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

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ISSN: 2056-9890

exo-4-[(1H-Benzimidazol-2-yl)meth­yl]-10-oxa-4-aza­tri­cyclo­[5.2.1.02,6]decane-3,5-dione

aZhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China, and bCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
*Correspondence e-mail: sky51@zjnu.cn

(Received 29 April 2011; accepted 4 July 2011; online 9 July 2011)

In the title compound, C16H15N3O3, the dihedral angle between the approximately planar benzimidazolyl group (r.m.s. deviation = 0.010 Å) and the pyrrolidine ring is 78.20 (6)°. The C—C—N bond angle of the bridging CH2 group is 112.14 (16)°. In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming infinite chains parallel to [101] and [10[\overline{1}]].

Related literature

For the bioactivity of norcantharidin (systematic name 4,10-dioxatricyclo­[5.2.1.02,6]decane-3,5-dione), see: Wang (1989[Wang, G.-S. (1989). J. Ethnopharmacol. 26, 147-162.]). For the use of norcantharidin in synthesis, see: Hill et al. (2007[Hill, T. A., Stewart, S. G., Ackland, S. P., Sauer, B., Gilbert, J., Ackland, S. P., Sakoff, J. A. & McCluskey, A. (2007). Bioorg. Med. Chem. 15, 6126-6134.]). For a related structure, see: Zhu & Lin (2009[Zhu, W.-Z. & Lin, Q.-Y. (2009). Acta Cryst. E65, o287.]).

[Scheme 1]

Experimental

Crystal data
  • C16H15N3O3

  • Mr = 297.31

  • Orthorhombic, F d d 2

  • a = 17.4294 (2) Å

  • b = 48.2746 (6) Å

  • c = 6.7947 (1) Å

  • V = 5717.04 (13) Å3

  • Z = 16

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 296 K

  • 0.24 × 0.17 × 0.10 mm

Data collection
  • Bruker SMART APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.981, Tmax = 0.990

  • 22741 measured reflections

  • 2159 independent reflections

  • 1690 reflections with I > 2σ(I)

  • Rint = 0.038

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.087

  • S = 1.04

  • 2159 reflections

  • 199 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.10 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯N2i 0.86 1.97 2.827 (2) 175
Symmetry code: (i) [x+{\script{1\over 4}}, -y+{\script{1\over 4}}, z+{\script{1\over 4}}].

Data collection: APEX2 (Bruker, 2006[Bruker (2006). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2006[Bruker (2006). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

Norcantharidin is an important compound that has a variety of bioactivities, such as protein kinase inhibition and antitumor activity (Wang, 1989). As a contribution to structure-activity studies in this field, the title compound, (I), a norcantharidin imide (Hill et al., 2007), was synthesized and investigated by X-ray crystallography. A related norcantharidin imide was reported by Zhu & Lin (2009).

X-ray crystallography confirmed the anticipated molecular structure and the atom connectivity for the title compound, as illustrated in Fig. 1. The norcantharidin imide and the benzimidazole moiety of (I) are rigid and feature usual bond lengths and angles. The dihedral angle between the flat benzimidazolyl group (C9—C15,N1,N2) and the pyrrolidine ring (C1,C2,C7,C8,N3) is 78.20 (6)°. The bond angle of the bridging CH2 group is C15—C16—N3 = 112.1 (2)°. In the crystal structure the molecules are linked via the hydrogen bond N1—H1A···N2i, N1···N2i = 2.827 (2) Å ((i): x+1/4, -y+1/4, z+1/4), to form infinite hydrogen bonded chains parallel to [101] and [101].

Related literature top

For the bioactivity of norcantharidin (systematic name 4,10-dioxatricyclo[5.2.1.02,6]decane-3,5-dione), see: Wang (1989). For the use of norcantharidin in synthesis, see: Hill et al. (2007). For a related structure, see: Zhu & Lin (2009).

Experimental top

A mixture of 0.5 mmol norcantharidin, 0.5 mmol 2-(aminomethyl)benzimidazole, 0.5 mmol cadmium acetate as a promoter, and 10 mL distilled water was sealed in a 25 mL Teflon-lined stainless vessel and heated at 433 K for 3 d, then cooled slowly to room temperature. The solution was filtered and gave then block-like transparent crystals.

Refinement top

The structure was solved by direct methods and successive Fourier difference synthesis. The H atoms were positioned geometrically and refined using a riding model [aromatic C—H = 0.93 Å, aliphatic C—H = 0.97Å, and N—H = 0.86 Å, Uiso(H) = 1.2Ueq(C, N)]. In the absence of significant anomalous scattering, the Friedel pairs of the polar structure were merged.

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of the molecule of (I) showing the atom-labelling scheme with displacement ellipsoids drawn at 30% probability.
exo-8-[(1H-Benzimidazol-2-yl)methyl]-10-oxa-8- azatricyclo[4.3.0.12,5]decane-7,9-dione top
Crystal data top
C16H15N3O3F(000) = 2496
Mr = 297.31Dx = 1.382 Mg m3
Orthorhombic, Fdd2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: F 2 -2dCell parameters from 5637 reflections
a = 17.4294 (2) Åθ = 2.5–29.8°
b = 48.2746 (6) ŵ = 0.10 mm1
c = 6.7947 (1) ÅT = 296 K
V = 5717.04 (13) Å3Block, colourless
Z = 160.24 × 0.17 × 0.10 mm
Data collection top
Bruker SMART APEXII CCD
diffractometer
2159 independent reflections
Radiation source: fine-focus sealed tube1690 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.038
ω scansθmax = 29.8°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 2424
Tmin = 0.981, Tmax = 0.990k = 6766
22741 measured reflectionsl = 98
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.087 w = 1/[σ2(Fo2) + (0.0448P)2 + 1.1097P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2159 reflectionsΔρmax = 0.10 e Å3
199 parametersΔρmin = 0.17 e Å3
1 restraintAbsolute structure: 1753 Friedel pairs were merged
Primary atom site location: structure-invariant direct methods
Crystal data top
C16H15N3O3V = 5717.04 (13) Å3
Mr = 297.31Z = 16
Orthorhombic, Fdd2Mo Kα radiation
a = 17.4294 (2) ŵ = 0.10 mm1
b = 48.2746 (6) ÅT = 296 K
c = 6.7947 (1) Å0.24 × 0.17 × 0.10 mm
Data collection top
Bruker SMART APEXII CCD
diffractometer
2159 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1690 reflections with I > 2σ(I)
Tmin = 0.981, Tmax = 0.990Rint = 0.038
22741 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0351 restraint
wR(F2) = 0.087H-atom parameters constrained
S = 1.04Δρmax = 0.10 e Å3
2159 reflectionsΔρmin = 0.17 e Å3
199 parametersAbsolute structure: 1753 Friedel pairs were merged
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
N20.06276 (8)0.10833 (3)0.2792 (3)0.0454 (4)
N10.04528 (8)0.11596 (3)0.4450 (3)0.0428 (4)
H1A0.08930.12290.47400.051*
N30.02809 (8)0.16452 (3)0.1037 (3)0.0431 (4)
O20.07386 (9)0.14915 (3)0.1930 (3)0.0629 (4)
O10.00312 (11)0.18963 (4)0.3811 (3)0.0765 (5)
O30.02560 (7)0.22474 (3)0.0973 (2)0.0556 (4)
C10.07375 (10)0.16595 (3)0.0624 (3)0.0439 (4)
C20.12089 (10)0.19215 (3)0.0513 (3)0.0431 (4)
H2B0.17610.18870.06340.052*
C30.09207 (12)0.21403 (4)0.1970 (3)0.0527 (5)
H3A0.08130.20680.32880.063*
C40.14630 (14)0.23883 (4)0.1956 (5)0.0713 (7)
H4A0.19950.23300.20160.086*
H4B0.13570.25130.30410.086*
C50.12741 (14)0.25219 (4)0.0024 (4)0.0700 (7)
H5A0.10880.27100.01390.084*
H5B0.17160.25230.08920.084*
C60.06469 (12)0.23307 (4)0.0784 (4)0.0552 (5)
H6A0.03110.24170.17630.066*
C70.09930 (11)0.20533 (4)0.1463 (3)0.0464 (5)
H7A0.14340.20770.23410.056*
C80.03878 (12)0.18644 (4)0.2306 (3)0.0492 (5)
C160.02831 (10)0.14281 (4)0.1375 (4)0.0519 (5)
H16A0.07600.15110.18140.062*
H16B0.03840.13330.01450.062*
C150.00198 (10)0.12236 (3)0.2871 (3)0.0410 (4)
C90.06167 (9)0.09153 (3)0.4452 (3)0.0391 (4)
C100.11496 (11)0.07221 (4)0.5106 (3)0.0488 (5)
H10A0.15970.06870.44020.059*
C110.09925 (12)0.05847 (4)0.6828 (4)0.0571 (5)
H11A0.13390.04530.72880.068*
C120.03280 (13)0.06372 (5)0.7903 (4)0.0600 (6)
H12A0.02470.05430.90780.072*
C130.02144 (11)0.08263 (4)0.7270 (3)0.0526 (5)
H13A0.06600.08610.79840.063*
C140.00597 (10)0.09617 (3)0.5518 (3)0.0395 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N20.0332 (7)0.0520 (8)0.0510 (10)0.0018 (6)0.0111 (7)0.0068 (8)
N10.0308 (7)0.0445 (7)0.0532 (10)0.0010 (6)0.0124 (8)0.0003 (7)
N30.0394 (8)0.0408 (7)0.0490 (10)0.0022 (6)0.0058 (7)0.0065 (7)
O20.0768 (10)0.0467 (7)0.0652 (11)0.0086 (7)0.0172 (9)0.0142 (8)
O10.0876 (11)0.0950 (13)0.0468 (11)0.0081 (9)0.0214 (10)0.0072 (9)
O30.0472 (7)0.0489 (7)0.0708 (11)0.0026 (6)0.0051 (8)0.0100 (7)
C10.0451 (9)0.0351 (8)0.0514 (12)0.0021 (7)0.0074 (9)0.0015 (8)
C20.0380 (9)0.0387 (8)0.0525 (11)0.0014 (7)0.0062 (9)0.0002 (8)
C30.0624 (12)0.0469 (10)0.0489 (13)0.0087 (9)0.0070 (11)0.0047 (9)
C40.0740 (15)0.0457 (10)0.094 (2)0.0098 (10)0.0194 (15)0.0099 (13)
C50.0703 (13)0.0407 (9)0.099 (2)0.0100 (10)0.0017 (15)0.0043 (12)
C60.0576 (12)0.0427 (9)0.0654 (15)0.0041 (8)0.0085 (11)0.0086 (10)
C70.0447 (10)0.0481 (9)0.0466 (12)0.0029 (8)0.0035 (9)0.0034 (9)
C80.0493 (11)0.0568 (11)0.0414 (12)0.0011 (9)0.0015 (10)0.0022 (9)
C160.0386 (9)0.0511 (10)0.0660 (15)0.0073 (8)0.0002 (10)0.0147 (10)
C150.0324 (8)0.0416 (8)0.0490 (12)0.0040 (7)0.0080 (8)0.0041 (8)
C90.0334 (8)0.0393 (8)0.0444 (11)0.0033 (6)0.0079 (8)0.0022 (8)
C100.0394 (9)0.0502 (10)0.0570 (14)0.0041 (8)0.0060 (9)0.0017 (9)
C110.0535 (11)0.0506 (10)0.0671 (15)0.0001 (8)0.0027 (12)0.0114 (11)
C120.0610 (12)0.0633 (12)0.0558 (14)0.0089 (10)0.0030 (11)0.0175 (11)
C130.0470 (11)0.0628 (11)0.0480 (12)0.0076 (9)0.0156 (10)0.0025 (10)
C140.0333 (8)0.0388 (8)0.0463 (12)0.0042 (7)0.0079 (8)0.0021 (8)
Geometric parameters (Å, º) top
N2—C151.317 (2)C5—C61.521 (3)
N2—C91.389 (2)C5—H5A0.9700
N1—C151.348 (3)C5—H5B0.9700
N1—C141.381 (2)C6—C71.540 (3)
N1—H1A0.8600C6—H6A0.9800
N3—C81.378 (3)C7—C81.507 (3)
N3—C11.383 (3)C7—H7A0.9800
N3—C161.455 (2)C16—C151.490 (3)
O2—C11.202 (2)C16—H16A0.9700
O1—C81.206 (3)C16—H16B0.9700
O3—C61.432 (3)C9—C101.389 (3)
O3—C31.438 (3)C9—C141.402 (2)
C1—C21.510 (2)C10—C111.373 (3)
C2—C31.532 (3)C10—H10A0.9300
C2—C71.533 (3)C11—C121.393 (3)
C2—H2B0.9800C11—H11A0.9300
C3—C41.525 (3)C12—C131.383 (3)
C3—H3A0.9800C12—H12A0.9300
C4—C51.528 (4)C13—C141.385 (3)
C4—H4A0.9700C13—H13A0.9300
C4—H4B0.9700
C15—N2—C9104.80 (15)C5—C6—H6A113.7
C15—N1—C14107.39 (14)C7—C6—H6A113.7
C15—N1—H1A126.3C8—C7—C2104.70 (15)
C14—N1—H1A126.3C8—C7—C6111.46 (16)
C8—N3—C1113.23 (15)C2—C7—C6101.23 (17)
C8—N3—C16123.08 (17)C8—C7—H7A112.9
C1—N3—C16123.63 (17)C2—C7—H7A112.9
C6—O3—C396.35 (15)C6—C7—H7A112.9
O2—C1—N3124.71 (16)O1—C8—N3124.0 (2)
O2—C1—C2126.96 (19)O1—C8—C7127.3 (2)
N3—C1—C2108.33 (16)N3—C8—C7108.75 (17)
C1—C2—C3111.50 (17)N3—C16—C15112.14 (16)
C1—C2—C7104.94 (16)N3—C16—H16A109.2
C3—C2—C7101.50 (14)C15—C16—H16A109.2
C1—C2—H2B112.7N3—C16—H16B109.2
C3—C2—H2B112.7C15—C16—H16B109.2
C7—C2—H2B112.7H16A—C16—H16B107.9
O3—C3—C4102.38 (16)N2—C15—N1113.22 (17)
O3—C3—C2101.96 (16)N2—C15—C16125.23 (18)
C4—C3—C2109.49 (19)N1—C15—C16121.52 (16)
O3—C3—H3A113.9C10—C9—N2129.97 (16)
C4—C3—H3A113.9C10—C9—C14120.28 (17)
C2—C3—H3A113.9N2—C9—C14109.74 (15)
C3—C4—C5101.72 (19)C11—C10—C9117.63 (18)
C3—C4—H4A111.4C11—C10—H10A121.2
C5—C4—H4A111.4C9—C10—H10A121.2
C3—C4—H4B111.4C10—C11—C12121.7 (2)
C5—C4—H4B111.4C10—C11—H11A119.2
H4A—C4—H4B109.3C12—C11—H11A119.2
C6—C5—C4101.42 (18)C13—C12—C11121.7 (2)
C6—C5—H5A111.5C13—C12—H12A119.1
C4—C5—H5A111.5C11—C12—H12A119.1
C6—C5—H5B111.5C12—C13—C14116.48 (19)
C4—C5—H5B111.5C12—C13—H13A121.8
H5A—C5—H5B109.3C14—C13—H13A121.8
O3—C6—C5103.2 (2)N1—C14—C13132.96 (17)
O3—C6—C7101.06 (15)N1—C14—C9104.84 (16)
C5—C6—C7110.35 (16)C13—C14—C9122.19 (18)
O3—C6—H6A113.7
C8—N3—C1—O2179.8 (2)C16—N3—C8—O10.5 (3)
C16—N3—C1—O22.6 (3)C1—N3—C8—C70.7 (2)
C8—N3—C1—C20.9 (2)C16—N3—C8—C7177.93 (16)
C16—N3—C1—C2176.28 (16)C2—C7—C8—O1176.4 (2)
O2—C1—C2—C371.9 (2)C6—C7—C8—O167.8 (3)
N3—C1—C2—C3106.99 (19)C2—C7—C8—N32.0 (2)
O2—C1—C2—C7179.06 (19)C6—C7—C8—N3110.60 (19)
N3—C1—C2—C72.10 (19)C8—N3—C16—C1577.7 (2)
C6—O3—C3—C455.9 (2)C1—N3—C16—C15105.4 (2)
C6—O3—C3—C257.41 (16)C9—N2—C15—N10.1 (2)
C1—C2—C3—O377.96 (19)C9—N2—C15—C16178.43 (18)
C7—C2—C3—O333.32 (17)C14—N1—C15—N20.4 (2)
C1—C2—C3—C4174.13 (18)C14—N1—C15—C16178.74 (17)
C7—C2—C3—C474.6 (2)N3—C16—C15—N255.2 (3)
O3—C3—C4—C535.0 (2)N3—C16—C15—N1126.70 (19)
C2—C3—C4—C572.7 (2)C15—N2—C9—C10179.28 (19)
C3—C4—C5—C61.0 (2)C15—N2—C9—C140.14 (19)
C3—O3—C6—C555.61 (16)N2—C9—C10—C11179.60 (19)
C3—O3—C6—C758.61 (15)C14—C9—C10—C111.0 (3)
C4—C5—C6—O333.5 (2)C9—C10—C11—C120.6 (3)
C4—C5—C6—C773.8 (2)C10—C11—C12—C131.3 (4)
C1—C2—C7—C82.40 (19)C11—C12—C13—C140.4 (3)
C3—C2—C7—C8113.79 (16)C15—N1—C14—C13178.2 (2)
C1—C2—C7—C6118.36 (16)C15—N1—C14—C90.44 (19)
C3—C2—C7—C62.16 (17)C12—C13—C14—N1179.8 (2)
O3—C6—C7—C873.7 (2)C12—C13—C14—C91.3 (3)
C5—C6—C7—C8177.5 (2)C10—C9—C14—N1179.13 (16)
O3—C6—C7—C237.14 (17)N2—C9—C14—N10.36 (19)
C5—C6—C7—C271.6 (2)C10—C9—C14—C132.0 (3)
C1—N3—C8—O1177.7 (2)N2—C9—C14—C13178.48 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N2i0.861.972.827 (2)175
Symmetry code: (i) x+1/4, y+1/4, z+1/4.

Experimental details

Crystal data
Chemical formulaC16H15N3O3
Mr297.31
Crystal system, space groupOrthorhombic, Fdd2
Temperature (K)296
a, b, c (Å)17.4294 (2), 48.2746 (6), 6.7947 (1)
V3)5717.04 (13)
Z16
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.24 × 0.17 × 0.10
Data collection
DiffractometerBruker SMART APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.981, 0.990
No. of measured, independent and
observed [I > 2σ(I)] reflections
22741, 2159, 1690
Rint0.038
(sin θ/λ)max1)0.699
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.087, 1.04
No. of reflections2159
No. of parameters199
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.10, 0.17
Absolute structure1753 Friedel pairs were merged

Computer programs: APEX2 (Bruker, 2006), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N2i0.861.972.827 (2)175
Symmetry code: (i) x+1/4, y+1/4, z+1/4.
 

Acknowledgements

The authors thank for the financial support from the Natural Science Foundation of Zhejiang Province, China (Grant No. Y407301).

References

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First citationZhu, W.-Z. & Lin, Q.-Y. (2009). Acta Cryst. E65, o287.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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