Redetermination of 3-deaza­uracil

Portalone, G.

doi:10.1107/S1600536808014578

organic compounds

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

doi:10.1107/S1600536808014578

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Redetermination of 3-deazauracil

Gustavo Portalone ^a ^*

^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 ); 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

Crystal data

C₅H₅NO₂
M_r = 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 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ) T_min = 0.924, T_max = 0.983
77963 measured reflections
1085 independent reflections
1043 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.13 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); 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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808014578/kp2171sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808014578/kp2171Isup2.hkl

checkCIF report

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.

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

	Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level.
	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

C₅H₅NO₂	D_x = 1.419 Mg m⁻³
M_r = 111.10	Melting point: 477 K
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 43477 reflections
a = 5.3393 (1) Å	θ = 2.9–32.3°
b = 8.6454 (1) Å	µ = 0.11 mm⁻¹
c = 11.2652 (2) Å	T = 298 K
V = 520.01 (1) Å³	Tablets, colourless
Z = 4	0.20 × 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 source	1043 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.025
Detector resolution: 16.0696 pixels mm^-1	θ_max = 32.4°, θ_min = 3.0°
ω and ϕ scans	h = −8→7
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)	k = −13→12
T_min = 0.924, T_max = 0.983	l = −16→16
77963 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.112	All H-atom parameters refined
S = 1.10	w = 1/[σ²(F_o²) + (0.0765P)² + 0.037P] where P = (F_o² + 2F_c²)/3
1085 reflections	(Δ/σ)_max < 0.001
93 parameters	Δρ_max = 0.22 e Å⁻³
0 restraints	Δρ_min = −0.13 e Å⁻³

Crystal data top

C₅H₅NO₂	V = 520.01 (1) Å³
M_r = 111.10	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.3393 (1) Å	µ = 0.11 mm⁻¹
b = 8.6454 (1) Å	T = 298 K
c = 11.2652 (2) Å	0.20 × 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)
T_min = 0.924, T_max = 0.983	R_int = 0.025
77963 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.112	All H-atom parameters refined
S = 1.10	Δρ_max = 0.22 e Å⁻³
1085 reflections	Δρ_min = −0.13 e Å⁻³
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

	x	y	z	U_iso*/U_eq
O1	0.5630 (2)	0.19169 (12)	0.88298 (9)	0.0418 (3)
O2	0.8080 (2)	−0.31430 (11)	0.76490 (11)	0.0423 (3)
H2	0.667 (4)	−0.302 (3)	0.711 (2)	0.056 (6)*
N1	0.9062 (2)	0.07483 (13)	0.96127 (9)	0.0329 (2)
H1	0.935 (5)	0.163 (3)	1.000 (2)	0.052 (6)*
C2	0.7058 (2)	0.07410 (13)	0.88575 (10)	0.0289 (2)
C3	0.6712 (2)	−0.06036 (13)	0.81646 (10)	0.0287 (2)
H3	0.523 (4)	−0.072 (2)	0.763 (2)	0.056 (6)*
C4	0.8348 (2)	−0.18253 (14)	0.82563 (11)	0.0299 (3)
C5	1.0428 (3)	−0.17405 (17)	0.90371 (13)	0.0363 (3)
H5	1.161 (4)	−0.263 (3)	0.9032 (17)	0.054 (6)*
C6	1.0714 (3)	−0.04424 (17)	0.96924 (12)	0.0362 (3)
H6	1.212 (4)	−0.021 (2)	1.0225 (18)	0.045 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0522 (6)	0.0310 (4)	0.0421 (5)	0.0126 (5)	−0.0071 (5)	−0.0089 (4)
O2	0.0473 (6)	0.0304 (4)	0.0493 (5)	0.0056 (5)	−0.0048 (5)	−0.0116 (4)
N1	0.0378 (5)	0.0301 (5)	0.0308 (5)	−0.0046 (4)	−0.0035 (4)	−0.0040 (4)
C2	0.0330 (5)	0.0261 (5)	0.0277 (5)	0.0007 (5)	0.0004 (4)	−0.0020 (4)
C3	0.0291 (5)	0.0270 (5)	0.0301 (5)	0.0014 (4)	−0.0025 (4)	−0.0041 (4)
C4	0.0307 (6)	0.0269 (5)	0.0321 (5)	0.0003 (5)	0.0013 (4)	−0.0020 (4)
C5	0.0306 (6)	0.0352 (6)	0.0432 (6)	0.0044 (5)	−0.0041 (5)	0.0007 (5)
C6	0.0318 (6)	0.0400 (6)	0.0369 (6)	−0.0037 (5)	−0.0070 (5)	0.0015 (5)

Geometric parameters (Å, º) top

O1—C2	1.2713 (15)	C3—C4	1.3746 (16)
O2—C4	1.3366 (15)	C3—H3	1.00 (2)
O2—H2	0.97 (2)	C4—C5	1.4187 (19)
N1—C6	1.3587 (17)	C5—C6	1.3519 (19)
N1—C2	1.3668 (17)	C5—H5	1.00 (2)
N1—H1	0.89 (2)	C6—H6	0.98 (2)
C2—C3	1.4123 (15)

C4—O2—H2	107.8 (14)	O2—C4—C3	123.25 (11)
C6—N1—C2	123.08 (10)	O2—C4—C5	116.44 (11)
C6—N1—H1	120.3 (16)	C3—C4—C5	120.30 (11)
C2—N1—H1	116.2 (16)	C6—C5—C4	118.02 (12)
O1—C2—N1	118.75 (10)	C6—C5—H5	125.0 (13)
O1—C2—C3	124.48 (12)	C4—C5—H5	117.0 (13)
N1—C2—C3	116.76 (11)	C5—C6—N1	121.30 (12)
C4—C3—C2	120.51 (11)	C5—C6—H6	126.0 (12)
C4—C3—H3	118.3 (12)	N1—C6—H6	112.6 (12)
C2—C3—H3	121.1 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, −z+3/2; (ii) x+1/2, −y+1/2, −z+2.

Experimental details

Crystal data
Chemical formula	C₅H₅NO₂
M_r	111.10
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	298
a, b, c (Å)	5.3393 (1), 8.6454 (1), 11.2652 (2)
V (Å³)	520.01 (1)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.20 × 0.15 × 0.15

Data collection
Diffractometer	Oxford Diffraction Xcalibur S CCD diffractometer
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2006)
T_min, T_max	0.924, 0.983
No. of measured, independent and observed [I > 2σ(I)] reflections	77963, 1085, 1043
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.753

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.112, 1.10
No. of reflections	1085
No. of parameters	93
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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−1/2, −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

	3Deazur						Uracil
	This work^a	This work^b	LTND^c	PND^d	X-N^e	XRD^f	XRD^g
N1-C2	1.3668 (17)	1.3696 (13)	1.362 (3)	1.332 (6)	1.362 (6)	1.360 (4)	1.371 (3)
N1-C6	1.3587 (17)	1.3577 (15)	1.355 (3)	1.356 (6)	1.367 (7)	1.359 (4)	1.358 (2)
C2-C3	1.4123 (15)	1.4141 (11)	1.414 (3)	1.409 (7)	1.409 (6)	1.412 (4)	—
C5-C6	1.3519 (19)	1.3587 (15)	1.360 (4)	1.350 (8)	1.355 (7)	1.348 (4)	1.340 (2)
C3-C4	1.3746 (16)	1.3860 (12)	1.385 (4)	1.381 (7)	1.375 (7)	1.381 (4)	—
C4-C5	1.4187 (19)	1.4183 (15)	1.411 (4)	1.417 (8)	1.400 (7)	1.411 (4)	1.430 (3)
C2-O1	1.2713 (15)	1.2735 (12)	1.266 (4)	1.268 (7)	1.266 (6)	1.262 (4)	1.215 (2)
C4-O2	1.3366 (15)	1.3342 (11)	1.322 (4)	1.345 (8)	1.346 (5)	1.319 (3)	1.245 (2)
O2···O1ⁱ	2.5886 (16)	2.5843 (16)	2.563 (4)	2.575 (11)	2.581 (6)	2.550 (4)	—
N1···O1ⁱⁱ	2.8024 (14)	2.7998 (12)	2.785 (3)	2.776 (8)	2.796 (5)	2.807 (4)	2.861 (2)
O2-H2···O1ⁱ	171.3 (16)	172.8 (9)	177.7 (7)	174.6 (13)	166 (4)	—	—
N1-H1···O1ⁱⁱ	160.6 (15)	164.7 (8)	165.5 (6)	164.0 (10)	158 (4)	156	171 (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'.

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