Literature DB >> 25844224

Crystal structure of ethyl 5''-fluoro-2'',3-dioxo-6',7',8',8a'-tetra-hydro-2'H,3H,5'H-di-spiro-[benzo[b]thio-phene-2,1'-indol-izine-3',3''-indoline]-2'-carboxyl-ate.

R Raja1, J Govindaraj2, M Suresh3, R Raghunathan3, A SubbiahPandi1.   

Abstract

In the title compound, C25H23FN2O4S, the fused piperidine ring of the octa-hydro-indolizine ring system adopts a chair conformation and the five-membered ring has a twisted conformation on the N-C(spiro) bond. The mean planes of the benzo-thio-phene and indoline ring systems are inclined to the mean plane of the pyrrolidine ring by 83.1 (1) and 84.9 (1)°, respectively, and to each other by 29.37 (17)°. In the crystal, mol-ecules are linked via pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(8) ring motif. The dimers are linked via C-H⋯O hydrogen bonds, forming slabs lying parallel to (100). The packing between the slabs features a short [2.734 (2) Å] F⋯F contact.

Entities:  

Keywords:  F⋯F inter­actions; benzo­thio­phene; crystal structure; di­spiro; hydrogen bonds; indoline; indolizine

Year:  2015        PMID: 25844224      PMCID: PMC4350745          DOI: 10.1107/S2056989015002121

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


Related literature

For the biological activity of indole derivatives, see: Barden (2011 ▸); Oudard et al. (2011 ▸); Beale (2011 ▸); Aanandhi et al. (2008 ▸); Muthukumar et al. (2008 ▸). For crystal structures of similar compounds, see: Savithri et al. (2014 ▸).

Experimental

Crystal data

C25H23FN2O4S M = 466.51 Monoclinic, a = 13.877 (2) Å b = 11.8999 (19) Å c = 15.426 (4) Å β = 116.463 (4)° V = 2280.5 (8) Å3 Z = 4 Mo Kα radiation μ = 0.19 mm−1 T = 293 K 0.30 × 0.30 × 0.30 mm

Data collection

Bruker SMART APEXII area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▸) T min = 0.947, T max = 0.955 32121 measured reflections 4784 independent reflections 3652 reflections with I > 2σ(I) R int = 0.033

Refinement

R[F 2 > 2σ(F 2)] = 0.044 wR(F 2) = 0.119 S = 1.04 4784 reflections 303 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.38 e Å−3 Δρmin = −0.24 e Å−3

Data collection: APEX2 (Bruker, 2008 ▸); cell refinement: SAINT (Bruker, 2008 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: PLATON (Spek, 2009 ▸); software used to prepare material for publication: SHELXL2014 and PLATON (Spek, 2009 ▸). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015002121/su5063sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015002121/su5063Isup2.hkl Click here for additional data file. . DOI: 10.1107/S2056989015002121/su5063fig1.tif The mol­ecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 30% probability level. Click here for additional data file. b . DOI: 10.1107/S2056989015002121/su5063fig2.tif A view along the b axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in these inter­actions have been omitted for clarity). CCDC reference: 1046671 Additional supporting information: crystallographic information; 3D view; checkCIF report
C25H23FN2O4SF(000) = 976
Mr = 466.51Dx = 1.359 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 13.877 (2) ÅCell parameters from 3238 reflections
b = 11.8999 (19) Åθ = 1.6–25.0°
c = 15.426 (4) ŵ = 0.19 mm1
β = 116.463 (4)°T = 293 K
V = 2280.5 (8) Å3Block, colourless
Z = 40.30 × 0.30 × 0.30 mm
Bruker SMART APEXII area-detector diffractometer4784 independent reflections
Radiation source: fine-focus sealed tube3652 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
ω and φ scansθmax = 26.6°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −17→17
Tmin = 0.947, Tmax = 0.955k = −15→15
32121 measured reflectionsl = −19→19
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.119w = 1/[σ2(Fo2) + (0.0484P)2 + 1.3589P] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
4784 reflectionsΔρmax = 0.38 e Å3
303 parametersΔρmin = −0.24 e Å3
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
xyzUiso*/Ueq
S10.35506 (4)0.59504 (4)0.45922 (4)0.04126 (16)
F10.07518 (12)1.08370 (13)0.02567 (10)0.0707 (5)
O10.42901 (14)0.75803 (15)0.29676 (15)0.0677 (5)
O20.32609 (12)0.60522 (12)0.24108 (12)0.0484 (4)
O30.06507 (11)0.61184 (12)0.25149 (11)0.0497 (4)
O40.42650 (12)0.85900 (12)0.48990 (10)0.0464 (4)
N10.18102 (13)0.86296 (13)0.36986 (11)0.0320 (4)
N20.39881 (14)1.00547 (14)0.38496 (13)0.0413 (4)
H20.453 (2)1.047 (2)0.4226 (18)0.055 (7)*
C10.3758 (4)0.4290 (3)0.2058 (4)0.1166 (15)
H1A0.42270.38980.18540.175*
H1B0.30320.42480.15570.175*
H1C0.37990.39500.26380.175*
C20.4091 (2)0.5476 (2)0.2250 (2)0.0677 (8)
H2A0.47810.55380.28170.081*
H2B0.41550.58010.17010.081*
C30.34861 (16)0.70724 (17)0.27985 (16)0.0401 (5)
C40.25734 (14)0.74688 (15)0.29925 (13)0.0308 (4)
H40.19210.74070.23770.037*
C50.23753 (14)0.67371 (15)0.37302 (13)0.0305 (4)
C60.10876 (18)0.73457 (18)0.44935 (17)0.0459 (5)
H6A0.12250.66620.48730.055*
H6B0.04430.72360.38900.055*
C70.0934 (2)0.8330 (2)0.50504 (19)0.0569 (6)
H7A0.02970.82030.51460.068*
H7B0.15480.83800.56830.068*
C80.0813 (2)0.9427 (2)0.45076 (19)0.0553 (6)
H8A0.01290.94260.39300.066*
H8B0.08061.00460.49140.066*
C90.17105 (19)0.96107 (17)0.42185 (17)0.0454 (5)
H9A0.15571.02700.38090.054*
H9B0.23830.97370.47920.054*
C100.20346 (16)0.76111 (15)0.42910 (14)0.0336 (4)
H100.26600.77610.49120.040*
C110.26183 (14)0.86879 (15)0.33304 (13)0.0298 (4)
C120.23884 (15)0.95884 (15)0.25758 (13)0.0315 (4)
C130.15370 (16)0.97322 (17)0.16708 (14)0.0381 (5)
H130.09700.92230.14210.046*
C140.15659 (17)1.06670 (19)0.11540 (15)0.0443 (5)
C150.23724 (19)1.14452 (19)0.14926 (17)0.0499 (6)
H150.23491.20640.11160.060*
C160.32277 (18)1.13050 (18)0.24034 (17)0.0467 (5)
H160.37881.18220.26520.056*
C170.32165 (16)1.03742 (16)0.29245 (14)0.0358 (4)
C180.37352 (15)0.90668 (16)0.41243 (14)0.0346 (4)
C190.14945 (14)0.58543 (15)0.31808 (14)0.0331 (4)
C200.18285 (15)0.47195 (16)0.35464 (14)0.0344 (4)
C210.11991 (19)0.37579 (17)0.32308 (17)0.0464 (5)
H210.04850.38080.27670.056*
C220.1637 (2)0.27384 (19)0.3607 (2)0.0601 (7)
H220.12210.20900.34040.072*
C230.2707 (2)0.26735 (18)0.4297 (2)0.0589 (7)
H230.30020.19730.45370.071*
C240.33419 (19)0.36132 (18)0.46330 (17)0.0474 (5)
H240.40530.35560.51010.057*
C250.28901 (16)0.46518 (16)0.42540 (14)0.0349 (4)
U11U22U33U12U13U23
S10.0304 (2)0.0319 (3)0.0474 (3)−0.0023 (2)0.0046 (2)0.0043 (2)
F10.0645 (9)0.0798 (11)0.0452 (8)−0.0036 (8)0.0042 (7)0.0238 (7)
O10.0545 (10)0.0552 (10)0.1114 (15)−0.0150 (8)0.0533 (11)−0.0126 (10)
O20.0471 (9)0.0390 (8)0.0651 (10)0.0031 (7)0.0304 (8)−0.0106 (7)
O30.0325 (7)0.0351 (8)0.0596 (10)−0.0030 (6)0.0009 (7)−0.0007 (7)
O40.0420 (8)0.0379 (8)0.0404 (8)−0.0110 (6)0.0013 (6)0.0069 (6)
N10.0370 (8)0.0234 (8)0.0375 (9)−0.0013 (6)0.0184 (7)−0.0005 (6)
N20.0395 (9)0.0313 (9)0.0403 (9)−0.0136 (8)0.0063 (8)0.0003 (7)
C10.159 (4)0.0526 (19)0.188 (4)0.030 (2)0.123 (4)−0.005 (2)
C20.0676 (17)0.0603 (16)0.094 (2)0.0148 (14)0.0527 (16)−0.0084 (15)
C30.0392 (11)0.0346 (11)0.0480 (12)−0.0025 (9)0.0208 (9)−0.0010 (9)
C40.0295 (9)0.0270 (9)0.0330 (10)−0.0038 (7)0.0112 (8)−0.0033 (7)
C50.0257 (9)0.0241 (9)0.0365 (10)−0.0021 (7)0.0093 (8)0.0006 (7)
C60.0538 (13)0.0395 (12)0.0549 (13)−0.0007 (10)0.0336 (11)0.0064 (10)
C70.0713 (17)0.0557 (15)0.0614 (15)0.0034 (13)0.0456 (14)0.0020 (12)
C80.0738 (17)0.0443 (13)0.0642 (15)0.0102 (12)0.0455 (14)−0.0025 (12)
C90.0647 (14)0.0286 (10)0.0512 (13)0.0016 (10)0.0333 (11)−0.0036 (9)
C100.0379 (10)0.0264 (9)0.0347 (10)−0.0021 (8)0.0145 (8)0.0017 (8)
C110.0301 (9)0.0252 (9)0.0304 (9)−0.0041 (7)0.0101 (8)−0.0010 (7)
C120.0343 (10)0.0264 (9)0.0348 (10)−0.0018 (8)0.0162 (8)−0.0013 (8)
C130.0374 (10)0.0397 (11)0.0349 (10)−0.0035 (9)0.0141 (9)0.0007 (9)
C140.0432 (12)0.0489 (13)0.0354 (11)0.0049 (10)0.0127 (9)0.0086 (10)
C150.0589 (14)0.0420 (12)0.0505 (13)0.0003 (11)0.0259 (11)0.0169 (10)
C160.0495 (13)0.0345 (11)0.0534 (13)−0.0098 (9)0.0205 (11)0.0053 (10)
C170.0377 (10)0.0298 (10)0.0389 (11)−0.0031 (8)0.0161 (9)0.0013 (8)
C180.0351 (10)0.0275 (9)0.0364 (10)−0.0064 (8)0.0117 (8)−0.0015 (8)
C190.0280 (9)0.0267 (9)0.0414 (11)−0.0035 (7)0.0126 (8)−0.0040 (8)
C200.0347 (10)0.0266 (9)0.0427 (11)−0.0019 (8)0.0180 (9)−0.0011 (8)
C210.0468 (12)0.0335 (11)0.0554 (13)−0.0079 (9)0.0198 (11)−0.0049 (10)
C220.0697 (17)0.0259 (11)0.0760 (17)−0.0098 (11)0.0246 (14)−0.0020 (11)
C230.0758 (17)0.0253 (11)0.0736 (17)0.0053 (11)0.0313 (14)0.0067 (11)
C240.0468 (12)0.0377 (11)0.0536 (13)0.0078 (10)0.0186 (11)0.0079 (10)
C250.0374 (10)0.0273 (9)0.0416 (11)0.0004 (8)0.0191 (9)0.0015 (8)
S1—C251.753 (2)C7—H7A0.9700
S1—C51.8362 (18)C7—H7B0.9700
F1—C141.356 (2)C8—C91.515 (3)
O1—C31.191 (3)C8—H8A0.9700
O2—C31.328 (2)C8—H8B0.9700
O2—C21.454 (3)C9—H9A0.9700
O3—C191.205 (2)C9—H9B0.9700
O4—C181.228 (2)C10—H100.9800
N1—C91.458 (2)C11—C121.508 (3)
N1—C101.465 (2)C11—C181.554 (2)
N1—C111.467 (2)C12—C131.380 (3)
N2—C181.348 (2)C12—C171.390 (3)
N2—C171.402 (3)C13—C141.380 (3)
N2—H20.87 (3)C13—H130.9300
C1—C21.474 (4)C14—C151.365 (3)
C1—H1A0.9600C15—C161.387 (3)
C1—H1B0.9600C15—H150.9300
C1—H1C0.9600C16—C171.373 (3)
C2—H2A0.9700C16—H160.9300
C2—H2B0.9700C19—C201.457 (3)
C3—C41.501 (3)C20—C211.389 (3)
C4—C111.533 (2)C20—C251.391 (3)
C4—C51.552 (3)C21—C221.365 (3)
C4—H40.9800C21—H210.9300
C5—C191.547 (2)C22—C231.391 (4)
C5—C101.555 (3)C22—H220.9300
C6—C101.513 (3)C23—C241.374 (3)
C6—C71.523 (3)C23—H230.9300
C6—H6A0.9700C24—C251.391 (3)
C6—H6B0.9700C24—H240.9300
C7—C81.520 (3)
C25—S1—C593.21 (9)C8—C9—H9B109.7
C3—O2—C2117.57 (19)H9A—C9—H9B108.2
C9—N1—C10111.42 (15)N1—C10—C6109.79 (16)
C9—N1—C11116.84 (15)N1—C10—C5103.83 (15)
C10—N1—C11107.09 (14)C6—C10—C5118.85 (16)
C18—N2—C17111.63 (16)N1—C10—H10108.0
C18—N2—H2123.8 (16)C6—C10—H10108.0
C17—N2—H2124.2 (16)C5—C10—H10108.0
C2—C1—H1A109.5N1—C11—C12113.40 (15)
C2—C1—H1B109.5N1—C11—C499.47 (14)
H1A—C1—H1B109.5C12—C11—C4116.58 (15)
C2—C1—H1C109.5N1—C11—C18112.01 (15)
H1A—C1—H1C109.5C12—C11—C18101.29 (14)
H1B—C1—H1C109.5C4—C11—C18114.69 (15)
O2—C2—C1106.6 (2)C13—C12—C17119.70 (18)
O2—C2—H2A110.4C13—C12—C11131.32 (17)
C1—C2—H2A110.4C17—C12—C11108.98 (16)
O2—C2—H2B110.4C14—C13—C12116.89 (19)
C1—C2—H2B110.4C14—C13—H13121.6
H2A—C2—H2B108.6C12—C13—H13121.6
O1—C3—O2124.9 (2)F1—C14—C15117.2 (2)
O1—C3—C4126.0 (2)F1—C14—C13118.98 (19)
O2—C3—C4109.08 (17)C15—C14—C13123.8 (2)
C3—C4—C11117.05 (16)C14—C15—C16119.4 (2)
C3—C4—C5114.26 (16)C14—C15—H15120.3
C11—C4—C5105.98 (15)C16—C15—H15120.3
C3—C4—H4106.3C17—C16—C15117.5 (2)
C11—C4—H4106.3C17—C16—H16121.2
C5—C4—H4106.3C15—C16—H16121.2
C19—C5—C4109.53 (15)C16—C17—C12122.62 (19)
C19—C5—C10113.40 (15)C16—C17—N2127.73 (19)
C4—C5—C10103.29 (14)C12—C17—N2109.64 (17)
C19—C5—S1106.29 (12)O4—C18—N2125.60 (18)
C4—C5—S1115.26 (13)O4—C18—C11125.97 (17)
C10—C5—S1109.29 (13)N2—C18—C11108.26 (16)
C10—C6—C7108.01 (18)O3—C19—C20126.31 (17)
C10—C6—H6A110.1O3—C19—C5121.35 (17)
C7—C6—H6A110.1C20—C19—C5112.32 (15)
C10—C6—H6B110.1C21—C20—C25120.52 (18)
C7—C6—H6B110.1C21—C20—C19125.85 (18)
H6A—C6—H6B108.4C25—C20—C19113.60 (16)
C8—C7—C6111.02 (19)C22—C21—C20119.5 (2)
C8—C7—H7A109.4C22—C21—H21120.3
C6—C7—H7A109.4C20—C21—H21120.3
C8—C7—H7B109.4C21—C22—C23119.7 (2)
C6—C7—H7B109.4C21—C22—H22120.1
H7A—C7—H7B108.0C23—C22—H22120.1
C9—C8—C7112.5 (2)C24—C23—C22122.0 (2)
C9—C8—H8A109.1C24—C23—H23119.0
C7—C8—H8A109.1C22—C23—H23119.0
C9—C8—H8B109.1C23—C24—C25118.1 (2)
C7—C8—H8B109.1C23—C24—H24120.9
H8A—C8—H8B107.8C25—C24—H24120.9
N1—C9—C8109.79 (18)C20—C25—C24120.17 (18)
N1—C9—H9A109.7C20—C25—S1114.38 (14)
C8—C9—H9A109.7C24—C25—S1125.45 (16)
N1—C9—H9B109.7
C3—O2—C2—C1165.9 (3)C4—C11—C12—C17−128.26 (18)
C2—O2—C3—O15.0 (4)C18—C11—C12—C17−3.1 (2)
C2—O2—C3—C4−174.5 (2)C17—C12—C13—C140.4 (3)
O1—C3—C4—C117.5 (3)C11—C12—C13—C14179.6 (2)
O2—C3—C4—C11−172.97 (16)C12—C13—C14—F1179.32 (19)
O1—C3—C4—C5−117.2 (2)C12—C13—C14—C15−0.8 (3)
O2—C3—C4—C562.3 (2)F1—C14—C15—C16−179.5 (2)
C3—C4—C5—C19−94.74 (18)C13—C14—C15—C160.6 (4)
C11—C4—C5—C19134.87 (15)C14—C15—C16—C170.0 (4)
C3—C4—C5—C10144.15 (16)C15—C16—C17—C12−0.3 (3)
C11—C4—C5—C1013.77 (18)C15—C16—C17—N2179.6 (2)
C3—C4—C5—S125.0 (2)C13—C12—C17—C160.1 (3)
C11—C4—C5—S1−105.36 (15)C11—C12—C17—C16−179.2 (2)
C25—S1—C5—C19−1.52 (14)C13—C12—C17—N2−179.83 (18)
C25—S1—C5—C4−123.05 (14)C11—C12—C17—N20.8 (2)
C25—S1—C5—C10121.20 (13)C18—N2—C17—C16−177.7 (2)
C10—C6—C7—C854.8 (3)C18—N2—C17—C122.3 (2)
C6—C7—C8—C9−51.8 (3)C17—N2—C18—O4−179.8 (2)
C10—N1—C9—C8−58.9 (2)C17—N2—C18—C11−4.3 (2)
C11—N1—C9—C8177.59 (17)N1—C11—C18—O458.7 (3)
C7—C8—C9—N152.5 (3)C12—C11—C18—O4179.9 (2)
C9—N1—C10—C664.7 (2)C4—C11—C18—O4−53.7 (3)
C11—N1—C10—C6−166.38 (16)N1—C11—C18—N2−116.76 (18)
C9—N1—C10—C5−167.21 (16)C12—C11—C18—N24.4 (2)
C11—N1—C10—C5−38.31 (17)C4—C11—C18—N2130.83 (18)
C7—C6—C10—N1−61.1 (2)C4—C5—C19—O3−49.5 (3)
C7—C6—C10—C5179.72 (18)C10—C5—C19—O365.3 (2)
C19—C5—C10—N1−104.87 (17)S1—C5—C19—O3−174.61 (17)
C4—C5—C10—N113.58 (17)C4—C5—C19—C20128.87 (17)
S1—C5—C10—N1136.76 (13)C10—C5—C19—C20−116.35 (18)
C19—C5—C10—C617.4 (2)S1—C5—C19—C203.7 (2)
C4—C5—C10—C6135.84 (18)O3—C19—C20—C21−4.7 (4)
S1—C5—C10—C6−100.99 (18)C5—C19—C20—C21177.0 (2)
C9—N1—C11—C12−63.7 (2)O3—C19—C20—C25173.4 (2)
C10—N1—C11—C12170.60 (15)C5—C19—C20—C25−4.8 (2)
C9—N1—C11—C4171.82 (16)C25—C20—C21—C22−1.3 (3)
C10—N1—C11—C446.10 (17)C19—C20—C21—C22176.8 (2)
C9—N1—C11—C1850.2 (2)C20—C21—C22—C23−0.4 (4)
C10—N1—C11—C18−75.51 (17)C21—C22—C23—C241.5 (4)
C3—C4—C11—N1−164.31 (16)C22—C23—C24—C25−0.9 (4)
C5—C4—C11—N1−35.55 (17)C21—C20—C25—C241.9 (3)
C3—C4—C11—C1273.4 (2)C19—C20—C25—C24−176.41 (19)
C5—C4—C11—C12−157.80 (15)C21—C20—C25—S1−178.07 (17)
C3—C4—C11—C18−44.7 (2)C19—C20—C25—S13.6 (2)
C5—C4—C11—C1884.10 (18)C23—C24—C25—C20−0.8 (3)
N1—C11—C12—C13−62.1 (3)C23—C24—C25—S1179.14 (19)
C4—C11—C12—C1352.5 (3)C5—S1—C25—C20−1.11 (17)
C18—C11—C12—C13177.7 (2)C5—S1—C25—C24179.0 (2)
N1—C11—C12—C17117.10 (18)
D—H···AD—HH···AD···AD—H···A
N2—H2···O4i0.87 (3)1.96 (3)2.834 (2)179 (2)
C1—H1A···O1ii0.962.503.401 (4)156
Table 1

Hydrogen-bond geometry (, )

DHA DHHA D A DHA
N2H2O4i 0.87(3)1.96(3)2.834(2)179(2)
C1H1AO1ii 0.962.503.401(4)156

Symmetry codes: (i) ; (ii) .

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Journal:  Biol Pharm Bull       Date:  2008-07       Impact factor: 2.233

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Journal:  Acta Crystallogr C Struct Chem       Date:  2015-01-01       Impact factor: 1.172

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

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