Benzyl 4-C-nitro­so­methyl-β-D-arabino­pyran­oside

The title compound [systematic name: (2R,3S,4S,5R)-2-(benzyl­oxy)-5-(nitro­methyl)-3,4,5,6-tetra­hydro-2H-pyran-3,4,5-triol], C₁₃H₁₇NO₇, has the nitro­so­methyl group in the equatorial position. The bond lengths and angles are as expected.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.058
• wR factor = 0.052
• Data-to-parameter ratio = 8.9

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT035_ALERT_1_A No _chemical_absolute_configuration info given .          ?

Alert level C
ABSMU01_ALERT_1_C  The ratio of given/expected absorption coefficient lies
               outside the range 0.99 <> 1.01
            Calculated value of mu =     0.125
            Value of mu given      =     0.120
RINTA01_ALERT_3_C  The value of Rint is greater than 0.10
            Rint given   0.136
PLAT020_ALERT_3_C The value of Rint is greater than 0.10 .........       0.14
PLAT150_ALERT_1_C Volume as Calculated Differs from that Given ...     653.50 Ang-3
PLAT162_ALERT_4_C Missing or Zero su (esd) on y-coordinate for ...         O5
PLAT220_ALERT_2_C Large Non-Solvent    O     Ueq(max)/Ueq(min) ...       3.12 Ratio
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          3
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1
              C13 H17 N O7

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           28.28
           From the CIF: _reflns_number_total               1781
           Count of symmetry unique reflns         1784
           Completeness (_total/calc)             99.83%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present           no

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

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

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Computing details

Data collection: SMART (Siemens, 1995); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1997 ) and KRYSTAL (Hazell, 1995); program(s) used to refine structure: modified ORFLS (Busing, 1962) and KRYSTAL; molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and KRYSTAL; software used to prepare material for publication: KRYSTAL.

(2R,3S,4S,5R)-2-(Benzyloxy)-5-(nitromethyl)tetrahydro-2H-pyran-3,4,5-triol

Crystal data

C13H17NO7	F(000) = 316
Mr = 299.28	Dx = 1.521 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 2950 reflections
a = 11.497 (3) Å	θ = 2.1–30.0°
b = 5.538 (1) Å	µ = 0.12 mm^−1
c = 11.603 (3) Å	T = 120 K
β = 117.792 (5)°	Needle, colourless
V = 653.5 (3) Å^3	0.50 × 0.10 × 0.05 mm
Z = 2

Data collection

Siemens SMART CCD diffractometer	1692 reflections with I > 0.01
Radiation source: x-ray tube	Rint = 0.136
Graphite monochromator	θmax = 28.3°, θmin = 2.1°
ω rotation scans with narrow frames	h = −15→15
8029 measured reflections	k = −7→7
1781 independent reflections	l = −15→15

Refinement

Refinement on F	0 constraints
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.058	w = 1/{[σcs(F^2 + B) + (1 + A)F^2]^1/2- |F|}^2 where A = 0.03, B = 1.0
wR(F^2) = 0.052	(Δ/σ)max < 0.001
S = 0.99	Δρmax = 0.43 (10) e Å^−3
1692 reflections	Δρmin = −0.35 (10) e Å^−3
190 parameters	Extinction correction: B-C type 1 Lorentzian isotropic Becker and Coppens (1974)
0 restraints	Extinction coefficient: 120 (16)

Special details

Refinement. Hydrogen atoms on O atoms located from difference map, on carbon atoms in calculated positions with C—H = 0.95 A and U_iso 20% bigger than U_eq for the carbon atom to which they were attached.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.1130 (2)	0.1376 (5)	0.2904 (2)	0.016 (2)
O2	−0.0195 (2)	−0.4377 (6)	0.3323 (2)	0.018 (2)
O3	0.1869 (2)	−0.3386 (6)	0.5919 (2)	0.019 (2)
O4	0.1820 (2)	0.1609 (5)	0.5607 (2)	0.016 (2)
O5	0.1239 (2)	−0.2437	0.2091 (2)	0.016 (1)
O6	0.5014 (3)	0.3145 (8)	0.6003 (3)	0.050 (2)
O7	0.4557 (3)	0.3133 (7)	0.7591 (3)	0.036 (2)
N1	0.4553 (3)	0.2200 (7)	0.6647 (3)	0.024 (2)
C1	0.0536 (3)	−0.0945 (7)	0.2523 (3)	0.016 (2)
C2	0.0494 (3)	−0.2150 (7)	0.3669 (3)	0.015 (2)
C3	0.1882 (3)	−0.2410 (7)	0.4805 (3)	0.015 (2)
C4	0.2519 (3)	0.0097 (7)	0.5151 (3)	0.014 (2)
C5	0.2446 (3)	0.1229 (7)	0.3931 (3)	0.015 (2)
C6	0.1191 (3)	−0.1658 (8)	0.0900 (3)	0.017 (2)
C7	0.2061 (3)	−0.3201 (7)	0.0568 (3)	0.015 (2)
C8	0.2602 (4)	−0.5344 (7)	0.1229 (4)	0.019 (2)
C9	0.3371 (3)	−0.6767 (8)	0.0878 (4)	0.023 (2)
C10	0.3599 (4)	−0.6101 (8)	−0.0155 (4)	0.025 (2)
C11	0.3067 (4)	−0.3985 (8)	−0.0808 (4)	0.025 (2)
C12	0.2307 (3)	−0.2534 (8)	−0.0449 (3)	0.020 (2)
C13	0.3926 (4)	−0.0224 (7)	0.6222 (3)	0.017 (2)
HO2	0.0312	−0.5379	0.3209	0.020*
HO3	0.1877	−0.4911	0.5801	0.020*
HO4	0.1562	0.0739	0.6056	0.020*
H1	−0.0337	−0.0758	0.1841	0.019*
H2	0.0022	−0.1105	0.3951	0.018*
H3	0.2387	−0.3424	0.4549	0.017*
H5a	0.2803	0.2813	0.4134	0.018*
H5b	0.2950	0.0281	0.3644	0.018*
H6a	0.1479	−0.0029	0.0988	0.021*
H6b	0.0313	−0.1770	0.0221	0.021*
H8	0.2442	−0.5829	0.1928	0.022*
H9	0.3746	−0.8213	0.1344	0.027*
H10	0.4115	−0.7096	−0.0406	0.030*
H11	0.3222	−0.3512	−0.1512	0.030*
H12	0.1953	−0.1069	−0.0903	0.024*
H13a	0.3923	−0.1036	0.6942	0.020*
H13b	0.4408	−0.1150	0.5900	0.020*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.020 (1)	0.007 (1)	0.023 (1)	0.000 (1)	0.011 (1)	0.001 (1)
O2	0.020 (1)	0.008 (1)	0.030 (1)	−0.002 (1)	0.015 (1)	−0.003 (1)
O3	0.031 (1)	0.008 (1)	0.023 (1)	0.000 (1)	0.018 (1)	0.002 (1)
O4	0.023 (1)	0.008 (1)	0.027 (1)	0.000 (1)	0.019 (1)	−0.001 (1)
O5	0.021 (1)	0.009 (1)	0.021 (1)	0.002 (1)	0.012 (1)	0.001 (1)
O6	0.051 (2)	0.066 (2)	0.033 (2)	−0.038 (2)	0.019 (2)	0.002 (2)
O7	0.037 (2)	0.029 (2)	0.043 (2)	−0.005 (1)	0.018 (1)	−0.018 (1)
N1	0.023 (2)	0.022 (2)	0.025 (2)	−0.005 (1)	0.010 (1)	0.003 (1)
C1	0.018 (2)	0.011 (1)	0.021 (2)	0.000 (1)	0.011 (1)	−0.002 (1)
C2	0.019 (2)	0.008 (2)	0.023 (2)	−0.002 (1)	0.014 (1)	−0.003 (1)
C3	0.018 (1)	0.007 (1)	0.020 (2)	0.001 (1)	0.011 (1)	0.001 (1)
C4	0.018 (2)	0.007 (1)	0.020 (2)	0.000 (1)	0.011 (1)	−0.003 (1)
C5	0.021 (2)	0.005 (1)	0.022 (2)	−0.002 (1)	0.013 (1)	−0.001 (1)
C6	0.021 (2)	0.015 (2)	0.017 (2)	0.001 (1)	0.009 (1)	0.002 (1)
C7	0.015 (1)	0.013 (2)	0.018 (2)	−0.003 (1)	0.008 (1)	−0.002 (1)
C8	0.023 (2)	0.013 (1)	0.021 (2)	−0.003 (1)	0.011 (2)	0.000 (1)
C9	0.025 (2)	0.015 (2)	0.030 (2)	0.001 (1)	0.015 (2)	−0.001 (2)
C10	0.023 (2)	0.025 (2)	0.031 (2)	−0.001 (2)	0.017 (2)	−0.004 (2)
C11	0.027 (2)	0.029 (2)	0.022 (2)	−0.004 (2)	0.014 (2)	−0.002 (2)
C12	0.022 (2)	0.019 (2)	0.016 (2)	−0.003 (1)	0.007 (1)	−0.001 (1)
C13	0.023 (2)	0.011 (1)	0.020 (2)	−0.002 (1)	0.012 (2)	−0.003 (1)

Geometric parameters (Å, º)

O5—C1	1.401 (4)	C10—C11	1.374 (6)
O5—C6	1.425 (4)	C11—C12	1.386 (5)
O2—C2	1.419 (4)	O2—HO2	0.859
O3—C3	1.407 (4)	O3—HO3	0.856
O4—C4	1.422 (4)	O4—HO4	0.858
O1—C1	1.426 (4)	C1—H1	0.950
O1—C5	1.426 (4)	C2—H2	0.950
O6—N1	1.217 (4)	C3—H3	0.950
O7—N1	1.210 (4)	C5—H5a	0.950
N1—C13	1.495 (4)	C5—H5b	0.950
C1—C2	1.508 (5)	C6—H6a	0.950
C2—C3	1.531 (5)	C6—H6b	0.950
C3—C4	1.534 (4)	C8—H8	0.950
C4—C5	1.514 (4)	C9—H9	0.950
C4—C13	1.523 (5)	C10—H10	0.950
C6—C7	1.496 (4)	C11—H11	0.950
C7—C12	1.385 (5)	C12—H12	0.950
C7—C8	1.392 (5)	C13—H13a	0.950
C8—C9	1.380 (5)	C13—H13b	0.950
C9—C10	1.391 (5)
C6—O5—C1	113.6 (3)	O5—C1—H1	109.1
C5—O1—C1	112.1 (2)	O1—C1—H1	109.1
O6—N1—O7	123.6 (3)	C2—C1—H1	109.1
C13—N1—O7	118.6 (3)	O2—C2—H2	107.1
C13—N1—O6	117.7 (3)	C1—C2—H2	107.1
O1—C1—O5	111.7 (2)	C3—C2—H2	107.1
C2—C1—O5	108.4 (3)	O3—C3—H3	109.3
C2—C1—O1	109.4 (3)	C2—C3—H3	109.3
C1—C2—O2	112.2 (3)	C4—C3—H3	109.3
C3—C2—O2	112.5 (3)	H5b—C5—H5a	109.5
C3—C2—C1	110.6 (3)	O1—C5—H5a	108.8
C2—C3—O3	112.0 (3)	C4—C5—H5a	108.8
C4—C3—O3	108.4 (3)	O1—C5—H5b	108.8
C4—C3—C2	108.6 (3)	C4—C5—H5b	108.8
C5—C4—O4	108.0 (3)	H6b—C6—H6a	109.5
C13—C4—O4	109.6 (3)	O5—C6—H6a	109.2
C3—C4—O4	110.3 (3)	C7—C6—H6a	109.2
C13—C4—C5	112.7 (3)	O5—C6—H6b	109.2
C3—C4—C5	108.6 (3)	C7—C6—H6b	109.2
C3—C4—C13	107.7 (3)	C9—C8—H8	119.8
C4—C5—O1	112.3 (2)	C7—C8—H8	119.8
C7—C6—O5	110.4 (3)	C8—C9—H9	119.8
C8—C7—C12	118.7 (3)	C10—C9—H9	119.8
C6—C7—C12	119.6 (3)	C11—C10—H10	120.4
C6—C7—C8	121.7 (3)	C9—C10—H10	120.4
C7—C8—C9	120.5 (3)	C10—C11—H11	119.7
C10—C9—C8	120.5 (3)	C12—C11—H11	119.7
C9—C10—C11	119.1 (3)	C11—C12—H12	119.7
C12—C11—C10	120.6 (3)	C7—C12—H12	119.7
C7—C12—C11	120.6 (3)	H13b—C13—H13a	109.5
C4—C13—N1	109.1 (3)	N1—C13—H13a	109.5
C2—O2—HO2	106.0	C4—C13—H13a	109.5
C3—O3—HO3	103.2	N1—C13—H13b	109.5
C4—O4—HO4	108.1	C4—C13—H13b	109.5