2-Acet­amido-4,5-di­nitro­toluene: a test mol­ecule for the CCDC `Blind Structure Prediction Test, 2004'

Watkin, D.J.; Motherwell, W.D.S.; Copper, R.I.; Pantos, S.

doi:10.1107/S1600536804028491

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 60| Part 12| December 2004| Pages o2295-o2297

https://doi.org/10.1107/S1600536804028491

ADDENDA AND ERRATA
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2-Acetamido-4,5-dinitrotoluene: a test molecule for the CCDC `Blind Structure Prediction Test, 2004'

David J. Watkin,^a ^* W. D. S. Motherwell,^b Richard I. Copper ^a and Stefan Pantos ^a

^aChemical Crystallography, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, and ^bCambridge Crystallographic Data Centre, 12 Union Rd, Cambridge CB2 1EZ, England
^*Correspondence e-mail: david.watkin@chem.no.ac.uk

(Received 29 October 2004; accepted 4 November 2004; online 13 November 2004)

The structure of the title compound, C₉H₉N₃O₅, was determined as one of a group of five related compounds in order to assess its suitability as a test material for the 2004 Cambridge Crystallographic Data Centre `Blind Structure Prediction Test'.

Comment

The Cambridge Crystallographic Data Centre `Blind Structure Prediction Tests' are carried out periodically by a number of participating groups in order to evaluate developments in structure prediction techniques. As part of the preparations for the 2004 test, five well crystalline samples whose crystal structure was previously unknown were provided by Professor Angelo Gavezzotti. The materials were from a collection of nitrotoluene derivatives synthesized by Wilhelm Koerner about a century ago and retrieved from a depository at the University of Milan. The structures and analyses of several other materials from this collection have recently been discussed (Demartin et al., 2004 ).

The sample consisted of a mixture of crushed and broken fragments and some glass-clear pale yellow lath-shaped crystals. These were always long, and generally very thin. Attempts were made to obtain a roughly isometric sample, but the specimens inevitably cleaved freely parallel to their long length if any attempt was made to cut them into shorter lengths. Full data sets were collected for three samples [(1) 0.02 × 0.22 × 0.48 mm, 0.0021 mm³; (2) 0.04 × 0.06 × 2.0 mm, 0.0048 mm³; and (3) 0.04 × 0.15 × 0.83 mm, 0.0049 mm³]. The first two samples were collected at 190 K and refined to R(all data) of 7.99 and 7.44%. The third sample was measured at 150 K and refined to 4.25%. Comparison of the atomic parameters for the first (smallest crystal) and third (most isometric crystal; Fig. 1) refinements had a mean atomic discrepancy of 0.0018 Å and an r.m.s. atomic discrepancy of 0.008 Å for the non-H atoms. The discrepancies between the U_eq values were larger, but probably not strictly comparable because of the temperature differences. The computed absorption corrections for the third sample perpendicular to the long axis are insignificant; it is presumed that the minimum and maximum scale factors reported by the multiscan calculation (SCALEPACK) are due to changes in illuminated volume (Görbitz, 1999 ). The results reported here are for the third sample only.

As reported by Demartin et al. (2004), the nitro groups are not coplanar with the benzene ring (Fig. 2). Those authors found that the torsion angles for a nitro group adjacent to another nitro group on one side and an H atom on the other fall in the interval 27–41°. In this case, the torsion angles are C1—C2—N12—O14 = 22.87 (19)° and C2—C1—N15—O17 = 52.08 (18)°. The acetamide group is itself almost planar [C10—C8—N7—C5 = 173.10 (12)°], but also inclined to the benzene ring [C6—C5—N7—C8 = −41.46 (19)°]. Hydrogen bonding between atom H71 of one molecule and O9 of an adjacent molecule causes the structure to consist of chains parallel to the b axis (Fig. 3). The benzene rings lie parallel to each other other with a perpendicular separation of 3.58 Å (Fig. 4). Other intermolecular contacts are unexceptional.

Figure 1
Perspective views of the crystal of (3), showing indices of principal faces and their relationship to the diffractometer axes.

Figure 2
The molecule of the title compound, with displacement ellipsoids drawn at the 50% probability level. H-atom radii are proportional to U_iso.

Figure 3
Packing diagram of the title compound, viewed parallel to the a axis, showing the hydrogen bonding as dashed lines.

Figure 4
Part of the packing of the title compound, showing the parallel stacking of the benzene rings. The dashed line indicates a hydrogen bond.

Experimental

Crystals were obtained by slow evaporation of an ethanol solution

Crystal data

C₉H₉N₃O₅
M_r = 239.19
Monoclinic, P2₁/n
a = 12.5693 (4) Å
b = 4.8531 (1) Å
c = 17.2663 (5) Å
β = 99.1624 (15)°
V = 1039.81 (5) Å³
Z = 4
D_x = 1.528 Mg m⁻³
Mo Kα radiation
Cell parameters from 2364 reflections
θ = 5–27°
μ = 0.13 mm⁻¹
T = 150 K
Lath, pale yellow
0.83 × 0.15 × 0.04 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997 ) T_min = 0.61, T_max = 0.99
4326 measured reflections
2357 independent reflections
2356 reflections with I > 3σ(I)
R_int = 0.035
θ_max = 27.5°
h = −16 → 16
k = −6 → 5
l = −22 → 22

Refinement

Refinement on F²
R[F² > 2σ(F²)]= 0.051
wR(F²) = 0.095
S = 1.00
2356 reflections
182 parameters
Only coordinates of H atoms refined
w = 1/[σ²(F²) + 0.04 + 0.35p] where p = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max = 0.001
Δρ_max = 0.37 e Å⁻³
Δρ_min = −0.31 e Å⁻³
Extinction correction: Larson (1970 )
Extinction coefficient: 140 (20)

Table 1
Selected geometric parameters (Å, °)

C1—C2	1.3958 (18)
C1—C6	1.3723 (19)
C1—N15	1.4716 (17)
C2—C3	1.3812 (19)
C2—N12	1.4597 (17)
C3—C4	1.3961 (19)
C4—C5	1.4008 (18)
C4—C11	1.5029 (19)
C5—C6	1.3976 (19)
C5—N7	1.4075 (17)
N7—C8	1.3638 (18)
C8—O9	1.2222 (18)
C8—C10	1.500 (2)
N12—O13	1.2313 (15)
N12—O14	1.2273 (16)
N15—O16	1.2216 (15)
N15—O17	1.2202 (15)

C2—C1—C6	120.39 (12)
C2—C1—N15	122.09 (12)
C6—C1—N15	117.28 (11)
C1—C2—C3	119.86 (12)
C1—C2—N12	121.60 (12)
C3—C2—N12	118.32 (11)
C2—C3—C4	120.96 (12)
C3—C4—C5	118.30 (12)
C3—C4—C11	119.68 (12)
C5—C4—C11	122.01 (12)
C4—C5—C6	120.78 (12)
C4—C5—N7	119.76 (12)
C6—C5—N7	119.43 (11)
C5—C6—C1	119.70 (12)
C5—N7—C8	124.40 (12)
N7—C8—O9	121.95 (13)
N7—C8—C10	115.49 (12)
O9—C8—C10	122.56 (13)
C2—N12—O13	118.02 (11)
C2—N12—O14	117.94 (11)
O13—N12—O14	124.00 (12)
C1—N15—O16	117.18 (11)
C1—N15—O17	117.65 (11)
O16—N15—O17	125.09 (12)

Table 2
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N7—H71⋯O9ⁱ	0.868 (19)	2.002 (19)	2.8632 (17)	171.2 (15)
Symmetry code: (i) x,y-1,z.

All H atoms were seen in the difference electron-density map. Their positions and isotropic displacement parameters were regularized by several cycles of refinement using slack restraints, after which the refinement was completed using riding constraints. Reflection $[\overline {13}]$ ,3,10 was omitted from the final refinement.

Data collection: COLLECT (Nonius, 1997–2001 ); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks 3, global. DOI: https://doi.org/10.1107/S1600536804028491/bt6562sup1.cif

Structure factors: contains datablock 3. DOI: https://doi.org/10.1107/S1600536804028491/bt65623sup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1997); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

2-Acetamido-4,5-dinitrotoluene top

Crystal data top

C₉H₉N₃O₅	F(000) = 496
M_r = 239.19	D_x = 1.528 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 12.5693 (4) Å	Cell parameters from 2364 reflections
b = 4.8531 (1) Å	θ = 5–27°
c = 17.2663 (5) Å	µ = 0.13 mm⁻¹
β = 99.1624 (15)°	T = 150 K
V = 1039.81 (5) Å³	Plate, pale yellow
Z = 4	0.83 × 0.15 × 0.04 mm

Data collection top

Nonius KappaCCD diffractometer	2356 reflections with I > −3.00u(I)
Graphite monochromator	R_int = 0.035
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997)	h = −16→16
T_min = 0.61, T_max = 0.99	k = −6→5
4326 measured reflections	l = −22→22
2357 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	Only H-atom coordinates refined
R[F² > 2σ(F²)] = 0.051	P = [max(F_o²,0) + 2F_c²]/3, w = 1/[σ²(F²) + 0.04 + 0.35p] (SHELXL97; Sheldrick, 1997)
wR(F²) = 0.095	(Δ/σ)_max = 0.001
S = 1.00	Δρ_max = 0.37 e Å⁻³
2356 reflections	Δρ_min = −0.31 e Å⁻³
182 parameters	Extinction correction: Larson (1970)
52 restraints	Extinction coefficient: 140 (20)
Primary atom site location: structure-invariant direct methods

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

	x	y	z	U_iso*/U_eq
C1	−0.11506 (10)	0.5271 (3)	0.17555 (8)	0.0182
C2	−0.07828 (10)	0.4023 (3)	0.11195 (7)	0.0192
C3	0.00466 (11)	0.2129 (3)	0.12487 (8)	0.0205
C4	0.05362 (10)	0.1462 (3)	0.20090 (8)	0.0198
C5	0.01694 (10)	0.2778 (3)	0.26388 (8)	0.0189
C6	−0.06721 (10)	0.4688 (3)	0.25086 (8)	0.0185
N7	0.06289 (9)	0.2109 (3)	0.34133 (6)	0.0205
C8	0.08507 (11)	0.3977 (3)	0.40072 (8)	0.0219
O9	0.07499 (9)	0.6455 (2)	0.38929 (6)	0.0323
C10	0.12180 (13)	0.2780 (3)	0.48059 (9)	0.0286
C11	0.14477 (11)	−0.0576 (3)	0.21299 (9)	0.0250
N12	−0.11868 (9)	0.4843 (2)	0.03128 (6)	0.0218
O13	−0.10806 (9)	0.3212 (2)	−0.02157 (6)	0.0294
O14	−0.15783 (9)	0.7153 (2)	0.02014 (6)	0.0301
N15	−0.21145 (9)	0.7037 (2)	0.16568 (6)	0.0198
O16	−0.20321 (8)	0.9276 (2)	0.19842 (6)	0.0290
O17	−0.29429 (8)	0.6111 (2)	0.12828 (6)	0.0301
H71	0.0726 (13)	0.038 (4)	0.3533 (10)	0.0290*
H31	0.0307 (9)	0.134 (2)	0.0806 (7)	0.0247*
H61	−0.0945 (9)	0.553 (2)	0.2935 (7)	0.0230*
H3	0.1484 (12)	0.093 (3)	0.4774 (9)	0.0343*
H4	0.0593 (11)	0.272 (3)	0.5080 (9)	0.0345*
H5	0.1738 (11)	0.394 (3)	0.5115 (9)	0.0352*
H6	0.1765 (12)	−0.086 (3)	0.1679 (8)	0.0346*
H7	0.2010 (11)	0.004 (3)	0.2535 (8)	0.0337*
H8	0.1236 (12)	−0.233 (3)	0.2305 (9)	0.0344*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0174 (6)	0.0154 (6)	0.0223 (6)	−0.0008 (5)	0.0050 (5)	0.0002 (5)
C2	0.0217 (6)	0.0182 (6)	0.0182 (6)	−0.0019 (5)	0.0045 (5)	0.0009 (5)
C3	0.0232 (7)	0.0171 (6)	0.0227 (6)	−0.0009 (5)	0.0083 (5)	−0.0011 (5)
C4	0.0200 (6)	0.0149 (7)	0.0249 (7)	−0.0021 (5)	0.0053 (5)	−0.0002 (5)
C5	0.0207 (6)	0.0147 (6)	0.0212 (6)	−0.0031 (5)	0.0033 (5)	0.0007 (5)
C6	0.0196 (6)	0.0166 (6)	0.0202 (6)	−0.0017 (5)	0.0058 (5)	−0.0012 (5)
N7	0.0259 (6)	0.0134 (6)	0.0212 (6)	0.0006 (5)	0.0011 (5)	0.0016 (5)
C8	0.0237 (7)	0.0183 (7)	0.0233 (7)	0.0002 (6)	0.0028 (5)	0.0000 (5)
O9	0.0494 (7)	0.0154 (5)	0.0288 (5)	0.0007 (5)	−0.0037 (5)	0.0006 (4)
C10	0.0367 (8)	0.0231 (8)	0.0238 (7)	0.0032 (7)	−0.0017 (6)	0.0011 (6)
C11	0.0244 (7)	0.0207 (7)	0.0303 (7)	0.0025 (6)	0.0057 (6)	0.0002 (6)
N12	0.0233 (6)	0.0223 (6)	0.0209 (6)	0.0000 (5)	0.0066 (5)	0.0017 (5)
O13	0.0382 (6)	0.0301 (6)	0.0207 (5)	0.0005 (5)	0.0073 (4)	−0.0062 (4)
O14	0.0384 (6)	0.0262 (6)	0.0266 (5)	0.0084 (5)	0.0081 (4)	0.0062 (4)
N15	0.0204 (6)	0.0204 (6)	0.0193 (5)	0.0007 (5)	0.0056 (4)	0.0010 (5)
O16	0.0276 (5)	0.0185 (5)	0.0421 (6)	0.0018 (4)	0.0090 (5)	−0.0051 (5)
O17	0.0212 (5)	0.0397 (6)	0.0275 (5)	0.0012 (5)	−0.0022 (4)	−0.0069 (5)

Geometric parameters (Å, º) top

C1—C2	1.3958 (18)	N7—H71	0.868 (19)
C1—C6	1.3723 (19)	C8—O9	1.2222 (18)
C1—N15	1.4716 (17)	C8—C10	1.500 (2)
C2—C3	1.3812 (19)	C10—H3	0.965 (13)
C2—N12	1.4597 (17)	C10—H4	0.979 (12)
C3—C4	1.3961 (19)	C10—H5	0.958 (13)
C3—H31	0.957 (12)	C11—H6	0.939 (12)
C4—C5	1.4008 (18)	C11—H7	0.960 (12)
C4—C11	1.5029 (19)	C11—H8	0.954 (13)
C5—C6	1.3976 (19)	N12—O13	1.2313 (15)
C5—N7	1.4075 (17)	N12—O14	1.2273 (16)
C6—H61	0.951 (12)	N15—O16	1.2216 (15)
N7—C8	1.3638 (18)	N15—O17	1.2202 (15)

C2—C1—C6	120.39 (12)	N7—C8—O9	121.95 (13)
C2—C1—N15	122.09 (12)	N7—C8—C10	115.49 (12)
C6—C1—N15	117.28 (11)	O9—C8—C10	122.56 (13)
C1—C2—C3	119.86 (12)	C8—C10—H3	111.6 (9)
C1—C2—N12	121.60 (12)	C8—C10—H4	107.6 (9)
C3—C2—N12	118.32 (11)	H3—C10—H4	108.0 (11)
C2—C3—C4	120.96 (12)	C8—C10—H5	111.6 (10)
C2—C3—H31	118.8 (8)	H3—C10—H5	111.6 (12)
C4—C3—H31	120.1 (8)	H4—C10—H5	106.1 (11)
C3—C4—C5	118.30 (12)	C4—C11—H6	113.3 (10)
C3—C4—C11	119.68 (12)	C4—C11—H7	110.6 (9)
C5—C4—C11	122.01 (12)	H6—C11—H7	106.7 (11)
C4—C5—C6	120.78 (12)	C4—C11—H8	112.6 (9)
C4—C5—N7	119.76 (12)	H6—C11—H8	108.1 (12)
C6—C5—N7	119.43 (11)	H7—C11—H8	104.9 (11)
C5—C6—C1	119.70 (12)	C2—N12—O13	118.02 (11)
C5—C6—H61	121.0 (8)	C2—N12—O14	117.94 (11)
C1—C6—H61	119.2 (8)	O13—N12—O14	124.00 (12)
C5—N7—C8	124.40 (12)	C1—N15—O16	117.18 (11)
C5—N7—H71	118.1 (11)	C1—N15—O17	117.65 (11)
C8—N7—H71	117.3 (11)	O16—N15—O17	125.09 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N7—H71···O9ⁱ	0.868 (19)	2.002 (19)	2.8632 (17)	171.2 (15)

Symmetry code: (i) x, y−1, z.

Acknowledgements

We thank Professor Angelo Gavezzotti for obtaining the samples, Professor Lucio Merlini, Director of the Dipartimento di Scienze Molecolari Agroalimentari of the University of Milano, for generously donating the samples, and Professor Anna Arnoldi for help in the retrieval of the crystals.

References

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