Crystal structure and Hirshfeld surface analysis of 2-methyl-3-nitro-N-[(E)-(5-nitro­thio­phen-2-yl)methyl­idene]aniline

The title compound is a Schiff base formed from 5-nitro­thio­phene-2-carbaldehyde and 2-methyl-3-nitro­aniline. In the crystal, the mol­ecules are linked by weak C—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.053
• wR factor = 0.129
• Data-to-parameter ratio = 21.1

checkCIF/PLATON results

No syntax errors found



Alert level C
STRVA01_ALERT_4_C           Flack test results are ambiguous.
           From the CIF: _refine_ls_abs_structure_Flack    0.590
           From the CIF: _refine_ls_abs_structure_Flack_su    0.150
PLAT048_ALERT_1_C MoietyFormula Not Given (or Incomplete) ........     Please Check
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of         N3 Check
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00527 Ang.
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      4.944 Check
PLAT907_ALERT_2_C Flack x > 0.5, Structure Needs to be Inverted? .       0.59 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          3 Report

Alert level G
PLAT033_ALERT_4_G Flack x Value Deviates > 3.0 * sigma from Zero .      0.590 Note
PLAT063_ALERT_4_G Crystal Size Possibly too Large for Beam Size ..       0.75 mm
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT380_ALERT_4_G Incorrectly? Oriented X(sp2)-Methyl Moiety .....         C1 Check
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          2 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 Info

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

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   5 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: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA(Stoe & Cie, 2002); data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXT2017/1 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2017/1 (Sheldrick, 2015b); molecular graphics: PLATON (Spek, 2020); software used to prepare material for publication: WinGX (Farrugia, 2012).

2-Methyl-3-nitro-N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline

Crystal data

C12H9N3O4S	Dx = 1.496 Mg m^−3
Mr = 291.28	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 6261 reflections
a = 7.1335 (4) Å	θ = 2.2–30.9°
b = 11.7297 (6) Å	µ = 0.27 mm^−1
c = 15.4593 (7) Å	T = 293 K
V = 1293.54 (11) Å^3	Stick, yellow
Z = 4	0.75 × 0.39 × 0.14 mm
F(000) = 600

Data collection

Stoe IPDS 2 diffractometer	3930 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	2258 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm^-1	Rint = 0.049
rotation method scans	θmax = 30.5°, θmin = 2.2°
Absorption correction: integration (X-RED32; Stoe & Cie, 2002)	h = −8→10
Tmin = 0.839, Tmax = 0.966	k = −16→12
6707 measured reflections	l = −22→20

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.053	w = 1/[σ^2(Fo^2) + (0.063P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.129	(Δ/σ)max < 0.001
S = 0.91	Δρmax = 0.33 e Å^−3
3930 reflections	Δρmin = −0.19 e Å^−3
186 parameters	Absolute structure: Refined as an inversion twin.
0 restraints	Absolute structure parameter: 0.59 (15)

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.

Refinement. Refined as a two-component inversion twin

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

	x	y	z	Uiso*/Ueq
S1	0.63801 (15)	0.83820 (8)	0.62698 (6)	0.0504 (3)
N2	0.6540 (5)	0.6808 (2)	0.47460 (18)	0.0437 (7)
N1	0.7061 (6)	0.2794 (3)	0.3994 (3)	0.0637 (10)
O2	0.8371 (6)	0.2537 (3)	0.4460 (2)	0.0886 (11)
O1	0.5937 (6)	0.2119 (3)	0.3708 (3)	0.0988 (13)
C8	0.7015 (6)	0.7831 (3)	0.4567 (2)	0.0432 (8)
C7	0.6589 (5)	0.5963 (3)	0.4097 (2)	0.0397 (7)
C9	0.6899 (5)	0.8708 (3)	0.5213 (2)	0.0431 (8)
C6	0.6287 (6)	0.6186 (3)	0.3229 (2)	0.0487 (9)
H6	0.610040	0.693392	0.304891	0.058*
C3	0.6828 (5)	0.4000 (3)	0.3749 (3)	0.0474 (8)
N3	0.6315 (7)	1.0145 (4)	0.7400 (3)	0.0756 (12)
C2	0.6860 (5)	0.4834 (3)	0.4389 (2)	0.0423 (8)
C4	0.6524 (7)	0.4210 (3)	0.2888 (2)	0.0549 (9)
H4	0.649811	0.361601	0.249035	0.066*
O3	0.5983 (7)	0.9420 (5)	0.7941 (2)	0.1054 (15)
C12	0.6570 (6)	0.9799 (3)	0.6526 (2)	0.0537 (10)
C11	0.7002 (6)	1.0482 (3)	0.5853 (3)	0.0575 (11)
H11	0.714508	1.126873	0.589073	0.069*
O4	0.6437 (7)	1.1168 (4)	0.7564 (3)	0.1149 (15)
C10	0.7204 (6)	0.9856 (3)	0.5095 (3)	0.0520 (10)
H10	0.751275	1.017854	0.456431	0.062*
C1	0.7131 (7)	0.4585 (4)	0.5333 (3)	0.0559 (10)
H1A	0.710488	0.528510	0.565450	0.084*
H1B	0.614362	0.409413	0.553194	0.084*
H1C	0.831809	0.421538	0.541751	0.084*
C5	0.6258 (7)	0.5321 (4)	0.2626 (2)	0.0573 (10)
H5	0.606041	0.548561	0.204434	0.069*
H8	0.747 (5)	0.807 (3)	0.403 (2)	0.034 (9)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0561 (5)	0.0487 (5)	0.0465 (4)	−0.0019 (5)	−0.0005 (5)	−0.0003 (4)
N2	0.0474 (16)	0.0390 (15)	0.0448 (15)	−0.0002 (14)	0.0051 (14)	−0.0033 (12)
N1	0.075 (3)	0.0406 (18)	0.075 (3)	0.0010 (19)	0.002 (2)	−0.0039 (17)
O2	0.110 (3)	0.0465 (17)	0.109 (3)	0.012 (2)	−0.021 (3)	0.0103 (18)
O1	0.120 (3)	0.0470 (17)	0.130 (3)	−0.0226 (19)	−0.015 (3)	−0.009 (2)
C8	0.052 (2)	0.0367 (18)	0.0407 (18)	0.0013 (15)	0.0051 (16)	0.0002 (14)
C7	0.0433 (19)	0.0334 (15)	0.0424 (17)	−0.0017 (16)	0.0050 (16)	−0.0029 (13)
C9	0.042 (2)	0.0383 (17)	0.0490 (19)	0.0033 (14)	−0.0003 (15)	−0.0014 (15)
C6	0.062 (2)	0.0445 (18)	0.0400 (18)	0.007 (2)	−0.0010 (19)	0.0059 (14)
C3	0.050 (2)	0.0368 (17)	0.055 (2)	0.0010 (15)	0.0040 (19)	0.0005 (17)
N3	0.070 (2)	0.093 (3)	0.063 (2)	0.006 (3)	−0.006 (2)	−0.032 (2)
C2	0.045 (2)	0.0399 (18)	0.0423 (18)	−0.0028 (15)	0.0037 (15)	−0.0006 (15)
C4	0.064 (3)	0.050 (2)	0.050 (2)	0.002 (2)	0.005 (2)	−0.0148 (17)
O3	0.131 (4)	0.134 (4)	0.052 (2)	0.012 (3)	0.006 (2)	−0.010 (2)
C12	0.050 (2)	0.056 (2)	0.055 (2)	0.004 (2)	−0.0073 (19)	−0.0194 (18)
C11	0.064 (3)	0.038 (2)	0.070 (3)	0.0038 (18)	−0.004 (2)	−0.0101 (19)
O4	0.141 (4)	0.101 (3)	0.102 (3)	0.004 (3)	−0.007 (3)	−0.063 (3)
C10	0.061 (2)	0.0366 (19)	0.058 (2)	−0.0001 (17)	−0.0024 (19)	0.0013 (17)
C1	0.073 (3)	0.046 (2)	0.048 (2)	0.000 (2)	0.002 (2)	0.0085 (17)
C5	0.073 (3)	0.063 (2)	0.0361 (18)	0.002 (3)	−0.001 (2)	−0.0028 (17)

Geometric parameters (Å, º)

S1—C12	1.714 (4)	C3—C2	1.392 (5)
S1—C9	1.718 (4)	N3—O3	1.216 (6)
N2—C8	1.277 (4)	N3—O4	1.230 (6)
N2—C7	1.411 (4)	N3—C12	1.423 (5)
N1—O1	1.211 (5)	C2—C1	1.501 (5)
N1—O2	1.218 (5)	C4—C5	1.377 (6)
N1—C3	1.474 (5)	C4—H4	0.9300
C8—C9	1.435 (5)	C12—C11	1.349 (6)
C8—H8	0.93 (4)	C11—C10	1.391 (6)
C7—C6	1.384 (5)	C11—H11	0.9300
C7—C2	1.412 (5)	C10—H10	0.9300
C9—C10	1.376 (5)	C1—H1A	0.9600
C6—C5	1.378 (5)	C1—H1B	0.9600
C6—H6	0.9300	C1—H1C	0.9600
C3—C4	1.371 (5)	C5—H5	0.9300
C12—S1—C9	89.25 (18)	C3—C2—C1	123.8 (3)
C8—N2—C7	120.0 (3)	C7—C2—C1	120.8 (3)
O1—N1—O2	124.3 (4)	C3—C4—C5	118.6 (3)
O1—N1—C3	117.3 (4)	C3—C4—H4	120.7
O2—N1—C3	118.4 (4)	C5—C4—H4	120.7
N2—C8—C9	120.5 (3)	C11—C12—N3	126.4 (4)
N2—C8—H8	124 (2)	C11—C12—S1	114.6 (3)
C9—C8—H8	115 (2)	N3—C12—S1	119.0 (3)
C6—C7—N2	123.5 (3)	C12—C11—C10	111.1 (4)
C6—C7—C2	120.6 (3)	C12—C11—H11	124.5
N2—C7—C2	115.8 (3)	C10—C11—H11	124.5
C10—C9—C8	126.9 (4)	C9—C10—C11	112.9 (4)
C10—C9—S1	112.2 (3)	C9—C10—H10	123.5
C8—C9—S1	120.9 (3)	C11—C10—H10	123.6
C5—C6—C7	121.3 (3)	C2—C1—H1A	109.5
C5—C6—H6	119.4	C2—C1—H1B	109.5
C7—C6—H6	119.4	H1A—C1—H1B	109.5
C4—C3—C2	124.5 (3)	C2—C1—H1C	109.5
C4—C3—N1	116.1 (3)	H1A—C1—H1C	109.5
C2—C3—N1	119.4 (4)	H1B—C1—H1C	109.5
O3—N3—O4	123.7 (5)	C4—C5—C6	119.7 (4)
O3—N3—C12	118.6 (4)	C4—C5—H5	120.2
O4—N3—C12	117.7 (5)	C6—C5—H5	120.2
C3—C2—C7	115.4 (3)
C7—N2—C8—C9	177.5 (3)	N2—C7—C2—C3	177.4 (3)
C8—N2—C7—C6	−30.4 (6)	C6—C7—C2—C1	−178.2 (4)
C8—N2—C7—C2	153.2 (4)	N2—C7—C2—C1	−1.7 (6)
N2—C8—C9—C10	−173.9 (4)	C2—C3—C4—C5	1.0 (7)
N2—C8—C9—S1	7.5 (5)	N1—C3—C4—C5	178.7 (4)
C12—S1—C9—C10	0.4 (3)	O3—N3—C12—C11	−177.8 (5)
C12—S1—C9—C8	179.2 (3)	O4—N3—C12—C11	2.5 (8)
N2—C7—C6—C5	−176.7 (4)	O3—N3—C12—S1	0.6 (7)
C2—C7—C6—C5	−0.5 (7)	O4—N3—C12—S1	−179.2 (4)
O1—N1—C3—C4	−47.0 (6)	C9—S1—C12—C11	0.0 (4)
O2—N1—C3—C4	132.2 (4)	C9—S1—C12—N3	−178.6 (4)
O1—N1—C3—C2	130.8 (4)	N3—C12—C11—C10	178.1 (4)
O2—N1—C3—C2	−50.0 (6)	S1—C12—C11—C10	−0.3 (5)
C4—C3—C2—C7	−1.2 (6)	C8—C9—C10—C11	−179.3 (4)
N1—C3—C2—C7	−178.8 (3)	S1—C9—C10—C11	−0.7 (4)
C4—C3—C2—C1	177.9 (4)	C12—C11—C10—C9	0.6 (5)
N1—C3—C2—C1	0.3 (6)	C3—C4—C5—C6	−0.5 (7)
C6—C7—C2—C3	0.9 (6)	C7—C6—C5—C4	0.3 (7)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8···O4^i	0.93 (4)	2.56 (4)	3.492 (5)	176 (3)

Symmetry code: (i) −x+3/2, −y+2, z−1/2.