organic compounds
3-Hydroxy-3-(2-oxo-2,3-dihydro-1H-indol-3-yl)-2,3-dihydro-1H-indol-2-one
aDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, bChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, cChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, eChemistry Department, Faculty of Science, Sohag University, Sohag-82534, Egypt, and fChemistry Department, College of Education, Salahaddin University-Hawler, Erbil, Kurdistan Region, Iraq
*Correspondence e-mail: shaabankamel@yahoo.com
The conformation of the title molecule, C16H12N2O3, is partly determined by an intramolecular C=O⋯π interaction between one carbonyl group and the five-membered ring of the other indolinone moiety. The crystal packing consists of layers parallel to (001) formed by a combination of N—H⋯O and O—H⋯O hydrogen bonds and π–π stacking interactions. Both the N—H⋯O and O—H⋯O hydrogen bonds generate inversion dimers.
Keywords: crystal structure; hydrogen bond; π–π stacking; indolinone; isatin; dimerization.
CCDC reference: 1529856
Structure description
Indole scaffold compounds are synthetically important substrates that can be used for the synthesis of a large variety of ). Recently, isatin derivatives have attracted strong interest in organic and medicinal chemistry due to their potent biological and pharmacological activities including antitumor (Premanathan et al., 2012; Havrylyuk et al., 2011), antimicrobial (Singh et al., 2010; Ali & Alam, 1994; Pandeya et al., 1999b), anti-inflammatory and analgesic (Abele et al., 2003; Mondal, et al., 2010), antimycobacterial (Aboul-Fadl et al., 2010; Sriram et al., 2006), anticonvulsant (Malawska, 2005), antiviral (Selvam et al., 2006; Selvam et al., 2008; Abbas et al., 2013), anthelmintic (Suresh et al., 2011), anti-HIV applications (Pandeya et al., 1999a) and anti-oxidant (Andreani et al., 2010; Kiran et al. 2013). In this context, the present study reports the synthesis and determination of the title bis-indole derivative.
and as raw material for drug synthesis (Grewal, 2014In the title compound (Fig. 1), the indolinone moieties are close to being planar, with r.m.s. deviations of the nine atoms from the mean plane being 0.025 Å for the ring system containing atom N1 and 0.014 Å for that containing atom N2. The dihedral angle between the mean planes of the two indolinone moieties is 58.69 (3)°. The conformation of the molecule is determined in part by a C=O⋯π interaction between the C10=O3 carbonyl group and the C1/C6/C7/C8/N1 ring (Fig. 1 and Table 1).
The bond lengths and angles of the title compound are comparable with those reported for related compounds such as (3E)-3-[(4-butylphenyl)imino]-1,3-dihydro-2H-indol-2-one (Akkurt et al., 2003), 2-oxo-2,3-dihydro-1H-indol-3-one nicotinoylhydrazone (Ali et al., 2005) and 3-(2-amino-1-methyl-4-4,5-dihydro-1H-imidazol-5-yl)-3-hydroxy-1-phenylindolin-2-one ethanol solvate (Penthala et al., 2009).
The N2—H2B⋯O3 and the O2—H2A⋯O1 hydrogen bonds (Table 1) generate inversion dimers with R22(8) and R22(10) ring motifs, respectively (Fig. 2). The other N1—H1⋯O3 contact also forms an inversion dimer but, in this case, with an R22(14) motif. A combination of N1—H1⋯O3 and N2—H2B⋯O3 hydrogen bonds generate zigzag chains of molecules running parallel to the b-axis direction which are formed into sheets parallel to (001) by pairwise O2—H2A⋯O1 hydrogen bonds (Figs. 2 and 3). The layer formation is assisted by complementary π–π stacking interactions [Cg2⋯Cg3 = 3.571 (1) Å] between the C11–C16 and C16/C9/C10/C11/N2 rings (Fig. 4).
Synthesis and crystallization
The title compound was obtained (Fig. 5) as a major product during an an attempt to synthesize a new tridentate ONO-dibasic hydrazone (1) derived from the condensation of phenyl alanine with isatin by the following procedures:
A methanolic solution (15 ml) of isatin (1 mmol) was added dropwise to an aqueous/methanolic (1:1) (10 ml) solution of phenyl alanine at room temperature. The reaction mixture was refluxed at 353 K (monitored by TLC) for 2 h, resulting in the formation of a dark-red precipitate. The precipitate was extracted by filtration and washed many times with water and diethyl ether then dried in an oven. The final product was recystallized in hot methanol to furnish good quality dark-red crystals of 3-hydroxy-3-(2-oxo-2,3-dihydro-1H-indol-3-yl)-2,3-dihydro-1H-indol-2-one (2) in 84% yield. Phenyl alanine may act as a to activate the isatin causing dimerization in the aqueous/methanolic media.
Refinement
Crystal data, data collection and structure . The hydroxyl hydrogen did not refine satisfactorily although definitely located in a difference map, possibly due to unresolved disorder. Consequently it was placed in a calculated position (SHELXL HFIX 147 instruction) and included as a riding contribution.
details are summarized in Table 2
|
Structural data
CCDC reference: 1529856
https://doi.org/10.1107/S2414314617001390/sj4085sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617001390/sj4085Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314617001390/sj4085Isup3.cml
Data collection: APEX3 (Bruker, 2016); cell
SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C16H12N2O3 | Z = 2 |
Mr = 280.28 | F(000) = 292 |
Triclinic, P1 | Dx = 1.451 Mg m−3 |
a = 7.7193 (3) Å | Cu Kα radiation, λ = 1.54178 Å |
b = 8.6977 (3) Å | Cell parameters from 6334 reflections |
c = 9.5907 (4) Å | θ = 4.6–72.4° |
α = 90.457 (2)° | µ = 0.84 mm−1 |
β = 95.070 (2)° | T = 150 K |
γ = 90.627 (2)° | Column, dark yellow-orange |
V = 641.34 (4) Å3 | 0.14 × 0.07 × 0.05 mm |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2487 independent reflections |
Radiation source: INCOATEC IµS micro-focus source | 2137 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.033 |
Detector resolution: 10.4167 pixels mm-1 | θmax = 72.4°, θmin = 4.6° |
ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Bruker, 2016) | k = −10→10 |
Tmin = 0.89, Tmax = 0.96 | l = −11→11 |
8464 measured reflections |
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)] = 0.039 | Hydrogen site location: mixed |
wR(F2) = 0.101 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.043P)2 + 0.3252P] where P = (Fo2 + 2Fc2)/3 |
2487 reflections | (Δ/σ)max < 0.001 |
235 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
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. |
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 > 2sigma(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. The hydroxyl hydrogen did not refine satisfactorily although definitely located in a difference map, possibly due to unresolved disorder. Consequently it was placed in a calculated position (SHELXL HFIX 147 instruction) and included as a riding contribution. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.78629 (14) | 1.05555 (13) | 0.52109 (12) | 0.0311 (3) | |
O2 | 0.94772 (15) | 0.94251 (13) | 0.26711 (13) | 0.0311 (3) | |
H2A | 1.0265 | 0.9586 | 0.3319 | 0.047* | |
O3 | 0.58356 (14) | 0.70275 (12) | 0.52877 (12) | 0.0272 (3) | |
N1 | 0.56106 (17) | 1.03152 (15) | 0.34911 (14) | 0.0252 (3) | |
H1 | 0.491 (3) | 1.105 (3) | 0.388 (2) | 0.052 (6)* | |
N2 | 0.69437 (18) | 0.50298 (15) | 0.40763 (14) | 0.0248 (3) | |
H2B | 0.613 (3) | 0.433 (3) | 0.423 (2) | 0.051 (6)* | |
C1 | 0.5182 (2) | 0.93711 (17) | 0.23090 (16) | 0.0243 (3) | |
C2 | 0.3649 (2) | 0.9328 (2) | 0.14575 (18) | 0.0306 (4) | |
H2 | 0.266 (3) | 1.000 (2) | 0.162 (2) | 0.033 (5)* | |
C3 | 0.3529 (2) | 0.8279 (2) | 0.03503 (19) | 0.0341 (4) | |
H3 | 0.246 (3) | 0.824 (2) | −0.025 (2) | 0.042 (6)* | |
C4 | 0.4899 (2) | 0.7319 (2) | 0.01088 (18) | 0.0334 (4) | |
H4 | 0.474 (3) | 0.656 (2) | −0.070 (2) | 0.037 (5)* | |
C5 | 0.6447 (2) | 0.73867 (19) | 0.09783 (17) | 0.0281 (4) | |
H5 | 0.743 (3) | 0.672 (2) | 0.084 (2) | 0.033 (5)* | |
C6 | 0.6578 (2) | 0.84201 (17) | 0.20856 (16) | 0.0230 (3) | |
C7 | 0.80112 (19) | 0.87379 (17) | 0.32288 (16) | 0.0224 (3) | |
C8 | 0.71796 (19) | 0.99649 (17) | 0.41294 (17) | 0.0239 (3) | |
C9 | 0.85503 (19) | 0.73274 (17) | 0.41305 (16) | 0.0225 (3) | |
H9 | 0.928 (2) | 0.7736 (19) | 0.5023 (18) | 0.022 (4)* | |
C10 | 0.69513 (19) | 0.64824 (17) | 0.45866 (16) | 0.0222 (3) | |
C11 | 0.8409 (2) | 0.47612 (17) | 0.33341 (16) | 0.0233 (3) | |
C12 | 0.8850 (2) | 0.34313 (19) | 0.26664 (18) | 0.0289 (4) | |
H12 | 0.812 (3) | 0.251 (2) | 0.267 (2) | 0.033 (5)* | |
C13 | 1.0385 (2) | 0.3456 (2) | 0.20033 (19) | 0.0326 (4) | |
H13 | 1.073 (3) | 0.257 (2) | 0.153 (2) | 0.039 (5)* | |
C14 | 1.1432 (2) | 0.4764 (2) | 0.20282 (19) | 0.0336 (4) | |
H14 | 1.251 (3) | 0.476 (2) | 0.159 (2) | 0.039 (5)* | |
C15 | 1.0967 (2) | 0.6096 (2) | 0.27092 (18) | 0.0288 (4) | |
H15 | 1.169 (2) | 0.701 (2) | 0.273 (2) | 0.031 (5)* | |
C16 | 0.94318 (19) | 0.60941 (17) | 0.33510 (16) | 0.0229 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0273 (6) | 0.0304 (6) | 0.0357 (7) | −0.0045 (5) | 0.0043 (5) | −0.0121 (5) |
O2 | 0.0265 (6) | 0.0299 (6) | 0.0382 (7) | −0.0054 (5) | 0.0111 (5) | −0.0011 (5) |
O3 | 0.0281 (6) | 0.0223 (5) | 0.0331 (6) | 0.0003 (4) | 0.0133 (5) | −0.0023 (4) |
N1 | 0.0236 (6) | 0.0220 (6) | 0.0306 (7) | 0.0002 (5) | 0.0065 (5) | −0.0039 (5) |
N2 | 0.0262 (7) | 0.0193 (6) | 0.0302 (7) | −0.0027 (5) | 0.0102 (5) | −0.0015 (5) |
C1 | 0.0257 (8) | 0.0217 (7) | 0.0265 (8) | −0.0028 (6) | 0.0076 (6) | −0.0003 (6) |
C2 | 0.0259 (8) | 0.0344 (9) | 0.0321 (9) | 0.0018 (7) | 0.0057 (7) | 0.0022 (7) |
C3 | 0.0291 (8) | 0.0430 (10) | 0.0297 (9) | −0.0039 (7) | −0.0001 (7) | 0.0009 (7) |
C4 | 0.0391 (9) | 0.0346 (9) | 0.0263 (9) | −0.0015 (7) | 0.0021 (7) | −0.0041 (7) |
C5 | 0.0326 (8) | 0.0258 (8) | 0.0265 (8) | 0.0017 (7) | 0.0058 (6) | −0.0016 (6) |
C6 | 0.0235 (7) | 0.0203 (7) | 0.0258 (8) | −0.0031 (6) | 0.0058 (6) | 0.0016 (6) |
C7 | 0.0202 (7) | 0.0195 (7) | 0.0283 (8) | −0.0042 (6) | 0.0075 (6) | −0.0019 (6) |
C8 | 0.0229 (7) | 0.0187 (7) | 0.0310 (8) | −0.0052 (6) | 0.0086 (6) | −0.0018 (6) |
C9 | 0.0203 (7) | 0.0214 (7) | 0.0263 (8) | −0.0015 (6) | 0.0050 (6) | −0.0033 (6) |
C10 | 0.0233 (7) | 0.0203 (7) | 0.0235 (7) | −0.0001 (6) | 0.0043 (6) | 0.0001 (6) |
C11 | 0.0247 (7) | 0.0222 (7) | 0.0236 (8) | 0.0018 (6) | 0.0053 (6) | 0.0004 (6) |
C12 | 0.0358 (9) | 0.0218 (8) | 0.0298 (8) | 0.0012 (7) | 0.0074 (7) | −0.0013 (6) |
C13 | 0.0384 (9) | 0.0281 (9) | 0.0327 (9) | 0.0070 (7) | 0.0100 (7) | −0.0042 (7) |
C14 | 0.0296 (9) | 0.0364 (9) | 0.0367 (9) | 0.0052 (7) | 0.0127 (7) | −0.0032 (7) |
C15 | 0.0237 (8) | 0.0287 (8) | 0.0347 (9) | −0.0005 (7) | 0.0067 (6) | −0.0019 (7) |
C16 | 0.0226 (7) | 0.0213 (7) | 0.0250 (7) | 0.0010 (6) | 0.0030 (6) | −0.0014 (6) |
O1—C8 | 1.2275 (19) | C5—C6 | 1.382 (2) |
O2—C7 | 1.4217 (18) | C5—H5 | 0.97 (2) |
O2—H2A | 0.8400 | C6—C7 | 1.509 (2) |
O3—C10 | 1.2348 (18) | C7—C9 | 1.546 (2) |
N1—C8 | 1.347 (2) | C7—C8 | 1.548 (2) |
N1—C1 | 1.408 (2) | C9—C16 | 1.505 (2) |
N1—H1 | 0.94 (2) | C9—C10 | 1.528 (2) |
N2—C10 | 1.3510 (19) | C9—H9 | 1.039 (17) |
N2—C11 | 1.4091 (19) | C11—C12 | 1.378 (2) |
N2—H2B | 0.90 (3) | C11—C16 | 1.395 (2) |
C1—C2 | 1.378 (2) | C12—C13 | 1.394 (2) |
C1—C6 | 1.396 (2) | C12—H12 | 0.97 (2) |
C2—C3 | 1.391 (3) | C13—C14 | 1.387 (3) |
C2—H2 | 0.99 (2) | C13—H13 | 0.95 (2) |
C3—C4 | 1.388 (3) | C14—C15 | 1.392 (2) |
C3—H3 | 0.97 (2) | C14—H14 | 0.97 (2) |
C4—C5 | 1.396 (2) | C15—C16 | 1.383 (2) |
C4—H4 | 1.02 (2) | C15—H15 | 0.96 (2) |
C7—O2—H2A | 109.5 | O1—C8—N1 | 126.03 (14) |
C8—N1—C1 | 111.47 (13) | O1—C8—C7 | 125.72 (14) |
C8—N1—H1 | 120.7 (14) | N1—C8—C7 | 108.20 (13) |
C1—N1—H1 | 127.6 (14) | C16—C9—C10 | 102.45 (12) |
C10—N2—C11 | 111.35 (13) | C16—C9—C7 | 113.88 (13) |
C10—N2—H2B | 123.3 (14) | C10—C9—C7 | 110.84 (12) |
C11—N2—H2B | 125.3 (14) | C16—C9—H9 | 114.1 (9) |
C2—C1—C6 | 122.38 (15) | C10—C9—H9 | 108.2 (10) |
C2—C1—N1 | 127.82 (14) | C7—C9—H9 | 107.2 (9) |
C6—C1—N1 | 109.80 (14) | O3—C10—N2 | 125.26 (14) |
C1—C2—C3 | 117.15 (16) | O3—C10—C9 | 126.29 (14) |
C1—C2—H2 | 122.0 (11) | N2—C10—C9 | 108.44 (13) |
C3—C2—H2 | 120.9 (11) | C12—C11—C16 | 122.28 (15) |
C4—C3—C2 | 121.50 (16) | C12—C11—N2 | 128.31 (15) |
C4—C3—H3 | 120.7 (12) | C16—C11—N2 | 109.41 (13) |
C2—C3—H3 | 117.8 (12) | C11—C12—C13 | 117.30 (16) |
C3—C4—C5 | 120.50 (16) | C11—C12—H12 | 120.7 (11) |
C3—C4—H4 | 118.5 (11) | C13—C12—H12 | 121.9 (11) |
C5—C4—H4 | 121.0 (11) | C14—C13—C12 | 121.20 (15) |
C6—C5—C4 | 118.51 (15) | C14—C13—H13 | 118.8 (13) |
C6—C5—H5 | 119.3 (11) | C12—C13—H13 | 119.9 (13) |
C4—C5—H5 | 122.2 (11) | C13—C14—C15 | 120.69 (16) |
C5—C6—C1 | 119.95 (15) | C13—C14—H14 | 120.5 (12) |
C5—C6—C7 | 131.78 (14) | C15—C14—H14 | 118.8 (12) |
C1—C6—C7 | 108.24 (13) | C16—C15—C14 | 118.65 (16) |
O2—C7—C6 | 110.72 (12) | C16—C15—H15 | 120.3 (11) |
O2—C7—C9 | 111.02 (12) | C14—C15—H15 | 121.0 (11) |
C6—C7—C9 | 114.49 (12) | C15—C16—C11 | 119.85 (14) |
O2—C7—C8 | 107.89 (12) | C15—C16—C9 | 131.84 (14) |
C6—C7—C8 | 102.04 (12) | C11—C16—C9 | 108.31 (13) |
C9—C7—C8 | 110.15 (12) | ||
C8—N1—C1—C2 | 175.44 (16) | C6—C7—C9—C16 | 67.76 (16) |
C8—N1—C1—C6 | −4.44 (19) | C8—C7—C9—C16 | −177.95 (12) |
C6—C1—C2—C3 | 0.4 (2) | O2—C7—C9—C10 | −173.39 (12) |
N1—C1—C2—C3 | −179.48 (16) | C6—C7—C9—C10 | −47.12 (17) |
C1—C2—C3—C4 | −0.3 (3) | C8—C7—C9—C10 | 67.17 (15) |
C2—C3—C4—C5 | −0.2 (3) | C11—N2—C10—O3 | −179.33 (14) |
C3—C4—C5—C6 | 0.4 (3) | C11—N2—C10—C9 | 1.48 (17) |
C4—C5—C6—C1 | −0.3 (2) | C16—C9—C10—O3 | 178.65 (15) |
C4—C5—C6—C7 | 177.50 (16) | C7—C9—C10—O3 | −59.5 (2) |
C2—C1—C6—C5 | −0.1 (2) | C16—C9—C10—N2 | −2.16 (16) |
N1—C1—C6—C5 | 179.79 (14) | C7—C9—C10—N2 | 119.69 (14) |
C2—C1—C6—C7 | −178.38 (15) | C10—N2—C11—C12 | −179.90 (16) |
N1—C1—C6—C7 | 1.50 (17) | C10—N2—C11—C16 | −0.08 (18) |
C5—C6—C7—O2 | 68.9 (2) | C16—C11—C12—C13 | 0.4 (2) |
C1—C6—C7—O2 | −113.13 (14) | N2—C11—C12—C13 | −179.79 (16) |
C5—C6—C7—C9 | −57.6 (2) | C11—C12—C13—C14 | 0.6 (3) |
C1—C6—C7—C9 | 120.45 (14) | C12—C13—C14—C15 | −0.6 (3) |
C5—C6—C7—C8 | −176.54 (17) | C13—C14—C15—C16 | −0.5 (3) |
C1—C6—C7—C8 | 1.48 (15) | C14—C15—C16—C11 | 1.5 (2) |
C1—N1—C8—O1 | −177.15 (15) | C14—C15—C16—C9 | −178.43 (16) |
C1—N1—C8—C7 | 5.31 (17) | C12—C11—C16—C15 | −1.5 (2) |
O2—C7—C8—O1 | −65.0 (2) | N2—C11—C16—C15 | 178.67 (14) |
C6—C7—C8—O1 | 178.37 (15) | C12—C11—C16—C9 | 178.46 (15) |
C9—C7—C8—O1 | 56.38 (19) | N2—C11—C16—C9 | −1.37 (17) |
O2—C7—C8—N1 | 112.59 (14) | C10—C9—C16—C15 | −177.95 (17) |
C6—C7—C8—N1 | −4.09 (15) | C7—C9—C16—C15 | 62.3 (2) |
C9—C7—C8—N1 | −126.08 (13) | C10—C9—C16—C11 | 2.10 (16) |
O2—C7—C9—C16 | −58.50 (16) | C7—C9—C16—C11 | −117.65 (14) |
Cg1 is the centroid of the C1,C6,C7,C8,N1 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2A···O1i | 0.84 | 1.93 | 2.7575 (17) | 167 |
N1—H1···O3ii | 0.94 (2) | 1.96 (2) | 2.8644 (17) | 161 (2) |
N2—H2B···O3iii | 0.90 (3) | 2.00 (3) | 2.8882 (18) | 173 (2) |
C10—O3···Cg1 | 1.24 (1) | 2.92 (1) | 3.0414 (13) | 73 (1) |
Symmetry codes: (i) −x+2, −y+2, −z+1; (ii) −x+1, −y+2, −z+1; (iii) −x+1, −y+1, −z+1. |
Acknowledgements
The support of NSF–MRI Grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.
References
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