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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

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

aKey Laboratory for Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China, and bDepartment of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
*Correspondence e-mail: shangpeihua05@mail.tsinghua.org.cn

(Received 19 March 2008; accepted 23 April 2008; online 21 June 2008)

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[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.]); Ganem (1966[Ganem, B. (1966). Acc. Chem. Res. 29, 340-347.]); Katzen (1979[Katzen, H. M. (1979). J. Biol. Chem. 254, 2983-2992.]); Bridiau et al. (2007[Bridiau, N., Benmansour, M., Legoy, M. D. & Maugard, T. (2007). Tetrahedron, 63. 4178-4183.]); Ojala et al. (2000[Ojala, W. H., Oatman, J. M. & Ojala, C. R. (2000). Carbohydr. Res. 326, 104-112.]).

[Scheme 1]

Experimental

Crystal data
  • C11H14ClNO3

  • Mr = 243.68

  • Orthorhombic, P 21 21 21

  • 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)

  • Rint = 0.025

  • 3 standard reflections every 97 reflections intensity decay: none

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 880 Friedel pairs

  • Flack parameter: 0.09 (11)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2C⋯O3i 0.82 1.93 2.739 (2) 170
O3—H3B⋯O1i 0.82 1.98 2.797 (2) 175
N1—H1B⋯O2ii 0.92 2.08 2.994 (3) 173
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: XSCANS (Bruker, 1997[Bruker (1997). XSCANS. Bruker AXS Inc.,Madison, Wisconsin, USA.]); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. View of the title compound, with displacement ellipsoids drawn at the 35% probability level.
N-(4-Chlorophenyl)-2-deoxy-α-L-ribopyranosylamine top
Crystal data top
C11H14ClNO3F(000) = 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 = 4.9–12.5°
b = 7.9857 (9) ŵ = 0.32 mm1
c = 22.496 (3) ÅT = 295 K
V = 1173.2 (3) Å3Prism, colorless
Z = 40.4 × 0.2 × 0.1 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.026
Radiation source: fine-focus sealed tubeθmax = 25.5°, θmin = 2.7°
Graphite monochromatorh = 77
ω scansk = 99
2581 measured reflectionsl = 2727
2172 independent reflections3 standard reflections every 97 reflections
1690 reflections with I > 2σ(I) intensity decay: none
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)] = 0.037H-atom parameters constrained
wR(F2) = 0.084 w = 1/[σ2(Fo2) + (0.005P)2 + 0.4P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
2172 reflectionsΔρmax = 0.15 e Å3
147 parametersΔρmin = 0.17 e Å3
0 restraintsAbsolute structure: Flack (1983), 880 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.09 (11)
Crystal data top
C11H14ClNO3V = 1173.2 (3) Å3
Mr = 243.68Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.5305 (8) ŵ = 0.32 mm1
b = 7.9857 (9) ÅT = 295 K
c = 22.496 (3) Å0.4 × 0.2 × 0.1 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.026
2581 measured reflections3 standard reflections every 97 reflections
2172 independent reflections intensity decay: none
1690 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.084Δρmax = 0.15 e Å3
S = 1.03Δρmin = 0.17 e Å3
2172 reflectionsAbsolute structure: Flack (1983), 880 Friedel pairs
147 parametersAbsolute structure parameter: 0.09 (11)
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
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)
H1B0.03050.48230.19160.059*
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*
H2B0.00710.79600.18130.055*
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)
C100.1245 (5)0.0904 (4)0.08970 (12)0.0580 (8)
H10A0.23480.01720.09280.070*
C110.1145 (5)0.2305 (3)0.12566 (12)0.0527 (7)
H11A0.21980.25180.15250.063*
Atomic displacement parameters (Å2) top
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, º) top
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, º) top
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, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H14ClNO3
Mr243.68
Crystal system, space groupOrthorhombic, P212121
Temperature (K)295
a, b, c (Å)6.5305 (8), 7.9857 (9), 22.496 (3)
V3)1173.2 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.32
Crystal size (mm)0.4 × 0.2 × 0.1
Data collection
DiffractometerBruker P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2581, 2172, 1690
Rint0.026
(sin θ/λ)max1)0.605
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.084, 1.03
No. of reflections2172
No. of parameters147
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.15, 0.17
Absolute structureFlack (1983), 880 Friedel pairs
Absolute structure parameter0.09 (11)

Computer programs: XSCANS (Bruker, 1997), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2C···O3i0.821.932.739 (2)169.6
O3—H3B···O1i0.821.982.797 (2)175.2
N1—H1B···O2ii0.922.082.994 (3)172.7
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y1/2, z+1/2.
 

Acknowledgements

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

References

First citationBridiau, N., Benmansour, M., Legoy, M. D. & Maugard, T. (2007). Tetrahedron, 63. 4178–4183.  Google Scholar
First citationBruker (1997). XSCANS. Bruker AXS Inc.,Madison, Wisconsin, USA.  Google Scholar
First citationDurette, 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.  CrossRef CAS PubMed Web of Science Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationGanem, B. (1966). Acc. Chem. Res. 29, 340–347.  CrossRef Web of Science Google Scholar
First citationKatzen, H. M. (1979). J. Biol. Chem. 254, 2983–2992.  CAS PubMed Web of Science Google Scholar
First citationOjala, W. H., Oatman, J. M. & Ojala, C. R. (2000). Carbohydr. Res. 326, 104–112.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds