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

Shang, P.-H.; Cheng, C.-M.; Yang, Y.-C.; Wang, R.-J.; Zhao, Y.-F.

doi:10.1107/S1600536808011616

organic compounds

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ISSN: 2056-9890

Volume 64| Part 7| July 2008| Page o1317

doi:10.1107/S1600536808011616

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

Pei-Hua Shang,^a Chang-Mei Cheng,^a ^* Yong-Chong Yang,^a Ru-Ji Wang ^b and Yu-Fen Zhao ^a

^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 ); Ganem (1966 ); Katzen (1979 ); Bridiau et al. (2007 ); Ojala et al. (2000 ).

Experimental

Crystal data

C₁₁H₁₄ClNO₃
M_r = 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)
R_int = 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
Δρ_max = 0.15 e Å⁻³
Δρ_min = −0.17 e Å⁻³
Absolute structure: Flack (1983 ), 880 Friedel pairs
Flack parameter: 0.09 (11)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

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

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

checkCIF report

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.

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

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

C₁₁H₁₄ClNO₃	F(000) = 512
M_r = 243.68	D_x = 1.380 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 37 reflections
a = 6.5305 (8) Å	θ = 4.9–12.5°
b = 7.9857 (9) Å	µ = 0.32 mm⁻¹
c = 22.496 (3) Å	T = 295 K
V = 1173.2 (3) Å³	Prism, colorless
Z = 4	0.4 × 0.2 × 0.1 mm

Data collection top

Bruker P4 diffractometer	R_int = 0.026
Radiation source: fine-focus sealed tube	θ_max = 25.5°, θ_min = 2.7°
Graphite monochromator	h = −7→7
ω scans	k = −9→9
2581 measured reflections	l = −27→27
2172 independent reflections	3 standard reflections every 97 reflections
1690 reflections with I > 2σ(I)	intensity decay: none

Refinement top

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)] = 0.037	H-atom parameters constrained
wR(F²) = 0.084	w = 1/[σ²(F_o²) + (0.005P)² + 0.4P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max < 0.001
2172 reflections	Δρ_max = 0.15 e Å⁻³
147 parameters	Δρ_min = −0.17 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 880 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.09 (11)

Crystal data top

C₁₁H₁₄ClNO₃	V = 1173.2 (3) Å³
M_r = 243.68	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.5305 (8) Å	µ = 0.32 mm⁻¹
b = 7.9857 (9) Å	T = 295 K
c = 22.496 (3) Å	0.4 × 0.2 × 0.1 mm

Data collection top

Bruker P4 diffractometer	R_int = 0.026
2581 measured reflections	3 standard reflections every 97 reflections
2172 independent reflections	intensity decay: none
1690 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.037	H-atom parameters constrained
wR(F²) = 0.084	Δρ_max = 0.15 e Å⁻³
S = 1.03	Δρ_min = −0.17 e Å⁻³
2172 reflections	Absolute structure: Flack (1983), 880 Friedel pairs
147 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
Cl1	0.01956 (18)	−0.12260 (10)	0.00675 (4)	0.0884 (3)
O1	0.3998 (2)	0.56562 (19)	0.16726 (7)	0.0425 (4)
O2	0.2117 (3)	1.0211 (2)	0.23361 (8)	0.0482 (5)
H2C	0.2839	1.1049	0.2316	0.058*
O3	0.5280 (3)	0.7894 (2)	0.25924 (7)	0.0477 (4)
H3B	0.5420	0.8705	0.2812	0.057*
N1	0.0604 (3)	0.4754 (3)	0.16049 (9)	0.0495 (6)
H1B	−0.0305	0.4823	0.1916	0.059*
C1	0.1909 (4)	0.6147 (3)	0.15314 (11)	0.0412 (6)
H1A	0.1850	0.6517	0.1116	0.049*
C2	0.1280 (4)	0.7577 (3)	0.19294 (12)	0.0457 (6)
H2A	0.1197	0.7179	0.2336	0.055*
H2B	−0.0071	0.7960	0.1813	0.055*
C3	0.2759 (4)	0.9032 (3)	0.19013 (10)	0.0392 (6)
H3A	0.2653	0.9554	0.1508	0.047*
C4	0.4948 (4)	0.8459 (3)	0.19940 (10)	0.0412 (6)
H4A	0.5884	0.9386	0.1906	0.049*
C5	0.5384 (4)	0.7017 (3)	0.15789 (11)	0.0451 (6)
H5A	0.5270	0.7400	0.1171	0.054*
H5B	0.6776	0.6631	0.1641	0.054*
C6	0.0505 (4)	0.3402 (3)	0.12239 (11)	0.0450 (6)
C7	0.2014 (5)	0.3069 (4)	0.08000 (12)	0.0549 (7)
H7A	0.3118	0.3797	0.0761	0.066*
C8	0.1893 (5)	0.1674 (4)	0.04379 (12)	0.0591 (8)
H8A	0.2906	0.1472	0.0156	0.071*
C9	0.0287 (6)	0.0594 (3)	0.04936 (11)	0.0567 (8)
C10	−0.1245 (5)	0.0904 (4)	0.08970 (12)	0.0580 (8)
H10A	−0.2348	0.0172	0.0928	0.070*
C11	−0.1145 (5)	0.2305 (3)	0.12566 (12)	0.0527 (7)
H11A	−0.2198	0.2518	0.1525	0.063*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.1371 (9)	0.0575 (4)	0.0707 (5)	0.0048 (6)	−0.0236 (6)	−0.0194 (4)
O1	0.0405 (9)	0.0404 (9)	0.0464 (9)	−0.0016 (8)	−0.0010 (8)	−0.0021 (8)
O2	0.0471 (11)	0.0378 (10)	0.0595 (10)	−0.0028 (9)	0.0080 (9)	−0.0056 (9)
O3	0.0561 (11)	0.0442 (9)	0.0429 (9)	0.0035 (10)	−0.0106 (9)	−0.0058 (8)
N1	0.0488 (13)	0.0482 (12)	0.0515 (12)	−0.0157 (11)	0.0108 (11)	−0.0106 (11)
C1	0.0396 (13)	0.0424 (13)	0.0417 (13)	−0.0043 (12)	−0.0045 (11)	0.0018 (12)
C2	0.0380 (14)	0.0423 (14)	0.0568 (15)	−0.0025 (11)	−0.0008 (12)	−0.0025 (13)
C3	0.0419 (14)	0.0359 (13)	0.0399 (12)	0.0022 (11)	−0.0002 (11)	0.0037 (11)
C4	0.0392 (14)	0.0423 (13)	0.0422 (12)	−0.0042 (12)	0.0011 (11)	0.0017 (10)
C5	0.0415 (14)	0.0480 (13)	0.0457 (13)	−0.0077 (13)	0.0025 (12)	−0.0025 (12)
C6	0.0501 (15)	0.0422 (13)	0.0427 (13)	−0.0043 (13)	−0.0031 (12)	0.0007 (11)
C7	0.0566 (17)	0.0569 (17)	0.0513 (15)	−0.0107 (16)	0.0078 (15)	−0.0060 (14)
C8	0.073 (2)	0.0582 (18)	0.0464 (15)	0.0010 (18)	0.0044 (15)	−0.0038 (14)
C9	0.085 (2)	0.0446 (14)	0.0408 (13)	0.0014 (17)	−0.0127 (16)	−0.0011 (12)
C10	0.0685 (19)	0.0525 (17)	0.0529 (16)	−0.0179 (16)	−0.0067 (15)	0.0033 (15)
C11	0.0533 (16)	0.0551 (17)	0.0497 (15)	−0.0173 (15)	0.0028 (14)	−0.0034 (14)

Geometric parameters (Å, º) top

Cl1—C9	1.742 (3)	C3—H3A	0.9800
O1—C5	1.430 (3)	C4—C5	1.510 (3)
O1—C1	1.454 (3)	C4—H4A	0.9800
O2—C3	1.421 (3)	C5—H5A	0.9700
O2—H2C	0.8200	C5—H5B	0.9700
O3—C4	1.436 (3)	C6—C11	1.391 (4)
O3—H3B	0.8200	C6—C7	1.397 (4)
N1—C6	1.380 (3)	C7—C8	1.382 (4)
N1—C1	1.411 (3)	C7—H7A	0.9300
N1—H1B	0.9195	C8—C9	1.364 (4)
C1—C2	1.508 (3)	C8—H8A	0.9300
C1—H1A	0.9800	C9—C10	1.373 (4)
C2—C3	1.512 (3)	C10—C11	1.382 (4)
C2—H2A	0.9700	C10—H10A	0.9300
C2—H2B	0.9700	C11—H11A	0.9300
C3—C4	1.515 (3)

C5—O1—C1	110.91 (18)	O3—C4—H4A	109.4
C3—O2—H2C	109.5	C5—C4—H4A	109.4
C4—O3—H3B	109.5	C3—C4—H4A	109.4
C6—N1—C1	124.9 (2)	O1—C5—C4	111.7 (2)
C6—N1—H1B	119.3	O1—C5—H5A	109.3
C1—N1—H1B	115.6	C4—C5—H5A	109.3
N1—C1—O1	109.19 (19)	O1—C5—H5B	109.3
N1—C1—C2	111.3 (2)	C4—C5—H5B	109.3
O1—C1—C2	109.23 (19)	H5A—C5—H5B	107.9
N1—C1—H1A	109.0	N1—C6—C11	119.7 (2)
O1—C1—H1A	109.0	N1—C6—C7	122.7 (2)
C2—C1—H1A	109.0	C11—C6—C7	117.6 (2)
C1—C2—C3	112.6 (2)	C8—C7—C6	121.0 (3)
C1—C2—H2A	109.1	C8—C7—H7A	119.5
C3—C2—H2A	109.1	C6—C7—H7A	119.5
C1—C2—H2B	109.1	C9—C8—C7	120.0 (3)
C3—C2—H2B	109.1	C9—C8—H8A	120.0
H2A—C2—H2B	107.8	C7—C8—H8A	120.0
O2—C3—C2	107.00 (19)	C8—C9—C10	120.5 (3)
O2—C3—C4	112.6 (2)	C8—C9—Cl1	120.2 (2)
C2—C3—C4	111.4 (2)	C10—C9—Cl1	119.3 (2)
O2—C3—H3A	108.6	C9—C10—C11	119.9 (3)
C2—C3—H3A	108.6	C9—C10—H10A	120.1
C4—C3—H3A	108.6	C11—C10—H10A	120.1
O3—C4—C5	108.14 (19)	C10—C11—C6	121.0 (3)
O3—C4—C3	111.5 (2)	C10—C11—H11A	119.5
C5—C4—C3	108.8 (2)	C6—C11—H11A	119.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, −z+1/2; (ii) −x, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₁H₁₄ClNO₃
M_r	243.68
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	295
a, b, c (Å)	6.5305 (8), 7.9857 (9), 22.496 (3)
V (Å³)	1173.2 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.32
Crystal size (mm)	0.4 × 0.2 × 0.1

Data collection
Diffractometer	Bruker P4 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	2581, 2172, 1690
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.605

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.084, 1.03
No. of reflections	2172
No. of parameters	147
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.17
Absolute structure	Flack (1983), 880 Friedel pairs
Absolute structure parameter	0.09 (11)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2C···O3ⁱ	0.82	1.93	2.739 (2)	169.6
O3—H3B···O1ⁱ	0.82	1.98	2.797 (2)	175.2
N1—H1B···O2ⁱⁱ	0.92	2.08	2.994 (3)	172.7

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

Acknowledgements

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

References

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