Literature DB >> 21581936

3-O-Benzyl-6-O-benzoyl-1,2-O-isopropil-idene-5-C-nitro-methyl-a-d-glucofuran-ose.

Begoña Pampín, Laura Valencia, Juan C Estévez, Ramón J Estévez.   

Abstract

The title compound, C(24)H(27)NO(9), is one of the epimers of the Henry reaction of 3-O-benzyl-6-O-benzoyl-2-O-isopropyl-idene-a-d-glucofuran-5-one with nitro-methane. The conformation of the five membered rings is as expected from the precursor compound and the mol-ecule is folded with a dihedral angle of 51.4 (2)° between the aromatic rings. One O-H⋯O hydrogen bond and some intra-molecular and inter-molecular C-H⋯O inter-actions are observed in the structure.

Entities:  

Year:  2009        PMID: 21581936      PMCID: PMC2968333          DOI: 10.1107/S1600536808043353

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the preparation of 3-O-benzyl-6-O-benzoyl-1,2-isopro­pyl­idene-a-d-xilo-hexofuran-5-one, the precursor of the title compound, and for the Henry reaction of the title compound with nitro­methane, see: Yoshikawa et al. (1990 ▶). For background to nitro­sugars as precursors of a wide range of natural and synthetic products, see: Chakraborty et al. (2002 ▶); Gruner et al. (2002 ▶); Lillelund et al. (2002 ▶); Ogawa & Morikawa (2005 ▶).

Experimental

Crystal data

C24H27NO9 M = 473.47 Orthorhombic, a = 9.5080 (12) Å b = 11.8190 (16) Å c = 21.395 (3) Å V = 2404.3 (5) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 113 (2) K 0.47 × 0.29 × 0.13 mm

Data collection

Bruker SMART CCD 1000 diffractometer Absorption correction: multi-scan (SADABS; Sheldrick 1996 ▶) T min = 0.626, T max = 0.982 4735 measured reflections 2692 independent reflections 1940 reflections with I > 2σ(I) R int = 0.037

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.131 S = 1.10 2692 reflections 313 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.25 e Å−3 Δρmin = −0.30 e Å−3 Data collection: SMART (Bruker, 1998 ▶); cell refinement: SAINT (Bruker, 1998 ▶); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX publication routines (Farrugia, 1999 ▶). Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536808043353/zl2144sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808043353/zl2144Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C24H27NO9Dx = 1.308 Mg m3
Mr = 473.47Mo Kα radiation, λ = 0.71069 Å
Orthorhombic, P212121Cell parameters from 915 reflections
a = 9.5080 (12) Åθ = 2.6–24.4°
b = 11.8190 (16) ŵ = 0.10 mm1
c = 21.395 (3) ÅT = 113 K
V = 2404.3 (5) Å3Prism, colourless
Z = 40.47 × 0.29 × 0.13 mm
F(000) = 1000
Bruker SMART CCD 1000 diffractometer2692 independent reflections
Radiation source: fine-focus sealed tube1940 reflections with I > 2σ(I)
graphiteRint = 0.037
ω scansθmax = 26.0°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick 1996)h = −11→11
Tmin = 0.626, Tmax = 0.982k = 0→14
4735 measured reflectionsl = 0→26
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.131H atoms treated by a mixture of independent and constrained refinement
S = 1.10w = 1/[σ2(Fo2) + (0.0583P)2 + 1.021P] where P = (Fo2 + 2Fc2)/3
2692 reflections(Δ/σ)max < 0.001
313 parametersΔρmax = 0.25 e Å3
1 restraintΔρmin = −0.30 e Å3
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.
xyzUiso*/Ueq
O10.1700 (3)0.0030 (2)0.56353 (12)0.0391 (7)
C20.0591 (5)0.0120 (3)0.61034 (19)0.0402 (11)
O30.0623 (3)0.1268 (2)0.62962 (11)0.0348 (7)
C40.1148 (5)0.1931 (3)0.57862 (16)0.0302 (9)
H40.03970.22280.55030.036*
C50.2170 (4)0.1109 (3)0.54653 (16)0.0303 (9)
H50.21430.12060.50010.036*
C60.2093 (4)0.2840 (3)0.60556 (16)0.0288 (9)
H60.16770.31970.64370.035*
C70.3420 (5)0.2167 (3)0.62059 (15)0.0283 (9)
H70.32650.17460.66060.034*
O80.3531 (3)0.1354 (2)0.57021 (11)0.0308 (6)
O90.2419 (3)0.3664 (2)0.55803 (10)0.0315 (6)
C100.1342 (5)0.4495 (3)0.54682 (17)0.0337 (10)
H10A0.04610.41060.53470.040*
H10B0.16320.49860.51160.040*
C110.1070 (5)0.5218 (3)0.60372 (16)0.0308 (9)
C12−0.0205 (5)0.5153 (4)0.63417 (18)0.0382 (10)
H12−0.09400.46990.61770.046*
C13−0.0408 (6)0.5759 (4)0.6894 (2)0.0477 (12)
H13−0.12860.57160.71040.057*
C140.0640 (6)0.6412 (4)0.7134 (2)0.0443 (11)
H140.04900.68160.75120.053*
C150.1910 (5)0.6489 (3)0.6834 (2)0.0422 (11)
H150.26400.69420.70050.051*
C160.2130 (5)0.5899 (3)0.62766 (18)0.0363 (10)
H160.30010.59650.60620.044*
C170.4799 (5)0.2818 (3)0.62561 (15)0.0279 (9)
C180.4703 (5)0.3727 (3)0.67693 (15)0.0318 (9)
H18A0.55780.41820.67780.038*
H18B0.39030.42400.66840.038*
O190.4505 (3)0.3165 (2)0.73631 (10)0.0330 (7)
C200.4824 (5)0.3802 (3)0.78726 (16)0.0307 (9)
C210.4595 (5)0.3169 (3)0.84646 (16)0.0317 (9)
C220.3918 (6)0.2137 (4)0.8481 (2)0.0571 (15)
H220.36110.17990.81020.069*
C230.3680 (7)0.1590 (5)0.9043 (2)0.0663 (17)
H230.32220.08760.90510.080*
C240.4120 (6)0.2096 (4)0.95958 (18)0.0497 (13)
H240.39150.17480.99850.060*
C250.4849 (5)0.3097 (4)0.95812 (17)0.0416 (11)
H250.51930.34170.99590.050*
C260.5087 (5)0.3643 (3)0.90188 (16)0.0369 (10)
H260.55840.43410.90110.044*
O270.5252 (4)0.4754 (2)0.78355 (11)0.0436 (8)
O280.5152 (3)0.3409 (2)0.56949 (11)0.0339 (7)
C290.5974 (4)0.1972 (3)0.63705 (18)0.0324 (9)
H29A0.58290.15930.67780.039*
H29B0.59630.13860.60400.039*
N300.7345 (4)0.2559 (3)0.63692 (16)0.0411 (9)
O310.8021 (3)0.2601 (3)0.58777 (14)0.0529 (9)
O320.7732 (4)0.3030 (3)0.68513 (14)0.0516 (9)
C330.0979 (8)−0.0629 (4)0.6645 (2)0.0663 (17)
H33A0.1894−0.03960.68120.099*
H33B0.1033−0.14170.65040.099*
H33C0.0264−0.05630.69730.099*
C34−0.0801 (5)−0.0168 (4)0.5813 (2)0.0530 (13)
H34A−0.1544−0.01090.61290.080*
H34B−0.0771−0.09420.56490.080*
H34C−0.09980.03600.54700.080*
H280.434 (3)0.366 (4)0.561 (2)0.060 (17)*
U11U22U33U12U13U23
O10.046 (2)0.0339 (14)0.0374 (14)−0.0003 (14)0.0047 (14)−0.0101 (12)
C20.048 (3)0.034 (2)0.039 (2)−0.002 (2)0.008 (2)−0.0016 (18)
O30.0463 (19)0.0312 (13)0.0269 (12)0.0023 (14)0.0063 (13)0.0019 (11)
C40.038 (3)0.0319 (18)0.0208 (17)0.0002 (18)0.0030 (17)0.0013 (15)
C50.034 (3)0.033 (2)0.0232 (17)−0.0006 (18)−0.0012 (17)−0.0028 (15)
C60.040 (3)0.0282 (18)0.0180 (16)0.0042 (18)0.0027 (16)0.0009 (14)
C70.039 (3)0.0308 (19)0.0148 (16)0.0034 (18)0.0016 (16)−0.0045 (13)
O80.0351 (18)0.0345 (13)0.0228 (12)0.0046 (13)−0.0043 (11)−0.0092 (10)
O90.0398 (18)0.0338 (13)0.0208 (11)0.0091 (13)0.0017 (12)0.0046 (10)
C100.039 (3)0.036 (2)0.0263 (18)0.0090 (19)−0.0026 (18)0.0021 (15)
C110.035 (3)0.0298 (19)0.0282 (18)0.0045 (18)−0.0009 (18)0.0070 (15)
C120.033 (3)0.045 (2)0.036 (2)0.003 (2)0.0000 (19)0.0016 (18)
C130.040 (3)0.062 (3)0.040 (2)0.011 (3)0.011 (2)0.001 (2)
C140.051 (3)0.046 (2)0.036 (2)0.009 (2)0.000 (2)−0.0074 (19)
C150.054 (3)0.031 (2)0.041 (2)0.003 (2)−0.006 (2)−0.0039 (18)
C160.041 (3)0.0318 (19)0.036 (2)0.0028 (19)0.0047 (19)0.0073 (17)
C170.040 (3)0.0274 (18)0.0167 (15)0.0017 (18)−0.0014 (16)0.0017 (13)
C180.043 (3)0.034 (2)0.0186 (16)0.000 (2)−0.0009 (17)0.0042 (14)
O190.052 (2)0.0317 (13)0.0157 (11)−0.0066 (14)−0.0016 (12)−0.0007 (10)
C200.038 (3)0.032 (2)0.0218 (16)−0.0028 (19)−0.0013 (17)−0.0042 (14)
C210.038 (3)0.037 (2)0.0201 (16)−0.0037 (19)0.0004 (17)−0.0006 (15)
C220.085 (4)0.060 (3)0.027 (2)−0.034 (3)−0.009 (2)0.0057 (19)
C230.087 (5)0.071 (3)0.040 (2)−0.043 (3)−0.010 (3)0.019 (2)
C240.057 (3)0.068 (3)0.024 (2)−0.007 (3)0.001 (2)0.014 (2)
C250.057 (3)0.048 (2)0.0192 (17)0.006 (2)−0.0037 (19)−0.0037 (16)
C260.051 (3)0.0364 (19)0.0231 (17)0.000 (2)−0.0005 (18)−0.0038 (15)
O270.079 (2)0.0289 (14)0.0231 (12)−0.0101 (16)−0.0052 (14)−0.0029 (10)
O280.040 (2)0.0450 (16)0.0169 (11)0.0035 (14)0.0009 (12)0.0047 (11)
C290.029 (3)0.038 (2)0.0301 (19)0.0012 (19)−0.0031 (18)0.0020 (16)
N300.042 (2)0.047 (2)0.0340 (18)0.0058 (19)−0.0066 (17)0.0115 (16)
O310.039 (2)0.079 (2)0.0404 (17)0.0084 (18)0.0052 (15)0.0129 (16)
O320.056 (2)0.061 (2)0.0387 (16)−0.0149 (18)−0.0148 (16)0.0018 (15)
C330.107 (5)0.042 (2)0.050 (3)0.010 (3)0.009 (3)0.011 (2)
C340.048 (3)0.049 (3)0.062 (3)−0.011 (2)0.009 (3)−0.009 (2)
O1—C51.400 (5)C17—O281.429 (4)
O1—C21.458 (5)C17—C291.519 (5)
C2—O31.419 (5)C17—C181.539 (5)
C2—C341.502 (7)C18—O191.446 (4)
C2—C331.505 (6)C18—H18A0.9900
O3—C41.433 (4)C18—H18B0.9900
C4—C61.515 (5)O19—C201.359 (4)
C4—C51.536 (5)C20—O271.199 (5)
C4—H41.0000C20—C211.487 (5)
C5—O81.419 (5)C21—C221.379 (6)
C5—H51.0000C21—C261.393 (5)
C6—O91.442 (4)C22—C231.385 (6)
C6—C71.526 (6)C22—H220.9500
C6—H61.0000C23—C241.391 (6)
C7—O81.448 (4)C23—H230.9500
C7—C171.524 (6)C24—C251.371 (6)
C7—H71.0000C24—H240.9500
O9—C101.439 (5)C25—C261.384 (5)
C10—C111.510 (5)C25—H250.9500
C10—H10A0.9900C26—H260.9500
C10—H10B0.9900O28—H280.84 (2)
C11—C121.378 (6)C29—N301.476 (6)
C11—C161.388 (6)C29—H29A0.9900
C12—C131.394 (6)C29—H29B0.9900
C12—H120.9500N30—O321.228 (4)
C13—C141.361 (7)N30—O311.233 (5)
C13—H130.9500C33—H33A0.9800
C14—C151.370 (7)C33—H33B0.9800
C14—H140.9500C33—H33C0.9800
C15—C161.398 (6)C34—H34A0.9800
C15—H150.9500C34—H34B0.9800
C16—H160.9500C34—H34C0.9800
C5—O1—C2110.1 (3)C15—C16—H16120.1
O3—C2—O1104.7 (3)O28—C17—C29106.5 (3)
O3—C2—C34110.9 (4)O28—C17—C7112.9 (3)
O1—C2—C34109.7 (3)C29—C17—C7108.2 (3)
O3—C2—C33109.5 (4)O28—C17—C18105.8 (3)
O1—C2—C33108.0 (4)C29—C17—C18112.8 (3)
C34—C2—C33113.7 (4)C7—C17—C18110.6 (3)
C2—O3—C4108.0 (3)O19—C18—C17108.3 (3)
O3—C4—C6107.7 (3)O19—C18—H18A110.0
O3—C4—C5102.4 (3)C17—C18—H18A110.0
C6—C4—C5104.1 (3)O19—C18—H18B110.0
O3—C4—H4113.8C17—C18—H18B110.0
C6—C4—H4113.8H18A—C18—H18B108.4
C5—C4—H4113.8C20—O19—C18114.9 (3)
O1—C5—O8112.6 (3)O27—C20—O19122.9 (3)
O1—C5—C4104.9 (3)O27—C20—C21125.3 (3)
O8—C5—C4106.8 (3)O19—C20—C21111.8 (3)
O1—C5—H5110.8C22—C21—C26119.5 (3)
O8—C5—H5110.8C22—C21—C20122.3 (3)
C4—C5—H5110.8C26—C21—C20118.2 (3)
O9—C6—C4109.8 (3)C21—C22—C23120.8 (4)
O9—C6—C7108.8 (3)C21—C22—H22119.6
C4—C6—C7101.6 (3)C23—C22—H22119.6
O9—C6—H6112.0C22—C23—C24119.2 (4)
C4—C6—H6112.0C22—C23—H23120.4
C7—C6—H6112.0C24—C23—H23120.4
O8—C7—C17109.0 (3)C25—C24—C23120.3 (4)
O8—C7—C6104.4 (3)C25—C24—H24119.9
C17—C7—C6117.6 (3)C23—C24—H24119.9
O8—C7—H7108.5C24—C25—C26120.3 (4)
C17—C7—H7108.5C24—C25—H25119.8
C6—C7—H7108.5C26—C25—H25119.8
C5—O8—C7109.6 (3)C25—C26—C21119.8 (4)
C10—O9—C6115.2 (3)C25—C26—H26120.1
O9—C10—C11112.0 (3)C21—C26—H26120.1
O9—C10—H10A109.2C17—O28—H2897 (4)
C11—C10—H10A109.2N30—C29—C17109.9 (3)
O9—C10—H10B109.2N30—C29—H29A109.7
C11—C10—H10B109.2C17—C29—H29A109.7
H10A—C10—H10B107.9N30—C29—H29B109.7
C12—C11—C16119.8 (4)C17—C29—H29B109.7
C12—C11—C10120.0 (4)H29A—C29—H29B108.2
C16—C11—C10120.1 (4)O32—N30—O31122.8 (4)
C11—C12—C13119.6 (4)O32—N30—C29118.4 (4)
C11—C12—H12120.2O31—N30—C29118.7 (3)
C13—C12—H12120.2C2—C33—H33A109.5
C14—C13—C12120.7 (5)C2—C33—H33B109.5
C14—C13—H13119.7H33A—C33—H33B109.5
C12—C13—H13119.7C2—C33—H33C109.5
C13—C14—C15120.4 (4)H33A—C33—H33C109.5
C13—C14—H14119.8H33B—C33—H33C109.5
C15—C14—H14119.8C2—C34—H34A109.5
C14—C15—C16119.9 (4)C2—C34—H34B109.5
C14—C15—H15120.1H34A—C34—H34B109.5
C16—C15—H15120.1C2—C34—H34C109.5
C11—C16—C15119.7 (4)H34A—C34—H34C109.5
C11—C16—H16120.1H34B—C34—H34C109.5
C5—O1—C2—O3−11.5 (4)C12—C13—C14—C150.5 (7)
C5—O1—C2—C34107.5 (4)C13—C14—C15—C160.3 (7)
C5—O1—C2—C33−128.2 (4)C12—C11—C16—C151.9 (6)
O1—C2—O3—C427.8 (4)C10—C11—C16—C15−174.4 (3)
C34—C2—O3—C4−90.4 (4)C14—C15—C16—C11−1.5 (6)
C33—C2—O3—C4143.4 (4)O8—C7—C17—O2859.3 (4)
C2—O3—C4—C6−141.4 (4)C6—C7—C17—O28−59.2 (4)
C2—O3—C4—C5−32.0 (4)O8—C7—C17—C29−58.3 (4)
C2—O1—C5—O8107.9 (3)C6—C7—C17—C29−176.8 (3)
C2—O1—C5—C4−7.8 (4)O8—C7—C17—C18177.6 (3)
O3—C4—C5—O123.9 (4)C6—C7—C17—C1859.1 (4)
C6—C4—C5—O1136.0 (3)O28—C17—C18—O19−173.6 (3)
O3—C4—C5—O8−95.8 (3)C29—C17—C18—O19−57.5 (4)
C6—C4—C5—O816.3 (3)C7—C17—C18—O1963.8 (4)
O3—C4—C6—O9−168.4 (3)C17—C18—O19—C20160.9 (3)
C5—C4—C6—O983.3 (3)C18—O19—C20—O27−0.8 (6)
O3—C4—C6—C776.5 (3)C18—O19—C20—C21−180.0 (4)
C5—C4—C6—C7−31.8 (3)O27—C20—C21—C22170.7 (5)
O9—C6—C7—O8−79.1 (3)O19—C20—C21—C22−10.1 (6)
C4—C6—C7—O836.6 (3)O27—C20—C21—C26−9.3 (7)
O9—C6—C7—C1741.7 (4)O19—C20—C21—C26169.9 (4)
C4—C6—C7—C17157.5 (3)C26—C21—C22—C232.2 (8)
O1—C5—O8—C7−107.4 (3)C20—C21—C22—C23−177.8 (5)
C4—C5—O8—C77.3 (4)C21—C22—C23—C240.6 (10)
C17—C7—O8—C5−154.4 (3)C22—C23—C24—C25−3.5 (9)
C6—C7—O8—C5−27.9 (3)C23—C24—C25—C263.5 (8)
C4—C6—O9—C1080.2 (4)C24—C25—C26—C21−0.6 (7)
C7—C6—O9—C10−169.4 (3)C22—C21—C26—C25−2.2 (7)
C6—O9—C10—C1162.9 (4)C20—C21—C26—C25177.7 (4)
O9—C10—C11—C12−113.6 (4)O28—C17—C29—N3053.6 (4)
O9—C10—C11—C1662.6 (4)C7—C17—C29—N30175.3 (3)
C16—C11—C12—C13−1.1 (6)C18—C17—C29—N30−62.1 (4)
C10—C11—C12—C13175.2 (4)C17—C29—N30—O3282.8 (4)
C11—C12—C13—C14−0.1 (6)C17—C29—N30—O31−93.9 (4)
D—H···AD—HH···AD···AD—H···A
O28—H28···O90.84 (2)1.83 (3)2.628 (4)157 (5)
C4—H4···O31i1.002.443.084 (5)122
C5—H5···O28ii1.002.453.189 (5)130
C5—H5···O31ii1.002.493.352 (5)144
C18—H18A···O320.992.463.000 (6)114
C22—H22···O190.952.412.739 (5)100
C24—H24···O1iii0.952.593.445 (5)151
C26—H26···O8iv0.952.603.514 (5)162
C29—H29A···O190.992.572.907 (5)100
C29—H29A···O27v0.992.543.334 (5)137
C29—H29B···O80.992.422.824 (5)104
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O28—H28⋯O90.84 (2)1.83 (3)2.628 (4)157 (5)
C4—H4⋯O31i1.002.443.084 (5)122
C5—H5⋯O28ii1.002.453.189 (5)130
C5—H5⋯O31ii1.002.493.352 (5)144
C18—H18A⋯O320.992.463.000 (6)114
C24—H24⋯O1iii0.952.593.445 (5)151
C26—H26⋯O8iv0.952.603.514 (5)162
C29—H29A⋯O27v0.992.543.334 (5)137

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

  4 in total

Review 1.  Recent developments of transition-state analogue glycosidase inhibitors of non-natural product origin.

Authors:  Vinni H Lillelund; Henrik H Jensen; Xifu Liang; Mikael Bols
Journal:  Chem Rev       Date:  2002-02       Impact factor: 60.622

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

Review 3.  Carbohydrate-based mimetics in drug design: sugar amino acids and carbohydrate scaffolds.

Authors:  Sibylle A W Gruner; Elsa Locardi; Elisabeth Lohof; Horst Kessler
Journal:  Chem Rev       Date:  2002-02       Impact factor: 60.622

Review 4.  Sugar amino acids and their uses in designing bioactive molecules.

Authors:  Tushar K Chakraborty; Subhash Ghosh; Sarva Jayaprakash
Journal:  Curr Med Chem       Date:  2002-02       Impact factor: 4.530

  4 in total

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