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Acta Cryst. (2012). E68, o3098    [ doi:10.1107/S1600536812040895 ]

Methyl 2-(3,5-dinitrobenzamido)-3-methylbutanoate

X. Li and Y. Zhao

Abstract top

In the title compound, C13H15N3O7, the dihedral angle between the amide plane (r.m.s. deviation = 0.008 Å) and the benzene ring is 33.2 (2)°. In the crystal, molecules are connected by N-H...O=C hydrogen bonds, forming a chain along the b-axis direction.

Comment top

Nitro and ester groups widely exist in variety of biologically active compounds that could be used as prodrugs (Sykes et al., 1999). We synthesized the title compound and determined its crystal structure (Fig. 1) whereas its biological activily is planned to be examined as well. In the crystal of the title compound, the carbonyl group acts as an acceptor and the amide group is a proton donor in the intermolecular N–H···O=C hydrogen bond, forming a chain along the b axis (Table 1, Fig. 2).

Related literature top

Nitro and ester groups occur widely in many biologically active compounds, see: Sykes et al. (1999).

Experimental top

To a solution of methyl 2-amino-3-methylbutanoate hydrochloride (0.8 g, 5 mmol) and triethylamine (0.5 mL) in dry methylene chloride (100 mL) was added to 3,5-dinitrobenzoyl chloride (1.1 g, 5 mmol)in dry methylene chloride (50 mL) at 273 K. The mixture was allowed to warm to room temperature for 0.5 h. After concentrating, the residue was subjected to chromatography(petroleum ether/ acetone, 4:1) to provide the product as a white crystal (1.2 g, 71.1%).

Refinement top

The C-bound H-atoms were included in calculated positions and treated as riding atoms: C—H = 0.93, 0.96 and 0.98 Å for CH(aromatic), CH3 and CH(methine) H-atoms, respectively,and N—H =0.86 Å, with Uiso(H)= k τimes Ueq(parent C-atom, N), where k = 1.5 for CH3 H-atoms and k = 1.2 for all other H-atoms. The absolute configuration can be assigned to be R according to the known chirality of the precursor, only.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. A view of the molecular strcuture of the title compound; the displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. A view of the hydrogen bonded chain running in the [100] direction. The hydrogen bonds are shown as dashed lines.
Methyl 2-(3,5-dinitrobenzamido)-3-methylbutanoate top
Crystal data top
C13H15N3O7F(000) = 680
Mr = 325.28Dx = 1.394 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 9233 reflections
a = 7.060 (2) Åθ = 1.0–22.7°
b = 9.412 (3) ŵ = 0.12 mm1
c = 23.321 (6) ÅT = 296 K
V = 1549.8 (7) Å3Block, colourless
Z = 40.43 × 0.32 × 0.30 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer
3580 independent reflections
Radiation source: fine-focus sealed tube3003 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
phi and ω scansθmax = 27.7°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 79
Tmin = 0.660, Tmax = 0.746k = 1212
9197 measured reflectionsl = 2630
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.131H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0802P)2 + 0.1123P]
where P = (Fo2 + 2Fc2)/3
3580 reflections(Δ/σ)max < 0.001
208 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = 0.18 e Å3
Crystal data top
C13H15N3O7V = 1549.8 (7) Å3
Mr = 325.28Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.060 (2) ŵ = 0.12 mm1
b = 9.412 (3) ÅT = 296 K
c = 23.321 (6) Å0.43 × 0.32 × 0.30 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer
3580 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
3003 reflections with I > 2σ(I)
Tmin = 0.660, Tmax = 0.746Rint = 0.023
9197 measured reflectionsθmax = 27.7°
Refinement top
R[F2 > 2σ(F2)] = 0.045H-atom parameters constrained
wR(F2) = 0.131Δρmax = 0.20 e Å3
S = 1.03Δρmin = 0.18 e Å3
3580 reflectionsAbsolute structure: ?
208 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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. C10, C11, C13 and C12 belong to terminal alkyl chains which show signs of disorder and have higher thermal parameters.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C11.2857 (3)0.28856 (19)0.10037 (8)0.0526 (4)
C21.2504 (3)0.23672 (19)0.15455 (8)0.0503 (4)
H2A1.33900.18010.17320.060*
C31.0795 (2)0.27084 (17)0.18071 (7)0.0453 (4)
C40.9487 (3)0.35376 (18)0.15216 (8)0.0469 (4)
H4A0.83500.37850.16960.056*
C50.9895 (3)0.39948 (18)0.09717 (7)0.0495 (4)
C61.1576 (3)0.3692 (2)0.07014 (8)0.0521 (4)
H6A1.18340.40150.03330.062*
C71.0425 (2)0.21140 (17)0.23943 (7)0.0460 (4)
C80.8869 (3)0.2398 (2)0.33103 (8)0.0557 (4)
H8A0.94650.14660.33580.067*
C90.9790 (4)0.3399 (3)0.37526 (9)0.0671 (6)
C100.5694 (5)0.3567 (4)0.3394 (2)0.1160 (12)
H15A0.43650.33900.34420.174*
H15B0.59020.40490.30360.174*
H15C0.61420.41490.37030.174*
C110.5992 (4)0.1150 (4)0.29434 (14)0.0947 (9)
H14A0.46560.10190.29980.142*
H14B0.66270.02530.29830.142*
H14C0.62210.15260.25670.142*
C121.0720 (6)0.3594 (4)0.47134 (13)0.1166 (13)
H12A1.06680.30690.50660.175*
H12B1.00720.44830.47600.175*
H12C1.20180.37690.46130.175*
C130.6744 (4)0.2186 (3)0.33924 (11)0.0735 (6)
H13A0.65600.17460.37690.088*
N11.4675 (3)0.2555 (2)0.07277 (9)0.0671 (5)
N20.8475 (3)0.48375 (18)0.06597 (7)0.0613 (4)
N50.9379 (2)0.29050 (15)0.27435 (6)0.0506 (4)
H5A0.90000.37280.26320.061*
O11.5804 (3)0.1847 (3)0.09906 (10)0.0990 (6)
O21.4962 (3)0.3026 (2)0.02520 (8)0.0877 (6)
O30.8739 (3)0.5050 (2)0.01510 (7)0.0856 (5)
O40.7125 (3)0.5274 (2)0.09269 (7)0.0781 (5)
O51.1072 (2)0.09485 (13)0.25244 (6)0.0596 (4)
O60.9809 (3)0.2774 (2)0.42582 (6)0.0897 (6)
O71.0395 (5)0.4534 (3)0.36573 (10)0.1163 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0540 (10)0.0489 (9)0.0547 (10)0.0103 (8)0.0075 (8)0.0126 (8)
C20.0526 (9)0.0426 (8)0.0556 (10)0.0011 (7)0.0013 (8)0.0040 (7)
C30.0525 (9)0.0375 (7)0.0460 (8)0.0054 (7)0.0006 (7)0.0030 (7)
C40.0503 (9)0.0439 (8)0.0464 (8)0.0035 (7)0.0001 (7)0.0047 (7)
C50.0614 (10)0.0427 (8)0.0445 (8)0.0027 (8)0.0047 (8)0.0028 (7)
C60.0639 (11)0.0497 (9)0.0426 (8)0.0102 (8)0.0046 (8)0.0043 (7)
C70.0500 (9)0.0402 (8)0.0477 (8)0.0039 (7)0.0024 (7)0.0004 (7)
C80.0658 (11)0.0549 (10)0.0463 (9)0.0091 (9)0.0023 (8)0.0045 (8)
C90.0770 (14)0.0720 (13)0.0523 (11)0.0169 (12)0.0047 (10)0.0061 (9)
C100.0821 (19)0.094 (2)0.172 (4)0.0177 (17)0.034 (2)0.017 (2)
C110.0834 (18)0.099 (2)0.102 (2)0.0206 (17)0.0107 (15)0.0137 (17)
C120.152 (3)0.130 (3)0.0680 (16)0.019 (3)0.0295 (19)0.0348 (17)
C130.0736 (14)0.0762 (14)0.0707 (13)0.0033 (12)0.0113 (11)0.0167 (11)
N10.0613 (10)0.0632 (10)0.0769 (12)0.0070 (9)0.0174 (9)0.0107 (9)
N20.0743 (11)0.0594 (9)0.0504 (9)0.0028 (9)0.0069 (8)0.0018 (7)
N50.0629 (9)0.0432 (7)0.0456 (7)0.0071 (7)0.0047 (6)0.0055 (6)
O10.0641 (10)0.1110 (14)0.1218 (16)0.0183 (11)0.0206 (10)0.0107 (13)
O20.0948 (13)0.0910 (12)0.0773 (11)0.0046 (11)0.0372 (10)0.0117 (9)
O30.1103 (15)0.0954 (12)0.0511 (8)0.0146 (12)0.0049 (9)0.0146 (8)
O40.0800 (11)0.0881 (11)0.0661 (9)0.0258 (9)0.0040 (8)0.0041 (8)
O50.0776 (9)0.0431 (6)0.0580 (7)0.0098 (6)0.0016 (7)0.0035 (6)
O60.1274 (15)0.0904 (11)0.0512 (8)0.0167 (12)0.0109 (9)0.0112 (8)
O70.162 (2)0.0923 (13)0.0946 (14)0.0369 (15)0.0343 (14)0.0015 (12)
Geometric parameters (Å, º) top
C1—C61.375 (3)C9—O61.318 (3)
C1—C21.377 (3)C10—C131.497 (4)
C1—N11.469 (3)C10—H15A0.9600
C2—C31.390 (3)C10—H15B0.9600
C2—H2A0.9300C10—H15C0.9600
C3—C41.380 (3)C11—C131.526 (4)
C3—C71.502 (2)C11—H14A0.9600
C4—C51.383 (3)C11—H14B0.9600
C4—H4A0.9300C11—H14C0.9600
C5—C61.373 (3)C12—O61.462 (3)
C5—N21.471 (3)C12—H12A0.9600
C6—H6A0.9300C12—H12B0.9600
C7—O51.226 (2)C12—H12C0.9600
C7—N51.328 (2)C13—H13A0.9800
C8—N51.451 (2)N1—O11.206 (3)
C8—C131.525 (3)N1—O21.212 (3)
C8—C91.541 (3)N2—O41.211 (2)
C8—H8A0.9800N2—O31.217 (2)
C9—O71.171 (3)N5—H5A0.8600
C6—C1—C2123.15 (18)H15A—C10—H15B109.5
C6—C1—N1117.83 (18)C13—C10—H15C109.5
C2—C1—N1119.02 (19)H15A—C10—H15C109.5
C1—C2—C3118.55 (18)H15B—C10—H15C109.5
C1—C2—H2A120.7C13—C11—H14A109.5
C3—C2—H2A120.7C13—C11—H14B109.5
C4—C3—C2119.99 (17)H14A—C11—H14B109.5
C4—C3—C7122.29 (16)C13—C11—H14C109.5
C2—C3—C7117.70 (16)H14A—C11—H14C109.5
C3—C4—C5118.94 (17)H14B—C11—H14C109.5
C3—C4—H4A120.5O6—C12—H12A109.5
C5—C4—H4A120.5O6—C12—H12B109.5
C6—C5—C4122.75 (17)H12A—C12—H12B109.5
C6—C5—N2118.28 (16)O6—C12—H12C109.5
C4—C5—N2118.97 (17)H12A—C12—H12C109.5
C5—C6—C1116.59 (17)H12B—C12—H12C109.5
C5—C6—H6A121.7C10—C13—C8111.9 (2)
C1—C6—H6A121.7C10—C13—C11112.6 (3)
O5—C7—N5123.84 (16)C8—C13—C11109.9 (2)
O5—C7—C3119.61 (16)C10—C13—H13A107.4
N5—C7—C3116.54 (14)C8—C13—H13A107.4
N5—C8—C13113.70 (18)C11—C13—H13A107.4
N5—C8—C9107.70 (17)O1—N1—O2123.8 (2)
C13—C8—C9114.29 (18)O1—N1—C1118.12 (19)
N5—C8—H8A106.9O2—N1—C1118.0 (2)
C13—C8—H8A106.9O4—N2—O3124.5 (2)
C9—C8—H8A106.9O4—N2—C5117.71 (17)
O7—C9—O6125.0 (2)O3—N2—C5117.81 (19)
O7—C9—C8125.7 (2)C7—N5—C8120.85 (15)
O6—C9—C8109.3 (2)C7—N5—H5A119.6
C13—C10—H15A109.5C8—N5—H5A119.6
C13—C10—H15B109.5C9—O6—C12114.7 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···O5i0.862.122.949 (2)161
Symmetry code: (i) x+2, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···O5i0.862.122.949 (2)161.2
Symmetry code: (i) x+2, y+1/2, z+1/2.
Acknowledgements top

The author thanks North China University of Water Source and Electric Power for supporting this study.

references
References top

Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Sykes, B. M., Atwell, G. J., Hogg, A., Wilson, W. R., O'Connor, C. J. & Denny, W. A. (1999). J. Med. Chem. 42, 346–355.

Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.