Download citation
Download citation
link to html
The title chiral compound, C12H12N2O2, was prepared by an intra­molecular cyclization reaction of (S)-methyl 1-(2-nitro­benz­yl)-5-oxopyrrolidine-2-carboxyl­ate in the presence of EtOH/Fe. In the mol­ecule, the seven-membered ring adopts a twist-boat conformation, while the five-membered ring shows a typical envelope conformation. The crystal structure is stabilized by inter­molecular N—H...O hydrogen bonding.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807054979/xu2346sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807054979/xu2346Isup2.hkl
Contains datablock I

CCDC reference: 672866

Key indicators

  • Single-crystal X-ray study
  • T = 187 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.036
  • wR factor = 0.093
  • Data-to-parameter ratio = 7.5

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) ..... 7.51 PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ?
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 25.62 From the CIF: _reflns_number_total 1089 Count of symmetry unique reflns 1093 Completeness (_total/calc) 99.63% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4 = . S PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 3 ALERT level C = Check and explain 3 ALERT level G = General alerts; check 2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are naturally occurring compounds isolated from various streptomyces (Kamal et al., 2002; Thurston & Bose, 1994). Such compounds have potential as regulators of gene expression with possible application as therapeutic agents in the treatment of certain genetic disorders including some cancers (Mishra et al., 2007; Mérour et al., 1994). As PBDs compounds are of great pharmaceutical importance, we determined the title chiral compound's crystal structure.

The molecular is shown in Fig. 1. The bond lengths and angles are within normal ranges. PBD ring involves in a twisted conformation (Arora, 1979). The seven-membered ring C6—C11—C12—N1—C4—C5—N2 (substituted diazepine) is far from planar, and its shape approximates to a twist boat. In this description applied to the title compound (Fig. 1), atoms C5, C12, N1 and N2 form the bottom of the boat (deviation from the mean C5/N1/C12/N2 plane = 0.090 (2) Å), C4 the prow, and C6 and C11 the stern [deviations from the C5/C12/N1/N2 mean plane = 0.655, 0.951, 0.932 Å, respectively]. The bond length of the carbonyl groups C1=O1 and C5=O2 of 1.213 (3) and 1.224 (3) Å, respectively, are somewhat longer than typical carbonyl bonds. This may be due to the fact that atoms O1 and O2 participate in intermolecular van der Waals forces. The five-membered ring N1—C1—C2—C3—C4 (substituted pyrrole) is non-planar and adopts nearly envelope conformation (deviation from the mean C4/N1/C1/C2 plane = 0.013 (5) Å). The C3 atom is located above the plane [deviations from the C4/N1/C1/C2 mean plane = 0.378 Å]. Atom C4 of the title molecule is chiral: S configuration was assigned to this atom based on the known chirality of the equivalent atom in the starting material.

The molecules are linked by an intermolecular hydrogen bond between N2–H2 and O2 (–X+1, y, z) (Table 1, Fig. 2).

Related literature top

For general background, see: Kamal et al. (2002); Mérour et al. (1994); Mishra et al. (2007); Thurston & Bose (1994). For a related structure, see: Arora (1979).

Experimental top

(S)-1-(2-Nitrobenzyl)-5-oxopyrrolidine-2-carboxylic acid methyl ester (5.56 g, 20 mmol) was dissolved in ethanol (100 ml). Fe (2.51 g, 45 mmol) was added and the solution was heated to reflux for 30 min. The mixture was filtered and the filtrate was concentrated under vacuum. The pure product was obtained through silica gel chromatography (eluant: petroleum ether/ethyl acetate, 1:1). Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a dilute solution of the title compound in ethyl acetate at room temperature.

Refinement top

All H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with N—H = 0.88 Å, C—H = 0.95, 0.99 and 1.00 Å for phenyl, methylene and tertiary H atoms, respectively, Uiso(H) = 1.2Ueq(C,N). Based on known chirality of the equivalent atom in the starting material, the S chirality at C4 was assigned. Friedels pairs were merged.

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (Siemens, 1990); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures top
[Figure 1] Fig. 1. The structure of the title compound(I), showing 30% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] Fig. 2. The molecular packing of (I), the molecular packing viewed along the b axis, H atoms not involved in hydrogen bonding have been omitted.
(S)-2,3,5,10,11,11a-Hexahydro-1H-pyrrolo[2,1-c][1,4]benzodiazepine-3,11-dione top
Crystal data top
C12H12N2O2F(000) = 456
Mr = 216.24Dx = 1.372 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
a = 16.280 (2) ÅCell parameters from 1769 reflections
b = 6.2848 (9) Åθ = 2.7–25.5°
c = 11.1016 (15) ŵ = 0.10 mm1
β = 112.810 (2)°T = 187 K
V = 1047.0 (3) Å3Block, colorless
Z = 40.36 × 0.17 × 0.13 mm
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
1046 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.021
Graphite monochromatorθmax = 25.6°, θmin = 2.0°
ϕ and ω scansh = 1916
2870 measured reflectionsk = 77
1089 independent reflectionsl = 813
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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.093H-atom parameters constrained
S = 1.17 w = 1/[σ2(Fo2) + (0.0528P)2 + 0.3158P]
where P = (Fo2 + 2Fc2)/3
1089 reflections(Δ/σ)max < 0.001
145 parametersΔρmax = 0.20 e Å3
1 restraintΔρmin = 0.17 e Å3
Crystal data top
C12H12N2O2V = 1047.0 (3) Å3
Mr = 216.24Z = 4
Monoclinic, C2Mo Kα radiation
a = 16.280 (2) ŵ = 0.10 mm1
b = 6.2848 (9) ÅT = 187 K
c = 11.1016 (15) Å0.36 × 0.17 × 0.13 mm
β = 112.810 (2)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
1046 reflections with I > 2σ(I)
2870 measured reflectionsRint = 0.021
1089 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0361 restraint
wR(F2) = 0.093H-atom parameters constrained
S = 1.17Δρmax = 0.20 e Å3
1089 reflectionsΔρmin = 0.17 e Å3
145 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
C10.65320 (15)0.9090 (4)0.9102 (2)0.0281 (5)
C20.61760 (16)0.7804 (4)0.9947 (2)0.0313 (6)
H2A0.56890.85771.00830.038*
H2B0.66540.75041.08090.038*
C30.58320 (16)0.5751 (4)0.9194 (2)0.0308 (6)
H3A0.51810.58250.86880.037*
H3B0.59640.45170.97950.037*
C40.63361 (15)0.5576 (4)0.8278 (2)0.0249 (5)
H40.68860.47000.87000.030*
C50.57841 (15)0.4697 (4)0.6922 (2)0.0251 (5)
C60.71544 (15)0.4757 (4)0.6450 (2)0.0251 (5)
C70.76369 (16)0.3207 (4)0.6119 (2)0.0294 (5)
H70.73520.19450.56860.035*
C80.85484 (18)0.3519 (5)0.6431 (3)0.0342 (6)
H80.88850.24630.62120.041*
C90.89569 (16)0.5354 (5)0.7053 (3)0.0366 (6)
H90.95770.55560.72730.044*
C100.84635 (16)0.6912 (5)0.7360 (2)0.0330 (6)
H100.87490.81790.77830.040*
C110.75563 (15)0.6642 (4)0.7055 (2)0.0270 (5)
C120.70051 (17)0.8408 (4)0.7277 (2)0.0301 (5)
H12A0.73920.96580.76430.036*
H12B0.65400.88340.64280.036*
N10.65789 (13)0.7786 (3)0.81665 (19)0.0268 (5)
N20.62252 (12)0.4396 (4)0.61258 (18)0.0274 (5)
H20.59110.39340.53310.033*
O10.67442 (13)1.0953 (3)0.9227 (2)0.0395 (5)
O20.49882 (10)0.4306 (3)0.65628 (16)0.0328 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0213 (10)0.0298 (14)0.0313 (12)0.0030 (10)0.0081 (9)0.0003 (10)
C20.0262 (11)0.0376 (14)0.0336 (12)0.0003 (11)0.0155 (10)0.0049 (12)
C30.0291 (12)0.0369 (14)0.0314 (12)0.0040 (11)0.0170 (10)0.0015 (11)
C40.0241 (11)0.0252 (12)0.0261 (11)0.0006 (10)0.0105 (9)0.0013 (10)
C50.0244 (11)0.0233 (11)0.0284 (11)0.0005 (9)0.0111 (9)0.0035 (10)
C60.0250 (11)0.0316 (13)0.0207 (10)0.0004 (10)0.0110 (9)0.0025 (10)
C70.0319 (12)0.0311 (14)0.0289 (11)0.0022 (11)0.0157 (9)0.0000 (10)
C80.0323 (12)0.0407 (15)0.0353 (13)0.0066 (11)0.0193 (10)0.0057 (11)
C90.0223 (11)0.0529 (18)0.0368 (13)0.0018 (12)0.0140 (10)0.0063 (13)
C100.0291 (12)0.0385 (14)0.0317 (13)0.0098 (11)0.0121 (10)0.0011 (12)
C110.0285 (12)0.0300 (14)0.0263 (11)0.0016 (11)0.0147 (9)0.0035 (10)
C120.0363 (12)0.0253 (12)0.0328 (12)0.0040 (11)0.0178 (10)0.0013 (10)
N10.0283 (10)0.0248 (10)0.0291 (10)0.0020 (8)0.0131 (8)0.0006 (9)
N20.0223 (9)0.0354 (11)0.0235 (9)0.0055 (9)0.0078 (7)0.0047 (9)
O10.0433 (11)0.0269 (10)0.0508 (11)0.0014 (8)0.0210 (9)0.0054 (9)
O20.0199 (8)0.0461 (11)0.0329 (8)0.0053 (8)0.0107 (6)0.0001 (9)
Geometric parameters (Å, º) top
C1—O11.213 (3)C6—C111.393 (3)
C1—N11.348 (3)C6—N21.431 (3)
C1—C21.514 (4)C7—C81.401 (4)
C2—C31.521 (4)C7—H70.9500
C2—H2A0.9900C8—C91.376 (4)
C2—H2B0.9900C8—H80.9500
C3—C41.538 (3)C9—C101.390 (4)
C3—H3A0.9900C9—H90.9500
C3—H3B0.9900C10—C111.392 (3)
C4—N11.462 (3)C10—H100.9500
C4—C51.527 (3)C11—C121.507 (4)
C4—H41.0000C12—N11.463 (3)
C5—O21.224 (3)C12—H12A0.9900
C5—N21.351 (3)C12—H12B0.9900
C6—C71.387 (4)N2—H20.8800
O1—C1—N1125.2 (3)C6—C7—C8119.4 (3)
O1—C1—C2127.2 (3)C6—C7—H7120.3
N1—C1—C2107.6 (2)C8—C7—H7120.3
C1—C2—C3105.10 (19)C9—C8—C7120.0 (2)
C1—C2—H2A110.7C9—C8—H8120.0
C3—C2—H2A110.7C7—C8—H8120.0
C1—C2—H2B110.7C8—C9—C10120.1 (2)
C3—C2—H2B110.7C8—C9—H9120.0
H2A—C2—H2B108.8C10—C9—H9120.0
C2—C3—C4104.26 (19)C9—C10—C11120.9 (3)
C2—C3—H3A110.9C9—C10—H10119.5
C4—C3—H3A110.9C11—C10—H10119.5
C2—C3—H3B110.9C10—C11—C6118.5 (2)
C4—C3—H3B110.9C10—C11—C12120.9 (2)
H3A—C3—H3B108.9C6—C11—C12120.5 (2)
N1—C4—C5109.59 (19)N1—C12—C11112.4 (2)
N1—C4—C3102.69 (19)N1—C12—H12A109.1
C5—C4—C3114.64 (18)C11—C12—H12A109.1
N1—C4—H4109.9N1—C12—H12B109.1
C5—C4—H4109.9C11—C12—H12B109.1
C3—C4—H4109.9H12A—C12—H12B107.8
O2—C5—N2121.6 (2)C1—N1—C12122.7 (2)
O2—C5—C4122.5 (2)C1—N1—C4114.5 (2)
N2—C5—C4115.91 (18)C12—N1—C4121.72 (19)
C7—C6—C11121.1 (2)C5—N2—C6126.30 (18)
C7—C6—N2118.3 (2)C5—N2—H2116.9
C11—C6—N2120.6 (2)C6—N2—H2116.9
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.882.062.871 (2)153
Symmetry code: (i) x+1, y, z+1.

Experimental details

Crystal data
Chemical formulaC12H12N2O2
Mr216.24
Crystal system, space groupMonoclinic, C2
Temperature (K)187
a, b, c (Å)16.280 (2), 6.2848 (9), 11.1016 (15)
β (°) 112.810 (2)
V3)1047.0 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.36 × 0.17 × 0.13
Data collection
DiffractometerBruker SMART APEX CCD area-detector
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2870, 1089, 1046
Rint0.021
(sin θ/λ)max1)0.608
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.093, 1.17
No. of reflections1089
No. of parameters145
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.17

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1999), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL-Plus (Siemens, 1990).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.882.062.871 (2)153
Symmetry code: (i) x+1, y, z+1.
 

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds