3-Methyl-5-nitro­uracil

The mol­ecules of the title compound, C₅H₅N₃O₄, are approximately planar. The nitro group makes a dihedral angle of 1.3 (4)° with the plane of the six-membered ring. This coplanar disposition is a reason for the changes in valence angles in the vicinity of the nitro group. Mol­ecules are connected into dimers by means of N—H...O hydrogen bonds, and these dimers make larger structures with the help of relatively short C—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.045
• wR factor = 0.128
• Data-to-parameter ratio = 10.1

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT732_ALERT_1_B Angle   Calc   118.9(16), Rep    118.7(2) ......       8.00 su-Rat
              C2   -N1   -H1      1.555   1.555   1.555

Alert level C
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N5
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.27
PLAT432_ALERT_2_C Short Inter X...Y Contact  O4     ..  C6      ..       2.96 Ang.

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

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

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Computing details

Data collection: KM-4 Software (Kuma Diffraction, 1991); cell refinement: KM-4 Software; data reduction: KM-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97.

3-Methyl-5-nitrouracil

Crystal data

C5H5N3O4	F(000) = 352
Mr = 171.12	Dx = 1.679 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 50 reflections
a = 5.7510 (12) Å	θ = 4–32°
b = 10.176 (2) Å	µ = 0.15 mm^−1
c = 11.775 (2) Å	T = 295 K
β = 100.69 (3)°	Block, colourless
V = 677.1 (2) Å^3	0.4 × 0.2 × 0.1 mm
Z = 4

Data collection

Kuma KM-4 diffractometer	Rint = 0.066
Radiation source: fine-focus sealed tube	θmax = 25.1°, θmin = 2.7°
Graphite monochromator	h = −6→6
ω–2θ scans	k = 0→12
1256 measured reflections	l = 0→14
1196 independent reflections	2 standard reflections every 100 reflections
926 reflections with I > 2σ(I)	intensity decay: 0.3%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.045	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.128	w = 1/[σ^2(Fo^2) + (0.0911P)^2 + 0.05P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
1196 reflections	Δρmax = 0.22 e Å^−3
119 parameters	Δρmin = −0.27 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.067 (11)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.3041 (3)	0.10318 (16)	0.58178 (12)	0.0400 (5)
H1	0.305 (4)	0.085 (2)	0.514 (2)	0.052 (6)*
C2	0.4814 (3)	0.05458 (18)	0.66604 (14)	0.0374 (5)
O2	0.6399 (3)	−0.01339 (15)	0.64165 (11)	0.0545 (5)
N3	0.4690 (3)	0.08839 (14)	0.77744 (11)	0.0339 (4)
C31	0.6539 (3)	0.0368 (2)	0.86989 (15)	0.0439 (5)
H31A	0.6011	−0.0405	0.9018	0.082 (5)*
H31B	0.6728	0.0990	0.9328	0.082 (5)*
H31C	0.8032	0.0313	0.8459	0.082 (5)*
C4	0.2863 (3)	0.16141 (16)	0.81129 (14)	0.0347 (5)
O4	0.2850 (3)	0.17753 (14)	0.91292 (10)	0.0532 (5)
C5	0.1152 (3)	0.21061 (17)	0.71467 (14)	0.0357 (5)
N5	−0.0782 (3)	0.29368 (16)	0.73154 (13)	0.0436 (5)
O51	−0.2155 (3)	0.3304 (2)	0.64614 (14)	0.0964 (8)
O52	−0.1018 (3)	0.32526 (15)	0.82795 (12)	0.0563 (5)
C6	0.1302 (3)	0.17918 (18)	0.60439 (15)	0.0380 (5)
H6	0.019 (4)	0.210 (2)	0.5393 (16)	0.044 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0510 (10)	0.0492 (9)	0.0215 (8)	0.0049 (7)	0.0114 (6)	−0.0016 (7)
C2	0.0449 (10)	0.0405 (10)	0.0293 (9)	0.0000 (8)	0.0130 (8)	−0.0020 (7)
O2	0.0567 (9)	0.0723 (10)	0.0374 (8)	0.0197 (8)	0.0159 (6)	−0.0053 (7)
N3	0.0405 (8)	0.0359 (8)	0.0261 (7)	0.0006 (6)	0.0083 (6)	0.0004 (6)
C31	0.0449 (11)	0.0531 (11)	0.0327 (9)	0.0047 (9)	0.0050 (8)	0.0026 (8)
C4	0.0465 (10)	0.0327 (9)	0.0270 (8)	−0.0012 (8)	0.0120 (7)	−0.0009 (7)
O4	0.0727 (10)	0.0637 (10)	0.0241 (7)	0.0213 (8)	0.0115 (6)	−0.0018 (6)
C5	0.0421 (10)	0.0359 (9)	0.0311 (9)	0.0019 (8)	0.0119 (7)	0.0017 (7)
N5	0.0510 (10)	0.0450 (9)	0.0368 (9)	0.0063 (7)	0.0131 (7)	0.0035 (7)
O51	0.1026 (15)	0.139 (2)	0.0447 (9)	0.0795 (14)	0.0072 (9)	0.0111 (10)
O52	0.0586 (9)	0.0696 (10)	0.0445 (8)	0.0154 (8)	0.0196 (7)	−0.0067 (7)
C6	0.0455 (10)	0.0421 (10)	0.0275 (9)	−0.0002 (9)	0.0092 (8)	0.0047 (8)

Geometric parameters (Å, º)

N1—C6	1.329 (2)	C31—H31C	0.95
N1—C2	1.376 (2)	C4—O4	1.209 (2)
N1—H1	0.82 (2)	C4—C5	1.449 (3)
C2—O2	1.220 (2)	C5—C6	1.356 (2)
C2—N3	1.371 (2)	C5—N5	1.440 (2)
N3—C4	1.404 (2)	N5—O52	1.212 (2)
N3—C31	1.470 (2)	N5—O51	1.216 (2)
C31—H31A	0.94	C6—H6	0.96 (2)
C31—H31B	0.96
C6—N1—C2	123.3 (2)	H31B—C31—H31C	107
C6—N1—H1	118 (2)	O4—C4—N3	119.7 (2)
C2—N1—H1	118.7 (2)	O4—C4—C5	127.0 (2)
O2—C2—N3	122.8 (2)	N3—C4—C5	113.3 (1)
O2—C2—N1	121.3 (2)	C6—C5—N5	117.3 (2)
N3—C2—N1	115.9 (2)	C6—C5—C4	121.1 (2)
C2—N3—C4	125.4 (2)	N5—C5—C4	121.6 (2)
C2—N3—C31	117.4 (2)	O52—N5—O51	121.7 (2)
C4—N3—C31	117.1 (1)	O52—N5—C5	120.6 (2)
N3—C31—H31A	111	O51—N5—C5	117.8 (2)
N3—C31—H31B	107	N1—C6—C5	120.9 (2)
H31A—C31—H31B	104	N1—C6—H6	117 (1)
N3—C31—H31C	112	C5—C6—H6	123 (1)
H31A—C31—H31C	116
C6—N1—C2—O2	−178.9 (2)	N3—C4—C5—C6	3.9 (3)
C6—N1—C2—N3	0.5 (3)	O4—C4—C5—N5	3.2 (3)
O2—C2—N3—C4	−177.1 (2)	N3—C4—C5—N5	−176.6 (2)
N1—C2—N3—C4	3.5 (3)	C6—C5—N5—O52	179.9 (2)
O2—C2—N3—C31	−1.4 (3)	C4—C5—N5—O52	0.4 (3)
N1—C2—N3—C31	179.2 (2)	C6—C5—N5—O51	0.0 (3)
C2—N3—C4—O4	174.7 (2)	C4—C5—N5—O51	−179.5 (2)
C31—N3—C4—O4	−1.0 (3)	C2—N1—C6—C5	−1.8 (3)
C2—N3—C4—C5	−5.5 (3)	N5—C5—C6—N1	179.8 (2)
C31—N3—C4—C5	178.8 (2)	C4—C5—C6—N1	−0.6 (3)
O4—C4—C5—C6	−176.3 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^i	0.82 (2)	2.05 (2)	2.859 (2)	169 (2)
C31—H31A···O51^ii	0.95	2.55	3.260 (3)	132
C31—H31A···O4^iii	0.95	2.57	3.330 (2)	138
C31—H31B···O51^iv	0.97	2.58	3.474 (3)	155
C6—H6···O52^v	0.96 (2)	2.48 (2)	3.281 (3)	141 (2)
C6—H6···O4^v	0.96 (2)	2.59 (2)	2.958 (2)	103 (1)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, y−1/2, −z+3/2; (iii) −x+1, −y, −z+2; (iv) x+1, −y+1/2, z+1/2; (v) x, −y+1/2, z−1/2.