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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): o1317.
Published online 2008 June 21. doi:  10.1107/S1600536808011616
PMCID: PMC2961724

N-(4-Chloro­phen­yl)-2-de­oxy-α-l-ribo­pyran­osylamine

Abstract

In the crystal structure of the title compound, C11H14ClNO3, inter­molecular hydrogen bonds link mol­ecules in the ab plane, forming layers that stack along the c axis.

Related literature

For related literature, see: Durette et al. (1978 [triangle]); Ganem (1966 [triangle]); Katzen (1979 [triangle]); Bridiau et al. (2007 [triangle]); Ojala et al. (2000 [triangle]).

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Object name is e-64-o1317-scheme1.jpg

Experimental

Crystal data

  • C11H14ClNO3
  • M r = 243.68
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1317-efi1.jpg
  • a = 6.5305 (8) Å
  • b = 7.9857 (9) Å
  • c = 22.496 (3) Å
  • V = 1173.2 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.32 mm−1
  • T = 295 (2) K
  • 0.4 × 0.2 × 0.1 mm

Data collection

  • Bruker P4 diffractometer
  • Absorption correction: none
  • 2581 measured reflections
  • 2172 independent reflections
  • 1690 reflections with I > 2σ(I)
  • R int = 0.025
  • 3 standard reflections every 97 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.084
  • S = 1.03
  • 2172 reflections
  • 147 parameters
  • H-atom parameters constrained
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.17 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 880 Friedel pairs
  • Flack parameter: 0.09 (11)

Data collection: XSCANS (Bruker, 1997 [triangle]); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808011616/pk2090sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808011616/pk2090Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We are grateful to the National Science Foundation of China (project grant No. 20132020).

supplementary crystallographic information

Comment

N-Alkyl and N-aryl glycosylamines have a wide range of biological activities (Katzen et al., 1979; Ganem, 1966), including insulin-like activity (Durette et al., 1978). They are important as junctures in glycoproteins (Ojala et al., 2000). Glycosylamines can exist either in cyclic or acyclic forms depending on reaction conditions and the particular amine used. Stereo-selective syntheses of N-aryl-glycosylamines are uncommon, but a one-pot stereoselective synthesis of beta-N-aryl-glycosides in aqueous buffers with purification by semi-preparative HPLC has been reported (Nicolas et al., 2007).

Recently, we found that 4-chlorobenzenamine reacted with 2-deoxy-L-ribose in methanol and water to give N-p-chlorophenyl-2-deoxy-α-L-ribopyranosylamine as the sole product. Herein we report the synthesis and structure (Fig. 1) of N-p-chlorophenyl-2-deoxy-α-L-ribopyranosylamine.

Experimental

The title compound was synthesized by the reaction of 4-chlorobenzenamine with 2-deoxy-L-ribose in a mixture of methanol and water. 4-chlorobenzenamine (0.93 g, 10 mmol) in a little methanol was added to a solution of 2-deoxy-L-ribose (1.34 g, 10 mmol) in 20 ml water, the solution was stirred at room temperature overnight. A white solid obtained by filtration was washed with ice water, then cold ether, and was dried under pressure. The solid was N-p-chlorophenyl-2-deoxy-α-L-ribopyranosylamine (yield: 70%). 1H NMR (300 MHz, DMSO-d6): δ 1.68 (m, 1H), 1.78 (m, 1H), 3.37 (d, 1H), 3.49 (s, 1H), 3.62 (q, 1H), 3.68 (m, 1H), 4.36 (d, 1H), 4.56 (m, 1H), 4.69 (d, 1H), 6.16 (d, 1H), 6.53 (d, 2H), 6.886 (d, 2H). 13C NMR (300 MHz, DMSO-d6): δ 144.2, 129.2, 125.3, 113.4, 80.3, 68.0, 66.8, 65.7, 34.7, 20.1.

Refinement

H atoms were placed in calculated positions with constrained distances of 0.98 Å (R3CH), 0.97 Å (R2CH2), 0.93 Å (R2CH), 0.82 Å (OH) and 0.9195 Å (NH). Uiso(H) values were set to 1.2Ueq of the attached atom.

Figures

Fig. 1.
View of the title compound, with displacement ellipsoids drawn at the 35% probability level.

Crystal data

C11H14ClNO3F000 = 512
Mr = 243.68Dx = 1.380 Mg m3
Orthorhombic, P212121Mo Kα radiation λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 37 reflections
a = 6.5305 (8) Åθ = 4.9–12.5º
b = 7.9857 (9) ŵ = 0.32 mm1
c = 22.496 (3) ÅT = 295 (2) K
V = 1173.2 (3) Å3Prism, colorless
Z = 40.4 × 0.2 × 0.1 mm

Data collection

Bruker P4 diffractometerRint = 0.026
Radiation source: fine-focus sealed tubeθmax = 25.5º
Monochromator: graphiteθmin = 2.7º
T = 295(2) Kh = −7→7
ω scansk = −9→9
Absorption correction: nonel = −27→27
2581 measured reflections3 standard reflections
2172 independent reflections every 97 reflections
1690 reflections with I > 2σ(I) intensity decay: none

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.037  w = 1/[σ2(Fo2) + (0.005P)2 + 0.4P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.084(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.15 e Å3
2172 reflectionsΔρmin = −0.17 e Å3
147 parametersExtinction correction: none
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 880 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.09 (11)

Special details

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)

xyzUiso*/Ueq
Cl10.01956 (18)−0.12260 (10)0.00675 (4)0.0884 (3)
O10.3998 (2)0.56562 (19)0.16726 (7)0.0425 (4)
O20.2117 (3)1.0211 (2)0.23361 (8)0.0482 (5)
H2C0.28391.10490.23160.058*
O30.5280 (3)0.7894 (2)0.25924 (7)0.0477 (4)
H3B0.54200.87050.28120.057*
N10.0604 (3)0.4754 (3)0.16049 (9)0.0495 (6)
H1B−0.03050.48230.19160.059*
C10.1909 (4)0.6147 (3)0.15314 (11)0.0412 (6)
H1A0.18500.65170.11160.049*
C20.1280 (4)0.7577 (3)0.19294 (12)0.0457 (6)
H2A0.11970.71790.23360.055*
H2B−0.00710.79600.18130.055*
C30.2759 (4)0.9032 (3)0.19013 (10)0.0392 (6)
H3A0.26530.95540.15080.047*
C40.4948 (4)0.8459 (3)0.19940 (10)0.0412 (6)
H4A0.58840.93860.19060.049*
C50.5384 (4)0.7017 (3)0.15789 (11)0.0451 (6)
H5A0.52700.74000.11710.054*
H5B0.67760.66310.16410.054*
C60.0505 (4)0.3402 (3)0.12239 (11)0.0450 (6)
C70.2014 (5)0.3069 (4)0.08000 (12)0.0549 (7)
H7A0.31180.37970.07610.066*
C80.1893 (5)0.1674 (4)0.04379 (12)0.0591 (8)
H8A0.29060.14720.01560.071*
C90.0287 (6)0.0594 (3)0.04936 (11)0.0567 (8)
C10−0.1245 (5)0.0904 (4)0.08970 (12)0.0580 (8)
H10A−0.23480.01720.09280.070*
C11−0.1145 (5)0.2305 (3)0.12566 (12)0.0527 (7)
H11A−0.21980.25180.15250.063*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.1371 (9)0.0575 (4)0.0707 (5)0.0048 (6)−0.0236 (6)−0.0194 (4)
O10.0405 (9)0.0404 (9)0.0464 (9)−0.0016 (8)−0.0010 (8)−0.0021 (8)
O20.0471 (11)0.0378 (10)0.0595 (10)−0.0028 (9)0.0080 (9)−0.0056 (9)
O30.0561 (11)0.0442 (9)0.0429 (9)0.0035 (10)−0.0106 (9)−0.0058 (8)
N10.0488 (13)0.0482 (12)0.0515 (12)−0.0157 (11)0.0108 (11)−0.0106 (11)
C10.0396 (13)0.0424 (13)0.0417 (13)−0.0043 (12)−0.0045 (11)0.0018 (12)
C20.0380 (14)0.0423 (14)0.0568 (15)−0.0025 (11)−0.0008 (12)−0.0025 (13)
C30.0419 (14)0.0359 (13)0.0399 (12)0.0022 (11)−0.0002 (11)0.0037 (11)
C40.0392 (14)0.0423 (13)0.0422 (12)−0.0042 (12)0.0011 (11)0.0017 (10)
C50.0415 (14)0.0480 (13)0.0457 (13)−0.0077 (13)0.0025 (12)−0.0025 (12)
C60.0501 (15)0.0422 (13)0.0427 (13)−0.0043 (13)−0.0031 (12)0.0007 (11)
C70.0566 (17)0.0569 (17)0.0513 (15)−0.0107 (16)0.0078 (15)−0.0060 (14)
C80.073 (2)0.0582 (18)0.0464 (15)0.0010 (18)0.0044 (15)−0.0038 (14)
C90.085 (2)0.0446 (14)0.0408 (13)0.0014 (17)−0.0127 (16)−0.0011 (12)
C100.0685 (19)0.0525 (17)0.0529 (16)−0.0179 (16)−0.0067 (15)0.0033 (15)
C110.0533 (16)0.0551 (17)0.0497 (15)−0.0173 (15)0.0028 (14)−0.0034 (14)

Geometric parameters (Å, °)

Cl1—C91.742 (3)C3—H3A0.9800
O1—C51.430 (3)C4—C51.510 (3)
O1—C11.454 (3)C4—H4A0.9800
O2—C31.421 (3)C5—H5A0.9700
O2—H2C0.8200C5—H5B0.9700
O3—C41.436 (3)C6—C111.391 (4)
O3—H3B0.8200C6—C71.397 (4)
N1—C61.380 (3)C7—C81.382 (4)
N1—C11.411 (3)C7—H7A0.9300
N1—H1B0.9195C8—C91.364 (4)
C1—C21.508 (3)C8—H8A0.9300
C1—H1A0.9800C9—C101.373 (4)
C2—C31.512 (3)C10—C111.382 (4)
C2—H2A0.9700C10—H10A0.9300
C2—H2B0.9700C11—H11A0.9300
C3—C41.515 (3)
C5—O1—C1110.91 (18)O3—C4—H4A109.4
C3—O2—H2C109.5C5—C4—H4A109.4
C4—O3—H3B109.5C3—C4—H4A109.4
C6—N1—C1124.9 (2)O1—C5—C4111.7 (2)
C6—N1—H1B119.3O1—C5—H5A109.3
C1—N1—H1B115.6C4—C5—H5A109.3
N1—C1—O1109.19 (19)O1—C5—H5B109.3
N1—C1—C2111.3 (2)C4—C5—H5B109.3
O1—C1—C2109.23 (19)H5A—C5—H5B107.9
N1—C1—H1A109.0N1—C6—C11119.7 (2)
O1—C1—H1A109.0N1—C6—C7122.7 (2)
C2—C1—H1A109.0C11—C6—C7117.6 (2)
C1—C2—C3112.6 (2)C8—C7—C6121.0 (3)
C1—C2—H2A109.1C8—C7—H7A119.5
C3—C2—H2A109.1C6—C7—H7A119.5
C1—C2—H2B109.1C9—C8—C7120.0 (3)
C3—C2—H2B109.1C9—C8—H8A120.0
H2A—C2—H2B107.8C7—C8—H8A120.0
O2—C3—C2107.00 (19)C8—C9—C10120.5 (3)
O2—C3—C4112.6 (2)C8—C9—Cl1120.2 (2)
C2—C3—C4111.4 (2)C10—C9—Cl1119.3 (2)
O2—C3—H3A108.6C9—C10—C11119.9 (3)
C2—C3—H3A108.6C9—C10—H10A120.1
C4—C3—H3A108.6C11—C10—H10A120.1
O3—C4—C5108.14 (19)C10—C11—C6121.0 (3)
O3—C4—C3111.5 (2)C10—C11—H11A119.5
C5—C4—C3108.8 (2)C6—C11—H11A119.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2C···O3i0.821.932.739 (2)170
O3—H3B···O1i0.821.982.797 (2)175
N1—H1B···O2ii0.922.082.994 (3)173

Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PK2090).

References

  • Bridiau, N., Benmansour, M., Legoy, M. D. & Maugard, T. (2007). Tetrahedron, 63 4178–4183.
  • Bruker (1997). XSCANS Bruker AXS Inc.,Madison, Wisconsin, USA.
  • Durette, P. L., Bugianesi, R. L., Ponpipom, M. M., Shen, T. Y., Cascieri, M. A., Glitzer, M. S. & Katzen, H. M. (1978). J. Med. Chem.21, 854–859. [PubMed]
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Ganem, B. (1966). Acc. Chem. Res.29, 340–347.
  • Katzen, H. M. (1979). J. Biol. Chem.254, 2983–2992. [PubMed]
  • Ojala, W. H., Oatman, J. M. & Ojala, C. R. (2000). Carbohydr. Res.326, 104–112. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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