(R)-4-[2-(Methyl-sulfanyl)pyrimidin-4-yl]-1-(tetra-hydro-furan-3-yl)-1H-pyrazol-5-amine.

The title compound, C(12)H(15)N(5)OS, was obtained by reaction of 2-(2-(methyl-thio)pyrimidin-4-yl)-3-oxopropane-nitrile with (tetra-hydro-furan-3-yl)hydrazine dihydro-chloride, and the racemic product was subsequently separated by chiral chromatography (first peak; [α](D) (20) = +51.3°). The chiral center at the substituted atom of the tetra-hydro-furanyl group has an R-configuration. The pyrimidine and pyrazolyl rings are almost coplanar, their mean planes forming a dihedral angle of 6.4 (1)°. One of the H atoms of the amino group participates in an intra-molecular hydrogen bond with the pyrimidine N atom in position 3. The second H atom is involved in an inter-molecular hydrogen bond, which links the mol-ecules into an infinite chain.

Related literature

For the structure of a related compound with a methyl-substituted amino group, see: Liu et al. (2009 ▶).

Experimental

Crystal data

C12H15N5OS

M = 277.35

Orthorhombic,

a = 15.479 (2) Å

b = 7.1217 (10) Å

c = 11.7802 (17) Å

V = 1298.6 (3) Å3

Z = 4

Mo Kα radiation

μ = 0.25 mm−1

T = 208 K

0.20 × 0.20 × 0.20 mm

Data collection

Bruker D8 APEXII CCD area-detector diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T min = 0.844, T max = 0.952

6570 measured reflections

3025 independent reflections

2844 reflections with I > 2σ(I)

R int = 0.043

Refinement

R[F 2 > 2σ(F 2)] = 0.041

wR(F 2) = 0.115

S = 1.07

3025 reflections

174 parameters

H-atom parameters constrained

Δρmax = 0.24 e Å−3

Δρmin = −0.35 e Å−3

Absolute structure: Flack (1983 ▶), 1180 Friedel pairs

Flack parameter: −0.05 (8)

Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-32 (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶).

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680900734X/tk2382sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680900734X/tk2382Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C12H15N5OS	F(000) = 584
Mr = 277.35	Dx = 1.419 Mg m−3
Orthorhombic, P21212	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 2ab	Cell parameters from 5004 reflections
a = 15.479 (2) Å	θ = 2.6–28.1°
b = 7.1217 (10) Å	µ = 0.25 mm−1
c = 11.7802 (17) Å	T = 208 K
V = 1298.6 (3) Å3	Block, yellow
Z = 4	0.20 × 0.20 × 0.20 mm

Bruker D8 APEXII CCD area-detector diffractometer	3025 independent reflections
Radiation source: fine-focus sealed tube	2844 reflections with I > 2σ(I)
graphite	Rint = 0.043
phi and ω scans	θmax = 28.1°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −20→19
Tmin = 0.844, Tmax = 0.952	k = −4→9
6570 measured reflections	l = −15→13

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.041	w = 1/[σ2(Fo2) + (0.0703P)2 + 0.0815P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.115	(Δ/σ)max = 0.001
S = 1.07	Δρmax = 0.24 e Å−3
3025 reflections	Δρmin = −0.35 e Å−3
174 parameters	Extinction correction: SHELXL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraints	Extinction coefficient: 0.058 (5)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1180 Friedel pairs
Secondary atom site location: difference Fourier map	Flack parameter: −0.05 (8)

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.

	x	y	z	Uiso*/Ueq
C1	0.61092 (15)	0.3862 (4)	1.04598 (18)	0.0592 (6)
H1A	0.6660	0.3550	1.0825	0.071*
H1B	0.5758	0.4600	1.0989	0.071*
C2	0.62567 (13)	0.4931 (3)	0.93597 (14)	0.0471 (4)
H2A	0.6760	0.5761	0.9418	0.057*
H2B	0.5748	0.5677	0.9154	0.057*
C3	0.64143 (10)	0.3354 (3)	0.85008 (15)	0.0414 (4)
H3	0.6054	0.3562	0.7818	0.050*
C4	0.61086 (12)	0.1571 (3)	0.91240 (18)	0.0514 (5)
H4A	0.5721	0.0835	0.8639	0.062*
H4B	0.6603	0.0785	0.9334	0.062*
C5	0.86860 (11)	0.3275 (3)	0.84766 (15)	0.0456 (4)
H5	0.9228	0.3341	0.8835	0.055*
C6	0.85782 (9)	0.3006 (3)	0.72974 (14)	0.0355 (4)
C7	0.76781 (9)	0.3006 (2)	0.71461 (13)	0.0341 (3)
C8	0.92276 (9)	0.2767 (2)	0.64376 (13)	0.0341 (3)
C9	1.01122 (10)	0.2623 (3)	0.66996 (14)	0.0427 (4)
H9	1.0308	0.2671	0.7454	0.051*
C10	1.06733 (10)	0.2412 (3)	0.58192 (16)	0.0466 (4)
H10	1.1264	0.2289	0.5987	0.056*
C11	0.95801 (10)	0.2531 (3)	0.45560 (14)	0.0371 (3)
C12	0.81445 (13)	0.2818 (3)	0.31648 (16)	0.0526 (5)
H12A	0.7888	0.1785	0.3583	0.079*
H12B	0.7917	0.2833	0.2398	0.079*
H12C	0.8006	0.3993	0.3539	0.079*
N1	0.73257 (8)	0.3241 (2)	0.81741 (12)	0.0393 (3)
N2	0.79452 (9)	0.3423 (3)	0.90197 (12)	0.0488 (4)
N3	0.72268 (9)	0.2815 (3)	0.61696 (12)	0.0493 (4)
H3A	0.6665	0.2841	0.6182	0.059*
H3B	0.7498	0.2667	0.5529	0.059*
N4	1.04322 (9)	0.2367 (3)	0.47231 (13)	0.0453 (4)
N5	0.89635 (8)	0.2704 (2)	0.53396 (11)	0.0341 (3)
O1	0.56646 (9)	0.2206 (3)	1.01145 (14)	0.0630 (5)
S1	0.92940 (3)	0.25258 (9)	0.31179 (4)	0.05191 (18)

	U11	U22	U33	U12	U13	U23
C1	0.0580 (12)	0.0835 (15)	0.0362 (10)	0.0152 (11)	0.0142 (8)	0.0072 (10)
C2	0.0412 (9)	0.0661 (12)	0.0340 (8)	0.0096 (8)	0.0063 (7)	0.0034 (8)
C3	0.0248 (7)	0.0669 (11)	0.0325 (8)	0.0036 (7)	0.0002 (6)	0.0017 (8)
C4	0.0343 (8)	0.0675 (12)	0.0523 (11)	−0.0037 (8)	0.0026 (7)	0.0040 (10)
C5	0.0288 (7)	0.0790 (13)	0.0290 (7)	−0.0006 (8)	−0.0025 (6)	−0.0024 (8)
C6	0.0258 (7)	0.0512 (9)	0.0293 (7)	−0.0007 (6)	−0.0009 (5)	0.0000 (7)
C7	0.0269 (7)	0.0473 (8)	0.0282 (7)	0.0005 (6)	−0.0020 (5)	−0.0004 (6)
C8	0.0262 (6)	0.0443 (8)	0.0320 (7)	−0.0002 (6)	0.0010 (5)	0.0008 (6)
C9	0.0277 (7)	0.0655 (11)	0.0350 (7)	0.0007 (7)	−0.0029 (6)	0.0006 (9)
C10	0.0259 (7)	0.0684 (11)	0.0456 (9)	0.0031 (9)	0.0023 (6)	−0.0035 (9)
C11	0.0315 (7)	0.0471 (8)	0.0327 (7)	−0.0020 (7)	0.0027 (5)	−0.0045 (8)
C12	0.0438 (9)	0.0754 (13)	0.0385 (9)	0.0067 (9)	−0.0061 (7)	−0.0041 (10)
N1	0.0254 (6)	0.0642 (9)	0.0282 (6)	0.0003 (6)	−0.0011 (5)	−0.0007 (6)
N2	0.0290 (6)	0.0884 (12)	0.0290 (7)	−0.0003 (7)	−0.0043 (5)	−0.0034 (8)
N3	0.0284 (6)	0.0917 (13)	0.0278 (6)	0.0010 (7)	−0.0043 (5)	−0.0065 (8)
N4	0.0293 (6)	0.0657 (9)	0.0408 (7)	−0.0002 (7)	0.0045 (5)	−0.0076 (9)
N5	0.0287 (6)	0.0435 (7)	0.0300 (6)	−0.0016 (5)	0.0020 (4)	−0.0026 (6)
O1	0.0460 (8)	0.0826 (11)	0.0604 (9)	0.0041 (8)	0.0233 (6)	0.0185 (8)
S1	0.0394 (2)	0.0852 (4)	0.0311 (2)	−0.0016 (2)	0.00439 (15)	−0.0075 (2)

C1—O1	1.425 (3)	C7—N1	1.339 (2)
C1—C2	1.520 (3)	C7—N3	1.353 (2)
C1—H1A	0.9800	C8—N5	1.357 (2)
C1—H1B	0.9800	C8—C9	1.407 (2)
C2—C3	1.531 (3)	C9—C10	1.361 (2)
C2—H2A	0.9800	C9—H9	0.9400
C2—H2B	0.9800	C10—N4	1.344 (2)
C3—N1	1.4644 (18)	C10—H10	0.9400
C3—C4	1.541 (3)	C11—N5	1.3334 (19)
C3—H3	0.9900	C11—N4	1.339 (2)
C4—O1	1.428 (3)	C11—S1	1.7510 (17)
C4—H4A	0.9800	C12—S1	1.792 (2)
C4—H4B	0.9800	C12—H12A	0.9700
C5—N2	1.317 (2)	C12—H12B	0.9700
C5—C6	1.412 (2)	C12—H12C	0.9700
C5—H5	0.9400	N1—N2	1.3888 (18)
C6—C7	1.4046 (19)	N3—H3A	0.8700
C6—C8	1.437 (2)	N3—H3B	0.8700
O1—C1—C2	104.11 (19)	N1—C7—C6	106.83 (13)
O1—C1—H1A	110.9	N3—C7—C6	128.32 (15)
C2—C1—H1A	110.9	N5—C8—C9	119.98 (14)
O1—C1—H1B	110.9	N5—C8—C6	117.70 (13)
C2—C1—H1B	110.9	C9—C8—C6	122.32 (14)
H1A—C1—H1B	109.0	C10—C9—C8	117.50 (15)
C1—C2—C3	102.70 (18)	C10—C9—H9	121.2
C1—C2—H2A	111.2	C8—C9—H9	121.2
C3—C2—H2A	111.2	N4—C10—C9	123.87 (14)
C1—C2—H2B	111.2	N4—C10—H10	118.1
C3—C2—H2B	111.2	C9—C10—H10	118.1
H2A—C2—H2B	109.1	N5—C11—N4	127.69 (15)
N1—C3—C2	111.55 (15)	N5—C11—S1	119.28 (12)
N1—C3—C4	112.07 (16)	N4—C11—S1	113.03 (12)
C2—C3—C4	103.93 (14)	S1—C12—H12A	109.5
N1—C3—H3	109.7	S1—C12—H12B	109.5
C2—C3—H3	109.7	H12A—C12—H12B	109.5
C4—C3—H3	109.7	S1—C12—H12C	109.5
O1—C4—C3	106.03 (18)	H12A—C12—H12C	109.5
O1—C4—H4A	110.5	H12B—C12—H12C	109.5
C3—C4—H4A	110.5	C7—N1—N2	112.28 (13)
O1—C4—H4B	110.5	C7—N1—C3	129.58 (14)
C3—C4—H4B	110.5	N2—N1—C3	118.13 (13)
H4A—C4—H4B	108.7	C5—N2—N1	104.20 (14)
N2—C5—C6	112.69 (15)	C7—N3—H3A	120.0
N2—C5—H5	123.7	C7—N3—H3B	120.0
C6—C5—H5	123.7	H3A—N3—H3B	120.0
C7—C6—C5	104.00 (14)	C11—N4—C10	114.37 (14)
C7—C6—C8	127.19 (14)	C11—N5—C8	116.57 (13)
C5—C6—C8	128.81 (14)	C1—O1—C4	105.25 (15)
N1—C7—N3	124.85 (14)	C11—S1—C12	102.76 (8)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N4i	0.87	2.19	2.9731 (19)	150
N3—H3B···N5	0.87	2.28	2.8616 (19)	124

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N4i	0.87	2.19	2.9731 (19)	150
N3—H3B⋯N5	0.87	2.28	2.8616 (19)	124

Symmetry code: (i) .