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

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.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.037
• wR factor = 0.084
• Data-to-parameter ratio = 14.8

checkCIF/PLATON results

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Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.47
           From the CIF: _reflns_number_total               2172
           Count of symmetry unique reflns         1292
           Completeness (_total/calc)            168.11%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       880
           Fraction of Friedel pairs measured     0.681
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     ...          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     ...          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     ...          S

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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.

Related literature

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

S2. 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.

S3. 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). U_iso(H) values were set to 1.2U_eq of the attached atom.

Computing details

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

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

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

Crystal data

C11H14ClNO3	F(000) = 512
Mr = 243.68	Dx = 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) Å^3	Prism, colorless
Z = 4	0.4 × 0.2 × 0.1 mm

Data collection

Bruker P4 diffractometer	Rint = 0.026
Radiation source: fine-focus sealed tube	θmax = 25.5°, θmin = 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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.037	H-atom parameters constrained
wR(F^2) = 0.084	w = 1/[σ^2(Fo^2) + (0.005P)^2 + 0.4P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max < 0.001
2172 reflections	Δρmax = 0.15 e Å^−3
147 parameters	Δρmin = −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)

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2C···O3^i	0.82	1.93	2.739 (2)	170
O3—H3B···O1^i	0.82	1.98	2.797 (2)	175
N1—H1B···O2^ii	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.