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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 1| January 2011| Pages o3-o4
https://doi.org/10.1107/S160053681004938X

3′-O-Acetyl-2′-de­­oxy­uridine

Bogdan Doboszewski,a Alexander Y. Nazarenkob* and Victor N. Nemykinc

aDepartamento de Química, Universidade Federal Rural de Pernambuco, 52171-900 Recife, PE, Brazil, bChemistry Department, State University of New York, College at Buffalo, 1300 Elmwood Ave, Buffalo, NY 14222-1095, USA, and cDepartment of Chemistry & Biochemistry, University of Minnesota Duluth, Duluth, Minnesota 55812-2496, USA
*Correspondence e-mail: nazareay@buffalostate.edu

(Received 24 November 2010; accepted 25 November 2010; online 4 December 2010)

In the two independent but very similar mol­ecules of the title compound, C11H14N2O6, both nucleobase fragments are nearly planar (both within 0.01 Å) while the furan­ose rings exhibit 2E-endo envelope conformations. In the crystal, the two 3′-O-acetyl-2′-de­oxy­uridine mol­ecules form a pseudosymmetric dimer of two bases connected via two nearly identical resonance-assisted N—H⋯O hydrogen bonds. The resulting pair is further connected with neighboring pairs via two similar O—H⋯O bonds involving the only hydroxyl group of the 2′-de­oxy­furan­ose fragment and the remaining carbonyl oxygen of the nucleobase. These inter­actions result in the formation of an infinite `double band' along the b axis that can be considered as a self-assembled analogue of a polynucleotide mol­ecule with non-canonical Watson–Crick base pairs. The infinite chains of 3′-O-acetyl-2′-de­oxy­uridine pairs are additionally held together by C—H⋯O inter­actions involving C atoms of the uracyl base and O atoms of carbonyl groups. Only weak C—H⋯O contacts exist between neighboring chains.

Related literature

For syntheses of this and similar compounds, see: Smrt & Sorm (1960[Smrt, J. & Sorm, F. (1960). Coll. Czech. Chem. Commun. 25, 553-558.]); Cabral et al. (2008[Cabral, N. L. D., Hoeltgebaum Thiesen, L. & Doboszewski, B. (2008). Nucleosides Nucleotides Nucl. Acids, 27, 931-948.]). For related structures of uridines, see: de Graaff et al. (1977[Graaff, R. A. G., Admiraal, G., Koen, E. H. & Romers, C. (1977). Acta Cryst. B33, 2459-2464.]); Green et al. (1975[Green, E. A., Rosenstein, R. D., Shiono, R., Abraham, D. J., Trus, B. L. & Marsh, R. E. (1975). Acta Cryst. B31, 102-107.]); Low & Wilson (1984[Low, J. N. & Wilson, C. C. (1984). Acta Cryst. C40, 1030-1032.]); Luo et al. (2007[Luo, Q., Tang, D.-H., Zhen, Z. & Liu, X.-H. (2007). Acta Cryst. E63, o4-o6.]); Marck et al. (1982[Marck, C., Lesyng, B. & Saenger, W. (1982). J. Mol. Struct. 82, 77-94.]); Rahman & Wilson (1972[Rahman, A. & Wilson, H. R. (1972). Acta Cryst. B28, 2260-2270.]); Suck et al. (1972[Suck, D., Saenger, W. & Hobbs, J. (1972). Biochim. Biophys. Acta, 259, 157-163.]). For conformations of five-membered rings, see: Schwarz (1973[Schwarz, J. C. P. (1973). J. Chem. Soc. Chem. Commun. pp. 505-508.]); Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]); Boeyens & Dobson (1987[Boeyens, J. C. A. & Dobson, S. M. (1987). Stereochemistry of Metallic Macrocycles, in Stereochemical and Stereophysical Behaviour of Macrocycles, edited by I. Bernal, pp. 2-102. Amsterdam: Elsevier.]). For analysis of absolute structure, see: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), Hooft et al. (2008[Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96-103.]). For hydrogen bonding in nucleotide chemistry, see: Gilli & Gilli (2009[Gilli, G. & Gilli, P. (2009). The Nature of the Hydrogen Bond. Oxford University Press.]); Desiraju & Steiner (1999[Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond in Structural Chemistry and Biology. Oxford University Press.]); Jeffrey (1997[Jeffrey, G. A. (1997). An Introduction to Hydrogen Bonding. Oxford University Press.]); Nagaswamy et al.(2000[Nagaswamy, U., Voss, N., Zhang, Z. & Fox, G. E. (2000). Nucleic Acid Res. 28, 375-376.]) and references therein. For similar UU-4-carbon­yl–imino pairs in RNA structures, see: Ban et al. (2000[Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000). Science, 289, 905-920.]); Jiang & Patel (1998[Jiang, L. & Patel, D. J. (1998). Nat. Struct. Biol. 5, 769-774.]).

[Scheme 1]

Experimental

Crystal data

  • C11H14N2O6

  • Mr = 270.24

  • Monoclinic, C 2

  • a = 22.8919 (4) Å

  • b = 6.8676 (1) Å

  • c = 17.2789 (12) Å

  • β = 111.307 (8)°

  • V = 2530.8 (2) Å3

  • Z = 8

  • Cu Kα radiation

  • μ = 1.00 mm−1

  • T = 291 K

  • 0.2 × 0.15 × 0.1 mm
Data collection

  • Rigaku R-AXIS RAPID II imaging plate diffractometer

  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.84, Tmax = 0.88

  • 11957 measured reflections

  • 4372 independent reflections

  • 2609 reflections with I > 2σ(I)

  • Rint = 0.069
Refinement

  • R[F2 > 2σ(F2)] = 0.048

  • wR(F2) = 0.149

  • S = 1.10

  • 4372 reflections

  • 346 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.24 e Å−3

  • Δρmin = −0.24 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1927 Friedel pairs

  • Flack parameter: 0.0 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O4—H1⋯O1i 0.82 1.98 2.798 (5) 173
N2—H2⋯O22ii 0.86 1.98 2.803 (5) 161
N22—H22⋯O2ii 0.86 1.99 2.817 (5) 160
O24—H24⋯O21iii 0.82 2.02 2.828 (5) 170
C3—H3A⋯O22iv 0.93 2.24 3.117 (6) 157
C23—H23A⋯O2v 0.93 2.39 3.254 (5) 154
C24—H24A⋯O21iii 0.93 2.59 3.381 (5) 143
C31—H31B⋯O26vi 0.96 2.56 3.428 (8) 150
Symmetry codes: (i) x, y-1, z; (ii) -x+1, y, -z+2; (iii) x, y+1, z; (iv) -x+1, y-1, -z+2; (v) -x+1, y+1, -z+2; (vi) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+1].

Data collection: CrystalClear-SM Expert (Rigaku, 2009[Rigaku (2009). CrystalClear-SM Expert. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S160053681004938X/zl2331sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053681004938X/zl2331Isup2.hkl

checkCIF report


Comment top

Modified nucleosides have received much attention as potential chemotherapeutic agents due to their ability to interfere with the polymerases engaged in replication processes in metastatic or virus invaded cells. In fact, most of the antiviral compounds approved for commercialization are nucleoside analogs which were obtained by modifications of the ribonucleosides or deoxyribonucleosides at a nucleobase moiety, at a carbohydrate moiety or at both of them. The title compound has attracted our attention as a possible intermediate in a synthesis of such agents.

The absolute structure of the title compound is known from the synthetic route which does not affect stereogenic atoms of the starting compound. Nevertheless, we preferred to obtain a direct experimental confirmation using X-ray diffractometry data. Because there are no heavy atoms in a chiral molecule of title compound, Cu Kα radiation was necessary for determination of the absolute structure.

In the crystal structure of title compound (Fig.1), all bond lengths and bond angles have standard dimensions.

The six-membered rings in both crystallographically independent molecules are flat within 0.01 Å. Figure 2 shows that the furanose ring in the first molecule adopts an envelope conformation with atoms O3, C7, C8, and C5 being within 0.02 Å from their mean plane, and atom C6 at a distance of 0.48 Å. A quantitative analysis of the ring conformations was performed using the method of Cremer and Pople (Cremer & Pople, 1975; Boeyens & Dobson, 1987) for the calculation of parameters of puckering. The polar parameters for the furanose ring are Q = 0.301 (4) and 0.320 (4) Å, Φ = 67.1 (8)° and 66.6 (7) ° for both independent molecules. These suggest the envelope conformation 2E (ideal Φ = 72°), slightly distorted towards twist 2T1 (Φ= 54°), with atoms C(6) and C(26) in corners of the respective envelopes. The conformation of the 3'-substituted 2'-deoxydeoxyuridine reported here is different from the conformation of the unsubstituted 2'-deoxyuridine molecule: in this case Φ = 83 and Φ = 89 ° for two independent molecules which is close to a twisted 2T3 conformation (Φ=90°) of the furanose ring (CSD code DOURID, Rahman & Wilson, 1972). An 2E conformation was observed in several other molecules of the uridine family (see, for example 2'-deoxy-3',5'-diacetyldeoxyuridine (WEVJOX, Luo et al., 2007) Φ = 67 °; 3,5-diacetyluridine (DAURID, de Graaff et al., 1977) Φ =76 °; and 2'-chloro-2'-deoxyuridine (CDURID, Suck et al., 1972) Φ =69 °). 3E and 3T2 conformations exist in uridine (BEURID10, Green et al., 1975) with Φ =282 ° and 273 °. Twisted conformations OT5 and 3T4 are observed in 2'deoxy-2'-fluorodeoxyuridine (BOFWIC, Marck et al., 1982) Φ =339 ° and 2,3,5-triacetyluridine (CIHNIK, Low & Wilson, 1984) Φ =313 °. Therefore, no direct correlation between the substituents, their properties, and the furanose ring conformation is obvious.

In the crystal of the title compound, the two independent acetyldeoxyuridine molecules form a pseudosymmetric dimer of two bases connected via two nearly identical N—H···O hydrogen bonds (Table 1, Figure 3). Such pseudosymmetric arrangment corresponds to a UU42 mode of base pairing (Jeffrey, 1997). Relatively short N···O separations (Table 1) demonstrate strong resonance-assisted hydrogen bonds. All eight cycle-forming atoms are located close to the mean plane (Figure 3), making possible π-delocalization of the resonance fragment. This observation is also supported by longer C=O bond lengths in the participating carbonyl groups (1.236 (5) and 1.230 (5) Å) when compared to the other carbonyl groups of the same nucleobase (1.223 (5) and 1.212 (5) Å).

The resulting dimer is further connected with neighboring dimers via two similar O—H···O bonds involving the only hydroxy group of deoxyfuranose fragment and the remaining carbonyl oxygen of the base. These interactions result in the formation of infinitive "double bands" along the b axis of the crystal cell (Figure 4). Such a structure can be considered as a primitive self-assembled analogue of an RNA polymer molecule with non-canonical Watson-Crick base pairs. Two examples of similar UU-4-carbonyl-immino pairs in RNA structures can be found in an NMR structure (Jiang & Patel, 1998) and in a low resolution solid state structure (Ban et al., 2000). More information about flipped pyrimidine-pyrimidine mismatches can be found in (Nagaswamy et al., 2000).

The infinitive chains of acetyldeoxyuridine pairs in the title compound are additionally kept together by CH···O interactions involving carbon atoms of the uracyl base and oxygen atoms of carbonyl groups (Table 1, Figure 4 and 5). Similar bonds were observed in various uracyl-containg structures (Desiraju & Steiner, 1999). A short intramolecular contact between carbonyl oxygen O1 and hydrogen atom H5A may additionaly stabilize the conformation of the molecule.

Only weak C—H···O contacts exist between neighboring chains.

Related literature top

For syntheses of this and similar compounds, see: Smrt & Sorm (1960); Cabral et al. (2008). For related structures of uridines, see: de Graaff et al. (1977); Green et al. (1975); Low & Wilson (1984); Luo et al. (2007); Marck et al. (1982); Rahman & Wilson (1972); Suck et al. (1972). For conformations of five-membered rings, see: Schwarz (1973); Cremer & Pople (1975); Boeyens & Dobson (1987). For analysis of absolute structure, see: Flack (1983), Hooft et al. (2008). For hydrogen bonding in nucleotide chemistry, see: Gilli & Gilli (2009); Desiraju & Steiner (1999); Jeffrey (1997); Nagaswamy et al.(2000) and references therein. For similar UU-4-carbonyl–imino pairs in RNA structures, see: Ban et al. (2000); Jiang & Patel (1998).

Experimental top

The synthesis of the title compound was accomplished via a transetherification procedure dubbed "protecting group transfer" (Cabral et al., 2008). 3'-Acetyl-2'-deoxyuridine obtained in this way showed the same properties as the one obtained before by an independent procedure (Smrt & Sorm, 1960). Crystallization from a hexane-acetone system yielded colourless crystals suitable for single-crystal diffractometry (m.p. 460–461 K).

Refinement top

The chirality of the title compound was known from the synthetic route; it was also examined using anomalous scattering. Analysis of the absolute structure using likelihood methods (Hooft et al., 2008) was performed using PLATON (Spek, 2009); 1867 Bijvoet pairs were employed. The results confirmed that the absolute structure had been correctly assigned: the probability that the structure is inverted is smaller than 10-11 with probability of racemic twinning at 0.001. Because no atom heavier than O is present, the standard deviation of the Flack parameter is relatively high. All H atoms were positioned geometrically with Uiso(H) = 1.2 or 1.5 Ueq(C).

Structure description top

Modified nucleosides have received much attention as potential chemotherapeutic agents due to their ability to interfere with the polymerases engaged in replication processes in metastatic or virus invaded cells. In fact, most of the antiviral compounds approved for commercialization are nucleoside analogs which were obtained by modifications of the ribonucleosides or deoxyribonucleosides at a nucleobase moiety, at a carbohydrate moiety or at both of them. The title compound has attracted our attention as a possible intermediate in a synthesis of such agents.

The absolute structure of the title compound is known from the synthetic route which does not affect stereogenic atoms of the starting compound. Nevertheless, we preferred to obtain a direct experimental confirmation using X-ray diffractometry data. Because there are no heavy atoms in a chiral molecule of title compound, Cu Kα radiation was necessary for determination of the absolute structure.

In the crystal structure of title compound (Fig.1), all bond lengths and bond angles have standard dimensions.

The six-membered rings in both crystallographically independent molecules are flat within 0.01 Å. Figure 2 shows that the furanose ring in the first molecule adopts an envelope conformation with atoms O3, C7, C8, and C5 being within 0.02 Å from their mean plane, and atom C6 at a distance of 0.48 Å. A quantitative analysis of the ring conformations was performed using the method of Cremer and Pople (Cremer & Pople, 1975; Boeyens & Dobson, 1987) for the calculation of parameters of puckering. The polar parameters for the furanose ring are Q = 0.301 (4) and 0.320 (4) Å, Φ = 67.1 (8)° and 66.6 (7) ° for both independent molecules. These suggest the envelope conformation 2E (ideal Φ = 72°), slightly distorted towards twist 2T1 (Φ= 54°), with atoms C(6) and C(26) in corners of the respective envelopes. The conformation of the 3'-substituted 2'-deoxydeoxyuridine reported here is different from the conformation of the unsubstituted 2'-deoxyuridine molecule: in this case Φ = 83 and Φ = 89 ° for two independent molecules which is close to a twisted 2T3 conformation (Φ=90°) of the furanose ring (CSD code DOURID, Rahman & Wilson, 1972). An 2E conformation was observed in several other molecules of the uridine family (see, for example 2'-deoxy-3',5'-diacetyldeoxyuridine (WEVJOX, Luo et al., 2007) Φ = 67 °; 3,5-diacetyluridine (DAURID, de Graaff et al., 1977) Φ =76 °; and 2'-chloro-2'-deoxyuridine (CDURID, Suck et al., 1972) Φ =69 °). 3E and 3T2 conformations exist in uridine (BEURID10, Green et al., 1975) with Φ =282 ° and 273 °. Twisted conformations OT5 and 3T4 are observed in 2'deoxy-2'-fluorodeoxyuridine (BOFWIC, Marck et al., 1982) Φ =339 ° and 2,3,5-triacetyluridine (CIHNIK, Low & Wilson, 1984) Φ =313 °. Therefore, no direct correlation between the substituents, their properties, and the furanose ring conformation is obvious.

In the crystal of the title compound, the two independent acetyldeoxyuridine molecules form a pseudosymmetric dimer of two bases connected via two nearly identical N—H···O hydrogen bonds (Table 1, Figure 3). Such pseudosymmetric arrangment corresponds to a UU42 mode of base pairing (Jeffrey, 1997). Relatively short N···O separations (Table 1) demonstrate strong resonance-assisted hydrogen bonds. All eight cycle-forming atoms are located close to the mean plane (Figure 3), making possible π-delocalization of the resonance fragment. This observation is also supported by longer C=O bond lengths in the participating carbonyl groups (1.236 (5) and 1.230 (5) Å) when compared to the other carbonyl groups of the same nucleobase (1.223 (5) and 1.212 (5) Å).

The resulting dimer is further connected with neighboring dimers via two similar O—H···O bonds involving the only hydroxy group of deoxyfuranose fragment and the remaining carbonyl oxygen of the base. These interactions result in the formation of infinitive "double bands" along the b axis of the crystal cell (Figure 4). Such a structure can be considered as a primitive self-assembled analogue of an RNA polymer molecule with non-canonical Watson-Crick base pairs. Two examples of similar UU-4-carbonyl-immino pairs in RNA structures can be found in an NMR structure (Jiang & Patel, 1998) and in a low resolution solid state structure (Ban et al., 2000). More information about flipped pyrimidine-pyrimidine mismatches can be found in (Nagaswamy et al., 2000).

The infinitive chains of acetyldeoxyuridine pairs in the title compound are additionally kept together by CH···O interactions involving carbon atoms of the uracyl base and oxygen atoms of carbonyl groups (Table 1, Figure 4 and 5). Similar bonds were observed in various uracyl-containg structures (Desiraju & Steiner, 1999). A short intramolecular contact between carbonyl oxygen O1 and hydrogen atom H5A may additionaly stabilize the conformation of the molecule.

Only weak C—H···O contacts exist between neighboring chains.

For syntheses of this and similar compounds, see: Smrt & Sorm (1960); Cabral et al. (2008). For related structures of uridines, see: de Graaff et al. (1977); Green et al. (1975); Low & Wilson (1984); Luo et al. (2007); Marck et al. (1982); Rahman & Wilson (1972); Suck et al. (1972). For conformations of five-membered rings, see: Schwarz (1973); Cremer & Pople (1975); Boeyens & Dobson (1987). For analysis of absolute structure, see: Flack (1983), Hooft et al. (2008). For hydrogen bonding in nucleotide chemistry, see: Gilli & Gilli (2009); Desiraju & Steiner (1999); Jeffrey (1997); Nagaswamy et al.(2000) and references therein. For similar UU-4-carbonyl–imino pairs in RNA structures, see: Ban et al. (2000); Jiang & Patel (1998).

Computing details top

Data collection: CrystalClear-SM Expert (Rigaku, 2009); cell refinement: CrystalClear-SM Expert (Rigaku, 2009); data reduction: CrystalClear-SM Expert (Rigaku, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Two molecules of the title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
[Figure 2] Fig. 2. Conformation of deoxyfuranose ring of molecule 1: mean plane through the C5, C7, C8, and O3 atoms.
[Figure 3] Fig. 3. Geometry of resonance-enhanced hydrogen bonding between two uracyl bases.
[Figure 4] Fig. 4. Two pairs of acetyldeoxyuridine molecules connected via N—H···O hydrogen bonds (blue), O—H···O hydrogen bonds (red) and C—H···O hydrogen bonds (black).
[Figure 5] Fig. 5. An infinitive chain of acetyldeoxyuridine pairs. View along the a axis.
[Figure 6] Fig. 6. Packing of the title molecules. View along the b axis.
[Figure 7] Fig. 7. A five-pair fragment of infinitive band of 3'-O-acetyl-2'-deoxyuridine molecules.
(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)- 2-(hydroxymethyl)tetrahydrofuran-3-yl acetate top
Crystal data top
C11H14N2O6F(000) = 1136
Mr = 270.24Dx = 1.418 Mg m−3
Monoclinic, C2Melting point: 461 K
Hall symbol: C 2yCu Kα radiation, λ = 1.54187 Å
a = 22.8919 (4) ÅCell parameters from 9690 reflections
b = 6.8676 (1) Åθ = 6.8–68.2°
c = 17.2789 (12) ŵ = 1.00 mm−1
β = 111.307 (8)°T = 291 K
V = 2530.8 (2) Å3Block, colourless
Z = 80.2 × 0.15 × 0.1 mm
Data collection top
Rigaku R-AXIS RAPID II imaging plate
diffractometer		4372 independent reflections
Radiation source: fine-focus sealed tube2609 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.069
Detector resolution: 10 pixels mm-1θmax = 67.0°, θmin = 6.8°
ω scansh = −27→22
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		k = −8→7
Tmin = 0.84, Tmax = 0.88l = −17→20
11957 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.048 w = 1/[σ2(Fo2) + (0.0552P)2 + 0.1596P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.149(Δ/σ)max < 0.001
S = 1.10Δρmax = 0.24 e Å−3
4372 reflectionsΔρmin = −0.24 e Å−3
346 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.0016 (2)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 1927 Friedel pairs
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.0 (2)
Crystal data top
C11H14N2O6V = 2530.8 (2) Å3
Mr = 270.24Z = 8
Monoclinic, C2Cu Kα radiation
a = 22.8919 (4) ŵ = 1.00 mm−1
b = 6.8676 (1) ÅT = 291 K
c = 17.2789 (12) Å0.2 × 0.15 × 0.1 mm
β = 111.307 (8)°
Data collection top
Rigaku R-AXIS RAPID II imaging plate
diffractometer		4372 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		2609 reflections with I > 2σ(I)
Tmin = 0.84, Tmax = 0.88Rint = 0.069
11957 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.149Δρmax = 0.24 e Å−3
S = 1.10Δρmin = −0.24 e Å−3
4372 reflectionsAbsolute structure: Flack (1983), 1927 Friedel pairs
346 parametersAbsolute structure parameter: 0.0 (2)
1 restraint
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
O10.46379 (15)0.4346 (4)0.81776 (18)0.0769 (9)
O20.40640 (14)0.0919 (4)1.00331 (19)0.0794 (9)
O30.46084 (12)−0.0505 (4)0.68957 (16)0.0697 (8)
O40.54767 (15)−0.3837 (5)0.7567 (2)0.0912 (11)
H10.5257−0.44390.77690.137*
O50.56917 (13)0.1405 (4)0.63582 (18)0.0689 (8)
O60.59476 (16)−0.0887 (6)0.5611 (2)0.0920 (11)
N10.46541 (16)0.1042 (5)0.8110 (2)0.0590 (9)
N20.43469 (16)0.2568 (5)0.9092 (2)0.0631 (9)
H20.42670.36310.92970.076*
C10.45611 (19)0.2760 (6)0.8447 (2)0.0562 (10)
C20.4246 (2)0.0868 (7)0.9442 (3)0.0698 (12)
C30.4369 (2)−0.0844 (7)0.9075 (3)0.0809 (15)
H3A0.4314−0.20610.92740.097*
C40.4567 (2)−0.0696 (7)0.8439 (3)0.0743 (13)
H4A0.4649−0.18360.82060.089*
C50.48799 (18)0.1107 (6)0.7418 (2)0.0563 (10)
H5A0.47430.23220.71070.068*
C60.55755 (18)0.0894 (6)0.7668 (2)0.0612 (11)
H6A0.57490.01000.81630.073*
H6B0.57810.21530.77670.073*
C70.56437 (19)−0.0114 (6)0.6914 (2)0.0609 (11)
H7A0.6012−0.09650.70820.073*
C80.5048 (2)−0.1272 (6)0.6545 (3)0.0640 (11)
H8A0.4877−0.10630.59430.077*
C90.5126 (2)−0.3445 (7)0.6714 (3)0.0788 (14)
H9A0.4716−0.40470.65590.095*
H9B0.5339−0.40160.63750.095*
C100.5876 (2)0.0811 (9)0.5732 (3)0.0784 (14)
C110.5960 (3)0.2490 (9)0.5245 (3)0.110 (2)
H11A0.63660.24160.52010.164*
H11B0.59280.36800.55180.164*
H11C0.56410.24620.46990.164*
O210.70463 (14)0.1998 (4)0.87917 (18)0.0703 (8)
O220.61778 (17)0.5604 (4)1.0291 (2)0.1020 (13)
O230.78772 (13)0.6734 (4)0.82972 (16)0.0676 (8)
O240.71663 (15)1.0090 (5)0.7407 (2)0.0874 (10)
H240.71811.06620.78300.131*
O250.76788 (13)0.4633 (5)0.65709 (18)0.0737 (9)
O260.80745 (19)0.6677 (7)0.5882 (2)0.1077 (13)
N210.71512 (15)0.5305 (5)0.87739 (19)0.0575 (9)
N220.66228 (16)0.3867 (5)0.9545 (2)0.0647 (9)
H220.65020.28280.97220.078*
C210.6952 (2)0.3601 (7)0.9015 (3)0.0588 (11)
C220.6469 (2)0.5612 (7)0.9816 (3)0.0710 (13)
C230.6674 (2)0.7311 (6)0.9510 (2)0.0638 (12)
H23A0.65860.85440.96630.077*
C240.6993 (2)0.7113 (5)0.9002 (2)0.0610 (11)
H24A0.71140.82280.87940.073*
C250.74536 (19)0.5179 (6)0.8160 (2)0.0582 (10)
H25A0.76790.39400.82250.070*
C260.69949 (18)0.5388 (7)0.7270 (2)0.0625 (11)
H26A0.68280.41340.70340.075*
H26B0.66510.62480.72380.075*
C270.73937 (19)0.6245 (6)0.6843 (2)0.0614 (11)
H27A0.71480.70690.63750.074*
C280.7886 (2)0.7422 (6)0.7511 (3)0.0641 (11)
H28A0.82980.71400.74850.077*
C290.7786 (2)0.9609 (7)0.7462 (3)0.0813 (14)
H29A0.80871.02180.79510.098*
H29B0.78561.01130.69790.098*
C300.7987 (2)0.5034 (9)0.6061 (3)0.0817 (15)
C310.8202 (2)0.3226 (9)0.5769 (3)0.108 (2)
H31A0.84280.35650.54170.162*
H31B0.78460.24430.54630.162*
H31C0.84720.25060.62400.162*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.111 (2)0.0498 (18)0.092 (2)−0.0016 (18)0.0627 (19)0.0023 (17)
O20.103 (2)0.065 (2)0.098 (2)0.0078 (17)0.070 (2)0.0114 (17)
O30.0616 (17)0.0763 (19)0.0791 (19)−0.0050 (16)0.0350 (15)−0.0208 (16)
O40.087 (2)0.080 (2)0.102 (2)−0.0043 (18)0.0301 (19)0.0241 (19)
O50.080 (2)0.0643 (19)0.0775 (19)0.0011 (16)0.0471 (16)0.0052 (16)
O60.108 (3)0.099 (3)0.087 (2)−0.001 (2)0.058 (2)−0.018 (2)
N10.077 (2)0.045 (2)0.072 (2)0.0068 (17)0.0471 (19)0.0022 (17)
N20.085 (2)0.045 (2)0.078 (2)0.0013 (18)0.052 (2)0.0004 (18)
C10.064 (3)0.048 (2)0.069 (3)0.000 (2)0.039 (2)0.000 (2)
C20.084 (3)0.060 (3)0.080 (3)0.002 (2)0.048 (3)0.005 (3)
C30.119 (4)0.049 (3)0.106 (4)0.007 (3)0.078 (3)0.005 (3)
C40.101 (4)0.047 (3)0.095 (3)−0.006 (2)0.059 (3)0.001 (2)
C50.064 (3)0.052 (2)0.065 (2)−0.004 (2)0.038 (2)−0.003 (2)
C60.061 (2)0.065 (3)0.068 (2)−0.005 (2)0.036 (2)−0.007 (2)
C70.061 (3)0.057 (3)0.074 (3)0.001 (2)0.035 (2)0.005 (2)
C80.078 (3)0.058 (3)0.059 (2)−0.001 (2)0.029 (2)−0.005 (2)
C90.090 (3)0.063 (3)0.089 (3)−0.006 (3)0.040 (3)−0.010 (3)
C100.077 (3)0.097 (4)0.073 (3)−0.011 (3)0.040 (3)−0.016 (3)
C110.135 (5)0.127 (5)0.091 (4)−0.033 (4)0.069 (4)0.012 (4)
O210.092 (2)0.0456 (18)0.086 (2)0.0012 (16)0.0480 (17)−0.0062 (16)
O220.160 (3)0.062 (2)0.141 (3)0.013 (2)0.124 (3)0.006 (2)
O230.0711 (18)0.0721 (19)0.0663 (17)−0.0189 (15)0.0328 (14)−0.0018 (15)
O240.084 (2)0.081 (3)0.103 (3)0.0105 (18)0.0398 (18)−0.015 (2)
O250.083 (2)0.077 (2)0.078 (2)−0.0012 (18)0.0493 (17)−0.0081 (17)
O260.119 (3)0.125 (3)0.107 (3)0.007 (3)0.074 (2)0.025 (3)
N210.067 (2)0.052 (2)0.063 (2)0.0026 (16)0.0364 (17)0.0013 (17)
N220.084 (2)0.050 (2)0.082 (2)0.0043 (18)0.055 (2)0.0060 (18)
C210.071 (3)0.050 (3)0.060 (2)−0.005 (2)0.030 (2)0.001 (2)
C220.098 (4)0.049 (3)0.077 (3)0.010 (2)0.045 (3)0.004 (2)
C230.087 (3)0.046 (3)0.072 (3)0.007 (2)0.045 (3)−0.001 (2)
C240.083 (3)0.040 (2)0.069 (3)0.002 (2)0.038 (2)0.005 (2)
C250.064 (2)0.053 (3)0.068 (3)−0.001 (2)0.038 (2)0.003 (2)
C260.061 (3)0.065 (3)0.066 (3)−0.006 (2)0.029 (2)−0.007 (2)
C270.064 (3)0.062 (3)0.064 (2)0.004 (2)0.031 (2)−0.002 (2)
C280.066 (3)0.064 (3)0.076 (3)−0.001 (2)0.043 (2)0.003 (2)
C290.093 (4)0.071 (3)0.093 (3)−0.008 (3)0.048 (3)−0.006 (3)
C300.068 (3)0.108 (5)0.076 (3)−0.004 (3)0.034 (3)−0.002 (3)
C310.092 (4)0.141 (6)0.113 (4)−0.020 (4)0.063 (3)−0.052 (4)
Geometric parameters (Å, º) top
O1—C11.223 (5)O21—C211.212 (5)
O2—C21.236 (5)O22—C221.230 (5)
O3—C51.421 (5)O23—C251.404 (4)
O3—C81.449 (4)O23—C281.445 (4)
O4—C91.425 (5)O24—C291.425 (5)
O4—H10.8200O24—H240.8200
O5—C101.358 (5)O25—C301.342 (5)
O5—C71.449 (5)O25—C271.447 (5)
O6—C101.207 (6)O26—C301.206 (6)
N1—C41.367 (5)N21—C211.375 (5)
N1—C11.366 (5)N21—C241.390 (5)
N1—C51.467 (4)N21—C251.464 (5)
N2—C21.373 (5)N22—C221.379 (5)
N2—C11.376 (4)N22—C211.392 (5)
N2—H20.8600N22—H220.8600
C2—C31.412 (6)C22—C231.429 (6)
C3—C41.336 (5)C23—C241.337 (5)
C3—H3A0.9300C23—H23A0.9300
C4—H4A0.9300C24—H24A0.9300
C5—C61.498 (5)C25—C261.522 (5)
C5—H5A0.9800C25—H25A0.9800
C6—C71.532 (5)C26—C271.488 (5)
C6—H6A0.9700C26—H26A0.9700
C6—H6B0.9700C26—H26B0.9700
C7—C81.506 (6)C27—C281.520 (6)
C7—H7A0.9800C27—H27A0.9800
C8—C91.519 (6)C28—C291.517 (7)
C8—H8A0.9800C28—H28A0.9800
C9—H9A0.9700C29—H29A0.9700
C9—H9B0.9700C29—H29B0.9700
C10—C111.482 (7)C30—C311.489 (7)
C11—H11A0.9600C31—H31A0.9600
C11—H11B0.9600C31—H31B0.9600
C11—H11C0.9600C31—H31C0.9600
C5—O3—C8109.8 (3)C25—O23—C28109.6 (3)
C9—O4—H1109.5C29—O24—H24109.5
C10—O5—C7115.6 (4)C30—O25—C27117.6 (4)
C4—N1—C1120.5 (3)C21—N21—C24121.7 (3)
C4—N1—C5120.9 (4)C21—N21—C25117.7 (3)
C1—N1—C5118.5 (3)C24—N21—C25119.9 (3)
C2—N2—C1127.2 (4)C22—N22—C21127.1 (4)
C2—N2—H2116.4C22—N22—H22116.4
C1—N2—H2116.4C21—N22—H22116.4
O1—C1—N1122.7 (4)O21—C21—N21124.0 (4)
O1—C1—N2122.5 (4)O21—C21—N22122.0 (4)
N1—C1—N2114.7 (4)N21—C21—N22114.0 (4)
O2—C2—N2120.1 (4)O22—C22—N22119.3 (4)
O2—C2—C3125.3 (4)O22—C22—C23125.5 (4)
N2—C2—C3114.6 (4)N22—C22—C23115.2 (4)
C4—C3—C2119.3 (4)C24—C23—C22119.4 (4)
C4—C3—H3A120.4C24—C23—H23A120.3
C2—C3—H3A120.4C22—C23—H23A120.3
C3—C4—N1123.5 (4)C23—C24—N21122.5 (4)
C3—C4—H4A118.2C23—C24—H24A118.7
N1—C4—H4A118.2N21—C24—H24A118.7
O3—C5—N1107.0 (3)O23—C25—N21108.2 (3)
O3—C5—C6106.3 (3)O23—C25—C26106.2 (3)
N1—C5—C6114.5 (3)N21—C25—C26113.1 (3)
O3—C5—H5A109.6O23—C25—H25A109.7
N1—C5—H5A109.6N21—C25—H25A109.7
C6—C5—H5A109.6C26—C25—H25A109.7
C5—C6—C7103.0 (3)C27—C26—C25102.5 (3)
C5—C6—H6A111.2C27—C26—H26A111.3
C7—C6—H6A111.2C25—C26—H26A111.3
C5—C6—H6B111.2C27—C26—H26B111.3
C7—C6—H6B111.2C25—C26—H26B111.3
H6A—C6—H6B109.1H26A—C26—H26B109.2
O5—C7—C8112.0 (3)O25—C27—C26106.8 (3)
O5—C7—C6107.1 (3)O25—C27—C28110.8 (3)
C8—C7—C6104.0 (3)C26—C27—C28104.6 (3)
O5—C7—H7A111.2O25—C27—H27A111.4
C8—C7—H7A111.2C26—C27—H27A111.4
C6—C7—H7A111.2C28—C27—H27A111.4
O3—C8—C7106.9 (3)O23—C28—C29108.8 (4)
O3—C8—C9109.1 (4)O23—C28—C27106.3 (3)
C7—C8—C9114.3 (4)C29—C28—C27115.4 (4)
O3—C8—H8A108.8O23—C28—H28A108.7
C7—C8—H8A108.8C29—C28—H28A108.7
C9—C8—H8A108.8C27—C28—H28A108.7
O4—C9—C8111.6 (4)O24—C29—C28111.1 (4)
O4—C9—H9A109.3O24—C29—H29A109.4
C8—C9—H9A109.3C28—C29—H29A109.4
O4—C9—H9B109.3O24—C29—H29B109.4
C8—C9—H9B109.3C28—C29—H29B109.4
H9A—C9—H9B108.0H29A—C29—H29B108.0
O6—C10—O5122.0 (5)O26—C30—O25122.4 (5)
O6—C10—C11126.8 (5)O26—C30—C31125.9 (5)
O5—C10—C11111.2 (5)O25—C30—C31111.6 (5)
C10—C11—H11A109.5C30—C31—H31A109.5
C10—C11—H11B109.5C30—C31—H31B109.5
H11A—C11—H11B109.5H31A—C31—H31B109.5
C10—C11—H11C109.5C30—C31—H31C109.5
H11A—C11—H11C109.5H31A—C31—H31C109.5
H11B—C11—H11C109.5H31B—C31—H31C109.5
C4—N1—C1—O1179.5 (4)C24—N21—C21—O21175.5 (4)
C5—N1—C1—O12.5 (6)C25—N21—C21—O214.8 (6)
C4—N1—C1—N2−3.3 (6)C24—N21—C21—N22−4.2 (6)
C5—N1—C1—N2179.8 (3)C25—N21—C21—N22−174.8 (3)
C2—N2—C1—O1−179.8 (4)C22—N22—C21—O21−177.5 (4)
C2—N2—C1—N13.0 (6)C22—N22—C21—N212.1 (6)
C1—N2—C2—O2178.5 (4)C21—N22—C22—O22−179.5 (4)
C1—N2—C2—C3−1.3 (7)C21—N22—C22—C230.1 (7)
O2—C2—C3—C4−179.8 (5)O22—C22—C23—C24179.3 (4)
N2—C2—C3—C4−0.1 (7)N22—C22—C23—C24−0.3 (6)
C2—C3—C4—N1−0.5 (8)C22—C23—C24—N21−1.8 (7)
C1—N1—C4—C32.3 (7)C21—N21—C24—C234.3 (6)
C5—N1—C4—C3179.2 (4)C25—N21—C24—C23174.7 (4)
C8—O3—C5—N1−144.8 (3)C28—O23—C25—N21−144.4 (3)
C8—O3—C5—C6−22.1 (4)C28—O23—C25—C26−22.7 (4)
C4—N1—C5—O336.1 (5)C21—N21—C25—O23−151.1 (3)
C1—N1—C5—O3−146.9 (3)C24—N21—C25—O2338.1 (5)
C4—N1—C5—C6−81.4 (5)C21—N21—C25—C2691.5 (4)
C1—N1—C5—C695.6 (5)C24—N21—C25—C26−79.3 (5)
O3—C5—C6—C731.3 (4)O23—C25—C26—C2732.7 (4)
N1—C5—C6—C7149.2 (3)N21—C25—C26—C27151.3 (3)
C10—O5—C7—C8−78.8 (5)C30—O25—C27—C26170.3 (4)
C10—O5—C7—C6167.8 (3)C30—O25—C27—C28−76.3 (5)
C5—C6—C7—O590.1 (4)C25—C26—C27—O2588.0 (4)
C5—C6—C7—C8−28.7 (4)C25—C26—C27—C28−29.6 (4)
C5—O3—C8—C73.2 (4)C25—O23—C28—C29128.5 (4)
C5—O3—C8—C9127.3 (4)C25—O23—C28—C273.6 (4)
O5—C7—C8—O3−99.0 (4)O25—C27—C28—O23−97.5 (4)
C6—C7—C8—O316.3 (4)C26—C27—C28—O2317.3 (4)
O5—C7—C8—C9140.2 (4)O25—C27—C28—C29141.8 (4)
C6—C7—C8—C9−104.5 (4)C26—C27—C28—C29−103.5 (4)
O3—C8—C9—O4−72.2 (5)O23—C28—C29—O24−68.0 (5)
C7—C8—C9—O447.4 (6)C27—C28—C29—O2451.4 (5)
C7—O5—C10—O65.4 (7)C27—O25—C30—O266.2 (7)
C7—O5—C10—C11−175.3 (4)C27—O25—C30—C31−174.6 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H1···O1i0.821.982.798 (5)173
N2—H2···O22ii0.861.982.803 (5)161
N22—H22···O2ii0.861.992.817 (5)160
O24—H24···O21iii0.822.022.828 (5)170
C3—H3A···O22iv0.932.243.117 (6)157
C23—H23A···O2v0.932.393.254 (5)154
C24—H24A···O21iii0.932.593.381 (5)143
C31—H31B···O26vi0.962.563.428 (8)150
Symmetry codes: (i) x, y−1, z; (ii) −x+1, y, −z+2; (iii) x, y+1, z; (iv) −x+1, y−1, −z+2; (v) −x+1, y+1, −z+2; (vi) −x+3/2, y−1/2, −z+1.

Experimental details

Crystal data
Chemical formulaC11H14N2O6
Mr270.24
Crystal system, space groupMonoclinic, C2
Temperature (K)291
a, b, c (Å)22.8919 (4), 6.8676 (1), 17.2789 (12)
β (°) 111.307 (8)
V (Å3)2530.8 (2)
Z8
Radiation typeCu Kα
µ (mm−1)1.00
Crystal size (mm)0.2 × 0.15 × 0.1
Data collection
DiffractometerRigaku R-AXIS RAPID II imaging plate
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.84, 0.88
No. of measured, independent and
observed [I > 2σ(I)] reflections		11957, 4372, 2609
Rint0.069
(sin θ/λ)max (Å−1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.149, 1.10
No. of reflections4372
No. of parameters346
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.24, −0.24
Absolute structureFlack (1983), 1927 Friedel pairs
Absolute structure parameter0.0 (2)

Computer programs: CrystalClear-SM Expert (Rigaku, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H1···O1i0.821.982.798 (5)173
N2—H2···O22ii0.861.9822.803 (5)161
N22—H22···O2ii0.861.992.817 (5)160
O24—H24···O21iii0.822.022.828 (5)170
C3—H3A···O22iv0.932.243.117 (6)157
C23—H23A···O2v0.932.393.254 (5)154
C24—H24A···O21iii0.932.593.381 (5)143
C31—H31B···O26vi0.962.563.428 (8)150
Symmetry codes: (i) x, y−1, z; (ii) −x+1, y, −z+2; (iii) x, y+1, z; (iv) −x+1, y−1, −z+2; (v) −x+1, y+1, −z+2; (vi) −x+3/2, y−1/2, −z+1.
 

Acknowledgements

This study was supported by the NSF (grant CHE-0922366 for X-ray diffractometer) and by SUNY (grant No 1073053).

References

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ISSN: 2056-9890
Volume 67| Part 1| January 2011| Pages o3-o4
https://doi.org/10.1107/S160053681004938X
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