1,3-Bis(2-oxoprop­yl)thymine

In the title compound [systematic name: 5-methyl-1,3-bis­(2-oxoprop­yl)pyrimidine-2,4(1H,3H)-dione], C₁₁H₁₄N₂O₄, the two 2-oxopropyl groups are nearly perpendicular to the planar thymine unit. One methyl group of oxopropyl substituent is disordered. In the crystal, C—H...O inter­actions help to connect the mol­ecules into (001) layers.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.042
• wR factor = 0.103
• Data-to-parameter ratio = 15.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      3.656 Check

Alert level G
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          3 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 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
   2 ALERT level G = General information/check it is not something unexpected

   0 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

---

Computing details

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

5-Methyl-1,3-bis(2-oxopropyl)pyrimidine-2,4(1H,3H)-dione

Crystal data

C11H14N2O4	Dx = 1.360 Mg m^−3
Mr = 238.24	Melting point: 412 K
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 13.9490 (9) Å	Cell parameters from 2683 reflections
b = 4.9891 (3) Å	θ = 3.0–25.8°
c = 17.3647 (11) Å	µ = 0.11 mm^−1
β = 105.693 (4)°	T = 173 K
V = 1163.41 (13) Å^3	Plate, colourless
Z = 4	0.2 × 0.15 × 0.08 mm
F(000) = 504

Data collection

Bruker PHOTON-100 CMOS diffractometer	2458 independent reflections
Radiation source: sealedtube	1889 reflections with I > 2σ(I)
Detector resolution: 10.4 pixels mm^-1	Rint = 0.051
ω scans	θmax = 26.7°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −17→17
Tmin = 0.769, Tmax = 0.862	k = −6→6
18736 measured reflections	l = −21→21

Refinement

Refinement on F^2	Primary atom site location: dual
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0421P)^2 + 0.5355P] where P = (Fo^2 + 2Fc^2)/3
2458 reflections	(Δ/σ)max < 0.001
163 parameters	Δρmax = 0.21 e Å^−3
0 restraints	Δρmin = −0.18 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. Methylene hydrogen atoms are refined with riding coordinates and with U_iso(H) = 1.2 U_iso(C); methyl hydrogen atoms are refined as rotating idealized methyl groups and with U_iso(H) = 1.5 U_iso(C).

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.83624 (10)	0.9143 (2)	0.36977 (7)	0.0433 (3)
O2	0.63791 (8)	1.2059 (2)	0.24695 (7)	0.0361 (3)
O3	0.92187 (8)	0.9349 (2)	0.18756 (7)	0.0378 (3)
O4	0.50121 (8)	1.2301 (2)	0.06408 (7)	0.0364 (3)
N1	0.62809 (9)	0.8661 (3)	0.15811 (7)	0.0258 (3)
N2	0.78007 (9)	1.0765 (3)	0.21574 (7)	0.0244 (3)
C1	0.35466 (13)	1.0758 (5)	0.09457 (13)	0.0579 (6)
H1A	0.333498	1.262010	0.097365	0.087*	0.43 (3)
H1B	0.343268	0.974481	0.139636	0.087*	0.43 (3)
H1C	0.316192	0.995262	0.044202	0.087*	0.43 (3)
H1D	0.328474	0.892492	0.090103	0.087*	0.57 (3)
H1E	0.318704	1.180021	0.047833	0.087*	0.57 (3)
H1F	0.345780	1.159240	0.143267	0.087*	0.57 (3)
C2	0.46300 (11)	1.0691 (3)	0.09839 (9)	0.0285 (4)
C3	0.52141 (11)	0.8459 (3)	0.14837 (10)	0.0291 (4)
H3A	0.50906 (19)	0.8483 (3)	0.2009 (7)	0.035*
H3B	0.4978 (3)	0.675 (2)	0.1234 (3)	0.035*
C4	0.67906 (11)	1.0595 (3)	0.20955 (9)	0.0252 (3)
C5	0.83796 (11)	1.2601 (3)	0.27622 (8)	0.0261 (3)
H5A	0.8008 (5)	1.422 (2)	0.27574 (8)	0.031*
H5B	0.8985 (8)	1.3054 (7)	0.26324 (18)	0.031*
C6	0.86268 (11)	1.1388 (3)	0.35899 (9)	0.0266 (3)
C7	0.91998 (12)	1.3150 (3)	0.42473 (9)	0.0316 (4)
H7A	0.8774 (5)	1.456 (2)	0.4341 (5)	0.047*
H7B	0.9756 (8)	1.392 (2)	0.4098 (3)	0.047*
H7C	0.9440 (8)	1.2108 (12)	0.4727 (6)	0.047*
C8	0.67438 (11)	0.7030 (3)	0.11540 (9)	0.0259 (3)
H8	0.6350 (7)	0.574 (2)	0.0796 (7)	0.031*
C9	0.77188 (11)	0.7166 (3)	0.12144 (8)	0.0250 (3)
C10	0.83202 (11)	0.9100 (3)	0.17581 (9)	0.0254 (3)
C11	0.82282 (13)	0.5375 (4)	0.07549 (10)	0.0347 (4)
H11A	0.7752 (6)	0.398 (2)	0.0469 (7)	0.052*
H11B	0.8811 (8)	0.449 (2)	0.1132 (4)	0.052*
H11C	0.8461 (8)	0.6461 (12)	0.0358 (6)	0.052*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0613 (9)	0.0324 (7)	0.0357 (7)	−0.0108 (6)	0.0122 (6)	0.0031 (5)
O2	0.0298 (6)	0.0419 (7)	0.0409 (7)	−0.0006 (5)	0.0169 (5)	−0.0137 (6)
O3	0.0215 (6)	0.0471 (8)	0.0452 (7)	0.0015 (5)	0.0095 (5)	−0.0046 (6)
O4	0.0377 (7)	0.0335 (7)	0.0383 (7)	−0.0051 (5)	0.0108 (5)	0.0024 (5)
N1	0.0200 (6)	0.0270 (7)	0.0309 (7)	−0.0016 (5)	0.0079 (5)	−0.0025 (6)
N2	0.0212 (6)	0.0294 (7)	0.0234 (6)	−0.0016 (5)	0.0073 (5)	−0.0028 (5)
C1	0.0299 (10)	0.0888 (17)	0.0564 (12)	0.0140 (10)	0.0142 (9)	0.0332 (12)
C2	0.0279 (8)	0.0338 (9)	0.0241 (7)	−0.0036 (7)	0.0075 (6)	−0.0053 (7)
C3	0.0213 (8)	0.0303 (9)	0.0366 (9)	−0.0047 (6)	0.0093 (6)	−0.0001 (7)
C4	0.0221 (7)	0.0288 (8)	0.0260 (7)	−0.0009 (6)	0.0086 (6)	0.0001 (6)
C5	0.0242 (8)	0.0285 (8)	0.0255 (8)	−0.0042 (6)	0.0064 (6)	−0.0023 (6)
C6	0.0237 (8)	0.0296 (8)	0.0278 (8)	0.0008 (6)	0.0091 (6)	0.0004 (7)
C7	0.0313 (9)	0.0361 (9)	0.0262 (8)	−0.0022 (7)	0.0058 (6)	0.0011 (7)
C8	0.0302 (8)	0.0248 (8)	0.0227 (7)	−0.0013 (6)	0.0074 (6)	−0.0010 (6)
C9	0.0295 (8)	0.0249 (8)	0.0217 (7)	0.0038 (6)	0.0087 (6)	0.0028 (6)
C10	0.0222 (8)	0.0304 (8)	0.0246 (7)	0.0038 (6)	0.0081 (6)	0.0050 (6)
C11	0.0383 (9)	0.0361 (10)	0.0340 (9)	0.0054 (8)	0.0168 (7)	−0.0022 (8)

Geometric parameters (Å, º)

O1—C6	1.2093 (19)	C2—C3	1.508 (2)
O2—C4	1.2191 (18)	C3—H3A	0.972 (12)
O3—C10	1.2205 (18)	C3—H3B	0.972 (12)
O4—C2	1.2066 (19)	C5—H5A	0.958 (12)
N1—C3	1.4551 (19)	C5—H5B	0.958 (12)
N1—C4	1.3749 (19)	C5—C6	1.511 (2)
N1—C8	1.3742 (19)	C6—C7	1.491 (2)
N2—C4	1.3864 (18)	C7—H7A	0.962 (10)
N2—C5	1.4612 (19)	C7—H7B	0.962 (10)
N2—C10	1.4027 (19)	C7—H7C	0.962 (10)
C1—H1A	0.9800	C8—H8	0.959 (17)
C1—H1B	0.9800	C8—C9	1.337 (2)
C1—H1C	0.9800	C9—C10	1.449 (2)
C1—H1D	0.9800	C9—C11	1.499 (2)
C1—H1E	0.9800	C11—H11A	0.997 (11)
C1—H1F	0.9800	C11—H11B	0.997 (11)
C1—C2	1.495 (2)	C11—H11C	0.997 (11)
C4—N1—C3	117.21 (12)	H3A—C3—H3B	107.8
C8—N1—C3	120.74 (13)	O2—C4—N1	122.08 (13)
C8—N1—C4	122.02 (12)	O2—C4—N2	122.48 (14)
C4—N2—C5	116.53 (12)	N1—C4—N2	115.44 (13)
C4—N2—C10	125.13 (13)	N2—C5—H5A	109.2
C10—N2—C5	117.87 (12)	N2—C5—H5B	109.2
H1A—C1—H1B	109.5	N2—C5—C6	111.84 (13)
H1A—C1—H1C	109.5	H5A—C5—H5B	107.9
H1A—C1—H1D	141.1	C6—C5—H5A	109.2
H1A—C1—H1E	56.3	C6—C5—H5B	109.2
H1A—C1—H1F	56.3	O1—C6—C5	121.18 (14)
H1B—C1—H1C	109.5	O1—C6—C7	123.40 (14)
H1B—C1—H1D	56.3	C7—C6—C5	115.42 (13)
H1B—C1—H1E	141.1	C6—C7—H7A	109.5
H1B—C1—H1F	56.3	C6—C7—H7B	109.5
H1C—C1—H1D	56.3	C6—C7—H7C	109.5
H1C—C1—H1E	56.3	H7A—C7—H7B	109.5
H1C—C1—H1F	141.1	H7A—C7—H7C	109.5
H1D—C1—H1E	109.5	H7B—C7—H7C	109.5
H1D—C1—H1F	109.5	N1—C8—H8	118.5
H1E—C1—H1F	109.5	C9—C8—N1	122.96 (14)
C2—C1—H1A	109.5	C9—C8—H8	118.5
C2—C1—H1B	109.5	C8—C9—C10	118.83 (14)
C2—C1—H1C	109.5	C8—C9—C11	123.13 (14)
C2—C1—H1D	109.5	C10—C9—C11	118.03 (13)
C2—C1—H1E	109.5	O3—C10—N2	120.12 (14)
C2—C1—H1F	109.5	O3—C10—C9	124.33 (14)
O4—C2—C1	122.64 (16)	N2—C10—C9	115.55 (12)
O4—C2—C3	122.26 (14)	C9—C11—H11A	109.5
C1—C2—C3	115.10 (14)	C9—C11—H11B	109.5
N1—C3—C2	113.07 (13)	C9—C11—H11C	109.5
N1—C3—H3A	109.0	H11A—C11—H11B	109.5
N1—C3—H3B	109.0	H11A—C11—H11C	109.5
C2—C3—H3A	109.0	H11B—C11—H11C	109.5
C2—C3—H3B	109.0
O4—C2—C3—N1	6.9 (2)	C5—N2—C4—O2	6.5 (2)
N1—C8—C9—C10	0.5 (2)	C5—N2—C4—N1	−173.64 (13)
N1—C8—C9—C11	179.45 (14)	C5—N2—C10—O3	−5.4 (2)
N2—C5—C6—O1	0.6 (2)	C5—N2—C10—C9	175.01 (12)
N2—C5—C6—C7	−178.80 (12)	C8—N1—C3—C2	−103.59 (16)
C1—C2—C3—N1	−173.11 (16)	C8—N1—C4—O2	179.34 (15)
C3—N1—C4—O2	1.3 (2)	C8—N1—C4—N2	−0.5 (2)
C3—N1—C4—N2	−178.54 (13)	C8—C9—C10—O3	178.02 (15)
C3—N1—C8—C9	179.04 (14)	C8—C9—C10—N2	−2.5 (2)
C4—N1—C3—C2	74.43 (17)	C10—N2—C4—O2	178.41 (14)
C4—N1—C8—C9	1.1 (2)	C10—N2—C4—N1	−1.7 (2)
C4—N2—C5—C6	79.50 (16)	C10—N2—C5—C6	−93.04 (15)
C4—N2—C10—O3	−177.28 (14)	C11—C9—C10—O3	−1.0 (2)
C4—N2—C10—C9	3.2 (2)	C11—C9—C10—N2	178.53 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3A···O2^i	0.97 (1)	2.56 (1)	3.304 (2)	134 (1)
C3—H3B···O4^ii	0.97 (1)	2.45 (1)	3.3820 (19)	160 (1)
C5—H5B···O3^iii	0.96 (1)	2.50 (1)	3.353 (2)	148 (1)
C7—H7A···O1^iv	0.96 (1)	2.54 (1)	3.2576 (19)	131 (1)
C7—H7B···O3^iii	0.96 (1)	2.50 (1)	3.370 (2)	150 (1)
C8—H8···O4^ii	0.96 (1)	2.50 (1)	3.3213 (19)	144 (1)

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