6-Methyl­uracil: a redetermination of polymorph (II)

6-Methyluracil, C₅H₆N₂O₂, exists in two crystalline phases: form (I), monoclinic, space group P2₁/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, mol­ecules form ribbons approximately running parallel to the c-axis direction through N—H...O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O⁻)=N—H⁺ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding inter­actions.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.048
• wR factor = 0.133
• Data-to-parameter ratio = 15.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      5.621 Check

Alert level G
PLAT012_ALERT_1_G N.O.K.   _shelx_res_checksum Found in CIF ......     Please Check
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          4 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   1 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   3 ALERT level G = General information/check it is not something unexpected

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: WinGX (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).

6-Methyluracil

Crystal data

C5H6N2O2	F(000) = 528
Mr = 126.12	Dx = 1.508 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.710689 Å
a = 20.572 (3) Å	Cell parameters from 2315 reflections
b = 3.9052 (5) Å	θ = 2.9–30.6°
c = 14.811 (3) Å	µ = 0.12 mm^−1
β = 110.95 (2)°	T = 298 K
V = 1111.2 (4) Å^3	Tablets, colourless
Z = 8	0.14 × 0.11 × 0.08 mm

Data collection

Agilent Xcalibur Sapphire3 diffractometer	1400 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source	1154 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.044
Detector resolution: 16.0696 pixels mm^-1	θmax = 28.5°, θmin = 3.0°
ω and φ scans	h = −27→27
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014)	k = −5→5
Tmin = 0.770, Tmax = 1.000	l = −19→19
8110 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.048	Hydrogen site location: mixed
wR(F^2) = 0.133	H atoms treated by a mixture of independent and constrained refinement
S = 1.11	w = 1/[σ^2(Fo^2) + (0.0609P)^2 + 0.4161P] where P = (Fo^2 + 2Fc^2)/3
1400 reflections	(Δ/σ)max < 0.001
91 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.17 e Å^−3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. The N-bound H atoms were located in a difference Fourier map and refined freely. All other H atoms were placed geometrically and refined using a riding atom approximation, with C–H = 0.97 Å, and with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(C) for methyl H atoms. A rotating model was used for the methyl groups.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.06097 (6)	0.5147 (3)	−0.06247 (9)	0.0486 (4)
O2	0.26885 (6)	0.0108 (3)	0.10454 (9)	0.0468 (3)
N1	0.07366 (7)	0.2401 (3)	0.07840 (9)	0.0380 (3)
H1	0.0293 (10)	0.304 (5)	0.0715 (13)	0.049 (5)*
C2	0.09750 (8)	0.3466 (4)	0.00759 (11)	0.0366 (4)
N3	0.16426 (6)	0.2545 (3)	0.02038 (9)	0.0361 (3)
H3	0.1820 (10)	0.333 (5)	−0.0258 (15)	0.057 (5)*
C4	0.20846 (7)	0.0710 (4)	0.09840 (11)	0.0357 (4)
C5	0.17907 (7)	−0.0298 (4)	0.16844 (11)	0.0372 (4)
H5	0.2066	−0.1641	0.2240	0.045*
C6	0.11357 (8)	0.0595 (4)	0.15811 (11)	0.0359 (4)
C7	0.08038 (9)	−0.0227 (5)	0.23014 (13)	0.0488 (5)
H7A	0.1100	−0.1790	0.2783	0.073*
H7B	0.0354	−0.1289	0.1975	0.073*
H7C	0.0742	0.1864	0.2615	0.073*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0372 (6)	0.0662 (8)	0.0451 (7)	0.0128 (5)	0.0178 (5)	0.0152 (5)
O2	0.0319 (6)	0.0639 (8)	0.0475 (7)	0.0091 (5)	0.0178 (5)	0.0105 (5)
N1	0.0300 (7)	0.0451 (7)	0.0423 (7)	0.0023 (5)	0.0171 (5)	0.0025 (6)
C2	0.0312 (7)	0.0414 (8)	0.0387 (8)	0.0008 (6)	0.0142 (6)	−0.0007 (6)
N3	0.0308 (6)	0.0435 (7)	0.0365 (7)	0.0021 (5)	0.0150 (5)	0.0031 (5)
C4	0.0304 (7)	0.0389 (7)	0.0383 (8)	−0.0006 (6)	0.0130 (6)	−0.0022 (6)
C5	0.0344 (8)	0.0416 (8)	0.0359 (8)	0.0005 (6)	0.0129 (6)	0.0038 (6)
C6	0.0369 (8)	0.0356 (7)	0.0385 (8)	−0.0035 (6)	0.0174 (6)	−0.0016 (6)
C7	0.0496 (10)	0.0552 (10)	0.0519 (11)	−0.0006 (7)	0.0308 (8)	0.0042 (7)

Geometric parameters (Å, º)

O1—C2	1.2308 (19)	C4—C5	1.430 (2)
O2—C4	1.2352 (18)	C5—C6	1.347 (2)
N1—C6	1.368 (2)	C5—H5	0.9700
N1—C2	1.372 (2)	C6—C7	1.493 (2)
N1—H1	0.91 (2)	C7—H7A	0.9701
C2—N3	1.3657 (19)	C7—H7B	0.9701
N3—C4	1.3872 (19)	C7—H7C	0.9701
N3—H3	0.93 (2)
C6—N1—C2	123.21 (13)	C6—C5—C4	120.79 (14)
C6—N1—H1	120.2 (12)	C6—C5—H5	119.6
C2—N1—H1	116.6 (12)	C5—C6—N1	119.92 (14)
O1—C2—N3	122.54 (14)	C5—C6—C7	123.91 (15)
O1—C2—N1	121.93 (14)	N1—C6—C7	116.16 (13)
N3—C2—N1	115.53 (14)	C6—C7—H7A	109.5
C2—N3—C4	125.36 (13)	C6—C7—H7B	109.5
C2—N3—H3	116.6 (12)	H7A—C7—H7B	109.5
C4—N3—H3	117.9 (12)	C6—C7—H7C	109.5
O2—C4—N3	120.14 (14)	H7A—C7—H7C	109.5
O2—C4—C5	124.69 (14)	H7B—C7—H7C	109.5
N3—C4—C5	115.16 (13)
C6—N1—C2—O1	−178.53 (14)	O2—C4—C5—C6	177.08 (14)
C6—N1—C2—N3	1.3 (2)	N3—C4—C5—C6	−1.6 (2)
O1—C2—N3—C4	178.78 (14)	C4—C5—C6—N1	1.9 (2)
N1—C2—N3—C4	−1.0 (2)	C4—C5—C6—C7	−177.22 (14)
C2—N3—C4—O2	−177.57 (14)	C2—N1—C6—C5	−1.8 (2)
C2—N3—C4—C5	1.2 (2)	C2—N1—C6—C7	177.42 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.91 (2)	1.95 (2)	2.8594 (17)	174.0 (16)
N3—H3···O2^ii	0.93 (2)	1.90 (2)	2.8246 (18)	171.5 (18)

Symmetry codes: (i) −x, −y+1, −z; (ii) −x+1/2, −y+1/2, −z.