3-[(6-Chloro­pyridin-3-yl)meth­yl]-2-thioxo-2,3,5,6-tetra­hydro­pyrimidin-4(1H)-one

The tetra­hydro­pyrimidine ring of the title mol­ecule, C₁₀H₁₀ClN₃OS, adopts a half-chair conformation. In the crystal structure, mol­ecules are linked through N—H...S hydrogen bonding, forming a one-dimensional structure.

Key indicators

• Single-crystal X-ray study
• T = 294 K
• R factor = 0.049
• wR factor = 0.146
• Data-to-parameter ratio = 14.6

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Computing details

Data collection: SMART (Bruker, 1998); 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 (Bruker, 1999); software used to prepare material for publication: SHELXTL.

3-[(6-Chloropyridin-3-yl)methyl]-2-thioxo-2,3,5,6-tetrahydropyrimidin-4(1H)-one

Crystal data

C10H10ClN3OS	F(000) = 528
Mr = 255.72	Dx = 1.408 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1449 reflections
a = 10.131 (3) Å	θ = 2.5–21.0°
b = 5.7977 (14) Å	µ = 0.47 mm^−1
c = 20.957 (5) Å	T = 294 K
β = 101.562 (4)°	Needle, colorless
V = 1205.9 (5) Å^3	0.24 × 0.20 × 0.10 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer	2470 independent reflections
Radiation source: fine-focus sealed tube	1277 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.034
φ and ω scans	θmax = 26.4°, θmin = 2.0°
Absorption correction: multi-scan (SABABS; Sheldrick, 1996)	h = −10→12
Tmin = 0.895, Tmax = 0.954	k = −7→5
6496 measured reflections	l = −26→25

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)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.146	w = 1/[σ^2(Fo^2) + (0.0614P)^2 + 0.3547P] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max = 0.001
2470 reflections	Δρmax = 0.25 e Å^−3
169 parameters	Δρmin = −0.24 e Å^−3
8 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0031 (19)

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	Occ. (<1)
S1	0.98460 (10)	0.3609 (2)	0.09604 (4)	0.0982 (5)
Cl1	0.36045 (11)	0.4397 (2)	0.24228 (5)	0.1150 (5)
O1	0.6241 (3)	−0.2187 (5)	0.03536 (12)	0.1079 (10)
N1	0.8558 (3)	0.2570 (5)	−0.02128 (13)	0.0744 (9)
H1A	0.901 (3)	0.360 (6)	−0.0349 (17)	0.089*
N2	0.7897 (2)	0.0472 (4)	0.06012 (11)	0.0587 (7)
C1	0.8710 (3)	0.2151 (5)	0.04145 (15)	0.0598 (8)
C2	0.7853 (12)	0.116 (3)	−0.0759 (7)	0.078 (4)	0.453 (14)
H2A	0.8385	−0.0180	−0.0825	0.094*	0.453 (14)
H2B	0.7658	0.2050	−0.1159	0.094*	0.453 (14)
C3	0.6566 (11)	0.045 (3)	−0.0549 (6)	0.081 (4)	0.453 (14)
H3A	0.6069	−0.0631	−0.0862	0.097*	0.453 (14)
H3B	0.6003	0.1789	−0.0531	0.097*	0.453 (14)
C2'	0.7328 (13)	0.1882 (16)	−0.0652 (5)	0.078 (3)	0.547 (14)
H2'A	0.7433	0.2039	−0.1099	0.093*	0.547 (14)
H2'B	0.6589	0.2862	−0.0588	0.093*	0.547 (14)
C3'	0.7029 (13)	−0.0599 (16)	−0.0513 (5)	0.075 (3)	0.547 (14)
H3'A	0.6186	−0.1076	−0.0789	0.090*	0.547 (14)
H3'B	0.7741	−0.1594	−0.0601	0.090*	0.547 (14)
C4	0.6937 (4)	−0.0760 (6)	0.01649 (17)	0.0783 (10)
C5	0.7974 (3)	−0.0065 (5)	0.12936 (14)	0.0655 (9)
H5A	0.8839	0.0446	0.1541	0.079*
H5B	0.7924	−0.1723	0.1345	0.079*
C6	0.6877 (3)	0.1047 (5)	0.15670 (12)	0.0530 (7)
C7	0.6365 (3)	0.3181 (5)	0.13526 (14)	0.0583 (8)
H7	0.6695	0.3936	0.1025	0.070*
C8	0.4871 (3)	0.3105 (6)	0.21018 (16)	0.0674 (9)
C9	0.5360 (4)	0.0967 (6)	0.23275 (15)	0.0886 (13)	0.46 (3)
H9	0.5022	0.0210	0.2652	0.106*	0.46 (3)
N3	0.5369 (3)	0.4208 (5)	0.16196 (16)	0.0787 (12)	0.46 (3)
N3'	0.5360 (4)	0.0967 (6)	0.23275 (15)	0.0886 (13)	0.54 (3)
C9'	0.5369 (3)	0.4208 (5)	0.16196 (16)	0.0787 (12)	0.54 (3)
H9'	0.5035	0.5648	0.1473	0.094*	0.54 (3)
C10	0.6369 (4)	−0.0019 (5)	0.20568 (14)	0.0653 (9)
H10	0.6715	−0.1445	0.2210	0.078*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0945 (8)	0.1388 (10)	0.0629 (6)	−0.0603 (7)	0.0195 (5)	−0.0257 (6)
Cl1	0.0950 (8)	0.1483 (11)	0.1073 (9)	−0.0031 (7)	0.0338 (7)	−0.0253 (7)
O1	0.128 (2)	0.0932 (19)	0.0926 (18)	−0.0588 (17)	−0.0026 (16)	0.0104 (15)
N1	0.071 (2)	0.090 (2)	0.0597 (18)	−0.0285 (15)	0.0065 (14)	0.0017 (15)
N2	0.0577 (15)	0.0571 (15)	0.0563 (15)	−0.0085 (12)	−0.0004 (12)	0.0024 (12)
C1	0.0474 (17)	0.070 (2)	0.062 (2)	−0.0046 (15)	0.0095 (15)	−0.0073 (16)
C2	0.060 (8)	0.100 (8)	0.070 (6)	−0.006 (6)	0.002 (6)	−0.016 (6)
C3	0.084 (7)	0.095 (8)	0.054 (5)	−0.024 (6)	−0.007 (5)	0.001 (6)
C2'	0.054 (6)	0.124 (9)	0.049 (5)	−0.023 (5)	−0.004 (4)	0.017 (5)
C3'	0.074 (6)	0.078 (6)	0.067 (5)	−0.017 (5)	0.000 (5)	−0.012 (5)
C4	0.083 (3)	0.075 (2)	0.072 (2)	−0.026 (2)	0.0047 (19)	−0.0051 (19)
C5	0.068 (2)	0.0597 (19)	0.0608 (19)	−0.0009 (15)	−0.0055 (16)	0.0143 (15)
C6	0.0631 (19)	0.0440 (16)	0.0441 (16)	−0.0130 (14)	−0.0083 (14)	0.0066 (13)
C7	0.0612 (19)	0.0519 (18)	0.0601 (18)	−0.0095 (15)	0.0078 (16)	0.0152 (15)
C8	0.068 (2)	0.072 (2)	0.059 (2)	−0.0141 (17)	0.0050 (17)	−0.0110 (17)
C9	0.108 (3)	0.096 (3)	0.059 (2)	−0.030 (2)	0.0106 (19)	−0.0004 (19)
N3	0.076 (2)	0.071 (2)	0.081 (2)	−0.0124 (17)	−0.0027 (18)	0.0050 (17)
N3'	0.108 (3)	0.096 (3)	0.059 (2)	−0.030 (2)	0.0106 (19)	−0.0004 (19)
C9'	0.076 (2)	0.071 (2)	0.081 (2)	−0.0124 (17)	−0.0027 (18)	0.0050 (17)
C10	0.090 (2)	0.0513 (18)	0.0477 (17)	−0.0117 (17)	−0.0032 (17)	0.0074 (15)

Geometric parameters (Å, º)

S1—C1	1.679 (3)	C2'—H2'A	0.9700
Cl1—C8	1.734 (4)	C2'—H2'B	0.9700
O1—C4	1.204 (4)	C3'—C4	1.445 (11)
N1—C1	1.315 (4)	C3'—H3'A	0.9700
N1—C2'	1.449 (11)	C3'—H3'B	0.9700
N1—C2	1.472 (14)	C5—C6	1.495 (4)
N1—H1A	0.83 (3)	C5—H5A	0.9700
N2—C1	1.381 (4)	C5—H5B	0.9700
N2—C4	1.391 (4)	C6—C7	1.381 (4)
N2—C5	1.471 (4)	C6—C10	1.383 (4)
C2—C3	1.515 (9)	C7—N3	1.383 (4)
C2—H2A	0.9700	C7—H7	0.9300
C2—H2B	0.9700	C8—N3	1.374 (4)
C3—C4	1.626 (14)	C8—C9	1.382 (5)
C3—H3A	0.9700	C9—C10	1.388 (5)
C3—H3B	0.9700	C9—H9	0.9300
C2'—C3'	1.510 (8)	C10—H10	0.9300
C1—N1—C2'	119.8 (5)	C2'—C3'—H3'A	110.1
C1—N1—C2	128.1 (6)	C4—C3'—H3'B	110.1
C2'—N1—C2	29.6 (4)	C2'—C3'—H3'B	110.1
C1—N1—H1A	121 (2)	H3'A—C3'—H3'B	108.5
C2'—N1—H1A	116 (2)	O1—C4—N2	121.0 (3)
C2—N1—H1A	110 (2)	O1—C4—C3'	121.6 (4)
C1—N2—C4	123.6 (3)	N2—C4—C3'	116.0 (5)
C1—N2—C5	120.8 (2)	O1—C4—C3	123.7 (5)
C4—N2—C5	115.6 (3)	N2—C4—C3	112.7 (6)
N1—C1—N2	117.2 (3)	C3'—C4—C3	27.9 (5)
N1—C1—S1	121.0 (2)	N2—C5—C6	113.0 (2)
N2—C1—S1	121.9 (2)	N2—C5—H5A	109.0
N1—C2—C3	103.7 (10)	C6—C5—H5A	109.0
N1—C2—H2A	111.0	N2—C5—H5B	109.0
C3—C2—H2A	111.0	C6—C5—H5B	109.0
N1—C2—H2B	111.0	H5A—C5—H5B	107.8
C3—C2—H2B	111.0	C7—C6—C10	118.1 (3)
H2A—C2—H2B	109.0	C7—C6—C5	121.4 (3)
C2—C3—C4	109.3 (10)	C10—C6—C5	120.5 (3)
C2—C3—H3A	109.8	C6—C7—N3	120.7 (3)
C4—C3—H3A	109.8	C6—C7—H7	119.7
C2—C3—H3B	109.8	N3—C7—H7	119.7
C4—C3—H3B	109.8	N3—C8—C9	120.7 (3)
H3A—C3—H3B	108.3	N3—C8—Cl1	119.5 (3)
N1—C2'—C3'	108.7 (8)	C9—C8—Cl1	119.8 (3)
N1—C2'—H2'A	109.9	C8—C9—C10	118.2 (3)
C3'—C2'—H2'A	109.9	C8—C9—H9	120.9
N1—C2'—H2'B	109.9	C10—C9—H9	120.9
C3'—C2'—H2'B	109.9	C8—N3—C7	120.1 (3)
H2'A—C2'—H2'B	108.3	C6—C10—C9	122.3 (3)
C4—C3'—C2'	107.8 (8)	C6—C10—H10	118.9
C4—C3'—H3'A	110.1	C9—C10—H10	118.9
C2'—N1—C1—N2	19.7 (7)	C2'—C3'—C4—O1	151.2 (8)
C2—N1—C1—N2	−14.8 (9)	C2'—C3'—C4—N2	−41.8 (13)
C2'—N1—C1—S1	−160.2 (6)	C2'—C3'—C4—C3	48.0 (11)
C2—N1—C1—S1	165.3 (7)	C2—C3—C4—O1	−152.1 (11)
C4—N2—C1—N1	−0.5 (5)	C2—C3—C4—N2	45.9 (15)
C5—N2—C1—N1	−178.4 (3)	C2—C3—C4—C3'	−57.1 (13)
C4—N2—C1—S1	179.4 (2)	C1—N2—C5—C6	99.9 (3)
C5—N2—C1—S1	1.6 (4)	C4—N2—C5—C6	−78.1 (3)
C1—N1—C2—C3	43.7 (17)	N2—C5—C6—C7	−33.4 (4)
C2'—N1—C2—C3	−40.5 (12)	N2—C5—C6—C10	148.3 (3)
N1—C2—C3—C4	−53.7 (17)	C10—C6—C7—N3	−0.3 (4)
C1—N1—C2'—C3'	−49.0 (13)	C5—C6—C7—N3	−178.7 (3)
C2—N1—C2'—C3'	66.6 (16)	N3—C8—C9—C10	0.4 (4)
N1—C2'—C3'—C4	57.3 (15)	Cl1—C8—C9—C10	179.7 (2)
C1—N2—C4—O1	−179.0 (3)	C9—C8—N3—C7	0.2 (5)
C5—N2—C4—O1	−1.0 (5)	Cl1—C8—N3—C7	−179.1 (2)
C1—N2—C4—C3'	14.0 (7)	C6—C7—N3—C8	−0.3 (4)
C5—N2—C4—C3'	−168.1 (6)	C7—C6—C10—C9	1.0 (4)
C1—N2—C4—C3	−16.5 (7)	C5—C6—C10—C9	179.4 (3)
C5—N2—C4—C3	161.5 (6)	C8—C9—C10—C6	−1.0 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···S1^i	0.83 (3)	2.49 (3)	3.315 (3)	169 (3)

Symmetry code: (i) −x+2, −y+1, −z.