organic compounds
An orthorhombic polymorph of 6-deoxy-6-iodo-1,2:3,4-di-O-isopropylidene-α-D-galactopyranoside
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bSyngene International Ltd, Biocon Park, Plot Nos. 2 & 3, Bommasandra 4th Phase, Jigani Link Rd, Bangalore 560 100, India, cDepartment of Printing, Manipal Institute of Technology, Manipal 576 104, India, and dDepartment of Chemistry, National Institute of Technology-Karnataka, Surathkal, Mangalore 575 025, India
*Correspondence e-mail: hkfun@usm.my
The title compound, C12H19IO5, is the orthorhombic polymorph of a previously reported monoclinic form [Krajewski et al. (1987). Bull. Pol. Acad. Sci. Chem. 35, 91–102]. The dihedral angles between the six-membered ring and the two five-membered rings are 67.66 (14) and 71.79 (13)°, whereas the dihedral angle between the five-membered rings is 74.41 (12)°, indicating that all three rings are twisted from each other. The six-membered ring has a twist-boat conformation while both of the five-membered rings have envelope conformations. The is stabilized by a network of C—H⋯O contacts linking the molecules into a two-dimensional array parallel to the ab plane.
Related literature
For the monoclinic polymorph of the title compound, see: Krajewski et al. (1987). For the synthesis and biological evaluation of 6-substituted purines, see: Gambogi Braga et al. (2007). For halogenation reagent systems, see: Classon et al. (1988). For the synthesis of perosamine derivatives, see: Stevens et al. (1970). For the synthesis of labilose, see: Westwood et al. (1967). For ring conformations and ring puckering analysis, see: Boeyens (1978); Cremer & Pople (1975). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; 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 and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536809029031/tk2509sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809029031/tk2509Isup2.hkl
Triphenylphosphine (0.53 g, 1.9 mmol) and imidazole (0.4 g, 5.7 mmol) was added to the mixture of 1,2,3,4-di-O-isopropylidine-α-D-galactopyranoside (0.5 g, 1.9 mmol) in toluene: acetonitrile (2: 1, 10 ml). The mixture was heated to 70 °C. Iodine (0.6 g, 3.8 mmol) was then added portion-wise for a period of 30 min and mixture was further stirred for 2 hours. The completion of the reaction was confirmed by TLC (30% EtOAc/hexane, Rf - 0.6). The brown reaction mixture was concentrated under vacuum and the residue was purified by using 25% ethylacetate in petroleum ether to get desired compound as white crystals. (Yield 600 mg, 83%, m.p. 334–336 K).
C-bound H atoms were positioned geometrically [C—H = 0.96–0.98 Å] and refined using a riding model, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(methyl-C). A rotating group model was used for the methyl groups.
The maximum and minimum residual electron density peaks of 0.87 and -1.24 eÅ-3, respectively, were located 0.85 Å and 0.52 Å from the H8A and I1 atoms, respectively.
Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); 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) and PLATON (Spek, 2009).C12H19IO5 | F(000) = 736 |
Mr = 370.17 | Dx = 1.707 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 6517 reflections |
a = 7.3595 (1) Å | θ = 3.0–30.1° |
b = 11.5145 (2) Å | µ = 2.23 mm−1 |
c = 16.9945 (2) Å | T = 100 K |
V = 1440.13 (4) Å3 | Block, colourless |
Z = 4 | 0.17 × 0.11 × 0.11 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 7509 independent reflections |
Radiation source: fine-focus sealed tube | 6211 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
ϕ and ω scans | θmax = 37.5°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −12→12 |
Tmin = 0.703, Tmax = 0.785 | k = −19→17 |
27359 measured reflections | l = −28→29 |
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)] = 0.035 | H-atom parameters constrained |
wR(F2) = 0.096 | w = 1/[σ2(Fo2) + (0.0418P)2 + 0.1348P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.003 |
7509 reflections | Δρmax = 0.87 e Å−3 |
167 parameters | Δρmin = −1.24 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 3286 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.020 (19) |
C12H19IO5 | V = 1440.13 (4) Å3 |
Mr = 370.17 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.3595 (1) Å | µ = 2.23 mm−1 |
b = 11.5145 (2) Å | T = 100 K |
c = 16.9945 (2) Å | 0.17 × 0.11 × 0.11 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 7509 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 6211 reflections with I > 2σ(I) |
Tmin = 0.703, Tmax = 0.785 | Rint = 0.046 |
27359 measured reflections |
R[F2 > 2σ(F2)] = 0.035 | H-atom parameters constrained |
wR(F2) = 0.096 | Δρmax = 0.87 e Å−3 |
S = 1.07 | Δρmin = −1.24 e Å−3 |
7509 reflections | Absolute structure: Flack (1983), 3286 Friedel pairs |
167 parameters | Absolute structure parameter: −0.020 (19) |
0 restraints |
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
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. |
x | y | z | Uiso*/Ueq | ||
I1 | 0.48767 (2) | −0.062287 (16) | 0.585388 (10) | 0.02322 (5) | |
O1 | 0.3941 (3) | 0.30650 (19) | 0.54871 (11) | 0.0202 (4) | |
O2 | 0.4126 (2) | 0.41053 (17) | 0.66190 (11) | 0.0174 (4) | |
O3 | −0.0095 (3) | 0.31453 (16) | 0.74636 (10) | 0.0169 (3) | |
O4 | 0.0869 (3) | 0.13209 (18) | 0.77122 (12) | 0.0181 (4) | |
O5 | 0.2158 (2) | 0.16776 (16) | 0.61095 (11) | 0.0162 (3) | |
C1 | 0.2269 (3) | 0.2856 (2) | 0.58845 (16) | 0.0166 (4) | |
H1A | 0.1256 | 0.3041 | 0.5532 | 0.020* | |
C2 | 0.4873 (3) | 0.4031 (2) | 0.58404 (14) | 0.0167 (4) | |
C3 | 0.2281 (3) | 0.3722 (2) | 0.65788 (15) | 0.0166 (4) | |
H3A | 0.1476 | 0.4379 | 0.6466 | 0.020* | |
C4 | 0.1835 (3) | 0.3209 (3) | 0.73797 (15) | 0.0167 (4) | |
H4A | 0.2335 | 0.3710 | 0.7793 | 0.020* | |
C5 | −0.0464 (3) | 0.2160 (2) | 0.79401 (15) | 0.0165 (4) | |
C6 | 0.2485 (3) | 0.1941 (2) | 0.75132 (13) | 0.0152 (5) | |
H6A | 0.3359 | 0.1907 | 0.7948 | 0.018* | |
C7 | 0.3309 (3) | 0.1412 (2) | 0.67660 (15) | 0.0165 (5) | |
H7A | 0.4522 | 0.1737 | 0.6677 | 0.020* | |
C8 | 0.3433 (4) | 0.0106 (3) | 0.68407 (16) | 0.0194 (5) | |
H8A | 0.2220 | −0.0221 | 0.6864 | 0.023* | |
H8B | 0.4059 | −0.0092 | 0.7325 | 0.023* | |
C9 | 0.4481 (4) | 0.5139 (3) | 0.53734 (17) | 0.0235 (6) | |
H9A | 0.3193 | 0.5267 | 0.5353 | 0.035* | |
H9B | 0.4945 | 0.5057 | 0.4848 | 0.035* | |
H9C | 0.5058 | 0.5787 | 0.5626 | 0.035* | |
C10 | 0.6874 (4) | 0.3785 (3) | 0.59115 (18) | 0.0220 (5) | |
H10A | 0.7049 | 0.3032 | 0.6142 | 0.033* | |
H10B | 0.7430 | 0.4364 | 0.6240 | 0.033* | |
H10C | 0.7421 | 0.3804 | 0.5399 | 0.033* | |
C11 | −0.0254 (4) | 0.2444 (3) | 0.88146 (15) | 0.0241 (5) | |
H11A | 0.0946 | 0.2739 | 0.8910 | 0.036* | |
H11B | −0.0440 | 0.1753 | 0.9120 | 0.036* | |
H11C | −0.1136 | 0.3018 | 0.8963 | 0.036* | |
C12 | −0.2321 (4) | 0.1723 (3) | 0.77260 (18) | 0.0205 (5) | |
H12A | −0.2307 | 0.1435 | 0.7196 | 0.031* | |
H12B | −0.3183 | 0.2346 | 0.7766 | 0.031* | |
H12C | −0.2662 | 0.1109 | 0.8078 | 0.031* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.02406 (8) | 0.02602 (9) | 0.01959 (7) | 0.00713 (7) | 0.00446 (7) | 0.00100 (6) |
O1 | 0.0212 (9) | 0.0223 (10) | 0.0170 (8) | −0.0053 (8) | 0.0033 (7) | −0.0029 (8) |
O2 | 0.0136 (7) | 0.0220 (10) | 0.0167 (8) | −0.0033 (6) | 0.0016 (6) | −0.0022 (7) |
O3 | 0.0124 (7) | 0.0161 (7) | 0.0222 (7) | −0.0003 (6) | 0.0014 (6) | 0.0023 (6) |
O4 | 0.0133 (8) | 0.0188 (9) | 0.0223 (9) | 0.0002 (6) | 0.0036 (7) | 0.0023 (7) |
O5 | 0.0169 (8) | 0.0149 (9) | 0.0166 (7) | −0.0011 (6) | −0.0038 (6) | 0.0004 (7) |
C1 | 0.0177 (9) | 0.0178 (12) | 0.0143 (9) | −0.0010 (8) | −0.0028 (9) | −0.0001 (9) |
C2 | 0.0173 (9) | 0.0193 (10) | 0.0134 (8) | −0.0026 (8) | 0.0025 (11) | 0.0023 (8) |
C3 | 0.0145 (10) | 0.0180 (12) | 0.0172 (10) | −0.0018 (8) | 0.0006 (8) | −0.0008 (9) |
C4 | 0.0127 (9) | 0.0207 (13) | 0.0167 (10) | −0.0020 (8) | 0.0012 (8) | −0.0009 (9) |
C5 | 0.0150 (10) | 0.0179 (12) | 0.0166 (10) | 0.0003 (8) | 0.0014 (8) | 0.0017 (8) |
C6 | 0.0125 (9) | 0.0197 (13) | 0.0135 (10) | −0.0002 (8) | −0.0011 (7) | 0.0007 (9) |
C7 | 0.0127 (10) | 0.0218 (13) | 0.0149 (10) | −0.0004 (8) | −0.0003 (8) | 0.0005 (9) |
C8 | 0.0186 (11) | 0.0227 (14) | 0.0170 (11) | 0.0044 (9) | 0.0011 (9) | 0.0041 (10) |
C9 | 0.0251 (13) | 0.0236 (14) | 0.0218 (12) | −0.0012 (10) | 0.0004 (10) | 0.0054 (11) |
C10 | 0.0175 (10) | 0.0292 (15) | 0.0193 (11) | 0.0012 (9) | 0.0031 (10) | 0.0007 (11) |
C11 | 0.0227 (13) | 0.0313 (15) | 0.0182 (10) | 0.0003 (11) | 0.0021 (10) | −0.0010 (10) |
C12 | 0.0170 (11) | 0.0200 (14) | 0.0245 (13) | −0.0021 (9) | 0.0014 (9) | 0.0036 (11) |
I1—C8 | 2.155 (3) | C5—C11 | 1.530 (4) |
O1—C1 | 1.424 (3) | C6—C7 | 1.533 (4) |
O1—C2 | 1.438 (3) | C6—H6A | 0.9800 |
O2—C3 | 1.430 (3) | C7—C8 | 1.512 (4) |
O2—C2 | 1.435 (3) | C7—H7A | 0.9800 |
O3—C5 | 1.420 (3) | C8—H8A | 0.9700 |
O3—C4 | 1.429 (3) | C8—H8B | 0.9700 |
O4—C6 | 1.428 (3) | C9—H9A | 0.9600 |
O4—C5 | 1.431 (3) | C9—H9B | 0.9600 |
O5—C1 | 1.412 (3) | C9—H9C | 0.9600 |
O5—C7 | 1.434 (3) | C10—H10A | 0.9600 |
C1—C3 | 1.545 (4) | C10—H10B | 0.9600 |
C1—H1A | 0.9800 | C10—H10C | 0.9600 |
C2—C10 | 1.505 (4) | C11—H11A | 0.9600 |
C2—C9 | 1.530 (4) | C11—H11B | 0.9600 |
C3—C4 | 1.519 (4) | C11—H11C | 0.9600 |
C3—H3A | 0.9800 | C12—H12A | 0.9600 |
C4—C6 | 1.554 (4) | C12—H12B | 0.9600 |
C4—H4A | 0.9800 | C12—H12C | 0.9600 |
C5—C12 | 1.501 (4) | ||
C1—O1—C2 | 110.17 (19) | C7—C6—H6A | 110.4 |
C3—O2—C2 | 107.52 (19) | C4—C6—H6A | 110.4 |
C5—O3—C4 | 106.8 (2) | O5—C7—C8 | 108.2 (2) |
C6—O4—C5 | 107.3 (2) | O5—C7—C6 | 109.1 (2) |
C1—O5—C7 | 112.42 (19) | C8—C7—C6 | 110.4 (2) |
O5—C1—O1 | 109.9 (2) | O5—C7—H7A | 109.7 |
O5—C1—C3 | 114.4 (2) | C8—C7—H7A | 109.7 |
O1—C1—C3 | 104.4 (2) | C6—C7—H7A | 109.7 |
O5—C1—H1A | 109.3 | C7—C8—I1 | 110.61 (18) |
O1—C1—H1A | 109.3 | C7—C8—H8A | 109.5 |
C3—C1—H1A | 109.3 | I1—C8—H8A | 109.5 |
O2—C2—O1 | 104.41 (18) | C7—C8—H8B | 109.5 |
O2—C2—C10 | 108.2 (2) | I1—C8—H8B | 109.5 |
O1—C2—C10 | 110.8 (2) | H8A—C8—H8B | 108.1 |
O2—C2—C9 | 110.8 (2) | C2—C9—H9A | 109.5 |
O1—C2—C9 | 109.8 (2) | C2—C9—H9B | 109.5 |
C10—C2—C9 | 112.5 (2) | H9A—C9—H9B | 109.5 |
O2—C3—C4 | 106.4 (2) | C2—C9—H9C | 109.5 |
O2—C3—C1 | 104.0 (2) | H9A—C9—H9C | 109.5 |
C4—C3—C1 | 115.6 (2) | H9B—C9—H9C | 109.5 |
O2—C3—H3A | 110.2 | C2—C10—H10A | 109.5 |
C4—C3—H3A | 110.2 | C2—C10—H10B | 109.5 |
C1—C3—H3A | 110.2 | H10A—C10—H10B | 109.5 |
O3—C4—C3 | 108.9 (2) | C2—C10—H10C | 109.5 |
O3—C4—C6 | 104.1 (2) | H10A—C10—H10C | 109.5 |
C3—C4—C6 | 115.4 (2) | H10B—C10—H10C | 109.5 |
O3—C4—H4A | 109.4 | C5—C11—H11A | 109.5 |
C3—C4—H4A | 109.4 | C5—C11—H11B | 109.5 |
C6—C4—H4A | 109.4 | H11A—C11—H11B | 109.5 |
O3—C5—O4 | 104.70 (19) | C5—C11—H11C | 109.5 |
O3—C5—C12 | 107.7 (2) | H11A—C11—H11C | 109.5 |
O4—C5—C12 | 109.4 (2) | H11B—C11—H11C | 109.5 |
O3—C5—C11 | 111.4 (2) | C5—C12—H12A | 109.5 |
O4—C5—C11 | 109.8 (2) | C5—C12—H12B | 109.5 |
C12—C5—C11 | 113.5 (2) | H12A—C12—H12B | 109.5 |
O4—C6—C7 | 109.1 (2) | C5—C12—H12C | 109.5 |
O4—C6—C4 | 104.4 (2) | H12A—C12—H12C | 109.5 |
C7—C6—C4 | 112.0 (2) | H12B—C12—H12C | 109.5 |
O4—C6—H6A | 110.4 |
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8B···O2i | 0.97 | 2.42 | 3.377 (3) | 169 |
C12—H12C···O2ii | 0.96 | 2.60 | 3.477 (4) | 152 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, y−1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C12H19IO5 |
Mr | 370.17 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 7.3595 (1), 11.5145 (2), 16.9945 (2) |
V (Å3) | 1440.13 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.23 |
Crystal size (mm) | 0.17 × 0.11 × 0.11 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.703, 0.785 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 27359, 7509, 6211 |
Rint | 0.046 |
(sin θ/λ)max (Å−1) | 0.857 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.096, 1.07 |
No. of reflections | 7509 |
No. of parameters | 167 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.87, −1.24 |
Absolute structure | Flack (1983), 3286 Friedel pairs |
Absolute structure parameter | −0.020 (19) |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8B···O2i | 0.97 | 2.42 | 3.377 (3) | 169 |
C12—H12C···O2ii | 0.96 | 2.60 | 3.477 (4) | 152 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, y−1/2, −z+3/2. |
Footnotes
‡Thomson Reuters Researcher ID: A-3561-2009.
Acknowledgements
HKF and WCL thank Universiti Sains Malaysia (USM) for a Research University Golden Goose Grant (No. 1001/PFIZIK/811012). WCL thanks USM for a student assistantship. AMI is grateful to the Director, NITK, Surathkal, India, for providing research facilities
References
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Libilomycin, an antibiotic which inhibits the growth of Gram-positive bacteria (Westwood et al., 1967) and which is effective against certain tumor cells, is produced by the microorganism, streptomyces albosporeas (Stevens et al., 1970), and contains 6-iodo,6-deoxy-1,2,3,4-di-O-isopropylidine-α-D-galactopyranoside as a part of its structure (Classon et al., 1988). These intermediates are used for the synthesis of 6-substituted purines which show high activity against Leishmania amazonensis (Gambogi Braga et al., 2007). These results prompted us to synthesize the title compound, (I).
Compound (I), Fig. 1, crystallized in the orthorhombic space group P212121 but has been reported previously (Krajewski et al., 1987) in the monoclinic space group P21, with a = 11.157 (2) Å, b = 20.047 (4) Å, c = 14.188 (2) Å and β = 107.67 (1)°. The dihedral angles between the six-membered ring systems, ring A (C1/C3/C4/C6/C7/O5), and the five-membered ring systems [rings B (C1—C3/O1—O2) and C (C4—C6/O3—O4)] are 67.66 (14)° and 71.79 (13)°, repectively. Moreover, the dihedral angle between rings B and C is 74.41 (12)° indicating that all the three rings are twisted from each other. Ring A adopts the twist-boat conformation (Boeyens, 1978; Cremer & Pople, 1975) with puckering amplitude Q = 0.629 (2) Å, ϕ = 75.3 (3)° and θ = 325.6 (2)°. On the other hand, each of rings B and C adopt an envelope conformation with flap atoms O2 and C5, respectively, but having different puckering parameters. For ring B, the puckering amplitude Q = 0.285 (2) Å and ϕ = 294.9 (5)° whereas for ring C, the puckering amplitude Q = 0.323 (3) Å and ϕ = 150.8 (4)°.
The crystal packing (Fig. 2 & Fig. 3) is consolidated by C8—H8B···O2 and C12—H12C···O2 contacts (Table 1) that link the molecules into a 2-D array parallel to the ab plane.