Literature DB >> 26090182

Crystal structure of 2-nitro-N-(2-nitro-phen-yl)benzamide.

Rodolfo Moreno-Fuquen¹, Alexis Azcárate¹, Alan R Kennedy².

Abstract

In the title compound, C13H9N3O5, the mean plane of the non-H atoms of the central amide fragment C-N-C(=O)-C [r.m.s. deviation = 0.0442 Å] forms dihedral angles of 71.76 (6) and 24.29 (10)° with the C-bonded and N-bonded benzene rings, respectively. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds forming C(4) chains along [100]. Weak C-H⋯O contacts link the mol-ecules into (100) sheets containing edge-fused R 4 (4)(30) rings. Together, the N-H⋯O and C-H⋯O hydrogen bonds generate a three-dimensional network.

Entities: Chemical Disease Gene Species

Keywords: anticonvulsant properties; antimicrobial properties; benzamide; crystal structure; hydrogen bonding; inhibitors of diverse enzymes

Year: 2015 PMID： 26090182 PMCID： PMC4459296 DOI： 10.1107/S2056989015008695

Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun

Related literature

For anticonvulsant and antimicrobial properties of benzanilide compounds, see: Leander (1992 ▸); Ahles et al. (2004 ▸). For studies as selective inhibitors of diverse enzymes, see: Goldman et al. (2003 ▸); Weisberg et al. (2006 ▸). For related structures, see: Sun et al. (2009 ▸); Saeed & Simpson (2009 ▸); Moreno-Fuquen et al. (2014 ▸).

Experimental

Crystal data

C13H9N3O5 M = 287.23 Orthorhombic, a = 7.7564 (2) Å b = 12.1142 (4) Å c = 12.9355 (4) Å V = 1215.45 (6) Å3 Z = 4 Cu Kα radiation μ = 1.06 mm−1 T = 123 K 0.35 × 0.05 × 0.02 mm

Data collection

Oxford Diffraction Gemini S diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010 ▸) T min = 0.657, T max = 1.000 4952 measured reflections 2367 independent reflections 2259 reflections with I > 2σ(I) R int = 0.019

Refinement

R[F 2 > 2σ(F 2)] = 0.034 wR(F 2) = 0.088 S = 1.06 2367 reflections 195 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.20 e Å−3 Δρmin = −0.22 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸) and Mercury (Macrae et al., 2006 ▸); software used to prepare material for publication: WinGX (Farrugia, 2012 ▸). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989015008695/hb7415sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015008695/hb7415Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S2056989015008695/hb7415Isup3.cml Click here for additional data file. . DOI: 10.1107/S2056989015008695/hb7415fig1.tif The molecular structure of (I) with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius. Click here for additional data file. C x y z . DOI: 10.1107/S2056989015008695/hb7415fig2.tif Part of the crystal structure of (I), showing the formation of C(4) chains along [100] [symmetry code: (i) x − , −y + , −z + 1]. Click here for additional data file. x y z x y z . DOI: 10.1107/S2056989015008695/hb7415fig3.tif Part of the crystal structure of (I), showing the formation of (30) rings within a 2-D hydrogen-bonded network (dashed lines) running parallel to (100) [Symmetry codes: (ii) −x + , −y + 2, z − ; (iii) −x + , −y + 1, z − ]. CCDC reference: 1063243 Additional supporting information: crystallographic information; 3D view; checkCIF report

C₁₃H₉N₃O₅	D_x = 1.570 Mg m⁻³
M_r = 287.23	Melting point: 431(1) K
Orthorhombic, P2₁2₁2₁	Cu Kα radiation, λ = 1.54180 Å
a = 7.7564 (2) Å	Cell parameters from 2546 reflections
b = 12.1142 (4) Å	θ = 5.0–72.8°
c = 12.9355 (4) Å	µ = 1.06 mm⁻¹
V = 1215.45 (6) Å³	T = 123 K
Z = 4	Needle, yellow
F(000) = 592	0.35 × 0.05 × 0.02 mm

Oxford Diffraction Gemini S diffractometer	2367 independent reflections
Radiation source: fine-focus sealed tube	2259 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.019
ω scans	θ_max = 72.9°, θ_min = 6.8°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)	h = −7→9
T_min = 0.657, T_max = 1.000	k = −13→14
4952 measured reflections	l = −15→15

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.088	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0496P)² + 0.2131P] where P = (F_o² + 2F_c²)/3
2367 reflections	(Δ/σ)_max < 0.001
195 parameters	Δρ_max = 0.20 e Å⁻³
0 restraints	Δρ_min = −0.22 e Å⁻³

Experimental. CrysAlisPro, Agilent Technologies, Version 1.171.34.46 (release 25-11-2010 CrysAlis171 .NET) (compiled Nov 25 2010,17:55:46) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

	x	y	z	U_iso*/U_eq
O1	0.8757 (2)	0.69891 (13)	0.59755 (12)	0.0235 (4)
O2	0.6495 (2)	0.70531 (14)	0.25441 (12)	0.0304 (4)
O3	0.4638 (3)	0.58573 (16)	0.20009 (14)	0.0363 (5)
O4	0.5324 (2)	0.71871 (14)	0.68775 (13)	0.0297 (4)
O5	0.5249 (3)	0.84234 (16)	0.80856 (13)	0.0348 (5)
N1	0.6852 (2)	0.69018 (17)	0.46280 (14)	0.0215 (4)
N2	0.5754 (2)	0.61585 (17)	0.26036 (15)	0.0240 (4)
N3	0.5572 (2)	0.81237 (17)	0.71999 (15)	0.0248 (4)
C1	0.7127 (3)	0.85927 (19)	0.55862 (17)	0.0207 (5)
C2	0.6264 (3)	0.89486 (19)	0.64730 (17)	0.0212 (5)
C3	0.5993 (3)	1.0050 (2)	0.66891 (18)	0.0250 (5)
H3	0.5410	1.0265	0.7303	0.030*
C4	0.6585 (3)	1.0837 (2)	0.5998 (2)	0.0282 (5)
H4	0.6418	1.1600	0.6136	0.034*
C5	0.7424 (3)	1.0505 (2)	0.51017 (19)	0.0274 (5)
H5	0.7818	1.1045	0.4623	0.033*
C6	0.7695 (3)	0.9394 (2)	0.48978 (18)	0.0226 (5)
H6	0.8273	0.9180	0.4282	0.027*
H1N	0.607 (4)	0.734 (2)	0.427 (2)	0.030 (7)*
C7	0.7639 (3)	0.74034 (19)	0.54308 (17)	0.0202 (5)
C8	0.6909 (3)	0.57706 (19)	0.43817 (18)	0.0214 (5)
C9	0.6276 (3)	0.5389 (2)	0.34294 (17)	0.0223 (5)
C10	0.6114 (3)	0.4274 (2)	0.32093 (19)	0.0275 (5)
H10	0.5633	0.4042	0.2570	0.033*
C11	0.6657 (3)	0.3505 (2)	0.3926 (2)	0.0294 (5)
H11	0.6574	0.2738	0.3780	0.035*
C12	0.7325 (3)	0.3865 (2)	0.4863 (2)	0.0290 (5)
H12	0.7711	0.3338	0.5356	0.035*
C13	0.7437 (3)	0.4977 (2)	0.50897 (18)	0.0254 (5)
H13	0.7882	0.5203	0.5740	0.030*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0236 (8)	0.0239 (8)	0.0231 (8)	−0.0009 (7)	−0.0027 (6)	0.0021 (7)
O2	0.0379 (10)	0.0292 (9)	0.0242 (8)	−0.0038 (8)	0.0001 (7)	0.0028 (7)
O3	0.0408 (10)	0.0401 (11)	0.0278 (10)	−0.0036 (9)	−0.0132 (8)	−0.0007 (8)
O4	0.0346 (9)	0.0225 (9)	0.0321 (9)	−0.0046 (7)	0.0051 (7)	−0.0003 (8)
O5	0.0417 (10)	0.0421 (11)	0.0205 (9)	−0.0040 (8)	0.0053 (8)	−0.0024 (8)
N1	0.0251 (9)	0.0206 (10)	0.0188 (9)	0.0031 (8)	−0.0020 (8)	0.0000 (8)
N2	0.0258 (10)	0.0289 (10)	0.0173 (9)	0.0020 (8)	0.0012 (8)	−0.0017 (8)
N3	0.0228 (9)	0.0288 (11)	0.0227 (9)	−0.0009 (8)	0.0014 (8)	0.0017 (8)
C1	0.0198 (10)	0.0231 (12)	0.0191 (11)	−0.0015 (9)	−0.0041 (9)	0.0006 (9)
C2	0.0206 (10)	0.0243 (12)	0.0186 (11)	−0.0014 (9)	−0.0039 (9)	0.0005 (9)
C3	0.0246 (10)	0.0262 (12)	0.0241 (11)	−0.0001 (10)	−0.0020 (9)	−0.0047 (10)
C4	0.0292 (12)	0.0205 (11)	0.0347 (13)	0.0005 (10)	−0.0061 (11)	−0.0037 (10)
C5	0.0284 (12)	0.0254 (13)	0.0285 (12)	−0.0023 (10)	−0.0047 (10)	0.0056 (11)
C6	0.0229 (11)	0.0246 (13)	0.0204 (11)	−0.0002 (9)	0.0003 (9)	0.0001 (10)
C7	0.0205 (10)	0.0238 (12)	0.0164 (10)	−0.0024 (8)	0.0030 (9)	0.0015 (9)
C8	0.0195 (10)	0.0226 (11)	0.0221 (11)	−0.0004 (9)	0.0026 (9)	−0.0013 (9)
C9	0.0210 (11)	0.0255 (12)	0.0204 (11)	0.0027 (9)	0.0029 (9)	−0.0004 (9)
C10	0.0295 (11)	0.0288 (13)	0.0244 (12)	−0.0017 (10)	0.0019 (10)	−0.0052 (10)
C11	0.0354 (13)	0.0186 (11)	0.0341 (13)	0.0006 (10)	0.0024 (12)	−0.0052 (10)
C12	0.0326 (13)	0.0243 (13)	0.0300 (13)	0.0013 (10)	−0.0017 (10)	0.0032 (11)
C13	0.0287 (11)	0.0249 (13)	0.0225 (11)	0.0010 (9)	−0.0022 (10)	−0.0004 (10)

O1—C7	1.225 (3)	C4—C5	1.389 (4)
O2—N2	1.229 (3)	C4—H4	0.9500
O3—N2	1.221 (3)	C5—C6	1.388 (3)
O4—N3	1.224 (3)	C5—H5	0.9500
O5—N3	1.228 (3)	C6—H6	0.9500
N1—C7	1.349 (3)	C8—C13	1.389 (3)
N1—C8	1.408 (3)	C8—C9	1.405 (3)
N1—H1N	0.93 (3)	C9—C10	1.385 (3)
N2—C9	1.475 (3)	C10—C11	1.381 (4)
N3—C2	1.473 (3)	C10—H10	0.9500
C1—C6	1.389 (3)	C11—C12	1.388 (4)
C1—C2	1.396 (3)	C11—H11	0.9500
C1—C7	1.508 (3)	C12—C13	1.382 (4)
C2—C3	1.379 (3)	C12—H12	0.9500
C3—C4	1.386 (4)	C13—H13	0.9500
C3—H3	0.9500

C7—N1—C8	126.7 (2)	C5—C6—C1	120.5 (2)
C7—N1—H1N	115.1 (18)	C5—C6—H6	119.7
C8—N1—H1N	117.5 (17)	C1—C6—H6	119.7
O3—N2—O2	123.7 (2)	O1—C7—N1	125.4 (2)
O3—N2—C9	117.9 (2)	O1—C7—C1	120.1 (2)
O2—N2—C9	118.33 (19)	N1—C7—C1	114.4 (2)
O4—N3—O5	124.1 (2)	C13—C8—C9	117.0 (2)
O4—N3—C2	117.94 (19)	C13—C8—N1	122.2 (2)
O5—N3—C2	118.0 (2)	C9—C8—N1	120.5 (2)
C6—C1—C2	117.6 (2)	C10—C9—C8	122.2 (2)
C6—C1—C7	119.9 (2)	C10—C9—N2	116.3 (2)
C2—C1—C7	122.1 (2)	C8—C9—N2	121.5 (2)
C3—C2—C1	122.6 (2)	C11—C10—C9	119.5 (2)
C3—C2—N3	118.1 (2)	C11—C10—H10	120.3
C1—C2—N3	119.3 (2)	C9—C10—H10	120.3
C2—C3—C4	119.0 (2)	C10—C11—C12	119.2 (2)
C2—C3—H3	120.5	C10—C11—H11	120.4
C4—C3—H3	120.5	C12—C11—H11	120.4
C3—C4—C5	119.6 (2)	C13—C12—C11	121.0 (2)
C3—C4—H4	120.2	C13—C12—H12	119.5
C5—C4—H4	120.2	C11—C12—H12	119.5
C6—C5—C4	120.7 (2)	C12—C13—C8	121.1 (2)
C6—C5—H5	119.7	C12—C13—H13	119.5
C4—C5—H5	119.7	C8—C13—H13	119.5

C6—C1—C2—C3	−1.2 (3)	C6—C1—C7—N1	−72.2 (3)
C7—C1—C2—C3	171.1 (2)	C2—C1—C7—N1	115.7 (2)
C6—C1—C2—N3	177.28 (19)	C7—N1—C8—C13	16.9 (3)
C7—C1—C2—N3	−10.5 (3)	C7—N1—C8—C9	−169.1 (2)
O4—N3—C2—C3	157.7 (2)	C13—C8—C9—C10	2.5 (3)
O5—N3—C2—C3	−20.9 (3)	N1—C8—C9—C10	−171.9 (2)
O4—N3—C2—C1	−20.8 (3)	C13—C8—C9—N2	−177.2 (2)
O5—N3—C2—C1	160.5 (2)	N1—C8—C9—N2	8.4 (3)
C1—C2—C3—C4	0.6 (3)	O3—N2—C9—C10	28.9 (3)
N3—C2—C3—C4	−177.9 (2)	O2—N2—C9—C10	−149.3 (2)
C2—C3—C4—C5	0.4 (3)	O3—N2—C9—C8	−151.5 (2)
C3—C4—C5—C6	−0.8 (4)	O2—N2—C9—C8	30.4 (3)
C4—C5—C6—C1	0.1 (4)	C8—C9—C10—C11	−2.8 (3)
C2—C1—C6—C5	0.8 (3)	N2—C9—C10—C11	176.8 (2)
C7—C1—C6—C5	−171.6 (2)	C9—C10—C11—C12	1.2 (4)
C8—N1—C7—O1	12.8 (4)	C10—C11—C12—C13	0.7 (4)
C8—N1—C7—C1	−171.3 (2)	C11—C12—C13—C8	−1.0 (4)
C6—C1—C7—O1	103.9 (3)	C9—C8—C13—C12	−0.5 (3)
C2—C1—C7—O1	−68.2 (3)	N1—C8—C13—C12	173.7 (2)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O1ⁱ	0.93 (3)	2.00 (3)	2.859 (2)	154 (2)
C5—H5···O5ⁱⁱ	0.95	2.57	3.427 (3)	150
C10—H10···O1ⁱⁱⁱ	0.95	2.46	3.271 (3)	144

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N1H1NO1ⁱ	0.93(3)	2.00(3)	2.859(2)	154(2)
C5H5O5ⁱⁱ	0.95	2.57	3.427(3)	150
C10H10O1ⁱⁱⁱ	0.95	2.46	3.271(3)	144

Symmetry codes: (i) ; (ii) ; (iii) .

7 in total

Review 1. Chronic myeloid leukemia--advances in biology and new approaches to treatment.

Authors: John M Goldman; Junia V Melo
Journal: N Engl J Med Date: 2003-10-09 Impact factor: 91.245

2. A short history of SHELX.

Authors: George M Sheldrick
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

3. Interaction of the anticonvulsant ameltolide with standard anticonvulsants.

Authors: J D Leander
Journal: Epilepsia Date: 1992 Jul-Aug Impact factor: 5.864

4. Quality of life impact of three different doses of suramin in patients with metastatic hormone-refractory prostate carcinoma: results of Intergroup O159/Cancer and Leukemia Group B 9480.

Authors: Tim A Ahles; James E Herndon; Eric J Small; Nicholas J Vogelzang; Alice B Kornblith; Mark J Ratain; Walter Stadler; David Palchak; M Ernest Marshall; George Wilding; Daniel Petrylak; Jimmie C Holland
Journal: Cancer Date: 2004-11-15 Impact factor: 6.860