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

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ISSN: 2056-9890

(S,Z)-1-Chloro-3-[(3,4,5-trimeth­­oxy­benzyl­­idene)amino]­propan-2-ol

aKey Laboratory of Drug Targeting of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China, and bBioengineering College, Xihua University, Chengdu 610039, People's Republic of China
*Correspondence e-mail: wyong@scu.edu.cn

(Received 8 November 2010; accepted 20 December 2010; online 8 January 2011)

In the title compound, C13H18ClNO4, the two meth­oxy groups at the meta positions of the attached benzene ring are close to being coplanar with the ring [the meth­oxy C atoms deviate by 0.267 (7) and 0.059 (7) Å], whereas the third meth­oxy group at the para position is not coplanar with the benzene ring [methoxy C atom deviates by 1.100 (6) Å]. In the crystal, mol­ecules are linked into a chain along the a axis by O—H⋯N hydrogen bonds.

Related literature

The title compound is an inter­mediate for the synthesis of linezolid [systematic name (S)-N{3-[3-fluoro-4-(morpholin-4-yl)phen­yl]-2-oxo-1,3-oxazolidin-5-yl}meth­yl)acetamide], which is currently used in the treatment of serious multi-drug resistant Gram-positive bacterial infections caused by strains of staphylococci, streptococci and enterococci, see: Brickner et al. (1996[Brickner, S. J., Hutchinson, D. K., Barbachyn, M. R., Manninen, P. R., Ulanowicz, D. A., Garmon, S. A., Grega, K. C., Hendges, S. K., Toops, D. S., Ford, C. W. & Zurenko, G. E. (1996). J. Med. Chem. 39, 673-679.]); Perrault et al. (2002[Perrault, W. R., Pearlman, B. A. & Godrej, D. B. (2002). WO Patent 02085849.]). For synthetic procedures, see: Imbordino et al. (2007[Imbordino, R. J., Perrault, W. R. & Reeder, M. R. (2007). WO Patent 116284.]); Zhao et al. (2006[Zhao, X. Y., Ma, Y. R. & Xu, Z. (2006). West China J. Pharm. Sci. 22, 180-181.]).

[Scheme 1]

Experimental

Crystal data
  • C13H18ClNO4

  • Mr = 287.73

  • Orthorhombic, P 21 21 21

  • a = 6.5332 (12) Å

  • b = 8.888 (2) Å

  • c = 25.29 (3) Å

  • V = 1468.7 (16) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.27 mm−1

  • T = 296 K

  • 0.32 × 0.28 × 0.20 mm

Data collection
  • Xcalibur, Eos diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]) Tmin = 0.760, Tmax = 1.0

  • 3967 measured reflections

  • 2695 independent reflections

  • 1599 reflections with I > 2σ(I)

  • Rint = 0.045

Refinement
  • R[F2 > 2σ(F2)] = 0.051

  • wR(F2) = 0.126

  • S = 1.06

  • 2695 reflections

  • 176 parameters

  • H-atom parameters constrained

  • Δρmax = 0.32 e Å−3

  • Δρmin = −0.21 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 931 Friedel pairs

  • Flack parameter: 0.18 (13)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯N1i 0.82 2.08 2.870 (4) 162
Symmetry code: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1].

Data collection: CrysAlis PRO (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]); software used to prepare material for publication: OLEX2.

Supporting information


Comment top

The optically active S,Z-1-chloro-3-(3,4,5-trimethoxybenzylideneamino) propan-2-ol is a key intermediate for synthesizing Linezolid. Linezolid is a potent, synthetic oxazolidinone, which is currently used in the treatment of serious multi-drug resistant Gram-positive bacterial infections caused by strains of staphylococci, streptococci, and enterococci (Brickner et al., 1996; Perrault et al., 2002). Our interests in synthesizing Linezolid prompted us to develop an efficient methodology for synthesizing S,Z-1-chloro-3-(3,4,5-trimethoxybenzylideneamino)propan-2-ol. In our synthetic work, we obtained the title compound, whose spectral data corresponds with that reported in the literature (Imbordino et al., 2007; Zhao et al., 2006). Its crystal structure is reported here. The two methoxy groups at the meta positions are approximately coplanar with the attached benzene ring, and the C(methoxy) atoms, C11 and C13, are -0.2672 (65) and -0.0588 (73) Å from the plane of benzene ring. Whereas the third methoxy group at the para position is not coplanar with the ring, and the distance of the C(methoxy) atom, C12, is -1.1003 (64) Å. An intermolecular O—H···N hydrogen bond is observed. The molecules are linked into a chain along the a axis by O—H···N hydrogen bonds.

Related literature top

The title compound is an intermediate for the synthesis of linezolid [systematic name (S)-N{3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide], which is currently used in the treatment of serious multi-drug resistant Gram-positive bacterial infections caused by strains of staphylococci, streptococci and enterococci, see: Brickner et al. (1996); Perrault et al. (2002). For synthetic procedures, see: Imbordino et al. (2007); Zhao et al. (2006).

Experimental top

To a stirred solution of 3,4,5-trimethoxybenzaldehyde (20.0 g,102 mmol) in 200 ml of methyl tert-butyl ether at room temperature was added concentrated ammonia water (12 ml,161 mmol). After 1 h, to this stirred solution at room temperature was added, dropwise over 20 min, the solution of S-2-(chloromethyl)oxirane (8 ml, 102 mmol) in 200 ml of methyl tert-butyl ether. After 24 h, the organic layer was separated and dried (MgSO4) and then concentrated under reduced pressure. The residue is dispersed in methyl tert-butyl ether, and left to crystallize 17.3 g (yield 58.8%) of S,Z-1-chloro-3-(3,4,5-trimethoxybenzylideneamino)propan-2-ol. Colourless crystals suitable for X-ray analysis were obtained by slow evaporation in methanol at room temperature.

Refinement top

All H atoms were positioned geometrically (C—H = 0.93–0.96 Å) and refined using a riding model, with Uiso(H) = 1.2–1.5Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. A packing diagram for the title compound.
(S,Z)-1-Chloro-3-[(3,4,5-trimethoxybenzylidene)amino]propan-2-ol top
Crystal data top
C13H18ClNO4F(000) = 608
Mr = 287.73Dx = 1.301 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ac 2abCell parameters from 699 reflections
a = 6.5332 (12) Åθ = 3.1–29.2°
b = 8.888 (2) ŵ = 0.27 mm1
c = 25.29 (3) ÅT = 296 K
V = 1468.7 (16) Å3Block, colourless
Z = 40.32 × 0.28 × 0.20 mm
Data collection top
Xcalibur, Eos
diffractometer
2695 independent reflections
Radiation source: Enhance (Mo) X-ray Source1599 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.045
Detector resolution: 16.0874 pixels mm-1θmax = 26.4°, θmin = 3.2°
ω scansh = 88
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction 2009)
k = 116
Tmin = 0.760, Tmax = 1.0l = 2031
3967 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.126 w = 1/[σ2(Fo2) + (0.0534P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2695 reflectionsΔρmax = 0.32 e Å3
176 parametersΔρmin = 0.21 e Å3
0 restraintsAbsolute structure: Flack (1983), 931 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.18 (13)
Crystal data top
C13H18ClNO4V = 1468.7 (16) Å3
Mr = 287.73Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.5332 (12) ŵ = 0.27 mm1
b = 8.888 (2) ÅT = 296 K
c = 25.29 (3) Å0.32 × 0.28 × 0.20 mm
Data collection top
Xcalibur, Eos
diffractometer
2695 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction 2009)
1599 reflections with I > 2σ(I)
Tmin = 0.760, Tmax = 1.0Rint = 0.045
3967 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.126Δρmax = 0.32 e Å3
S = 1.06Δρmin = 0.21 e Å3
2695 reflectionsAbsolute structure: Flack (1983), 931 Friedel pairs
176 parametersAbsolute structure parameter: 0.18 (13)
0 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl11.17509 (19)0.37018 (14)0.54369 (7)0.1140 (6)
O10.8309 (4)0.7058 (3)0.49115 (10)0.0664 (7)
H10.92640.74360.47490.100*
O40.0299 (4)0.9974 (3)0.65900 (10)0.0669 (8)
O20.3609 (4)0.7987 (3)0.80796 (10)0.0644 (7)
O30.0912 (4)0.9855 (3)0.76403 (10)0.0617 (7)
N10.5915 (4)0.6334 (3)0.58064 (11)0.0465 (7)
C11.0430 (6)0.4919 (4)0.49923 (16)0.0734 (12)
H1B1.14170.54730.47820.088*
H1A0.95990.43220.47540.088*
C20.9080 (5)0.6012 (4)0.52862 (13)0.0488 (8)
H20.98930.65460.55530.059*
C30.7283 (5)0.5258 (4)0.55492 (15)0.0522 (9)
H3A0.65190.46960.52860.063*
H3B0.77830.45490.58110.063*
C40.5835 (5)0.6308 (4)0.63124 (14)0.0488 (9)
H40.67020.56400.64850.059*
C50.4496 (5)0.7237 (3)0.66425 (13)0.0395 (8)
C60.4721 (5)0.7140 (4)0.71966 (13)0.0484 (9)
H60.57070.65030.73390.058*
C70.3478 (5)0.7990 (4)0.75334 (14)0.0472 (9)
C80.2026 (5)0.8932 (3)0.73163 (14)0.0465 (8)
C90.1786 (5)0.9004 (4)0.67608 (14)0.0466 (8)
C100.3006 (5)0.8172 (4)0.64293 (14)0.0467 (9)
H100.28350.82340.60650.056*
C110.4771 (6)0.6841 (5)0.83311 (14)0.0685 (11)
H11C0.46680.69520.87080.103*
H11B0.61790.69240.82260.103*
H11A0.42510.58740.82290.103*
C120.0824 (6)0.9189 (5)0.78748 (19)0.0875 (15)
H12C0.14990.99130.80960.131*
H12B0.04070.83420.80840.131*
H12A0.17480.88590.76030.131*
C130.0084 (8)1.0060 (6)0.60329 (18)0.0896 (15)
H13C0.10081.08750.59620.134*
H13A0.06820.91330.59140.134*
H13B0.11811.02300.58490.134*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0817 (7)0.0840 (8)0.1764 (16)0.0268 (7)0.0172 (9)0.0122 (9)
O10.0611 (14)0.0825 (17)0.0555 (17)0.0065 (15)0.0092 (14)0.0266 (15)
O40.0658 (15)0.0730 (18)0.0620 (19)0.0251 (14)0.0078 (15)0.0007 (15)
O20.0800 (18)0.0735 (16)0.0397 (16)0.0194 (15)0.0047 (14)0.0117 (13)
O30.0610 (15)0.0594 (15)0.0647 (17)0.0101 (14)0.0073 (14)0.0150 (13)
N10.0467 (14)0.0528 (16)0.0401 (18)0.0021 (15)0.0038 (14)0.0074 (14)
C10.067 (2)0.070 (3)0.083 (3)0.005 (2)0.023 (2)0.007 (2)
C20.0478 (17)0.057 (2)0.042 (2)0.0037 (17)0.0064 (17)0.0005 (18)
C30.055 (2)0.055 (2)0.046 (2)0.0042 (18)0.0125 (18)0.0002 (18)
C40.0481 (18)0.051 (2)0.047 (2)0.0039 (18)0.0028 (18)0.0086 (18)
C50.0405 (17)0.0397 (17)0.038 (2)0.0011 (15)0.0052 (16)0.0014 (15)
C60.0463 (18)0.0483 (18)0.051 (2)0.0055 (17)0.0026 (18)0.0024 (18)
C70.054 (2)0.0466 (18)0.041 (2)0.0003 (18)0.0017 (18)0.0044 (17)
C80.0449 (17)0.0445 (18)0.050 (2)0.0021 (18)0.0023 (18)0.0055 (18)
C90.0443 (17)0.0461 (19)0.049 (2)0.0012 (19)0.0062 (18)0.0010 (17)
C100.0470 (17)0.0483 (18)0.045 (2)0.0022 (17)0.0018 (17)0.0001 (17)
C110.072 (2)0.087 (3)0.047 (2)0.008 (2)0.002 (2)0.007 (2)
C120.060 (2)0.103 (3)0.100 (4)0.011 (2)0.022 (3)0.005 (3)
C130.094 (3)0.104 (4)0.071 (3)0.039 (3)0.022 (3)0.002 (3)
Geometric parameters (Å, º) top
Cl1—C11.783 (4)C4—C51.464 (5)
O1—H10.8200C5—C61.412 (5)
O1—C21.420 (4)C5—C101.389 (5)
O4—C91.369 (4)C6—H60.9300
O4—C131.433 (5)C6—C71.398 (5)
O2—C71.384 (4)C7—C81.379 (5)
O2—C111.420 (4)C8—C91.415 (5)
O3—C81.369 (4)C9—C101.373 (5)
O3—C121.410 (4)C10—H100.9300
N1—C31.462 (4)C11—H11C0.9600
N1—C41.281 (4)C11—H11B0.9600
C1—H1B0.9700C11—H11A0.9600
C1—H1A0.9700C12—H12C0.9600
C1—C21.508 (5)C12—H12B0.9600
C2—H20.9800C12—H12A0.9600
C2—C31.507 (4)C13—H13C0.9600
C3—H3A0.9700C13—H13A0.9600
C3—H3B0.9700C13—H13B0.9600
C4—H40.9300
Cl1—C1—H1B109.4C2—C3—H3B109.1
Cl1—C1—H1A109.4C3—C2—C1112.7 (3)
O1—C2—C1107.5 (3)C3—C2—H2109.5
O1—C2—H2109.5H3A—C3—H3B107.8
O1—C2—C3108.0 (3)C4—N1—C3117.2 (3)
O4—C9—C8114.9 (3)C5—C4—H4117.1
O4—C9—C10123.9 (3)C5—C6—H6119.6
O4—C13—H13C109.5C5—C10—H10120.3
O4—C13—H13A109.5C6—C5—C4118.0 (3)
O4—C13—H13B109.5C7—O2—C11118.8 (3)
O2—C7—C6124.8 (3)C7—C6—C5120.7 (3)
O2—C11—H11C109.5C7—C6—H6119.6
O2—C11—H11B109.5C7—C8—C9119.9 (3)
O2—C11—H11A109.5C8—O3—C12115.3 (3)
O3—C8—C7119.4 (3)C8—C7—O2116.2 (3)
O3—C8—C9120.6 (3)C8—C7—C6119.0 (3)
O3—C12—H12C109.5C9—O4—C13117.9 (3)
O3—C12—H12B109.5C9—C10—C5119.5 (3)
O3—C12—H12A109.5C9—C10—H10120.3
N1—C3—C2112.5 (3)C10—C5—C4122.3 (3)
N1—C3—H3A109.1C10—C5—C6119.7 (3)
N1—C3—H3B109.1C10—C9—C8121.2 (3)
N1—C4—H4117.1H11C—C11—H11B109.5
N1—C4—C5125.7 (3)H11C—C11—H11A109.5
C1—C2—H2109.5H11B—C11—H11A109.5
H1B—C1—H1A108.0H12C—C12—H12B109.5
C2—O1—H1109.5H12C—C12—H12A109.5
C2—C1—Cl1111.3 (3)H12B—C12—H12A109.5
C2—C1—H1B109.4H13C—C13—H13A109.5
C2—C1—H1A109.4H13C—C13—H13B109.5
C2—C3—H3A109.1H13A—C13—H13B109.5
Cl1—C1—C2—O1172.3 (2)C5—C6—C7—O2178.8 (3)
Cl1—C1—C2—C368.8 (4)C5—C6—C7—C80.2 (5)
O1—C2—C3—N157.9 (4)C6—C5—C10—C90.8 (5)
O4—C9—C10—C5178.9 (3)C6—C7—C8—O3174.9 (3)
O2—C7—C8—O33.9 (4)C6—C7—C8—C91.3 (5)
O2—C7—C8—C9180.0 (3)C7—C8—C9—O4179.9 (3)
O3—C8—C9—O44.0 (4)C7—C8—C9—C101.4 (5)
O3—C8—C9—C10174.8 (3)C8—C9—C10—C50.3 (5)
N1—C4—C5—C6175.3 (3)C10—C5—C6—C70.9 (5)
N1—C4—C5—C106.1 (5)C11—O2—C7—C613.6 (5)
C1—C2—C3—N1176.5 (3)C11—O2—C7—C8167.7 (3)
C3—N1—C4—C5176.9 (3)C12—O3—C8—C784.2 (4)
C4—N1—C3—C2111.9 (3)C12—O3—C8—C999.6 (4)
C4—C5—C6—C7179.5 (3)C13—O4—C9—C8177.6 (4)
C4—C5—C10—C9179.4 (3)C13—O4—C9—C103.7 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N1i0.822.082.870 (4)162
Symmetry code: (i) x+1/2, y+3/2, z+1.

Experimental details

Crystal data
Chemical formulaC13H18ClNO4
Mr287.73
Crystal system, space groupOrthorhombic, P212121
Temperature (K)296
a, b, c (Å)6.5332 (12), 8.888 (2), 25.29 (3)
V3)1468.7 (16)
Z4
Radiation typeMo Kα
µ (mm1)0.27
Crystal size (mm)0.32 × 0.28 × 0.20
Data collection
DiffractometerXcalibur, Eos
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction 2009)
Tmin, Tmax0.760, 1.0
No. of measured, independent and
observed [I > 2σ(I)] reflections
3967, 2695, 1599
Rint0.045
(sin θ/λ)max1)0.625
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.126, 1.06
No. of reflections2695
No. of parameters176
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.32, 0.21
Absolute structureFlack (1983), 931 Friedel pairs
Absolute structure parameter0.18 (13)

Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N1i0.822.082.870 (4)162
Symmetry code: (i) x+1/2, y+3/2, z+1.
 

Acknowledgements

The authors thank the NSFC (81072532) for financial support and Professor Zhihua Mao (Sichuan University) for the X-ray measurements.

References

First citationBrickner, S. J., Hutchinson, D. K., Barbachyn, M. R., Manninen, P. R., Ulanowicz, D. A., Garmon, S. A., Grega, K. C., Hendges, S. K., Toops, D. S., Ford, C. W. & Zurenko, G. E. (1996). J. Med. Chem. 39, 673–679.  CrossRef CAS PubMed Web of Science Google Scholar
First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationImbordino, R. J., Perrault, W. R. & Reeder, M. R. (2007). WO Patent 116284.  Google Scholar
First citationOxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.  Google Scholar
First citationPerrault, W. R., Pearlman, B. A. & Godrej, D. B. (2002). WO Patent 02085849.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZhao, X. Y., Ma, Y. R. & Xu, Z. (2006). West China J. Pharm. Sci. 22, 180–181.  Google Scholar

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COMMUNICATIONS
ISSN: 2056-9890
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