organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 7| July 2011| Pages o1714-o1715

N′-[(E)-2-Meth­­oxy­benzyl­­idene]pyrazine-2-carbohydrazide

aFundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos – Farmanguinhos, R. Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, RJ, Brazil, bCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil, cCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland, and dDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: edward.tiekink@gmail.com

(Received 13 June 2011; accepted 13 June 2011; online 18 June 2011)

In the title compound, C13H12N4O2, all the non-H atoms lie on a crystallographic mirror plane and an intra­molecular N—H⋯N hydrogen bond generates an S(5) ring; the conformation about the imine bond [1.280 (3) Å] is E. In the crystal, mol­ecules assemble into a two-dimensional array via C—H⋯O(carbon­yl) and C—H⋯N(pyrazine) contacts. Layers stack along the b-axis direction via weak ππ inter­actions between pyrazine rings [ring centroid distance = 3.8028 (8) Å].

Related literature

For background to the anti-mycobacterial activity of pyrazin­amide derivatives, see: Chaisson et al. (2002[Chaisson, R. E., Armstrong, J., Stafford, J., Golub, J. & Bur, S. (2002). J. Am. Med. Assoc. 288, 165-166.]); Gordin et al. (2000[Gordin, F., Chaisson, R. E., Matts, J. P., Miller, C., Garcia, M. de L., Hafner, R., Valdespino, J. L., Coberly, J., Schechter, M., Klukowicz, A. J., Barry, M. A. & O'Brien, R. J. (2000). J. Am. Med. Assoc. 283, 1445-1450.]); de Souza (2006[Souza, M. V. N. de (2006). Rec. Pat. Anti. Infect. Drug Disc, 1, 33-45.]); Pinheiro et al. (2007[Pinheiro, A. C., Kaiser, C. R., Lourenco, M. C. S., De Souza, M. V. N., Wardell, J. L. & Wardell, S. M. S. V. (2007). J. Chem. Res. pp. 180-184.]). For related structures of pyrazine­carbonyl­hydrazones, see: Baddeley et al. (2009[Baddeley, T. C., Howie, R. A., Lima, C. H. da S., Kaiser, C. R., de Souza, M. V. N., Wardell, J. L. & Wardell, S. M. S. V. (2009). Z. Kristallogr. 224, 506-514.]); Howie et al. (2010a[Howie, R. A., Lima, C. H. S., Kaiser, C. R., de Souza, M. V. N., Wardell, J. L. & Wardell, S. M. S. V. (2010a). Z. Kristallogr. 225, 245-252.],b[Howie, R. A., Lima, C. H. S., Kaiser, C. R., de Souza, M. V. N., Wardell, J. L. & Wardell, S. M. S. V. (2010b). Z. Kristallogr. 225, 349-358.]).

[Scheme 1]

Experimental

Crystal data
  • C13H12N4O2

  • Mr = 256.27

  • Monoclinic, P 21 /m

  • a = 7.7615 (6) Å

  • b = 6.4257 (4) Å

  • c = 12.2480 (9) Å

  • β = 93.893 (3)°

  • V = 609.44 (8) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 120 K

  • 0.46 × 0.24 × 0.01 mm

Data collection
  • Nonius KappaCCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2007[Sheldrick, G. M. (2007). SADABS. University of Göttingen, Germany.]) Tmin = 0.594, Tmax = 0.746

  • 7850 measured reflections

  • 1481 independent reflections

  • 1032 reflections with I > 2σ(I)

  • Rint = 0.074

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.147

  • S = 1.03

  • 1481 reflections

  • 122 parameters

  • 4 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.31 e Å−3

  • Δρmin = −0.29 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3n⋯N1 0.88 (2) 2.27 (2) 2.685 (3) 109 (2)
C2—H2⋯O1i 0.95 2.57 3.160 (3) 121
C3—H3⋯O1i 0.95 2.44 3.103 (3) 127
C9—H9⋯N2ii 0.95 2.56 3.437 (3) 153
Symmetry codes: (i) x+1, y, z; (ii) x-1, y, z-1.

Data collection: COLLECT (Hooft, 1998[Hooft, R. W. W. (1998). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]), DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

Pyrazinamide has well known anti-mycobacterial activity and it is the one of the most important drugs used in tuberculosis treatment (Chaisson et al., 2002; Gordin et al., 2000; de Souza, 2006). Various derivatives have been prepared and their anti-tuberculosis properties studied (Pinheiro et al., 2007). Among the reported crystal structures of pyrazinamide derivatives are those of pyrazinecarbonylhydrazones (Baddeley et al., 2009; Howie et al. 2010a, 2010b). In continuation of previous work, we now wish to report on the crystal structure of the title compound, (I).

All non-hydrogen atoms in (I) lie on a crystallographic mirror plane, Fig. 1. The formation of intramolecular N3—H···N1 and C6—H···O2 contacts, Table 1, contributes to the stability of the planar conformation. The configuration about the N4C6 bond [1.280 (3) Å] is E. The most prominent contacts in the crystal packing are of the type C—H···O and C—H···N, Table 1. The C—H···O contacts lead to chains along the a direction and involve the bifurcated carbonyl-O1 atom. Chains are linked in the c direction by C—H···N2(pyrazinyl) contacts with the result that a two-dimensional array is formed in the ac plane, Fig. 2. Layers stack along the b direction stabilized by weak ππ interactions formed between pyrazinyl rings [ring centroid(N1,N2,C1–C4)···ring centroid(N1,N2,C1—C4)i = 3.8028 (8) Å for i: 1 - x, -1/2 + y, 2 - z], Fig. 3.

Related literature top

For background to the anti-mycobacterial activity of pyrazinamide derivatives, see: Chaisson et al. (2002); Gordin et al. (2000); de Souza (2006); Pinheiro et al. (2007). For related structures of pyrazinecarbonylhydrazones, see: Baddeley et al. (2009); Howie et al. (2010a,b).

Experimental top

Solutions of 2-pyrazinehydrazide (0.72 mmol) in water (10 ml), and 2-methoxybenzaldehyde (0.79 mmol) in ethanol (10 ml) were mixed and the reaction mixture was stirred at ambient temperature, until TLC indicated reaction was complete. The solvent was removed under reduced pressure and the residue was washed with cold diethyl ether (30 ml) and recrystallized from ethanol to yield colourless plates of (I). Yield: 52%; M.pt.: 453–454 K. 1H NMR (400 MHz, DMSO-d6) δ: 12.35 (1H, s, NH), 9.26 (1H, s, H3), 9.00 (1H, s, H6), 8.92 (1H, s, H5), 8.80 (1H, s, NCH), 7.91 (1H, d, J=7.5 Hz, H60), 7.45 (1H, t, J=7.5, H40), 7.12 (1H, d, J=7.5 Hz, H3'), 7.04 (1H, t, J=7.5 Hz, H5'), 3.87 (3H, s, OCH3) p.p.m.. 13C NMR (100 MHz, DMSO-d6) δ: 160.5, 148.8, 148.2, 144.7, 144.4, 143.7, 133.5, 133.2, 132.2, 128.4, 127.8, 124.1, 55.4 p.p.m. MS/ESI: [M—H]: 255. IR (KBr pellets): \v 3300 (N—H); 1680 (CO) cm-1.

Refinement top

The C-bound H atoms were geometrically placed (C—H = 0.95–0.98 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The N-bound atom was refined with N—H = 0.88±0.01 Å, and with Uiso(H) = 1.2Ueq(N). One reflection, i.e. (011), was omitted from the final refinement owing to poor agreement.

Computing details top

Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997), DIAMOND (Brandenburg, 2006); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing displacement ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. View of the supramolecular array in the ac plane in the crystal structure of (I). The C—H···O and C—H···N contacts are shown as orange and blue dashed lines, respectively.
[Figure 3] Fig. 3. A view in projection down the b axis of the unit-cell contents of (I) with the C—H···N contacts shown as blue dashed lines.
N'-[(E)-2-Methoxybenzylidene]pyrazine-2-carbohydrazide top
Crystal data top
C13H12N4O2F(000) = 268
Mr = 256.27Dx = 1.397 Mg m3
Monoclinic, P21/mMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybCell parameters from 6063 reflections
a = 7.7615 (6) Åθ = 2.9–27.5°
b = 6.4257 (4) ŵ = 0.10 mm1
c = 12.2480 (9) ÅT = 120 K
β = 93.893 (3)°Plate, colourless
V = 609.44 (8) Å30.46 × 0.24 × 0.01 mm
Z = 2
Data collection top
Nonius KappaCCD area-detector
diffractometer
1481 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode1032 reflections with I > 2σ(I)
10 cm confocal mirrors monochromatorRint = 0.074
Detector resolution: 9.091 pixels mm-1θmax = 27.4°, θmin = 3.0°
ϕ and ω scansh = 99
Absorption correction: multi-scan
(SADABS; Sheldrick, 2007)
k = 88
Tmin = 0.594, Tmax = 0.746l = 1415
7850 measured reflections
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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.147H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.087P)2]
where P = (Fo2 + 2Fc2)/3
1481 reflections(Δ/σ)max = 0.006
122 parametersΔρmax = 0.31 e Å3
4 restraintsΔρmin = 0.29 e Å3
Crystal data top
C13H12N4O2V = 609.44 (8) Å3
Mr = 256.27Z = 2
Monoclinic, P21/mMo Kα radiation
a = 7.7615 (6) ŵ = 0.10 mm1
b = 6.4257 (4) ÅT = 120 K
c = 12.2480 (9) Å0.46 × 0.24 × 0.01 mm
β = 93.893 (3)°
Data collection top
Nonius KappaCCD area-detector
diffractometer
1481 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2007)
1032 reflections with I > 2σ(I)
Tmin = 0.594, Tmax = 0.746Rint = 0.074
7850 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0524 restraints
wR(F2) = 0.147H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.31 e Å3
1481 reflectionsΔρmin = 0.29 e Å3
122 parameters
Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.1276 (2)0.25000.91441 (14)0.0329 (5)
O20.0786 (2)0.25000.36159 (13)0.0288 (5)
N10.5591 (2)0.25000.83175 (16)0.0220 (5)
N20.6293 (3)0.25001.06050 (16)0.0240 (5)
N30.2321 (2)0.25000.74474 (15)0.0200 (5)
H3N0.327 (2)0.25000.7099 (19)0.024*
N40.0712 (2)0.25000.68916 (15)0.0193 (4)
C10.4324 (3)0.25000.90152 (18)0.0185 (5)
C20.7208 (3)0.25000.87780 (19)0.0227 (5)
H20.81480.25000.83200.027*
C30.7549 (3)0.25000.99078 (19)0.0235 (5)
H30.87170.25001.01950.028*
C40.4676 (3)0.25001.01421 (18)0.0206 (5)
H40.37380.25001.06020.025*
C50.2483 (3)0.25000.85506 (18)0.0199 (5)
C60.0729 (3)0.25000.58476 (18)0.0210 (5)
H60.18030.25000.55190.025*
C70.0876 (3)0.25000.51541 (19)0.0203 (5)
C80.0819 (3)0.25000.40041 (19)0.0214 (5)
C90.2344 (3)0.25000.3333 (2)0.0265 (6)
H90.23040.25000.25600.032*
C100.3910 (3)0.25000.3800 (2)0.0362 (7)
H100.49490.25000.33430.043*
C110.3992 (3)0.25000.4929 (2)0.0440 (8)
H110.50780.25000.52430.053*
C120.2482 (3)0.25000.5589 (2)0.0325 (6)
H120.25420.25000.63610.039*
C130.088612 (1)0.25000.244660 (1)0.0341 (6)
H13A0.21080.25000.22920.051*
H13B0.03280.37540.21350.051*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0181 (9)0.0612 (11)0.0196 (9)0.0000.0021 (7)0.000
O20.0280 (10)0.0415 (10)0.0168 (9)0.0000.0011 (7)0.000
N10.0167 (10)0.0290 (10)0.0200 (10)0.0000.0011 (8)0.000
N20.0238 (11)0.0287 (10)0.0190 (11)0.0000.0020 (8)0.000
N30.0144 (10)0.0297 (10)0.0154 (10)0.0000.0028 (7)0.000
N40.0164 (10)0.0217 (9)0.0191 (10)0.0000.0041 (8)0.000
C10.0175 (12)0.0199 (11)0.0180 (12)0.0000.0003 (9)0.000
C20.0170 (11)0.0301 (12)0.0207 (12)0.0000.0017 (9)0.000
C30.0166 (12)0.0312 (12)0.0221 (13)0.0000.0039 (10)0.000
C40.0192 (12)0.0261 (11)0.0164 (11)0.0000.0002 (9)0.000
C50.0176 (12)0.0234 (11)0.0184 (12)0.0000.0004 (9)0.000
C60.0205 (12)0.0227 (11)0.0194 (12)0.0000.0008 (9)0.000
C70.0218 (12)0.0200 (11)0.0182 (11)0.0000.0049 (9)0.000
C80.0257 (13)0.0188 (11)0.0192 (12)0.0000.0015 (9)0.000
C90.0339 (14)0.0244 (12)0.0195 (12)0.0000.0102 (11)0.000
C100.0234 (13)0.0512 (16)0.0317 (15)0.0000.0145 (11)0.000
C110.0200 (14)0.079 (2)0.0323 (16)0.0000.0017 (12)0.000
C120.0262 (14)0.0484 (15)0.0227 (13)0.0000.0003 (11)0.000
C130.0406 (16)0.0459 (15)0.0160 (13)0.0000.0030 (11)0.000
Geometric parameters (Å, º) top
O1—C51.224 (3)C4—H40.9500
O2—C81.363 (3)C6—C71.459 (3)
O2—C131.4395 (16)C6—H60.9500
N1—C21.341 (3)C7—C121.388 (3)
N1—C11.346 (3)C7—C81.412 (3)
N2—C31.339 (3)C8—C91.394 (3)
N2—C41.342 (3)C9—C101.378 (4)
N3—C51.348 (3)C9—H90.9500
N3—N41.381 (2)C10—C111.388 (4)
N3—H3N0.875 (10)C10—H100.9500
N4—C61.280 (3)C11—C121.377 (4)
C1—C41.389 (3)C11—H110.9500
C1—C51.502 (3)C12—H120.9500
C2—C31.391 (3)C13—H13A0.9800
C2—H20.9500C13—H13B0.9800
C3—H30.9500
C8—O2—C13117.35 (16)N4—C6—H6119.5
C2—N1—C1115.86 (19)C7—C6—H6119.5
C3—N2—C4115.54 (19)C12—C7—C8118.2 (2)
C5—N3—N4120.89 (17)C12—C7—C6122.0 (2)
C5—N3—H3N117.6 (17)C8—C7—C6119.8 (2)
N4—N3—H3N121.5 (17)O2—C8—C9123.6 (2)
C6—N4—N3114.97 (17)O2—C8—C7116.0 (2)
N1—C1—C4121.9 (2)C9—C8—C7120.3 (2)
N1—C1—C5118.47 (19)C10—C9—C8119.5 (2)
C4—C1—C5119.63 (19)C10—C9—H9120.2
N1—C2—C3121.9 (2)C8—C9—H9120.2
N1—C2—H2119.1C9—C10—C11121.0 (2)
C3—C2—H2119.1C9—C10—H10119.5
N2—C3—C2122.5 (2)C11—C10—H10119.5
N2—C3—H3118.8C12—C11—C10119.3 (2)
C2—C3—H3118.8C12—C11—H11120.4
N2—C4—C1122.4 (2)C10—C11—H11120.4
N2—C4—H4118.8C11—C12—C7121.7 (2)
C1—C4—H4118.8C11—C12—H12119.1
O1—C5—N3124.9 (2)C7—C12—H12119.1
O1—C5—C1121.5 (2)O2—C13—H13A108.1
N3—C5—C1113.65 (18)O2—C13—H13B109.6
N4—C6—C7121.02 (19)H13A—C13—H13B109.4
C5—N3—N4—C6180.0N4—C6—C7—C120.0
C2—N1—C1—C40.000 (1)N4—C6—C7—C8180.0
C2—N1—C1—C5180.0C13—O2—C8—C90.0
C1—N1—C2—C30.000 (1)C13—O2—C8—C7180.0
C4—N2—C3—C20.000 (1)C12—C7—C8—O2180.0
N1—C2—C3—N20.000 (1)C6—C7—C8—O20.0
C3—N2—C4—C10.000 (1)C12—C7—C8—C90.0
N1—C1—C4—N20.000 (1)C6—C7—C8—C9180.0
C5—C1—C4—N2180.0O2—C8—C9—C10180.0
N4—N3—C5—O10.0C7—C8—C9—C100.0
N4—N3—C5—C1180.0C8—C9—C10—C110.0
N1—C1—C5—O1180.0C9—C10—C11—C120.0
C4—C1—C5—O10.0C10—C11—C12—C70.0
N1—C1—C5—N30.0C8—C7—C12—C110.0
C4—C1—C5—N3180.0C6—C7—C12—C11180.0
N3—N4—C6—C7180.0
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3n···N10.88 (2)2.27 (2)2.685 (3)109 (2)
C2—H2···O1i0.952.573.160 (3)121
C3—H3···O1i0.952.443.103 (3)127
C9—H9···N2ii0.952.563.437 (3)153
Symmetry codes: (i) x+1, y, z; (ii) x1, y, z1.

Experimental details

Crystal data
Chemical formulaC13H12N4O2
Mr256.27
Crystal system, space groupMonoclinic, P21/m
Temperature (K)120
a, b, c (Å)7.7615 (6), 6.4257 (4), 12.2480 (9)
β (°) 93.893 (3)
V3)609.44 (8)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.46 × 0.24 × 0.01
Data collection
DiffractometerNonius KappaCCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2007)
Tmin, Tmax0.594, 0.746
No. of measured, independent and
observed [I > 2σ(I)] reflections
7850, 1481, 1032
Rint0.074
(sin θ/λ)max1)0.647
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.147, 1.03
No. of reflections1481
No. of parameters122
No. of restraints4
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.31, 0.29

Computer programs: , DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), DIAMOND (Brandenburg, 2006), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3n···N10.882 (18)2.27 (2)2.685 (3)108.9 (19)
C2—H2···O1i0.952.573.160 (3)121
C3—H3···O1i0.952.443.103 (3)127
C9—H9···N2ii0.952.563.437 (3)153
Symmetry codes: (i) x+1, y, z; (ii) x1, y, z1.
 

Footnotes

Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.

Acknowledgements

The use of the EPSRC X-ray crystallographic service at the University of Southampton, England, and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from CAPES (Brazil).

References

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Volume 67| Part 7| July 2011| Pages o1714-o1715
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