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In the title compound, C12H19N3O7S, the xylo­pyran­osyl ring adopts a chair conformation. All the substituents are in equatorial positions. There are four intramolecular interactions forming four closed rings. C—H...O and N—H...S interactions link the mol­ecules into a three-dimensional framework.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804005641/ci6345sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536804005641/ci6345Isup2.hkl
Contains datablock I

CCDC reference: 238788

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.007 Å
  • R factor = 0.052
  • wR factor = 0.133
  • Data-to-parameter ratio = 12.7

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT241_ALERT_2_C Check High U(eq) as Compared to Neighbors .... C5 PLAT242_ALERT_2_C Check Low U(eq) as Compared to Neighbors .... C9 PLAT242_ALERT_2_C Check Low U(eq) as Compared to Neighbors .... C11 PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 7
Alert level G REFLT03_ALERT_4_G WARNING: Large fraction of Friedel related reflns may be needed to determine absolute structure From the CIF: _diffrn_reflns_theta_max 26.41 From the CIF: _reflns_number_total 2772 Count of symmetry unique reflns 1977 Completeness (_total/calc) 140.21% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 795 Fraction of Friedel pairs measured 0.402 Are heavy atom types Z>Si present yes
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995) and PLATON (Spek, 1990).

N-Amino-N-(2,3,4-tri-O-acetyl-β-D-xylopyranosyl)thiocarbamide top
Crystal data top
C12H19N3O7SF(000) = 736
Mr = 349.36Dx = 1.339 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2yCell parameters from 2772 reflections
a = 22.560 (8) Åθ = 1.6–26.4°
b = 5.4253 (19) ŵ = 0.22 mm1
c = 15.057 (5) ÅT = 293 K
β = 109.886 (6)°Needle, yellow
V = 1733.0 (10) Å30.26 × 0.14 × 0.12 mm
Z = 4
Data collection top
Simens SMART CCD area detector
diffractometer
2772 independent reflections
Radiation source: fine-focus sealed tube2023 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
Detector resolution: 8.33 pixels mm-1θmax = 26.4°, θmin = 1.4°
ω scansh = 2728
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
k = 65
Tmin = 0.944, Tmax = 0.974l = 1818
5020 measured reflections
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)] = 0.052H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.133 w = 1/[σ2(Fo2) + (0.0525P)2 + 1.2246P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max < 0.001
2772 reflectionsΔρmax = 0.22 e Å3
219 parametersΔρmin = 0.20 e Å3
3 restraintsAbsolute structure: Flack (1983), 803 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.07 (16)
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
S10.16639 (6)0.4786 (3)0.00763 (8)0.0597 (4)
N10.16984 (17)0.6742 (8)0.1725 (3)0.0541 (11)
H10.18870.76710.22010.065*
N20.22948 (17)0.8595 (8)0.0984 (3)0.0531 (11)
H20.24430.86980.05290.064*
N30.2488 (2)1.0312 (9)0.1728 (3)0.0598 (11)
H3A0.2909 (6)1.020 (10)0.194 (3)0.070 (16)*
H3B0.237 (3)1.187 (4)0.158 (5)0.10 (2)*
O10.06247 (15)0.6522 (8)0.1394 (3)0.0777 (13)
O20.18131 (13)0.2893 (6)0.3168 (2)0.0468 (7)
O30.24585 (18)0.5951 (8)0.3861 (3)0.0831 (13)
O40.07665 (15)0.3095 (6)0.3827 (2)0.0521 (8)
O50.0720 (3)0.0950 (9)0.3906 (3)0.1173 (19)
O60.03621 (14)0.2252 (7)0.2124 (2)0.0616 (10)
O70.10189 (15)0.4549 (7)0.2588 (3)0.0708 (10)
C10.11979 (19)0.5185 (11)0.1778 (3)0.0528 (13)
H1A0.11810.36740.14140.063*
C20.12846 (18)0.4543 (10)0.2801 (3)0.0446 (10)
H2A0.13470.60380.31880.053*
C30.07198 (19)0.3096 (9)0.2848 (3)0.0450 (11)
H30.07420.13990.26390.054*
C40.00990 (19)0.4222 (10)0.2271 (3)0.0558 (14)
H40.00070.56320.25960.067*
C50.0102 (2)0.4929 (16)0.1298 (4)0.0828 (19)
H5A0.01350.34600.09510.099*
H5B0.02890.57620.09490.099*
C60.18884 (19)0.6826 (9)0.0973 (3)0.0435 (11)
C70.2376 (2)0.3827 (11)0.3718 (3)0.0520 (12)
C80.2849 (2)0.1839 (10)0.4081 (4)0.0705 (16)
H8A0.31270.22650.47020.106*
H8B0.30890.16450.36670.106*
H8C0.26370.03210.41090.106*
C90.0771 (2)0.1000 (11)0.4267 (4)0.0581 (13)
C100.0850 (3)0.1412 (12)0.5278 (3)0.0748 (18)
H10A0.06840.00260.55130.112*
H10B0.06270.28770.53360.112*
H10C0.12900.16010.56370.112*
C110.0896 (2)0.2661 (10)0.2297 (3)0.0484 (12)
C120.1291 (2)0.0416 (11)0.2087 (4)0.0741 (17)
H12A0.16670.07000.22360.111*
H12B0.10600.09310.24590.111*
H12C0.14040.00210.14280.111*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0526 (6)0.0835 (9)0.0501 (6)0.0014 (7)0.0268 (5)0.0060 (7)
N10.048 (2)0.078 (3)0.044 (2)0.008 (2)0.0265 (18)0.003 (2)
N20.054 (2)0.063 (3)0.059 (2)0.001 (2)0.040 (2)0.003 (2)
N30.057 (3)0.062 (3)0.070 (3)0.002 (2)0.034 (2)0.006 (3)
O10.0438 (19)0.123 (4)0.071 (2)0.008 (2)0.0259 (18)0.043 (2)
O20.0408 (16)0.047 (2)0.0535 (18)0.0024 (14)0.0169 (14)0.0065 (16)
O30.064 (2)0.052 (3)0.116 (4)0.0129 (19)0.008 (2)0.012 (2)
O40.068 (2)0.051 (2)0.0507 (18)0.0050 (16)0.0365 (17)0.0025 (17)
O50.215 (6)0.052 (3)0.090 (3)0.010 (3)0.058 (4)0.006 (3)
O60.0440 (18)0.065 (2)0.083 (2)0.0058 (17)0.0309 (17)0.011 (2)
O70.062 (2)0.056 (2)0.112 (3)0.001 (2)0.052 (2)0.002 (2)
C10.040 (2)0.077 (4)0.047 (2)0.002 (2)0.0223 (19)0.007 (3)
C20.043 (2)0.054 (3)0.043 (2)0.003 (2)0.0216 (18)0.000 (2)
C30.044 (2)0.056 (3)0.042 (2)0.003 (2)0.0233 (19)0.005 (2)
C40.040 (2)0.068 (4)0.067 (3)0.003 (2)0.029 (2)0.001 (3)
C50.040 (3)0.140 (6)0.065 (3)0.008 (4)0.013 (2)0.028 (4)
C60.034 (2)0.061 (3)0.041 (2)0.015 (2)0.0194 (19)0.011 (2)
C70.051 (3)0.055 (3)0.051 (3)0.007 (2)0.018 (2)0.005 (2)
C80.062 (3)0.062 (4)0.074 (4)0.004 (3)0.005 (3)0.000 (3)
C90.056 (3)0.056 (4)0.066 (3)0.004 (3)0.024 (3)0.000 (3)
C100.070 (4)0.104 (5)0.054 (3)0.000 (3)0.026 (3)0.019 (3)
C110.042 (3)0.053 (3)0.052 (3)0.004 (2)0.017 (2)0.019 (2)
C120.054 (3)0.068 (4)0.096 (4)0.005 (3)0.020 (3)0.013 (3)
Geometric parameters (Å, º) top
S1—C61.685 (5)C1—H1A0.98
N1—C61.342 (5)C2—C31.519 (6)
N1—C11.434 (6)C2—H2A0.98
N1—H10.86C3—C41.504 (6)
N2—C61.324 (6)C3—H30.98
N2—N31.407 (6)C4—C51.517 (7)
N2—H20.86C4—H40.98
N3—H3A0.90 (3)C5—H5A0.97
N3—H3B0.89 (3)C5—H5B0.97
O1—C11.423 (6)C7—C81.484 (7)
O1—C51.429 (7)C8—H8A0.96
O2—C71.357 (6)C8—H8B0.96
O2—C21.442 (5)C8—H8C0.96
O3—C71.175 (6)C9—C101.488 (7)
O4—C91.314 (6)C10—H10A0.96
O4—C31.442 (5)C10—H10B0.96
O5—C91.177 (7)C10—H10C0.96
O6—C111.335 (5)C11—C121.478 (7)
O6—C41.455 (6)C12—H12A0.96
O7—C111.184 (6)C12—H12B0.96
C1—C21.525 (5)C12—H12C0.96
C6—N1—C1123.4 (4)O1—C5—C4109.2 (4)
C6—N1—H1118.3O1—C5—H5A109.8
C1—N1—H1118.3C4—C5—H5A109.8
C6—N2—N3121.1 (3)O1—C5—H5B109.8
C6—N2—H2119.5C4—C5—H5B109.8
N3—N2—H2119.5H5A—C5—H5B108.3
N2—N3—H3A104 (3)N2—C6—N1115.6 (4)
N2—N3—H3B116 (4)N2—C6—S1120.3 (3)
H3A—N3—H3B110 (6)N1—C6—S1124.0 (4)
C1—O1—C5109.7 (5)O3—C7—O2122.3 (5)
C7—O2—C2118.8 (4)O3—C7—C8126.6 (5)
C9—O4—C3120.1 (4)O2—C7—C8111.1 (5)
C11—O6—C4119.7 (4)C7—C8—H8A109.5
O1—C1—N1107.5 (4)C7—C8—H8B109.5
O1—C1—C2108.3 (3)H8A—C8—H8B109.5
N1—C1—C2111.0 (4)C7—C8—H8C109.5
O1—C1—H1A110.0H8A—C8—H8C109.5
N1—C1—H1A110.0H8B—C8—H8C109.5
C2—C1—H1A110.0O5—C9—O4124.2 (5)
O2—C2—C3105.0 (4)O5—C9—C10124.5 (6)
O2—C2—C1109.5 (3)O4—C9—C10111.3 (5)
C3—C2—C1110.1 (3)C9—C10—H10A109.5
O2—C2—H2A110.7C9—C10—H10B109.5
C3—C2—H2A110.7H10A—C10—H10B109.5
C1—C2—H2A110.7C9—C10—H10C109.5
O4—C3—C4108.7 (3)H10A—C10—H10C109.5
O4—C3—C2106.1 (3)H10B—C10—H10C109.5
C4—C3—C2113.2 (4)O7—C11—O6123.8 (4)
O4—C3—H3109.6O7—C11—C12126.4 (4)
C4—C3—H3109.6O6—C11—C12109.9 (5)
C2—C3—H3109.6C11—C12—H12A109.5
O6—C4—C3105.5 (4)C11—C12—H12B109.5
O6—C4—C5106.1 (4)H12A—C12—H12B109.5
C3—C4—C5110.6 (4)C11—C12—H12C109.5
O6—C4—H4111.5H12A—C12—H12C109.5
C3—C4—H4111.5H12B—C12—H12C109.5
C5—C4—H4111.5
C5—O1—C1—N1171.3 (4)O4—C3—C4—O681.8 (4)
C5—O1—C1—C268.8 (5)C2—C3—C4—O6160.6 (3)
C6—N1—C1—O188.6 (5)O4—C3—C4—C5164.0 (5)
C6—N1—C1—C2153.2 (4)C2—C3—C4—C546.4 (6)
C7—O2—C2—C3142.0 (4)C1—O1—C5—C468.1 (6)
C7—O2—C2—C199.9 (4)O6—C4—C5—O1169.2 (5)
O1—C1—C2—O2171.9 (4)C3—C4—C5—O155.3 (7)
N1—C1—C2—O270.4 (5)N3—N2—C6—N12.4 (6)
O1—C1—C2—C357.0 (5)N3—N2—C6—S1179.9 (3)
N1—C1—C2—C3174.7 (4)C1—N1—C6—N2171.1 (4)
C9—O4—C3—C4113.6 (5)C1—N1—C6—S111.5 (6)
C9—O4—C3—C2124.3 (4)C2—O2—C7—O34.6 (7)
O2—C2—C3—O475.9 (4)C2—O2—C7—C8176.1 (4)
C1—C2—C3—O4166.4 (4)C3—O4—C9—O52.4 (8)
O2—C2—C3—C4165.0 (3)C3—O4—C9—C10177.6 (4)
C1—C2—C3—C447.3 (5)C4—O6—C11—O71.7 (7)
C11—O6—C4—C3130.9 (4)C4—O6—C11—C12179.3 (4)
C11—O6—C4—C5111.8 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O30.862.573.117 (6)123
N1—H1···N30.862.252.630 (6)107
N2—H2···S1i0.862.553.322 (5)150
N3—H3A···O7ii0.90 (3)2.31 (3)3.198 (6)174 (4)
N3—H3B···S1iii0.89 (3)2.78 (6)3.520 (5)142 (5)
C1—H1A···S10.982.663.090 (5)107
C3—H3···O50.982.312.712 (7)104
C4—H4···O70.982.352.727 (6)102
C8—H8C···O3iv0.962.413.300 (7)154
C12—H12B···O7iv0.962.463.281 (7)144
Symmetry codes: (i) x+1/2, y+1/2, z; (ii) x+1/2, y+1/2, z; (iii) x, y+1, z; (iv) x, y1, z.
 

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