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ISSN: 2056-9890
Volume 70| Part 2| February 2014| Pages o108-o109

2,6-Di­chloro-9-(2′,3′,5′-tri-O-acetyl-β-D-ribo­furanos­yl)-9H-purine

aDepartment of Material Science and Applied Chemistry, Riga Technical University, 14/24 Azenes street, Riga, LV-1007, Latvia, and bLatvian Institute of Organic Synthesis, 21 Aizkraukles street, Riga, LV-1006, Latvia
*Correspondence e-mail: irina.novosjolova@rtu.lv

(Received 9 December 2013; accepted 23 December 2013; online 4 January 2014)

The title synthetic analog of purine nucleosides, C16H16Cl2N4O7, has its acetyl­ated β-furan­ose ring in a 3′β-envelope conformation, with the corresponding C atom deviating by 0.602 (5) Å from the rest of the ring. The planar part of the furan­ose ring forms a dihedral angle of 65.0 (1)° with the mean plane of the purine bicycle. In the crystal, mol­ecules form a three-dimensional network through multiple C—H⋯O and C—H⋯N hydrogen bonds and C—H⋯π interactions.

Related literature

For applications of 9-(2′,3′,5′-tri-O-acetyl-β-D-ribo­furanos­yl)-2,6-di­chloro-9H-purine in synthesis, see: Caner & Vilarrasa (2010[Caner, J. & Vilarrasa, J. (2010). J. Org. Chem. 75, 4880-4883.]); Korboukh et al. (2012[Korboukh, I., Hull-Ryde, E. A., Rittiner, J. E., Randhawa, A. S., Coleman, J., Fitzpatrick, B. J., Setola, V., Janzen, W. P., Frye, S. V., Zylka, M. J. & Jin, J. (2012). J. Med. Chem. 55, 6467-6477.]). For the synthesis, see: Vorbrüggen (1995[Vorbrüggen, H. (1995). Acc. Chem. Res. 28, 509-520.]); Robins & Uznański (1981[Robins, M. J. & Uznański, B. (1981). Can. J. Chem. 59, 2608-2611.]); Nair & Richardson (1982[Nair, V. & Richardson, S. G. (1982). Synthesis, 8, 670-672.]); Francom et al. (2002[Francom, P., Janeba, Z., Shibuya, S. & Robins, M. J. (2002). J. Org. Chem. 67, 6788-6796.]); Francom & Robins (2003[Francom, P. & Robins, M. J. (2003). J. Org. Chem. 68, 666-669.]); Gerster & Robins (1966[Gerster, J. F. & Robins, R. K. (1966). J. Org. Chem. 31, 3258-3262.]). The conditions were improved by using our previous studies (Kovalovs et al., 2013[Kovalovs, A., Novosjolova, I., Bizdēna, Ē., Bižāne, I., Skardziute, L., Kazlauskas, K., Jursenas, S. & Turks, M. (2013). Tetrahedron Lett. 54, 850-853.]; Novosjolova et al., 2013[Novosjolova, I., Bizdēna, Ē. & Turks, M. (2013). Tetrahedron Lett. 54, 6557-6561.]). For the biological activity of purine nucleosides, their anti­cancer and anti­viral activity and use as agonists and antagonists of adenosine receptors, see: Lech-Maranda et al. (2006[Lech-Maranda, E., Korycka, A. & Robak, T. (2006). Mini Rev. Med. Chem. 6, 575-581.]); Robak et al. (2009[Robak, T., Korycka, A., Lech-Maranda, E. & Robak, P. (2009). Molecules, 14, 1183-1226.]); Gumina et al. (2003[Gumina, G., Choi, Y. & Chu, C. (2003). Recent advances in antiviral nucleosides, in Antiviral Nucleosides: Chiral Synthesis and Chemotherapy, edited by C. K. Chu, pp. 1-76. Amsterdam: Elsevier.]); Fredholm et al. (2011[Fredholm, B. B., IJzerman, A. P., Jacobson, K. A., Linden, J. & Muller, C. E. (2011). Pharmacol. Rev. 63, 1-34.]); Elzein & Zablocki (2008[Elzein, E. & Zablocki, J. (2008). Expert Opin. Investig. Drugs, 17, 1901-1910.]). For the structure of another 2,6-di­chloro­purine ribonucleoside, 9-(2′-de­oxy-3′,5′-di-O-4-meth­oxy­benzoyl-β-D-ribo­furanos­yl)-2,6-di­chloro-9H-purine, see:Yang et al. (2012[Yang, F., Zhu, Y. & Yu, B. (2012). Chem. Commun. 48, 7097-7099.]). The purine heterocycle is known to form ππ stacking inter­actions in related structures, see: Sternglanz & Bugg (1975[Sternglanz, H. & Bugg, C. E. (1975). Acta Cryst. B31, 2888-2891.]). For standard bond lengths, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). The nature of hydrogen bonding is described by Gilli (2002[Gilli, G. (2002). In Fundamentals of Crystallography, edited by C. Giacovazzo, pp. 585-666. Oxford Univercity Press.]). For a description of the Cambridge Structural Database, see: Allen (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]).

[Scheme 1]

Experimental

Crystal data
  • C16H16Cl2N4O7

  • Mr = 447.23

  • Monoclinic, P 21

  • a = 10.1324 (2) Å

  • b = 9.6887 (3) Å

  • c = 10.5399 (2) Å

  • β = 106.537 (2)°

  • V = 991.90 (4) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.37 mm−1

  • T = 296 K

  • 0.38 × 0.32 × 0.15 mm

Data collection
  • Nonius KappaCCD diffractometer

  • 3898 measured reflections

  • 3898 independent reflections

  • 2846 reflections with I > 2σ(I)

Refinement
  • R[F2 > 2σ(F2)] = 0.046

  • wR(F2) = 0.107

  • S = 1.02

  • 3898 reflections

  • 265 parameters

  • H-atom parameters constrained

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.20 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1518 Friedel pairs

  • Absolute structure parameter: 0.00 (7)

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C4/C5/N7/C8/N9 imidazole ring.

D—H⋯A D—H H⋯A DA D—H⋯A
C8—H8⋯O15′ 0.93 2.52 3.265 (4) 137
C8—H8⋯O14′i 0.93 2.56 3.350 (4) 143
C1′—H1⋯N1ii 0.98 2.48 3.355 (5) 148
C9′—H9B⋯O18′iii 0.96 2.51 3.434 (4) 161
C13′—H13B⋯N7iv 0.96 2.54 3.502 (5) 175
C5′—H5ACgi 0.97 2.69 3.454 136
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+2]; (ii) [-x+2, y+{\script{1\over 2}}, -z+1]; (iii) x-1, y, z-1; (iv) x-1, y, z.

Data collection: KappaCCD Server Software (Nonius, 1997[Nonius (1997). KappaCCD Server Software. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinovski & Minor, 1997[Otwinovski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO (Otwinovski & Minor, 1997[Otwinovski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXL97, PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


1. Comment top

Purine nucleosides are well known of their biological activity: anti­cancer and anti­viral activities, and as agonists and antagonists of adenosine receptors (Lech-Maranda et al. (2006), Robak et al. (2009), Gumina et al. (2003), Fredholm et al. (2011), Elzein & Zablocki (2008).

There is only one example of similar crystal structure of 2,6-di­chloro­purine ribonucleoside (9-(2'-de­oxy-3',5'-di-O-4-meth­oxy­benzoyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine) in literature (Yang et al., 2012, CSD refcode KEBWOF). Search of the Cambridge Structural Database (CSD, Version 1.15; Allen, 2002) indicated that there are only 4 (CSD refcodes: CLPURB, JEMHUF, PUPZAC, ZEXWEE) entries of 2- or 6-chloro substituted derivatives from over 300 crystal structures of 9-(ribo­furan­osyl)-9H-purines. The bond lengths (Allen et al., 1987) and angles in the molecule of are close to standard values. The furan­ose cycle adopts an envelope conformation. Atoms C2', C1', O6' and C4' of furan­ose lie in same plane (denoted as plane A), 2'- and 5'-O-acetyl groups are on opposite sides of the A plane, while 3'-O-acetyl group lies close to the A plane. The C3' deviates from the A by 0.602 (5) Å. The dihedral angle between the least-square planes of the purine system and four planar atoms (C2', C1', O6' and C4') of furan­ose cycle is 65.0 (1)°. The main torsion angles describing the location of purine system in respect to furan­ose ring are: C8—N9—C1'—O6' (6.9 (4)°); C8—N9—C1'—C2' (-111.1 (3)°); C4—N9—C1'—O6' (-168.8 (3)°); C4—N9—C1'—C2' (73.2 (4)°). Regardless of the fact that purine heterocycle is known to form ππ stacking inter­actions in related structures (Sternglanz & Bugg, 1975), such inter­action was not observed in the crystals of the title compound. Moderate hydrogen bonds type C—H···O and C— H···N are present to form and stabilize three-dimensional architecture (Table 1).

The 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine 1 was synthesized by method of Vorbrüggen glycosyl­ation of 2,6-di­chloro­purine (Vorbrüggen, 1995). The conditions were improved by using our previous studies (Kovalovs et al., 2013; Novosjolova et al., 2013).

2. Experimental top

Single crystals of 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine were grown from an ethanol solution by slow evaporation in ambient temperature. 1H-NMR and 13C-NMR spectra were recorded at 300 MHz and at 75.5 MHz, respectively. The proton signals for residual non-deuterated solvents (δ 7.26 for CDCl3) and carbon signals (δ 77.1 for CDCl3) were used as an inter­nal references for 1H-NMR and 13C-NMR spectra, respectively. Coupling constants are reported in Hz. Analytical thin layer chromatography (TLC) was performed on Kieselgel 60 F254 glass plates precoated with a 0.25 mm thickness of silica gel. Dry MeCN was obtained by distillation over CaH2. Commercial reagents were used as received.

9-(2',3',5'-Tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine (3). N,O-Bis(tri­methyl­silyl)acetamide (5.60 mL, 22.7 mmol) was added to a stirred suspension of 2,6-di­chloro­purine (2) (4.02 g, 21.2 mmol) in dry aceto­nitrile (50 mL). The resulting mixture was stirred at 40 °C for 30 min until a clear solution was obtained. Solution of tetra-O-acetyl-D-ribo­furan­ose (1) (6.77 g, 21.3 mmol) in dry aceto­nitrile (35 mL) was then added, followed by TMSOTf (0.80 mL, 4.4 mmol). The resulting reaction mixture was stirred at 75-80 °C for 2.5-3 h (TLC control). Then it was cooled to ambient temperature and ethanol (1 mL) was added and the mixture was stirred for 15 min at the same temperature followed by evaporation under reduced pressure. The residue was dissolved in CH2Cl2 (100 mL) washed with saturated aqueous solution of NaHCO3 (3 × 25 mL) and water (1 × 25 mL), dried over anh. Na2SO4. Evaporation under reduced pressure provided product 3 (8.95 g, 95%) as a slightly yellow powder. The title compound was crystallized from ethanol, mp 158-160 °C [lit.: 159-161 °C (Gerster & Robins, 1966)]. The other analytical data of 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine are consistent with those reported earlier (Francom et al., 2002; Caner & Vilarrasa, 2010). Rf=0.45 (Toluene/EtOAc 1:2), IR (KBr), ν, cm-1: 2976, 2924, 1773, 1742, 1593, 1560, 1381, 1367, 1245, 1229, 1200, 1137, 1100, 1061; 1H-NMR (300 MHz, CDCl3) δ (ppm): 8.29 (s, 1H, H—C(8)), 6.21 (d, 1H, 3J1'-2' = 5.6 Hz, H—C(1')), 5.79 (t, 1H, 3J1'-2' = 3J2'-3' = 5.6 Hz, H—C(2')), 5.57 (dd, 1H, 3J2'-3' = 5.6 Hz, 3J3'-4' = 4.4 Hz, H—C(3')), 4.47 (quartet, 1H, 3J3'-4' = 3J4'-5' = 4.4 Hz, H—C(4')), 4.41 (d, 2H, 3J4'-5' = 4.4 Hz, H—C(5')), 2.16, 2.14, 2.09 (3s, 9H, H3COOC-C(2',3',5')); 13C-NMR (75.5 MHz, CDCl3) δ (ppm): 170.2, 169.5, 169.4, 153.3, 152.6, 152.2, 143.9, 131.3, 86.5, 80.8, 73.2, 70.5, 62.8, 20.7, 20.5, 20.3.

3. Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. All non-hydrogen atoms were refined anisotropically. All hydrogen atoms were positioned geometrically with C—H distances ranging from 0.93 Å to 0.98 Å and refined as riding on their parent atoms with Uiso (H) = 1.5Ueq (C) for methyl groups and Uiso (H) = 1.2Ueq (C) for others.

Related literature top

For applications of 9-(2',3',5'-tri-O-acetyl-β-D-ribofuranosyl)-2,6-dichloro-9H-purine in synthesis, see: Caner & Vilarrasa (2010); Korboukh et al. (2012). For the synthesis, see: Vorbrüggen (1995); Robins & Uznański (1981); Nair & Richardson (1982); Francom et al. (2002); Francom & Robins (2003); Gerster & Robins (1966). The conditions were improved by using our previous studies (Kovalovs et al., 2013; Novosjolova et al., 2013). For the biological activity of purine nucleosides, their anticancer and antiviral activity and use as agonists and antagonists of adenosine receptors, see: Lech-Maranda et al. (2006); Robak et al. (2009); Gumina et al. (2003); Fredholm et al. (2011); Elzein & Zablocki (2008). For the structure of another 2,6-dichloropurine ribonucleoside, 9-(2'-deoxy-3',5'-di-O-4-methoxybenzoyl-β-D-ribofuranosyl)-2,6-dichloro-9H-purine, see:Yang et al. (2012). The purine heterocycle is known to form ππ stacking interactions in related structures, see: Sternglanz & Bugg (1975). For standard bond lengths, see: Allen et al. (1987). The nature of hydrogen bonding is described by Gilli (2002). For a description of the Cambridge Structural Database, see: Allen (2002).

Structure description top

Purine nucleosides are well known of their biological activity: anti­cancer and anti­viral activities, and as agonists and antagonists of adenosine receptors (Lech-Maranda et al. (2006), Robak et al. (2009), Gumina et al. (2003), Fredholm et al. (2011), Elzein & Zablocki (2008).

There is only one example of similar crystal structure of 2,6-di­chloro­purine ribonucleoside (9-(2'-de­oxy-3',5'-di-O-4-meth­oxy­benzoyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine) in literature (Yang et al., 2012, CSD refcode KEBWOF). Search of the Cambridge Structural Database (CSD, Version 1.15; Allen, 2002) indicated that there are only 4 (CSD refcodes: CLPURB, JEMHUF, PUPZAC, ZEXWEE) entries of 2- or 6-chloro substituted derivatives from over 300 crystal structures of 9-(ribo­furan­osyl)-9H-purines. The bond lengths (Allen et al., 1987) and angles in the molecule of are close to standard values. The furan­ose cycle adopts an envelope conformation. Atoms C2', C1', O6' and C4' of furan­ose lie in same plane (denoted as plane A), 2'- and 5'-O-acetyl groups are on opposite sides of the A plane, while 3'-O-acetyl group lies close to the A plane. The C3' deviates from the A by 0.602 (5) Å. The dihedral angle between the least-square planes of the purine system and four planar atoms (C2', C1', O6' and C4') of furan­ose cycle is 65.0 (1)°. The main torsion angles describing the location of purine system in respect to furan­ose ring are: C8—N9—C1'—O6' (6.9 (4)°); C8—N9—C1'—C2' (-111.1 (3)°); C4—N9—C1'—O6' (-168.8 (3)°); C4—N9—C1'—C2' (73.2 (4)°). Regardless of the fact that purine heterocycle is known to form ππ stacking inter­actions in related structures (Sternglanz & Bugg, 1975), such inter­action was not observed in the crystals of the title compound. Moderate hydrogen bonds type C—H···O and C— H···N are present to form and stabilize three-dimensional architecture (Table 1).

The 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine 1 was synthesized by method of Vorbrüggen glycosyl­ation of 2,6-di­chloro­purine (Vorbrüggen, 1995). The conditions were improved by using our previous studies (Kovalovs et al., 2013; Novosjolova et al., 2013).

Single crystals of 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine were grown from an ethanol solution by slow evaporation in ambient temperature. 1H-NMR and 13C-NMR spectra were recorded at 300 MHz and at 75.5 MHz, respectively. The proton signals for residual non-deuterated solvents (δ 7.26 for CDCl3) and carbon signals (δ 77.1 for CDCl3) were used as an inter­nal references for 1H-NMR and 13C-NMR spectra, respectively. Coupling constants are reported in Hz. Analytical thin layer chromatography (TLC) was performed on Kieselgel 60 F254 glass plates precoated with a 0.25 mm thickness of silica gel. Dry MeCN was obtained by distillation over CaH2. Commercial reagents were used as received.

9-(2',3',5'-Tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine (3). N,O-Bis(tri­methyl­silyl)acetamide (5.60 mL, 22.7 mmol) was added to a stirred suspension of 2,6-di­chloro­purine (2) (4.02 g, 21.2 mmol) in dry aceto­nitrile (50 mL). The resulting mixture was stirred at 40 °C for 30 min until a clear solution was obtained. Solution of tetra-O-acetyl-D-ribo­furan­ose (1) (6.77 g, 21.3 mmol) in dry aceto­nitrile (35 mL) was then added, followed by TMSOTf (0.80 mL, 4.4 mmol). The resulting reaction mixture was stirred at 75-80 °C for 2.5-3 h (TLC control). Then it was cooled to ambient temperature and ethanol (1 mL) was added and the mixture was stirred for 15 min at the same temperature followed by evaporation under reduced pressure. The residue was dissolved in CH2Cl2 (100 mL) washed with saturated aqueous solution of NaHCO3 (3 × 25 mL) and water (1 × 25 mL), dried over anh. Na2SO4. Evaporation under reduced pressure provided product 3 (8.95 g, 95%) as a slightly yellow powder. The title compound was crystallized from ethanol, mp 158-160 °C [lit.: 159-161 °C (Gerster & Robins, 1966)]. The other analytical data of 9-(2',3',5'-tri-O-acetyl-β-D-ribo­furan­osyl)-2,6-di­chloro-9H-purine are consistent with those reported earlier (Francom et al., 2002; Caner & Vilarrasa, 2010). Rf=0.45 (Toluene/EtOAc 1:2), IR (KBr), ν, cm-1: 2976, 2924, 1773, 1742, 1593, 1560, 1381, 1367, 1245, 1229, 1200, 1137, 1100, 1061; 1H-NMR (300 MHz, CDCl3) δ (ppm): 8.29 (s, 1H, H—C(8)), 6.21 (d, 1H, 3J1'-2' = 5.6 Hz, H—C(1')), 5.79 (t, 1H, 3J1'-2' = 3J2'-3' = 5.6 Hz, H—C(2')), 5.57 (dd, 1H, 3J2'-3' = 5.6 Hz, 3J3'-4' = 4.4 Hz, H—C(3')), 4.47 (quartet, 1H, 3J3'-4' = 3J4'-5' = 4.4 Hz, H—C(4')), 4.41 (d, 2H, 3J4'-5' = 4.4 Hz, H—C(5')), 2.16, 2.14, 2.09 (3s, 9H, H3COOC-C(2',3',5')); 13C-NMR (75.5 MHz, CDCl3) δ (ppm): 170.2, 169.5, 169.4, 153.3, 152.6, 152.2, 143.9, 131.3, 86.5, 80.8, 73.2, 70.5, 62.8, 20.7, 20.5, 20.3.

For applications of 9-(2',3',5'-tri-O-acetyl-β-D-ribofuranosyl)-2,6-dichloro-9H-purine in synthesis, see: Caner & Vilarrasa (2010); Korboukh et al. (2012). For the synthesis, see: Vorbrüggen (1995); Robins & Uznański (1981); Nair & Richardson (1982); Francom et al. (2002); Francom & Robins (2003); Gerster & Robins (1966). The conditions were improved by using our previous studies (Kovalovs et al., 2013; Novosjolova et al., 2013). For the biological activity of purine nucleosides, their anticancer and antiviral activity and use as agonists and antagonists of adenosine receptors, see: Lech-Maranda et al. (2006); Robak et al. (2009); Gumina et al. (2003); Fredholm et al. (2011); Elzein & Zablocki (2008). For the structure of another 2,6-dichloropurine ribonucleoside, 9-(2'-deoxy-3',5'-di-O-4-methoxybenzoyl-β-D-ribofuranosyl)-2,6-dichloro-9H-purine, see:Yang et al. (2012). The purine heterocycle is known to form ππ stacking interactions in related structures, see: Sternglanz & Bugg (1975). For standard bond lengths, see: Allen et al. (1987). The nature of hydrogen bonding is described by Gilli (2002). For a description of the Cambridge Structural Database, see: Allen (2002).

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 1. All non-hydrogen atoms were refined anisotropically. All hydrogen atoms were positioned geometrically with C—H distances ranging from 0.93 Å to 0.98 Å and refined as riding on their parent atoms with Uiso (H) = 1.5Ueq (C) for methyl groups and Uiso (H) = 1.2Ueq (C) for others.

Computing details top

Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: SCALEPACK (Otwinovski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinovski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound showing 50% probability displacement ellipsoids and the atom-numbering (hydrogen atoms are shown as small spheres of arbitrary radii)
[Figure 2] Fig. 2. Packing diagram of the title compound viewed down the b axis
2,6-Dichloro-9-(2',3',5'-tri-O-acetyl-β-D-ribofuranosyl)-9H-purine top
Crystal data top
C16H16Cl2N4O7F(000) = 460
Mr = 447.23Dx = 1.497 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 17407 reflections
a = 10.1324 (2) Åθ = 1.0–27.5°
b = 9.6887 (3) ŵ = 0.37 mm1
c = 10.5399 (2) ÅT = 296 K
β = 106.537 (2)°Prism, colorless
V = 991.90 (4) Å30.38 × 0.32 × 0.15 mm
Z = 2
Data collection top
Nonius KappaCCD
diffractometer
2846 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.000
Graphite monochromatorθmax = 27.5°, θmin = 2.0°
CCD scansh = 1313
3898 measured reflectionsk = 1112
3898 independent reflectionsl = 1313
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)] = 0.046H-atom parameters constrained
wR(F2) = 0.107 w = 1/[σ2(Fo2) + (0.0352P)2 + 0.3514P]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
3898 reflectionsΔρmax = 0.22 e Å3
265 parametersΔρmin = 0.20 e Å3
0 restraintsAbsolute structure: Flack (1983), 1518 Friedel pairs
0 constraintsAbsolute structure parameter: 0.00 (7)
Primary atom site location: structure-invariant direct methods
Crystal data top
C16H16Cl2N4O7V = 991.90 (4) Å3
Mr = 447.23Z = 2
Monoclinic, P21Mo Kα radiation
a = 10.1324 (2) ŵ = 0.37 mm1
b = 9.6887 (3) ÅT = 296 K
c = 10.5399 (2) Å0.38 × 0.32 × 0.15 mm
β = 106.537 (2)°
Data collection top
Nonius KappaCCD
diffractometer
2846 reflections with I > 2σ(I)
3898 measured reflectionsRint = 0.000
3898 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.107Δρmax = 0.22 e Å3
S = 1.02Δρmin = 0.20 e Å3
3898 reflectionsAbsolute structure: Flack (1983), 1518 Friedel pairs
265 parametersAbsolute structure parameter: 0.00 (7)
0 restraints
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
N11.0850 (3)0.1139 (3)0.4785 (3)0.0535 (8)
C20.9650 (4)0.1787 (4)0.4602 (3)0.0508 (9)
N30.9178 (3)0.2553 (3)0.5399 (2)0.0458 (6)
C41.0170 (3)0.2704 (3)0.6574 (3)0.0404 (7)
C51.1477 (3)0.2135 (4)0.6915 (3)0.0429 (8)
C61.1761 (4)0.1309 (4)0.5952 (3)0.0510 (9)
N71.2211 (3)0.2508 (3)0.8196 (3)0.0506 (7)
C81.1331 (3)0.3266 (4)0.8596 (3)0.0473 (8)
H81.15400.36710.94300.057*
N91.0071 (2)0.3404 (3)0.7669 (2)0.0405 (6)
Cl101.32958 (12)0.04548 (15)0.62312 (11)0.0892 (4)
Cl110.85038 (11)0.15549 (12)0.30379 (9)0.0733 (3)
C1'0.8877 (3)0.4205 (4)0.7769 (3)0.0409 (7)
H10.85740.48270.70080.049*
C2'0.7695 (3)0.3282 (4)0.7845 (3)0.0397 (7)
H20.76420.24210.73440.048*
C3'0.8034 (3)0.3062 (3)0.9343 (3)0.0385 (7)
H30.87720.23800.96390.046*
C4'0.8537 (3)0.4472 (3)0.9862 (3)0.0382 (7)
H40.77330.50630.97860.046*
C5'0.9455 (3)0.4570 (4)1.1251 (3)0.0432 (8)
H5A0.97880.55091.14370.052*
H5B0.89460.43251.18700.052*
O6'0.9264 (2)0.4982 (2)0.89486 (18)0.0402 (5)
O7'0.6460 (2)0.4081 (2)0.74576 (19)0.0490 (6)
C8'0.5479 (3)0.3728 (4)0.6337 (3)0.0520 (9)
C9'0.4297 (4)0.4704 (5)0.6096 (4)0.0696 (12)
H9A0.46160.56270.60310.104*
H9C0.38950.46510.68160.104*
H9B0.36200.44620.52850.104*
O10'0.5636 (3)0.2809 (4)0.5649 (3)0.0967 (11)
O11'0.6883 (2)0.2701 (2)0.9804 (2)0.0458 (6)
C12'0.6474 (4)0.1370 (4)0.9636 (3)0.0504 (9)
C13'0.5286 (4)0.1098 (5)1.0189 (5)0.0826 (15)
H13A0.51880.01221.02880.124*
H13B0.44560.14620.95970.124*
H13C0.54550.15381.10370.124*
O14'0.7012 (3)0.0544 (3)0.9110 (3)0.0775 (8)
O15'1.0599 (2)0.3644 (2)1.13994 (18)0.0441 (5)
C16'1.1551 (3)0.3677 (4)1.2595 (3)0.0499 (8)
C17'1.2746 (4)0.2794 (4)1.2628 (3)0.0618 (10)
H17A1.35700.33421.28650.093*
H17B1.26300.23931.17700.093*
H17C1.28160.20751.32700.093*
O18'1.1385 (3)0.4370 (4)1.3478 (2)0.0909 (10)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.063 (2)0.055 (2)0.0498 (17)0.0015 (15)0.0270 (14)0.0050 (14)
C20.064 (2)0.052 (2)0.0376 (17)0.0083 (19)0.0173 (14)0.0028 (16)
N30.0551 (17)0.0437 (17)0.0444 (15)0.0010 (13)0.0239 (12)0.0023 (13)
C40.0511 (19)0.0378 (19)0.0362 (16)0.0014 (15)0.0189 (13)0.0051 (14)
C50.0451 (19)0.046 (2)0.0406 (16)0.0016 (15)0.0166 (13)0.0040 (15)
C60.057 (2)0.050 (2)0.0533 (19)0.0053 (17)0.0275 (16)0.0000 (17)
N70.0465 (16)0.0552 (19)0.0495 (15)0.0014 (14)0.0126 (12)0.0009 (14)
C80.050 (2)0.048 (2)0.0437 (17)0.0015 (16)0.0143 (14)0.0012 (15)
N90.0450 (15)0.0425 (16)0.0363 (13)0.0033 (12)0.0154 (11)0.0016 (12)
Cl100.0712 (7)0.1099 (11)0.0907 (7)0.0324 (7)0.0299 (6)0.0156 (7)
Cl110.0824 (7)0.0903 (9)0.0433 (5)0.0046 (6)0.0118 (4)0.0139 (5)
C1'0.0501 (18)0.0420 (19)0.0319 (14)0.0100 (15)0.0137 (12)0.0040 (14)
C2'0.0413 (17)0.0406 (19)0.0364 (15)0.0043 (14)0.0096 (12)0.0049 (14)
C3'0.0383 (16)0.0419 (19)0.0366 (15)0.0032 (14)0.0130 (12)0.0013 (14)
C4'0.0405 (16)0.0397 (19)0.0357 (14)0.0054 (14)0.0129 (12)0.0043 (14)
C5'0.0492 (18)0.044 (2)0.0364 (15)0.0030 (15)0.0116 (13)0.0055 (14)
O6'0.0493 (12)0.0367 (13)0.0371 (11)0.0013 (10)0.0162 (9)0.0035 (9)
O7'0.0426 (12)0.0597 (17)0.0380 (11)0.0133 (11)0.0005 (9)0.0104 (10)
C8'0.044 (2)0.060 (3)0.0451 (18)0.0044 (17)0.0028 (14)0.0038 (18)
C9'0.047 (2)0.084 (3)0.065 (2)0.011 (2)0.0044 (16)0.006 (2)
O10'0.079 (2)0.096 (3)0.089 (2)0.0098 (18)0.0174 (16)0.048 (2)
O11'0.0382 (12)0.0531 (16)0.0492 (12)0.0009 (11)0.0174 (9)0.0004 (11)
C12'0.044 (2)0.054 (2)0.0484 (18)0.0001 (18)0.0050 (14)0.0148 (18)
C13'0.053 (3)0.109 (4)0.087 (3)0.016 (2)0.022 (2)0.027 (3)
O14'0.0762 (19)0.0504 (18)0.112 (2)0.0012 (16)0.0364 (17)0.0004 (17)
O15'0.0455 (12)0.0469 (14)0.0356 (10)0.0033 (10)0.0049 (9)0.0040 (10)
C16'0.051 (2)0.048 (2)0.0401 (18)0.0036 (17)0.0029 (14)0.0044 (17)
C17'0.056 (2)0.062 (3)0.057 (2)0.006 (2)0.0006 (16)0.0030 (19)
O18'0.087 (2)0.120 (3)0.0482 (14)0.026 (2)0.0101 (13)0.0346 (18)
Geometric parameters (Å, º) top
N1—C61.321 (4)C4'—C5'1.497 (4)
N1—C21.333 (4)C4'—H40.9800
C2—N31.308 (4)C5'—O15'1.439 (4)
C2—Cl111.740 (3)C5'—H5A0.9700
N3—C41.363 (4)C5'—H5B0.9700
C4—N91.367 (4)O7'—C8'1.354 (4)
C4—C51.384 (4)C8'—O10'1.187 (4)
C5—C61.386 (4)C8'—C9'1.489 (5)
C5—N71.391 (4)C9'—H9A0.9600
C6—Cl101.712 (4)C9'—H9C0.9600
N7—C81.314 (4)C9'—H9B0.9600
C8—N91.376 (4)O11'—C12'1.351 (5)
C8—H80.9300C12'—O14'1.190 (4)
N9—C1'1.466 (4)C12'—C13'1.502 (5)
C1'—O6'1.409 (4)C13'—H13A0.9600
C1'—C2'1.515 (5)C13'—H13B0.9600
C1'—H10.9800C13'—H13C0.9600
C2'—O7'1.429 (4)O15'—C16'1.352 (3)
C2'—C3'1.532 (4)C16'—O18'1.198 (4)
C2'—H20.9800C16'—C17'1.475 (5)
C3'—O11'1.429 (3)C17'—H17A0.9600
C3'—C4'1.505 (5)C17'—H17B0.9600
C3'—H30.9800C17'—H17C0.9600
C4'—O6'1.455 (3)
C6—N1—C2116.3 (3)C5'—C4'—C3'117.7 (3)
N3—C2—N1131.2 (3)O6'—C4'—H4108.3
N3—C2—Cl11114.5 (3)C5'—C4'—H4108.3
N1—C2—Cl11114.3 (2)C3'—C4'—H4108.3
C2—N3—C4109.5 (3)O15'—C5'—C4'108.9 (2)
N3—C4—N9127.5 (3)O15'—C5'—H5A109.9
N3—C4—C5126.6 (3)C4'—C5'—H5A109.9
N9—C4—C5105.9 (3)O15'—C5'—H5B109.9
C4—C5—C6115.0 (3)C4'—C5'—H5B109.9
C4—C5—N7110.9 (3)H5A—C5'—H5B108.3
C6—C5—N7134.1 (3)C1'—O6'—C4'109.7 (2)
N1—C6—C5121.2 (3)C8'—O7'—C2'118.5 (3)
N1—C6—Cl10117.4 (2)O10'—C8'—O7'122.0 (3)
C5—C6—Cl10121.4 (3)O10'—C8'—C9'127.8 (3)
C8—N7—C5103.5 (3)O7'—C8'—C9'110.1 (3)
N7—C8—N9113.8 (3)C8'—C9'—H9A109.5
N7—C8—H8123.1C8'—C9'—H9C109.5
N9—C8—H8123.1H9A—C9'—H9C109.5
C4—N9—C8105.9 (3)C8'—C9'—H9B109.5
C4—N9—C1'125.7 (2)H9A—C9'—H9B109.5
C8—N9—C1'128.2 (3)H9C—C9'—H9B109.5
O6'—C1'—N9108.5 (2)C12'—O11'—C3'116.1 (3)
O6'—C1'—C2'107.2 (2)O14'—C12'—O11'122.6 (3)
N9—C1'—C2'111.8 (3)O14'—C12'—C13'126.0 (4)
O6'—C1'—H1109.8O11'—C12'—C13'111.5 (4)
N9—C1'—H1109.8C12'—C13'—H13A109.5
C2'—C1'—H1109.8C12'—C13'—H13B109.5
O7'—C2'—C1'107.8 (3)H13A—C13'—H13B109.5
O7'—C2'—C3'106.9 (2)C12'—C13'—H13C109.5
C1'—C2'—C3'100.8 (2)H13A—C13'—H13C109.5
O7'—C2'—H2113.5H13B—C13'—H13C109.5
C1'—C2'—H2113.5C16'—O15'—C5'115.2 (2)
C3'—C2'—H2113.5O18'—C16'—O15'121.1 (3)
O11'—C3'—C4'108.8 (2)O18'—C16'—C17'127.1 (3)
O11'—C3'—C2'114.8 (2)O15'—C16'—C17'111.8 (3)
C4'—C3'—C2'101.7 (2)C16'—C17'—H17A109.5
O11'—C3'—H3110.4C16'—C17'—H17B109.5
C4'—C3'—H3110.4H17A—C17'—H17B109.5
C2'—C3'—H3110.4C16'—C17'—H17C109.5
O6'—C4'—C5'109.5 (2)H17A—C17'—H17C109.5
O6'—C4'—C3'104.5 (2)H17B—C17'—H17C109.5
C6—N1—C2—N32.3 (6)O6'—C1'—C2'—O7'82.0 (3)
C6—N1—C2—Cl11178.7 (3)N9—C1'—C2'—O7'159.2 (2)
N1—C2—N3—C43.0 (5)O6'—C1'—C2'—C3'29.8 (3)
Cl11—C2—N3—C4178.0 (2)N9—C1'—C2'—C3'89.0 (3)
C2—N3—C4—N9178.6 (3)O7'—C2'—C3'—O11'44.0 (4)
C2—N3—C4—C50.9 (5)C1'—C2'—C3'—O11'156.5 (3)
N3—C4—C5—C61.5 (5)O7'—C2'—C3'—C4'73.3 (3)
N9—C4—C5—C6176.6 (3)C1'—C2'—C3'—C4'39.2 (3)
N3—C4—C5—N7180.0 (3)O11'—C3'—C4'—O6'157.0 (2)
N9—C4—C5—N71.9 (4)C2'—C3'—C4'—O6'35.5 (3)
C2—N1—C6—C50.8 (5)O11'—C3'—C4'—C5'81.3 (3)
C2—N1—C6—Cl10178.4 (3)C2'—C3'—C4'—C5'157.2 (2)
C4—C5—C6—N12.4 (5)O6'—C4'—C5'—O15'65.6 (3)
N7—C5—C6—N1179.6 (4)C3'—C4'—C5'—O15'53.4 (3)
C4—C5—C6—Cl10176.8 (3)N9—C1'—O6'—C4'112.7 (3)
N7—C5—C6—Cl101.2 (6)C2'—C1'—O6'—C4'8.2 (3)
C4—C5—N7—C80.9 (4)C5'—C4'—O6'—C1'144.5 (2)
C6—C5—N7—C8177.2 (4)C3'—C4'—O6'—C1'17.6 (3)
C5—N7—C8—N90.4 (4)C1'—C2'—O7'—C8'115.0 (3)
N3—C4—N9—C8179.9 (3)C3'—C2'—O7'—C8'137.4 (3)
C5—C4—N9—C82.0 (3)C2'—O7'—C8'—O10'2.6 (5)
N3—C4—N9—C1'3.4 (5)C2'—O7'—C8'—C9'178.7 (3)
C5—C4—N9—C1'178.5 (3)C4'—C3'—O11'—C12'168.0 (2)
N7—C8—N9—C41.6 (4)C2'—C3'—O11'—C12'78.9 (3)
N7—C8—N9—C1'177.9 (3)C3'—O11'—C12'—O14'1.6 (5)
C4—N9—C1'—O6'168.8 (3)C3'—O11'—C12'—C13'178.4 (3)
C8—N9—C1'—O6'6.9 (4)C4'—C5'—O15'—C16'176.9 (3)
C4—N9—C1'—C2'73.2 (4)C5'—O15'—C16'—O18'4.7 (5)
C8—N9—C1'—C2'111.1 (3)C5'—O15'—C16'—C17'174.8 (3)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C4/C5/N7/C8/N9 imidazole ring.
D—H···AD—HH···AD···AD—H···A
C8—H8···O150.932.523.265 (4)137
C8—H8···O14i0.932.563.350 (4)143
C1—H1···N1ii0.982.483.355 (5)148
C9—H9B···O18iii0.962.513.434 (4)161
C13—H13B···N7iv0.962.543.502 (5)175
C5—H5A···Cgi0.972.693.454136
Symmetry codes: (i) x+2, y+1/2, z+2; (ii) x+2, y+1/2, z+1; (iii) x1, y, z1; (iv) x1, y, z.
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C4/C5/N7/C8/N9 imidazole ring.
D—H···AD—HH···AD···AD—H···A
C8—H8···O15'0.932.523.265 (4)137
C8—H8···O14'i0.932.563.350 (4)143
C1'—H1···N1ii0.982.483.355 (5)148
C9'—H9B···O18'iii0.962.513.434 (4)161
C13'—H13B···N7iv0.962.543.502 (5)175
C5'—H5A···Cgi0.972.693.454136
Symmetry codes: (i) x+2, y+1/2, z+2; (ii) x+2, y+1/2, z+1; (iii) x1, y, z1; (iv) x1, y, z.
 

Acknowledgements

IN thanks the European Social Fund within the project `Support for the implementation of doctoral studies at Riga Technical University' for a scholarship and ERDF project 2DP/2.1.1.2.0/10/APIA/VI4AA/003 for the opportunity to present this work at the 14th Tetra­hedron Symposium.

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ISSN: 2056-9890
Volume 70| Part 2| February 2014| Pages o108-o109
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