Literature DB >> 22969650

(3'R)-3'-Benzyl-2',3'-dihydro-1H-spiro-[indole-3,1'-naphtho-[2,3-c]pyrrole]-2,4',9'-trione.

Garima Sharma, S Vasanth Kumar, Habibah A Wahab, Mohd Mustaqim Rosli, Hoong-Kun Fun.   

Abstract

In the title compound, C(26)H(18)N(2)O(3), the maximum deviations from planarity for the tetra-hydro-1H-naphtho-[2,3-c]pyrrole and indoline rings systems are 0.091 (1) and 0.012 (2) Å, respectively. These ring systems make a dihedral angle of 89.95 (6)° with each other and they make dihedral angles of 73.42 (8) and 71.28 (9)°, respectively, with the benzene ring. In the crystal, inversion dimers linked by pairs of N-H⋯O hydrogen bonds generate R(2) (2)(8) loops and C-H⋯O inter-actions connect the dimers into corrugated sheets lying parallel to the bc plane.

Entities:  

Year:  2012        PMID: 22969650      PMCID: PMC3435804          DOI: 10.1107/S1600536812036227

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For a related structure, see: Sharma et al. (2012 ▶). For the biological activity of naphtho­quinones, see: Babula et al. (2007 ▶). For 1,3-cyclo­addition reactions involving naphtho­quinones, see: Chen et al. (2011 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C26H18N2O3 M = 406.42 Monoclinic, a = 10.2317 (4) Å b = 26.2823 (8) Å c = 7.8406 (3) Å β = 109.122 (2)° V = 1992.10 (12) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.36 × 0.20 × 0.10 mm

Data collection

Bruker SMART APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.968, T max = 0.992 19577 measured reflections 5742 independent reflections 3338 reflections with I > 2σ(I) R int = 0.069

Refinement

R[F 2 > 2σ(F 2)] = 0.064 wR(F 2) = 0.178 S = 1.02 5742 reflections 288 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.45 e Å−3 Δρmin = −0.27 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812036227/hb6939sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812036227/hb6939Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812036227/hb6939Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C26H18N2O3F(000) = 848
Mr = 406.42Dx = 1.355 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2917 reflections
a = 10.2317 (4) Åθ = 3.6–30.0°
b = 26.2823 (8) ŵ = 0.09 mm1
c = 7.8406 (3) ÅT = 100 K
β = 109.122 (2)°Plate, yellow
V = 1992.10 (12) Å30.36 × 0.20 × 0.10 mm
Z = 4
Bruker SMART APEXII CCD diffractometer5742 independent reflections
Radiation source: fine-focus sealed tube3338 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.069
φ and ω scansθmax = 30.0°, θmin = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −14→14
Tmin = 0.968, Tmax = 0.992k = −36→36
19577 measured reflectionsl = −10→10
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.064Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.178H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.0823P)2 + 0.2374P] where P = (Fo2 + 2Fc2)/3
5742 reflections(Δ/σ)max < 0.001
288 parametersΔρmax = 0.45 e Å3
0 restraintsΔρmin = −0.27 e Å3
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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.
xyzUiso*/Ueq
O10.63086 (17)0.24596 (6)−0.1639 (2)0.0425 (4)
O20.99431 (16)0.12903 (5)0.32957 (19)0.0322 (3)
O30.90923 (16)0.05795 (5)−0.09244 (19)0.0303 (3)
N10.6184 (2)0.08098 (7)−0.0952 (2)0.0323 (4)
N20.89813 (19)0.01158 (6)0.1530 (2)0.0279 (4)
C10.2987 (2)0.10602 (8)−0.0342 (3)0.0326 (5)
H1A0.27160.0806−0.12530.039*
C20.2518 (2)0.10324 (8)0.1128 (3)0.0350 (5)
H2A0.19160.07650.12040.042*
C30.2923 (2)0.13924 (8)0.2481 (3)0.0334 (5)
H3A0.26100.13720.34940.040*
C40.3785 (2)0.17823 (8)0.2351 (3)0.0358 (5)
H4A0.40740.20300.32830.043*
C50.4237 (2)0.18162 (8)0.0863 (3)0.0322 (5)
H5A0.48180.20900.07780.039*
C60.3846 (2)0.14535 (7)−0.0502 (3)0.0277 (4)
C70.4355 (2)0.14789 (8)−0.2108 (3)0.0326 (5)
H7A0.42260.1830−0.25880.039*
H7B0.37720.1252−0.30650.039*
C80.5876 (2)0.13280 (8)−0.1709 (3)0.0292 (5)
H8A0.60770.1336−0.28740.035*
C90.6946 (2)0.16499 (7)−0.0368 (3)0.0259 (4)
C100.7108 (2)0.22060 (8)−0.0448 (3)0.0301 (5)
C110.8288 (2)0.24382 (7)0.0988 (3)0.0299 (5)
C120.8434 (3)0.29669 (8)0.1069 (3)0.0393 (6)
H12A0.77670.31750.02310.047*
C130.9546 (3)0.31879 (9)0.2366 (4)0.0457 (7)
H13A0.96320.35480.24310.055*
C141.0541 (3)0.28861 (9)0.3576 (3)0.0432 (6)
H14A1.13170.30400.44420.052*
C151.0407 (2)0.23625 (8)0.3524 (3)0.0351 (5)
H15A1.10870.21580.43580.042*
C160.9273 (2)0.21352 (7)0.2246 (3)0.0284 (4)
C170.9102 (2)0.15717 (7)0.2248 (3)0.0250 (4)
C180.7843 (2)0.13671 (7)0.0901 (3)0.0243 (4)
C190.7453 (2)0.08120 (7)0.0663 (3)0.0247 (4)
C200.7310 (2)0.05476 (7)0.2298 (3)0.0286 (4)
C210.6447 (2)0.06580 (8)0.3289 (3)0.0351 (5)
H21A0.58210.09360.29750.042*
C220.6529 (3)0.03456 (9)0.4769 (3)0.0410 (6)
H22A0.59560.04120.54840.049*
C230.7448 (3)−0.00613 (9)0.5190 (3)0.0410 (6)
H23A0.7485−0.02700.61940.049*
C240.8312 (3)−0.01737 (8)0.4200 (3)0.0348 (5)
H24A0.8933−0.04540.45010.042*
C250.8228 (2)0.01413 (7)0.2749 (3)0.0276 (4)
C260.8609 (2)0.04958 (7)0.0286 (3)0.0248 (4)
H1N10.551 (3)0.0684 (11)−0.059 (4)0.065 (9)*
H1N20.968 (3)−0.0123 (9)0.156 (3)0.045 (7)*
U11U22U33U12U13U23
O10.0417 (10)0.0389 (9)0.0539 (10)0.0140 (7)0.0252 (8)0.0197 (7)
O20.0299 (9)0.0331 (8)0.0342 (8)0.0021 (6)0.0110 (7)0.0021 (6)
O30.0354 (9)0.0290 (7)0.0322 (8)0.0062 (6)0.0188 (7)0.0033 (5)
N10.0287 (10)0.0337 (10)0.0345 (10)0.0016 (8)0.0103 (8)−0.0007 (7)
N20.0326 (10)0.0244 (9)0.0290 (9)0.0045 (7)0.0135 (8)0.0022 (6)
C10.0332 (13)0.0290 (11)0.0310 (11)−0.0018 (9)0.0043 (9)−0.0041 (8)
C20.0327 (13)0.0322 (11)0.0382 (12)−0.0071 (9)0.0092 (10)0.0050 (9)
C30.0292 (12)0.0418 (12)0.0321 (11)−0.0005 (9)0.0141 (9)0.0014 (9)
C40.0338 (13)0.0426 (12)0.0345 (12)−0.0083 (10)0.0161 (10)−0.0112 (9)
C50.0269 (12)0.0357 (11)0.0384 (12)−0.0089 (9)0.0164 (10)−0.0084 (9)
C60.0214 (10)0.0328 (10)0.0275 (10)0.0036 (8)0.0058 (8)−0.0008 (8)
C70.0288 (12)0.0405 (12)0.0285 (11)0.0042 (9)0.0092 (9)−0.0013 (8)
C80.0302 (12)0.0353 (11)0.0253 (10)0.0051 (9)0.0133 (9)0.0022 (8)
C90.0282 (11)0.0264 (10)0.0292 (10)0.0035 (8)0.0176 (8)0.0033 (7)
C100.0316 (12)0.0301 (10)0.0373 (11)0.0073 (9)0.0233 (10)0.0089 (8)
C110.0363 (12)0.0254 (10)0.0397 (12)0.0003 (8)0.0287 (10)0.0015 (8)
C120.0479 (15)0.0277 (11)0.0605 (15)0.0024 (10)0.0424 (13)0.0036 (9)
C130.0623 (18)0.0263 (11)0.0695 (17)−0.0098 (11)0.0503 (15)−0.0101 (11)
C140.0493 (15)0.0423 (13)0.0521 (15)−0.0191 (11)0.0358 (13)−0.0163 (11)
C150.0357 (13)0.0368 (12)0.0420 (12)−0.0088 (9)0.0253 (10)−0.0075 (9)
C160.0314 (11)0.0270 (10)0.0362 (11)−0.0033 (8)0.0240 (10)−0.0035 (8)
C170.0260 (11)0.0268 (10)0.0283 (10)0.0011 (8)0.0171 (8)−0.0003 (7)
C180.0261 (11)0.0253 (9)0.0268 (10)0.0016 (8)0.0161 (8)0.0001 (7)
C190.0268 (11)0.0241 (9)0.0266 (10)0.0010 (8)0.0132 (8)−0.0002 (7)
C200.0344 (12)0.0281 (10)0.0266 (10)−0.0029 (8)0.0143 (9)−0.0004 (8)
C210.0396 (14)0.0348 (11)0.0369 (12)−0.0029 (10)0.0207 (10)−0.0021 (9)
C220.0489 (16)0.0439 (13)0.0389 (13)−0.0104 (11)0.0262 (11)−0.0029 (10)
C230.0563 (17)0.0388 (12)0.0316 (12)−0.0112 (11)0.0193 (11)0.0026 (9)
C240.0453 (14)0.0282 (10)0.0295 (11)−0.0045 (9)0.0103 (10)0.0025 (8)
C250.0346 (12)0.0234 (9)0.0270 (10)−0.0045 (8)0.0132 (9)−0.0020 (7)
C260.0266 (11)0.0235 (9)0.0254 (10)0.0007 (8)0.0101 (8)−0.0015 (7)
O1—C101.219 (2)C9—C101.475 (3)
O2—C171.225 (2)C10—C111.485 (3)
O3—C261.225 (2)C11—C121.397 (3)
N1—C81.478 (3)C11—C161.404 (3)
N1—C191.487 (3)C12—C131.381 (4)
N1—H1N10.89 (3)C12—H12A0.9500
N2—C261.361 (2)C13—C141.390 (4)
N2—C251.413 (3)C13—H13A0.9500
N2—H1N20.95 (3)C14—C151.382 (3)
C1—C21.388 (3)C14—H14A0.9500
C1—C61.389 (3)C15—C161.395 (3)
C1—H1A0.9500C15—H15A0.9500
C2—C31.380 (3)C16—C171.491 (3)
C2—H2A0.9500C17—C181.474 (3)
C3—C41.378 (3)C18—C191.508 (3)
C3—H3A0.9500C19—C201.507 (3)
C4—C51.391 (3)C19—C261.552 (3)
C4—H4A0.9500C20—C211.384 (3)
C5—C61.391 (3)C20—C251.389 (3)
C5—H5A0.9500C21—C221.402 (3)
C6—C71.513 (3)C21—H21A0.9500
C7—C81.536 (3)C22—C231.390 (4)
C7—H7A0.9900C22—H22A0.9500
C7—H7B0.9900C23—C241.387 (3)
C8—C91.505 (3)C23—H23A0.9500
C8—H8A1.0000C24—C251.386 (3)
C9—C181.336 (3)C24—H24A0.9500
C8—N1—C19110.48 (16)C11—C12—H12A119.9
C8—N1—H1N1112.6 (19)C12—C13—C14120.3 (2)
C19—N1—H1N1106 (2)C12—C13—H13A119.8
C26—N2—C25111.33 (17)C14—C13—H13A119.8
C26—N2—H1N2122.5 (15)C15—C14—C13120.3 (2)
C25—N2—H1N2126.2 (15)C15—C14—H14A119.8
C2—C1—C6121.01 (19)C13—C14—H14A119.8
C2—C1—H1A119.5C14—C15—C16119.9 (2)
C6—C1—H1A119.5C14—C15—H15A120.0
C3—C2—C1120.3 (2)C16—C15—H15A120.0
C3—C2—H2A119.9C15—C16—C11119.91 (19)
C1—C2—H2A119.9C15—C16—C17119.7 (2)
C4—C3—C2119.5 (2)C11—C16—C17120.43 (19)
C4—C3—H3A120.3O2—C17—C18121.16 (17)
C2—C3—H3A120.3O2—C17—C16122.93 (19)
C3—C4—C5120.4 (2)C18—C17—C16115.90 (17)
C3—C4—H4A119.8C9—C18—C17123.79 (18)
C5—C4—H4A119.8C9—C18—C19110.90 (18)
C6—C5—C4120.7 (2)C17—C18—C19125.13 (17)
C6—C5—H5A119.6N1—C19—C20114.94 (17)
C4—C5—H5A119.6N1—C19—C18103.35 (15)
C1—C6—C5118.11 (19)C20—C19—C18115.91 (15)
C1—C6—C7120.54 (18)N1—C19—C26110.06 (15)
C5—C6—C7121.34 (19)C20—C19—C26101.98 (15)
C6—C7—C8114.88 (17)C18—C19—C26110.74 (16)
C6—C7—H7A108.5C21—C20—C25121.35 (19)
C8—C7—H7A108.5C21—C20—C19129.63 (19)
C6—C7—H7B108.5C25—C20—C19109.01 (17)
C8—C7—H7B108.5C20—C21—C22117.8 (2)
H7A—C7—H7B107.5C20—C21—H21A121.1
N1—C8—C9103.11 (16)C22—C21—H21A121.1
N1—C8—C7112.82 (18)C23—C22—C21119.9 (2)
C9—C8—C7116.98 (17)C23—C22—H22A120.0
N1—C8—H8A107.8C21—C22—H22A120.0
C9—C8—H8A107.8C24—C23—C22122.4 (2)
C7—C8—H8A107.8C24—C23—H23A118.8
C18—C9—C10121.58 (19)C22—C23—H23A118.8
C18—C9—C8111.86 (17)C25—C24—C23116.9 (2)
C10—C9—C8126.40 (18)C25—C24—H24A121.6
O1—C10—C9121.2 (2)C23—C24—H24A121.6
O1—C10—C11122.08 (19)C24—C25—C20121.6 (2)
C9—C10—C11116.72 (18)C24—C25—N2128.7 (2)
C12—C11—C16119.4 (2)C20—C25—N2109.71 (17)
C12—C11—C10119.4 (2)O3—C26—N2126.73 (19)
C16—C11—C10121.17 (18)O3—C26—C19125.32 (17)
C13—C12—C11120.1 (2)N2—C26—C19107.95 (16)
C13—C12—H12A119.9
C6—C1—C2—C3−1.3 (3)C10—C9—C18—C19−179.17 (16)
C1—C2—C3—C40.7 (3)C8—C9—C18—C19−3.6 (2)
C2—C3—C4—C50.5 (3)O2—C17—C18—C9−174.50 (18)
C3—C4—C5—C6−1.1 (3)C16—C17—C18—C95.6 (3)
C2—C1—C6—C50.7 (3)O2—C17—C18—C190.2 (3)
C2—C1—C6—C7179.80 (19)C16—C17—C18—C19−179.66 (16)
C4—C5—C6—C10.5 (3)C8—N1—C19—C20130.56 (17)
C4—C5—C6—C7−178.6 (2)C8—N1—C19—C183.3 (2)
C1—C6—C7—C8−105.2 (2)C8—N1—C19—C26−115.02 (17)
C5—C6—C7—C873.9 (3)C9—C18—C19—N10.2 (2)
C19—N1—C8—C9−5.1 (2)C17—C18—C19—N1−175.10 (17)
C19—N1—C8—C7−132.25 (18)C9—C18—C19—C20−126.48 (19)
C6—C7—C8—N157.3 (2)C17—C18—C19—C2058.2 (2)
C6—C7—C8—C9−62.1 (2)C9—C18—C19—C26118.02 (18)
N1—C8—C9—C185.4 (2)C17—C18—C19—C26−57.3 (2)
C7—C8—C9—C18129.81 (19)N1—C19—C20—C21−61.8 (3)
N1—C8—C9—C10−179.28 (18)C18—C19—C20—C2158.8 (3)
C7—C8—C9—C10−54.8 (3)C26—C19—C20—C21179.2 (2)
C18—C9—C10—O1177.88 (19)N1—C19—C20—C25118.20 (19)
C8—C9—C10—O13.0 (3)C18—C19—C20—C25−121.20 (19)
C18—C9—C10—C11−2.1 (3)C26—C19—C20—C25−0.8 (2)
C8—C9—C10—C11−177.06 (17)C25—C20—C21—C220.0 (3)
O1—C10—C11—C125.0 (3)C19—C20—C21—C22−180.0 (2)
C9—C10—C11—C12−174.99 (17)C20—C21—C22—C23−0.5 (3)
O1—C10—C11—C16−173.87 (18)C21—C22—C23—C240.4 (4)
C9—C10—C11—C166.1 (3)C22—C23—C24—C250.2 (3)
C16—C11—C12—C130.7 (3)C23—C24—C25—C20−0.6 (3)
C10—C11—C12—C13−178.23 (18)C23—C24—C25—N2179.8 (2)
C11—C12—C13—C141.2 (3)C21—C20—C25—C240.5 (3)
C12—C13—C14—C15−1.7 (3)C19—C20—C25—C24−179.47 (18)
C13—C14—C15—C160.4 (3)C21—C20—C25—N2−179.80 (19)
C14—C15—C16—C111.5 (3)C19—C20—C25—N20.2 (2)
C14—C15—C16—C17−177.37 (18)C26—N2—C25—C24−179.7 (2)
C12—C11—C16—C15−2.0 (3)C26—N2—C25—C200.7 (2)
C10—C11—C16—C15176.84 (18)C25—N2—C26—O3178.67 (19)
C12—C11—C16—C17176.85 (17)C25—N2—C26—C19−1.2 (2)
C10—C11—C16—C17−4.3 (3)N1—C19—C26—O358.9 (3)
C15—C16—C17—O2−2.4 (3)C20—C19—C26—O3−178.64 (19)
C11—C16—C17—O2178.71 (18)C18—C19—C26—O3−54.7 (3)
C15—C16—C17—C18177.45 (17)N1—C19—C26—N2−121.22 (17)
C11—C16—C17—C18−1.4 (2)C20—C19—C26—N21.2 (2)
C10—C9—C18—C17−3.8 (3)C18—C19—C26—N2125.13 (17)
C8—C9—C18—C17171.80 (17)
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O3i0.95 (3)1.92 (3)2.840 (2)164 (2)
C5—H5A···O1ii0.952.413.038 (3)123
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N2—H1N2⋯O3i 0.95 (3)1.92 (3)2.840 (2)164 (2)
C5—H5A⋯O1ii 0.952.413.038 (3)123

Symmetry codes: (i) ; (ii) .

  4 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

Review 2.  [Naphthoquinones and their pharmacological properties].

Authors:  P Babula; V Adam; L Havel; R Kizek
Journal:  Ceska Slov Farm       Date:  2007-06

3.  (1S,3R)-3-Isobutyl-2,3-dihydro-spiro[benzo[f]isoindole-1,3'-indoline]-2',4,9-trione methanol monosolvate.

Authors:  Garima Sharma; S Vasanth Kumar; Habibah A Wahab; Mohd Mustaqim Rosli; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-07-25

4.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  4 in total

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