5-Benz­yl-6-meth­yl-2-thioxo-2,3-dihydro­pyrimidin-4(1H)-one

Hu, S.-L.; Yin, G.-D.; Wu, A.-X.

doi:10.1107/S1600536805020921

5-Benzyl-6-methyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one

In the title compound, C₁₂H₁₂N₂OS, the dihedral angle between the benzene and pyrimidine rings is 84.1 (1)°. The molecules are linked by centrosymmetric pairs of N—H

O [N

O = 2.817 (2) Å] and N—H

S [N

S = 3.357 (2) Å] hydrogen bonds to form chains.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805020921/wk6057sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536805020921/wk6057Isup2.hkl Contains datablock I

CCDC reference: 276172

checkCIF report

Key indicators

Single-crystal X-ray study
T = 292 K
Mean (C-C) = 0.004 Å
R factor = 0.048
wR factor = 0.123
Data-to-parameter ratio = 15.6

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.67 Ratio
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C11

   0 ALERT level A = In general: serious problem
   0 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
   2 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

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SMART; data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Brker, 2001); software used to prepare material for publication: SHELXTL.

5-benzyl-6-methyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one top

Crystal data top

C₁₂H₁₂N₂OS	F(000) = 488
M_r = 232.30	D_x = 1.332 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P2yn	Cell parameters from 1539 reflections
a = 5.8779 (9) Å	θ = 2.7–23.4°
b = 29.800 (4) Å	µ = 0.26 mm⁻¹
c = 7.2160 (11) Å	T = 292 K
β = 113.622 (2)°	Block, colorless
V = 1158.1 (3) Å³	0.20 × 0.08 × 0.06 mm
Z = 4

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2274 independent reflections
Radiation source: fine-focus sealed tube	1753 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
0.3° ω scans	θ_max = 26.1°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	h = −7→4
T_min = 0.950, T_max = 0.985	k = −32→36
5152 measured reflections	l = −8→8

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)] = 0.048	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.123	H-atom parameters constrained
S = 1.03	w = 1/[σ²(F_o²) + (0.058P)² + 0.2016P] where P = (F_o² + 2F_c²)/3
2274 reflections	(Δ/σ)_max < 0.001
146 parameters	Δρ_max = 0.20 e Å⁻³
0 restraints	Δρ_min = −0.16 e Å⁻³

Special details top

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
C2	0.5675 (4)	0.00697 (7)	0.7906 (3)	0.0412 (5)
C4	0.2035 (4)	0.05504 (7)	0.6485 (3)	0.0458 (5)
C5	0.3509 (4)	0.09261 (7)	0.7549 (3)	0.0436 (5)
C6	0.5918 (4)	0.08551 (7)	0.8763 (3)	0.0449 (5)
C7	0.7674 (5)	0.11984 (8)	1.0091 (4)	0.0670 (7)
H7A	0.7063	0.1493	0.9613	0.100*
H7B	0.9279	0.1159	1.0059	0.100*
H7C	0.7807	0.1163	1.1453	0.100*
C8	0.2217 (4)	0.13688 (8)	0.7296 (3)	0.0540 (6)
H8A	0.3069	0.1545	0.8509	0.065*
H8B	0.0544	0.1315	0.7195	0.065*
C9	0.2055 (4)	0.16450 (7)	0.5496 (3)	0.0486 (6)
C10	0.0270 (5)	0.19793 (9)	0.4811 (5)	0.0763 (8)
H10	−0.0810	0.2023	0.5448	0.092*
C11	0.0078 (8)	0.22450 (11)	0.3210 (6)	0.1104 (14)
H11	−0.1138	0.2466	0.2767	0.132*
C12	0.1634 (9)	0.21904 (13)	0.2262 (6)	0.1088 (14)
H12	0.1495	0.2374	0.1181	0.131*
C13	0.3407 (7)	0.18634 (12)	0.2904 (4)	0.0866 (10)
H13	0.4480	0.1825	0.2257	0.104*
C14	0.3618 (5)	0.15881 (9)	0.4521 (3)	0.0599 (7)
H14	0.4822	0.1364	0.4943	0.072*
N1	0.6932 (3)	0.04336 (6)	0.8898 (3)	0.0456 (4)
H1	0.8477	0.0401	0.9672	0.055*
N3	0.3240 (3)	0.01424 (6)	0.6757 (2)	0.0449 (4)
H3	0.2366	−0.0086	0.6143	0.054*
O1	−0.0202 (3)	0.05739 (6)	0.5398 (3)	0.0626 (5)
S1	0.69904 (11)	−0.043343 (19)	0.80797 (9)	0.0515 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C2	0.0386 (11)	0.0476 (13)	0.0346 (10)	−0.0022 (10)	0.0117 (9)	0.0043 (9)
C4	0.0417 (12)	0.0481 (14)	0.0436 (11)	0.0034 (10)	0.0128 (10)	0.0038 (10)
C5	0.0449 (13)	0.0430 (13)	0.0417 (11)	0.0005 (10)	0.0160 (10)	0.0030 (9)
C6	0.0472 (13)	0.0423 (13)	0.0447 (11)	−0.0024 (10)	0.0180 (11)	0.0004 (9)
C7	0.0553 (15)	0.0546 (16)	0.0797 (17)	−0.0091 (12)	0.0151 (14)	−0.0149 (13)
C8	0.0512 (14)	0.0523 (14)	0.0568 (14)	0.0047 (11)	0.0197 (12)	−0.0069 (11)
C9	0.0436 (13)	0.0365 (12)	0.0503 (12)	−0.0054 (10)	0.0027 (10)	−0.0057 (10)
C10	0.0615 (17)	0.0496 (16)	0.094 (2)	0.0118 (14)	0.0057 (15)	0.0007 (15)
C11	0.097 (3)	0.057 (2)	0.125 (3)	0.009 (2)	−0.009 (2)	0.029 (2)
C12	0.111 (3)	0.082 (3)	0.085 (2)	−0.037 (2)	−0.010 (2)	0.035 (2)
C13	0.087 (2)	0.096 (2)	0.0639 (17)	−0.030 (2)	0.0163 (16)	0.0091 (17)
C14	0.0572 (15)	0.0581 (16)	0.0540 (14)	−0.0035 (13)	0.0115 (12)	0.0034 (12)
N1	0.0333 (9)	0.0473 (11)	0.0472 (10)	−0.0002 (8)	0.0068 (8)	0.0005 (8)
N3	0.0394 (10)	0.0413 (10)	0.0436 (9)	−0.0018 (8)	0.0059 (8)	−0.0002 (8)
O1	0.0416 (9)	0.0563 (11)	0.0700 (11)	0.0058 (8)	0.0016 (8)	−0.0024 (8)
S1	0.0452 (4)	0.0462 (4)	0.0546 (4)	0.0043 (3)	0.0111 (3)	0.0014 (3)

Geometric parameters (Å, º) top

C2—N1	1.346 (3)	C8—H8B	0.9700
C2—N3	1.354 (3)	C9—C14	1.373 (3)
C2—S1	1.668 (2)	C9—C10	1.386 (3)
C4—O1	1.234 (3)	C10—C11	1.367 (5)
C4—N3	1.381 (3)	C10—H10	0.9300
C4—C5	1.435 (3)	C11—C12	1.353 (5)
C5—C6	1.350 (3)	C11—H11	0.9300
C5—C8	1.497 (3)	C12—C13	1.365 (5)
C6—N1	1.377 (3)	C12—H12	0.9300
C6—C7	1.496 (3)	C13—C14	1.391 (4)
C7—H7A	0.9600	C13—H13	0.9300
C7—H7B	0.9600	C14—H14	0.9300
C7—H7C	0.9600	N1—H1	0.8600
C8—C9	1.508 (3)	N3—H3	0.8600
C8—H8A	0.9700

N1—C2—N3	114.66 (19)	C14—C9—C10	118.2 (2)
N1—C2—S1	123.03 (16)	C14—C9—C8	123.3 (2)
N3—C2—S1	122.31 (16)	C10—C9—C8	118.5 (2)
O1—C4—N3	119.7 (2)	C11—C10—C9	120.8 (3)
O1—C4—C5	123.8 (2)	C11—C10—H10	119.6
N3—C4—C5	116.45 (19)	C9—C10—H10	119.6
C6—C5—C4	118.4 (2)	C12—C11—C10	120.9 (3)
C6—C5—C8	124.5 (2)	C12—C11—H11	119.5
C4—C5—C8	117.02 (19)	C10—C11—H11	119.5
C5—C6—N1	120.04 (19)	C11—C12—C13	119.5 (3)
C5—C6—C7	125.7 (2)	C11—C12—H12	120.2
N1—C6—C7	114.24 (19)	C13—C12—H12	120.2
C6—C7—H7A	109.5	C12—C13—C14	120.3 (3)
C6—C7—H7B	109.5	C12—C13—H13	119.8
H7A—C7—H7B	109.5	C14—C13—H13	119.8
C6—C7—H7C	109.5	C9—C14—C13	120.3 (3)
H7A—C7—H7C	109.5	C9—C14—H14	119.9
H7B—C7—H7C	109.5	C13—C14—H14	119.9
C5—C8—C9	116.11 (19)	C2—N1—C6	124.58 (19)
C5—C8—H8A	108.3	C2—N1—H1	117.7
C9—C8—H8A	108.3	C6—N1—H1	117.7
C5—C8—H8B	108.3	C2—N3—C4	125.75 (19)
C9—C8—H8B	108.3	C2—N3—H3	117.1
H8A—C8—H8B	107.4	C4—N3—H3	117.1

O1—C4—C5—C6	177.2 (2)	C9—C10—C11—C12	−0.4 (5)
N3—C4—C5—C6	−1.6 (3)	C10—C11—C12—C13	0.5 (6)
O1—C4—C5—C8	−0.2 (3)	C11—C12—C13—C14	0.0 (5)
N3—C4—C5—C8	−178.99 (18)	C10—C9—C14—C13	0.6 (3)
C4—C5—C6—N1	2.5 (3)	C8—C9—C14—C13	−178.2 (2)
C8—C5—C6—N1	179.68 (19)	C12—C13—C14—C9	−0.5 (4)
C4—C5—C6—C7	−175.4 (2)	N3—C2—N1—C6	−1.6 (3)
C8—C5—C6—C7	1.8 (3)	S1—C2—N1—C6	178.81 (16)
C6—C5—C8—C9	96.4 (3)	C5—C6—N1—C2	−0.8 (3)
C4—C5—C8—C9	−86.3 (3)	C7—C6—N1—C2	177.3 (2)
C5—C8—C9—C14	−21.2 (3)	N1—C2—N3—C4	2.6 (3)
C5—C8—C9—C10	160.0 (2)	S1—C2—N3—C4	−177.84 (16)
C14—C9—C10—C11	−0.1 (4)	O1—C4—N3—C2	−179.91 (19)
C8—C9—C10—C11	178.7 (3)	C5—C4—N3—C2	−1.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O1ⁱ	0.86	1.96	2.817 (2)	176
N1—H1···S1ⁱⁱ	0.86	2.51	3.3574 (19)	171

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

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5-Benz­yl-6-meth­yl-2-thioxo-2,3-dihydro­pyrimidin-4(1H)-one

Supporting information

Key indicators

checkCIF/PLATON results

5-Benzyl-6-methyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one