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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 72| Part 5| May 2016| Pages 624-627

Crystal structure of a nucleoside model for the inter­strand cross-link formed by the reaction of 2′-de­­oxy­guanosine and an abasic site in duplex DNA

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a125 Chemistry Bldg, University of Missouri-Columbia, MO 65211, USA
*Correspondence e-mail: gatesk@missouri.edu

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 25 February 2016; accepted 26 March 2016; online 5 April 2016)

The title compound, 9-[(2R,4S,5R)-4-hy­droxy-5-(hy­droxy­meth­yl)tetra­hydro­furan-2-yl]-2-{[(2R,4S,5R)-4-meth­oxy-5-(meth­oxy­meth­yl)tetra­hydro­furan-2-yl]amino}-1H-purin-6(9H)-one, C17H25N5O7, crystallizes with two independent mol­ecules (A and B) in the asymmetric unit. In the crystal, the guanosine moieties of mol­ecules A and B are linked by N—H⋯N and O—H⋯N hydrogen-bonding inter­actions, forming ribbons which are stacked to form columns along [100]. These columns are then linked by O—H⋯O hydrogen bonds between the ribose moieties and numerous C—H⋯O inter­actions to complete the three-dimensional structure.

1. Chemical context

Recent work has characterized a structurally novel set of inter­strand DNA–DNA cross-links involving reaction of the ubiquitous DNA abasic lesion with a nucleobase on the opposing strand of the double helix (Catalano et al., 2015[Catalano, M. J., Liu, S., Andersen, N., Yang, Z., Johnson, K. M., Price, N. A., Wang, Y. & Gates, K. S. (2015). J. Am. Chem. Soc. 137, 3933-3945.]; Dutta et al., 2007[Dutta, S., Chowdhury, G. & Gates, K. S. (2007). J. Am. Chem. Soc. 129, 1852-1853.]; Gamboa Varela & Gates, 2015[Gamboa Varela, J. & Gates, K. S. (2015). Angew. Chem. Int. Ed. 54, 7666-7669.]; Johnson et al., 2013[Johnson, K. M., Price, N. E., Wang, J., Fekry, M. I., Dutta, S., Seiner, D. R., Wang, Y. & Gates, K. S. (2013). J. Am. Chem. Soc. 135, 1015-1025.]; Price et al., 2014[Price, N. E., Johnson, K. M., Wang, J., Fekry, M. I., Wang, Y. & Gates, K. S. (2014). J. Am. Chem. Soc. 136, 3483-3490.], 2015[Price, N. E., Catalano, M. J., Liu, S., Wang, Y. & Gates, K. S. (2015). Nucleic Acids Res. 43, 3434-3441.]; Yang et al., 2015[Yang, Z., Price, N. E., Johnson, K. M. & Gates, K. S. (2015). Biochemistry, 54, 4259-4266.]; Zhang et al., 2015[Zhang, X., Price, N. E., Fang, X., Yang, Z., Gu, L. Q. & Gates, K. S. (2015). ACS Nano, 9, 11812-11819.]). Evidence indicates that the covalent attachment is forged between the anomeric carbon of the abasic sugar and the exocyclic amino group of either a guanine, adenine, or N4-amino­cytosine residue (Catalano et al., 2015[Catalano, M. J., Liu, S., Andersen, N., Yang, Z., Johnson, K. M., Price, N. A., Wang, Y. & Gates, K. S. (2015). J. Am. Chem. Soc. 137, 3933-3945.]; Dutta et al., 2007[Dutta, S., Chowdhury, G. & Gates, K. S. (2007). J. Am. Chem. Soc. 129, 1852-1853.]; Gamboa Varela & Gates, 2015[Gamboa Varela, J. & Gates, K. S. (2015). Angew. Chem. Int. Ed. 54, 7666-7669.]; Johnson et al., 2013[Johnson, K. M., Price, N. E., Wang, J., Fekry, M. I., Dutta, S., Seiner, D. R., Wang, Y. & Gates, K. S. (2013). J. Am. Chem. Soc. 135, 1015-1025.]; Price et al., 2014[Price, N. E., Johnson, K. M., Wang, J., Fekry, M. I., Wang, Y. & Gates, K. S. (2014). J. Am. Chem. Soc. 136, 3483-3490.], 2015[Price, N. E., Catalano, M. J., Liu, S., Wang, Y. & Gates, K. S. (2015). Nucleic Acids Res. 43, 3434-3441.]; Yang et al., 2015[Yang, Z., Price, N. E., Johnson, K. M. & Gates, K. S. (2015). Biochemistry, 54, 4259-4266.]). This type of glycosidic linkage involving the exocyclic amino group of a nucleobase is reminiscent of that found in the natural products anicemycin, spicamycin, and septacidin (Acton et al., 1977[Acton, E. M., Ryan, K. J. & Luetzow, A. E. (1977). J. Med. Chem. 20, 1362-1371.]; Igarashi et al., 2005[Igarashi, Y., Ootsu, K., Onaka, H., Fujita, T., Uehara, Y. & Furumai, T. (2005). J. Antibiot. 58, 322-326.]; Suzuki et al., 2002[Suzuki, T., Suzuki, S. T., Yamada, I., Koashi, Y., Yamada, K. & Chida, N. (2002). J. Org. Chem. 67, 2874-2880.]).

[Scheme 1]

Here we present single crystal X-ray crystallographic analysis of a nucleoside analog, (I)[link], of the 2′-de­oxy­guanosine/abasic site cross-link. This structure corroborates an earlier two-dimensional NMR analysis (Catalano et al., 2015[Catalano, M. J., Liu, S., Andersen, N., Yang, Z., Johnson, K. M., Price, N. A., Wang, Y. & Gates, K. S. (2015). J. Am. Chem. Soc. 137, 3933-3945.]) concluding that the 2-de­oxy­ribose unit attached at the exocyclic N2-amino group of the guanine residue exists in the cyclic amino­glycoside form.

2. Structural commentary

The two independent mol­ecules (A and B) of (I)[link] are shown in Fig. 1[link] as they are oriented in the crystal, while Fig. 2[link] shows an overlay to illustrate the differences in orientation and conformation of the furan­ose rings. Ring puckering analysis, after Cremer & Pople as calculated using PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) indicates the furan­ose rings attached to N4 positions in the two mol­ecules to be half-chairs in both mol­ecules, but with the maximum variance from planarity occurring between C7 and C8 in mol­ecule A and C6 and C7 in mol­ecule B [Q(2) = 0.367 (2), Φ(2) = 88.0 (4)° for mol­ecule A and Q(2) = 0.347 (2), Φ(2) = 60.6 (4)° for mol­ecule B]. The disposition of these furan­ose rings relative to the purine rings can be described by the torsion angle C2—N4—C6—O2, which is 70.9 (3)° in mol­ecule A and 61.7 (3)° in mol­ecule B. The furan­ose ring attached to the N5 position in mol­ecule A is again a half-chair, with the maximum deviation from planarity between C11A and C12A [Q(2) = 3.41 (2), Φ(2) = 62.2 (3)°], while this furan­ose ring in mol­ecule B is an envelope with C11B at the flap [Q(2) = 0.422 (2), Φ(2) = 45.4 (3)°]. The disposition of these furan­ose rings relative to the purine rings can be described by the angle C1—N5—C11—O5, which is −87.4 (2)° in mol­ecule A and −93.7 (2)° in mol­ecule B.

[Figure 1]
Figure 1
The mol­ecular structure of (I)[link] showing 50% displacement ellipsoids.
[Figure 2]
Figure 2
Overlay plot of the two mol­ecules in (I). A molecule in orange and B molecule in blue.

3. Supra­molecular features

In the crystal, the two mol­ecules form infinite ribbons along the ac diagonal of the unit cell, with the A mol­ecules on one side of the ribbon and the B mol­ecules on the other. The mol­ecules are staggered such that each A mol­ecule forms hydrogen bonds to two B mol­ecules and each B mol­ecule forms hydrogen bonds (Table 1[link]) to two A mol­ecules, fully involving the N1, N3, N5 and O1 atoms. These ribbons are then stacked to form slabs propagating in the ac plane and one half the b dimension in thickness. The de­oxy­ribose moieties occupy the outsides of these slabs and are linked via hydrogen bonds to twofold screw-related slabs, resulting in a herringbone pattern in the three-dimensional structure as seen in Fig. 3[link].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1A—H1A⋯N3B 0.88 1.92 2.789 (2) 170
O3A—H3A⋯O5Ai 0.84 2.07 2.897 (2) 167
O4A—H4A⋯O3Bii 0.84 2.01 2.847 (2) 178
N5A—H5A⋯O1B 0.88 2.23 3.058 (2) 157
C5A—H5A1⋯O1Biii 0.95 2.63 3.284 (3) 126
C7A—H7A1⋯N2A 0.99 2.46 3.172 (3) 128
C8A—H8A⋯O7Ai 1.00 2.39 3.316 (3) 153
C12A—H12A⋯O1Aiv 0.99 2.61 3.432 (3) 141
C12A—H12B⋯O1B 0.99 2.55 3.426 (3) 147
C16A—H16A⋯O4Av 0.98 2.47 3.401 (3) 158
C16A—H16B⋯O6Av 0.98 2.54 3.222 (3) 127
C16A—H16C⋯O2Avi 0.98 2.50 3.356 (3) 146
C17A—H17A⋯O3Avi 0.98 2.65 3.610 (3) 168
C17A—H17B⋯O2Aiv 0.98 2.60 3.573 (3) 175
N1B—H1B⋯N3Avi 0.88 1.94 2.808 (2) 166
O3B—H3B⋯O5Bvii 0.84 1.99 2.817 (2) 169
O4B—H4B⋯N2B 0.84 2.38 3.180 (3) 158
N5B—H5B⋯O1Avi 0.88 2.19 3.027 (2) 159
C5B—H5B1⋯O1A 0.95 2.60 3.269 (3) 127
C8B—H8B⋯O7Bvii 1.00 2.49 3.363 (3) 146
C11B—H11B⋯O4B 1.00 2.59 3.251 (3) 124
C12B—H12C⋯O1Avi 0.99 2.55 3.363 (3) 140
C12B—H12D⋯O1Bv 0.99 2.45 3.424 (3) 167
C14B—H14B⋯O4B 1.00 2.61 3.272 (3) 123
C17B—H17E⋯O2Bv 0.98 2.48 3.456 (3) 176
Symmetry codes: (i) x-1, y, z; (ii) [-x+1, y+{\script{1\over 2}}, -z]; (iii) x-1, y, z-1; (iv) x, y, z+1; (v) x+1, y, z; (vi) x+1, y, z+1; (vii) x, y, z-1.
[Figure 3]
Figure 3
The packing in (I)[link] along the c axis showing the formation of hydrogen-bonded chains (A mol­ecules green, B mol­ecules blue).

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.36, update February 2015; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]) for de­oxy­guanosine analogues with exocyclic amine substitution revealed three crystal structures (Morr et al., 1991[Morr, M., Ernst, L. & Schomburg, D. (1991). Liebigs Ann. Chem. 1991, 615-631.]; Fujino et al., 2010[Fujino, T., Tsunaka, N., Guillot-Nieckowski, M., Nakanishi, W., Iwamoto, T., Nakamura, E. & Isobe, H. (2010). Tetrahedron Lett. 51, 2036-2038.]). In all these crystal structures, the five-membered 2-de­oxy­ribo­furan­ose rings have envelope conformations, as in the title compound.

5. Synthesis and crystallization

2′-De­oxy­guanosine (199 mg, 0.75 mmol) and 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose (110 mg, 0.74 mmol) were dissolved in 0.8 ml of a 3:1 mixture of DMSO and 25 mM sodium phosphate buffer (pH 7.0) in a round-bottom flask. The flask was heated to 333 K and the mixture stirred for 22 h. The solvent removed in vacuo and the product purified by column chromatography on silica gel eluted with 0–15% methanol in di­chloro­methane (Rf = 0.30, 15% methanol/di­chloro­methane) to yield 36 mg (12% yield) of the title compound as a colorless oil. The precursor 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose was synthesized according to previously reported procedures (Deriaz et al., 1949[Deriaz, R. E., Overend, W. G., Stacey, M. & Wiggins, L. F. (1949). J. Chem. Soc. pp. 2836-2841.]; Olsson et al., 1998[Olsson, R., Rundström, P. & Frejd, T. (1998). J. Chem. Soc. Perkin Trans. 1, pp. 785-790.]). The title compound was crystallized by vapour diffusion, a 2 ml vial containing the title compound in methanol being placed in a 20 ml vial containing hexa­nes at room temperature for several days.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms were placed geometrically (C—H = 0.95 or 0.98 Å) and refined as riding with Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C17H25N5O7
Mr 411.42
Crystal system, space group Monoclinic, P21
Temperature (K) 100
a, b, c (Å) 8.1817 (1), 26.4033 (5), 8.8800 (2)
β (°) 98.023 (1)
V3) 1899.52 (6)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.96
Crystal size (mm) 0.15 × 0.08 × 0.08
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.])
Tmin, Tmax 0.86, 0.93
No. of measured, independent and observed [I > 2σ(I)] reflections 26696, 6862, 6644
Rint 0.029
(sin θ/λ)max−1) 0.617
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.072, 1.04
No. of reflections 6862
No. of parameters 531
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.23, −0.17
Absolute structure Flack x determined using 2923 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.08 (5)
Computer programs: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS2013 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2013 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), X-SEED, Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.], CIFTAB (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Chemical context top

Recent work has characterized a structurally novel set of inter­strand DNA–DNA cross-links involving reaction of the ubiquitous DNA abasic lesion with a nucleobase on the opposing strand of the double helix (Catalano et al., 2015; Dutta et al., 2007; Gamboa Varela & Gates, 2015; Johnson et al., 2013; Price et al., 2014, 2015; Yang et al., 2015; Zhang et al., 2015). Evidence indicates that the covalent attachment is forged between the anomeric carbon of the abasic sugar and the exocyclic amino group of either a guanine, adenine, or N4-amino­cytosine residue (Catalano et al., 2015; Dutta et al., 2007; Gamboa Varela & Gates, 2015; Johnson et al., 2013; Price et al., 2014, 2015; Yang et al., 2015). This type of glycosidic linkage involving the exocyclic amino group of a nucleobase is reminiscent of that found in the natural products anicemycin, spicamycin, and septacidin (Acton et al., 1977; Igarashi et al., 2005; Suzuki et al., 2002). Here we present single crystal X-ray crystallographic analysis of a nucleoside analog, (I), of the 2'-de­oxy­guanosine/abasic site cross-link. This structure corroborates an earlier two-dimensional NMR analysis (Catalano et al., 2015) concluding that the 2-de­oxy­ribose unit attached at the exocyclic N2-amino group of the guanine residue exists in the cyclic amino­glycoside form.

Structural commentary top

The two independent molecules (A and B) of (I) are shown in Fig. 1 as they are oriented in the crystal, while Fig. 2 shows an overlay to illustrate the differences in orientation and conformation of the furan­ose rings. Ring puckering analysis, after Cremer & Pople as calculated using PLATON (Spek, 2009) indicates the furan­ose rings attached to N4 positions in the two molecules to be half-chairs in both molecules, but with the maximum variance from planarity occurring between C7 and C8 in molecule A and C6 and C7 in molecule B [Q(2) = 0.367 (2), Φ(2) = 88.0 (4)° for molecule A and Q(2) = 0.347 (2), Φ(2) = 60.6 (4)° for molecule B]. The disposition of these furan­ose rings relative to the purine rings can be described by the torsion angle C2—N4—C6—O2, which is 70.9 (3)° in molecule A and 61.7 (3)° in molecule B. The furan­ose ring attached to the N5 position in molecule A is again a half-chair, with the maximum deviation from planarity between C11A and C12A [Q(2) = 3.41 (2), Φ(2) = 62.2 (3)°], while this furan­ose ring in molecule B is an envelope with C11B at the flap [ Q(2) = 0.422 (2), Φ(2) = 45.4 (3)°]. The disposition of these furan­ose rings relative to the purine rings can be described by the angle C1—N5—C11—O5, which is -87.4 (2)° in molecule A and -93.7 (2)° in molecule B.

Supra­molecular features top

In the crystal, the two molecules form infinite ribbons along the ac diagonal of the unit cell, with the A molecules on one side of the ribbon and the B molecules on the other. The molecules are staggered such that each A molecule forms hydrogen bonds to two B molecules and each B molecule forms hydrogen bonds to two A molecules, fully involving the N1, N3, N5 and O1 atoms. These ribbons are then stacked to form slabs propagating in the ac plane and one half the b dimension in thickness. The de­oxy­ribose moieties occupy the outsides of these slabs and are linked via hydrogen bonds to twofold screw-related slabs, resulting in a herringbone pattern in the three-dimensional structure as seen in Fig. 3.

Database survey top

A search of the Cambridge Structural Database (CSD, Version 5.36, update February 2015; Groom & Allen, 2014) for de­oxy­guanosine analogues with exocyclic amine substitution revealed three crystal structures (Morr et al., 1991; Fujino et al., 2010). In all these crystal structures, the five-membered 2-de­oxy­ribo­furan­ose rings have envelope conformations, as in the title compound.

Synthesis and crystallization top

2′-De­oxy­guanosine (199 mg, 0.75 mmol) and 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose (110 mg, 0.74 mmol) were dissolved in 0.8 ml of a 3:1 mixture of DMSO and 25 mM sodium phosphate buffer (pH 7.0) in a round-bottom flask. The flask was heated to 333 K and the mixture stirred for 22 h. The solvent removed in vacuo and the product purified by column chromatography on silica gel eluted with 0–15% methanol in di­chloro­methane (Rf = 0.30, 15% methanol/di­chloro­methane) to yield 36 mg (12% yield) of the title compound as a colorless oil. The precursor 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose was synthesized according to previously reported procedures (Deriaz et al., 1949; Olsson et al., 1998). The title compound was crystallized by vapour diffusion, a 2 ml vial containing the title compound in methanol being placed in a 20 ml vial containing hexanes at room temperature for several days.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2.

Structure description top

Recent work has characterized a structurally novel set of inter­strand DNA–DNA cross-links involving reaction of the ubiquitous DNA abasic lesion with a nucleobase on the opposing strand of the double helix (Catalano et al., 2015; Dutta et al., 2007; Gamboa Varela & Gates, 2015; Johnson et al., 2013; Price et al., 2014, 2015; Yang et al., 2015; Zhang et al., 2015). Evidence indicates that the covalent attachment is forged between the anomeric carbon of the abasic sugar and the exocyclic amino group of either a guanine, adenine, or N4-amino­cytosine residue (Catalano et al., 2015; Dutta et al., 2007; Gamboa Varela & Gates, 2015; Johnson et al., 2013; Price et al., 2014, 2015; Yang et al., 2015). This type of glycosidic linkage involving the exocyclic amino group of a nucleobase is reminiscent of that found in the natural products anicemycin, spicamycin, and septacidin (Acton et al., 1977; Igarashi et al., 2005; Suzuki et al., 2002). Here we present single crystal X-ray crystallographic analysis of a nucleoside analog, (I), of the 2'-de­oxy­guanosine/abasic site cross-link. This structure corroborates an earlier two-dimensional NMR analysis (Catalano et al., 2015) concluding that the 2-de­oxy­ribose unit attached at the exocyclic N2-amino group of the guanine residue exists in the cyclic amino­glycoside form.

The two independent molecules (A and B) of (I) are shown in Fig. 1 as they are oriented in the crystal, while Fig. 2 shows an overlay to illustrate the differences in orientation and conformation of the furan­ose rings. Ring puckering analysis, after Cremer & Pople as calculated using PLATON (Spek, 2009) indicates the furan­ose rings attached to N4 positions in the two molecules to be half-chairs in both molecules, but with the maximum variance from planarity occurring between C7 and C8 in molecule A and C6 and C7 in molecule B [Q(2) = 0.367 (2), Φ(2) = 88.0 (4)° for molecule A and Q(2) = 0.347 (2), Φ(2) = 60.6 (4)° for molecule B]. The disposition of these furan­ose rings relative to the purine rings can be described by the torsion angle C2—N4—C6—O2, which is 70.9 (3)° in molecule A and 61.7 (3)° in molecule B. The furan­ose ring attached to the N5 position in molecule A is again a half-chair, with the maximum deviation from planarity between C11A and C12A [Q(2) = 3.41 (2), Φ(2) = 62.2 (3)°], while this furan­ose ring in molecule B is an envelope with C11B at the flap [ Q(2) = 0.422 (2), Φ(2) = 45.4 (3)°]. The disposition of these furan­ose rings relative to the purine rings can be described by the angle C1—N5—C11—O5, which is -87.4 (2)° in molecule A and -93.7 (2)° in molecule B.

In the crystal, the two molecules form infinite ribbons along the ac diagonal of the unit cell, with the A molecules on one side of the ribbon and the B molecules on the other. The molecules are staggered such that each A molecule forms hydrogen bonds to two B molecules and each B molecule forms hydrogen bonds to two A molecules, fully involving the N1, N3, N5 and O1 atoms. These ribbons are then stacked to form slabs propagating in the ac plane and one half the b dimension in thickness. The de­oxy­ribose moieties occupy the outsides of these slabs and are linked via hydrogen bonds to twofold screw-related slabs, resulting in a herringbone pattern in the three-dimensional structure as seen in Fig. 3.

A search of the Cambridge Structural Database (CSD, Version 5.36, update February 2015; Groom & Allen, 2014) for de­oxy­guanosine analogues with exocyclic amine substitution revealed three crystal structures (Morr et al., 1991; Fujino et al., 2010). In all these crystal structures, the five-membered 2-de­oxy­ribo­furan­ose rings have envelope conformations, as in the title compound.

Synthesis and crystallization top

2′-De­oxy­guanosine (199 mg, 0.75 mmol) and 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose (110 mg, 0.74 mmol) were dissolved in 0.8 ml of a 3:1 mixture of DMSO and 25 mM sodium phosphate buffer (pH 7.0) in a round-bottom flask. The flask was heated to 333 K and the mixture stirred for 22 h. The solvent removed in vacuo and the product purified by column chromatography on silica gel eluted with 0–15% methanol in di­chloro­methane (Rf = 0.30, 15% methanol/di­chloro­methane) to yield 36 mg (12% yield) of the title compound as a colorless oil. The precursor 3,5-bis-O-methyl-2-de­oxy-D-ribo­furan­ose was synthesized according to previously reported procedures (Deriaz et al., 1949; Olsson et al., 1998). The title compound was crystallized by vapour diffusion, a 2 ml vial containing the title compound in methanol being placed in a 20 ml vial containing hexanes at room temperature for several days.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: X-SEED, Barbour, 2001; software used to prepare material for publication: CIFTAB (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing 50% displacement ellipsoids.
[Figure 2] Fig. 2. Overlay plot of the two molecules in (I)
[Figure 3] Fig. 3. The packing in (I) showing the formation of hydrogen-bonded chains (A molecules green, B molecules blue).
9-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-2-{[(2R,4S,5R)-4-methoxy-5-(methoxymethyl)tetrahydrofuran-2-yl]amino}-1H-purin-6(9H)-one top
Crystal data top
C17H25N5O7F(000) = 872
Mr = 411.42Dx = 1.439 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
a = 8.1817 (1) ÅCell parameters from 9940 reflections
b = 26.4033 (5) Åθ = 5.3–72.2°
c = 8.8800 (2) ŵ = 0.96 mm1
β = 98.023 (1)°T = 100 K
V = 1899.52 (6) Å3Prism, colourless
Z = 40.15 × 0.08 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer
6644 reflections with I > 2σ(I)
Radiation source: Incoatec micro focus Cu tubeRint = 0.029
ω and phi scansθmax = 72.2°, θmin = 3.4°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
h = 1010
Tmin = 0.86, Tmax = 0.93k = 3131
26696 measured reflectionsl = 910
6862 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.027 w = 1/[σ2(Fo2) + (0.0424P)2 + 0.3476P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.072(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.23 e Å3
6862 reflectionsΔρmin = 0.17 e Å3
531 parametersAbsolute structure: Flack x determined using 2923 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute structure parameter: 0.08 (5)
Crystal data top
C17H25N5O7V = 1899.52 (6) Å3
Mr = 411.42Z = 4
Monoclinic, P21Cu Kα radiation
a = 8.1817 (1) ŵ = 0.96 mm1
b = 26.4033 (5) ÅT = 100 K
c = 8.8800 (2) Å0.15 × 0.08 × 0.08 mm
β = 98.023 (1)°
Data collection top
Bruker APEXII CCD
diffractometer
6862 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
6644 reflections with I > 2σ(I)
Tmin = 0.86, Tmax = 0.93Rint = 0.029
26696 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.072Δρmax = 0.23 e Å3
S = 1.04Δρmin = 0.17 e Å3
6862 reflectionsAbsolute structure: Flack x determined using 2923 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
531 parametersAbsolute structure parameter: 0.08 (5)
1 restraint
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O1A0.34576 (17)0.46915 (6)0.12995 (17)0.0168 (3)
N1A0.3499 (2)0.50765 (6)0.1022 (2)0.0146 (3)
H1A0.44930.49550.13170.017*
C1A0.2806 (2)0.53738 (8)0.2030 (2)0.0140 (4)
O2A0.1409 (2)0.64849 (6)0.01984 (18)0.0223 (3)
N2A0.1339 (2)0.55894 (7)0.1729 (2)0.0155 (4)
C2A0.0560 (3)0.54690 (8)0.0330 (2)0.0150 (4)
O3A0.44313 (19)0.65756 (6)0.18573 (19)0.0221 (3)
H3A0.50510.64600.24540.027*
N3A0.0017 (2)0.51309 (7)0.2041 (2)0.0170 (4)
C3A0.1129 (2)0.51624 (8)0.0744 (2)0.0148 (4)
O4A0.0015 (2)0.72195 (6)0.3635 (2)0.0298 (4)
H4A0.02530.75010.32350.036*
N4A0.0978 (2)0.56295 (7)0.0324 (2)0.0177 (4)
C4A0.2740 (2)0.49535 (7)0.0439 (2)0.0138 (4)
O5A0.37552 (18)0.62783 (6)0.42933 (16)0.0176 (3)
N5A0.3711 (2)0.54372 (7)0.3418 (2)0.0163 (4)
H5A0.46470.52720.36420.020*
C5A0.1246 (3)0.54152 (8)0.1750 (2)0.0192 (4)
H5A10.22200.54680.24490.023*
O6A0.23353 (18)0.61868 (6)0.75564 (18)0.0227 (3)
C6A0.2089 (3)0.59897 (8)0.0258 (3)0.0185 (4)
H6A0.31790.59800.04100.022*
O7A0.69231 (18)0.63615 (6)0.60640 (19)0.0221 (3)
C7A0.2373 (3)0.59060 (8)0.1890 (3)0.0184 (4)
H7A10.13720.57700.25140.022*
H7A20.33090.56730.19480.022*
C8A0.2764 (3)0.64379 (8)0.2388 (2)0.0182 (4)
H8A0.25070.64760.35160.022*
C9A0.1612 (3)0.67599 (8)0.1574 (2)0.0189 (4)
H9A0.21520.70930.12930.023*
C10A0.0085 (3)0.68527 (9)0.2482 (3)0.0245 (5)
H10A0.05180.65310.29510.029*
H10B0.08530.69700.17870.029*
C11A0.3171 (2)0.57690 (8)0.4527 (2)0.0156 (4)
H11A0.19380.57670.44290.019*
C12A0.3901 (3)0.56396 (8)0.6145 (2)0.0182 (4)
H12A0.32280.53810.65810.022*
H12B0.50450.55130.61900.022*
C13A0.3861 (2)0.61397 (8)0.6978 (2)0.0167 (4)
H13A0.48040.61610.78230.020*
C14A0.4064 (3)0.65359 (8)0.5738 (2)0.0175 (4)
H14A0.32300.68110.57690.021*
C15A0.5775 (3)0.67638 (9)0.5938 (3)0.0218 (4)
H15A0.59170.69790.50530.026*
H15B0.59470.69760.68660.026*
C16A0.8590 (3)0.65335 (11)0.6422 (3)0.0301 (5)
H16A0.87990.68020.57110.045*
H16B0.93460.62500.63380.045*
H16C0.87660.66660.74630.045*
C17A0.2364 (3)0.65893 (11)0.8622 (3)0.0289 (5)
H17A0.33240.65510.94070.043*
H17B0.13520.65810.90960.043*
H17C0.24350.69130.80970.043*
O1B0.72354 (17)0.51384 (5)0.47267 (17)0.0168 (3)
N1B0.9716 (2)0.47201 (6)0.50184 (19)0.0139 (3)
H1B0.99710.48550.59270.017*
C1B1.0833 (2)0.43911 (7)0.4530 (2)0.0136 (4)
O2B0.9310 (2)0.32766 (6)0.07593 (19)0.0219 (3)
N2B1.0610 (2)0.41620 (6)0.3193 (2)0.0153 (4)
C2B0.9168 (3)0.42949 (8)0.2340 (2)0.0150 (4)
O3B1.09413 (19)0.31769 (6)0.23244 (18)0.0220 (3)
H3B1.15710.33060.28900.026*
N3B0.6634 (2)0.46447 (7)0.1606 (2)0.0188 (4)
C3B0.7979 (2)0.46230 (8)0.2729 (2)0.0159 (4)
O4B1.2568 (3)0.31747 (9)0.2436 (2)0.0452 (5)
H4B1.19200.33770.27790.054*
N4B0.8528 (2)0.41146 (7)0.0918 (2)0.0186 (4)
C4B0.8210 (2)0.48559 (8)0.4184 (2)0.0143 (4)
O5B1.32491 (17)0.34807 (6)0.57774 (18)0.0175 (3)
N5B1.2221 (2)0.43116 (7)0.5529 (2)0.0159 (3)
H5B1.23340.44680.64130.019*
C5B0.7002 (3)0.43335 (9)0.0558 (3)0.0215 (5)
H5B10.62870.42660.03580.026*
O6B1.67925 (19)0.36348 (6)0.43876 (18)0.0216 (3)
C6B0.9187 (3)0.37405 (8)0.0034 (2)0.0185 (4)
H6B0.84020.36990.09950.022*
O7B1.5367 (2)0.31343 (6)0.84948 (19)0.0252 (3)
C7B1.0893 (3)0.38469 (8)0.0431 (3)0.0198 (4)
H7B11.16150.40020.04350.024*
H7B21.08450.40720.13280.024*
C8B1.1484 (3)0.33176 (8)0.0781 (2)0.0191 (4)
H8B1.27090.32870.05250.023*
C9B1.0581 (3)0.29760 (9)0.0248 (3)0.0226 (5)
H9B1.00710.26830.03570.027*
C10B1.1657 (4)0.27835 (11)0.1641 (3)0.0360 (6)
H10C1.09580.26180.23220.043*
H10D1.24270.25260.13370.043*
C11B1.3507 (3)0.39806 (8)0.5188 (2)0.0157 (4)
H11B1.35000.39630.40620.019*
C12B1.5222 (3)0.41144 (8)0.5959 (3)0.0191 (4)
H12C1.52180.42040.70410.023*
H12D1.57000.43980.54360.023*
C13B1.6149 (3)0.36211 (8)0.5792 (2)0.0177 (4)
H13B1.70500.35720.66640.021*
C14B1.4792 (3)0.32117 (8)0.5795 (3)0.0178 (4)
H14B1.47380.30090.48380.021*
C15B1.5051 (3)0.28550 (9)0.7128 (3)0.0227 (5)
H15C1.40550.26430.71420.027*
H15D1.59950.26280.70330.027*
C16B1.5735 (3)0.28046 (11)0.9765 (3)0.0331 (6)
H16D1.48560.25520.97520.050*
H16E1.58140.30021.07080.050*
H16F1.67880.26330.97110.050*
C17B1.7854 (3)0.32160 (10)0.4226 (3)0.0271 (5)
H17D1.87560.32120.50770.041*
H17E1.83120.32480.32670.041*
H17F1.72250.29000.42210.041*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O1A0.0171 (7)0.0182 (7)0.0155 (7)0.0035 (6)0.0033 (5)0.0025 (6)
N1A0.0120 (7)0.0159 (8)0.0155 (9)0.0028 (6)0.0006 (6)0.0015 (6)
C1A0.0148 (9)0.0128 (9)0.0142 (10)0.0002 (7)0.0018 (7)0.0013 (7)
O2A0.0304 (9)0.0195 (8)0.0191 (8)0.0039 (6)0.0108 (6)0.0007 (6)
N2A0.0152 (8)0.0175 (9)0.0134 (9)0.0031 (6)0.0008 (7)0.0026 (7)
C2A0.0152 (9)0.0136 (10)0.0158 (10)0.0012 (7)0.0005 (7)0.0019 (7)
O3A0.0198 (8)0.0247 (8)0.0234 (8)0.0066 (6)0.0078 (6)0.0027 (6)
N3A0.0174 (8)0.0183 (9)0.0148 (9)0.0033 (7)0.0001 (7)0.0032 (7)
C3A0.0170 (9)0.0137 (9)0.0134 (10)0.0018 (8)0.0014 (8)0.0032 (7)
O4A0.0448 (10)0.0194 (8)0.0243 (9)0.0047 (7)0.0011 (7)0.0001 (7)
N4A0.0172 (8)0.0195 (9)0.0154 (9)0.0053 (7)0.0012 (7)0.0036 (7)
C4A0.0152 (10)0.0127 (10)0.0139 (10)0.0012 (7)0.0032 (8)0.0005 (7)
O5A0.0227 (7)0.0174 (7)0.0123 (7)0.0008 (6)0.0009 (5)0.0013 (6)
N5A0.0139 (8)0.0201 (9)0.0142 (9)0.0039 (6)0.0003 (6)0.0034 (7)
C5A0.0169 (10)0.0228 (11)0.0166 (11)0.0045 (8)0.0027 (8)0.0048 (8)
O6A0.0163 (7)0.0333 (9)0.0194 (8)0.0025 (6)0.0060 (6)0.0082 (7)
C6A0.0163 (9)0.0200 (11)0.0185 (11)0.0069 (8)0.0005 (8)0.0024 (8)
O7A0.0153 (7)0.0240 (8)0.0268 (9)0.0015 (6)0.0027 (6)0.0011 (6)
C7A0.0172 (10)0.0172 (11)0.0211 (11)0.0001 (8)0.0037 (8)0.0002 (8)
C8A0.0203 (10)0.0201 (11)0.0148 (10)0.0015 (8)0.0047 (8)0.0008 (8)
C9A0.0257 (11)0.0157 (10)0.0165 (10)0.0038 (8)0.0073 (8)0.0009 (8)
C10A0.0259 (12)0.0182 (11)0.0297 (13)0.0001 (9)0.0052 (10)0.0023 (9)
C11A0.0150 (9)0.0167 (10)0.0149 (10)0.0005 (7)0.0015 (7)0.0028 (8)
C12A0.0206 (10)0.0201 (10)0.0137 (10)0.0017 (8)0.0024 (8)0.0002 (8)
C13A0.0139 (9)0.0227 (11)0.0134 (10)0.0007 (8)0.0012 (7)0.0029 (8)
C14A0.0185 (10)0.0172 (10)0.0163 (10)0.0037 (8)0.0004 (8)0.0042 (8)
C15A0.0257 (11)0.0193 (11)0.0207 (11)0.0025 (9)0.0043 (9)0.0023 (9)
C16A0.0209 (11)0.0458 (15)0.0230 (12)0.0085 (10)0.0010 (9)0.0059 (11)
C17A0.0229 (11)0.0410 (14)0.0238 (12)0.0011 (10)0.0065 (9)0.0138 (10)
O1B0.0172 (7)0.0172 (7)0.0163 (7)0.0052 (6)0.0031 (6)0.0026 (6)
N1B0.0149 (8)0.0147 (8)0.0119 (8)0.0022 (6)0.0009 (6)0.0038 (6)
C1B0.0148 (9)0.0122 (9)0.0140 (10)0.0001 (7)0.0033 (7)0.0005 (7)
O2B0.0261 (8)0.0176 (8)0.0243 (8)0.0016 (6)0.0113 (6)0.0048 (6)
N2B0.0137 (8)0.0171 (9)0.0148 (9)0.0019 (6)0.0010 (6)0.0028 (7)
C2B0.0169 (9)0.0146 (10)0.0136 (10)0.0007 (8)0.0022 (7)0.0021 (8)
O3B0.0278 (8)0.0215 (8)0.0183 (8)0.0035 (6)0.0094 (6)0.0033 (6)
N3B0.0168 (8)0.0222 (9)0.0166 (9)0.0042 (7)0.0003 (7)0.0038 (7)
C3B0.0144 (9)0.0162 (10)0.0168 (10)0.0017 (8)0.0014 (8)0.0016 (8)
O4B0.0386 (11)0.0665 (15)0.0278 (10)0.0170 (10)0.0056 (8)0.0101 (10)
N4B0.0168 (9)0.0227 (9)0.0153 (9)0.0048 (7)0.0013 (7)0.0068 (7)
C4B0.0154 (9)0.0128 (9)0.0147 (10)0.0004 (7)0.0024 (7)0.0014 (7)
O5B0.0139 (7)0.0165 (7)0.0226 (8)0.0023 (6)0.0037 (6)0.0013 (6)
N5B0.0172 (8)0.0162 (8)0.0137 (8)0.0038 (7)0.0004 (6)0.0042 (6)
C5B0.0185 (10)0.0270 (12)0.0174 (11)0.0039 (9)0.0028 (8)0.0053 (9)
O6B0.0225 (8)0.0239 (8)0.0200 (8)0.0048 (6)0.0084 (6)0.0045 (6)
C6B0.0212 (11)0.0186 (11)0.0151 (10)0.0027 (8)0.0002 (8)0.0061 (8)
O7B0.0264 (8)0.0281 (9)0.0207 (8)0.0003 (7)0.0018 (6)0.0081 (7)
C7B0.0246 (11)0.0175 (10)0.0181 (11)0.0018 (8)0.0055 (8)0.0025 (8)
C8B0.0204 (10)0.0202 (11)0.0175 (11)0.0020 (8)0.0054 (8)0.0025 (8)
C9B0.0305 (12)0.0183 (11)0.0208 (11)0.0022 (9)0.0098 (9)0.0036 (8)
C10B0.0506 (16)0.0338 (14)0.0241 (13)0.0162 (12)0.0067 (11)0.0026 (11)
C11B0.0174 (10)0.0146 (10)0.0151 (10)0.0013 (7)0.0018 (8)0.0003 (7)
C12B0.0156 (10)0.0195 (11)0.0220 (11)0.0002 (8)0.0023 (8)0.0036 (8)
C13B0.0149 (10)0.0209 (11)0.0174 (11)0.0028 (8)0.0028 (8)0.0004 (8)
C14B0.0160 (9)0.0167 (10)0.0210 (11)0.0035 (8)0.0040 (8)0.0011 (8)
C15B0.0201 (10)0.0200 (11)0.0280 (12)0.0021 (8)0.0034 (9)0.0031 (9)
C16B0.0261 (12)0.0417 (15)0.0298 (13)0.0035 (11)0.0019 (10)0.0187 (11)
C17B0.0263 (12)0.0291 (13)0.0281 (12)0.0092 (10)0.0118 (9)0.0021 (10)
Geometric parameters (Å, º) top
O1A—C4A1.238 (3)O1B—C4B1.237 (3)
N1A—C1A1.371 (3)N1B—C1B1.374 (3)
N1A—C4A1.397 (3)N1B—C4B1.393 (3)
N1A—H1A0.8800N1B—H1B0.8800
C1A—N2A1.321 (3)C1B—N2B1.323 (3)
C1A—N5A1.357 (3)C1B—N5B1.356 (3)
O2A—C6A1.425 (3)O2B—C6B1.409 (3)
O2A—C9A1.450 (3)O2B—C9B1.432 (3)
N2A—C2A1.353 (3)N2B—C2B1.356 (3)
C2A—N4A1.377 (3)C2B—C3B1.382 (3)
C2A—C3A1.380 (3)C2B—N4B1.382 (3)
O3A—C8A1.427 (3)O3B—C8B1.429 (3)
O3A—H3A0.8400O3B—H3B0.8400
N3A—C5A1.309 (3)N3B—C5B1.308 (3)
N3A—C3A1.382 (3)N3B—C3B1.379 (3)
C3A—C4A1.420 (3)C3B—C4B1.420 (3)
O4A—C10A1.417 (3)O4B—C10B1.405 (4)
O4A—H4A0.8400O4B—H4B0.8400
N4A—C5A1.376 (3)N4B—C5B1.373 (3)
N4A—C6A1.460 (3)N4B—C6B1.452 (3)
O5A—C14A1.443 (2)O5B—C11B1.446 (3)
O5A—C11A1.452 (3)O5B—C14B1.447 (2)
N5A—C11A1.433 (3)N5B—C11B1.433 (3)
N5A—H5A0.8800N5B—H5B0.8800
C5A—H5A10.9500C5B—H5B10.9500
O6A—C13A1.420 (3)O6B—C13B1.420 (3)
O6A—C17A1.421 (3)O6B—C17B1.426 (3)
C6A—C7A1.515 (3)C6B—C7B1.513 (3)
C6A—H6A1.0000C6B—H6B1.0000
O7A—C15A1.412 (3)O7B—C15B1.413 (3)
O7A—C16A1.431 (3)O7B—C16B1.424 (3)
C7A—C8A1.520 (3)C7B—C8B1.525 (3)
C7A—H7A10.9900C7B—H7B10.9900
C7A—H7A20.9900C7B—H7B20.9900
C8A—C9A1.524 (3)C8B—C9B1.544 (3)
C8A—H8A1.0000C8B—H8B1.0000
C9A—C10A1.525 (3)C9B—C10B1.503 (4)
C9A—H9A1.0000C9B—H9B1.0000
C10A—H10A0.9900C10B—H10C0.9900
C10A—H10B0.9900C10B—H10D0.9900
C11A—C12A1.516 (3)C11B—C12B1.514 (3)
C11A—H11A1.0000C11B—H11B1.0000
C12A—C13A1.516 (3)C12B—C13B1.525 (3)
C12A—H12A0.9900C12B—H12C0.9900
C12A—H12B0.9900C12B—H12D0.9900
C13A—C14A1.544 (3)C13B—C14B1.550 (3)
C13A—H13A1.0000C13B—H13B1.0000
C14A—C15A1.512 (3)C14B—C15B1.505 (3)
C14A—H14A1.0000C14B—H14B1.0000
C15A—H15A0.9900C15B—H15C0.9900
C15A—H15B0.9900C15B—H15D0.9900
C16A—H16A0.9800C16B—H16D0.9800
C16A—H16B0.9800C16B—H16E0.9800
C16A—H16C0.9800C16B—H16F0.9800
C17A—H17A0.9800C17B—H17D0.9800
C17A—H17B0.9800C17B—H17E0.9800
C17A—H17C0.9800C17B—H17F0.9800
C1A—N1A—C4A124.64 (17)C1B—N1B—C4B124.95 (17)
C1A—N1A—H1A117.7C1B—N1B—H1B117.5
C4A—N1A—H1A117.7C4B—N1B—H1B117.5
N2A—C1A—N5A119.73 (18)N2B—C1B—N5B120.96 (18)
N2A—C1A—N1A124.14 (18)N2B—C1B—N1B123.93 (18)
N5A—C1A—N1A116.13 (17)N5B—C1B—N1B115.11 (18)
C6A—O2A—C9A109.66 (16)C6B—O2B—C9B109.15 (17)
C1A—N2A—C2A112.51 (17)C1B—N2B—C2B112.52 (17)
N2A—C2A—N4A126.92 (19)N2B—C2B—C3B127.64 (19)
N2A—C2A—C3A127.70 (19)N2B—C2B—N4B127.58 (19)
N4A—C2A—C3A105.38 (18)C3B—C2B—N4B104.73 (18)
C8A—O3A—H3A109.5C8B—O3B—H3B109.5
C5A—N3A—C3A104.51 (18)C5B—N3B—C3B104.43 (17)
C2A—C3A—N3A110.89 (18)N3B—C3B—C2B111.34 (19)
C2A—C3A—C4A119.30 (18)N3B—C3B—C4B129.16 (19)
N3A—C3A—C4A129.73 (19)C2B—C3B—C4B119.33 (19)
C10A—O4A—H4A109.5C10B—O4B—H4B109.5
C5A—N4A—C2A106.28 (17)C5B—N4B—C2B106.50 (17)
C5A—N4A—C6A124.53 (18)C5B—N4B—C6B123.40 (18)
C2A—N4A—C6A128.96 (18)C2B—N4B—C6B129.95 (18)
O1A—C4A—N1A121.03 (18)O1B—C4B—N1B121.23 (19)
O1A—C4A—C3A127.38 (19)O1B—C4B—C3B127.16 (19)
N1A—C4A—C3A111.59 (17)N1B—C4B—C3B111.59 (17)
C14A—O5A—C11A109.25 (15)C11B—O5B—C14B106.31 (15)
C1A—N5A—C11A121.20 (17)C1B—N5B—C11B121.92 (18)
C1A—N5A—H5A119.4C1B—N5B—H5B119.0
C11A—N5A—H5A119.4C11B—N5B—H5B119.0
N3A—C5A—N4A112.93 (18)N3B—C5B—N4B112.99 (18)
N3A—C5A—H5A1123.5N3B—C5B—H5B1123.5
N4A—C5A—H5A1123.5N4B—C5B—H5B1123.5
C13A—O6A—C17A111.90 (16)C13B—O6B—C17B112.00 (17)
O2A—C6A—N4A108.59 (17)O2B—C6B—N4B107.89 (18)
O2A—C6A—C7A106.39 (17)O2B—C6B—C7B105.90 (17)
N4A—C6A—C7A115.46 (18)N4B—C6B—C7B116.03 (18)
O2A—C6A—H6A108.7O2B—C6B—H6B108.9
N4A—C6A—H6A108.7N4B—C6B—H6B108.9
C7A—C6A—H6A108.7C7B—C6B—H6B108.9
C15A—O7A—C16A112.43 (18)C15B—O7B—C16B110.76 (19)
C6A—C7A—C8A102.12 (17)C6B—C7B—C8B101.90 (17)
C6A—C7A—H7A1111.3C6B—C7B—H7B1111.4
C8A—C7A—H7A1111.3C8B—C7B—H7B1111.4
C6A—C7A—H7A2111.3C6B—C7B—H7B2111.4
C8A—C7A—H7A2111.3C8B—C7B—H7B2111.4
H7A1—C7A—H7A2109.2H7B1—C7B—H7B2109.3
O3A—C8A—C7A111.70 (18)O3B—C8B—C7B111.64 (18)
O3A—C8A—C9A109.09 (17)O3B—C8B—C9B107.79 (17)
C7A—C8A—C9A102.03 (17)C7B—C8B—C9B102.92 (17)
O3A—C8A—H8A111.2O3B—C8B—H8B111.4
C7A—C8A—H8A111.2C7B—C8B—H8B111.4
C9A—C8A—H8A111.2C9B—C8B—H8B111.4
O2A—C9A—C8A105.75 (17)O2B—C9B—C10B107.12 (19)
O2A—C9A—C10A108.82 (17)O2B—C9B—C8B107.00 (17)
C8A—C9A—C10A114.59 (18)C10B—C9B—C8B114.3 (2)
O2A—C9A—H9A109.2O2B—C9B—H9B109.4
C8A—C9A—H9A109.2C10B—C9B—H9B109.4
C10A—C9A—H9A109.2C8B—C9B—H9B109.4
O4A—C10A—C9A111.51 (19)O4B—C10B—C9B111.9 (2)
O4A—C10A—H10A109.3O4B—C10B—H10C109.2
C9A—C10A—H10A109.3C9B—C10B—H10C109.2
O4A—C10A—H10B109.3O4B—C10B—H10D109.2
C9A—C10A—H10B109.3C9B—C10B—H10D109.2
H10A—C10A—H10B108.0H10C—C10B—H10D107.9
N5A—C11A—O5A109.19 (17)N5B—C11B—O5B109.36 (17)
N5A—C11A—C12A113.26 (17)N5B—C11B—C12B115.06 (18)
O5A—C11A—C12A104.50 (16)O5B—C11B—C12B102.84 (16)
N5A—C11A—H11A109.9N5B—C11B—H11B109.8
O5A—C11A—H11A109.9O5B—C11B—H11B109.8
C12A—C11A—H11A109.9C12B—C11B—H11B109.8
C13A—C12A—C11A103.50 (17)C11B—C12B—C13B101.47 (17)
C13A—C12A—H12A111.1C11B—C12B—H12C111.5
C11A—C12A—H12A111.1C13B—C12B—H12C111.5
C13A—C12A—H12B111.1C11B—C12B—H12D111.5
C11A—C12A—H12B111.1C13B—C12B—H12D111.5
H12A—C12A—H12B109.0H12C—C12B—H12D109.3
O6A—C13A—C12A109.43 (17)O6B—C13B—C12B108.29 (17)
O6A—C13A—C14A112.71 (17)O6B—C13B—C14B111.87 (18)
C12A—C13A—C14A103.35 (16)C12B—C13B—C14B103.26 (16)
O6A—C13A—H13A110.4O6B—C13B—H13B111.0
C12A—C13A—H13A110.4C12B—C13B—H13B111.0
C14A—C13A—H13A110.4C14B—C13B—H13B111.0
O5A—C14A—C15A109.66 (17)O5B—C14B—C15B110.05 (17)
O5A—C14A—C13A106.95 (16)O5B—C14B—C13B106.37 (16)
C15A—C14A—C13A112.09 (17)C15B—C14B—C13B114.55 (18)
O5A—C14A—H14A109.4O5B—C14B—H14B108.6
C15A—C14A—H14A109.4C15B—C14B—H14B108.6
C13A—C14A—H14A109.4C13B—C14B—H14B108.6
O7A—C15A—C14A107.74 (17)O7B—C15B—C14B109.74 (18)
O7A—C15A—H15A110.2O7B—C15B—H15C109.7
C14A—C15A—H15A110.2C14B—C15B—H15C109.7
O7A—C15A—H15B110.2O7B—C15B—H15D109.7
C14A—C15A—H15B110.2C14B—C15B—H15D109.7
H15A—C15A—H15B108.5H15C—C15B—H15D108.2
O7A—C16A—H16A109.5O7B—C16B—H16D109.5
O7A—C16A—H16B109.5O7B—C16B—H16E109.5
H16A—C16A—H16B109.5H16D—C16B—H16E109.5
O7A—C16A—H16C109.5O7B—C16B—H16F109.5
H16A—C16A—H16C109.5H16D—C16B—H16F109.5
H16B—C16A—H16C109.5H16E—C16B—H16F109.5
O6A—C17A—H17A109.5O6B—C17B—H17D109.5
O6A—C17A—H17B109.5O6B—C17B—H17E109.5
H17A—C17A—H17B109.5H17D—C17B—H17E109.5
O6A—C17A—H17C109.5O6B—C17B—H17F109.5
H17A—C17A—H17C109.5H17D—C17B—H17F109.5
H17B—C17A—H17C109.5H17E—C17B—H17F109.5
C4A—N1A—C1A—N2A1.4 (3)C4B—N1B—C1B—N2B0.2 (3)
C4A—N1A—C1A—N5A177.84 (18)C4B—N1B—C1B—N5B179.83 (18)
N5A—C1A—N2A—C2A176.82 (19)N5B—C1B—N2B—C2B178.87 (19)
N1A—C1A—N2A—C2A2.4 (3)N1B—C1B—N2B—C2B1.1 (3)
C1A—N2A—C2A—N4A179.8 (2)C1B—N2B—C2B—C3B0.8 (3)
C1A—N2A—C2A—C3A0.3 (3)C1B—N2B—C2B—N4B177.6 (2)
N2A—C2A—C3A—N3A179.8 (2)C5B—N3B—C3B—C2B0.2 (3)
N4A—C2A—C3A—N3A0.1 (2)C5B—N3B—C3B—C4B175.1 (2)
N2A—C2A—C3A—C4A2.9 (3)N2B—C2B—C3B—N3B176.7 (2)
N4A—C2A—C3A—C4A177.03 (18)N4B—C2B—C3B—N3B0.7 (2)
C5A—N3A—C3A—C2A0.2 (2)N2B—C2B—C3B—C4B0.9 (3)
C5A—N3A—C3A—C4A176.3 (2)N4B—C2B—C3B—C4B176.47 (19)
N2A—C2A—N4A—C5A179.5 (2)N2B—C2B—N4B—C5B176.1 (2)
C3A—C2A—N4A—C5A0.4 (2)C3B—C2B—N4B—C5B1.3 (2)
N2A—C2A—N4A—C6A4.8 (4)N2B—C2B—N4B—C6B0.6 (4)
C3A—C2A—N4A—C6A175.1 (2)C3B—C2B—N4B—C6B176.8 (2)
C1A—N1A—C4A—O1A178.41 (19)C1B—N1B—C4B—O1B176.86 (19)
C1A—N1A—C4A—C3A1.7 (3)C1B—N1B—C4B—C3B1.8 (3)
C2A—C3A—C4A—O1A176.6 (2)N3B—C3B—C4B—O1B1.6 (4)
N3A—C3A—C4A—O1A0.3 (4)C2B—C3B—C4B—O1B176.5 (2)
C2A—C3A—C4A—N1A3.6 (3)N3B—C3B—C4B—N1B177.0 (2)
N3A—C3A—C4A—N1A179.8 (2)C2B—C3B—C4B—N1B2.0 (3)
N2A—C1A—N5A—C11A5.3 (3)N2B—C1B—N5B—C11B0.3 (3)
N1A—C1A—N5A—C11A175.39 (18)N1B—C1B—N5B—C11B179.74 (18)
C3A—N3A—C5A—N4A0.5 (3)C3B—N3B—C5B—N4B1.0 (3)
C2A—N4A—C5A—N3A0.6 (3)C2B—N4B—C5B—N3B1.5 (3)
C6A—N4A—C5A—N3A175.6 (2)C6B—N4B—C5B—N3B177.4 (2)
C9A—O2A—C6A—N4A138.45 (17)C9B—O2B—C6B—N4B153.74 (17)
C9A—O2A—C6A—C7A13.6 (2)C9B—O2B—C6B—C7B28.9 (2)
C5A—N4A—C6A—O2A103.0 (2)C5B—N4B—C6B—O2B113.2 (2)
C2A—N4A—C6A—O2A70.9 (3)C2B—N4B—C6B—O2B61.7 (3)
C5A—N4A—C6A—C7A137.7 (2)C5B—N4B—C6B—C7B128.3 (2)
C2A—N4A—C6A—C7A48.4 (3)C2B—N4B—C6B—C7B56.9 (3)
O2A—C6A—C7A—C8A31.8 (2)O2B—C6B—C7B—C8B36.8 (2)
N4A—C6A—C7A—C8A152.34 (18)N4B—C6B—C7B—C8B156.41 (19)
C6A—C7A—C8A—O3A79.6 (2)C6B—C7B—C8B—O3B85.4 (2)
C6A—C7A—C8A—C9A36.8 (2)C6B—C7B—C8B—C9B30.0 (2)
C6A—O2A—C9A—C8A10.4 (2)C6B—O2B—C9B—C10B131.8 (2)
C6A—O2A—C9A—C10A113.18 (18)C6B—O2B—C9B—C8B8.8 (2)
O3A—C8A—C9A—O2A88.60 (19)O3B—C8B—C9B—O2B103.77 (19)
C7A—C8A—C9A—O2A29.7 (2)C7B—C8B—C9B—O2B14.3 (2)
O3A—C8A—C9A—C10A151.55 (18)O3B—C8B—C9B—C10B137.8 (2)
C7A—C8A—C9A—C10A90.2 (2)C7B—C8B—C9B—C10B104.1 (2)
O2A—C9A—C10A—O4A165.83 (17)O2B—C9B—C10B—O4B68.9 (3)
C8A—C9A—C10A—O4A76.0 (2)C8B—C9B—C10B—O4B49.4 (3)
C1A—N5A—C11A—O5A87.4 (2)C1B—N5B—C11B—O5B93.7 (2)
C1A—N5A—C11A—C12A156.64 (19)C1B—N5B—C11B—C12B151.2 (2)
C14A—O5A—C11A—N5A148.25 (16)C14B—O5B—C11B—N5B163.87 (16)
C14A—O5A—C11A—C12A26.8 (2)C14B—O5B—C11B—C12B41.2 (2)
N5A—C11A—C12A—C13A154.32 (17)N5B—C11B—C12B—C13B162.67 (18)
O5A—C11A—C12A—C13A35.6 (2)O5B—C11B—C12B—C13B43.9 (2)
C17A—O6A—C13A—C12A167.04 (19)C17B—O6B—C13B—C12B172.60 (18)
C17A—O6A—C13A—C14A78.6 (2)C17B—O6B—C13B—C14B74.3 (2)
C11A—C12A—C13A—O6A89.7 (2)C11B—C12B—C13B—O6B88.8 (2)
C11A—C12A—C13A—C14A30.6 (2)C11B—C12B—C13B—C14B30.0 (2)
C11A—O5A—C14A—C15A128.97 (18)C11B—O5B—C14B—C15B146.08 (17)
C11A—O5A—C14A—C13A7.2 (2)C11B—O5B—C14B—C13B21.5 (2)
O6A—C13A—C14A—O5A102.90 (18)O6B—C13B—C14B—O5B109.88 (18)
C12A—C13A—C14A—O5A15.1 (2)C12B—C13B—C14B—O5B6.4 (2)
O6A—C13A—C14A—C15A136.89 (18)O6B—C13B—C14B—C15B128.32 (19)
C12A—C13A—C14A—C15A105.08 (19)C12B—C13B—C14B—C15B115.5 (2)
C16A—O7A—C15A—C14A173.67 (18)C16B—O7B—C15B—C14B175.77 (18)
O5A—C14A—C15A—O7A66.7 (2)O5B—C14B—C15B—O7B69.6 (2)
C13A—C14A—C15A—O7A51.9 (2)C13B—C14B—C15B—O7B50.2 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1A—H1A···N3B0.881.922.789 (2)170
O3A—H3A···O5Ai0.842.072.897 (2)167
O4A—H4A···O3Bii0.842.012.847 (2)178
N5A—H5A···O1B0.882.233.058 (2)157
C5A—H5A1···O1Biii0.952.633.284 (3)126
C7A—H7A1···N2A0.992.463.172 (3)128
C8A—H8A···O7Ai1.002.393.316 (3)153
C12A—H12A···O1Aiv0.992.613.432 (3)141
C12A—H12B···O1B0.992.553.426 (3)147
C16A—H16A···O4Av0.982.473.401 (3)158
C16A—H16B···O6Av0.982.543.222 (3)127
C16A—H16C···O2Avi0.982.503.356 (3)146
C17A—H17A···O3Avi0.982.653.610 (3)168
C17A—H17B···O2Aiv0.982.603.573 (3)175
N1B—H1B···N3Avi0.881.942.808 (2)166
O3B—H3B···O5Bvii0.841.992.817 (2)169
O4B—H4B···N2B0.842.383.180 (3)158
N5B—H5B···O1Avi0.882.193.027 (2)159
C5B—H5B1···O1A0.952.603.269 (3)127
C8B—H8B···O7Bvii1.002.493.363 (3)146
C11B—H11B···O4B1.002.593.251 (3)124
C12B—H12C···O1Avi0.992.553.363 (3)140
C12B—H12D···O1Bv0.992.453.424 (3)167
C14B—H14B···O4B1.002.613.272 (3)123
C17B—H17E···O2Bv0.982.483.456 (3)176
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1/2, z; (iii) x1, y, z1; (iv) x, y, z+1; (v) x+1, y, z; (vi) x+1, y, z+1; (vii) x, y, z1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1A—H1A···N3B0.881.922.789 (2)170
O3A—H3A···O5Ai0.842.072.897 (2)167
O4A—H4A···O3Bii0.842.012.847 (2)178
N5A—H5A···O1B0.882.233.058 (2)157
C5A—H5A1···O1Biii0.952.633.284 (3)126
C7A—H7A1···N2A0.992.463.172 (3)128
C8A—H8A···O7Ai1.002.393.316 (3)153
C12A—H12A···O1Aiv0.992.613.432 (3)141
C12A—H12B···O1B0.992.553.426 (3)147
C16A—H16A···O4Av0.982.473.401 (3)158
C16A—H16B···O6Av0.982.543.222 (3)127
C16A—H16C···O2Avi0.982.503.356 (3)146
C17A—H17A···O3Avi0.982.653.610 (3)168
C17A—H17B···O2Aiv0.982.603.573 (3)175
N1B—H1B···N3Avi0.881.942.808 (2)166
O3B—H3B···O5Bvii0.841.992.817 (2)169
O4B—H4B···N2B0.842.383.180 (3)158
N5B—H5B···O1Avi0.882.193.027 (2)159
C5B—H5B1···O1A0.952.603.269 (3)127
C8B—H8B···O7Bvii1.002.493.363 (3)146
C11B—H11B···O4B1.002.593.251 (3)124
C12B—H12C···O1Avi0.992.553.363 (3)140
C12B—H12D···O1Bv0.992.453.424 (3)167
C14B—H14B···O4B1.002.613.272 (3)123
C17B—H17E···O2Bv0.982.483.456 (3)176
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1/2, z; (iii) x1, y, z1; (iv) x, y, z+1; (v) x+1, y, z; (vi) x+1, y, z+1; (vii) x, y, z1.

Experimental details

Crystal data
Chemical formulaC17H25N5O7
Mr411.42
Crystal system, space groupMonoclinic, P21
Temperature (K)100
a, b, c (Å)8.1817 (1), 26.4033 (5), 8.8800 (2)
β (°) 98.023 (1)
V3)1899.52 (6)
Z4
Radiation typeCu Kα
µ (mm1)0.96
Crystal size (mm)0.15 × 0.08 × 0.08
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2008)
Tmin, Tmax0.86, 0.93
No. of measured, independent and
observed [I > 2σ(I)] reflections
26696, 6862, 6644
Rint0.029
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.072, 1.04
No. of reflections6862
No. of parameters531
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.23, 0.17
Absolute structureFlack x determined using 2923 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Absolute structure parameter0.08 (5)

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS2013 (Sheldrick, 2008), SHELXL2013 (Sheldrick, 2015), X-SEED, Barbour, 2001, CIFTAB (Sheldrick, 2008).

 

References

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Volume 72| Part 5| May 2016| Pages 624-627
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