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CHEMISTRY
ISSN: 2053-2296

1,N6-Etheno-2′-de­­oxy­tubercidin hemihydrate

aLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany, and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany, bLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany, and cAnorganische Chemie II, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
*Correspondence e-mail: frank.seela@uni-osnabrueck.de

(Received 21 January 2011; accepted 10 February 2011; online 16 February 2011)

The title compound [systematic name: 7-(2-de­oxy-β-D-erythro-pentofuranos­yl)-7H-imidazo[1,2-c]pyrrolo­[2,3-d]py­rimi­dine hemihydrate], 2C13H14N4O3·H2O or (I)·0.5H2O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water mol­ecule by hydrogen bonds. The N-glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I-1) and −107.0 (2)° for conformer (I-2). The sugar moiety adopts an unusual N-type (C3′-endo) sugar pucker for 2′-de­oxy­ribonucleosides, with P = 36.8 (2)° and τm = 40.6 (1)° for conformer (I-1), and P = 34.5 (2)° and τm = 41.4 (1)° for conformer (I-2). Both conformers and the solvent mol­ecule participate in the formation of a three-dimensional pattern with a `chain'-like arrangement of the conformers. The structure is stabilized by inter­molecular O—H⋯O and O—H⋯N hydrogen bonds, together with weak C—H⋯O contacts.

Comment

Etheno adducts have proved to be biomarkers for DNA damage arising from reactions of endogenous lipid peroxidation, chloro­ethyl­ene oxide or chloro­acetaldehyde (Bolt, 1994[Bolt, H. M. (1994). DNA Adducts: Identification and Biological Significance, Vol. 125, edited by K. Hemminki, A. Dipple, D. E. G. Shuker, F. F. Kadlubar, D. Segerback & H. Bartsch, pp. 141-150. Lyon: IARC.]). They are also thought to initiate vinyl-chloride- and urethane-induced tumours because of their miscoding capability, leading to point mutations (Arab et al., 2009[Arab, K., Pedersen, M., Nair, J., Meerang, M., Knudsen, L. E. & Bartsch, H. (2009). Carcinogenesis, 30, 282-285.]; Pandya & Moriya, 1996[Pandya, G. A. & Moriya, M. (1996). Biochemistry, 35, 11487-11492.]). 1,N6-Etheno-2′-de­oxy­tubercidin, (I)[link], and the corresponding congener 1,N6-ethenoadenosine, (III), can be considered as 7-deaza­purine or purine pyrrole ring annelation products with a [1,2-c]-ring connectivity (purine numbering is used throughout this discussion). By enlarging the aromatic system, these tricyclic nucleosides show strong fluorescence with quantum yields higher than 0.5 (Seela et al., 2007[Seela, F., Schweinberger, E., Xu, K., Sirivolu, V. R., Rosemeyer, H. & Becker, E.-M. (2007). Tetrahedron, 63, 3471-3482.]). Their propensity to fluorescence makes these compounds valuable for probing the biochemical and biophysical properties of nucleosides, nucleotides and nucleic acids (Bielecki et al., 2000[Bielecki, L., Skalski, B., Zagorowska, I., Verrall, R. E. & Adamiak, R. W. (2000). Nucleosides Nucleotides Nucleic Acids, 19, 1735-1750.]; Inoue et al., 1981[Inoue, Y., Kuramochi, T. & Imakubo, K. (1981). Chem. Lett. 10, 1161-1164.]; Paulsen & Winter­meyer, 1984[Paulsen, H. & Wintermeyer, W. (1984). Eur. J. Biochem. 138, 125-130.]; Secrist et al., 1972[Secrist, J. A., Barrio, J. R., Leonard, N. J. & Weber, G. (1972). Biochemistry, 11, 3499-3506.]; Seela et al., 2007[Seela, F., Schweinberger, E., Xu, K., Sirivolu, V. R., Rosemeyer, H. & Becker, E.-M. (2007). Tetrahedron, 63, 3471-3482.]). The 7-deaza­purine nucleoside, (I)[link], shows extraordinary stability in acidic and in alkaline media compared to its `purine' counterpart, (III) (Seela et al., 2007[Seela, F., Schweinberger, E., Xu, K., Sirivolu, V. R., Rosemeyer, H. & Becker, E.-M. (2007). Tetrahedron, 63, 3471-3482.]). The synthesis of the title compound, (I)[link], which was prepared from 2′-de­oxy­tubercidin with chloro­acetaldehyde, was reported previously (Seela et al., 2007[Seela, F., Schweinberger, E., Xu, K., Sirivolu, V. R., Rosemeyer, H. & Becker, E.-M. (2007). Tetrahedron, 63, 3471-3482.]). The single-crystal structure of (I)[link] is studied herein and is compared to the closely related crystal structures of 2′-de­oxy­tubercidin [(IIa) and (IIb); Zabel et al., 1987[Zabel, V., Saenger, W. & Seela, F. (1987). Acta Cryst. C43, 131-134.]], 1,N6-ethenoadenosine [(III); Jaskólski, 1982[Jaskólski, M. (1982). Acta Cryst. B38, 3171-3174.]] and 7-deaza-2,8-diaza-1,N6-ethenoadenosine [(IV); Lin et al., 2004[Lin, W., Seela, F., Eickmeier, H. & Reuter, H. (2004). Acta Cryst. C60, o566-o568.]].

[Scheme 1]

In the asymmetric unit of (I)·0.5H2O, two conformers with a slightly different sugar puckering exist which are connected through a water mol­ecule by hydrogen bonds. They are defined as types 1 and 2, and denoted (I-1) and (I-2), respectively. The three-dimensional structures of the mol­ecules of (I-1) and (I-2) are shown in Figs. 1[link] and 2[link], and selected geometric parameters are summarized in Table 1[link].

Conformers (I-1) and (I-2) exhibit almost identical torsion angles χ (O4′—C1′—N9—C4) of −107.7 (2) and −107.0 (2)°, respectively, which indicate conformations situated between anti and high-anti (IUPAC-IUB Joint Commission on Biochemical Nomenclature, 1983[IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9-15.]). These values are close to that of the water-free crystal of (IIa) [χ = −104.4 (2)°], whereas the torsion angle of dihydrate (IIb) [χ = −115.5 (3)°] falls into the anti range (Zabel et al., 1987[Zabel, V., Saenger, W. & Seela, F. (1987). Acta Cryst. C43, 131-134.]). The length of the glycosylic N9—C1′ bond is 1.451 (2) Å for (I-1) and 1.449 (2) Å for (I-2), which is almost identical to the bond length observed for 2′-de­oxy­tubercidin [1.449 (2) Å in (IIa) and 1.446 (4) Å in (IIb); Zabel et al., 1987[Zabel, V., Saenger, W. & Seela, F. (1987). Acta Cryst. C43, 131-134.]]. The parent ribonucleoside, (III), adopts a slightly longer glycosylic bond [1.455 (4) Å; Jaskólski, 1982[Jaskólski, M. (1982). Acta Cryst. B38, 3171-3174.]].

The heterocyclic base moiety of 1,N6-ethenoadenosine, (III), forms a `U'-shaped structure when looking from the edge side, with a maximum deviation of 0.064 (4) Å out of the plane (Jaskólski, 1982[Jaskólski, M. (1982). Acta Cryst. B38, 3171-3174.]). In contrast, the 7-deaza­purine moieties of (I-1) and (I-2) are nearly planar. The r.m.s. deviations of the ring atoms from their calculated least-squares planes are 0.0121 Å for (I-1) and 0.0206 Å for (I-2). Maximum deviations of 0.0185 (2) and 0.0365 (2) Å were found for atom C112 of (I-1) and atom N29 of (I-2), respectively.

For both conformers, the torsion angle about the exocyclic C4′—C5′ bond, which is defined as γ (O5′—C5′—C4′—C3′), adopts an anti­periplanar (gauche, trans) conformation with γ = −168.7 (2)° for (I-1) and γ = −167.1 (2)° for (I-2). In the crystal structures of (IIa) and (IIb), the torsion angles γ are also within the anti­periplanar range [−179.6 (2) and −173.6 (3)°; trans] (Zabel et al., 1987[Zabel, V., Saenger, W. & Seela, F. (1987). Acta Cryst. C43, 131-134.]).

Usually, the sugar conformation of ribonucleosides adopts the N-type pucker, whereas 2′-de­oxy­ribonucleosides prefer the S conformation. In solution, the predominant conformation of compound (I)[link] shows the S-type conformation (75% S). The sugar conformation of compound (I)[link] was determined from the vicinal 3J(H,H) coupling constants of the 1H NMR spectra measured in D2O, applying the program PSEUROT6.3 (Van Wijk et al., 1999[Van Wijk, L., Haasnoot, C. A. G., de Leeuw, F. A. A. M., Huckriede, B. D., Westra Hoekzema, A. J. A. & Altona, C. (1999). PSEUROT6.3. Leiden Institute of Chemistry, Leiden University, The Netherlands.]). It has to be noted that both conformers exhibit sugar moieties with the N conformation in the crystalline state. For conformer (I-1), the sugar pucker is 4T3 (C4′-exo–C3′-endo) (Altona & Sundaralingam, 1972[Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212.]), with a phase angle of pseudorotation of P = 36.8 (2)° and a maximum amplitude of puckering of τm = 40.6 (1)°. In conformer (I-2), the sugar moiety adopts a slightly different N-type sugar pucker (3T4; C3′-endo–C4′-exo), with P = 34.5 (2)° and τm = 41.4 (1)°. In contrast, the parent 2′-de­oxy­tubercidins, (IIa) and (IIb), adopt S conformations with P = 186.6 (2) (3T2; C3′-exo–C2′-endo) and 215.1 (3)° (3T4; C3′-exo–C4′-endo), respectively. A similar influence on the sugar conformation was also found for the ribonucleoside 1,N6-etheno derivatives, (III) and (IV), which adopt the S conformation (C2′-endo) instead of the usual N-type conformation of ribonucleosides. The ribose ring of nucleoside (III) is characterized by P = 163.5° (2T3; C2′-endo–C3′-exo) and τm = 44.3° (Jaskólski, 1982[Jaskólski, M. (1982). Acta Cryst. B38, 3171-3174.]), while P = 183.4° (3T2; C3′-exo–C2′-endo) and τm = 42.4° for compound (IV) (Lin et al., 2004[Lin, W., Seela, F., Eickmeier, H. & Reuter, H. (2004). Acta Cryst. C60, o566-o568.]).

The title compound forms a three-dimensional network, which is generated by numerous hydrogen bonds involving conformers (I-1) and (I-2) and the water mol­ecule (Fig. 3[link] and Table 2[link]). Within the ac plane, (I-1) and (I-2) are located in a `chain'-like arrangement. Each chain is composed of mol­ecules of identical conformation, either (I-1) or (I-2), and the chains are ordered in an alternating fashion. Furthermore, within the chains, the individual mol­ecules are arranged in a head-to-tail fashion. The different chains are connected to each other via hydrogen bonding between the two conformers. The individual chains are also stabilized by hydrogen bonds, while the water molecule participates in both intra- and interchain hydrogen bonds. Conformers (I-1) and (I-2) show a different hydrogen-bonding pattern. Hydrogen bonds are formed to neighbouring mol­ecules of identical conformation (O13′—H13′⋯O15′i, O15′—H15′⋯N112ii, O23′—H23′⋯O25′iii and O25′—H25′⋯N212iv; for symmetry codes and geometry see Table 2[link]), while those to the water mol­ecule (O100) employ different atoms as acceptors. For (I-1), atom O15′ functions as acceptor (O100—H102⋯O15′i), whereas atom O23′ is the acceptor for (I-2) (O100—H101⋯O23′). Additional weak contacts (Steiner, 2002[Steiner, T. (2002). Angew. Chem. Int. Ed. 41, 48-76.]) were observed for both conformers, including that of conformer (I-2) to atom O100 of the water mol­ecule (C210—H210⋯O100vi, C12—H12⋯O13′v and C22—H22⋯O23′vi).

[Figure 1]
Figure 1
Perspective views of (a) conformer (I-1) and (b) conformer (I-2), showing the atom-numbering schemes. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary size.
[Figure 2]
Figure 2
Overlay of mol­ecules (I-1) and (I-2).
[Figure 3]
Figure 3
The crystal packing showing the inter­molecular hydrogen-bonding network (parallel to the ac plane).

Experimental

Compound (I)[link] was synthesized as reported previously (Seela et al., 2007[Seela, F., Schweinberger, E., Xu, K., Sirivolu, V. R., Rosemeyer, H. & Becker, E.-M. (2007). Tetrahedron, 63, 3471-3482.]). Slow crystallization from aqueous methanol afforded (I)·0.5H2O as colourless crystals (m.p. 442 K). For the diffraction experiment, a single crystal was mounted on a MiTeGen MicroMountsfibre in a thin smear of oil.

Crystal data
  • 2C13H14N4O3·H2O

  • Mr = 566.58

  • Monoclinic, C 2

  • a = 19.6476 (12) Å

  • b = 5.2979 (3) Å

  • c = 26.3354 (16) Å

  • β = 106.865 (3)°

  • V = 2623.4 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 130 K

  • 0.30 × 0.20 × 0.10 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2 (Version 2008/5), SADABS (Version 2008/1) and SAINT (Version 7.56a). Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.969, Tmax = 0.989

  • 46138 measured reflections

  • 4214 independent reflections

  • 3987 reflections with I > 2σ(I)

  • Rint = 0.033

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.106

  • S = 1.12

  • 4214 reflections

  • 374 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.33 e Å−3

  • Absolute structure: established by known chemical absolute configuration

Table 1
Selected geometric parameters (Å, °)

N11—C16 1.396 (3)
C16—N112 1.322 (2)
N19—C11′ 1.451 (2)
N21—C26 1.394 (3)
C26—N212 1.325 (2)
N29—C21′ 1.449 (2)
O13′—C13′—C14′ 112.06 (17)
O15′—C15′—C14′ 111.68 (18)
O23′—C23′—C24′ 111.71 (16)
O25′—C25′—C24′ 110.91 (17)
C12—N11—C16—N112 178.6 (2)
C14—C15—C16—N112 −179.5 (2)
C14—N19—C11′—O14′ −107.7 (2)
C13′—C14′—C15′—O15′ −168.66 (16)
C22—N21—C26—N212 176.1 (2)
C24—C25—C26—N212 −177.3 (2)
C24—N29—C21′—O24′ −107.0 (2)
C23′—C24′—C25′—O25′ −167.05 (16)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O13′—H13′⋯O15′i 0.84 2.01 2.800 (2) 156
O15′—H15′⋯N112ii 0.84 1.87 2.705 (2) 175
O23′—H23′⋯O25′iii 0.84 1.84 2.665 (2) 165
O25′—H25′⋯N212iv 0.84 1.84 2.675 (2) 174
O100—H101⋯O23′ 0.96 1.91 2.823 (3) 157
O100—H102⋯O15′i 0.96 1.92 2.868 (2) 169
C12—H12⋯O13′v 0.95 2.37 3.241 (3) 153
C22—H22⋯O23′vi 0.95 2.47 3.295 (3) 145
C210—H210⋯O100vi 0.95 2.47 3.230 (4) 138
Symmetry codes: (i) x, y+1, z; (ii) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z]; (iii) x, y-1, z; (iv) [-x+{\script{1\over 2}}], [y+{\script{1\over 2}}, -z+1]; (v) -x+1, y-1, -z; (vi) -x+1, y+1, -z+1.

In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Refinement of the Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]) parameter led to inconclusive values for this parameter [0.2 (7)]. Therefore, Friedel equivalents (2881) were merged before the final refinement. The known configuration of the parent mol­ecule was used to define the enanti­omer employed in the refined model.

All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms were placed in geometrically idealized positions (C—H = 0.95–1.00 Å) and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C). The OH groups were refined as rigid groups, allowed to rotate but not tip (AFIX 147 instruction in the XL routine of SHELXTL; Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), with O—H = 0.84 Å and Uiso(H) = 1.5Ueq(O). The water H atoms were located from difference maps, and the parameters of the water H atoms were first refined freely. Owing to the low reflection/refined parameter ratio, the O—H distances were constrained [AFIX 3 (m = 0)] to 0.96 Å and with Uiso(H) = 1.5Ueq(O) in the final cycles of refinement.

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2 (Version 2008/5), SADABS (Version 2008/1) and SAINT (Version 7.56a). Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). APEX2 (Version 2008/5), SADABS (Version 2008/1) and SAINT (Version 7.56a). Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: DIAMOND (Brandenburg, 1999[Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Etheno adducts have proved to be biomarkers for DNA damage arising from reactions of endogenous lipid peroxidation, chloroethylene oxide or chloroacetaldehyde (Bolt, 1994). They are also thought to initiate vinyl-chloride- and urethane-induced tumours because of their miscoding capability, leading to point mutations (Arab et al., 2009; Pandya & Moriya, 1996). 1,N6-Etheno-2'-deoxytubercidin, (I), and the corresponding congener 1,N6-ethenoadenosine, (III), can be considered as 7-deazapurine or purine pyrrole ring annelation products with a [1,2-c]-ring connectivity (purine numbering is used throughout this discussion). By enlarging the aromatic system, these tricyclic nucleosides show strong fluorescence with quantum yields higher than 0.5 (Seela et al., 2007). Their propensity to fluorescence makes these compounds valuable for probing the biochemical and biophysical properties of nucleosides, nucleotides and nucleic acids (Bielecki et al., 2000; Inoue et al., 1981; Paulsen & Wintermeyer, 1984; Secrist et al., 1972; Seela et al., 2007). The 7-deazapurine nucleoside, (I), shows extraordinary stability in acidic and in alkaline media compared to its `purine' counterpart, (III) (Seela et al., 2007). The synthesis of the title compound, (I), which was prepared from 2'-deoxytubercidin with chloroacetaldehyde, was reported earlier (Seela et al., 2007). The single-crystal structure of (I) is studied herein and is compared to the closely related crystal structures of 2'-deoxytubercidin, [(IIa) and (IIb)] (Zabel et al., 1987), 1,N6-ethenoadenosine, (III) (Jaskólski, 1982), and 7-deaza-2,8-diaza-1,N6-ethenoadenosine, (IV) (Lin et al., 2004).

In the asymmetric unit of (I)2.H2O, two conformational states with a slightly different sugar puckering exist which are connected through water molecules by hydrogen bonds. They are defined as types 1 and 2, and denoted (I-1) and (I-2), respectively. The three-dimensional structures of the molecules of (I-1) and (I-2) are shown in Figs. 1 and 2, [respectively?], and selected geometric parameters are summarized in Table 1.

Conformers (I-1) and (I-2) exhibit almost identical torsion angles χ (O4'—C1'—N9—C4) of -107.7 (2) and -107.0 (2)°, respectively; referring to conformations situated between anti and high-anti (IUPAC-IUB Joint Commission on Biochemical Nomenclature, 1983). These values are close to that of the water-free crystal of (IIa) [χ = -104 (2)°], whereas the torsion angle of dihydrate, (IIb) [χ = -115.5 (3)°], falls into the anti range (Zabel et al., 1987). The length of the glycosylic bond N9—C1' is 1.451 (2) Å for (I-1) and 1.449 (2) Å for (I-2), which is almost identical to the bond length observed for 2'-deoxytubercidin [(IIa): 1.449 (2) Å; (IIb): 1.446 (4) Å; Zabel et al., 1987]. The parent ribonucleoside, (III), adopts a slightly longer glycosylic bond [1.455 (4) Å] (Jaskólski, 1982).

The heterocyclic base moiety of 1,N6-ethenoadenosine, (III), forms a `U'-shaped structure when looking from the edge side with a maximum deviation of 0.064 (4) Å out of the plane (Jaskólski, 1982). In contrast, the 7-deazapurine moieties of (I-1) and (I-2) are nearly planar. The r.m.s. deviations of the ring atoms from their calculated least-squares planes are 0.0121 Å for (I-1) and 0.0206 Å for (I-2). Maximum deviations were found for atom C112 of (I-1) with -0.0185 (2) Å and for atom N29 (I-2) with -0.0365 (2) Å.

For both conformers, the torsion angle about the exocyclic C4'—C5' bond, which is defined as γ (O5'—C5'—C4'—C3'), adopts an -antiperiplanar (gauche, trans) conformation with γ = -168.7 (2)° for (I-1) and γ = -167.1 (2)° for (I-2). In the crystal structures of (IIa) and (IIb), the torsion angles γ are also within the antiperiplanar range [-179.6 (2)°, -173.6 (3)°; trans] (Zabel et al., 1987).

Usually, the sugar conformation of ribonucleosides adopts the N-type pucker whereas 2'-deoxyribonucleosides prefer the S conformation. In solution, the predominant conformation of compound (I) shows the S-type conformation (75% S). The sugar conformation of compound (I) was determined from the vicinal 3J(H,H) coupling constants of the 1H NMR spectra measured in D2O, applying the program PSEUROT6.3 (Van Wijk et al., 1999). It has to be noted that both conformers exhibit sugar moieties with the N conformation in the crystalline state. For conformer (I-1), the sugar pucker is 3T4 (C3'-endo-C4'-exo) (Altona & Sundaralingam, 1972) with a phase angle of pseudorotation of P = 36.8° and a maximum amplitude of puckering of τm = 40.6°. In conformer (I-2), the sugar moiety adopts a slightly different N-type sugar pucker with P = 34.5° and τm = 41.4°. In contrast, the parent 2'-deoxytubercidins, (IIa) and (IIb), adopt S conformations with P = 186.6° and 215.1°, respectively (C2'-endo-C1'-exo, 2T1). A similar influence on the sugar conformation was also found for the ribonucleoside 1,N6-etheno derivatives, (III) and (IV), which adopt the S conformation (C2'-endo-C3'-exo; 3T2) instead of the usual N-type conformation of ribonucleosides. The ribose ring of nucleoside (III) is characterized by P = 163.5° with τm = 44.3° (Jaskólski, 1982), and P = 183.4° with τm = 42.4° for compound (IV) (Lin et al., 2004).

The title compound forms a three-dimensional network, which is generated by numerous hydrogen bonds involving the two conformers (I-1) and (I-2) and the water molecule (Fig. 3 and Table 2). Within the ac plane, the conformers (I-1) and (I-2) are located in a `chain'- like arrangement. Each chain is composed of molecules of identical conformation, either (I-1) or (I-2), and the chains are ordered in an alternating fashion. Furthermore, within the chains, the individual molecules are arranged in a head-to-tail fashion. The different chains are connected to each other via hydrogen bonding of the two conformers. The individual chains are also stabilized by hydrogen bonds. In both cases, the water molecule participates in hydrogen bonding. Conformers (I-1) and (I-2) show a different hydrogen-bonding pattern. Hydrogen bonds are formed to neighbouring molecules of identical conformation (O13'—H13'···O15'i, O15'—H15'···N112ii, O23'—H23'···O25'iii, O25'—H25'···N212iv; for symmetry codes and geometry see Table 2), while those to the water molecule employ different atoms as acceptors. For (I-1), atom O15' functions as acceptor (O100—H102···O15'i), whereas atom O23' is the acceptor for (I-2) (O100—H101···O23'). Additional weak contacts (Steiner, 2002) were observed for both conformers, including that of conformer (I-2) to oxygen O100 of the water molecule (C210—H210···O100vi, C12—H12···O13'v, C22—H22···O23'vi).

Related literature top

For related literature, see: Altona & Sundaralingam (1972); Arab et al. (2009); Bielecki et al. (2000); Bolt (1994); IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983); Inoue et al. (1981); Jaskólski (1982); Lin et al. (2004); Pandya & Moriya (1996); Paulsen & Wintermeyer (1984); Secrist et al. (1972); Seela et al. (2007); Steiner (2002); Van Wijk, Haasnoot, de Leeuw, Huckriede, Westra Hoekzema & Altona (1999); Zabel et al. (1987).

Experimental top

Compound (I) was synthesized as reported previously (Seela et al., 2007). Slow crystallization from aqueous methanol afforded (I).H2O as colourless crystals (m.p. 442 K). For the diffraction experiment, a single crystal was mounted on a MiTeGen MicroMountsfibre in a thin smear of oil.

Refinement top

In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Refinement of the Flack parameter led to inconclusive values for this parameter [0.2 (7)]. Therefore, Friedel equivalents (2881) were merged before the final refinement. The known configuration of the parent molecule was used to define the enantiomer employed in the refined model.

All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms were placed in geometrically idealized positions (C—H = 0.95–1.00 Å) and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C). The OH groups were refined as rigid groups, allowed to rotate but not tip (AFIX 147) with O—H = 0.84 Å and U(H) = 1.5Ueq(O). The water H atoms were located from difference maps, and the parameters of the water H atoms were first refined freely. Owing to the low reflection/refined parameter ratio, the O—H distances were constrained [AFIX 3 (m = 0)] to 0.96 Å and Uiso(H) = 1.5Ueq(O) in the final cycles of refinement.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Perspective views of (a) molecule (I-1) and (b) molecule (I-2), showing the atom-numbering schemes. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary size
[Figure 2] Fig. 2. Overlay of molecules (I-1) and (I-2).
[Figure 3] Fig. 3. The crystal packing showing the intermolecular hydrogen-bonding network (parallel to ac plane).
7-(2-deoxy-β-D-erythro-pentofuranosyl)-7H-imidazo[1,2-c]pyrrolo[2,3-d]pyrimidine hemihydrate (1,N6-etheno-2'-deoxytubercidin hemihydrate top
Crystal data top
2C13H14N4O3·H2OF(000) = 1192
Mr = 566.58Dx = 1.434 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2yCell parameters from 9960 reflections
a = 19.6476 (12) Åθ = 3.1–30.2°
b = 5.2979 (3) ŵ = 0.11 mm1
c = 26.3354 (16) ÅT = 130 K
β = 106.865 (3)°Block, colourless
V = 2623.4 (3) Å30.30 × 0.20 × 0.10 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
4214 independent reflections
Radiation source: fine-focus sealed tube3987 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
ϕ and ω scansθmax = 30.0°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 2727
Tmin = 0.969, Tmax = 0.989k = 67
46138 measured reflectionsl = 3737
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)] = 0.039H-atom parameters constrained
wR(F2) = 0.106 w = 1/[σ2(Fo2) + (0.0528P)2 + 2.1726P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max < 0.001
4214 reflectionsΔρmax = 0.33 e Å3
374 parametersΔρmin = 0.33 e Å3
1 restraintAbsolute structure: established by known chemical absolute configuration
Primary atom site location: structure-invariant direct methods
Crystal data top
2C13H14N4O3·H2OV = 2623.4 (3) Å3
Mr = 566.58Z = 4
Monoclinic, C2Mo Kα radiation
a = 19.6476 (12) ŵ = 0.11 mm1
b = 5.2979 (3) ÅT = 130 K
c = 26.3354 (16) Å0.30 × 0.20 × 0.10 mm
β = 106.865 (3)°
Data collection top
Bruker APEXII CCD
diffractometer
4214 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
3987 reflections with I > 2σ(I)
Tmin = 0.969, Tmax = 0.989Rint = 0.033
46138 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0391 restraint
wR(F2) = 0.106H-atom parameters constrained
S = 1.12Δρmax = 0.33 e Å3
4214 reflectionsΔρmin = 0.33 e Å3
374 parametersAbsolute structure: established by known chemical absolute configuration
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
N110.30649 (9)0.2198 (4)0.14311 (6)0.0187 (3)
C120.37027 (11)0.2977 (5)0.10879 (8)0.0211 (4)
H120.39690.42360.12030.025*
N130.39545 (9)0.2056 (4)0.06125 (7)0.0199 (3)
C140.35434 (10)0.0236 (4)0.04813 (7)0.0164 (4)
C150.28979 (10)0.0733 (4)0.07974 (8)0.0170 (4)
C160.26376 (10)0.0329 (4)0.13084 (8)0.0174 (4)
C170.26837 (11)0.2648 (4)0.04969 (8)0.0204 (4)
H170.22660.36500.06070.024*
C180.31983 (11)0.2761 (5)0.00191 (8)0.0212 (4)
H180.31940.38780.02620.025*
N190.37253 (9)0.1013 (4)0.00059 (7)0.0176 (3)
C1100.27289 (11)0.2997 (5)0.19499 (8)0.0224 (4)
H1100.28860.42570.21470.027*
C1110.21312 (11)0.1577 (5)0.21093 (8)0.0224 (4)
H1110.17950.16920.24510.027*
N1120.20674 (9)0.0069 (4)0.17148 (7)0.0209 (4)
C11'0.43588 (10)0.0517 (4)0.04298 (7)0.0163 (4)
H11C0.46840.06120.03040.020*
C12'0.47629 (11)0.2920 (5)0.06714 (8)0.0204 (4)
H12B0.52800.27320.07230.024*
H12C0.45870.44060.04430.024*
O13'0.51496 (8)0.4410 (3)0.15925 (6)0.0222 (3)
H13'0.49700.53620.17740.033*
C13'0.46005 (10)0.3168 (4)0.12039 (8)0.0176 (4)
H13C0.41380.40640.11550.021*
C14'0.45317 (10)0.0405 (4)0.13421 (7)0.0166 (4)
H14A0.50160.03680.14720.020*
O14'0.41504 (8)0.0729 (3)0.08456 (5)0.0197 (3)
C15'0.41325 (11)0.0018 (4)0.17449 (8)0.0197 (4)
H15B0.43170.11480.20480.024*
H15C0.36230.03690.15810.024*
O15'0.42026 (8)0.2549 (3)0.19342 (6)0.0209 (3)
H15'0.38020.32520.18460.031*
N210.41692 (9)1.0061 (4)0.64906 (6)0.0190 (3)
C220.45326 (11)1.0822 (5)0.61436 (8)0.0227 (4)
H220.48771.21230.62510.027*
N230.44254 (9)0.9838 (4)0.56751 (7)0.0217 (4)
C240.39205 (10)0.7990 (4)0.55514 (7)0.0171 (4)
C250.35263 (10)0.7033 (4)0.58726 (8)0.0167 (4)
C260.36720 (10)0.8110 (4)0.63846 (8)0.0178 (4)
C270.30727 (11)0.5113 (5)0.55762 (8)0.0206 (4)
H270.27400.41260.56890.025*
C280.32117 (10)0.4973 (5)0.50961 (8)0.0208 (4)
H280.29860.38510.48160.025*
N290.37295 (9)0.6710 (4)0.50806 (7)0.0181 (3)
C2100.42418 (11)1.0875 (5)0.70082 (8)0.0235 (4)
H2100.45401.21860.71970.028*
C2110.37954 (11)0.9389 (5)0.71828 (8)0.0241 (4)
H2110.37350.95070.75270.029*
N2120.34363 (9)0.7673 (4)0.67997 (7)0.0211 (4)
C21'0.40203 (10)0.7148 (4)0.46418 (7)0.0169 (4)
H21B0.44500.82510.47640.020*
C22'0.42207 (10)0.4712 (4)0.44016 (8)0.0193 (4)
H22B0.46900.48760.43360.023*
H22C0.42310.32480.46370.023*
O23'0.38386 (8)0.3114 (3)0.34860 (6)0.0193 (3)
H23'0.35140.21160.33280.029*
C23'0.36256 (10)0.4444 (4)0.38811 (7)0.0163 (4)
H23C0.32010.36160.39460.020*
C24'0.34657 (10)0.7205 (4)0.37314 (8)0.0152 (3)
H24A0.38500.79080.35930.018*
O24'0.34914 (7)0.8411 (3)0.42234 (5)0.0182 (3)
C25'0.27543 (10)0.7644 (4)0.33290 (8)0.0173 (4)
H25B0.26880.64140.30360.021*
H25C0.23710.73750.34980.021*
O25'0.27071 (7)1.0146 (3)0.31212 (6)0.0190 (3)
H25'0.23321.08320.31460.029*
O1000.47493 (10)0.5675 (5)0.30043 (8)0.0422 (5)
H1010.43630.52040.31390.063*
H1020.45360.64410.26650.063*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N110.0186 (7)0.0210 (9)0.0177 (7)0.0020 (7)0.0071 (6)0.0021 (7)
C120.0192 (9)0.0215 (10)0.0227 (9)0.0044 (8)0.0065 (7)0.0026 (8)
N130.0179 (7)0.0214 (9)0.0211 (8)0.0043 (7)0.0067 (6)0.0015 (7)
C140.0165 (8)0.0176 (9)0.0163 (8)0.0003 (8)0.0067 (6)0.0006 (7)
C150.0168 (8)0.0165 (9)0.0192 (8)0.0008 (7)0.0077 (7)0.0008 (7)
C160.0174 (8)0.0167 (9)0.0197 (8)0.0029 (7)0.0080 (7)0.0012 (8)
C170.0213 (9)0.0201 (10)0.0211 (9)0.0051 (8)0.0084 (7)0.0000 (8)
C180.0229 (9)0.0207 (10)0.0219 (9)0.0042 (8)0.0097 (7)0.0018 (8)
N190.0179 (7)0.0192 (8)0.0165 (7)0.0024 (7)0.0060 (6)0.0009 (7)
C1100.0254 (9)0.0267 (11)0.0156 (8)0.0002 (9)0.0067 (7)0.0031 (8)
C1110.0225 (9)0.0286 (12)0.0168 (8)0.0000 (9)0.0067 (7)0.0002 (8)
N1120.0189 (7)0.0254 (9)0.0178 (7)0.0025 (7)0.0047 (6)0.0007 (7)
C11'0.0164 (8)0.0170 (9)0.0161 (8)0.0009 (7)0.0058 (6)0.0004 (7)
C12'0.0229 (9)0.0198 (10)0.0202 (9)0.0067 (8)0.0089 (7)0.0011 (8)
O13'0.0228 (7)0.0216 (8)0.0216 (7)0.0056 (6)0.0058 (5)0.0057 (6)
C13'0.0182 (8)0.0171 (9)0.0183 (8)0.0033 (7)0.0065 (7)0.0016 (8)
C14'0.0185 (8)0.0158 (9)0.0159 (8)0.0036 (7)0.0056 (7)0.0018 (7)
O14'0.0252 (7)0.0186 (7)0.0158 (6)0.0081 (6)0.0065 (5)0.0019 (6)
C15'0.0238 (9)0.0186 (10)0.0187 (8)0.0033 (8)0.0092 (7)0.0024 (8)
O15'0.0215 (7)0.0215 (8)0.0199 (7)0.0053 (6)0.0064 (5)0.0021 (6)
N210.0189 (7)0.0209 (9)0.0170 (7)0.0038 (7)0.0049 (6)0.0021 (7)
C220.0216 (9)0.0254 (11)0.0223 (9)0.0087 (9)0.0085 (7)0.0035 (9)
N230.0198 (7)0.0244 (10)0.0215 (8)0.0069 (8)0.0069 (6)0.0030 (8)
C240.0145 (7)0.0188 (9)0.0176 (8)0.0005 (8)0.0042 (6)0.0007 (8)
C250.0125 (7)0.0192 (9)0.0180 (8)0.0012 (7)0.0037 (6)0.0014 (8)
C260.0142 (7)0.0190 (9)0.0201 (8)0.0001 (7)0.0046 (7)0.0004 (8)
C270.0189 (8)0.0214 (10)0.0211 (9)0.0061 (8)0.0049 (7)0.0005 (8)
C280.0189 (8)0.0216 (10)0.0206 (9)0.0071 (8)0.0039 (7)0.0021 (8)
N290.0155 (7)0.0206 (8)0.0178 (7)0.0040 (7)0.0045 (6)0.0004 (7)
C2100.0233 (9)0.0291 (11)0.0175 (9)0.0048 (9)0.0052 (7)0.0058 (9)
C2110.0230 (9)0.0308 (12)0.0186 (9)0.0010 (9)0.0064 (7)0.0024 (9)
N2120.0196 (7)0.0257 (10)0.0189 (7)0.0027 (7)0.0070 (6)0.0004 (7)
C21'0.0147 (8)0.0199 (9)0.0155 (8)0.0011 (7)0.0036 (6)0.0006 (7)
C22'0.0183 (8)0.0188 (10)0.0192 (8)0.0042 (8)0.0030 (7)0.0006 (8)
O23'0.0223 (6)0.0169 (7)0.0211 (7)0.0019 (6)0.0098 (5)0.0021 (6)
C23'0.0178 (8)0.0149 (9)0.0167 (8)0.0018 (7)0.0058 (7)0.0005 (7)
C24'0.0166 (8)0.0137 (9)0.0158 (8)0.0015 (7)0.0052 (6)0.0009 (7)
O24'0.0203 (6)0.0176 (7)0.0150 (6)0.0040 (6)0.0024 (5)0.0010 (5)
C25'0.0174 (8)0.0162 (9)0.0176 (8)0.0015 (7)0.0042 (7)0.0000 (7)
O25'0.0185 (6)0.0192 (7)0.0197 (6)0.0044 (6)0.0060 (5)0.0034 (6)
O1000.0315 (9)0.0542 (14)0.0414 (10)0.0025 (10)0.0114 (8)0.0174 (10)
Geometric parameters (Å, º) top
N11—C121.379 (3)N21—C261.394 (3)
N11—C161.396 (3)N21—C2101.397 (3)
N11—C1101.399 (3)C22—N231.299 (3)
C12—N131.300 (3)C22—H220.9500
C12—H120.9500N23—C241.364 (3)
N13—C141.365 (3)C24—N291.367 (3)
C14—N191.369 (3)C24—C251.397 (3)
C14—C151.397 (3)C25—C261.415 (3)
C15—C161.410 (3)C25—C271.426 (3)
C15—C171.423 (3)C26—N2121.325 (2)
C16—N1121.322 (2)C27—C281.371 (3)
C17—C181.368 (3)C27—H270.9500
C17—H170.9500C28—N291.381 (3)
C18—N191.382 (3)C28—H280.9500
C18—H180.9500N29—C21'1.449 (2)
N19—C11'1.451 (2)C210—C2111.354 (3)
C110—C1111.355 (3)C210—H2100.9500
C110—H1100.9500C211—N2121.389 (3)
C111—N1121.390 (3)C211—H2110.9500
C111—H1110.9500C21'—O24'1.441 (2)
C11'—O14'1.436 (2)C21'—C22'1.538 (3)
C11'—C12'1.537 (3)C21'—H21B1.0000
C11'—H11C1.0000C22'—C23'1.529 (3)
C12'—C13'1.531 (3)C22'—H22B0.9900
C12'—H12B0.9900C22'—H22C0.9900
C12'—H12C0.9900O23'—C23'1.417 (2)
O13'—C13'1.416 (2)O23'—H23'0.8400
O13'—H13'0.8400C23'—C24'1.524 (3)
C13'—C14'1.524 (3)C23'—H23C1.0000
C13'—H13C1.0000C24'—O24'1.432 (2)
C14'—O14'1.437 (2)C24'—C25'1.507 (3)
C14'—C15'1.508 (3)C24'—H24A1.0000
C14'—H14A1.0000C25'—O25'1.427 (3)
C15'—O15'1.423 (3)C25'—H25B0.9900
C15'—H15B0.9900C25'—H25C0.9900
C15'—H15C0.9900O25'—H25'0.8400
O15'—H15'0.8400O100—H1010.9601
N21—C221.373 (3)O100—H1020.9602
C12—N11—C16123.65 (17)C22—N21—C210129.30 (19)
C12—N11—C110129.14 (19)C26—N21—C210106.95 (17)
C16—N11—C110107.19 (17)N23—C22—N21122.8 (2)
N13—C12—N11122.59 (19)N23—C22—H22118.6
N13—C12—H12118.7N21—C22—H22118.6
N11—C12—H12118.7C22—N23—C24114.90 (18)
C12—N13—C14114.89 (18)N23—C24—N29124.18 (18)
N13—C14—N19123.81 (17)N23—C24—C25127.47 (19)
N13—C14—C15127.61 (18)N29—C24—C25108.33 (18)
N19—C14—C15108.55 (18)C24—C25—C26115.85 (18)
C14—C15—C16115.92 (18)C24—C25—C27107.20 (17)
C14—C15—C17107.12 (17)C26—C25—C27136.94 (19)
C16—C15—C17136.95 (19)N212—C26—N21110.89 (18)
N112—C16—N11110.55 (18)N212—C26—C25133.9 (2)
N112—C16—C15134.1 (2)N21—C26—C25115.23 (17)
N11—C16—C15115.33 (17)C28—C27—C25106.45 (18)
C18—C17—C15106.49 (18)C28—C27—H27126.8
C18—C17—H17126.8C25—C27—H27126.8
C15—C17—H17126.8C27—C28—N29109.68 (19)
C17—C18—N19110.01 (19)C27—C28—H28125.2
C17—C18—H18125.0N29—C28—H28125.2
N19—C18—H18125.0C24—N29—C28108.33 (17)
C14—N19—C18107.82 (17)C24—N29—C21'125.18 (17)
C14—N19—C11'124.89 (17)C28—N29—C21'126.48 (18)
C18—N19—C11'127.28 (17)C211—C210—N21105.0 (2)
C111—C110—N11104.81 (19)C211—C210—H210127.5
C111—C110—H110127.6N21—C210—H210127.5
N11—C110—H110127.6C210—C211—N212112.09 (19)
C110—C111—N112112.01 (19)C210—C211—H211124.0
C110—C111—H111124.0N212—C211—H211124.0
N112—C111—H111124.0C26—N212—C211105.04 (18)
C16—N112—C111105.44 (18)O24'—C21'—N29108.68 (15)
O14'—C11'—N19108.50 (15)O24'—C21'—C22'106.79 (15)
O14'—C11'—C12'107.01 (15)N29—C21'—C22'113.64 (18)
N19—C11'—C12'113.50 (18)O24'—C21'—H21B109.2
O14'—C11'—H11C109.2N29—C21'—H21B109.2
N19—C11'—H11C109.2C22'—C21'—H21B109.2
C12'—C11'—H11C109.2C23'—C22'—C21'103.08 (16)
C13'—C12'—C11'103.30 (16)C23'—C22'—H22B111.1
C13'—C12'—H12B111.1C21'—C22'—H22B111.1
C11'—C12'—H12B111.1C23'—C22'—H22C111.1
C13'—C12'—H12C111.1C21'—C22'—H22C111.1
C11'—C12'—H12C111.1H22B—C22'—H22C109.1
H12B—C12'—H12C109.1C23'—O23'—H23'109.5
C13'—O13'—H13'109.5O23'—C23'—C24'111.71 (16)
O13'—C13'—C14'112.06 (17)O23'—C23'—C22'113.13 (16)
O13'—C13'—C12'112.60 (16)C24'—C23'—C22'100.92 (16)
C14'—C13'—C12'101.13 (17)O23'—C23'—H23C110.3
O13'—C13'—H13C110.3C24'—C23'—H23C110.3
C14'—C13'—H13C110.3C22'—C23'—H23C110.3
C12'—C13'—H13C110.3O24'—C24'—C25'110.45 (15)
O14'—C14'—C15'109.74 (16)O24'—C24'—C23'104.08 (15)
O14'—C14'—C13'104.09 (15)C25'—C24'—C23'114.18 (17)
C15'—C14'—C13'114.29 (17)O24'—C24'—H24A109.3
O14'—C14'—H14A109.5C25'—C24'—H24A109.3
C15'—C14'—H14A109.5C23'—C24'—H24A109.3
C13'—C14'—H14A109.5C24'—O24'—C21'108.25 (15)
C11'—O14'—C14'108.23 (15)O25'—C25'—C24'110.91 (17)
O15'—C15'—C14'111.68 (18)O25'—C25'—H25B109.5
O15'—C15'—H15B109.3C24'—C25'—H25B109.5
C14'—C15'—H15B109.3O25'—C25'—H25C109.5
O15'—C15'—H15C109.3C24'—C25'—H25C109.5
C14'—C15'—H15C109.3H25B—C25'—H25C108.0
H15B—C15'—H15C107.9C25'—O25'—H25'109.5
C15'—O15'—H15'109.5H101—O100—H102106.0
C22—N21—C26123.62 (18)
C16—N11—C12—N131.4 (3)C26—N21—C22—N232.5 (4)
C110—N11—C12—N13179.8 (2)C210—N21—C22—N23177.7 (2)
N11—C12—N13—C140.8 (3)N21—C22—N23—C240.3 (3)
C12—N13—C14—N19178.1 (2)C22—N23—C24—N29179.7 (2)
C12—N13—C14—C150.5 (3)C22—N23—C24—C251.4 (3)
N13—C14—C15—C161.1 (3)N23—C24—C25—C260.2 (3)
N19—C14—C15—C16179.03 (18)N29—C24—C25—C26178.42 (18)
N13—C14—C15—C17178.0 (2)N23—C24—C25—C27179.3 (2)
N19—C14—C15—C170.1 (2)N29—C24—C25—C270.7 (2)
C12—N11—C16—N112178.6 (2)C22—N21—C26—N212176.1 (2)
C110—N11—C16—N1120.1 (2)C210—N21—C26—N2120.0 (2)
C12—N11—C16—C150.6 (3)C22—N21—C26—C253.9 (3)
C110—N11—C16—C15179.33 (18)C210—N21—C26—C25179.98 (19)
C14—C15—C16—N112179.5 (2)C24—C25—C26—N212177.3 (2)
C17—C15—C16—N1120.7 (4)C27—C25—C26—N2121.5 (4)
C14—C15—C16—N110.5 (3)C24—C25—C26—N212.6 (3)
C17—C15—C16—N11178.3 (2)C27—C25—C26—N21178.5 (2)
C14—C15—C17—C180.0 (2)C24—C25—C27—C280.4 (2)
C16—C15—C17—C18178.8 (2)C26—C25—C27—C28178.5 (2)
C15—C17—C18—N190.1 (3)C25—C27—C28—N290.0 (3)
N13—C14—N19—C18178.2 (2)N23—C24—N29—C28179.4 (2)
C15—C14—N19—C180.1 (2)C25—C24—N29—C280.8 (2)
N13—C14—N19—C11'2.7 (3)N23—C24—N29—C21'1.3 (3)
C15—C14—N19—C11'179.31 (18)C25—C24—N29—C21'179.90 (19)
C17—C18—N19—C140.1 (3)C27—C28—N29—C240.5 (3)
C17—C18—N19—C11'179.3 (2)C27—C28—N29—C21'179.8 (2)
C12—N11—C110—C111178.2 (2)C22—N21—C210—C211175.6 (2)
C16—N11—C110—C1110.4 (2)C26—N21—C210—C2110.3 (3)
N11—C110—C111—N1120.6 (3)N21—C210—C211—N2120.4 (3)
N11—C16—N112—C1110.3 (2)N21—C26—N212—C2110.2 (2)
C15—C16—N112—C111178.8 (2)C25—C26—N212—C211179.8 (2)
C110—C111—N112—C160.6 (3)C210—C211—N212—C260.4 (3)
C14—N19—C11'—O14'107.7 (2)C24—N29—C21'—O24'107.0 (2)
C18—N19—C11'—O14'71.3 (3)C28—N29—C21'—O24'72.2 (3)
C14—N19—C11'—C12'133.5 (2)C24—N29—C21'—C22'134.3 (2)
C18—N19—C11'—C12'47.5 (3)C28—N29—C21'—C22'46.5 (3)
O14'—C11'—C12'—C13'12.9 (2)O24'—C21'—C22'—C23'14.6 (2)
N19—C11'—C12'—C13'106.80 (18)N29—C21'—C22'—C23'105.17 (18)
C11'—C12'—C13'—O13'151.50 (17)C21'—C22'—C23'—O23'152.70 (17)
C11'—C12'—C13'—C14'31.74 (19)C21'—C22'—C23'—C24'33.22 (19)
O13'—C13'—C14'—O14'160.61 (15)O23'—C23'—C24'—O24'161.76 (15)
C12'—C13'—C14'—O14'40.46 (18)C22'—C23'—C24'—O24'41.27 (18)
O13'—C13'—C14'—C15'79.7 (2)O23'—C23'—C24'—C25'77.7 (2)
C12'—C13'—C14'—C15'160.16 (16)C22'—C23'—C24'—C25'161.76 (16)
N19—C11'—O14'—C14'135.80 (17)C25'—C24'—O24'—C21'156.46 (16)
C12'—C11'—O14'—C14'13.0 (2)C23'—C24'—O24'—C21'33.49 (19)
C15'—C14'—O14'—C11'156.64 (17)N29—C21'—O24'—C24'134.58 (17)
C13'—C14'—O14'—C11'33.9 (2)C22'—C21'—O24'—C24'11.6 (2)
O14'—C14'—C15'—O15'74.9 (2)O24'—C24'—C25'—O25'76.1 (2)
C13'—C14'—C15'—O15'168.66 (16)C23'—C24'—C25'—O25'167.05 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O13—H13···O15i0.842.012.800 (2)156
O15—H15···N112ii0.841.872.705 (2)175
O23—H23···O25iii0.841.842.665 (2)165
O25—H25···N212iv0.841.842.675 (2)174
O100—H101···O230.961.912.823 (3)157
O100—H102···O15i0.961.922.868 (2)169
C12—H12···O13v0.952.373.241 (3)153
C22—H22···O23vi0.952.473.295 (3)145
C210—H210···O100vi0.952.473.230 (4)138
Symmetry codes: (i) x, y+1, z; (ii) x+1/2, y1/2, z; (iii) x, y1, z; (iv) x+1/2, y+1/2, z+1; (v) x+1, y1, z; (vi) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formula2C13H14N4O3·H2O
Mr566.58
Crystal system, space groupMonoclinic, C2
Temperature (K)130
a, b, c (Å)19.6476 (12), 5.2979 (3), 26.3354 (16)
β (°) 106.865 (3)
V3)2623.4 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.30 × 0.20 × 0.10
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.969, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections
46138, 4214, 3987
Rint0.033
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.106, 1.12
No. of reflections4214
No. of parameters374
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.33, 0.33
Absolute structureEstablished by known chemical absolute configuration

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), DIAMOND (Brandenburg, 1999), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Selected geometric parameters (Å, º) top
N11—C161.396 (3)N21—C261.394 (3)
C16—N1121.322 (2)C26—N2121.325 (2)
N19—C11'1.451 (2)N29—C21'1.449 (2)
O13'—C13'—C14'112.06 (17)O23'—C23'—C24'111.71 (16)
O15'—C15'—C14'111.68 (18)O25'—C25'—C24'110.91 (17)
C12—N11—C16—N112178.6 (2)C22—N21—C26—N212176.1 (2)
C14—C15—C16—N112179.5 (2)C24—C25—C26—N212177.3 (2)
C14—N19—C11'—O14'107.7 (2)C24—N29—C21'—O24'107.0 (2)
C13'—C14'—C15'—O15'168.66 (16)C23'—C24'—C25'—O25'167.05 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O13'—H13'···O15'i0.842.012.800 (2)156.0
O15'—H15'···N112ii0.841.872.705 (2)174.7
O23'—H23'···O25'iii0.841.842.665 (2)165.3
O25'—H25'···N212iv0.841.842.675 (2)173.6
O100—H101···O23'0.961.912.823 (3)156.8
O100—H102···O15'i0.961.922.868 (2)168.7
C12—H12···O13'v0.952.373.241 (3)153.1
C22—H22···O23'vi0.952.473.295 (3)145.0
C210—H210···O100vi0.952.473.230 (4)137.5
Symmetry codes: (i) x, y+1, z; (ii) x+1/2, y1/2, z; (iii) x, y1, z; (iv) x+1/2, y+1/2, z+1; (v) x+1, y1, z; (vi) x+1, y+1, z+1.
 

References

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