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

The chiral center at the substituted atom of the tetra-hydro-furanyl ring in the title compound, C(13)H(17)N(5)OS, has an R configuration. The methyl-sulfanylpyrimidine group and the pyrazole ring are almost coplanar [the maximum deviation from this plane is 0.070 (4) Å], the N-Me substituent being displaced from the methyl-sulfanylpyrimidine-pyrazole plane by 0.880 (4) Å. The secondary amine group participates in an intra-molecular hydrogen bond with the pyrimidine N atom in position 3.

Related literature

For the structures of related pyrimidine derivatives with similar intra­molecular hydrogen bonds, see: Golic et al. (1993 ▶).

Experimental

Crystal data

C13H17N5OS

M = 291.38

Orthorhombic,

a = 6.6209 (4) Å

b = 14.0757 (9) Å

c = 14.6793 (10) Å

V = 1368.02 (15) Å3

Z = 4

Cu Kα radiation

μ = 2.14 mm−1

T = 100 K

0.12 × 0.10 × 0.06 mm

Data collection

Bruker Kappa APEXII CCD area-detector diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T min = 0.783, T max = 0.882

9765 measured reflections

2419 independent reflections

2388 reflections with I > 2σ(I)

R int = 0.021

Refinement

R[F 2 > 2σ(F 2)] = 0.021

wR(F 2) = 0.057

S = 1.06

2419 reflections

187 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.22 e Å−3

Δρmin = −0.16 e Å−3

Absolute structure: Flack (1983 ▶), 964 Friedel pairs

Flack parameter: 0.061 (12)

Data collection: APEX2 (Bruker–Nonius, 2004 ▶); cell refinement: SAINT (Bruker–Nonius, 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/S1600536809006369/tk2375sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006369/tk2375Isup2.hkl

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

C13H17N5OS	F(000) = 616
Mr = 291.38	Dx = 1.415 Mg m−3
Orthorhombic, P212121	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 8684 reflections
a = 6.6209 (4) Å	θ = 3.1–68.1°
b = 14.0757 (9) Å	µ = 2.14 mm−1
c = 14.6793 (10) Å	T = 100 K
V = 1368.02 (15) Å3	Block, colorless
Z = 4	0.12 × 0.10 × 0.06 mm

Bruker Kappa APEXII CCD area-detector diffractometer	2419 independent reflections
Radiation source: fine-focus sealed tube	2388 reflections with I > 2σ(I)
graphite	Rint = 0.021
φ and ω scans	θmax = 67.9°, θmin = 4.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −7→7
Tmin = 0.783, Tmax = 0.882	k = −16→16
9765 measured reflections	l = −11→17

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.021	w = 1/[σ2(Fo2) + (0.0319P)2 + 0.2281P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.057	(Δ/σ)max = 0.001
S = 1.06	Δρmax = 0.22 e Å−3
2419 reflections	Δρmin = −0.16 e Å−3
187 parameters	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraints	Extinction coefficient: 0.0024 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 964 Friedel pairs
Secondary atom site location: difference Fourier map	Flack parameter: 0.061 (12)

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	0.4029 (2)	0.30990 (12)	0.04871 (10)	0.0272 (3)
H1A	0.4395	0.2446	0.0676	0.033*
H1B	0.3269	0.3069	−0.0093	0.033*
C2	0.2806 (2)	0.35928 (10)	0.12196 (10)	0.0213 (3)
H2A	0.1860	0.3147	0.1519	0.026*
H2B	0.2034	0.4134	0.0966	0.026*
C3	0.4445 (2)	0.39343 (9)	0.18853 (8)	0.0167 (3)
H3	0.4133	0.4595	0.2093	0.020*
C4	0.6387 (2)	0.39367 (10)	0.12981 (10)	0.0214 (3)
H4A	0.7017	0.4575	0.1302	0.026*
H4B	0.7375	0.3472	0.1539	0.026*
C5	0.4646 (2)	0.19552 (9)	0.33361 (8)	0.0149 (3)
H5	0.4649	0.1289	0.3441	0.018*
C6	0.4610 (2)	0.26374 (9)	0.40411 (9)	0.0138 (3)
C7	0.4621 (2)	0.35123 (9)	0.35763 (8)	0.0135 (2)
C8	0.5746 (2)	0.52007 (10)	0.36114 (10)	0.0215 (3)
H8A	0.6704	0.4970	0.3153	0.032*
H8B	0.6490	0.5481	0.4122	0.032*
H8C	0.4865	0.5682	0.3338	0.032*
C9	0.4629 (2)	0.24930 (9)	0.50139 (9)	0.0135 (3)
C10	0.4728 (2)	0.15830 (9)	0.54074 (9)	0.0162 (3)
H10	0.4773	0.1026	0.5042	0.019*
C11	0.4755 (2)	0.15340 (9)	0.63402 (9)	0.0159 (3)
H11	0.4826	0.0924	0.6615	0.019*
C12	0.4595 (2)	0.31224 (9)	0.64505 (8)	0.0136 (2)
C13	0.4376 (2)	0.37321 (10)	0.82303 (9)	0.0210 (3)
H13A	0.3289	0.3262	0.8275	0.032*
H13B	0.4109	0.4256	0.8654	0.032*
H13C	0.5666	0.3432	0.8386	0.032*
N1	0.46330 (18)	0.33043 (7)	0.26754 (7)	0.0148 (2)
N2	0.46738 (18)	0.23371 (7)	0.25178 (8)	0.0166 (2)
N3	0.4520 (2)	0.44067 (7)	0.39416 (7)	0.0171 (2)
N4	0.46873 (18)	0.22994 (7)	0.68912 (7)	0.0153 (2)
N5	0.45642 (17)	0.32731 (7)	0.55510 (7)	0.0142 (2)
O1	0.57971 (18)	0.36833 (9)	0.03959 (7)	0.0318 (3)
S1	0.44904 (5)	0.41854 (2)	0.70856 (2)	0.01652 (9)
H3N	0.456 (3)	0.4369 (11)	0.4524 (10)	0.020*

	U11	U22	U33	U12	U13	U23
C1	0.0362 (9)	0.0310 (8)	0.0143 (7)	−0.0093 (7)	−0.0007 (6)	−0.0027 (6)
C2	0.0218 (7)	0.0245 (7)	0.0178 (7)	−0.0019 (6)	−0.0048 (6)	0.0038 (6)
C3	0.0195 (6)	0.0169 (6)	0.0136 (6)	0.0011 (6)	−0.0012 (6)	0.0028 (5)
C4	0.0232 (7)	0.0236 (7)	0.0173 (7)	−0.0037 (6)	0.0020 (6)	0.0017 (6)
C5	0.0144 (6)	0.0143 (6)	0.0160 (6)	0.0004 (6)	0.0003 (6)	−0.0005 (5)
C6	0.0117 (6)	0.0151 (6)	0.0146 (6)	−0.0003 (5)	0.0006 (6)	0.0005 (5)
C7	0.0099 (5)	0.0168 (6)	0.0139 (6)	0.0004 (5)	0.0020 (6)	0.0000 (5)
C8	0.0249 (8)	0.0185 (6)	0.0212 (7)	−0.0053 (6)	0.0008 (6)	0.0003 (5)
C9	0.0082 (6)	0.0170 (6)	0.0154 (6)	−0.0009 (5)	−0.0003 (6)	−0.0002 (5)
C10	0.0150 (6)	0.0153 (6)	0.0183 (6)	0.0006 (6)	−0.0001 (6)	0.0003 (5)
C11	0.0131 (6)	0.0156 (6)	0.0190 (6)	−0.0003 (5)	−0.0002 (6)	0.0036 (5)
C12	0.0096 (6)	0.0158 (6)	0.0154 (6)	−0.0008 (6)	−0.0005 (6)	0.0004 (5)
C13	0.0287 (8)	0.0208 (7)	0.0137 (6)	−0.0034 (6)	0.0004 (6)	0.0009 (5)
N1	0.0183 (5)	0.0138 (5)	0.0122 (5)	0.0015 (5)	0.0001 (5)	0.0010 (4)
N2	0.0186 (5)	0.0137 (5)	0.0176 (5)	0.0017 (5)	0.0003 (5)	−0.0018 (4)
N3	0.0240 (6)	0.0136 (5)	0.0137 (5)	−0.0014 (5)	0.0036 (5)	0.0002 (4)
N4	0.0135 (5)	0.0160 (5)	0.0164 (5)	0.0004 (5)	−0.0007 (5)	0.0017 (4)
N5	0.0136 (5)	0.0149 (5)	0.0141 (5)	−0.0005 (5)	0.0010 (5)	0.0013 (4)
O1	0.0363 (6)	0.0441 (7)	0.0152 (5)	−0.0122 (5)	0.0067 (5)	−0.0030 (5)
S1	0.02089 (16)	0.01483 (15)	0.01383 (15)	−0.00088 (14)	−0.00033 (14)	0.00007 (12)

C1—O1	1.4369 (18)	C8—N3	1.4639 (17)
C1—C2	1.515 (2)	C8—H8A	0.9800
C1—H1A	0.9900	C8—H8B	0.9800
C1—H1B	0.9900	C8—H8C	0.9800
C2—C3	1.5373 (19)	C9—N5	1.3525 (17)
C2—H2A	0.9900	C9—C10	1.4066 (18)
C2—H2B	0.9900	C10—C11	1.3710 (18)
C3—N1	1.4652 (15)	C10—H10	0.9500
C3—C4	1.5484 (19)	C11—N4	1.3479 (17)
C3—H3	1.0000	C11—H11	0.9500
C4—O1	1.4262 (18)	C12—N4	1.3282 (16)
C4—H4A	0.9900	C12—N5	1.3375 (16)
C4—H4B	0.9900	C12—S1	1.7644 (13)
C5—N2	1.3162 (16)	C13—S1	1.7990 (13)
C5—C6	1.4119 (17)	C13—H13A	0.9800
C5—H5	0.9500	C13—H13B	0.9800
C6—C7	1.4080 (17)	C13—H13C	0.9800
C6—C9	1.4425 (17)	N1—N2	1.3811 (14)
C7—N1	1.3545 (16)	N3—H3N	0.858 (15)
C7—N3	1.3700 (16)
O1—C1—C2	103.83 (12)	N3—C8—H8B	109.5
O1—C1—H1A	111.0	H8A—C8—H8B	109.5
C2—C1—H1A	111.0	N3—C8—H8C	109.5
O1—C1—H1B	111.0	H8A—C8—H8C	109.5
C2—C1—H1B	111.0	H8B—C8—H8C	109.5
H1A—C1—H1B	109.0	N5—C9—C10	120.10 (12)
C1—C2—C3	102.56 (12)	N5—C9—C6	117.54 (11)
C1—C2—H2A	111.3	C10—C9—C6	122.36 (12)
C3—C2—H2A	111.3	C11—C10—C9	117.16 (12)
C1—C2—H2B	111.3	C11—C10—H10	121.4
C3—C2—H2B	111.3	C9—C10—H10	121.4
H2A—C2—H2B	109.2	N4—C11—C10	123.96 (12)
N1—C3—C2	111.96 (11)	N4—C11—H11	118.0
N1—C3—C4	111.79 (11)	C10—C11—H11	118.0
C2—C3—C4	103.48 (10)	N4—C12—N5	128.31 (12)
N1—C3—H3	109.8	N4—C12—S1	118.95 (9)
C2—C3—H3	109.8	N5—C12—S1	112.74 (9)
C4—C3—H3	109.8	S1—C13—H13A	109.5
O1—C4—C3	106.78 (12)	S1—C13—H13B	109.5
O1—C4—H4A	110.4	H13A—C13—H13B	109.5
C3—C4—H4A	110.4	S1—C13—H13C	109.5
O1—C4—H4B	110.4	H13A—C13—H13C	109.5
C3—C4—H4B	110.4	H13B—C13—H13C	109.5
H4A—C4—H4B	108.6	C7—N1—N2	112.13 (10)
N2—C5—C6	113.04 (11)	C7—N1—C3	129.90 (11)
N2—C5—H5	123.5	N2—N1—C3	117.75 (10)
C6—C5—H5	123.5	C5—N2—N1	104.45 (10)
C7—C6—C5	103.86 (11)	C7—N3—C8	123.02 (12)
C7—C6—C9	127.08 (12)	C7—N3—H3N	109.4 (10)
C5—C6—C9	129.03 (12)	C8—N3—H3N	111.1 (11)
N1—C7—N3	125.53 (11)	C12—N4—C11	113.97 (11)
N1—C7—C6	106.50 (11)	C12—N5—C9	116.49 (11)
N3—C7—C6	127.87 (11)	C4—O1—C1	106.25 (11)
N3—C8—H8A	109.5	C12—S1—C13	101.21 (6)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N5	0.858 (15)	2.157 (15)	2.8510 (14)	137.9 (14)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N5	0.858 (15)	2.157 (15)	2.8510 (14)	137.9 (14)