organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296

A novel Janus-type AT nucleoside with benzoyl protecting groups forming a pleated-sheet structure

aLaboratory of Ethnopharmacology, Institute for Nanobiomedical Technology and Membrane Biology, Regenerative Medicine Research Center, West China Hospital, West China Medical School, Sichuan University, No. 1 Keyuansilu, Gaopeng Dadao, Chengdu, Sichuan 610041, People's Republic of China, and bAnalytical and Testing Center, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu 610064, People's Republic of China
*Correspondence e-mail: huangwen@scu.edu.cn, heyangqx@yahoo.com.cn

(Received 28 January 2011; accepted 27 March 2011; online 14 April 2011)

The title compound, 5-amino-8-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)pyrimido[4,5-d]pyrimidine-2,4(3H,8H)-dione methanol monosolvate, C32H25N5O9·CH4O, which crystallized slowly from methanol, exhibits an anti conformation with a glycosyl-bond torsion angle of χ = −141.28 (17)°. The furan­ose moiety adopts an N-type sugar puckering (3T4). The corresponding pseudo­rotation phase angle and maximum amplitude are P = 24.5 (2)° and τm = 38.3 (2)°, respectively. In the solid state, one methanol mol­ecule acts as a bridge joining adjacent nucleoside mol­ecules head-to-head, leading to a pleated-ribbon supra­molecular structure, with the base moieties located in the centre of the ribbon and the sugar residues protruding to the outside of the layers, as in a DNA helix. The pleated-ribbon supra­molecular structure is tethered together into a two-dimensional infinite pleated-sheet structure through aromatic stacking between the nucleobase planes and the benzene rings of the benzoyl protecting groups on the 5′-OH group of furanose.

Comment

Recently, a novel Janus-type GC (J-GC) nucleoside, (II)[link] (from the two-faced Roman god Janus), has been synthesized in our laboratory which showed anti­viral potential (Yang et al., 2011[Yang, H.-Z., Pan, M.-Y., Jiang, D.-W. & He, Y. (2011). Org. Biomol. Chem. 9, 1516-1522.]). The base moiety of J-GC has one face with a Watson–Crick donor–donor–acceptor (DDA) hydrogen-bond array of guanine and the other with an acceptor–acceptor–donor (AAD) hydrogen-bond array of cytosine. In principle, J-GC could pair with cytidine or guanosine via rotation of the glycosyl bond. At the same time, this J-GC nucleoside can also associate through self-complementary hydrogen-bond formation. This property has been employed to construct nano-architectures such as trimers (Sessler et al., 2003[Sessler, J., Jayawickramarajah, J., Sathiosatham, M., Sherman, C. & Brodbelt, J. (2003). Org. Lett. 5, 2627-2630.]), rosettes (Marsh et al., 1996[Marsh, A., Silvestri, M. & Lehn, J.-M. (1996). Chem. Commun. pp. 1527-1528.]; Fenniri et al., 2001[Fenniri, H., Mathivanan, P., Vidale, K. L., Sherman, D. M., Hallenga, K., Wood, K. V. & Stowell, J. G. (2001). J. Am. Chem. Soc. 123, 3854-3855.]) and regular noncovalent polymer arrays (Asadi et al., 2007[Asadi, A., Patrick, B. O. & Perrin, D. M. (2007). J. Org. Chem. 72, 466-475.]; Marsh et al., 1994[Marsh, A., Nolen, E., Gardinier, K. & Lehn, J. (1994). Tetrahedron Lett. 35, 397-400.]). In order to make full use of these properties to generate different supra­molecular structures in the field of nucleosides and oligonucleotides, we wish to expand these Janus nucleosides from a tridentate GC series to a bidentate AT series. Very few structures with the Janus-type AT base moiety have been reported (Tominaga et al., 1991[Tominaga, Y., Ohno, S., Kohra, S., Fujito, H. & Mazurae, H. (1991). J. Heterocycl. Chem. 28, 1039-1042.]; Asadi et al., 2007[Asadi, A., Patrick, B. O. & Perrin, D. M. (2007). J. Org. Chem. 72, 466-475.]). Consequently, we synthesized the Janus-type AT nucleoside (J-AT); the full synthetic route will be reported elsewhere. The base moiety of J-AT has one face with a Watson–Crick acceptor–donor (AD) hydrogen-bond array of adenine and the other with a donor–acceptor (DA) hydrogen-bond array of thymine. Inter­estingly, we have found for the first time that the solid-state structure of the benzoylated J-AT nucleoside, (I)[link], can form a pleated-sheet supra­structure, a finding that we report in this paper. The expected hydrogen-bond patterns of (I)[link] and (II)[link] are shown in the scheme[link] (arrows labelled A represent hydrogen-bond acceptors and those labelled D represent hydrogen-bond donors).

[Scheme 1]

The structure of (I)[link] is shown in Fig. 1[link], selected geometric parameters are listed in Table 1[link] and the hydrogen-bond geometry is listed in Table 2[link].

The pyrimido[4,5-d]pyrimidine ring is almost planar. For the thymine pyrimidine ring, the deviations of the ring atoms from the N1/C2/N3/C4/C10/C9 least-squares plane range from −0.009 (2) (for C2) to 0.016 (1) Å (for N1), with an r.m.s. deviation of 0.010 Å. The exocyclic atoms N11, O12 and O13 and the C1′ substituent group deviate from this plane by −0.135 (4), 0.067 (3), −0.043 (3) and −0.189 (4) Å, respectively. For the adenine pyrimidine ring, the deviations of the ring atoms from the C10/C9/N8/C7/N6/C5 least-squares plane range from −0.017 (1) (for C5) to 0.012 (1) Å (for C10), with an r.m.s. deviation of 0.011 Å. The deviations of exocyclic atoms N11, O12 and O13 from this ring are −0.135 (4), 0.055 (4) and −0.129 (4) Å, respectively. The dihedral angle between the two rings is 1.62 (11)°. Therefore, the parameters of each ring of the pyrimido[4,5-d]pyrimidine are quite close to those of canonical adenine (Lai & Marsh, 1972[Lai, T. F. & Marsh, R. E. (1972). Acta Cryst. B28, 1982-1989.]) and thymine (Ozeki et al., 1969[Ozeki, K., Sakabe, N. & Tanaka, J. (1969). Acta Cryst. B25, 1038-1045.]). The orientation of the nucleobase relative to the sugar ring (anti/syn conformation) in a normal N9-glycosyl­ated purine nucleoside system is defined by the torsion angle χ(O4′—C1′—N9—C4) (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983[IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9-15.]). When the pyrimidine ring of the purine is located outside the sugar plane the conformation is defined as anti, and when it is located inside the sugar plane the conformation is defined as syn. In the case of (I)[link], the anti/syn conformation is also defined by the torsion angle χ(O4′—C1′—N8—C9), which is −141.28 (17)°, with the thymine ring located outside the sugar ring. Therefore, (I)[link] adopts an anti conformation. Another conformational parameter of inter­est is the puckering of the ribofuran­ose moiety, which is defined by the pseudorotation phase angle and the maximum puckering amplitude (Altona & Sundaralingam, 1972[Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212.]). The values of these two parameters are P = 24.5 (2)° and τm = 38.3 (2)°, respectively. The corresponding sugar puckering mode is an asymmetrical twist of 3T4 in the north (3′-endo) region, which is in the normal range for a pyrimidine or purine ribonucleoside system. The orientation of the exocyclic 5′-hydroxy group relative to the ribofuran­ose ring is characterized by the torsion angle γ (O5′—C5′—C4′—C3′), which is 57.3 (3)° for (I)[link], corresponding to the +sc (gauche) conformation.

A very inter­esting phenomenon is that the inter­molecular connection of (I)[link] is not mediated through self-complementary Watson–Crick base pairs as proposed for J-GC base pairs (Fenniri et al., 2001[Fenniri, H., Mathivanan, P., Vidale, K. L., Sherman, D. M., Hallenga, K., Wood, K. V. & Stowell, J. G. (2001). J. Am. Chem. Soc. 123, 3854-3855.]; Marsh et al., 1996[Marsh, A., Silvestri, M. & Lehn, J.-M. (1996). Chem. Commun. pp. 1527-1528.]; Yang et al., 2011[Yang, H.-Z., Pan, M.-Y., Jiang, D.-W. & He, Y. (2011). Org. Biomol. Chem. 9, 1516-1522.]) (see scheme[link]). The unit cell of (I)[link] consists of four nucleoside mol­ecules and four methanol mol­ecules (Fig. 2[link]). Each nucleoside mol­ecule is involved in six intermolecular hydrogen bonds and one intramolecular N11—H11A⋯O12 interaction (Table 2[link] and Fig. 3[link]). Four inter­molecular hydrogen bonds act as the linking units, connecting adjacent nucleosides head-to-head in an antiparallel manner to form an undulating ribbon in one layer (Fig. 4[link]). The N3—H3⋯N6 hydrogen bond is not shown, owing to the large distance between atoms H3 and N6. Three of the linking units are highlighted by the small rect­angle in Fig. 4[link]: the first is formed between the H atom of the exocyclic amino group of one nucleoside mol­ecule and the O atom of the benzoyl group of the previous nucleoside mol­ecule in the chain; the second hydrogen bond is formed between the H atom of the exocyclic amino group of the nucleoside mol­ecule and the O atom of the methanol mol­ecule; and the third is formed between the H atom of the same methanol mol­ecule and the exocyclic O atom of the next nucleoside mol­ecule in the chain. This ribbon has a pleated linear structure, viewed along the [001] orientation, as shown in Fig. 5[link]. This arrangement is quite different from the flattened structures reported for 5,7-diamino-1-heptyl­pyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione and 5,7-diamino-1-butyl-1H-pyrido[4,3-d]pyrimidine-2,4-dione (Asadi et al., 2007[Asadi, A., Patrick, B. O. & Perrin, D. M. (2007). J. Org. Chem. 72, 466-475.]). In this pleated-ribbon structure, the base moieties are located in the centre of the ribbon and the sugar residues protrude to the outside of the layers (see Fig. 4[link]), as in a DNA helix. Finally, the layers are tethered together in a parallel fashion and stretched to form an infinite two-dimensional pleated-sheet structure through aromatic stacking between the nucleobase planes and the benzene rings of the benzoyl protecting groups on the 5′-OH group of furanose. Whether the special pleated-sheet structure exists at the RNA (or DNA) level will be explored in future studies.

[Figure 1]
Figure 1
A perspective view of (I)[link], showing the atom-labelling scheme and the intra­molecular hydrogen bond (dashed line). Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2]
Figure 2
An arrangement of the nucleoside and methanol mol­ecules in the unit cell of (I)[link], viewed along [100]. Hydrogen bonds have been omitted for clarity.
[Figure 3]
Figure 3
A detailed view of the hydrogen bonds surrounding one nucleoside mol­ecule. Hydrogen bonds are indicated by dashed lines. (In the electronic version of the paper, the bifurcated hydrogen bonds are shown in green and the hydrogen bonds with large distances are shown in yellow; the remaining hydrogen bonds are shown in black.) H atoms of (I)[link] and some groups which are not involved in hydrogen bonds have been omitted for clarity. (In the electronic version of the paper, atoms are coded as follows: red for oxygen, blue for nitro­gen, grey for carbon and white for hydrogen.) [Symmetry codes: (ii) −x, y − [{1\over 2}], −z + [{3 \over 2}]; (iii) −x + 1, y[{1 \over 2}], −z + [{3 \over 2}]; (iv) −x, y + [{1 \over 2}], −z + [{3 \over 2}]; (v) x − 1, y − 1, z.]
[Figure 4]
Figure 4
A packing diagram for (I)[link], viewed along [100]. Hydrogen bonds are indicated by dashed lines. The hydrogen-bond motif in the small rectangular frame is the linking unit. H atoms have been omitted for clarity.
[Figure 5]
Figure 5
A four-layered packing diagram for (I)[link], viewed along [001]. Hydrogen bonds are shown as dashed lines. H atoms have been omitted for clarity.

Experimental

Compound (I) was synthesized from bis(methylsulfanyl)methylenecyanamide. The detailed synthetic procedure will be reported elsewhere. Compound (I)[link] was dissolved in methanol at 323 K, and cooled slowly in steps of 0.5 K h−1 to ambient temperature in an incubator, giving colourless needle-shaped crystals suitable for single-crystal X-ray diffraction. A selected crystal of compound (I)[link] was protected in the mother liquor in a tiny glass tube and epoxy resin was used to minimize the loss of the solvent.

Crystal data
  • C32H25N5O9·CH4O

  • Mr = 655.61

  • Orthorhombic, P 21 21 21

  • a = 8.2526 (3) Å

  • b = 11.9486 (4) Å

  • c = 32.1865 (10) Å

  • V = 3173.82 (18) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 293 K

  • 0.42 × 0.36 × 0.20 mm

Data collection
  • Oxford Diffraction Xcalibur CCD diffractometer

  • Absorption correction: multi-scan [CrysAlis PRO (Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO. Version 1.171.33.66. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]); empirical absorption correction using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm]Tmin = 0.443, Tmax = 1.0

  • 9151 measured reflections

  • 6101 independent reflections

  • 4128 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.093

  • S = 0.91

  • 6101 reflections

  • 441 parameters

  • 4 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Selected torsion angles (°)

O4′—C1′—C2′—C3′ −19.90 (18)
O4′—C4′—C5′—O5′ −60.7 (2)
O12—C4—C10—C9 −177.1 (2)
N1—C9—C10—C5 178.17 (19)
N8—C9—C10—C4 −178.65 (16)
C2—N3—C4—O12 177.2 (2)
C3′—C4′—C5′—O5′ 57.3 (3)
C4—N3—C2—O13 179.1 (2)
C4—C10—C5—N6 −179.49 (17)
C7—N6—C5—N11 177.5 (2)
C7—N8—C1′—O4′ 34.4 (3)
C9—N1—C2—O13 −177.1 (2)
C9—N8—C1′—O4′ −141.28 (17)
C9—C10—C5—N11 −176.94 (19)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O10—H10⋯O13i 0.82 1.86 2.661 (3) 166
N3—H3⋯N6ii 0.86 2.40 3.113 (2) 141
N11—H11B⋯O10iii 0.87 (1) 1.96 (1) 2.835 (3) 176 (2)
N11—H11A⋯O7′ii 0.86 (1) 2.29 (2) 2.860 (2) 124 (2)
N11—H11A⋯O12 0.86 (1) 2.12 (2) 2.751 (2) 130 (2)
Symmetry codes: (i) x+1, y+1, z; (ii) [-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].

In the absence of suitable anomalous scattering, Friedel equivalents cannot be used to determine the absolute structure. The Flack parameter (Flack, 1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]) has an inconclusive value of 0.3 (9) with 2423 Friedel pairs. The known configuration of the D-ribofuran­ose derivatives was used to define the enantio­mer employed in the refined model. The amine H atoms at N11 were located in a difference Fourier map and were refined using N—H bond-length restraints of 0.86 (2) Å, a H⋯H distance restraint of 1.40 (4) Å, similarity restraints (s.u. of 0.02 Å) for the two C5⋯H distances and fixed Uiso(H) values of 0.05 Å2. All other H atoms were placed in geometrically idealized positions and treated as riding. For the hydroxy and methyl groups, O—H = 0.82 Å and C—H = 0.96 Å, with Uiso(H) = 1.5Ueq(O,C). For the remaining groups, C—H = 0.93 (aromatic), 0.97 (methylene) or 0.98 Å (methine) and N—H = 0.86 Å, with Uiso(H) = 1.2Ueq(C,N).

Data collection: CrysAlis PRO (Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO. Version 1.171.33.66. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]); software used to prepare material for publication: OLEX2.

Supporting information


Comment top

Recently, a novel Janus-type GC (J-GC) nucleoside, (II) (from the two-faced Roman god Janus), has been synthesized in our laboratory which showed antiviral potential (Yang et al., 2011). The base moiety of J-GC has one face with a Watson–Crick donor–donor–acceptor (DDA) hydrogen-bond array of guanine and the other face with an acceptor–acceptor–donor (AAD) hydrogen-bond array of cytosine. In principle, J-GC could pair with cytidine or guanosine via rotation of the glycosyl bond. At the same time, this J-GC nucleoside can also associate through self-supplementary hydrogen-bond formation. This property has been employed to construct nano-architectures such as trimers (Sessler et al., 2003), rosettes (Marsh et al., 1996; Fenniri et al., 2001) and regular noncovalent polymer arrays (Asadi et al., 2007' Marsh et al., 1994). In order to make full use of these properties to generate different supramolecular structures in the field of nucleosides and oligonucleotides, we wish to expand these Janus nucleosides from a tridentate GC series to a bidentate AT series. Very few structures with the Janus-type AT base moiety have been reported (Tominaga et al., 1991; Asadi et al., 2007). Consequently, we synthesized the Janus-type AT nucleoside (J-AT),; the full synthetic route will be reported elsewhere. The base moiety of J-AT has one face with a Watson–Crick acceptor–donor (AD) hydrogen-bond array of adenine and the other face with a donor–acceptor (DA) hydrogen-bond array of thymine. Interestingly, we have found for the first time that the solid-state structure of the benzolyted J-AT nucleoside, (I), can form a pleated sheet suprastructure, findings which we report in this paper. The expecting hydrogen-bonds patterns of compound (I) and (II) are shown in the scheme (the arrows of A represent the hydrogen bond acceptors; the arrows of D represent the hydrogen bond donors).

The single-crystal of compound (I) was obtained by dissolving it in hot methanol and cooling slowly to room temperature in an incubator, giving colourless needle crystals suitable for single-crystal X-ray diffraction. The structure of compound (I) is shown in Fig. 1, selected geometric parameters are listed in Table 1 and the hydrogen-bond geometry is listed in Table 2.

The pyrimido[4,5-d]pyrimidine ring is almost planar. For the thymine pyrimidine ring, the deviations of the ring atoms from the least-squares plane (N1/C2/N3/C4/C10/C9) range from -0.009 (2) (C2) to 0.016 (1) Å (N1), with an r.m.s. deviation of 0.010 Å. The exocyclic atoms N11, O12, O13 and the C1' substituent group deviate from this plane with distances of -0.135 (4), 0.067 (3), -0.043 (3) and -0.189 (4) Å. For the adenine pyrimidine ring, the deviations of the ring atoms from the least-squares plane (C10/C9/N8/C7/N6/C5) range from -0.017 (1) (C5) to 0.012 (1) (C10) Å, with an r.m.s. deviation of 0.011 Å. The deviations of exocyclic atoms N11, O12 and O13 from this ring are -0.135 (4), 0.055 (4) and -0.129 (4) Å, respectively. The dihedral angle between the two rings is 1.62 (11)°. Therefore, the parameters of each ring of the pyrimido[4,5-d]pyrimidine are quite close to those of canonical adenine (Lai & Marsh, 1972) and thymine (Ozeki et al., 1969). The orientation of the nucleobase relative to the sugar ring (anti/syn conformation) in a normal N9-glycosylated purine nucleoside system is defined by the torsion angle χ (O4'—C1'—N9— C4) (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983).When the pyrimidine ring of the purine is located outside of the sugar plane, the conformation is defined as anti; on the other hand, when the pyrimidine ring of purine is located inside of the sugar plane, the conformation is defined as syn. In the case of compound (I), the anti/syn conformation is also defined by the torsion angle χ (O4'—C1'—N8— C9) correspondingly which is -141.28 (17)°, with the thymine ring located outside the sugar ring. Therefore, compound (I) adopts an anti conformation. Another conformational parameter of interest is the puckering of the ribofuranose moiety which is defined by the pseudorotation phase angle and the maximum puckering amplitude (Altona & Sundaralingam, 1972). The values of these two parameters are P = 25.5 (2)°, τm = 38.3 (2)°, respectively. The corresponding sugar puckering mode is an asymmetrical twist of 3T 4 in the North (3'-endo) region, which is in the normal range of the pyrimidine or purine ribonucleoside system. The orientation of the exocyclic 5'-hydroxyl group relative to the ribofuranose ring is characterized by the torsion angle γ (O5'—C5'—C4'—C3'), which is 57.3 (3)° for compound (I) corresponding to the +sc (gauche) conformation.

A very interesting phenomenon is that the intermolecular connection of compound (I) is not mediated through self-complementary Watson–Crick base pairs as proposed in J-GC base pairs (Fenniri et al., 2001; Marsh et al., 1996; Yang et al., 2011) (scheme). The crystal cell of compound (I) consists of four nucleoside molecules and four methanol molecules (Fig. 2). There are seven hydrogen bonds on one nucleoside molecule which ware displayed in Fig.3. Six of them are intermolecular hydrogen bonds: O10—H10···O13, N3—H3···N6, N11—H11A···O7', N11—H11B···O10, N6···H3—N3 and O7'···H11A—N11. The remaining one is an intramolecular hydrogen bond formed between the N11—H11A and O12. Four intermolecular hydrogen bonds act as the repeated units connecting adjacent nucleosides head to head in an anti-parallel way to form a wavy ribbon in one layer (Fig. 4). The hydrogen bond N3—H3···N6 is not shown owing to the large distance between the H3 and N6 atoms. Three of them are highlighted in the red rectangle in Fig. 4: the first one is formed between the H atom of the exocyclic amino group of one nucleoside molecule and the O atom of the benzoyl group of the former nucleoside molecule; the second hydrogen bond is formed between the H atom of the exocyclic amino group of the nucleoside molecule and the O atom of the methanol molecule; the third one is formed between the H atom of the same methanol molecule and the exocyclic oxygen of the next nucleoside molecule. This wavy ribbon forms a three-dimensional pleated sheet structure when viewed along the [001] orientation as shown in Fig. 5. This arrangement is quite different from the flattened structure reported for 5,7-diamino-1-heptylpyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione and 5,7-diamino-1-butyl-1H-pyrido[4,3-d]pyrimidine-2,4-dione (Asadi et al., 2007). In this pleated sheet structure, the base moieties are located inside and the sugar residues located outside (see Fig. 4) as in a DNA helix. Finally, the layers are tethered together in a parallel fashion [ok as edited?] and stretched in all directions to form an infinite three-dimensional wall through short contacts. Whether the special pleated sheet structure exists in [at the?] RNA (or DNA) level will be explored in future studies.

Related literature top

For related literature, see: Altona & Sundaralingam (1972); Asadi et al. (2007); Fenniri et al. (2001); IUPAC–IUB Joint Commission on Biochemical Nomenclature (1983); Lai & Marsh (1972); Marsh et al. (1994, 1996); Ozeki et al. (1969); Sessler et al. (2003); Tominaga et al. (1991); Yang et al. (2011).

Experimental top

Compound (I) was dissolved in methanol at 323 K, and slowly cooled in steps of 0.5 K h-1 to ambient temperature in an incubator, giving colourless needle crystals suitable for single-crystal X-ray diffraction. The crystal of compound (I) was protected in the mother liquor in a tiny glass tube and the epoxy resin was used to minimize the loss of the solvent.

Refinement top

In the absence of suitable anomalous scattering, Friedel equivalents cannot be used to determine the absolute structure.The Flack parameter leads to an inconclusive value [the Flack parameter is 0.3 (9)]. The known configuration of the D-ribofuranose derivatives was used to define the enantiomer employed in the refined model. All H atoms were placed in geometrically idealized positions and treated as riding. For the OH and CH3 groups, the O—H distance is 0.82 Å, and the C—H distance is 0.96 Å, with Uiso(H) = 1.5Ueq(O, C). For the remaining groups, the C—H distance is 0.93–0.98 Å and the N—H distance is 0.857–0.874 Å, with Uiso(H) = 1.2Ueq (C, N).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. A perspective view of compound (I), showing the atom-labelling scheme and the intramolecular hydrogen bond (dashed line). Displacement ellipsoids are drawn at the 30% probability level. H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. An arrangement of the nucleoside and methanol molecules in the crystal cell of compound (I), viewed along [100]. The hydrogen bonds have been omitted for clarity.
[Figure 3] Fig. 3. A detailed view of the hydrogen bonds on one nucleoside molecule. Hydrogen bonds are indicated by dashed lines; the bifurcated hydrogen bonds are shown in green and the hydrogen bonds with large distances are shown in yellow. The remaining hydrogen bonds are shown in black. H atoms in compound (I) and some groups which are not involved in hydrogen bonds have been omitted for clarity. Atoms are coded as follows: red, oxygen; blue, nitrogen; grey, carbon; white, hydrogen.
[Figure 4] Fig. 4. A packing diagram of compound (I) viewed along [100]. Hydrogen bonds are indicated by dashed lines. The hydrogen-bond motif in the red rectangle frame is the repeated unit. H atoms have been omitted for clarity.
[Figure 5] Fig. 5. A four-layered packing diagram of compound (I), viewed along [001]. H atoms and short contacts have been omitted for clarity.
5-amino-8-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)pyrimido[4,5- d]pyrimidine-2,4(3H,8H)-dione methanol monosolvate top
Crystal data top
C32H25N5O9·CH4OF(000) = 1368
Mr = 655.61Dx = 1.372 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ac 2abCell parameters from 4443 reflections
a = 8.2526 (3) Åθ = 3.0–28.6°
b = 11.9486 (4) ŵ = 0.10 mm1
c = 32.1865 (10) ÅT = 293 K
V = 3173.82 (18) Å3Block, colourless
Z = 40.42 × 0.36 × 0.20 mm
Data collection top
Xcalibur, Eos
diffractometer
6101 independent reflections
Radiation source: fine-focus sealed tube4128 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
Detector resolution: 16.0874 pixels mm-1θmax = 26.4°, θmin = 3.0°
ω scansh = 510
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
k = 1214
Tmin = 0.443, Tmax = 1.0l = 4037
9151 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.093 w = 1/[σ2(Fo2) + (0.0545P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.91(Δ/σ)max = 0.001
6101 reflectionsΔρmax = 0.20 e Å3
441 parametersΔρmin = 0.17 e Å3
4 restraintsAbsolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.3 (9)
Crystal data top
C32H25N5O9·CH4OV = 3173.82 (18) Å3
Mr = 655.61Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.2526 (3) ŵ = 0.10 mm1
b = 11.9486 (4) ÅT = 293 K
c = 32.1865 (10) Å0.42 × 0.36 × 0.20 mm
Data collection top
Xcalibur, Eos
diffractometer
6101 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
4128 reflections with I > 2σ(I)
Tmin = 0.443, Tmax = 1.0Rint = 0.019
9151 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.093Δρmax = 0.20 e Å3
S = 0.91Δρmin = 0.17 e Å3
6101 reflectionsAbsolute structure: Flack (1983)
441 parametersAbsolute structure parameter: 0.3 (9)
4 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
O1'0.1064 (2)0.9166 (2)0.57869 (5)0.0981 (7)
O2'0.16180 (18)0.92186 (14)0.57869 (4)0.0602 (4)
O3'0.30283 (19)1.11731 (12)0.59472 (4)0.0536 (4)
O4'0.41924 (18)0.86301 (12)0.64316 (4)0.0509 (4)
O5'0.59502 (18)1.03297 (12)0.68253 (4)0.0574 (4)
O6'0.7952 (4)0.9171 (3)0.69536 (6)0.1580 (14)
O7'0.0843 (3)1.19406 (17)0.62259 (5)0.0988 (7)
O100.7211 (3)1.35557 (18)0.62921 (7)0.1071 (7)
H100.75641.41950.62720.161*
O120.1258 (2)0.60344 (14)0.77627 (4)0.0688 (5)
O130.1604 (2)0.56157 (16)0.63710 (5)0.0849 (6)
N10.0126 (2)0.69619 (14)0.65928 (5)0.0478 (4)
N30.1379 (2)0.58429 (16)0.70634 (5)0.0551 (5)
H30.20800.53170.70940.066*
N60.2396 (2)0.85321 (14)0.75736 (5)0.0477 (4)
N80.1959 (2)0.82240 (13)0.68565 (4)0.0425 (4)
N110.1053 (2)0.74897 (16)0.80589 (5)0.0535 (5)
C10.0181 (3)0.91044 (19)0.56044 (6)0.0534 (5)
C1'0.2495 (3)0.84454 (18)0.64265 (5)0.0482 (5)
H1'0.22670.77840.62560.058*
C20.0961 (3)0.6135 (2)0.66577 (6)0.0557 (6)
C2'0.1714 (3)0.94616 (18)0.62242 (5)0.0472 (5)
H2'0.06750.96760.63490.057*
C30.0371 (3)0.88356 (18)0.51572 (6)0.0517 (5)
C3'0.3025 (2)1.03413 (17)0.62692 (5)0.0444 (5)
H3'0.29811.06920.65440.053*
C40.0764 (2)0.63233 (18)0.74197 (6)0.0480 (5)
C4'0.4559 (2)0.96579 (18)0.62195 (6)0.0477 (5)
H4'0.47070.94930.59240.057*
C60.1716 (3)0.9130 (2)0.49378 (7)0.0738 (8)
H60.25430.95260.50680.089*
C5'0.6121 (3)1.0112 (2)0.63873 (7)0.0624 (6)
H5'B0.69850.95740.63420.075*
H5'A0.64021.07980.62430.075*
C80.1863 (4)0.8843 (3)0.45209 (7)0.0890 (9)
H80.27830.90520.43730.107*
C70.2670 (3)0.87387 (17)0.71838 (6)0.0479 (5)
H70.34270.92920.71240.057*
C110.0678 (4)0.8266 (3)0.43322 (8)0.0859 (9)
H110.07830.80690.40540.103*
C90.0778 (2)0.74186 (15)0.69249 (6)0.0387 (5)
C100.0425 (2)0.71700 (16)0.73433 (6)0.0399 (4)
C120.0664 (4)0.7970 (3)0.45441 (10)0.1094 (12)
H120.14780.75660.44120.131*
C130.0833 (4)0.8267 (3)0.49569 (8)0.0894 (9)
H130.17740.80780.50990.107*
C140.1853 (3)1.19359 (19)0.59607 (6)0.0553 (6)
C150.1917 (3)1.27433 (18)0.56114 (6)0.0526 (5)
C160.0966 (3)1.3687 (2)0.56331 (8)0.0733 (7)
H160.03121.38140.58640.088*
C170.0994 (4)1.4443 (3)0.53078 (10)0.0908 (9)
H170.03701.50900.53230.109*
C180.1920 (4)1.4253 (3)0.49675 (9)0.0922 (9)
H180.19101.47620.47490.111*
C190.2850 (4)1.3335 (3)0.49442 (8)0.0868 (9)
H190.34841.32120.47100.104*
C200.2875 (3)1.2568 (2)0.52666 (7)0.0687 (7)
H200.35341.19380.52510.082*
C210.6937 (3)0.9786 (2)0.70792 (8)0.0707 (7)
C220.6645 (3)1.0037 (2)0.75222 (7)0.0590 (6)
C230.5612 (3)1.0867 (2)0.76491 (8)0.0653 (6)
H230.50411.12890.74550.078*
C240.5428 (3)1.1070 (3)0.80733 (10)0.0811 (9)
H240.47341.16320.81640.097*
C250.6271 (4)1.0439 (3)0.83574 (10)0.0969 (10)
H250.61491.05760.86400.116*
C260.7278 (4)0.9620 (3)0.82271 (10)0.1052 (11)
H260.78440.91960.84210.126*
C270.7475 (4)0.9407 (3)0.78108 (8)0.0878 (9)
H270.81660.88380.77240.105*
C280.6092 (6)1.3387 (3)0.60040 (14)0.1419 (16)
H28A0.64911.28620.58030.213*
H28B0.58451.40830.58690.213*
H28C0.51301.30940.61310.213*
C50.1272 (2)0.77177 (16)0.76612 (6)0.0414 (5)
H11B0.160 (2)0.7844 (15)0.8251 (5)0.050*
H11A0.034 (2)0.7008 (15)0.8132 (6)0.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O1'0.0547 (10)0.190 (2)0.0499 (10)0.0053 (13)0.0024 (9)0.0181 (12)
O2'0.0529 (9)0.1033 (12)0.0245 (7)0.0130 (9)0.0018 (7)0.0056 (7)
O3'0.0575 (9)0.0618 (9)0.0415 (8)0.0022 (9)0.0098 (7)0.0117 (7)
O4'0.0526 (9)0.0574 (9)0.0426 (8)0.0039 (8)0.0160 (7)0.0041 (6)
O5'0.0494 (8)0.0704 (10)0.0525 (9)0.0050 (8)0.0048 (7)0.0061 (7)
O6'0.168 (2)0.237 (3)0.0693 (14)0.146 (3)0.0011 (15)0.0096 (15)
O7'0.1211 (16)0.1150 (15)0.0604 (11)0.0562 (14)0.0485 (12)0.0290 (10)
O100.130 (2)0.0960 (16)0.0952 (15)0.0033 (15)0.0450 (14)0.0166 (12)
O120.0765 (11)0.0941 (12)0.0357 (9)0.0300 (9)0.0116 (7)0.0062 (7)
O130.0976 (13)0.1168 (14)0.0404 (9)0.0545 (12)0.0191 (9)0.0028 (9)
N10.0548 (11)0.0605 (10)0.0281 (9)0.0089 (10)0.0031 (8)0.0021 (7)
N30.0507 (10)0.0760 (13)0.0384 (10)0.0207 (10)0.0039 (8)0.0075 (8)
N60.0581 (10)0.0558 (10)0.0294 (9)0.0081 (9)0.0068 (8)0.0051 (7)
N80.0525 (10)0.0470 (9)0.0281 (8)0.0059 (9)0.0089 (7)0.0022 (7)
N110.0605 (12)0.0708 (13)0.0291 (10)0.0150 (10)0.0037 (9)0.0011 (8)
C10.0525 (13)0.0724 (14)0.0354 (12)0.0049 (12)0.0023 (11)0.0051 (10)
C1'0.0604 (13)0.0589 (13)0.0251 (10)0.0102 (11)0.0131 (10)0.0065 (9)
C20.0548 (13)0.0764 (16)0.0360 (12)0.0115 (13)0.0089 (10)0.0061 (11)
C2'0.0479 (11)0.0712 (14)0.0225 (10)0.0062 (11)0.0069 (9)0.0019 (9)
C30.0615 (13)0.0586 (13)0.0350 (11)0.0021 (12)0.0054 (10)0.0038 (9)
C3'0.0524 (12)0.0535 (12)0.0273 (10)0.0016 (11)0.0049 (9)0.0031 (8)
C40.0460 (11)0.0621 (13)0.0358 (12)0.0035 (11)0.0005 (10)0.0038 (10)
C4'0.0494 (12)0.0620 (14)0.0317 (11)0.0031 (11)0.0088 (9)0.0063 (9)
C60.0789 (17)0.110 (2)0.0328 (12)0.0239 (17)0.0004 (12)0.0013 (12)
C5'0.0520 (13)0.0878 (17)0.0473 (14)0.0057 (14)0.0080 (11)0.0096 (12)
C80.102 (2)0.130 (2)0.0347 (13)0.020 (2)0.0072 (14)0.0055 (14)
C70.0572 (13)0.0503 (12)0.0360 (11)0.0104 (11)0.0107 (10)0.0066 (9)
C110.124 (3)0.101 (2)0.0329 (14)0.008 (2)0.0099 (16)0.0077 (13)
C90.0410 (11)0.0436 (11)0.0314 (10)0.0062 (10)0.0017 (8)0.0003 (8)
C100.0394 (10)0.0517 (11)0.0286 (10)0.0000 (10)0.0022 (8)0.0016 (8)
C120.116 (3)0.154 (3)0.0585 (19)0.049 (3)0.0145 (19)0.0302 (19)
C130.089 (2)0.124 (2)0.0557 (17)0.037 (2)0.0013 (15)0.0134 (15)
C140.0626 (14)0.0664 (14)0.0369 (12)0.0045 (14)0.0046 (11)0.0025 (10)
C150.0566 (13)0.0593 (14)0.0418 (12)0.0017 (13)0.0050 (10)0.0051 (9)
C160.0741 (17)0.0850 (18)0.0609 (16)0.0140 (16)0.0026 (13)0.0083 (13)
C170.087 (2)0.087 (2)0.098 (2)0.0224 (18)0.0055 (19)0.0323 (17)
C180.0802 (19)0.110 (2)0.086 (2)0.002 (2)0.0038 (17)0.0500 (18)
C190.088 (2)0.110 (2)0.0619 (17)0.005 (2)0.0180 (15)0.0303 (15)
C200.0750 (17)0.0809 (17)0.0502 (14)0.0094 (15)0.0115 (13)0.0152 (12)
C210.0602 (15)0.0870 (18)0.0650 (16)0.0250 (16)0.0012 (13)0.0045 (13)
C220.0460 (12)0.0753 (15)0.0557 (14)0.0013 (13)0.0022 (11)0.0097 (11)
C230.0452 (12)0.0763 (16)0.0744 (18)0.0063 (13)0.0034 (12)0.0185 (14)
C240.0580 (16)0.102 (2)0.084 (2)0.0157 (16)0.0078 (15)0.0399 (17)
C250.090 (2)0.137 (3)0.064 (2)0.027 (2)0.0082 (18)0.022 (2)
C260.103 (2)0.145 (3)0.067 (2)0.003 (3)0.0120 (18)0.0083 (19)
C270.0834 (19)0.116 (2)0.0638 (18)0.0215 (18)0.0092 (16)0.0017 (15)
C280.150 (3)0.089 (2)0.187 (4)0.028 (3)0.069 (3)0.009 (3)
C50.0443 (11)0.0504 (12)0.0294 (10)0.0019 (10)0.0050 (9)0.0006 (8)
Geometric parameters (Å, º) top
O1'—C11.186 (3)C6—C81.390 (3)
O2'—C11.331 (3)C5'—H5'B0.9700
O2'—C2'1.439 (2)C5'—H5'A0.9700
O3'—C3'1.436 (2)C8—H80.9300
O3'—C141.332 (3)C8—C111.342 (4)
O4'—C1'1.418 (3)C7—H70.9300
O4'—C4'1.437 (2)C11—H110.9300
O5'—C5'1.441 (2)C11—C121.348 (4)
O5'—C211.324 (3)C9—C101.409 (2)
O6'—C211.186 (3)C10—C51.401 (3)
O7'—C141.193 (3)C12—H120.9300
O10—H100.8200C12—C131.382 (4)
O10—C281.324 (4)C13—H130.9300
O12—C41.226 (2)C14—C151.482 (3)
O13—C21.232 (2)C15—C161.375 (3)
N1—C21.351 (3)C15—C201.379 (3)
N1—C91.315 (2)C16—H160.9300
N3—H30.8600C16—C171.384 (4)
N3—C21.395 (3)C17—H170.9300
N3—C41.379 (3)C17—C181.355 (4)
N6—C71.299 (2)C18—H180.9300
N6—C51.373 (2)C18—C191.341 (4)
N8—C1'1.477 (2)C19—H190.9300
N8—C71.354 (2)C19—C201.384 (3)
N8—C91.387 (2)C20—H200.9300
N11—C51.321 (2)C21—C221.477 (3)
N11—H11B0.874 (13)C22—C231.370 (3)
N11—H11A0.857 (13)C22—C271.378 (3)
C1—C31.483 (3)C23—H230.9300
C1'—H1'0.9800C23—C241.395 (4)
C1'—C2'1.521 (3)C24—H240.9300
C2'—H2'0.9800C24—C251.374 (4)
C2'—C3'1.516 (3)C25—H250.9300
C3—C61.362 (3)C25—C261.350 (4)
C3—C131.366 (3)C26—H260.9300
C3'—H3'0.9800C26—C271.374 (4)
C3'—C4'1.515 (3)C27—H270.9300
C4—C101.431 (3)C28—H28A0.9600
C4'—H4'0.9800C28—H28B0.9600
C4'—C5'1.500 (3)C28—H28C0.9600
C6—H60.9300
O1'—C1—O2'123.2 (2)C5'—C4'—H4'108.4
O1'—C1—C3125.9 (2)H5'B—C5'—H5'A108.2
O2'—C1—C3110.87 (19)C8—C6—H6119.7
O2'—C2'—C1'106.31 (16)C8—C11—H11119.8
O2'—C2'—H2'113.8C8—C11—C12120.3 (3)
O2'—C2'—C3'105.82 (14)C7—N6—C5116.79 (17)
O3'—C3'—C2'114.34 (16)C7—N8—C1'121.17 (17)
O3'—C3'—H3'110.9C7—N8—C9119.77 (15)
O3'—C3'—C4'107.17 (15)C11—C8—C6120.0 (3)
O3'—C14—C15113.23 (19)C11—C8—H8120.0
O4'—C1'—N8108.26 (17)C11—C12—H12119.9
O4'—C1'—H1'108.8C11—C12—C13120.1 (3)
O4'—C1'—C2'107.43 (17)C9—N1—C2116.70 (16)
O4'—C4'—C3'103.57 (15)C9—N8—C1'118.92 (15)
O4'—C4'—H4'108.4C9—C10—C4117.05 (17)
O4'—C4'—C5'108.58 (17)C12—C11—H11119.8
O5'—C5'—C4'109.49 (16)C12—C13—H13119.7
O5'—C5'—H5'B109.8C13—C3—C1119.3 (2)
O5'—C5'—H5'A109.8C13—C12—H12119.9
O5'—C21—C22113.3 (2)C14—O3'—C3'116.66 (16)
O6'—C21—O5'121.9 (2)C15—C16—H16120.4
O6'—C21—C22124.8 (2)C15—C16—C17119.2 (3)
O7'—C14—O3'122.4 (2)C15—C20—C19119.6 (3)
O7'—C14—C15124.4 (2)C15—C20—H20120.2
O10—C28—H28A109.5C16—C15—C14118.3 (2)
O10—C28—H28B109.5C16—C15—C20119.5 (2)
O10—C28—H28C109.5C16—C17—H17119.6
O12—C4—N3120.61 (18)C17—C16—H16120.4
O12—C4—C10125.56 (19)C17—C18—H18119.8
O13—C2—N1122.58 (19)C18—C17—C16120.7 (3)
O13—C2—N3117.9 (2)C18—C17—H17119.6
N1—C2—N3119.49 (18)C18—C19—H19119.7
N1—C9—N8116.50 (16)C18—C19—C20120.5 (3)
N1—C9—C10127.21 (18)C19—C18—C17120.4 (3)
N3—C4—C10113.82 (17)C19—C18—H18119.8
N6—C7—N8126.13 (19)C19—C20—H20120.2
N6—C7—H7116.9C20—C15—C14122.1 (2)
N6—C5—C10121.19 (16)C20—C19—H19119.7
N8—C1'—H1'108.8C21—O5'—C5'117.06 (18)
N8—C1'—C2'114.64 (16)C22—C23—H23120.5
N8—C7—H7116.9C22—C23—C24119.0 (3)
N8—C9—C10116.29 (16)C22—C27—H27120.1
N11—C5—N6115.93 (17)C23—C22—C21122.4 (2)
N11—C5—C10122.88 (18)C23—C22—C27120.3 (2)
C1—O2'—C2'120.07 (16)C23—C24—H24120.0
C1'—O4'—C4'109.59 (16)C24—C23—H23120.5
C1'—C2'—H2'113.8C24—C25—H25119.9
C2—N3—H3117.2C25—C24—C23120.1 (3)
C2'—C1'—H1'108.8C25—C24—H24120.0
C2'—C3'—H3'110.9C25—C26—H26119.7
C3—C6—H6119.7C25—C26—C27120.7 (3)
C3—C6—C8120.5 (2)C26—C25—C24120.2 (3)
C3—C13—C12120.5 (3)C26—C25—H25119.9
C3—C13—H13119.7C26—C27—C22119.8 (3)
C3'—C2'—C1'102.10 (16)C26—C27—H27120.1
C3'—C2'—H2'113.8C27—C22—C21117.3 (2)
C3'—C4'—H4'108.4C27—C26—H26119.7
C4—N3—H3117.2C28—O10—H10109.5
C4—N3—C2125.67 (18)H28A—C28—H28B109.5
C4'—C3'—C2'102.28 (15)H28A—C28—H28C109.5
C4'—C3'—H3'110.9H28B—C28—H28C109.5
C4'—C5'—H5'B109.8C5—N11—H11B120.9 (12)
C4'—C5'—H5'A109.8C5—N11—H11A119.8 (13)
C6—C3—C1122.2 (2)C5—C10—C4123.16 (17)
C6—C3—C13118.5 (2)C5—C10—C9119.75 (17)
C6—C8—H8120.0H11B—N11—H11A119.2 (19)
C5'—C4'—C3'119.05 (18)
O1'—C1—C3—C6157.8 (3)C3'—O3'—C14—O7'0.3 (3)
O1'—C1—C3—C1322.7 (4)C3'—O3'—C14—C15178.42 (18)
O2'—C1—C3—C625.3 (3)C3'—C4'—C5'—O5'57.3 (3)
O2'—C1—C3—C13154.2 (2)C4—N3—C2—O13179.1 (2)
O2'—C2'—C3'—O3'39.3 (2)C4—N3—C2—N10.5 (3)
O2'—C2'—C3'—C4'76.19 (17)C4—C10—C5—N6179.49 (17)
O3'—C3'—C4'—O4'158.71 (15)C4—C10—C5—N110.7 (3)
O3'—C3'—C4'—C5'80.7 (2)C4'—O4'—C1'—N8128.43 (16)
O3'—C14—C15—C16168.0 (2)C4'—O4'—C1'—C2'4.1 (2)
O3'—C14—C15—C2013.0 (3)C6—C3—C13—C121.8 (4)
O4'—C1'—C2'—O2'90.79 (18)C6—C8—C11—C120.6 (5)
O4'—C1'—C2'—C3'19.90 (18)C5'—O5'—C21—O6'2.1 (4)
O4'—C4'—C5'—O5'60.7 (2)C5'—O5'—C21—C22178.4 (2)
O5'—C21—C22—C238.7 (3)C8—C11—C12—C130.5 (6)
O5'—C21—C22—C27172.1 (2)C7—N6—C5—N11177.5 (2)
O6'—C21—C22—C23170.8 (3)C7—N6—C5—C102.3 (3)
O6'—C21—C22—C278.5 (5)C7—N8—C1'—O4'34.4 (3)
O7'—C14—C15—C1613.4 (4)C7—N8—C1'—C2'85.5 (2)
O7'—C14—C15—C20165.6 (3)C7—N8—C9—N1179.30 (18)
O12—C4—C10—C9177.1 (2)C7—N8—C9—C101.5 (3)
O12—C4—C10—C55.2 (3)C11—C12—C13—C31.7 (5)
N1—C9—C10—C40.4 (3)C9—N1—C2—O13177.1 (2)
N1—C9—C10—C5178.17 (19)C9—N1—C2—N32.5 (3)
N3—C4—C10—C91.5 (3)C9—N8—C1'—O4'141.28 (17)
N3—C4—C10—C5176.13 (18)C9—N8—C1'—C2'98.8 (2)
N8—C1'—C2'—O2'148.86 (16)C9—N8—C7—N62.3 (3)
N8—C1'—C2'—C3'100.45 (19)C9—C10—C5—N62.9 (3)
N8—C9—C10—C4178.65 (16)C9—C10—C5—N11176.94 (19)
N8—C9—C10—C50.9 (3)C13—C3—C6—C80.8 (4)
C1—O2'—C2'—C1'114.5 (2)C14—O3'—C3'—C2'73.8 (2)
C1—O2'—C2'—C3'137.44 (19)C14—O3'—C3'—C4'173.63 (17)
C1—C3—C6—C8178.7 (3)C14—C15—C16—C17179.2 (2)
C1—C3—C13—C12177.7 (3)C14—C15—C20—C19178.1 (2)
C1'—O4'—C4'—C3'26.60 (19)C15—C16—C17—C181.3 (5)
C1'—O4'—C4'—C5'154.05 (16)C16—C15—C20—C190.9 (4)
C1'—N8—C7—N6173.4 (2)C16—C17—C18—C191.3 (5)
C1'—N8—C9—N14.9 (3)C17—C18—C19—C200.2 (5)
C1'—N8—C9—C10174.23 (18)C18—C19—C20—C150.9 (5)
C1'—C2'—C3'—O3'150.34 (16)C20—C15—C16—C170.2 (4)
C1'—C2'—C3'—C4'34.87 (17)C21—O5'—C5'—C4'120.2 (2)
C2—N1—C9—N8176.56 (17)C21—C22—C23—C24178.6 (2)
C2—N1—C9—C102.5 (3)C21—C22—C27—C26178.5 (3)
C2—N3—C4—O12177.2 (2)C22—C23—C24—C250.2 (4)
C2—N3—C4—C101.5 (3)C23—C22—C27—C260.7 (4)
C2'—O2'—C1—O1'1.9 (3)C23—C24—C25—C260.1 (4)
C2'—O2'—C1—C3178.89 (17)C24—C25—C26—C270.0 (5)
C2'—C3'—C4'—O4'38.13 (17)C25—C26—C27—C220.4 (5)
C2'—C3'—C4'—C5'158.73 (17)C27—C22—C23—C240.6 (4)
C3—C6—C8—C110.4 (4)C5—N6—C7—N80.3 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O10—H10···O13i0.821.862.661 (3)166
N3—H3···N6ii0.862.403.113 (2)141
N11—H11B···O10iii0.87 (1)1.96 (1)2.835 (3)176 (2)
N11—H11A···O7ii0.86 (1)2.29 (2)2.860 (2)124 (2)
N11—H11A···O120.86 (1)2.12 (2)2.751 (2)130 (2)
Symmetry codes: (i) x+1, y+1, z; (ii) x, y1/2, z+3/2; (iii) x+1, y1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC32H25N5O9·CH4O
Mr655.61
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)8.2526 (3), 11.9486 (4), 32.1865 (10)
V3)3173.82 (18)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.42 × 0.36 × 0.20
Data collection
DiffractometerXcalibur, Eos
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2010) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
Tmin, Tmax0.443, 1.0
No. of measured, independent and
observed [I > 2σ(I)] reflections
9151, 6101, 4128
Rint0.019
(sin θ/λ)max1)0.625
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.093, 0.91
No. of reflections6101
No. of parameters441
No. of restraints4
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.20, 0.17
Absolute structureFlack (1983)
Absolute structure parameter0.3 (9)

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Selected torsion angles (º) top
O4'—C1'—C2'—C3'19.90 (18)C4—N3—C2—O13179.1 (2)
O4'—C4'—C5'—O5'60.7 (2)C4—C10—C5—N6179.49 (17)
O12—C4—C10—C9177.1 (2)C7—N6—C5—N11177.5 (2)
N1—C9—C10—C5178.17 (19)C7—N8—C1'—O4'34.4 (3)
N8—C9—C10—C4178.65 (16)C9—N1—C2—O13177.1 (2)
C2—N3—C4—O12177.2 (2)C9—N8—C1'—O4'141.28 (17)
C3'—C4'—C5'—O5'57.3 (3)C9—C10—C5—N11176.94 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O10—H10···O13i0.821.862.661 (3)165.5
N3—H3···N6ii0.862.403.113 (2)140.6
N11—H11B···O10iii0.874 (13)1.963 (13)2.835 (3)176.0 (17)
N11—H11A···O7'ii0.857 (13)2.288 (17)2.860 (2)124.3 (16)
N11—H11A···O120.857 (13)2.121 (18)2.751 (2)130.0 (16)
Symmetry codes: (i) x+1, y+1, z; (ii) x, y1/2, z+3/2; (iii) x+1, y1/2, z+3/2.
 

Acknowledgements

This work was supported by the National Natural Science Foundation of China (grant No. 20772087). The authors are grateful to the Analytical and Testing Center of Sichuan University for support of the X-ray laboratory and Mr Zhi-Hua Mao for kindly helping with the X-ray data analysis.

References

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