organic compounds
(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
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); Perrault et al. (2002). For synthetic procedures, see: Imbordino et al. (2007); Zhao et al. (2006).
Experimental
Crystal data
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Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell CrysAlis PRO; data reduction: CrysAlis PRO; 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.
Supporting information
10.1107/S1600536810053420/rn2076sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810053420/rn2076Isup2.hkl
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.
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).
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
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).Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level. | |
Fig. 2. A packing diagram for the title compound. |
C13H18ClNO4 | F(000) = 608 |
Mr = 287.73 | Dx = 1.301 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.7107 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 699 reflections |
a = 6.5332 (12) Å | θ = 3.1–29.2° |
b = 8.888 (2) Å | µ = 0.27 mm−1 |
c = 25.29 (3) Å | T = 296 K |
V = 1468.7 (16) Å3 | Block, colourless |
Z = 4 | 0.32 × 0.28 × 0.20 mm |
Xcalibur, Eos diffractometer | 2695 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 1599 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.045 |
Detector resolution: 16.0874 pixels mm-1 | θmax = 26.4°, θmin = 3.2° |
ω scans | h = −8→8 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction 2009) | k = −11→6 |
Tmin = 0.760, Tmax = 1.0 | l = −20→31 |
3967 measured 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)] = 0.051 | H-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 reflections | Δρmax = 0.32 e Å−3 |
176 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 931 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.18 (13) |
C13H18ClNO4 | V = 1468.7 (16) Å3 |
Mr = 287.73 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 6.5332 (12) Å | µ = 0.27 mm−1 |
b = 8.888 (2) Å | T = 296 K |
c = 25.29 (3) Å | 0.32 × 0.28 × 0.20 mm |
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 = 1.0 | Rint = 0.045 |
3967 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | H-atom parameters constrained |
wR(F2) = 0.126 | Δρmax = 0.32 e Å−3 |
S = 1.06 | Δρmin = −0.21 e Å−3 |
2695 reflections | Absolute structure: Flack (1983), 931 Friedel pairs |
176 parameters | Absolute structure parameter: 0.18 (13) |
0 restraints |
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 | ||
Cl1 | 1.17509 (19) | 0.37018 (14) | 0.54369 (7) | 0.1140 (6) | |
O1 | 0.8309 (4) | 0.7058 (3) | 0.49115 (10) | 0.0664 (7) | |
H1 | 0.9264 | 0.7436 | 0.4749 | 0.100* | |
O4 | 0.0299 (4) | 0.9974 (3) | 0.65900 (10) | 0.0669 (8) | |
O2 | 0.3609 (4) | 0.7987 (3) | 0.80796 (10) | 0.0644 (7) | |
O3 | 0.0912 (4) | 0.9855 (3) | 0.76403 (10) | 0.0617 (7) | |
N1 | 0.5915 (4) | 0.6334 (3) | 0.58064 (11) | 0.0465 (7) | |
C1 | 1.0430 (6) | 0.4919 (4) | 0.49923 (16) | 0.0734 (12) | |
H1B | 1.1417 | 0.5473 | 0.4782 | 0.088* | |
H1A | 0.9599 | 0.4322 | 0.4754 | 0.088* | |
C2 | 0.9080 (5) | 0.6012 (4) | 0.52862 (13) | 0.0488 (8) | |
H2 | 0.9893 | 0.6546 | 0.5553 | 0.059* | |
C3 | 0.7283 (5) | 0.5258 (4) | 0.55492 (15) | 0.0522 (9) | |
H3A | 0.6519 | 0.4696 | 0.5286 | 0.063* | |
H3B | 0.7783 | 0.4549 | 0.5811 | 0.063* | |
C4 | 0.5835 (5) | 0.6308 (4) | 0.63124 (14) | 0.0488 (9) | |
H4 | 0.6702 | 0.5640 | 0.6485 | 0.059* | |
C5 | 0.4496 (5) | 0.7237 (3) | 0.66425 (13) | 0.0395 (8) | |
C6 | 0.4721 (5) | 0.7140 (4) | 0.71966 (13) | 0.0484 (9) | |
H6 | 0.5707 | 0.6503 | 0.7339 | 0.058* | |
C7 | 0.3478 (5) | 0.7990 (4) | 0.75334 (14) | 0.0472 (9) | |
C8 | 0.2026 (5) | 0.8932 (3) | 0.73163 (14) | 0.0465 (8) | |
C9 | 0.1786 (5) | 0.9004 (4) | 0.67608 (14) | 0.0466 (8) | |
C10 | 0.3006 (5) | 0.8172 (4) | 0.64293 (14) | 0.0467 (9) | |
H10 | 0.2835 | 0.8234 | 0.6065 | 0.056* | |
C11 | 0.4771 (6) | 0.6841 (5) | 0.83311 (14) | 0.0685 (11) | |
H11C | 0.4668 | 0.6952 | 0.8708 | 0.103* | |
H11B | 0.6179 | 0.6924 | 0.8226 | 0.103* | |
H11A | 0.4251 | 0.5874 | 0.8229 | 0.103* | |
C12 | −0.0824 (6) | 0.9189 (5) | 0.78748 (19) | 0.0875 (15) | |
H12C | −0.1499 | 0.9913 | 0.8096 | 0.131* | |
H12B | −0.0407 | 0.8342 | 0.8084 | 0.131* | |
H12A | −0.1748 | 0.8859 | 0.7603 | 0.131* | |
C13 | −0.0084 (8) | 1.0060 (6) | 0.60329 (18) | 0.0896 (15) | |
H13C | −0.1008 | 1.0875 | 0.5962 | 0.134* | |
H13A | −0.0682 | 0.9133 | 0.5914 | 0.134* | |
H13B | 0.1181 | 1.0230 | 0.5849 | 0.134* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0817 (7) | 0.0840 (8) | 0.1764 (16) | 0.0268 (7) | 0.0172 (9) | 0.0122 (9) |
O1 | 0.0611 (14) | 0.0825 (17) | 0.0555 (17) | 0.0065 (15) | 0.0092 (14) | 0.0266 (15) |
O4 | 0.0658 (15) | 0.0730 (18) | 0.0620 (19) | 0.0251 (14) | −0.0078 (15) | 0.0007 (15) |
O2 | 0.0800 (18) | 0.0735 (16) | 0.0397 (16) | 0.0194 (15) | −0.0047 (14) | −0.0117 (13) |
O3 | 0.0610 (15) | 0.0594 (15) | 0.0647 (17) | 0.0101 (14) | 0.0073 (14) | −0.0150 (13) |
N1 | 0.0467 (14) | 0.0528 (16) | 0.0401 (18) | 0.0021 (15) | 0.0038 (14) | 0.0074 (14) |
C1 | 0.067 (2) | 0.070 (3) | 0.083 (3) | −0.005 (2) | 0.023 (2) | −0.007 (2) |
C2 | 0.0478 (17) | 0.057 (2) | 0.042 (2) | −0.0037 (17) | 0.0064 (17) | −0.0005 (18) |
C3 | 0.055 (2) | 0.055 (2) | 0.046 (2) | −0.0042 (18) | 0.0125 (18) | 0.0002 (18) |
C4 | 0.0481 (18) | 0.051 (2) | 0.047 (2) | 0.0039 (18) | 0.0028 (18) | 0.0086 (18) |
C5 | 0.0405 (17) | 0.0397 (17) | 0.038 (2) | −0.0011 (15) | 0.0052 (16) | 0.0014 (15) |
C6 | 0.0463 (18) | 0.0483 (18) | 0.051 (2) | 0.0055 (17) | −0.0026 (18) | 0.0024 (18) |
C7 | 0.054 (2) | 0.0466 (18) | 0.041 (2) | −0.0003 (18) | −0.0017 (18) | −0.0044 (17) |
C8 | 0.0449 (17) | 0.0445 (18) | 0.050 (2) | −0.0021 (18) | 0.0023 (18) | −0.0055 (18) |
C9 | 0.0443 (17) | 0.0461 (19) | 0.049 (2) | −0.0012 (19) | −0.0062 (18) | 0.0010 (17) |
C10 | 0.0470 (17) | 0.0483 (18) | 0.045 (2) | 0.0022 (17) | 0.0018 (17) | 0.0001 (17) |
C11 | 0.072 (2) | 0.087 (3) | 0.047 (2) | 0.008 (2) | −0.002 (2) | 0.007 (2) |
C12 | 0.060 (2) | 0.103 (3) | 0.100 (4) | 0.011 (2) | 0.022 (3) | −0.005 (3) |
C13 | 0.094 (3) | 0.104 (4) | 0.071 (3) | 0.039 (3) | −0.022 (3) | 0.002 (3) |
Cl1—C1 | 1.783 (4) | C4—C5 | 1.464 (5) |
O1—H1 | 0.8200 | C5—C6 | 1.412 (5) |
O1—C2 | 1.420 (4) | C5—C10 | 1.389 (5) |
O4—C9 | 1.369 (4) | C6—H6 | 0.9300 |
O4—C13 | 1.433 (5) | C6—C7 | 1.398 (5) |
O2—C7 | 1.384 (4) | C7—C8 | 1.379 (5) |
O2—C11 | 1.420 (4) | C8—C9 | 1.415 (5) |
O3—C8 | 1.369 (4) | C9—C10 | 1.373 (5) |
O3—C12 | 1.410 (4) | C10—H10 | 0.9300 |
N1—C3 | 1.462 (4) | C11—H11C | 0.9600 |
N1—C4 | 1.281 (4) | C11—H11B | 0.9600 |
C1—H1B | 0.9700 | C11—H11A | 0.9600 |
C1—H1A | 0.9700 | C12—H12C | 0.9600 |
C1—C2 | 1.508 (5) | C12—H12B | 0.9600 |
C2—H2 | 0.9800 | C12—H12A | 0.9600 |
C2—C3 | 1.507 (4) | C13—H13C | 0.9600 |
C3—H3A | 0.9700 | C13—H13A | 0.9600 |
C3—H3B | 0.9700 | C13—H13B | 0.9600 |
C4—H4 | 0.9300 | ||
Cl1—C1—H1B | 109.4 | C2—C3—H3B | 109.1 |
Cl1—C1—H1A | 109.4 | C3—C2—C1 | 112.7 (3) |
O1—C2—C1 | 107.5 (3) | C3—C2—H2 | 109.5 |
O1—C2—H2 | 109.5 | H3A—C3—H3B | 107.8 |
O1—C2—C3 | 108.0 (3) | C4—N1—C3 | 117.2 (3) |
O4—C9—C8 | 114.9 (3) | C5—C4—H4 | 117.1 |
O4—C9—C10 | 123.9 (3) | C5—C6—H6 | 119.6 |
O4—C13—H13C | 109.5 | C5—C10—H10 | 120.3 |
O4—C13—H13A | 109.5 | C6—C5—C4 | 118.0 (3) |
O4—C13—H13B | 109.5 | C7—O2—C11 | 118.8 (3) |
O2—C7—C6 | 124.8 (3) | C7—C6—C5 | 120.7 (3) |
O2—C11—H11C | 109.5 | C7—C6—H6 | 119.6 |
O2—C11—H11B | 109.5 | C7—C8—C9 | 119.9 (3) |
O2—C11—H11A | 109.5 | C8—O3—C12 | 115.3 (3) |
O3—C8—C7 | 119.4 (3) | C8—C7—O2 | 116.2 (3) |
O3—C8—C9 | 120.6 (3) | C8—C7—C6 | 119.0 (3) |
O3—C12—H12C | 109.5 | C9—O4—C13 | 117.9 (3) |
O3—C12—H12B | 109.5 | C9—C10—C5 | 119.5 (3) |
O3—C12—H12A | 109.5 | C9—C10—H10 | 120.3 |
N1—C3—C2 | 112.5 (3) | C10—C5—C4 | 122.3 (3) |
N1—C3—H3A | 109.1 | C10—C5—C6 | 119.7 (3) |
N1—C3—H3B | 109.1 | C10—C9—C8 | 121.2 (3) |
N1—C4—H4 | 117.1 | H11C—C11—H11B | 109.5 |
N1—C4—C5 | 125.7 (3) | H11C—C11—H11A | 109.5 |
C1—C2—H2 | 109.5 | H11B—C11—H11A | 109.5 |
H1B—C1—H1A | 108.0 | H12C—C12—H12B | 109.5 |
C2—O1—H1 | 109.5 | H12C—C12—H12A | 109.5 |
C2—C1—Cl1 | 111.3 (3) | H12B—C12—H12A | 109.5 |
C2—C1—H1B | 109.4 | H13C—C13—H13A | 109.5 |
C2—C1—H1A | 109.4 | H13C—C13—H13B | 109.5 |
C2—C3—H3A | 109.1 | H13A—C13—H13B | 109.5 |
Cl1—C1—C2—O1 | 172.3 (2) | C5—C6—C7—O2 | −178.8 (3) |
Cl1—C1—C2—C3 | −68.8 (4) | C5—C6—C7—C8 | −0.2 (5) |
O1—C2—C3—N1 | −57.9 (4) | C6—C5—C10—C9 | 0.8 (5) |
O4—C9—C10—C5 | 178.9 (3) | C6—C7—C8—O3 | −174.9 (3) |
O2—C7—C8—O3 | 3.9 (4) | C6—C7—C8—C9 | 1.3 (5) |
O2—C7—C8—C9 | −180.0 (3) | C7—C8—C9—O4 | 179.9 (3) |
O3—C8—C9—O4 | −4.0 (4) | C7—C8—C9—C10 | −1.4 (5) |
O3—C8—C9—C10 | 174.8 (3) | C8—C9—C10—C5 | 0.3 (5) |
N1—C4—C5—C6 | −175.3 (3) | C10—C5—C6—C7 | −0.9 (5) |
N1—C4—C5—C10 | 6.1 (5) | C11—O2—C7—C6 | −13.6 (5) |
C1—C2—C3—N1 | −176.5 (3) | C11—O2—C7—C8 | 167.7 (3) |
C3—N1—C4—C5 | −176.9 (3) | C12—O3—C8—C7 | −84.2 (4) |
C4—N1—C3—C2 | −111.9 (3) | C12—O3—C8—C9 | 99.6 (4) |
C4—C5—C6—C7 | −179.5 (3) | C13—O4—C9—C8 | −177.6 (4) |
C4—C5—C10—C9 | 179.4 (3) | C13—O4—C9—C10 | 3.7 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···N1i | 0.82 | 2.08 | 2.870 (4) | 162 |
Symmetry code: (i) x+1/2, −y+3/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C13H18ClNO4 |
Mr | 287.73 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 296 |
a, b, c (Å) | 6.5332 (12), 8.888 (2), 25.29 (3) |
V (Å3) | 1468.7 (16) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.27 |
Crystal size (mm) | 0.32 × 0.28 × 0.20 |
Data collection | |
Diffractometer | Xcalibur, Eos diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction 2009) |
Tmin, Tmax | 0.760, 1.0 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3967, 2695, 1599 |
Rint | 0.045 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.126, 1.06 |
No. of reflections | 2695 |
No. of parameters | 176 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.32, −0.21 |
Absolute structure | Flack (1983), 931 Friedel pairs |
Absolute structure parameter | 0.18 (13) |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···N1i | 0.82 | 2.08 | 2.870 (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
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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.