organic compounds
H-benzo[4,5]thiazolo[3,2-a]pyrimidine-3-carboxylate
of ethyl 4-(2,4-dichlorophenyl)-2-methyl-4aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, bInstitution of Excellence, University of Mysore, Manasagangotri, Mysore 570 006, India, and cDepartment of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570 006, India
*Correspondence e-mail: gunaunom@gmail.com
In the title compound, C20H16Cl2N2O2S, the pyrimidine ring has a screw-boat conformation. The attached dichlorophenyl ring is twisted at an angle of 89.29 (13)° with respect to the pyrimidine ring mean plane. The benzothiazole group is approximately planar (r.m.s. deviation = 0.008 Å) and inclined to the pyrimidine ring mean plane by 3.04 (10)°. The carboxylate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the O=C—O—C torsion angle of 3.2 (4) °. In the crystal, molecules are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming slabs lying parallel to (100).
Keywords: crystal structure; pyrimidine; benzothiazole; C—H⋯O hydrogen bonds; C—H⋯N hydrogen bonds.
CCDC reference: 1056200
1. Related literature
For general background and literature on the biological properties of pyrimidine derivatives, see: Kumar et al. (2002; Baraldi et al. (2002); Nasr & Gineinah (2002).
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2008); cell SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009).
Supporting information
CCDC reference: 1056200
https://doi.org/10.1107/S2056989015007033/su5114sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015007033/su5114Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989015007033/su5114Isup3.cml
Many pyrimidine derivatives are reported to have anti-bacterial, anti-tumor and anti-viral activities (Kumar et al., 2012; Baraldi et al., 2002; Nasr et al., 2002). In view of their important properties we synthesized the title compound and report herein on its crystal structure.
The molecular structure of the title compound is shown in Fig. 1. The pyrimidine ring [N1/C13/C12/C11/N10/C2] has a screw-boat conformation and its mean plane is inclined to the planar benzothiazole group [S3/C2/N10/C4—C9; r.m.s. deviation = 0.008 Å] by 3.04 (10) °. The dichlorophenyl ring [C15—C20] is twisted at an angle of 89.29 (13) ° with respect to the pyrimidine ring mean plane. The carboxylate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the torsion angle O24—C23—O25—C26 = 3.2 (4) °.
In the crystal, molecules are linked via C—H···O and C—H···N hydrogen bonds forming slabs lying parallel to (100); see Table 1 and Fig. 2.
A mixture of 2,4-dichloro benzaldehyde was treated with ethyl acetoacetate and 2-aminobenzothiazole in the presence of ammonium acetate in ethanol. The mixture was gently warmed in a water bath at 353 K until the colour changed and it was then kept aside overnight at room temperature. The completion of reaction was monitored by TLC. The solid obtained was separated and purified by means of
using hexane and ethyl acetate as The sample was recrystallized using a 1:1 mixture of ethanol and THF, yielding yellow block-like crystals.Many pyrimidine derivatives are reported to have anti-bacterial, anti-tumor and anti-viral activities (Kumar et al., 2012; Baraldi et al., 2002; Nasr et al., 2002). In view of their important properties we synthesized the title compound and report herein on its crystal structure.
The molecular structure of the title compound is shown in Fig. 1. The pyrimidine ring [N1/C13/C12/C11/N10/C2] has a screw-boat conformation and its mean plane is inclined to the planar benzothiazole group [S3/C2/N10/C4—C9; r.m.s. deviation = 0.008 Å] by 3.04 (10) °. The dichlorophenyl ring [C15—C20] is twisted at an angle of 89.29 (13) ° with respect to the pyrimidine ring mean plane. The carboxylate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the torsion angle O24—C23—O25—C26 = 3.2 (4) °.
In the crystal, molecules are linked via C—H···O and C—H···N hydrogen bonds forming slabs lying parallel to (100); see Table 1 and Fig. 2.
For general background and literature on the biological properties of pyrimidine derivatives, see: Kumar et al. (2002; Baraldi et al. (2002); Nasr & Gineinah (2002).
A mixture of 2,4-dichloro benzaldehyde was treated with ethyl acetoacetate and 2-aminobenzothiazole in the presence of ammonium acetate in ethanol. The mixture was gently warmed in a water bath at 353 K until the colour changed and it was then kept aside overnight at room temperature. The completion of reaction was monitored by TLC. The solid obtained was separated and purified by means of
using hexane and ethyl acetate as The sample was recrystallized using a 1:1 mixture of ethanol and THF, yielding yellow block-like crystals. detailsCrystal data, data collection and structure
details are summarized in Table 2. H atoms were positioned geometrically and allowed to ride on their parent atoms: C—H = 0.93-0.98 Å with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms.Data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).C20H16Cl2N2O2S | F(000) = 1728 |
Mr = 419.31 | Dx = 1.427 Mg m−3 |
Monoclinic, C2/c | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: -C 2yc | Cell parameters from 3114 reflections |
a = 38.654 (8) Å | θ = 5.1–64.1° |
b = 11.787 (3) Å | µ = 4.14 mm−1 |
c = 8.774 (2) Å | T = 296 K |
β = 102.415 (14)° | Block, yellow |
V = 3904.1 (15) Å3 | 0.30 × 0.27 × 0.25 mm |
Z = 8 |
Bruker SMART APEXII CCD diffractometer | 3114 independent reflections |
Radiation source: fine-focus sealed tube | 2519 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.042 |
ω and φ scans | θmax = 64.1°, θmin = 5.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | h = −43→44 |
Tmin = 0.370, Tmax = 0.424 | k = −12→12 |
10089 measured reflections | l = −10→9 |
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)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.139 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0772P)2 + 2.6744P] where P = (Fo2 + 2Fc2)/3 |
3114 reflections | (Δ/σ)max < 0.001 |
246 parameters | Δρmax = 0.36 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
C20H16Cl2N2O2S | V = 3904.1 (15) Å3 |
Mr = 419.31 | Z = 8 |
Monoclinic, C2/c | Cu Kα radiation |
a = 38.654 (8) Å | µ = 4.14 mm−1 |
b = 11.787 (3) Å | T = 296 K |
c = 8.774 (2) Å | 0.30 × 0.27 × 0.25 mm |
β = 102.415 (14)° |
Bruker SMART APEXII CCD diffractometer | 3114 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 2519 reflections with I > 2σ(I) |
Tmin = 0.370, Tmax = 0.424 | Rint = 0.042 |
10089 measured reflections |
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.139 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.36 e Å−3 |
3114 reflections | Δρmin = −0.31 e Å−3 |
246 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.29291 (6) | 0.8365 (2) | 0.6499 (3) | 0.0540 (6) | |
C2 | 0.29669 (6) | 0.7278 (2) | 0.6518 (3) | 0.0450 (6) | |
S3 | 0.267722 (17) | 0.63964 (6) | 0.72345 (9) | 0.0552 (3) | |
C4 | 0.28999 (6) | 0.5193 (2) | 0.6806 (3) | 0.0446 (6) | |
C5 | 0.28233 (7) | 0.4079 (2) | 0.7057 (3) | 0.0520 (7) | |
H5 | 0.2631 | 0.3891 | 0.7488 | 0.062* | |
C6 | 0.30359 (8) | 0.3250 (3) | 0.6658 (4) | 0.0561 (7) | |
H6 | 0.2990 | 0.2492 | 0.6832 | 0.067* | |
C7 | 0.33195 (8) | 0.3533 (2) | 0.5997 (4) | 0.0560 (7) | |
H7 | 0.3460 | 0.2958 | 0.5730 | 0.067* | |
C8 | 0.33984 (7) | 0.4649 (2) | 0.5723 (3) | 0.0484 (7) | |
H8 | 0.3589 | 0.4831 | 0.5276 | 0.058* | |
C9 | 0.31847 (6) | 0.5488 (2) | 0.6136 (3) | 0.0406 (6) | |
N10 | 0.32157 (5) | 0.66662 (18) | 0.5982 (2) | 0.0417 (5) | |
C11 | 0.35145 (6) | 0.7226 (2) | 0.5479 (3) | 0.0411 (6) | |
H11 | 0.3537 | 0.6908 | 0.4474 | 0.049* | |
C12 | 0.34297 (7) | 0.8489 (2) | 0.5275 (3) | 0.0463 (6) | |
C13 | 0.31608 (7) | 0.8979 (2) | 0.5811 (3) | 0.0513 (7) | |
C14 | 0.30725 (9) | 1.0217 (3) | 0.5713 (4) | 0.0694 (9) | |
H14A | 0.3263 | 1.0638 | 0.6345 | 0.104* | |
H14B | 0.2859 | 1.0344 | 0.6084 | 0.104* | |
H14C | 0.3038 | 1.0464 | 0.4649 | 0.104* | |
C15 | 0.38581 (6) | 0.7024 (2) | 0.6676 (3) | 0.0409 (6) | |
C16 | 0.38873 (7) | 0.7454 (2) | 0.8175 (3) | 0.0472 (6) | |
H16 | 0.3695 | 0.7836 | 0.8417 | 0.057* | |
C17 | 0.41907 (8) | 0.7332 (3) | 0.9307 (4) | 0.0608 (8) | |
H17 | 0.4205 | 0.7630 | 1.0300 | 0.073* | |
C18 | 0.44751 (8) | 0.6758 (3) | 0.8946 (4) | 0.0627 (8) | |
C19 | 0.44582 (7) | 0.6332 (3) | 0.7486 (4) | 0.0612 (8) | |
H19 | 0.4651 | 0.5953 | 0.7251 | 0.073* | |
C20 | 0.41531 (7) | 0.6470 (2) | 0.6369 (3) | 0.0491 (7) | |
Cl21 | 0.41503 (2) | 0.59197 (7) | 0.45153 (10) | 0.0706 (3) | |
Cl22 | 0.48585 (3) | 0.65809 (11) | 1.03772 (14) | 0.1075 (4) | |
C23 | 0.36748 (8) | 0.9170 (3) | 0.4592 (3) | 0.0556 (7) | |
O24 | 0.36870 (7) | 1.0189 (2) | 0.4524 (3) | 0.0880 (8) | |
O25 | 0.39033 (6) | 0.8507 (2) | 0.4043 (3) | 0.0734 (7) | |
C26 | 0.41805 (13) | 0.9061 (4) | 0.3433 (5) | 0.1021 (15) | |
H26A | 0.4088 | 0.9754 | 0.2903 | 0.122* | |
H26B | 0.4253 | 0.8568 | 0.2674 | 0.122* | |
C27 | 0.44862 (13) | 0.9328 (5) | 0.4666 (8) | 0.134 (2) | |
H27A | 0.4416 | 0.9836 | 0.5400 | 0.201* | |
H27B | 0.4665 | 0.9682 | 0.4221 | 0.201* | |
H27C | 0.4579 | 0.8642 | 0.5190 | 0.201* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0535 (13) | 0.0408 (15) | 0.0701 (16) | 0.0048 (10) | 0.0185 (12) | −0.0012 (11) |
C2 | 0.0429 (13) | 0.0401 (17) | 0.0513 (15) | 0.0021 (11) | 0.0086 (11) | −0.0025 (12) |
S3 | 0.0456 (4) | 0.0476 (5) | 0.0771 (5) | 0.0017 (3) | 0.0239 (3) | 0.0002 (3) |
C4 | 0.0394 (12) | 0.0424 (17) | 0.0512 (15) | −0.0019 (11) | 0.0077 (11) | 0.0004 (12) |
C5 | 0.0495 (15) | 0.0455 (18) | 0.0619 (17) | −0.0077 (13) | 0.0142 (13) | 0.0038 (13) |
C6 | 0.0656 (18) | 0.0351 (16) | 0.0682 (19) | −0.0063 (13) | 0.0155 (15) | 0.0017 (13) |
C7 | 0.0608 (17) | 0.0400 (18) | 0.0682 (19) | 0.0019 (13) | 0.0163 (15) | −0.0035 (14) |
C8 | 0.0491 (14) | 0.0408 (17) | 0.0574 (17) | −0.0014 (12) | 0.0162 (12) | −0.0049 (13) |
C9 | 0.0420 (13) | 0.0351 (15) | 0.0429 (14) | −0.0045 (11) | 0.0050 (11) | −0.0022 (11) |
N10 | 0.0421 (11) | 0.0343 (13) | 0.0502 (12) | −0.0013 (9) | 0.0136 (10) | −0.0016 (9) |
C11 | 0.0462 (13) | 0.0366 (15) | 0.0432 (14) | −0.0043 (11) | 0.0154 (11) | −0.0037 (11) |
C12 | 0.0538 (15) | 0.0379 (16) | 0.0450 (15) | −0.0023 (11) | 0.0058 (12) | 0.0034 (11) |
C13 | 0.0560 (16) | 0.0381 (16) | 0.0563 (17) | 0.0024 (12) | 0.0044 (13) | 0.0004 (12) |
C14 | 0.075 (2) | 0.0404 (19) | 0.092 (2) | 0.0083 (15) | 0.0153 (18) | 0.0044 (16) |
C15 | 0.0456 (13) | 0.0315 (14) | 0.0479 (14) | −0.0041 (11) | 0.0152 (11) | −0.0003 (11) |
C16 | 0.0526 (14) | 0.0401 (16) | 0.0513 (15) | 0.0009 (12) | 0.0165 (12) | −0.0034 (12) |
C17 | 0.0724 (19) | 0.057 (2) | 0.0495 (17) | −0.0046 (16) | 0.0048 (15) | −0.0073 (14) |
C18 | 0.0493 (16) | 0.063 (2) | 0.070 (2) | −0.0035 (15) | 0.0002 (14) | 0.0069 (16) |
C19 | 0.0433 (15) | 0.057 (2) | 0.085 (2) | 0.0012 (13) | 0.0171 (15) | 0.0003 (17) |
C20 | 0.0490 (14) | 0.0414 (16) | 0.0623 (17) | −0.0040 (12) | 0.0241 (13) | −0.0068 (13) |
Cl21 | 0.0700 (5) | 0.0747 (6) | 0.0771 (5) | −0.0009 (4) | 0.0375 (4) | −0.0252 (4) |
Cl22 | 0.0677 (6) | 0.1307 (10) | 0.1058 (8) | 0.0037 (6) | −0.0221 (5) | 0.0064 (7) |
C23 | 0.0678 (18) | 0.048 (2) | 0.0501 (17) | −0.0049 (14) | 0.0103 (14) | 0.0078 (13) |
O24 | 0.0960 (18) | 0.0479 (16) | 0.127 (2) | −0.0077 (12) | 0.0385 (16) | 0.0245 (14) |
O25 | 0.0905 (16) | 0.0654 (16) | 0.0767 (15) | −0.0168 (12) | 0.0455 (13) | −0.0005 (11) |
C26 | 0.126 (3) | 0.104 (3) | 0.098 (3) | −0.039 (3) | 0.071 (3) | −0.006 (2) |
C27 | 0.088 (3) | 0.143 (5) | 0.182 (6) | −0.025 (3) | 0.050 (4) | −0.008 (4) |
N1—C2 | 1.290 (4) | C14—H14A | 0.9600 |
N1—C13 | 1.387 (4) | C14—H14B | 0.9600 |
C2—N10 | 1.364 (3) | C14—H14C | 0.9600 |
C2—S3 | 1.741 (3) | C15—C20 | 1.390 (3) |
S3—C4 | 1.741 (3) | C15—C16 | 1.392 (4) |
C4—C5 | 1.375 (4) | C16—C17 | 1.372 (4) |
C4—C9 | 1.399 (3) | C16—H16 | 0.9300 |
C5—C6 | 1.369 (4) | C17—C18 | 1.384 (4) |
C5—H5 | 0.9300 | C17—H17 | 0.9300 |
C6—C7 | 1.387 (4) | C18—C19 | 1.365 (5) |
C6—H6 | 0.9300 | C18—Cl22 | 1.737 (3) |
C7—C8 | 1.383 (4) | C19—C20 | 1.371 (4) |
C7—H7 | 0.9300 | C19—H19 | 0.9300 |
C8—C9 | 1.385 (4) | C20—Cl21 | 1.748 (3) |
C8—H8 | 0.9300 | C23—O24 | 1.204 (4) |
C9—N10 | 1.403 (3) | C23—O25 | 1.343 (4) |
N10—C11 | 1.478 (3) | O25—C26 | 1.452 (4) |
C11—C15 | 1.524 (3) | C26—C27 | 1.455 (7) |
C11—C12 | 1.527 (4) | C26—H26A | 0.9700 |
C11—H11 | 0.9800 | C26—H26B | 0.9700 |
C12—C13 | 1.358 (4) | C27—H27A | 0.9600 |
C12—C23 | 1.465 (4) | C27—H27B | 0.9600 |
C13—C14 | 1.497 (4) | C27—H27C | 0.9600 |
C2—N1—C13 | 116.2 (2) | C13—C14—H14B | 109.5 |
N1—C2—N10 | 127.4 (2) | H14A—C14—H14B | 109.5 |
N1—C2—S3 | 121.2 (2) | C13—C14—H14C | 109.5 |
N10—C2—S3 | 111.4 (2) | H14A—C14—H14C | 109.5 |
C4—S3—C2 | 91.26 (12) | H14B—C14—H14C | 109.5 |
C5—C4—C9 | 121.3 (2) | C20—C15—C16 | 116.8 (2) |
C5—C4—S3 | 127.6 (2) | C20—C15—C11 | 124.7 (2) |
C9—C4—S3 | 111.0 (2) | C16—C15—C11 | 118.4 (2) |
C6—C5—C4 | 118.6 (3) | C17—C16—C15 | 121.9 (3) |
C6—C5—H5 | 120.7 | C17—C16—H16 | 119.0 |
C4—C5—H5 | 120.7 | C15—C16—H16 | 119.0 |
C5—C6—C7 | 120.5 (3) | C16—C17—C18 | 118.9 (3) |
C5—C6—H6 | 119.8 | C16—C17—H17 | 120.6 |
C7—C6—H6 | 119.7 | C18—C17—H17 | 120.6 |
C8—C7—C6 | 121.6 (3) | C19—C18—C17 | 121.0 (3) |
C8—C7—H7 | 119.2 | C19—C18—Cl22 | 119.7 (3) |
C6—C7—H7 | 119.2 | C17—C18—Cl22 | 119.3 (3) |
C7—C8—C9 | 117.9 (3) | C18—C19—C20 | 119.2 (3) |
C7—C8—H8 | 121.1 | C18—C19—H19 | 120.4 |
C9—C8—H8 | 121.1 | C20—C19—H19 | 120.4 |
C8—C9—C4 | 120.0 (2) | C19—C20—C15 | 122.2 (3) |
C8—C9—N10 | 127.8 (2) | C19—C20—Cl21 | 117.0 (2) |
C4—C9—N10 | 112.2 (2) | C15—C20—Cl21 | 120.9 (2) |
C2—N10—C9 | 114.1 (2) | O24—C23—O25 | 121.8 (3) |
C2—N10—C11 | 121.4 (2) | O24—C23—C12 | 127.0 (3) |
C9—N10—C11 | 124.0 (2) | O25—C23—C12 | 111.2 (3) |
N10—C11—C15 | 110.2 (2) | C23—O25—C26 | 117.7 (3) |
N10—C11—C12 | 108.0 (2) | O25—C26—C27 | 111.6 (4) |
C15—C11—C12 | 111.5 (2) | O25—C26—H26A | 109.3 |
N10—C11—H11 | 109.0 | C27—C26—H26A | 109.3 |
C15—C11—H11 | 109.0 | O25—C26—H26B | 109.3 |
C12—C11—H11 | 109.0 | C27—C26—H26B | 109.3 |
C13—C12—C23 | 121.3 (3) | H26A—C26—H26B | 108.0 |
C13—C12—C11 | 122.4 (2) | C26—C27—H27A | 109.5 |
C23—C12—C11 | 116.1 (2) | C26—C27—H27B | 109.5 |
C12—C13—N1 | 122.9 (3) | H27A—C27—H27B | 109.5 |
C12—C13—C14 | 125.2 (3) | C26—C27—H27C | 109.5 |
N1—C13—C14 | 111.9 (3) | H27A—C27—H27C | 109.5 |
C13—C14—H14A | 109.5 | H27B—C27—H27C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···N1i | 0.93 | 2.59 | 3.515 (4) | 176 |
C16—H16···O24ii | 0.93 | 2.53 | 3.180 (4) | 128 |
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) x, −y+2, z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···N1i | 0.93 | 2.59 | 3.515 (4) | 176 |
C16—H16···O24ii | 0.93 | 2.53 | 3.180 (4) | 128 |
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) x, −y+2, z+1/2. |
Acknowledgements
The authors are thankful to the Institution of Excellence, University of Mysore, for providing the single-crystal X-ray diffraction facility.
References
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