organic compounds
(11aS)-8-Hydroxy-7-methoxy-2,3,5,10,11,11a-hexahydro-1H-pyrrolo[2,1-c][1,4]benzodiazepine-3,11-dione
aSchool of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Mail Box 40, 103 Wenhua Road, Shenhe District, Shenyang 110016, People's Republic of China
*Correspondence e-mail: mscheng@syphu.edu.cn
The title chiral compound, C13H14N2O4, was prepared by an intracyclization reaction of methyl (S)-1-(4-hydroxy-5-methoxy-2-nitrobenzyl)-5-oxopyrrolidine-2-carboxylate in the presence of ethanol and iron. The five-membered substituted pyrrole ring adopts an approximate while the seven-membered substituted diazepine ring displays a twist-boat conformation. Intermolecular O—H⋯O and N—H⋯O hydrogen bonding helps to stabilize the crystal structure.
Related literature
For general background, see: Bose et al. (1992); Hu et al. (2001); Kamal et al. (2002); Thurston & Bose (1994). For a related structure, see: Cheng et al. (2007).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: SMART (Bruker, 1997); cell SAINT (Bruker, 1999); data reduction: SAINT; 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.
Supporting information
https://doi.org/10.1107/S1600536807066056/xu2391sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807066056/xu2391Isup2.hkl
(S)-1-(4-Hydroxy-5-mythoxy-2-nitrobenzyl)-5-oxopyrrolidine-2-carboxylic acid methyl ester (8.10 g, 25 mmol) was dissolved in ethanol (150 ml). Fe (3.36 g, 60 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
(eluant: petroleum ether/ethyl acetate, 2:1). Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a of the title compound in ethyl acetate at room temperature.All H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with N—H = 0.97 Å, O—H = 0.84 Å, and C—H = 0.95, 0.99, 0.98 and 1.00 Å for phenyl, methylene, methyl and tertiary H atoms, respectively, with Uiso(H) = xUeq(C,N,O), where x = 1.5 for methyl H and hydroxyl H, and x = 1.2 for all other H atoms. Based on known
of the equivalent atom in the starting material, the S at C10 was assigned. Friedels pairs were merged.Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are a group of potent, naturally occurring antitumor antibiotics produced by Streptomyces species (Kamal et al., 2002; Thurston & Bose, 1994). Naturally occurring Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) have attracted the attention of many researchers largely because of the potent anticancer activity exhibited in most of the compounds with this ring system (Hu et al., 2001; Bose et al., 1992). As PBDs compounds are of great pharmaceutical importance, we determined the title chiral compound's
The molecular is shown in Fig. 1 and the bond lengths and angles are within normal ranges. PBD ring involes in a twisted conformation, similar to a related structure (Cheng et al., 2007). The seven-membered ring C5—C4—C9—N2—C10—C8—N1 (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 C8, C9, N1 and N2 form the bottom of the boat (deviation from the mean N1/C9/N2/C8 plane = 0.125 (2) Å), C10 the prow, and C4 and C5 the stern [deviations from the C8/C9/N1/N2 mean plane = 0.567, 0.885, 0.948 Å, respectively]. The bond length of the carbonyl groups C8=O4 and C13=O3 of 1.228 (2) and 1.225 (3) Å, respectively, are somewhat longer than typical carbonyl bonds. This may be due to the fact that atoms O3 and O4 participate in intermolecular The five-membered ring N2—C10—C11—C12—C13 (substituted pyrrole) is non-planar and adopts nearly (deviation from the mean C10/N2/C13/C12 plane = 0.021 (5) Å). The C11 atom is located above the plane [deviations from the C10/N2/C13/C12 mean plane = 0.449 Å]. Atom C10 of the title molecule is chiral: S configuration was assigned to this atom based on the known of the equivalent atom in the starting material. In the intermolecular O—H···O and N—H···O hydrogen bonds link the molecules together (Table 1) and help to stabilize the structure.For general background, see: Bose et al. (1992); Hu et al. (2001); Kamal et al. (2002); Thurston & Bose (1994). For a related structure, see: Cheng et al. (2007).
Data collection: SMART (Bruker, 1997); cell
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).Fig. 1. The structure of the title compound, showing 30% probability displacement ellipsoids and the atom-numbering scheme. |
C13H14N2O4 | F(000) = 276 |
Mr = 262.26 | Dx = 1.454 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 2332 reflections |
a = 6.3819 (7) Å | θ = 3.0–25.3° |
b = 9.3139 (10) Å | µ = 0.11 mm−1 |
c = 10.3673 (11) Å | T = 187 K |
β = 103.621 (1)° | Block, colorless |
V = 598.90 (11) Å3 | 0.48 × 0.26 × 0.15 mm |
Z = 2 |
Bruker SMART APEX CCD area-detector diffractometer | 1149 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.013 |
Graphite monochromator | θmax = 25.3°, θmin = 3.0° |
φ and ω scans | h = −7→7 |
3169 measured reflections | k = −5→11 |
1168 independent reflections | l = −12→11 |
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)] = 0.030 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.074 | H-atom parameters constrained |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0425P)2 + 0.0991P] where P = (Fo2 + 2Fc2)/3 |
1168 reflections | (Δ/σ)max = 0.004 |
174 parameters | Δρmax = 0.14 e Å−3 |
1 restraint | Δρmin = −0.19 e Å−3 |
C13H14N2O4 | V = 598.90 (11) Å3 |
Mr = 262.26 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.3819 (7) Å | µ = 0.11 mm−1 |
b = 9.3139 (10) Å | T = 187 K |
c = 10.3673 (11) Å | 0.48 × 0.26 × 0.15 mm |
β = 103.621 (1)° |
Bruker SMART APEX CCD area-detector diffractometer | 1149 reflections with I > 2σ(I) |
3169 measured reflections | Rint = 0.013 |
1168 independent reflections |
R[F2 > 2σ(F2)] = 0.030 | 1 restraint |
wR(F2) = 0.074 | H-atom parameters constrained |
S = 1.12 | Δρmax = 0.14 e Å−3 |
1168 reflections | Δρmin = −0.19 e Å−3 |
174 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | −0.1968 (3) | 0.3136 (2) | 0.6150 (2) | 0.0254 (4) | |
C2 | 0.0218 (3) | 0.2900 (2) | 0.6730 (2) | 0.0283 (5) | |
C3 | 0.1550 (3) | 0.4061 (3) | 0.7152 (2) | 0.0290 (5) | |
H3 | 0.3026 | 0.3905 | 0.7566 | 0.035* | |
C4 | 0.0751 (3) | 0.5463 (3) | 0.6978 (2) | 0.0275 (5) | |
C5 | −0.1437 (3) | 0.5676 (2) | 0.6429 (2) | 0.0263 (4) | |
C6 | −0.2799 (4) | 0.4511 (3) | 0.6011 (2) | 0.0280 (5) | |
H6 | −0.4289 | 0.4662 | 0.5632 | 0.034* | |
C7 | 0.3005 (4) | 0.1165 (3) | 0.7439 (3) | 0.0375 (5) | |
H7A | 0.3303 | 0.1447 | 0.8375 | 0.056* | |
H7B | 0.3962 | 0.1695 | 0.6995 | 0.056* | |
H7C | 0.3253 | 0.0132 | 0.7374 | 0.056* | |
C8 | −0.1959 (3) | 0.8199 (2) | 0.7104 (2) | 0.0281 (5) | |
C9 | 0.2252 (3) | 0.6725 (2) | 0.7329 (2) | 0.0304 (5) | |
H9A | 0.3751 | 0.6369 | 0.7620 | 0.037* | |
H9B | 0.2159 | 0.7322 | 0.6528 | 0.037* | |
C10 | −0.0465 (3) | 0.7914 (3) | 0.8459 (2) | 0.0280 (5) | |
H10 | −0.1028 | 0.7076 | 0.8878 | 0.034* | |
C11 | −0.0166 (3) | 0.9189 (3) | 0.9420 (2) | 0.0360 (5) | |
H11A | −0.1253 | 0.9172 | 0.9962 | 0.043* | |
H11B | −0.0277 | 1.0112 | 0.8935 | 0.043* | |
C12 | 0.2116 (4) | 0.8965 (3) | 1.0287 (2) | 0.0402 (6) | |
H12A | 0.2842 | 0.9897 | 1.0540 | 0.048* | |
H12B | 0.2073 | 0.8425 | 1.1103 | 0.048* | |
C13 | 0.3266 (3) | 0.8111 (3) | 0.9419 (2) | 0.0310 (5) | |
N1 | −0.2336 (3) | 0.7085 (2) | 0.62395 (18) | 0.0314 (4) | |
H1A | −0.3508 | 0.7192 | 0.5458 | 0.038* | |
N2 | 0.1759 (3) | 0.76080 (19) | 0.83733 (17) | 0.0267 (4) | |
O1 | −0.3329 (2) | 0.20085 (17) | 0.57207 (15) | 0.0316 (4) | |
H1 | −0.2729 | 0.1238 | 0.6029 | 0.047* | |
O2 | 0.0812 (2) | 0.14895 (17) | 0.68141 (17) | 0.0352 (4) | |
O3 | 0.5206 (2) | 0.7896 (2) | 0.96020 (16) | 0.0416 (4) | |
O4 | −0.2877 (3) | 0.93534 (18) | 0.68144 (17) | 0.0373 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0268 (10) | 0.0274 (11) | 0.0211 (9) | −0.0026 (9) | 0.0038 (8) | −0.0001 (9) |
C2 | 0.0280 (11) | 0.0297 (11) | 0.0279 (11) | 0.0021 (9) | 0.0078 (8) | 0.0001 (9) |
C3 | 0.0229 (10) | 0.0323 (12) | 0.0309 (11) | 0.0032 (9) | 0.0047 (8) | −0.0027 (10) |
C4 | 0.0264 (10) | 0.0303 (11) | 0.0253 (10) | −0.0007 (9) | 0.0055 (8) | −0.0016 (9) |
C5 | 0.0284 (10) | 0.0255 (11) | 0.0228 (9) | 0.0015 (9) | 0.0017 (8) | 0.0005 (9) |
C6 | 0.0255 (10) | 0.0311 (12) | 0.0247 (10) | −0.0005 (9) | 0.0003 (8) | 0.0023 (9) |
C7 | 0.0272 (11) | 0.0336 (12) | 0.0514 (14) | 0.0057 (9) | 0.0092 (9) | 0.0039 (11) |
C8 | 0.0219 (9) | 0.0255 (11) | 0.0353 (11) | −0.0025 (9) | 0.0036 (8) | 0.0026 (10) |
C9 | 0.0271 (10) | 0.0322 (12) | 0.0320 (11) | −0.0021 (9) | 0.0070 (9) | −0.0034 (9) |
C10 | 0.0236 (10) | 0.0306 (11) | 0.0296 (11) | −0.0027 (9) | 0.0059 (8) | 0.0006 (9) |
C11 | 0.0305 (11) | 0.0423 (14) | 0.0357 (11) | −0.0042 (11) | 0.0086 (9) | −0.0097 (11) |
C12 | 0.0354 (12) | 0.0521 (16) | 0.0309 (11) | −0.0078 (11) | 0.0035 (9) | −0.0089 (11) |
C13 | 0.0272 (10) | 0.0333 (12) | 0.0295 (10) | −0.0055 (9) | 0.0010 (8) | 0.0034 (10) |
N1 | 0.0294 (9) | 0.0277 (10) | 0.0304 (9) | 0.0014 (9) | −0.0066 (7) | 0.0029 (9) |
N2 | 0.0216 (8) | 0.0298 (10) | 0.0273 (9) | −0.0013 (7) | 0.0027 (7) | −0.0013 (7) |
O1 | 0.0300 (8) | 0.0249 (8) | 0.0350 (8) | −0.0020 (7) | −0.0019 (6) | 0.0021 (7) |
O2 | 0.0277 (8) | 0.0272 (9) | 0.0477 (10) | 0.0039 (7) | 0.0029 (7) | −0.0019 (7) |
O3 | 0.0246 (8) | 0.0513 (11) | 0.0437 (10) | −0.0034 (8) | −0.0021 (7) | −0.0010 (9) |
O4 | 0.0328 (9) | 0.0254 (8) | 0.0482 (9) | 0.0019 (7) | −0.0013 (7) | 0.0036 (7) |
C1—O1 | 1.369 (3) | C8—C10 | 1.524 (3) |
C1—C6 | 1.381 (3) | C9—N2 | 1.452 (3) |
C1—C2 | 1.400 (3) | C9—H9A | 0.9900 |
C2—O2 | 1.364 (3) | C9—H9B | 0.9900 |
C2—C3 | 1.382 (3) | C10—N2 | 1.471 (3) |
C3—C4 | 1.398 (3) | C10—C11 | 1.532 (3) |
C3—H3 | 0.9500 | C10—H10 | 1.0000 |
C4—C5 | 1.392 (3) | C11—C12 | 1.535 (3) |
C4—C9 | 1.506 (3) | C11—H11A | 0.9900 |
C5—C6 | 1.394 (3) | C11—H11B | 0.9900 |
C5—N1 | 1.427 (3) | C12—C13 | 1.514 (3) |
C6—H6 | 0.9500 | C12—H12A | 0.9900 |
C7—O2 | 1.429 (3) | C12—H12B | 0.9900 |
C7—H7A | 0.9800 | C13—O3 | 1.224 (3) |
C7—H7B | 0.9800 | C13—N2 | 1.353 (3) |
C7—H7C | 0.9800 | N1—H1A | 0.9699 |
C8—O4 | 1.228 (3) | O1—H1 | 0.8400 |
C8—N1 | 1.355 (3) | ||
O1—C1—C6 | 118.58 (18) | C4—C9—H9B | 109.1 |
O1—C1—C2 | 120.7 (2) | H9A—C9—H9B | 107.8 |
C6—C1—C2 | 120.7 (2) | N2—C10—C8 | 112.39 (17) |
O2—C2—C3 | 126.32 (19) | N2—C10—C11 | 102.46 (16) |
O2—C2—C1 | 114.37 (19) | C8—C10—C11 | 114.80 (19) |
C3—C2—C1 | 119.3 (2) | N2—C10—H10 | 109.0 |
C2—C3—C4 | 120.79 (18) | C8—C10—H10 | 109.0 |
C2—C3—H3 | 119.6 | C11—C10—H10 | 109.0 |
C4—C3—H3 | 119.6 | C10—C11—C12 | 103.35 (19) |
C5—C4—C3 | 119.1 (2) | C10—C11—H11A | 111.1 |
C5—C4—C9 | 120.5 (2) | C12—C11—H11A | 111.1 |
C3—C4—C9 | 120.41 (19) | C10—C11—H11B | 111.1 |
C6—C5—C4 | 120.5 (2) | C12—C11—H11B | 111.1 |
C6—C5—N1 | 118.15 (18) | H11A—C11—H11B | 109.1 |
C4—C5—N1 | 121.28 (19) | C13—C12—C11 | 104.43 (18) |
C1—C6—C5 | 119.54 (19) | C13—C12—H12A | 110.9 |
C1—C6—H6 | 120.2 | C11—C12—H12A | 110.9 |
C5—C6—H6 | 120.2 | C13—C12—H12B | 110.9 |
O2—C7—H7A | 109.5 | C11—C12—H12B | 110.9 |
O2—C7—H7B | 109.5 | H12A—C12—H12B | 108.9 |
H7A—C7—H7B | 109.5 | O3—C13—N2 | 124.7 (2) |
O2—C7—H7C | 109.5 | O3—C13—C12 | 127.5 (2) |
H7A—C7—H7C | 109.5 | N2—C13—C12 | 107.80 (18) |
H7B—C7—H7C | 109.5 | C8—N1—C5 | 127.59 (17) |
O4—C8—N1 | 120.58 (19) | C8—N1—H1A | 117.1 |
O4—C8—C10 | 122.5 (2) | C5—N1—H1A | 114.5 |
N1—C8—C10 | 116.85 (19) | C13—N2—C9 | 123.76 (18) |
N2—C9—C4 | 112.66 (17) | C13—N2—C10 | 113.48 (18) |
N2—C9—H9A | 109.1 | C9—N2—C10 | 122.48 (16) |
C4—C9—H9A | 109.1 | C1—O1—H1 | 109.5 |
N2—C9—H9B | 109.1 | C2—O2—C7 | 117.41 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O4i | 0.84 | 1.95 | 2.707 (2) | 150 |
N1—H1A···O1ii | 0.97 | 2.11 | 3.023 (2) | 157.2 |
Symmetry codes: (i) x, y−1, z; (ii) −x−1, y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C13H14N2O4 |
Mr | 262.26 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 187 |
a, b, c (Å) | 6.3819 (7), 9.3139 (10), 10.3673 (11) |
β (°) | 103.621 (1) |
V (Å3) | 598.90 (11) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.48 × 0.26 × 0.15 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD area-detector |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3169, 1168, 1149 |
Rint | 0.013 |
(sin θ/λ)max (Å−1) | 0.602 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.074, 1.12 |
No. of reflections | 1168 |
No. of parameters | 174 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.14, −0.19 |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1999), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL-Plus (Siemens, 1990).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O4i | 0.84 | 1.95 | 2.707 (2) | 150.0 |
N1—H1A···O1ii | 0.97 | 2.11 | 3.023 (2) | 157.2 |
Symmetry codes: (i) x, y−1, z; (ii) −x−1, y+1/2, −z+1. |
References
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Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are a group of potent, naturally occurring antitumor antibiotics produced by Streptomyces species (Kamal et al., 2002; Thurston & Bose, 1994). Naturally occurring Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) have attracted the attention of many researchers largely because of the potent anticancer activity exhibited in most of the compounds with this ring system (Hu et al., 2001; Bose et al., 1992). As PBDs compounds are of great pharmaceutical importance, we determined the title chiral compound's crystal structure. The molecular is shown in Fig. 1 and the bond lengths and angles are within normal ranges. PBD ring involes in a twisted conformation, similar to a related structure (Cheng et al., 2007). The seven-membered ring C5—C4—C9—N2—C10—C8—N1 (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 C8, C9, N1 and N2 form the bottom of the boat (deviation from the mean N1/C9/N2/C8 plane = 0.125 (2) Å), C10 the prow, and C4 and C5 the stern [deviations from the C8/C9/N1/N2 mean plane = 0.567, 0.885, 0.948 Å, respectively]. The bond length of the carbonyl groups C8=O4 and C13=O3 of 1.228 (2) and 1.225 (3) Å, respectively, are somewhat longer than typical carbonyl bonds. This may be due to the fact that atoms O3 and O4 participate in intermolecular van der Waals forces. The five-membered ring N2—C10—C11—C12—C13 (substituted pyrrole) is non-planar and adopts nearly envelope conformation (deviation from the mean C10/N2/C13/C12 plane = 0.021 (5) Å). The C11 atom is located above the plane [deviations from the C10/N2/C13/C12 mean plane = 0.449 Å]. Atom C10 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. In the crystal structure, intermolecular O—H···O and N—H···O hydrogen bonds link the molecules together (Table 1) and help to stabilize the structure.