research communications
Crystal and geometry-optimized structure, and Hirshfeld surface analysis of 1-(2-bromoethyl)indoline-2,3-dione
aPostgraduate and Research Department of Physics, National College (Autonomous), Tiruchirappalli 620 001, Tamilnadu, India, bSchool of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamilnadu, India, and cLaboratorio de Políimeros, Centro de Química Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Complejo de Ciencias, ICUAP, Edif. 103H, 22 Sur y San Claudio, C.P. 72570 Puebla, Puebla, Mexico
*Correspondence e-mail: sunvag@gmail.com
In the title compound, C10H8BrNO2, the isatin (1H-indole-2,3-dione) moiety is nearly planar (r.m.s. deviation = 0.026 Å). In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming layers parallel to the ab plane, and enclosing R44(24) loops. There are a low percentage (19.3%) of intermolecular H⋯H contacts in the structure, as estimated by the analysis of Hirshfeld surfaces. This could be due to the presence of the Br atom, present in the bromoethylene group, which makes ca 18.7% Br⋯H contacts.
Keywords: crystal structure; isatin; C—H⋯O hydrogen bonds.
CCDC reference: 1508554
1. Chemical context
Isatin (1H-indole-2,3-dione) is an endogenous compound that has been identified in humans and possesses a wide range of biological activities, such as anxiogenic and sedative activities. It serves as a synthetically useful substrate which can be used to prepare a broad range of including molecules of pharmacological significance (Bekircan & Bektas, 2008). A variety of biological activities are associated with isatin, including central nervous system (CNS) activities (Raj, 2012). As part of our interest in the identification of bioactive compounds, we report herein on the synthesis, the and the geometry optimization and Hirshfeld surface analysis of the title isatin derivative, (I).
2. Structural commentary
The molecular structure of the title isatin derivative, (I), is illustrated in Fig. 1. It crystallized in the orthorhombic P212121 with an parameter of 0.015 (8). The bond lengths and angles of the isatin moiety are comparable with those reported for similar N-substituted isatin derivatives (Qachchachi et al., 2016a,b).
In compound (I), the isatin ring system is almost planar, with an r.m.s. deviation of the fitted atoms C1–C8/N1/O1/O2 of 0.026 Å. The sum of the bond angles around atom N1 is ca 360°, indicating little evidence for the presence of an sp3 lone pair.
3. Supramolecular features
In the crystal of (I), molecules are linked by C—H⋯O hydrogen bonds, viz C2—H2⋯O1 and C10—H10A⋯O2 (Table 1), which individually form C(6) and C(7) chains, respectively. Together they form layers parallel to the ab plane and enclose (24) loops (Table 1 and Fig. 2). An analysis of the crystal packing of (I) indicated that no further significant intermolecular interactions were present (PLATON; Spek, 2009).
4. Database survey
A search of the Cambridge Structural Database (Version 5.37, update May 2016; Groom et al., 2016) for N-substituted isatin derivatives yielded 58 hits. These include five reports of the structure of isatin itself and four reports of the structure of N-methylisatin. 13 of the structures involve an alkyl chain of two or more C atoms. The compound most similar to the title compound is 1-(3-bromopropyl)-1H-indole-2,3-dione (AKOBIN), whose structure was published very recently (Qachchachi et al., 2016a). A view of the structural overlap of this compound with that of compound (I) is shown in Fig. 3.
5. Geometry optimization
The geometry optimization of compound (I) was performed using the density functional theory (DFT) method with a 6-311++G** basis set. The in the solid state was used as the starting structure for the calculations. The DFT calculations are performed with the GAUSSIAN09 program package (Frisch et al., 2013). The resulting geometrical parameters are compared with those obtained from an X-ray crystallography study. A superimposed analysis of (I) with its optimized structure gives an r.m.s. deviation of 0.068 Å (Fig. 4). This indicates a twist leading to further separation between the isatin moiety and the benzene ring. Also, this suggests that the crystal packing could be influenced by the collective effect of the intermolecular interactions. To probe further, structure-based theoretical parameters, viz. HOMO and LUMO energy levels, total energy and were calculated and found to be −6.860 eV, −3.091 eV, −86134.81 eV and 7.2176 Debye, respectively. As a further structure-based test, semi-empirical molecular orbital calculations are carried out using the PM7 method in MOPAC2012 (Stewart, 2012; Maia et al., 2012). The PM7 method gave the HOMO and LUMO energy levels, total energy and as −9.276 eV, −1.271 eV, −2334.96 eV and 5.8952 Debye, respectively. Also, the superimposed analysis of the X-ray structure with the isolated molecule in the gas phase by the PM7 method gave an r.m.s. deviation of 0.211 Å. Further, the N1—C8 and N1—C1 (X-ray: 1.367 Å; DFT: 1.392 Å; PM7: 1.424 Å) bond lengths increased, while the bond angles O2—C7—C6 (X-ray: 131.3°; DFT: 130.8°; PM7: 131.2°) and O1—C8—N1 (X-ray: 127.4°; DFT: 126.8°; PM7: 123.8°) decreased. These confirm the influence of the packing interactions in the solid state of the molecule. The relative conformation about the bond joining the isatin and bromoethylene moieties of (I) is defined by the N1—C9—C10—Br1 torsion angle of 62.0 (5)°. This indicates that the conformation of the molecule is (+)-synclinal.
6. Hirshfeld surface analysis
A detailed Hirshfeld surface analysis is useful for identifing the various intermolecular interactions and intermolecular contacts present in crystal structures, with the aid of decomposed two-dimensional fingerprint plots. The Hirshfeld surface (HS) and the two-dimensional fingerprint plots were generated based on the di and de distances using Crystal Explorer (Wolff et al., 2012); di is the distance from the nearest atom inside the surface, while de is the distance from the HS to the nearest atom outside the surface. This analysis identified the various intermolecular contacts (O—H, H—H, C—H, C—C and H—Br) and their relative contributions in the The bond lengths (C—H = 1.083 Å, N—H = 1.009 Å and O—H = 0.983 Å) were adjusted to typical neutron diffraction values before the HS calculation (Venkatesan et al., 2015, 2016a,b). In Hirshfeld surface diagrams, the contacts with distances shorter than the sum of the van der Waals radii are indicated as red and the contacts with distances longer than the van der Waals radii are represented as blue, whereas the contacts with distances equal to the sum of the van der Waals radii are indicated as white. The HS area of compound (I) is shown in Fig. 5, and the respective points of intermolecular interactions are labelled.
Two-dimensional fingerprint plots are used to quantify and visualize the intermolecular interactions present in the . The result suggests that the share of intermolecular H⋯H contacts in (I) is about 19.3%. The low percentage could be attributed to the presence of the Br atom in the bromoethylene group, which makes ca 18.7% contacts with H atoms (Br⋯H). The next significant intermolecular contacts observed in the structure, i.e. O⋯H, C⋯H and C⋯C, have relative contributions of 30.6, 18.8 and 3.1%, respectively.
and the same for the title compound is shown in Fig. 67. Synthesis and crystallization
To a solution of 1-{2-[(2-bromoethyl)amino]phenyl}ethanone (1 equivalent) in DMSO were added I2 (0.1 equivalents) and TBHP (1 equivalent, 70% in H2O) at ambient temperature, and the mixture was heated to 353 K. The progress of the reaction was monitored by Upon completion, the reaction mixture was allowed to cool to ambient temperature and was quenched with aqueous sodium thiosulfate and ethyl acetate. The organic phase was separated, dried over Na2SO4, filtered and concentrated. The crude product was purified by silica-gel using hexane–ethyl acetate (9:1 v/v) as The title compound was obtained as a red solid (yield: 71%, 74.5 mg; m.p. 404–406 K). It was dissolved in a mixture of hexane–ethyl acetate (9:1 v/v) and left to slowly evaporate at room temperature, yielding brown block-like crystals after a period of 3 d.
8. Refinement
Crystal data, data collection and structure . C-bound H atoms were included in calculated positions and treated as riding, with C—H = 0.93–0.97 Å and Uiso(H) = 1.2Ueq(C).
details are summarized in Table 2Supporting information
CCDC reference: 1508554
https://doi.org/10.1107/S2056989016015760/su5327sup1.cif
contains datablocks I, Global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016015760/su5327Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989016015760/su5327Isup3.cml
Data collection: APEX2 (Bruker, 2004); cell
APEX2 (Bruker, 2004) and SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004) and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: QMOL (Gans & Shalloway, 2001) and Mercury (Macrae et al., 2008).; software used to prepare material for publication: WinGX (Farrugia, 2012) and PLATON (Spek, 2009).C10H8BrNO2 | Dx = 1.726 Mg m−3 |
Mr = 254.08 | Melting point: 406 K |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.6834 (2) Å | Cell parameters from 2844 reflections |
b = 12.9567 (7) Å | θ = 2.5–26.7° |
c = 16.1130 (8) Å | µ = 4.18 mm−1 |
V = 977.76 (8) Å3 | T = 293 K |
Z = 4 | Block, brown |
F(000) = 504 | 0.25 × 0.20 × 0.20 mm |
Bruker Kappa APEXII CCD diffractometer | 1663 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.037 |
ω and φ scan | θmax = 32.8°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Bruker, 2004) | h = −7→6 |
Tmin = 0.419, Tmax = 0.498 | k = −19→17 |
8226 measured reflections | l = −22→18 |
3150 independent reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.055 | H-atom parameters constrained |
wR(F2) = 0.084 | w = 1/[σ2(Fo2) + (0.0167P)2 + 0.3638P] where P = (Fo2 + 2Fc2)/3 |
S = 1.02 | (Δ/σ)max < 0.001 |
3150 reflections | Δρmax = 0.70 e Å−3 |
127 parameters | Δρmin = −0.59 e Å−3 |
0 restraints | Absolute structure: Flack x determined using 503 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.015 (8) |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.83217 (12) | 0.83821 (4) | 0.06227 (4) | 0.0609 (2) | |
O1 | 0.4527 (9) | 0.7005 (3) | 0.2349 (3) | 0.0719 (13) | |
O2 | 0.8447 (9) | 0.6409 (2) | 0.3684 (2) | 0.0688 (10) | |
N1 | 0.6516 (8) | 0.8607 (2) | 0.2584 (2) | 0.0378 (8) | |
C1 | 0.8490 (10) | 0.9005 (3) | 0.3156 (3) | 0.0326 (9) | |
C2 | 0.9288 (9) | 1.0020 (3) | 0.3268 (3) | 0.0429 (12) | |
H2 | 0.8520 | 1.0548 | 0.2947 | 0.051* | |
C3 | 1.1289 (12) | 1.0218 (4) | 0.3883 (3) | 0.0538 (14) | |
H3 | 1.1896 | 1.0894 | 0.3966 | 0.065* | |
C4 | 1.2414 (10) | 0.9446 (4) | 0.4377 (4) | 0.0572 (14) | |
H4 | 1.3755 | 0.9606 | 0.4783 | 0.069* | |
C5 | 1.1551 (10) | 0.8445 (4) | 0.4267 (3) | 0.0503 (11) | |
H5 | 1.2276 | 0.7920 | 0.4599 | 0.060* | |
C6 | 0.9592 (9) | 0.8233 (4) | 0.3656 (3) | 0.0362 (11) | |
C7 | 0.8222 (12) | 0.7276 (3) | 0.3414 (3) | 0.0447 (12) | |
C8 | 0.6167 (11) | 0.7569 (4) | 0.2703 (3) | 0.0458 (13) | |
C9 | 0.4985 (10) | 0.9198 (4) | 0.1964 (3) | 0.0464 (12) | |
H9A | 0.4179 | 0.9805 | 0.2227 | 0.056* | |
H9B | 0.3412 | 0.8784 | 0.1757 | 0.056* | |
C10 | 0.6765 (12) | 0.9533 (3) | 0.1248 (3) | 0.0499 (12) | |
H10A | 0.8325 | 0.9956 | 0.1451 | 0.060* | |
H10B | 0.5612 | 0.9955 | 0.0881 | 0.060* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.0714 (3) | 0.0570 (3) | 0.0543 (3) | −0.0008 (3) | 0.0059 (3) | −0.0069 (3) |
O1 | 0.090 (3) | 0.055 (2) | 0.071 (3) | −0.036 (2) | −0.003 (2) | −0.012 (2) |
O2 | 0.102 (3) | 0.0323 (18) | 0.072 (3) | 0.005 (2) | 0.013 (3) | 0.0138 (17) |
N1 | 0.042 (2) | 0.035 (2) | 0.036 (2) | −0.0055 (19) | −0.001 (2) | 0.0022 (16) |
C1 | 0.038 (2) | 0.032 (2) | 0.028 (2) | −0.001 (2) | 0.007 (2) | −0.0028 (18) |
C2 | 0.057 (3) | 0.029 (2) | 0.043 (3) | −0.001 (2) | 0.006 (2) | 0.000 (2) |
C3 | 0.069 (4) | 0.045 (3) | 0.047 (3) | −0.016 (3) | 0.011 (3) | −0.015 (3) |
C4 | 0.060 (3) | 0.078 (4) | 0.034 (3) | −0.011 (2) | 0.003 (3) | −0.007 (3) |
C5 | 0.053 (2) | 0.063 (3) | 0.036 (3) | 0.006 (3) | 0.004 (3) | 0.008 (3) |
C6 | 0.045 (2) | 0.038 (3) | 0.026 (3) | 0.002 (2) | 0.006 (2) | −0.001 (2) |
C7 | 0.060 (3) | 0.032 (2) | 0.043 (3) | 0.003 (3) | 0.017 (3) | 0.002 (2) |
C8 | 0.058 (3) | 0.038 (3) | 0.041 (3) | −0.011 (3) | 0.010 (3) | −0.005 (2) |
C9 | 0.041 (3) | 0.053 (3) | 0.045 (3) | 0.004 (2) | −0.004 (3) | 0.000 (3) |
C10 | 0.061 (3) | 0.040 (2) | 0.048 (3) | 0.005 (3) | −0.005 (3) | 0.005 (2) |
Br1—C10 | 1.942 (5) | C4—C5 | 1.370 (7) |
O1—C8 | 1.204 (6) | C4—H4 | 0.9300 |
O2—C7 | 1.210 (5) | C5—C6 | 1.373 (6) |
N1—C8 | 1.367 (5) | C5—H5 | 0.9300 |
N1—C1 | 1.404 (6) | C6—C7 | 1.449 (6) |
N1—C9 | 1.449 (6) | C7—C8 | 1.544 (7) |
C1—C2 | 1.380 (6) | C9—C10 | 1.488 (7) |
C1—C6 | 1.384 (6) | C9—H9A | 0.9700 |
C2—C3 | 1.388 (7) | C9—H9B | 0.9700 |
C2—H2 | 0.9300 | C10—H10A | 0.9700 |
C3—C4 | 1.382 (7) | C10—H10B | 0.9700 |
C3—H3 | 0.9300 | ||
C8—N1—C1 | 110.4 (4) | C1—C6—C7 | 107.2 (4) |
C8—N1—C9 | 123.9 (4) | O2—C7—C6 | 131.3 (5) |
C1—N1—C9 | 125.7 (4) | O2—C7—C8 | 123.3 (5) |
C2—C1—C6 | 120.7 (4) | C6—C7—C8 | 105.4 (4) |
C2—C1—N1 | 128.0 (4) | O1—C8—N1 | 127.4 (5) |
C6—C1—N1 | 111.2 (4) | O1—C8—C7 | 126.9 (5) |
C1—C2—C3 | 116.9 (4) | N1—C8—C7 | 105.7 (4) |
C1—C2—H2 | 121.5 | N1—C9—C10 | 114.3 (4) |
C3—C2—H2 | 121.5 | N1—C9—H9A | 108.7 |
C4—C3—C2 | 122.3 (5) | C10—C9—H9A | 108.7 |
C4—C3—H3 | 118.8 | N1—C9—H9B | 108.7 |
C2—C3—H3 | 118.8 | C10—C9—H9B | 108.7 |
C5—C4—C3 | 119.9 (5) | H9A—C9—H9B | 107.6 |
C5—C4—H4 | 120.1 | C9—C10—Br1 | 112.9 (3) |
C3—C4—H4 | 120.1 | C9—C10—H10A | 109.0 |
C4—C5—C6 | 118.6 (5) | Br1—C10—H10A | 109.0 |
C4—C5—H5 | 120.7 | C9—C10—H10B | 109.0 |
C6—C5—H5 | 120.7 | Br1—C10—H10B | 109.0 |
C5—C6—C1 | 121.5 (4) | H10A—C10—H10B | 107.8 |
C5—C6—C7 | 131.3 (5) | ||
C8—N1—C1—C2 | −175.9 (5) | C5—C6—C7—O2 | −0.3 (9) |
C9—N1—C1—C2 | 2.7 (7) | C1—C6—C7—O2 | −178.2 (6) |
C8—N1—C1—C6 | 2.1 (5) | C5—C6—C7—C8 | 178.1 (5) |
C9—N1—C1—C6 | −179.4 (4) | C1—C6—C7—C8 | 0.2 (5) |
C6—C1—C2—C3 | 1.9 (7) | C1—N1—C8—O1 | 175.8 (5) |
N1—C1—C2—C3 | 179.7 (4) | C9—N1—C8—O1 | −2.8 (8) |
C1—C2—C3—C4 | −1.2 (7) | C1—N1—C8—C7 | −1.8 (5) |
C2—C3—C4—C5 | −0.1 (8) | C9—N1—C8—C7 | 179.6 (4) |
C3—C4—C5—C6 | 0.7 (8) | O2—C7—C8—O1 | 2.0 (8) |
C4—C5—C6—C1 | 0.0 (7) | C6—C7—C8—O1 | −176.6 (5) |
C4—C5—C6—C7 | −177.6 (5) | O2—C7—C8—N1 | 179.6 (5) |
C2—C1—C6—C5 | −1.4 (7) | C6—C7—C8—N1 | 1.0 (5) |
N1—C1—C6—C5 | −179.5 (4) | C8—N1—C9—C10 | −107.9 (5) |
C2—C1—C6—C7 | 176.8 (4) | C1—N1—C9—C10 | 73.7 (6) |
N1—C1—C6—C7 | −1.3 (5) | N1—C9—C10—Br1 | 62.0 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1i | 0.93 | 2.41 | 3.286 (6) | 156 |
C10—H10A···O2ii | 0.97 | 2.42 | 3.309 (6) | 151 |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+2, y+1/2, −z+1/2. |
Acknowledgements
NS thanks the Sophisticated Analytical Instrumentation Facility (SAIF), Indian Institute of Technology Madras, India, for help with the data collection and Professor A. Ilangovan, School of Chemistry, Bharathidasan University, India, for fruitful discussions.
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