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

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 64| Part 6| June 2008| Pages o1107-o1108

Redetermination of 3-de­aza­uracil

aChemistry Department, "Sapienza" University of Rome, P.le A. Moro, 5, I-00185 Rome, Italy
*Correspondence e-mail: g.portalone@caspur.it

(Received 8 May 2008; accepted 14 May 2008; online 17 May 2008)

The crystal structure of the title compound, 4-hydr­oxy-2-pyridone, C5H5NO2, which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, 1688–1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of π-electron density through the mol­ecule. In the crystal structure, the mol­ecules are connected into chains by two strong O—H⋯O and N—H⋯O hydrogen bonds between the OH and NH groups and the carbonyl O atom.

Related literature

For previous structure determinations, see: Low & Wilson (1983[Low, J. N. & Wilson, C. C. (1983). Acta Cryst. C39, 1688-1690.]); Wilson et al. (1992[Wilson, C. C., Keen, D. & Stewart, N. S. (1992). J. Chem. Soc. Chem. Commun. pp. 1160-1162.]); Wilson (1994[Wilson, C. C. (1994). J. Chem. Crystallogr. 24, 371-373.], 2001[Wilson, C. C. (2001). J. Mol. Struct. 560, 239-246.]). For related literature, see: Stewart & Jensen (1967[Stewart, R. F. & Jensen, L. H. (1967). Acta Cryst. 23, 1102-1105.]): Robins et al. (1969[Robins, M. J., Currie, B. L., Robins, L. K. & Bloch, A. (1969). Proc. Am. Assoc. Cancer Res. 10, 73-79.]); Schwalbe & Saenger (1973[Schwalbe, C. H. & Saenger, W. (1973). Acta Cryst. B29, 61-69.]). For a general approach to the use of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supra­molecular reagents, see: Portalone et al. (1999[Portalone, G., Bencivenni, L., Colapietro, M., Pieretti, A. & Ramondo, F. (1999). Acta Chem. Scand. 53, 57-68.]); Portalone & Colapietro (2004[Portalone, G. & Colapietro, M. (2004). Acta Cryst. E60, o1165-o1166.], 2007[Portalone, G. & Colapietro, M. (2007). Acta Cryst. C63, o181-o184.] and references therein). For high-order refinement, see: Hirshfeld (1992[Hirshfeld, F. L. (1992). Accurate Molecular Structures. Their Determination and Importance, edited by A. Domenicano & I. Hargittai, pp 252-253. New York: Oxford University Press.]). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]); Motherwell et al. (1999[Motherwell, W. D. S., Shields, G. P. & Allen, F. H. (1999). Acta Cryst. B55, 1044-1056.]).

[Scheme 1]

Experimental

Crystal data
  • C5H5NO2

  • Mr = 111.10

  • Orthorhombic, P 21 21 21

  • a = 5.3393 (1) Å

  • b = 8.6454 (1) Å

  • c = 11.2652 (2) Å

  • V = 520.01 (1) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 298 (2) K

  • 0.20 × 0.15 × 0.15 mm

Data collection
  • Oxford Diffraction Xcalibur S CCD diffractometer

  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.924, Tmax = 0.983

  • 77963 measured reflections

  • 1085 independent reflections

  • 1043 reflections with I > 2σ(I)

  • Rint = 0.025

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.112

  • S = 1.10

  • 1085 reflections

  • 93 parameters

  • All H-atom parameters refined

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.13 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2⋯O1i 0.97 (2) 1.62 (2) 2.5886 (16) 171.3 (16)
N1—H1⋯O1ii 0.89 (2) 1.94 (2) 2.8024 (14) 160.6 (15)
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+2].

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

The crystal structure of the modified nucleic acid base 3-deazauracil, 3deazur, has been the subject of several structural studies using XD and ND techniques in order to localise the H atoms as accurately as possible and to define their functions; the very strong hydrogen bond is found in the structure, as also observed in the parent nucleoside (3-deazauridine) (Schwalbe & Saenger, 1973). This interaction might play a relevant role in the powerful cytostatic properties of the nucleoside (Robins et al., 1969). In the first crystal structure determination (XRD, Low & Wilson, 1983) 713 unique reflections were collected at ambient temperature on an automatic diffractometer. H atoms were localized by a difference Fourier map with the exception of the hydroxyl H2, and all but H1, which was fixed at its position as obtained from the difference map, were included as riding atoms at calculated positions. The final refinement led to R = 0.065, and standard deviations of 0.004Å in C—C bond lengths and 0.3° in bond angles. Subsequently, a joint X-ray and neutron diffraction blocked-matrix refinement, based on limited neutron single-crystal data (80) combined with 674 X-ray data, was reported (X—N, Wilson et al., 1992). This calculation, involving 94 refined parameters with all but the H atoms treated anisotropically, led to R = 0.075. Two years later, in a pulsed neutron single-crystal study (PND, Wilson, 1994), 119 parameters and 447 unique reflections [with I > 5σ(I)] yielded an R = 0.071, with a poor agreement between the geometrical parameters obtained from this and the previous experiments (e.g. the N1–C2 bond distance is 1.332 (6) in PND, 1.362 (6) in X—N and 1.360 (4) in XRD, Table 2). Finally, in a neutron single-crystal diffraction experiment at 100 K using a sample containing one crystal of 3-deazauracil and one of lead hydrogen arsenate (LTND, Wilson, 2001). 118 parameters and 1426 unique reflections [with I > 2σ(I)] yielded an R = 0.078. Again, some discrepancies between the geometrical parameters from this study and those from the previous structural determinations remain unsolved (e.g. the C4–O2 bond distance is 1.322 (4) in LTND, 1.345 (8) in PND, 1.346 (5) in X—N and 1.319 (3) in XRD, Table 2). and it was suggested the presence of tautomeric mixing.

As a part of a more general study of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents (Portalone et al., 1999; Portalone & Colapietro, 2004, 2007), and in view of the importance of the title compound, this paper reports a redetermination of the crystal structure with greater precision and accuracy.

The asymmetric unit of (I) comprises a planar independent molecule as 4-enol tautomer (Fig. 1). A comparison of the molecular geometry of 3-deazur (high θ refinement) with that reported for uracil (Stewart & Jensen, 1967), in conjunction with a detailed examination of Fourier maps, exclude the presence of tautomeric mixing (4-enol and 2-enol tautomers) and suggests some degree of delocalization of π-electron density through the 4-enol tautomer, which in turn strengthens the existing intermolecular hydrogen bonds (Portalone et al., 1999). Analysis of the crystal packing of (I) shows (Table 1) that the structure is stabilized by two strong independent intermolecular O—H···O and N—H···O interactions of descriptor C11(3) (Etter et al., 1990; Bernstein et al., 1995; Motherwell et al., 1999) between OH and NH moieties and the carbonyl O atom (O1i and O1ii) [symmetry code: (i) -x + 1, y - 1/2, -z + 3/2; (ii) x + 1/2, -y + 1/2, -z + 2] which link the molecules into chains (Fig. 2).

Related literature top

For previous structure determinations, see: Low & Wilson (1983); Wilson et al. (1992); Wilson (1994, 2001). For related literature, see: Stewart & Jensen (1967): Robins et al. (1969); Schwalbe & Saenger (1973). For a general approach to the use of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents, see: Portalone et al. (1999); Portalone & Colapietro (2004, 2007 and references therein). For high-order refinement, see: Hirshfeld (1992). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990); Bernstein et al. (1995); Motherwell et al. (1999).

Experimental top

3-deazauracil (0.1 mmol, Sigma Aldrich at 97% purity) was dissolved in water (9 mL) and heated under reflux for 3 h. After cooling the solution to an ambient temperature, crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of a solvent after a few days.

Refinement top

All H atoms were found in a difference map and refined isotropically. In the high θ refinement (Hirshfeld, 1992) 624 reflections having Hmin = 0.9 Å-1 and 74 parameters yielded the following results: R1 = 0.0339, wR2 = 0.0679, S = 1.190. H atoms were kept fixed at values deduced from the conventional refinement. In the absence of significant anomalous scattering in this light-atom study, Friedel pairs were merged.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level.
[Figure 2] Fig. 2. Crystal packing diagram for (I) viewed approximately down a. All atoms are shown as small spheres of arbitrary radii. Hydrogen bonding is indicated by dashed lines.
4-hydroxy-2-pyridone top
Crystal data top
C5H5NO2Dx = 1.419 Mg m3
Mr = 111.10Melting point: 477 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 43477 reflections
a = 5.3393 (1) Åθ = 2.9–32.3°
b = 8.6454 (1) ŵ = 0.11 mm1
c = 11.2652 (2) ÅT = 298 K
V = 520.01 (1) Å3Tablets, colourless
Z = 40.20 × 0.15 × 0.15 mm
F(000) = 232
Data collection top
Oxford Diffraction Xcalibur S CCD
diffractometer
1085 independent reflections
Radiation source: Enhance (Mo) X-ray source1043 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
Detector resolution: 16.0696 pixels mm-1θmax = 32.4°, θmin = 3.0°
ω and ϕ scansh = 87
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
k = 1312
Tmin = 0.924, Tmax = 0.983l = 1616
77963 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)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112All H-atom parameters refined
S = 1.10 w = 1/[σ2(Fo2) + (0.0765P)2 + 0.037P]
where P = (Fo2 + 2Fc2)/3
1085 reflections(Δ/σ)max < 0.001
93 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = 0.13 e Å3
Crystal data top
C5H5NO2V = 520.01 (1) Å3
Mr = 111.10Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.3393 (1) ŵ = 0.11 mm1
b = 8.6454 (1) ÅT = 298 K
c = 11.2652 (2) Å0.20 × 0.15 × 0.15 mm
Data collection top
Oxford Diffraction Xcalibur S CCD
diffractometer
1085 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
1043 reflections with I > 2σ(I)
Tmin = 0.924, Tmax = 0.983Rint = 0.025
77963 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.112All H-atom parameters refined
S = 1.10Δρmax = 0.22 e Å3
1085 reflectionsΔρmin = 0.13 e Å3
93 parameters
Special details top

Experimental. (CrysAlis RED; Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) (compiled Oct 18 2006,16:28:17) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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
O10.5630 (2)0.19169 (12)0.88298 (9)0.0418 (3)
O20.8080 (2)0.31430 (11)0.76490 (11)0.0423 (3)
H20.667 (4)0.302 (3)0.711 (2)0.056 (6)*
N10.9062 (2)0.07483 (13)0.96127 (9)0.0329 (2)
H10.935 (5)0.163 (3)1.000 (2)0.052 (6)*
C20.7058 (2)0.07410 (13)0.88575 (10)0.0289 (2)
C30.6712 (2)0.06036 (13)0.81646 (10)0.0287 (2)
H30.523 (4)0.072 (2)0.763 (2)0.056 (6)*
C40.8348 (2)0.18253 (14)0.82563 (11)0.0299 (3)
C51.0428 (3)0.17405 (17)0.90371 (13)0.0363 (3)
H51.161 (4)0.263 (3)0.9032 (17)0.054 (6)*
C61.0714 (3)0.04424 (17)0.96924 (12)0.0362 (3)
H61.212 (4)0.021 (2)1.0225 (18)0.045 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0522 (6)0.0310 (4)0.0421 (5)0.0126 (5)0.0071 (5)0.0089 (4)
O20.0473 (6)0.0304 (4)0.0493 (5)0.0056 (5)0.0048 (5)0.0116 (4)
N10.0378 (5)0.0301 (5)0.0308 (5)0.0046 (4)0.0035 (4)0.0040 (4)
C20.0330 (5)0.0261 (5)0.0277 (5)0.0007 (5)0.0004 (4)0.0020 (4)
C30.0291 (5)0.0270 (5)0.0301 (5)0.0014 (4)0.0025 (4)0.0041 (4)
C40.0307 (6)0.0269 (5)0.0321 (5)0.0003 (5)0.0013 (4)0.0020 (4)
C50.0306 (6)0.0352 (6)0.0432 (6)0.0044 (5)0.0041 (5)0.0007 (5)
C60.0318 (6)0.0400 (6)0.0369 (6)0.0037 (5)0.0070 (5)0.0015 (5)
Geometric parameters (Å, º) top
O1—C21.2713 (15)C3—C41.3746 (16)
O2—C41.3366 (15)C3—H31.00 (2)
O2—H20.97 (2)C4—C51.4187 (19)
N1—C61.3587 (17)C5—C61.3519 (19)
N1—C21.3668 (17)C5—H51.00 (2)
N1—H10.89 (2)C6—H60.98 (2)
C2—C31.4123 (15)
C4—O2—H2107.8 (14)O2—C4—C3123.25 (11)
C6—N1—C2123.08 (10)O2—C4—C5116.44 (11)
C6—N1—H1120.3 (16)C3—C4—C5120.30 (11)
C2—N1—H1116.2 (16)C6—C5—C4118.02 (12)
O1—C2—N1118.75 (10)C6—C5—H5125.0 (13)
O1—C2—C3124.48 (12)C4—C5—H5117.0 (13)
N1—C2—C3116.76 (11)C5—C6—N1121.30 (12)
C4—C3—C2120.51 (11)C5—C6—H6126.0 (12)
C4—C3—H3118.3 (12)N1—C6—H6112.6 (12)
C2—C3—H3121.1 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···O1i0.97 (2)1.62 (2)2.5886 (16)171.3 (16)
N1—H1···O1ii0.89 (2)1.94 (2)2.8024 (14)160.6 (15)
Symmetry codes: (i) x+1, y1/2, z+3/2; (ii) x+1/2, y+1/2, z+2.

Experimental details

Crystal data
Chemical formulaC5H5NO2
Mr111.10
Crystal system, space groupOrthorhombic, P212121
Temperature (K)298
a, b, c (Å)5.3393 (1), 8.6454 (1), 11.2652 (2)
V3)520.01 (1)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.20 × 0.15 × 0.15
Data collection
DiffractometerOxford Diffraction Xcalibur S CCD
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2006)
Tmin, Tmax0.924, 0.983
No. of measured, independent and
observed [I > 2σ(I)] reflections
77963, 1085, 1043
Rint0.025
(sin θ/λ)max1)0.753
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.112, 1.10
No. of reflections1085
No. of parameters93
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.22, 0.13

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···O1i0.97 (2)1.62 (2)2.5886 (16)171.3 (16)
N1—H1···O1ii0.89 (2)1.94 (2)2.8024 (14)160.6 (15)
Symmetry codes: (i) x+1, y1/2, z+3/2; (ii) x+1/2, y+1/2, z+2.
Comparison of selected interatomic distances and angles (Å,°) for the title compound and uracil top
3DeazurUracil
This workaThis workbLTNDcPNDdX-NeXRDfXRDg
N1-C21.3668 (17)1.3696 (13)1.362 (3)1.332 (6)1.362 (6)1.360 (4)1.371 (3)
N1-C61.3587 (17)1.3577 (15)1.355 (3)1.356 (6)1.367 (7)1.359 (4)1.358 (2)
C2-C31.4123 (15)1.4141 (11)1.414 (3)1.409 (7)1.409 (6)1.412 (4)
C5-C61.3519 (19)1.3587 (15)1.360 (4)1.350 (8)1.355 (7)1.348 (4)1.340 (2)
C3-C41.3746 (16)1.3860 (12)1.385 (4)1.381 (7)1.375 (7)1.381 (4)
C4-C51.4187 (19)1.4183 (15)1.411 (4)1.417 (8)1.400 (7)1.411 (4)1.430 (3)
C2-O11.2713 (15)1.2735 (12)1.266 (4)1.268 (7)1.266 (6)1.262 (4)1.215 (2)
C4-O21.3366 (15)1.3342 (11)1.322 (4)1.345 (8)1.346 (5)1.319 (3)1.245 (2)
O2···O1i2.5886 (16)2.5843 (16)2.563 (4)2.575 (11)2.581 (6)2.550 (4)
N1···O1ii2.8024 (14)2.7998 (12)2.785 (3)2.776 (8)2.796 (5)2.807 (4)2.861 (2)
O2-H2···O1i171.3 (16)172.8 (9)177.7 (7)174.6 (13)166 (4)
N1-H1···O1ii160.6 (15)164.7 (8)165.5 (6)164.0 (10)158 (4)156171 (1)
Notes: (a) `Conventional' refinement; (b) High θ refinement; (c) Low Temperature ND (Wilson, 2001); (d) Pulsed ND (Wilson, 1994); (e) Joint X-N (Wilson et al., 1992); (f) XRD (Low & Wilson, 1983); (g) XRD (Stewart & Jensen, 1967). Symmetry codes: (i) -x+1, y-1/2, -z+3/2; (ii) x+1/2, -y+1/2, -z+2.
 

Acknowledgements

We thank MIUR (Rome) for 2006 financial support of the project `X-ray diffractometry and spectrometry'.

References

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Volume 64| Part 6| June 2008| Pages o1107-o1108
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