Issue contents cross.png
Download PDF of article cross.png
Download CIF cross.png
3D view cross.png
Navigation cross.png
Highlighting cross.png
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation cross.png
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
Text
cross.png
share
Previous article cross.png
Next article cross.png
Previous article cross.png
Issue contents cross.png
Download PDF of article cross.png
Download CIF cross.png
3D view cross.png
Navigation cross.png
Highlighting cross.png
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation cross.png
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
Text
cross.png
share
Next article cross.png

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

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296
Volume 61| Part 9| September 2005| Pages o548-o550
doi:10.1107/S0108270105024406

N-(6-Amino-3,4-di­hydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)leucine: a three-dimensional hydrogen-bonded framework structure

CROSSMARK_Color_square_no_text.svg
Paloma Arranz Mascarós,a M. Luz Godino Salido,a M. Dolores Gutiérrez Valero,a John N. Lowb and Christopher Glidewellc*

aDepartamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071 Jaén, Spain, bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and cSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
*Correspondence e-mail: cg@st-andrews.ac.uk

(Received 28 July 2005; accepted 29 July 2005; online 20 August 2005)

In the title compound, C11H17N5O4, the bond distances show evidence of a highly polarized mol­ecular–electronic structure. The mol­ecules are linked into a three-dimensional framework by a combination of O—H⋯O and N—H⋯O hydrogen bonds, including a very short O—H⋯O hydrogen bond [H⋯O = 1.67 Å, O⋯O = 2.494 (2) Å and O—H⋯O = 166°].

Comment

We report here the structure of the title compound, (I)[link], which we briefly compare with the structures of its valine, methio­nine and threonine analogues, (II)[link]–(IV)[link], respectively (Low et al., 1999[Low, J. N., Godino, M. L., López, R., Pérez, A., Melguizo, M. & Cobo, J. (1999). Acta Cryst. C55, 1727-1730.], 2000[Low, J. N., López. M. D., Arranz Mascarós, P., Cobo Domingo, J., Godino, M. L., López Garzón, R., Gutiérrez, M. D., Melguizo, M., Ferguson, G. & Glidewell, C. (2000). Acta Cryst. B56, 882-892.]), and those of the glycine, serine and isoleucine analogues, (V)[link]–(VII)[link], respectively, which all crystallize as hydrates (Low et al., 1997[Low, J. N., Ferguson, G., López, R., Arranz, P., Cobo, J., Melguizo, M., Nogueras, M. & Sánchez, A. (1997). Acta Cryst. C53, 890-892.], 2000[Low, J. N., López. M. D., Arranz Mascarós, P., Cobo Domingo, J., Godino, M. L., López Garzón, R., Gutiérrez, M. D., Melguizo, M., Ferguson, G. & Glidewell, C. (2000). Acta Cryst. B56, 882-892.], 2001[Low, J. N., Cannon, D., Quesada, A., Marchal, A., Melguizo, M., Nogueras, M., Sánchez, A. & Glidewell, C. (2001). Acta Cryst. C57, 604-607.]). Compound (I)[link] thus differs from its isomer (VII)[link], which forms a 4:1 hydrate of overall composition 4C11H17N5O4·H2O.

[Scheme 1]

Within the mol­ecule of (I)[link] (Fig. 1[link]), the bond distances (Table 1[link]) in the heterocyclic ring and its immediate substituents are all very similar to the corresponding values in compounds (II)[link]–(VII)[link] and they provide evidence for extensive electronic polarization. In particular, the C5—N5 and N5—O5 distances in the C-nitroso group are very similar, the C4—C5 and C5—C6 bonds, which are formally single and double bonds, respectively, have distances identical within experimental uncertainly, and the C—N bonds involving atoms N1, N2 and N3, except for N2—C21, all have very similar distances, with the formally single C6—N6 bond shorter than the formally double N1=C2 bond. Taken together, these observations indicate a significant contribution to the overall mol­ecular–electronic structure from the polarized form (Ia). The C—O distances in the carboxyl group are consistent with the location of the acidic H atom deduced from the difference maps.

The combination of the high negative change on the nitroso O atom and the carboxylic acid functionality leads to a very short O—H⋯O hydrogen bond (Table 2[link]), which is also a feature of the analogues (II)[link]–(VI)[link], although not of (VII)[link], where the carboxyl group acts as hydrogen-bond donor to the water mol­ecule rather than to the nitroso O atom. The effect of the O—H⋯O hydrogen bond is to generate by translation a C(11) (Bernstein et al., 1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]) chain running parallel to the [001] direction (Fig. 2[link]). C(11) chains generated by translation also occur in (II)[link]–(IV)[link], while there are similar C(11) chains generated by a glide plane in (V)[link] and by a 21 screw axis in (VI)[link].

In addition, atom N2 in the mol­ecule at (x, y, z) acts as a hydrogen-bond donor to atom O4 in the mol­ecule at ([{1\over 2}] − x, 1 − y, [{1\over 2}] + z), so forming a C(6) chain running parallel to the [001] direction and generated by the 21 screw axis along ([{1\over 4}], [{1\over 2}], z) (Fig. 2[link]). The combination of the C(6) and C(11) chains along [001] generates a chain of edge-fused R33(17) rings (Fig. 2[link]).

Amino atom N6 acts as a double donor of hydrogen bonds. In addition to forming the intra­molecular S(6) motif characteristic of nitro­pyrimidine of this type, atom N6 in the mol­ecule at (x, y, z) acts as donor, via atom H6B, to carboxyl atom O22 in the mol­ecule at ([{1\over 2}] + x, [{1\over 2}] − y, 1 − z), so forming a C(9) chain running parallel to the [100] direction and generated by the 21 screw axis along (x, [{1\over 4}], [{1\over 2}]) (Fig. 3[link]). Thus, the inter­molecular N—H⋯O hydrogen bond with N2 as donor, acting alone, forms a chain along [001], while that with N6 as donor, again acting alone, forms a chain along [100]. However, the combination of the two inter­molecular N—H⋯O hydrogen bonds acting in concert forms a C44(26) chain running parallel to the [010] direction (Fig. 4[link]). The combination of the [100], [010] and [001] chains then generates a continuous three-dimensional framework.

The anhydrous analogues (II)[link]–(IV)[link] all form three-dimensional hydrogen-bonded frameworks, but these differ in the details of their formation from the framework in (I)[link] (Low et al., 1999[Low, J. N., Godino, M. L., López, R., Pérez, A., Melguizo, M. & Cobo, J. (1999). Acta Cryst. C55, 1727-1730.], 2000[Low, J. N., López. M. D., Arranz Mascarós, P., Cobo Domingo, J., Godino, M. L., López Garzón, R., Gutiérrez, M. D., Melguizo, M., Ferguson, G. & Glidewell, C. (2000). Acta Cryst. B56, 882-892.]). Similarly, the hydrates (V)[link]–(VII)[link] all form three-dimensional frameworks, again all of different construction (Low et al., 1997[Low, J. N., Ferguson, G., López, R., Arranz, P., Cobo, J., Melguizo, M., Nogueras, M. & Sánchez, A. (1997). Acta Cryst. C53, 890-892.], 2000[Low, J. N., López. M. D., Arranz Mascarós, P., Cobo Domingo, J., Godino, M. L., López Garzón, R., Gutiérrez, M. D., Melguizo, M., Ferguson, G. & Glidewell, C. (2000). Acta Cryst. B56, 882-892.], 2001[Low, J. N., Cannon, D., Quesada, A., Marchal, A., Melguizo, M., Nogueras, M., Sánchez, A. & Glidewell, C. (2001). Acta Cryst. C57, 604-607.]).

[Figure 1]
Figure 1
The mol­ecule of (I)[link], showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2]
Figure 2
Stereoview of part of the crystal structure of (I)[link], showing the formation of a chain of edge-fused R33(17) rings along [001]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.
[Figure 3]
Figure 3
Part of the crystal structure of (I)[link], showing the formation of a C(9) chain along [100]. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions ([{1\over 2}] + x, [{1\over 2}] − y, 1 − z) and (x − [{1\over 2}], [{1\over 2}] − y, 1 − z), respectively.
[Figure 4]
Figure 4
Stereoview of part of the crystal structure of (I)[link], showing the formation of a C44(26) chain along [010]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.

Experimental

The title compound was prepared by adding a suspension of 6-amino-3,4-dihydro-3-methyl-2-meth­oxy-5-nitroso-4-oxopyrimidine (5.00 g, 27.17 mmol) in acetonitrile (100 ml) to a suspension of L-leucine [(S)-2-amino-4-methyl­pentanoic acid; 3.90 g, 29.73 mmol] in aqueous KOH (60 ml of 0.5 M solution; 30.0 mmol). The mixture was stirred at 343 K for 1 h. The solution was then cooled to ambient temperature and the pH was adjusted to 3.0 by dropwise addition of aqueous HCl (0.1 M). After 8 h at room temperature, the orange crystalline solid which formed was collected by filtration and washed successively with water, ethanol and diethyl ether to yield the title compound (4.70 g, 16.60 mmol, 61%). Analysis found: C 45.9, H 5.6, N 25.1%; C11H17N5O4 requires: C 46.6, H, 6.0, N 24.7%.

Crystal data

  • C11H17N5O4

  • Mr = 283.30

  • Orthorhombic, P 21 21 21

  • a = 9.4395 (2) Å

  • b = 13.1565 (3) Å

  • c = 10.9581 (2) Å

  • V = 1360.89 (5) Å3

  • Z = 4

  • Dx = 1.383 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 1795 reflections

  • θ = 3.2–27.5°

  • μ = 0.11 mm−1

  • T = 120 (2) K

  • Lath, orange

  • 0.20 × 0.10 × 0.08 mm
Data collection

  • Nonius KappaCCD area-detector diffractometer

  • φ and ω scans

  • Absorption correction: multi-scan(SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.])Tmin = 0.982, Tmax = 0.992

  • 22570 measured reflections

  • 1795 independent reflections

  • 1644 reflections with I > 2σ(I)

  • Rint = 0.024

  • θmax = 27.5°

  • h = −12 → 12

  • k = −17 → 16

  • l = −14 → 14
Refinement

  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.106

  • S = 1.06

  • 1795 reflections

  • 185 parameters

  • H-atom parameters constrained

  • w = 1/[σ2(Fo2) + (0.0702P)2 + 0.2932P] where P = (Fo2 + 2Fc2)/3

  • (Δ/σ)max = 0.001

  • Δρmax = 0.32 e Å−3

  • Δρmin = −0.30 e Å−3

Table 1
Selected bond lengths (Å)[link]

N1—C2 1.324 (3)
C2—N3 1.379 (2)
N3—C4 1.407 (2)
C4—C5 1.459 (3)
C5—C6 1.455 (3)
C6—N1 1.345 (2)
C22—O21 1.308 (3)
C2—N2 1.337 (3)
N3—C3 1.466 (3)
C4—O4 1.222 (2)
C5—N5 1.328 (3)
N5—O5 1.297 (2)
C6—N6 1.312 (3)
C22—O22 1.215 (3)

Table 2
Hydrogen-bond geometry (Å, °)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O21—H21A⋯O5i 0.84 1.67 2.494 (2) 166
N2—H2⋯O4ii 0.88 2.15 2.958 (2) 153
N6—H6A⋯O22iii 0.88 2.07 2.924 (2) 163
N6—H6B⋯O5 0.88 1.97 2.598 (2) 127
Symmetry codes: (i) x, y, z+1; (ii) [{\script{1\over 2}}-x, 1-y, z+{\script{1\over 2}}]; (iii) [x+{\script{1\over 2}}, {\script{1\over 2}}-y, 1-z].

The space group P212121 was uniquely assigned from the systematic absences. All H atoms were located from difference maps and were subsequently treated as riding atoms, with C—H distances of 0.98 (CH3), 0.99 (CH2) or 1.00 Å (CH), N—H distances of 0.88 Å and O—H distances of 0.84 Å, and with Uiso(H) = 1.2Ueq(C,N), 1.5Ueq(C) for the methyl groups and 1.5Ueq(O). In the absence of significant anomalous scattering, the Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]) parameter was indeterminate (Flack & Bernardinelli, 2000[Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148.]), and hence the Friedel-equivalent reflections were merged prior to the final refinements. The correct absolute configuration was set by reference to the known absolute configuration of the L-leucine employed in the synthesis.

Data collection: COLLECT (Hooft, 1999[Hooft, R. W. W. (1999). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003[McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography Centre, Chemistry Department, NUI Galway, Ireland.]) and SHELXS97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); molecular graphics: PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999[Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S0108270105024406/sk1862sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S0108270105024406/sk1862Isup2.hkl


Comment top

We report here the structure of the title compound, (I), which we briefly compare with the structures of its valine, methionine and threonine analogues, (II)–(IV), respectively (Low et al., 1999, 2000), and those of the glycine, serine and isoleucine analogues, (V)–(VII), respectively, which all crystallize as hydrates (Low et al., 1997, 2000, 2001). Compound (I) thus differs from its isomer (VII), which forms a 4:1 hydrate of overall composition (C11H17N5O4)4·H2O.

Within the molecule of (I) (Fig. 1), the bond distances (Table 1) in the heterocyclic ring and its immediate substituents are all very similar to the corresponding values in compounds (II)–(VII) and they provide evidence for extensive electronic polarization. In particular, the C5—N5 and N5—O5 distances in the C-nitroso group are very similar, the C4—C5 and C5—C6 bonds, which are formally single and double bonds, respectively, have distances identical within experimental uncertainly, and the C—N bonds involving atoms N1, N2 and N3, except for N2—C21, all have very similar distances, with the formally single C6—N6 bond shorter than the formally double N1—C2 bond. Taken together, these observations indicate a significant contribution to the overall molecular-electronic structure from the polarized form (Ia). The C—O distances in the carboxyl group are consistent with the location of the acidic H atom deduced from the difference maps.

The combination of the high negative change on the nitroso O atom and the carboxylic acid functionality leads to a very short O—H···O hydrogen bond (Table 2), which is also a feature of the analogues (II)–(VI), although not of (VII), where the carboxyl group acts as hydrogen-bond donor to the water molecule rather than to the nitroso O atom. The effect of the O—H···O hydrogen bond is to generate by translation a C(11) (Bernstein et al., 1995) chain running parallel to the [001] direction (Fig. 2). C(11) chains generated by translation also occur in (II)–(IV), while there are similar C(11) chains generated by a glide plane in (V) and by a 21 screw axis in (VI).

In addition, atom N2 in the molecule at (x, y, z) acts as hydrogen-bond donor to atom O4 in the molecule at (1/2 − x, 1 − y, 1/2 + z), so forming a C(6) chain running parallel to the [001] direction and generated by the 21 screw axis along (1/4, 1/2, z) (Fig. 2). The combination of the C(6) and C(11) chains along [001] generates a chain of edge-fused R33(17) rings (Fig. 2).

The amino atom N6 acts as a double donor of hydrogen bonds. In addition to forming the intramolecular S(6) motif characteristic of nitropyrimidine of this type, atom N6 in the molecule at (x, y, z) acts as donor, via atom H6B, to carboxyl atom O22 in the molecule at (1/2 + x, 1/2 − y, 1 − z), so forming a C(9) chain running parallel to the [100] direction and generated by the 21 screw axis along (x, 1/4, 1/2) (Fig. 3). Thus, the intermolecular N—H···O hydrogen bond with N2 as donor, acting alone, forms a chain along [001], while that with N6 as donor, again acting alone, forms a chain along [100]. However, the combination of the two intermolecular N—H···O hydrogen bonds acting in concert forms a C22(13) chain running parallel to the [010] direction (Fig. 4). The combination of the [100], [010] and [001] chains then generates a continuous three-dimensional framework.

The anhydrous analogues (II)–(IV) all form three-dimensional hydrogen-bonded frameworks, but these differ in the details of their formation from the framework in (I) (Low et al., 1999, 2000). Similarly, the hydrates (V)–(VII) all form three-dimensional frameworks, again all of different construction (Low et al., 1997, 2000, 2001).

Experimental top

The title compound was prepared by adding a suspension of 6-amino-3,4-dihydro-3-methyl-2-methoxy-5-nitroso-4-oxopyrimidine (5.00 g, 27.17 mmol) in acetonitrile (100 ml) to a suspension of L-leucine [(S)-2-amino-4-methylpentanoic acid; 3.90 g, 29.73 mmol] in aqueous KOH (60 ml of 0.5 M solution; 30.0 mmol). The mixture was stirred at 343 K for 1 h. The solution was then cooled to ambient temperature and the pH was adjusted to 3.0 by dropwise addition of aqueous HCl (0.1 M). After 8 h at room temperature, the orange crystalline solid which formed was collected by filtration and washed successively with water, ethanol and diethyl ether to yield the title compound (4.70 g, 16.60 mmol, 61%). Analysis: found C 45.9, H 5.6, N 25.1%; C11H17N5O4 requires C 46.6, H, 6.0, N 24.7%.

Refinement top

The space group P212121 was uniquely assigned from the systematic absences. All H atoms were located from difference maps and were subsequently treated as riding atoms, with C—H distances of 0.98 Å (CH3), 0.99 Å (CH2) or 1.00 Å (CH), N—H distances of 0.88 Å and O—H distances of 0.84 Å, and with Uiso(H) = 1.2Ueq(C,N), or 1.5Ueq(C) for the methyl groups, and 1.5Ueq(O). In the absence of significant anomalous scattering, the Flack parameter (Flack, 1983) was indeterminate (Flack & Bernardinelli, 2000), and hence the Friedel-equivalent reflections were merged prior to the final refinements. The correct absolute configuration was set by reference to the known absolute configuration of the L-leucine employed in the synthesis.

Computing details top

Data collection: COLLECT (Hooft, 1999); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

Figures top
[Figure 1] Fig. 1. The molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. Stereoview of part of the crystal structure of (I), showing the formation of a chain of edge-fused R33(17) rings along [001]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.
[Figure 3] Fig. 3. Part of the crystal structure of (I), showing the formation of a C(9) chain along [100]. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (1/2 + x, 1/2 − y, 1 − z) and (x − 1/2, 1/2 − y, 1 − z), respectively.
[Figure 4] Fig. 4. Stereoview of part of the crystal structure of (I), showing the formation of a C22(13) chain along [010]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.
N-(6-Amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)leucine top
Crystal data top
C11H17N5O4F(000) = 600
Mr = 283.30Dx = 1.383 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1795 reflections
a = 9.4395 (2) Åθ = 3.2–27.5°
b = 13.1565 (3) ŵ = 0.11 mm−1
c = 10.9581 (2) ÅT = 120 K
V = 1360.89 (5) Å3Lath, orange
Z = 40.20 × 0.10 × 0.08 mm
Data collection top
Nonius KappaCCD area-detector
diffractometer		1795 independent reflections
Radiation source: Bruker Nonius FR91 rotating anode1644 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 3.2°
ϕ and ω scansh = −12→12
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		k = −17→16
Tmin = 0.982, Tmax = 0.992l = −14→14
22570 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.106H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0702P)2 + 0.2932P]
where P = (Fo2 + 2Fc2)/3
1795 reflections(Δ/σ)max = 0.001
185 parametersΔρmax = 0.32 e Å−3
0 restraintsΔρmin = −0.30 e Å−3
Crystal data top
C11H17N5O4V = 1360.89 (5) Å3
Mr = 283.30Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.4395 (2) ŵ = 0.11 mm−1
b = 13.1565 (3) ÅT = 120 K
c = 10.9581 (2) Å0.20 × 0.10 × 0.08 mm
Data collection top
Nonius KappaCCD area-detector
diffractometer		1795 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		1644 reflections with I > 2σ(I)
Tmin = 0.982, Tmax = 0.992Rint = 0.024
22570 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.106H-atom parameters constrained
S = 1.06Δρmax = 0.32 e Å−3
1795 reflectionsΔρmin = −0.30 e Å−3
185 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O40.17512 (16)0.42095 (12)0.10904 (13)0.0204 (3)
O50.44571 (17)0.22692 (12)−0.04938 (13)0.0223 (3)
O210.52219 (17)0.26060 (13)0.73658 (14)0.0267 (4)
O220.31846 (16)0.33891 (12)0.68781 (14)0.0228 (3)
N10.48741 (18)0.29307 (13)0.31541 (15)0.0169 (4)
N20.41713 (17)0.39787 (13)0.47036 (15)0.0168 (4)
N30.28601 (17)0.40236 (13)0.29227 (15)0.0163 (4)
N50.36042 (19)0.29343 (14)−0.00210 (16)0.0189 (4)
N60.56944 (19)0.19659 (14)0.15928 (16)0.0197 (4)
C20.3981 (2)0.36236 (16)0.35723 (18)0.0156 (4)
C30.1785 (2)0.46433 (17)0.35373 (19)0.0199 (4)
C40.2697 (2)0.38014 (15)0.16743 (18)0.0160 (4)
C50.3696 (2)0.30631 (16)0.11780 (18)0.0163 (4)
C60.4761 (2)0.26289 (15)0.19851 (18)0.0160 (4)
C210.5202 (2)0.35525 (16)0.55548 (18)0.0171 (4)
C220.4411 (2)0.31676 (16)0.66712 (18)0.0192 (4)
C230.6301 (2)0.43523 (18)0.5961 (2)0.0226 (5)
C240.7219 (2)0.47950 (19)0.4938 (2)0.0312 (6)
C250.8003 (3)0.3981 (2)0.4241 (3)0.0403 (7)
C260.8255 (3)0.5559 (2)0.5493 (3)0.0466 (8)
H20.36500.44950.49470.020*
H3A0.14120.42710.42420.030*
H3B0.10110.47910.29680.030*
H3C0.22130.52820.38130.030*
H6A0.63560.17390.20890.024*
H6B0.56590.17480.08340.024*
H210.57030.29710.51560.021*
H21A0.48320.25250.80480.040*
H23A0.57930.49180.63660.027*
H23B0.69330.40380.65760.027*
H240.65870.51650.43550.037*
H25A0.86190.42990.36300.060*
H25B0.73200.35350.38320.060*
H25C0.85800.35810.48080.060*
H26A0.89350.52000.60140.070*
H26B0.77310.60560.59830.070*
H26C0.87650.59120.48390.070*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O40.0167 (7)0.0240 (8)0.0205 (7)0.0030 (6)−0.0045 (6)0.0027 (6)
O50.0255 (7)0.0265 (8)0.0149 (7)0.0055 (6)−0.0004 (6)−0.0023 (6)
O210.0243 (8)0.0404 (10)0.0155 (7)0.0082 (8)0.0022 (6)0.0064 (7)
O220.0168 (7)0.0303 (8)0.0212 (7)−0.0001 (6)0.0043 (6)0.0025 (7)
N10.0144 (8)0.0219 (8)0.0144 (7)0.0028 (7)−0.0015 (7)−0.0001 (7)
N20.0134 (8)0.0223 (8)0.0147 (8)0.0031 (7)−0.0008 (7)−0.0004 (7)
N30.0105 (8)0.0219 (8)0.0164 (8)0.0023 (7)−0.0006 (7)−0.0011 (7)
N50.0181 (8)0.0222 (9)0.0164 (8)0.0005 (7)−0.0010 (7)−0.0008 (8)
N60.0181 (9)0.0262 (9)0.0147 (8)0.0068 (7)−0.0047 (7)−0.0018 (7)
C20.0124 (9)0.0198 (10)0.0145 (9)−0.0004 (8)0.0010 (7)0.0015 (8)
C30.0141 (9)0.0254 (11)0.0202 (10)0.0049 (8)0.0006 (8)0.0006 (8)
C40.0133 (9)0.0196 (10)0.0151 (9)−0.0028 (8)−0.0013 (8)0.0028 (8)
C50.0135 (9)0.0211 (10)0.0144 (9)−0.0007 (8)0.0015 (8)0.0027 (8)
C60.0131 (9)0.0205 (10)0.0144 (9)0.0002 (8)−0.0005 (8)0.0013 (8)
C210.0132 (9)0.0241 (10)0.0141 (9)0.0018 (8)−0.0020 (8)−0.0010 (8)
C220.0193 (10)0.0238 (11)0.0145 (9)−0.0010 (8)−0.0011 (8)−0.0025 (8)
C230.0159 (9)0.0286 (11)0.0234 (11)−0.0010 (9)−0.0022 (8)−0.0063 (9)
C240.0191 (12)0.0346 (13)0.0400 (14)−0.0052 (10)0.0013 (11)0.0011 (12)
C250.0253 (12)0.0529 (17)0.0426 (15)−0.0084 (12)0.0119 (12)−0.0090 (13)
C260.0301 (14)0.0379 (15)0.072 (2)−0.0082 (12)0.0000 (15)−0.0057 (15)
Geometric parameters (Å, º) top
N1—C21.324 (3)O21—H21A0.84
C2—N31.379 (2)C23—C241.532 (3)
N3—C41.407 (2)C23—H23A0.99
C4—C51.459 (3)C23—H23B0.99
C5—C61.455 (3)C24—C251.509 (4)
C6—N11.345 (2)C24—C261.529 (4)
C22—O211.308 (3)C24—H241.00
C2—N21.337 (3)C25—H25A0.98
N3—C31.466 (3)C25—H25B0.98
C4—O41.222 (2)C25—H25C0.98
C5—N51.328 (3)C26—H26A0.98
N5—O51.297 (2)C26—H26B0.98
C6—N61.312 (3)C26—H26C0.98
C22—O221.215 (3)C3—H3A0.98
N2—C211.460 (2)C3—H3B0.98
N2—H20.88C3—H3C0.98
C21—C221.520 (3)N6—H6A0.88
C21—C231.543 (3)N6—H6B0.88
C21—H211.00
C2—N1—C6118.83 (17)C24—C25—H25C109.5
N1—C2—N2118.42 (18)H25A—C25—H25C109.5
N1—C2—N3124.94 (18)H25B—C25—H25C109.5
N2—C2—N3116.64 (18)C24—C26—H26A109.5
C2—N2—C21123.23 (17)C24—C26—H26B109.5
C2—N2—H2118.4H26A—C26—H26B109.5
C21—N2—H2118.4C24—C26—H26C109.5
N2—C21—C22108.35 (16)H26A—C26—H26C109.5
N2—C21—C23111.74 (17)H26B—C26—H26C109.5
C22—C21—C23108.98 (16)C2—N3—C4120.43 (17)
N2—C21—H21109.2C2—N3—C3120.40 (16)
C22—C21—H21109.2C4—N3—C3119.10 (16)
C23—C21—H21109.2N3—C3—H3A109.5
C22—O21—H21A109.5N3—C3—H3B109.5
O22—C22—O21125.8 (2)H3A—C3—H3B109.5
O22—C22—C21122.6 (2)N3—C3—H3C109.5
O21—C22—C21111.67 (18)H3A—C3—H3C109.5
C24—C23—C21115.36 (18)H3B—C3—H3C109.5
C24—C23—H23A108.4O4—C4—N3119.84 (19)
C21—C23—H23A108.4O4—C4—C5124.71 (18)
C24—C23—H23B108.4N3—C4—C5115.44 (17)
C21—C23—H23B108.4N5—C5—C6126.6 (2)
H23A—C23—H23B107.5N5—C5—C4114.29 (18)
C25—C24—C26110.7 (2)C6—C5—C4118.77 (17)
C25—C24—C23112.2 (2)O5—N5—C5116.16 (19)
C26—C24—C23108.7 (2)N6—C6—N1117.04 (18)
C25—C24—H24108.4N6—C6—C5121.70 (18)
C26—C24—H24108.4N1—C6—C5121.17 (18)
C23—C24—H24108.4C6—N6—H6A120.0
C24—C25—H25A109.5C6—N6—H6B120.0
C24—C25—H25B109.5H6A—N6—H6B120.0
H25A—C25—H25B109.5
C6—N1—C2—N2−174.70 (18)N2—C2—N3—C3−12.0 (3)
C6—N1—C2—N34.6 (3)C2—N3—C4—O4−175.51 (18)
N1—C2—N2—C21−7.9 (3)C3—N3—C4—O47.6 (3)
N3—C2—N2—C21172.75 (17)C2—N3—C4—C55.5 (3)
C2—N2—C21—C22−119.5 (2)C3—N3—C4—C5−171.45 (17)
C2—N2—C21—C23120.4 (2)O4—C4—C5—N56.8 (3)
N2—C21—C22—O22−13.7 (3)N3—C4—C5—N5−174.26 (18)
C23—C21—C22—O22108.1 (2)O4—C4—C5—C6−179.3 (2)
N2—C21—C22—O21167.89 (17)N3—C4—C5—C6−0.3 (3)
C23—C21—C22—O21−70.3 (2)C6—C5—N5—O57.9 (3)
N2—C21—C23—C24−61.9 (2)C4—C5—N5—O5−178.71 (16)
C22—C21—C23—C24178.39 (19)C2—N1—C6—N6177.82 (19)
C21—C23—C24—C25−56.5 (3)C2—N1—C6—C51.1 (3)
C21—C23—C24—C26−179.32 (19)N5—C5—C6—N6−6.5 (3)
N1—C2—N3—C4−8.1 (3)C4—C5—C6—N6−179.61 (19)
N2—C2—N3—C4171.14 (18)N5—C5—C6—N1170.1 (2)
N1—C2—N3—C3168.75 (19)C4—C5—C6—N1−3.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O21—H21A···O5i0.841.672.494 (2)166
N2—H2···O4ii0.882.152.958 (2)153
N6—H6A···O22iii0.882.072.924 (2)163
N6—H6B···O50.881.972.598 (2)127
Symmetry codes: (i) x, y, z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x+1/2, −y+1/2, −z+1.

Experimental details

Crystal data
Chemical formulaC11H17N5O4
Mr283.30
Crystal system, space groupOrthorhombic, P212121
Temperature (K)120
a, b, c (Å)9.4395 (2), 13.1565 (3), 10.9581 (2)
V (Å3)1360.89 (5)
Z4
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.20 × 0.10 × 0.08
Data collection
DiffractometerNonius KappaCCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.982, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections		22570, 1795, 1644
Rint0.024
(sin θ/λ)max (Å−1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.106, 1.06
No. of reflections1795
No. of parameters185
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.32, −0.30

Computer programs: COLLECT (Hooft, 1999), DENZO (Otwinowski & Minor, 1997) and COLLECT, DENZO and COLLECT, OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997), OSCAIL and SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).

Selected bond lengths (Å) top
N1—C21.324 (3)C2—N21.337 (3)
C2—N31.379 (2)N3—C31.466 (3)
N3—C41.407 (2)C4—O41.222 (2)
C4—C51.459 (3)C5—N51.328 (3)
C5—C61.455 (3)N5—O51.297 (2)
C6—N11.345 (2)C6—N61.312 (3)
C22—O211.308 (3)C22—O221.215 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O21—H21A···O5i0.841.672.494 (2)166
N2—H2···O4ii0.882.152.958 (2)153
N6—H6A···O22iii0.882.072.924 (2)163
N6—H6B···O50.881.972.598 (2)127
Symmetry codes: (i) x, y, z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x+1/2, −y+1/2, −z+1.
 

Acknowledgements

The X-ray data were collected at the EPSRC X-ray Crystallographic Service, University of Southampton, England.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
 First citationFerguson, G. (1999). PRPKAPPA. University of Guelph, Canada.  Google Scholar
 First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationFlack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143–1148.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationHooft, R. W. W. (1999). COLLECT. Nonius BV, Delft, The Netherlands.  Google Scholar
 First citationLow, J. N., Cannon, D., Quesada, A., Marchal, A., Melguizo, M., Nogueras, M., Sánchez, A. & Glidewell, C. (2001). Acta Cryst. C57, 604–607.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationLow, J. N., Ferguson, G., López, R., Arranz, P., Cobo, J., Melguizo, M., Nogueras, M. & Sánchez, A. (1997). Acta Cryst. C53, 890–892.  CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationLow, J. N., Godino, M. L., López, R., Pérez, A., Melguizo, M. & Cobo, J. (1999). Acta Cryst. C55, 1727–1730.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationLow, J. N., López. M. D., Arranz Mascarós, P., Cobo Domingo, J., Godino, M. L., López Garzón, R., Gutiérrez, M. D., Melguizo, M., Ferguson, G. & Glidewell, C. (2000). Acta Cryst. B56, 882–892.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationMcArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography Centre, Chemistry Department, NUI Galway, Ireland.  Google Scholar
 First citationOtwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.  Google Scholar
 First citationSheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.  Google Scholar
 First citationSheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.  Google Scholar
 First citationSpek, A. L. (2003). J. Appl. Cryst. 36, 7–13.  Web of Science CrossRef CAS IUCr Journals Google Scholar

© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296
Volume 61| Part 9| September 2005| Pages o548-o550
doi:10.1107/S0108270105024406
Follow Acta Cryst. C
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS