039 (10)	−0.0011 (9)	−0.0114 (10)
C12	0.0308 (11)	0.0327 (11)	0.0247 (10)	−0.0010 (9)	−0.0013 (8)	0.0002 (8)
C13	0.0267 (10)	0.0306 (10)	0.0257 (10)	−0.0070 (8)	−0.0028 (8)	−0.0018 (8)
N1	0.0190 (8)	0.0260 (9)	0.0310 (9)	−0.0009 (6)	−0.0037 (7)	−0.0016 (7)
N2	0.0213 (8)	0.0277 (9)	0.0257 (8)	−0.0010 (7)	−0.0042 (7)	−0.0030 (7)
O1	0.0267 (7)	0.0334 (8)	0.0371 (8)	−0.0062 (6)	0.0010 (6)	0.0028 (7)
O2	0.0348 (8)	0.0320 (8)	0.0356 (8)	−0.0010 (6)	−0.0045 (6)	−0.0098 (7)
O3	0.0204 (7)	0.0324 (8)	0.0337 (8)	0.0005 (6)	−0.0017 (6)	−0.0003 (6)
F1	0.151 (2)	0.0382 (9)	0.0239 (7)	0.0278 (10)	0.0154 (9)	−0.0002 (6)
F2	0.0336 (7)	0.0457 (8)	0.0460 (8)	0.0053 (6)	−0.0056 (6)	0.0175 (7)
F3	0.0389 (8)	0.0567 (10)	0.0453 (8)	−0.0142 (7)	−0.0052 (6)	0.0251 (7)
F1'	0.151 (2)	0.0382 (9)	0.0239 (7)	0.0278 (10)	0.0154 (9)	−0.0002 (6)
F2'	0.0336 (7)	0.0457 (8)	0.0460 (8)	0.0053 (6)	−0.0056 (6)	0.0175 (7)
F3'	0.0389 (8)	0.0567 (10)	0.0453 (8)	−0.0142 (7)	−0.0052 (6)	0.0251 (7)
Cl1	0.0267 (3)	0.0273 (3)	0.0250 (3)	−0.00271 (18)	0.00002 (17)	0.00364 (17)

Geometric parameters (Å, º)

C1—C2	1.389 (3)	C8—N2	1.342 (3)
C1—C6	1.395 (3)	C9—N2	1.465 (3)
C1—C8	1.510 (3)	C9—C10	1.519 (3)
C2—C3	1.398 (3)	C9—H9A	0.9900
C2—Cl1	1.725 (2)	C9—H9B	0.9900
C3—C4	1.380 (3)	C10—C11	1.525 (3)
C3—N1	1.468 (3)	C10—H10A	0.9900
C4—C5	1.390 (3)	C10—H10B	0.9900
C4—H4	0.9500	C11—C12	1.522 (3)
C5—C6	1.386 (3)	C11—H11A	0.9900
C5—C7	1.497 (3)	C11—H11B	0.9900
C6—H6	0.9500	C12—C13	1.518 (3)
C7—F2'	1.304 (14)	C12—H12A	0.9900
C7—F3'	1.314 (14)	C12—H12B	0.9900
C7—F1	1.325 (3)	C13—N2	1.465 (2)
C7—F3	1.328 (3)	C13—H13A	0.9900
C7—F1'	1.332 (14)	C13—H13B	0.9900
C7—F2	1.336 (3)	N1—O2	1.225 (2)
C8—O3	1.234 (2)	N1—O1	1.229 (2)
C2—C1—C6	120.16 (18)	C10—C9—H9A	109.5
C2—C1—C8	119.82 (17)	N2—C9—H9B	109.5
C6—C1—C8	119.90 (17)	C10—C9—H9B	109.5
C1—C2—C3	118.92 (18)	H9A—C9—H9B	108.1
C1—C2—Cl1	117.93 (15)	C9—C10—C11	110.61 (19)
C3—C2—Cl1	123.13 (16)	C9—C10—H10A	109.5
C4—C3—C2	121.24 (18)	C11—C10—H10A	109.5
C4—C3—N1	116.41 (17)	C9—C10—H10B	109.5
C2—C3—N1	122.35 (18)	C11—C10—H10B	109.5
C3—C4—C5	119.32 (18)	H10A—C10—H10B	108.1
C3—C4—H4	120.3	C12—C11—C10	109.74 (18)
C5—C4—H4	120.3	C12—C11—H11A	109.7
C6—C5—C4	120.33 (18)	C10—C11—H11A	109.7
C6—C5—C7	120.58 (19)	C12—C11—H11B	109.7
C4—C5—C7	119.09 (18)	C10—C11—H11B	109.7
C5—C6—C1	119.98 (19)	H11A—C11—H11B	108.2
C5—C6—H6	120.0	C13—C12—C11	111.01 (18)
C1—C6—H6	120.0	C13—C12—H12A	109.4
F2'—C7—F3'	111.1 (19)	C11—C12—H12A	109.4
F1—C7—F3	107.69 (19)	C13—C12—H12B	109.4
F2'—C7—F1'	105.2 (19)	C11—C12—H12B	109.4
F3'—C7—F1'	104.0 (19)	H12A—C12—H12B	108.0
F1—C7—F2	105.98 (19)	N2—C13—C12	111.35 (17)
F3—C7—F2	105.59 (17)	N2—C13—H13A	109.4
F2'—C7—C5	112.3 (15)	C12—C13—H13A	109.4
F3'—C7—C5	113.2 (15)	N2—C13—H13B	109.4
F1—C7—C5	112.43 (17)	C12—C13—H13B	109.4
F3—C7—C5	112.80 (18)	H13A—C13—H13B	108.0
F1'—C7—C5	110.3 (15)	O2—N1—O1	124.48 (17)
F2—C7—C5	111.86 (17)	O2—N1—C3	117.04 (17)
O3—C8—N2	124.72 (18)	O1—N1—C3	118.44 (16)
O3—C8—C1	118.43 (18)	C8—N2—C13	120.26 (16)
N2—C8—C1	116.85 (17)	C8—N2—C9	124.74 (16)
N2—C9—C10	110.59 (18)	C13—N2—C9	114.89 (16)
N2—C9—H9A	109.5
C6—C1—C2—C3	1.9 (3)	C6—C5—C7—F1'	−47 (3)
C8—C1—C2—C3	−174.16 (17)	C4—C5—C7—F1'	133 (3)
C6—C1—C2—Cl1	−179.32 (15)	C6—C5—C7—F2	−99.4 (2)
C8—C1—C2—Cl1	4.6 (2)	C4—C5—C7—F2	80.3 (2)
C1—C2—C3—C4	−0.5 (3)	C2—C1—C8—O3	77.8 (2)
Cl1—C2—C3—C4	−179.22 (14)	C6—C1—C8—O3	−98.3 (2)
C1—C2—C3—N1	179.37 (16)	C2—C1—C8—N2	−102.6 (2)
Cl1—C2—C3—N1	0.6 (3)	C6—C1—C8—N2	81.4 (2)
C2—C3—C4—C5	−0.9 (3)	N2—C9—C10—C11	55.5 (3)
N1—C3—C4—C5	179.25 (16)	C9—C10—C11—C12	−56.9 (3)
C3—C4—C5—C6	0.9 (3)	C10—C11—C12—C13	55.8 (3)
C3—C4—C5—C7	−178.87 (18)	C11—C12—C13—N2	−53.4 (2)
C4—C5—C6—C1	0.5 (3)	C4—C3—N1—O2	36.6 (2)
C7—C5—C6—C1	−179.75 (18)	C2—C3—N1—O2	−143.29 (19)
C2—C1—C6—C5	−1.9 (3)	C4—C3—N1—O1	−141.34 (18)
C8—C1—C6—C5	174.13 (18)	C2—C3—N1—O1	38.8 (3)
C6—C5—C7—F2'	70 (2)	O3—C8—N2—C13	3.0 (3)
C4—C5—C7—F2'	−110 (2)	C1—C8—N2—C13	−176.62 (17)
C6—C5—C7—F3'	−163 (2)	O3—C8—N2—C9	179.0 (2)
C4—C5—C7—F3'	17 (2)	C1—C8—N2—C9	−0.6 (3)
C6—C5—C7—F1	141.5 (2)	C12—C13—N2—C8	−130.0 (2)
C4—C5—C7—F1	−38.8 (3)	C12—C13—N2—C9	53.6 (2)
C6—C5—C7—F3	19.5 (3)	C10—C9—N2—C8	129.2 (2)
C4—C5—C7—F3	−160.82 (18)	C10—C9—N2—C13	−54.6 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···O3^i	0.95	2.59	3.526 (3)	169
C9—H9A···O1^ii	0.99	2.45	3.361 (3)	154
C9—H9B···O1^iii	0.99	2.58	3.369 (3)	137
C13—H13A···Cg(C1–C6)^iv	0.99	2.92	3.447 (2)	114

Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+1/2, y+1/2, z; (iii) x, y+1, z; (iv) x+3/2, −y+1/2, −z.