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Crystal structure of 4-(4b,8a-di­hydro-9H-pyrido[3,4-b]indol-1-yl)-7-methyl-2H-chromen-2-one

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aDepartment of Chemistry, Karnatak University, Dharwad, India, and bDepartment of Physics, M. S. Ramaiah Institute of Technology, Bangalore, India
*Correspondence e-mail: anilgn@msrit.edu

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 4 December 2016; accepted 10 December 2016; online 1 January 2017)

The title compound, C21H14N2O2, was prepared by Pictet–Spengler cyclization of tryptamine and 4-formyl coumarin. In the mol­ecule, the dihedral angle between the mean planes of the coumarin and β-carboline ring systems is 63.8 (2)°. In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming chains along the b-axis direction. Within the chains, there are a number of offset ππ inter­actions present [shortest inter­centroid distance = 3.457 (2) Å].

1. Chemical context

Naturally occurring coumarins (Murry, 2002[Murry, R. D. H. (2002). The Naturally Occurring Coumarins, in Progress in the Chemistry of Organic Natural Products. Vienna: Springer-Verlag.]) and their deriv­atives have a vast number of applications in different areas. They are precursor reagents for synthetic anti-coagulants (Bairagi et al., 2012[Bairagi, S. H., Salaskar, P. P., Loke, S. D., Surve, N. N., Tandel, D. V. & Dusara, M. D. (2012). Int. J. Pharm. Res. 4, 16-19.]), the most notable being warfarin (Holbrook et al., 2005[Holbrook, A. M., Pereira, J. A., Labiris, R., McDonald, H., Douketis, J. D., Crowther, M. & Wells, P. S. (2005). Arch. Intern. Med. 165, 1095-1106.]). Coumarin dyes are also widely used in blue–green organic dyes (Schafer, 1990[Schafer, F. P. (1990). Editor. Dye Lasers, 3rd ed. Berlin: Springer-Verlag.]; Duarte & Hillman, 1990[Duarte, F. J. & Hillman, L. W. (1990). In Dye Laser Principles. New York: Academic Press.]; Duarte, 2003[Duarte, F. J. (2003). In Tunable Laser Optics, Appendix of Laser Dyes. New York: Elsevier Academic.]) and in OLED emitters (Duarte et al., 2005[Duarte, F. J., Liao, L. S. & Vaeth, K. M. (2005). Opt. Lett. 30, 3072-3074.]). Norharman is a β-carboline alkaloid which has the basic structural unit for a wide range of naturally occurring compounds, and is found in plants, animals and humans (Fekkes et al., 1992[Fekkes, D., Schouten, M. J., Pepplinkhuizen, L., Bruinvels, J., Lauwers, W. & Brinkman, U. A. (1992). Lancet, 339, 506.]). They are used widely as neurotoxins to Parkinson's disease (Kuhn et al., 1996[Kuhn, W., Müller, T., Groβe, H. & Rommelspacher, H. (1996). J. Neural Transm. 103, 1435-1440.]) and as mediators in the mutagenesis of DNA in the presence of another mol­ecule (Mori et al., 1996[Mori, M., Totsuka, Y., Fukutome, K., Yoshida, T., Sugimura, T. & Wakabayashi, K. (1996). Carcinogenesis, 17, 1499-1503.]). Given the ongoing research into the biological functions of norharman and the many related β-carboline derivatives, a single-crystal X-ray structure of norharman would be of use in theoretical modelling and related structural work. Norharman exhibits a one-dimensional herringbone motif (Thatcher & Douthwaite, 2011[Thatcher, R. J. & Douthwaite, R. E. (2011). Acta Cryst. C67, o241-o243.]). Due to their extensive natural occurrence and common biological origin, there are no reports on compounds which contain these two systems in a single mol­ecule. It was hence thought of considerable biological inter­est to synthesize new mol­ecules which contain both β-carboline and coumarin ring systems.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The coumarin (r.m.s. deviation = 0.019 Å) and β-carboline (r.m.s. deviation = 0.034 Å) ring systems exhibit an s-trans arrangement across the bridging C7—C6 bond; their mean planes are inclined to one another by 63.8 (2)°.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling and displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming chains along [010]; see Table 1[link] and Fig. 2[link]. Within the chains there are a number of offset ππ inter­actions present; the shortest inter­centroid distance of 3.457 (2) Å, involves rings N2/C18–C20/C22 of the β-carboline ring system and O1/C1–C3/C8/C9 of the coumarin system.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯N1i 0.86 2.47 2.994 (3) 120
Symmetry code: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A view along the a axis of the crystal packing of the title compound. The N—H⋯N hydrogen bonds are shown as dashed lines (see Table 1[link]), and the shortest offset ππ inter­actions by a double-headed arrow. For clarity, only H atom H2 (grey ball) has been included.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.37, last update May 2016; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) using 4,7-dimethyl-2H-chromen-2-one as the main skeleton revealed the presence of 66 structures. However, only six of these structures contain the 7-methyl-4-phenyl-2H-chromen-2-one nucleus (refcodes: BUFQUQ, FINNEX, GUFTUY, IFUMED, LENYIO, DUVVIB). There were no structures reported for a search of 7-methyl-4-(pyridin-2-yl)-2H-chromen-2-one skeleton.

5. Synthesis and crystallization

Acetic acid (10 ml) was added drop wise, at 273 K, to a mixture of tryptamine (1 eq) and 4-formyl coumarin (1 eq). The reaction mixture was stirred at room temperature for ca 12 h. After completion of the reaction, the solid that separated was filtered, washed several times with water and dried (yield >70%) to give the inter­mediate. This inter­mediate compound (1 eq) was taken in 10 ml of dry chloro­form and 2,3-di­chloro-5,6-di­cyano-1,4-benzo­quinone (2 eq) was added at inter­vals of 5 min in cold conditions, 273 K. Stirring was continued for ca 10 h. The reaction mixture was then quenched using aqueous sodium bicarbonate and extracted with chloro­form. The organic layer was washed 2–3 times with sodium bicarbonate, water and brine solution, dried using sodium sulfate, and concentrated to afford the crude title product. It was purified by flash chromatography using 230–400 mesh silica-gels (35% ethyl acetate in hexane mixture; yield 75%). The solid obtained was recrystallized from dichloromethane, giving colourless block-like crystals of the title compound on slow evaporation of the solvent

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms were positioned geometrically, with N—H = 0.86 Å and C—H = 0.93–0.96 Å, and constrained to ride on their parent atoms with Uiso(H) = 1.5Ueq(C-meth­yl) and 1.2Ueq(C,N) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula C21H14N2O2
Mr 326.34
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 10.6784 (8), 8.0954 (6), 17.9032 (14)
β (°) 98.105 (5)
V3) 1532.2 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.20 × 0.15 × 0.10
 
Data collection
Diffractometer Bruker SMART CCD area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2012[Bruker (2012). SMART, SAINT and SADABS. Bruker AXS Inc, Madison, Wisconsin, USA.])
Tmin, Tmax 0.941, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections 11601, 2848, 1446
Rint 0.059
(sin θ/λ)max−1) 0.606
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.060, 0.166, 0.94
No. of reflections 2848
No. of parameters 227
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.21, −0.27
Computer programs: SMART and SAINT (Bruker, 2012[Bruker (2012). SMART, SAINT and SADABS. Bruker AXS Inc, Madison, Wisconsin, USA.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows and WinGX (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

Data collection: SMART (Bruker, 2012); cell refinement: SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 2012) and PLATON (Spek, 2009).

4-(4b,8a-Dihydro-9H-pyrido[3,4-b]indol-1-yl)-7-methyl-2H-chromen-2-one top
Crystal data top
C21H14N2O2F(000) = 680
Mr = 326.34Dx = 1.415 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1990 reflections
a = 10.6784 (8) Åθ = 3.3–26.4°
b = 8.0954 (6) ŵ = 0.09 mm1
c = 17.9032 (14) ÅT = 296 K
β = 98.105 (5)°Block, colourless
V = 1532.2 (2) Å30.20 × 0.15 × 0.10 mm
Z = 4
Data collection top
Bruker SMART CCD area-detector
diffractometer
2848 independent reflections
Radiation source: fine-focus sealed tube1446 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.059
ω and φ scansθmax = 25.5°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2012)
h = 1211
Tmin = 0.941, Tmax = 0.971k = 99
11601 measured reflectionsl = 2121
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.060Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.166H-atom parameters constrained
S = 0.94 w = 1/[σ2(Fo2) + (0.0799P)2]
where P = (Fo2 + 2Fc2)/3
2848 reflections(Δ/σ)max < 0.001
227 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = 0.27 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.85044 (16)0.1787 (2)0.24656 (10)0.0445 (6)
O20.87191 (18)0.3169 (3)0.35363 (12)0.0602 (7)
N10.3818 (2)0.2835 (3)0.17822 (12)0.0413 (7)
N20.4360 (2)0.0447 (3)0.35591 (12)0.0407 (7)
H20.51490.02590.37070.049*
C10.7990 (3)0.2565 (4)0.30347 (17)0.0429 (8)
C20.6635 (2)0.2570 (3)0.29733 (15)0.0427 (8)
H2A0.62640.30550.33590.051*
C30.5878 (2)0.1912 (3)0.23877 (15)0.0341 (7)
C40.5774 (3)0.0283 (4)0.11849 (15)0.0401 (8)
H40.48950.02730.11260.048*
C50.6389 (3)0.0500 (4)0.06608 (15)0.0459 (8)
H50.59210.10470.02580.055*
C60.7705 (3)0.0486 (4)0.07241 (15)0.0427 (8)
C70.8384 (3)0.0291 (4)0.13369 (15)0.0431 (8)
H70.92630.03020.13950.052*
C80.6443 (2)0.1088 (3)0.18005 (15)0.0353 (7)
C90.7754 (2)0.1051 (4)0.18637 (15)0.0370 (7)
C100.8380 (3)0.1277 (4)0.01293 (17)0.0635 (10)
H10A0.9240.15090.03390.095*
H10B0.83690.05370.02910.095*
H10C0.79610.22870.00380.095*
C110.4475 (2)0.2009 (4)0.23601 (15)0.0356 (7)
C120.2541 (3)0.2974 (4)0.17666 (16)0.0464 (8)
H120.20930.35810.13760.056*
C130.1874 (3)0.2280 (4)0.22862 (17)0.0449 (8)
H130.10.23880.22420.054*
C140.1087 (3)0.0115 (4)0.37782 (19)0.0542 (9)
H140.03210.04820.35190.065*
C150.1115 (3)0.0820 (4)0.44170 (19)0.0595 (10)
H150.03610.11070.45870.071*
C160.2255 (3)0.1345 (4)0.48153 (18)0.0589 (9)
H160.22480.19610.52530.071*
C170.3403 (3)0.0978 (4)0.45785 (16)0.0489 (9)
H170.41660.13290.48470.059*
C180.2223 (3)0.0506 (4)0.35234 (15)0.0411 (8)
C190.3358 (3)0.0063 (4)0.39225 (15)0.0403 (7)
C200.2544 (2)0.1410 (3)0.28810 (16)0.0370 (7)
C220.3865 (2)0.1313 (3)0.29183 (15)0.0342 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0319 (11)0.0588 (15)0.0433 (12)0.0005 (10)0.0069 (9)0.0029 (11)
O20.0450 (13)0.0760 (18)0.0575 (14)0.0050 (12)0.0001 (11)0.0134 (13)
N10.0356 (14)0.0428 (17)0.0454 (15)0.0022 (12)0.0056 (11)0.0007 (13)
N20.0321 (13)0.0503 (18)0.0406 (14)0.0004 (12)0.0083 (11)0.0003 (13)
C10.0423 (18)0.044 (2)0.0434 (18)0.0038 (16)0.0090 (15)0.0018 (16)
C20.0376 (17)0.049 (2)0.0419 (18)0.0018 (15)0.0083 (14)0.0027 (16)
C30.0332 (15)0.0306 (19)0.0397 (16)0.0001 (13)0.0086 (13)0.0041 (14)
C40.0372 (16)0.043 (2)0.0409 (17)0.0026 (15)0.0071 (13)0.0029 (15)
C50.048 (2)0.048 (2)0.0419 (18)0.0040 (16)0.0066 (15)0.0008 (16)
C60.055 (2)0.037 (2)0.0376 (17)0.0076 (16)0.0135 (15)0.0056 (15)
C70.0359 (16)0.049 (2)0.0468 (18)0.0071 (15)0.0150 (14)0.0058 (16)
C80.0385 (17)0.0310 (19)0.0373 (16)0.0013 (14)0.0086 (13)0.0032 (14)
C90.0311 (16)0.041 (2)0.0393 (17)0.0008 (14)0.0060 (13)0.0051 (15)
C100.070 (2)0.071 (3)0.054 (2)0.0156 (19)0.0223 (17)0.0037 (19)
C110.0333 (16)0.036 (2)0.0382 (16)0.0008 (14)0.0086 (13)0.0025 (14)
C120.0383 (18)0.050 (2)0.0500 (19)0.0041 (16)0.0011 (15)0.0005 (16)
C130.0320 (16)0.045 (2)0.058 (2)0.0013 (15)0.0074 (15)0.0065 (17)
C140.0461 (19)0.048 (2)0.074 (2)0.0008 (17)0.0276 (17)0.0005 (19)
C150.064 (2)0.051 (2)0.073 (2)0.0048 (19)0.0414 (19)0.001 (2)
C160.078 (2)0.049 (2)0.056 (2)0.006 (2)0.0313 (19)0.0005 (18)
C170.059 (2)0.041 (2)0.0487 (19)0.0011 (17)0.0127 (16)0.0001 (16)
C180.0375 (17)0.037 (2)0.0509 (19)0.0006 (15)0.0157 (14)0.0048 (16)
C190.0418 (17)0.0379 (19)0.0440 (18)0.0030 (15)0.0157 (14)0.0038 (15)
C200.0310 (16)0.036 (2)0.0445 (17)0.0027 (14)0.0093 (13)0.0075 (15)
C220.0324 (16)0.033 (2)0.0372 (17)0.0017 (13)0.0059 (13)0.0078 (14)
Geometric parameters (Å, º) top
O1—C11.377 (3)C8—C91.389 (3)
O1—C91.383 (3)C10—H10A0.96
O2—C11.206 (3)C10—H10B0.96
N1—C111.344 (3)C10—H10C0.96
N1—C121.365 (3)C11—C221.388 (3)
N2—C221.384 (3)C12—C131.369 (4)
N2—C191.391 (3)C12—H120.93
N2—H20.86C13—C201.388 (4)
C1—C21.435 (4)C13—H130.93
C2—C31.341 (3)C14—C151.368 (4)
C2—H2A0.93C14—C181.392 (4)
C3—C81.447 (3)C14—H140.93
C3—C111.494 (3)C15—C161.388 (4)
C4—C51.374 (4)C15—H150.93
C4—C81.388 (3)C16—C171.385 (4)
C4—H40.93C16—H160.93
C5—C61.394 (4)C17—C191.384 (4)
C5—H50.93C17—H170.93
C6—C71.379 (4)C18—C191.396 (4)
C6—C101.510 (4)C18—C201.445 (4)
C7—C91.378 (4)C20—C221.405 (3)
C7—H70.93
C1—O1—C9121.7 (2)H10A—C10—H10C109.5
C11—N1—C12117.9 (2)H10B—C10—H10C109.5
C22—N2—C19108.0 (2)N1—C11—C22120.6 (2)
C22—N2—H2126N1—C11—C3117.7 (2)
C19—N2—H2126C22—C11—C3121.7 (2)
O2—C1—O1117.0 (3)C13—C12—N1124.5 (3)
O2—C1—C2126.4 (3)C13—C12—H12117.8
O1—C1—C2116.6 (3)N1—C12—H12117.8
C3—C2—C1123.3 (3)C12—C13—C20117.9 (3)
C3—C2—H2A118.4C12—C13—H13121
C1—C2—H2A118.4C20—C13—H13121
C2—C3—C8119.0 (2)C15—C14—C18118.8 (3)
C2—C3—C11119.7 (3)C15—C14—H14120.6
C8—C3—C11121.3 (2)C18—C14—H14120.6
C5—C4—C8121.1 (3)C14—C15—C16120.9 (3)
C5—C4—H4119.4C14—C15—H15119.6
C8—C4—H4119.4C16—C15—H15119.6
C4—C5—C6121.0 (3)C17—C16—C15121.8 (3)
C4—C5—H5119.5C17—C16—H16119.1
C6—C5—H5119.5C15—C16—H16119.1
C7—C6—C5118.6 (3)C16—C17—C19116.6 (3)
C7—C6—C10120.3 (3)C16—C17—H17121.7
C5—C6—C10121.0 (3)C19—C17—H17121.7
C6—C7—C9119.7 (3)C14—C18—C19119.5 (3)
C6—C7—H7120.1C14—C18—C20133.8 (3)
C9—C7—H7120.1C19—C18—C20106.7 (2)
C9—C8—C4117.0 (3)C17—C19—N2128.3 (3)
C9—C8—C3118.0 (2)C17—C19—C18122.3 (3)
C4—C8—C3124.9 (2)N2—C19—C18109.4 (2)
C7—C9—O1116.1 (2)C13—C20—C22118.0 (3)
C7—C9—C8122.5 (3)C13—C20—C18135.5 (3)
O1—C9—C8121.4 (2)C22—C20—C18106.4 (2)
C6—C10—H10A109.5C11—C22—N2129.7 (2)
C6—C10—H10B109.5C11—C22—C20120.9 (3)
H10A—C10—H10B109.5N2—C22—C20109.4 (2)
C6—C10—H10C109.5
C9—O1—C1—O2179.9 (2)C11—N1—C12—C132.4 (4)
C9—O1—C1—C20.2 (4)N1—C12—C13—C201.7 (4)
O2—C1—C2—C3178.1 (3)C18—C14—C15—C161.3 (5)
O1—C1—C2—C32.2 (4)C14—C15—C16—C171.2 (5)
C1—C2—C3—C82.8 (4)C15—C16—C17—C190.2 (4)
C1—C2—C3—C11178.5 (3)C15—C14—C18—C190.1 (4)
C8—C4—C5—C61.1 (4)C15—C14—C18—C20178.5 (3)
C4—C5—C6—C71.8 (4)C16—C17—C19—N2179.0 (3)
C4—C5—C6—C10177.1 (3)C16—C17—C19—C181.6 (4)
C5—C6—C7—C90.9 (4)C22—N2—C19—C17179.2 (3)
C10—C6—C7—C9178.0 (3)C22—N2—C19—C181.3 (3)
C5—C4—C8—C90.5 (4)C14—C18—C19—C171.6 (4)
C5—C4—C8—C3178.6 (3)C20—C18—C19—C17179.7 (3)
C2—C3—C8—C91.4 (4)C14—C18—C19—N2178.9 (3)
C11—C3—C8—C9179.8 (2)C20—C18—C19—N20.1 (3)
C2—C3—C8—C4176.6 (3)C12—C13—C20—C220.7 (4)
C11—C3—C8—C42.2 (4)C12—C13—C20—C18179.2 (3)
C6—C7—C9—O1179.3 (2)C14—C18—C20—C132.6 (6)
C6—C7—C9—C80.8 (4)C19—C18—C20—C13178.9 (3)
C1—O1—C9—C7179.1 (2)C14—C18—C20—C22177.4 (3)
C1—O1—C9—C81.0 (4)C19—C18—C20—C221.1 (3)
C4—C8—C9—C71.5 (4)N1—C11—C22—N2178.8 (2)
C3—C8—C9—C7179.7 (2)C3—C11—C22—N20.5 (4)
C4—C8—C9—O1178.6 (2)N1—C11—C22—C202.0 (4)
C3—C8—C9—O10.4 (4)C3—C11—C22—C20179.7 (2)
C12—N1—C11—C220.4 (4)C19—N2—C22—C11177.3 (3)
C12—N1—C11—C3177.9 (2)C19—N2—C22—C202.0 (3)
C2—C3—C11—N1118.4 (3)C13—C20—C22—C112.5 (4)
C8—C3—C11—N162.9 (3)C18—C20—C22—C11177.4 (2)
C2—C3—C11—C2260.0 (4)C13—C20—C22—N2178.1 (2)
C8—C3—C11—C22118.8 (3)C18—C20—C22—N21.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N1i0.862.472.994 (3)120
Symmetry code: (i) x+1, y1/2, z+1/2.
 

Acknowledgements

SS acknowledges Karnatak University for the data collection and support.

References

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