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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 8| August 2012| Page o2386
https://doi.org/10.1107/S1600536812029935

(R*)-Methyl 2-(2,6-dimeth­­oxy-3,5-di­nitro­benzamido)­propano­ate

Xiaofei Lia* and Yan Tonga

aCollege of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou 450008, People's Republic of China
*Correspondence e-mail: arphylee@126.com

(Received 3 June 2012; accepted 1 July 2012; online 7 July 2012)

In the title mol­ecule, C13H15N3O9, the nitro groups are tilted with respect to the benzene mean plane by 22.8 (3) and 31.6 (3)°. The meth­oxy groups are in a cis orientation relative to the ring. In the crystal, mol­ecules are linked by strong N—H⋯O hydrogen bonds into C(3) chains along [100].

Related literature

For the biological activity of related compounds or for their use as prodrugs, see: Sykes et al. (1999[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.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data

  • C13H15N3O9

  • Mr = 357.28

  • Orthorhombic, P 21 21 21

  • a = 4.6933 (10) Å

  • b = 17.501 (3) Å

  • c = 19.917 (4) Å

  • V = 1635.9 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 296 K

  • 0.31 × 0.30 × 0.09 mm
Data collection

  • Bruker APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.962, Tmax = 0.989

  • 9526 measured reflections

  • 3683 independent reflections

  • 2824 reflections with I > 2σ(I)

  • Rint = 0.025
Refinement

  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.153

  • S = 1.03

  • 3683 reflections

  • 226 parameters

  • H-atom parameters constrained

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N3—H3A⋯O2i 0.86 2.02 2.850 (2) 162
Symmetry code: (i) x+1, y, z.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536812029935/bx2416sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812029935/bx2416Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812029935/bx2416Isup3.cml

checkCIF report


Comment top

Amides and Imides widely exist in many biological activity compounds or could be used as prodrugs (Sykes et al., 1999). We synthesized the title compound and shall examine its biological activity. In the title molecule, C13H15N3O9, the nitro groups are tilted with respect to the benzene mean plane by 22.8 (3) and 31.6 (3)°. The methoxy groups are cis conformation. In the crystal structure the molecules are linked by strong N—H···O (H···O 2.02 Å; N···O 2.850 (2) Å; N—H···Oi 162° symmetry code: (i) 1+x, y, z) hydrogen bonds into C(3) chains along [100] (Bernstein et al., 1995).

Related literature top

For the biological activity in related compounds or as prodrugs, see: Sykes et al. (1999). For hydrogen-bond motifs, see: Bernstein et al. (1995). [ok as edited?]

Experimental top

To a solution of D-alanine methyl ester hydrochloride (0.7 g, 5 mmol) and triethylamine (0.5 ml) in dry methylene chloride (100 ml) was added 2,6-dimethoxy-3,5-dinitrobenzoyl chloride 1.4 g, 5 mmol in dry methylene chloride (50 ml) at 0°C. The mixture was allowed to warm to room temperature for 1 h. After concentration the residue was subjected to chromatography (petroleum ether/ ethyl acetate, 3:1) to provide the product as a yellow crystal (1.3 g, 74.5%).

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. Friedel pairs were merged and that absolute structure was determined relative to the known chiral centers.

Structure description top

Amides and Imides widely exist in many biological activity compounds or could be used as prodrugs (Sykes et al., 1999). We synthesized the title compound and shall examine its biological activity. In the title molecule, C13H15N3O9, the nitro groups are tilted with respect to the benzene mean plane by 22.8 (3) and 31.6 (3)°. The methoxy groups are cis conformation. In the crystal structure the molecules are linked by strong N—H···O (H···O 2.02 Å; N···O 2.850 (2) Å; N—H···Oi 162° symmetry code: (i) 1+x, y, z) hydrogen bonds into C(3) chains along [100] (Bernstein et al., 1995).

For the biological activity in related compounds or as prodrugs, see: Sykes et al. (1999). For hydrogen-bond motifs, see: Bernstein et al. (1995). [ok as edited?]

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 (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: SHELXTL (Sheldrick, 2008) and 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. Part of the crystal structure showing C(3) chains along [100] direction. The hydrogen bonds are shown as dashed lines.
(R*)-Methyl 2-(2,6-dimethoxy-3,5-dinitrobenzamido)propanoate top
Crystal data top
C13H15N3O9Dx = 1.451 Mg m−3
Mr = 357.28Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 9565 reflections
a = 4.6933 (10) Åθ = 1.0–27.5°
b = 17.501 (3) ŵ = 0.13 mm−1
c = 19.917 (4) ÅT = 296 K
V = 1635.9 (6) Å3Block, yellow
Z = 40.31 × 0.30 × 0.09 mm
F(000) = 744
Data collection top
Bruker APEXII CCD area-detector
diffractometer		3683 independent reflections
Radiation source: fine-focus sealed tube2824 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
φ and ω scansθmax = 27.5°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −5→6
Tmin = 0.962, Tmax = 0.989k = −22→15
9526 measured reflectionsl = −25→25
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) = 0.153H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.1P)2]
where P = (Fo2 + 2Fc2)/3
3683 reflections(Δ/σ)max = 0.002
226 parametersΔρmax = 0.22 e Å−3
0 restraintsΔρmin = −0.17 e Å−3
Crystal data top
C13H15N3O9V = 1635.9 (6) Å3
Mr = 357.28Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.6933 (10) ŵ = 0.13 mm−1
b = 17.501 (3) ÅT = 296 K
c = 19.917 (4) Å0.31 × 0.30 × 0.09 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer		3683 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		2824 reflections with I > 2σ(I)
Tmin = 0.962, Tmax = 0.989Rint = 0.025
9526 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.153H-atom parameters constrained
S = 1.03Δρmax = 0.22 e Å−3
3683 reflectionsΔρmin = −0.17 e Å−3
226 parameters
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.7640 (5)1.00166 (13)0.58894 (9)0.0458 (5)
H1A0.87711.00430.62720.055*
C20.6630 (5)1.06770 (14)0.56054 (9)0.0443 (5)
C30.4986 (5)1.06566 (13)0.50149 (9)0.0415 (5)
C40.4388 (4)0.99479 (13)0.47345 (9)0.0376 (4)
C50.5350 (5)0.92644 (13)0.50238 (10)0.0412 (5)
C60.6998 (5)0.93146 (13)0.56147 (9)0.0424 (5)
C70.6194 (8)1.17734 (18)0.44049 (16)0.0750 (9)
H7A0.52991.21920.41760.113*
H7B0.73601.14930.40950.113*
H7C0.73601.19670.47630.113*
C80.0896 (12)1.1761 (2)0.26985 (16)0.1048 (14)
H8A0.17191.22050.29050.157*
H8B−0.10551.17120.28360.157*
H8C0.09841.18130.22190.157*
C90.6995 (7)0.81397 (17)0.44691 (14)0.0634 (7)
H9A0.62470.76950.42480.095*
H9B0.81280.79850.48470.095*
H9C0.81540.84240.41600.095*
C100.3449 (5)0.97587 (18)0.28526 (10)0.0609 (7)
H10A0.51050.97710.25530.073*
C110.1574 (6)1.04345 (19)0.26521 (11)0.0605 (7)
C120.2859 (4)0.99044 (13)0.40660 (10)0.0414 (5)
C130.2023 (7)0.8995 (2)0.27420 (14)0.0836 (10)
H13A0.32950.85920.28750.125*
H13B0.15560.89380.22750.125*
H13C0.03140.89680.30060.125*
N10.7169 (6)1.13899 (13)0.59792 (10)0.0603 (6)
N20.7960 (5)0.86403 (13)0.59826 (9)0.0540 (5)
N30.4560 (4)0.98513 (13)0.35366 (8)0.0513 (5)
H3A0.63730.98720.35960.062*
O1−0.0446 (5)1.03749 (15)0.22813 (10)0.0861 (7)
O20.0251 (3)0.99289 (11)0.40308 (7)0.0561 (5)
O30.2451 (5)1.10947 (14)0.29000 (8)0.0787 (6)
O40.4046 (4)1.12770 (10)0.46763 (8)0.0550 (5)
O50.4680 (4)0.86110 (9)0.46968 (8)0.0529 (4)
O60.9142 (7)1.13948 (14)0.63661 (12)0.1064 (10)
O70.5635 (7)1.19271 (14)0.58904 (12)0.0949 (8)
O81.0181 (5)0.87020 (14)0.63012 (10)0.0811 (7)
O90.6518 (5)0.80595 (12)0.59661 (10)0.0734 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0423 (11)0.0649 (13)0.0303 (8)−0.0062 (11)−0.0056 (8)0.0043 (10)
C20.0437 (11)0.0547 (13)0.0345 (9)−0.0068 (10)−0.0009 (9)−0.0023 (9)
C30.0314 (10)0.0576 (13)0.0354 (9)−0.0007 (10)0.0013 (9)0.0037 (9)
C40.0228 (8)0.0588 (12)0.0310 (8)0.0009 (9)0.0004 (7)0.0008 (9)
C50.0260 (9)0.0566 (13)0.0410 (10)−0.0022 (9)0.0015 (9)−0.0031 (9)
C60.0336 (11)0.0581 (13)0.0354 (9)0.0022 (10)0.0008 (9)0.0048 (9)
C70.078 (2)0.0735 (19)0.0740 (17)0.0061 (16)0.0089 (16)0.0259 (14)
C80.129 (4)0.123 (3)0.0616 (17)0.032 (3)−0.001 (2)0.0052 (19)
C90.0620 (18)0.0638 (16)0.0644 (14)0.0038 (13)0.0064 (14)−0.0134 (12)
C100.0324 (11)0.118 (2)0.0326 (9)−0.0047 (13)0.0007 (9)−0.0132 (12)
C110.0410 (12)0.110 (2)0.0305 (9)−0.0086 (14)−0.0010 (10)0.0026 (12)
C120.0239 (10)0.0637 (14)0.0365 (9)−0.0017 (9)−0.0035 (7)−0.0036 (10)
C130.068 (2)0.125 (3)0.0582 (15)−0.001 (2)−0.0094 (16)−0.0271 (17)
N10.0736 (16)0.0621 (14)0.0453 (10)−0.0049 (12)−0.0063 (12)−0.0047 (10)
N20.0506 (12)0.0682 (14)0.0431 (10)0.0058 (11)−0.0007 (10)0.0072 (9)
N30.0228 (8)0.0949 (15)0.0361 (8)−0.0030 (9)−0.0030 (7)−0.0052 (9)
O10.0594 (12)0.1340 (19)0.0649 (11)−0.0156 (13)−0.0300 (11)0.0121 (12)
O20.0222 (7)0.1020 (13)0.0441 (7)−0.0014 (8)−0.0028 (6)−0.0035 (9)
O30.0758 (14)0.1116 (17)0.0487 (9)0.0014 (14)−0.0148 (10)−0.0017 (10)
O40.0494 (10)0.0585 (10)0.0571 (9)0.0025 (7)−0.0093 (8)0.0101 (8)
O50.0432 (9)0.0580 (9)0.0576 (9)−0.0037 (8)−0.0076 (8)−0.0111 (7)
O60.139 (3)0.0824 (15)0.0981 (15)−0.0124 (16)−0.0724 (18)−0.0102 (12)
O70.110 (2)0.0825 (15)0.0920 (14)0.0233 (15)−0.0242 (16)−0.0324 (12)
O80.0694 (14)0.0956 (15)0.0782 (13)0.0171 (12)−0.0322 (12)0.0102 (11)
O90.0795 (14)0.0658 (12)0.0747 (12)−0.0045 (11)−0.0042 (11)0.0178 (10)
Geometric parameters (Å, º) top
C1—C21.371 (3)C9—O51.438 (3)
C1—C61.378 (3)C9—H9A0.9600
C1—H1A0.9300C9—H9B0.9600
C2—C31.407 (3)C9—H9C0.9600
C2—N11.475 (3)C10—N31.468 (3)
C3—O41.352 (3)C10—C131.512 (5)
C3—C41.389 (3)C10—C111.527 (4)
C4—C51.402 (3)C10—H10A0.9800
C4—C121.514 (3)C11—O11.207 (3)
C5—O51.353 (3)C11—O31.322 (4)
C5—C61.411 (3)C12—O21.227 (2)
C6—N21.461 (3)C12—N31.326 (3)
C7—O41.436 (4)C13—H13A0.9600
C7—H7A0.9600C13—H13B0.9600
C7—H7B0.9600C13—H13C0.9600
C7—H7C0.9600N1—O71.197 (3)
C8—O31.433 (4)N1—O61.205 (3)
C8—H8A0.9600N2—O91.222 (3)
C8—H8B0.9600N2—O81.225 (3)
C8—H8C0.9600N3—H3A0.8600
C2—C1—C6120.80 (18)O5—C9—H9C109.5
C2—C1—H1A119.6H9A—C9—H9C109.5
C6—C1—H1A119.6H9B—C9—H9C109.5
C1—C2—C3120.86 (19)N3—C10—C13113.0 (2)
C1—C2—N1116.46 (19)N3—C10—C11111.2 (2)
C3—C2—N1122.5 (2)C13—C10—C11113.1 (2)
O4—C3—C4116.79 (17)N3—C10—H10A106.3
O4—C3—C2125.1 (2)C13—C10—H10A106.3
C4—C3—C2118.00 (18)C11—C10—H10A106.3
C3—C4—C5122.10 (17)O1—C11—O3123.3 (3)
C3—C4—C12119.61 (18)O1—C11—C10123.1 (3)
C5—C4—C12118.10 (19)O3—C11—C10113.6 (2)
O5—C5—C4116.62 (18)O2—C12—N3123.90 (18)
O5—C5—C6125.6 (2)O2—C12—C4121.40 (18)
C4—C5—C6117.79 (19)N3—C12—C4114.68 (16)
C1—C6—C5120.4 (2)C10—C13—H13A109.5
C1—C6—N2116.97 (18)C10—C13—H13B109.5
C5—C6—N2122.5 (2)H13A—C13—H13B109.5
O4—C7—H7A109.5C10—C13—H13C109.5
O4—C7—H7B109.5H13A—C13—H13C109.5
H7A—C7—H7B109.5H13B—C13—H13C109.5
O4—C7—H7C109.5O7—N1—O6123.4 (2)
H7A—C7—H7C109.5O7—N1—C2119.1 (2)
H7B—C7—H7C109.5O6—N1—C2117.4 (2)
O3—C8—H8A109.5O9—N2—O8124.0 (2)
O3—C8—H8B109.5O9—N2—C6119.2 (2)
H8A—C8—H8B109.5O8—N2—C6116.8 (2)
O3—C8—H8C109.5C12—N3—C10122.15 (17)
H8A—C8—H8C109.5C12—N3—H3A118.9
H8B—C8—H8C109.5C10—N3—H3A118.9
O5—C9—H9A109.5C11—O3—C8116.6 (3)
O5—C9—H9B109.5C3—O4—C7116.4 (2)
H9A—C9—H9B109.5C5—O5—C9117.5 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O2i0.862.022.850 (2)162
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC13H15N3O9
Mr357.28
Crystal system, space groupOrthorhombic, P212121
Temperature (K)296
a, b, c (Å)4.6933 (10), 17.501 (3), 19.917 (4)
V (Å3)1635.9 (6)
Z4
Radiation typeMo Kα
µ (mm−1)0.13
Crystal size (mm)0.31 × 0.30 × 0.09
Data collection
DiffractometerBruker APEXII CCD area-detector
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.962, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections		9526, 3683, 2824
Rint0.025
(sin θ/λ)max (Å−1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.153, 1.03
No. of reflections3683
No. of parameters226
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.22, −0.17

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O2i0.862.022.850 (2)162
Symmetry code: (i) x+1, y, z.
 

Acknowledgements

The authors thank Henan University of Traditional Chinese Medicine for supporting this study.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
 First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSykes, B. M., Atwell, G. J., Hogg, A., Wilson, W. R., O'Connor, C. J. & Denny, W. A. (1999). J. Med. Chem. 42, 346–355.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 8| August 2012| Page o2386
https://doi.org/10.1107/S1600536812029935
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