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(R)-N-Methyl-4-[2-(methyl­sulfan­yl)pyrimidin-4-yl]-1-(tetra­hydro­furan-3-yl)-1H-pyrazol-5-amine

aPfizer Global Research and Development, La Jolla Labs, 10614 Science Center Drive, San Diego, CA 92121, USA, and bDepartment of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
*Correspondence e-mail: alex.yanovsky@pfizer.com

(Received 19 February 2009; accepted 20 February 2009; online 28 February 2009)

The chiral center at the substituted atom of the tetra­hydro­furanyl ring in the title compound, C13H17N5OS, has an R configuration. The methyl­sulfanylpyrimidine 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 methyl­sulfanylpyrimidine-pyrazole plane by 0.880 (4) Å. The secondary amine group participates in an intra­molecular 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[Golic, L., Sinur, A. & Tisler, M. (1993). Acta Chim. Slov. 40, 281-288.]).

[Scheme 1]

Experimental

Crystal data
  • C13H17N5OS

  • Mr = 291.38

  • Orthorhombic, P 21 21 21

  • 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[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.783, Tmax = 0.882

  • 9765 measured reflections

  • 2419 independent reflections

  • 2388 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.021

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 964 Friedel pairs

  • Flack parameter: 0.061 (12)

Table 1
Hydrogen-bond geometry (Å, °)

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

Data collection: APEX2 (Bruker–Nonius, 2004[Bruker-Nonius (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker–Nonius, 2004[Bruker-Nonius (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-32 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

The title compound (I) was obtained by N-methylation of 4-(2-(methylsulfanyl)pyrimidin-4-yl)-1-(tetrahydrofuran-2-yl)-1H-pyrazol-5-amine with methyl iodide. The racemic product was then separated with the help of chiral chromatography; (I) was collected as the earlier fraction when eluted with isopropyl alcohol using the Chiralpak column (99% ee; [α]D20 = -191.4°)

The present X-ray study unambiguously established the R-configuration of the chiral center at the C3 atom (Fig. 1).

The methylsulfanylpyrimidine group and pyrazolyl ring lie approximately in one plane. The maximum deviation from this plane being 0.070 (4) Å for the C13 atom; the displacement of methyl-C8 atom from this plane is 0.880 (4) Å. The orientation of the tetrahydrofuran ring can be characterized by the dihedral angle of 98.1 (3)° formed by the pyrimidine-pyrazolyl plane with the C2—C3—C4 plane.

The secondary amino group forms an intramolecular hydrogen bond with the N5 atom of the pyrimidine ring, Table 1, the geometry of this bond is similar to that observed in ethyl (Z)-2-amino-3-(4-pyrimidinyl)propenoate (Golic et al., 1993).

Related literature top

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

Experimental top

A solution of -(2-(methylsulfanyl)pyrimidin-4-yl)-1-(tetrahydrofuran-2-yl)-1H-pyrazol-5-amine (8.32 g, 30.0 mmol) in anhydrous THF (80 ml) was added dropwise to a suspension of hexane-washed NaH (60% dispersion in mineral oil, 1.92 g, 48.0 mmol) in anhydrous THF (20 ml) at room temperature. The resulting orange reaction mixture was stirred under nitrogen for 30 minutes; thereafter MeI (5.96 g, 42.0 mmol) was added dropwise. The reaction mixture was stirred at room temperature under nitrogen overnight and then quenched with aqueous NH4Cl (100 ml). EtOAc (200 ml) was added and layers were separated. The organic extract was washed with brine, dried over sodium sulfate, and concentrated to give the crude product, which was purified by flash chromatography using 20–50% EtOAc in hexane to afford 5.85 g (67%) of yellow solid. The racemic product thus obtained was subjected to chiral chromatography on Chiralpak AS—H 21.2 x 250 mm column with 15% IPA in CO2 at 140 bar as eluent (temp = 35°C; flow = 60 ml/min; UV detection at 260 nm). Two fractions corresponding to each of the enantiomers (Peak1 and Peak2) were collected and evaporated to dryness; specific rotation [α]D20 was measured in methanol solution and yielded the values of -191.4° and +224.1°, respectively. The enantiomer collected as Peak 1 was recrystallized from EtOAc/hexane to yield single crystals.

Refinement top

All H atoms bonded to C atoms were placed in geometrically calculated positions (C—H 0.95 Å, 0.98 Å, 0.99 Å, and 1.00 Å for aromatic-, methyl-, methylene- and methyine-H atoms, respectively) and included in the refinement in the riding model approximation. The H3N atom was located in a difference Fourier map and refined isotropically [N3—H3N 0.858 (15) Å]. The Uiso(H) were set to 1.2Ueq of the carrying atom for non-methyl and amine, and 1.5Ueq for methyl-H atoms.

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); 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).

Figures top
[Figure 1] Fig. 1. Molecular structure of (I), showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius.
(R)-N-Methyl-4-[2-(methylsulfanyl)pyrimidin-4-yl]-1- (tetrahydrofuran-3-yl)-1H-pyrazol-5-amine top
Crystal data top
C13H17N5OSF(000) = 616
Mr = 291.38Dx = 1.415 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 8684 reflections
a = 6.6209 (4) Åθ = 3.1–68.1°
b = 14.0757 (9) ŵ = 2.14 mm1
c = 14.6793 (10) ÅT = 100 K
V = 1368.02 (15) Å3Block, colorless
Z = 40.12 × 0.10 × 0.06 mm
Data collection top
Bruker Kappa APEXII CCD area-detector
diffractometer
2419 independent reflections
Radiation source: fine-focus sealed tube2388 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
ϕ and ω scansθmax = 67.9°, θmin = 4.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 77
Tmin = 0.783, Tmax = 0.882k = 1616
9765 measured reflectionsl = 1117
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH 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 = 1.06Δρmax = 0.22 e Å3
2419 reflectionsΔρmin = 0.16 e Å3
187 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0024 (2)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 964 Friedel pairs
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.061 (12)
Crystal data top
C13H17N5OSV = 1368.02 (15) Å3
Mr = 291.38Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 6.6209 (4) ŵ = 2.14 mm1
b = 14.0757 (9) ÅT = 100 K
c = 14.6793 (10) Å0.12 × 0.10 × 0.06 mm
Data collection top
Bruker Kappa APEXII CCD area-detector
diffractometer
2419 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
2388 reflections with I > 2σ(I)
Tmin = 0.783, Tmax = 0.882Rint = 0.021
9765 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.021H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.057Δρmax = 0.22 e Å3
S = 1.06Δρmin = 0.16 e Å3
2419 reflectionsAbsolute structure: Flack (1983), 964 Friedel pairs
187 parametersAbsolute structure parameter: 0.061 (12)
0 restraints
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
xyzUiso*/Ueq
C10.4029 (2)0.30990 (12)0.04871 (10)0.0272 (3)
H1A0.43950.24460.06760.033*
H1B0.32690.30690.00930.033*
C20.2806 (2)0.35928 (10)0.12196 (10)0.0213 (3)
H2A0.18600.31470.15190.026*
H2B0.20340.41340.09660.026*
C30.4445 (2)0.39343 (9)0.18853 (8)0.0167 (3)
H30.41330.45950.20930.020*
C40.6387 (2)0.39367 (10)0.12981 (10)0.0214 (3)
H4A0.70170.45750.13020.026*
H4B0.73750.34720.15390.026*
C50.4646 (2)0.19552 (9)0.33361 (8)0.0149 (3)
H50.46490.12890.34410.018*
C60.4610 (2)0.26374 (9)0.40411 (9)0.0138 (3)
C70.4621 (2)0.35123 (9)0.35763 (8)0.0135 (2)
C80.5746 (2)0.52007 (10)0.36114 (10)0.0215 (3)
H8A0.67040.49700.31530.032*
H8B0.64900.54810.41220.032*
H8C0.48650.56820.33380.032*
C90.4629 (2)0.24930 (9)0.50139 (9)0.0135 (3)
C100.4728 (2)0.15830 (9)0.54074 (9)0.0162 (3)
H100.47730.10260.50420.019*
C110.4755 (2)0.15340 (9)0.63402 (9)0.0159 (3)
H110.48260.09240.66150.019*
C120.4595 (2)0.31224 (9)0.64505 (8)0.0136 (2)
C130.4376 (2)0.37321 (10)0.82303 (9)0.0210 (3)
H13A0.32890.32620.82750.032*
H13B0.41090.42560.86540.032*
H13C0.56660.34320.83860.032*
N10.46330 (18)0.33043 (7)0.26754 (7)0.0148 (2)
N20.46738 (18)0.23371 (7)0.25178 (8)0.0166 (2)
N30.4520 (2)0.44067 (7)0.39416 (7)0.0171 (2)
N40.46873 (18)0.22994 (7)0.68912 (7)0.0153 (2)
N50.45642 (17)0.32731 (7)0.55510 (7)0.0142 (2)
O10.57971 (18)0.36833 (9)0.03959 (7)0.0318 (3)
S10.44904 (5)0.41854 (2)0.70856 (2)0.01652 (9)
H3N0.456 (3)0.4369 (11)0.4524 (10)0.020*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0362 (9)0.0310 (8)0.0143 (7)0.0093 (7)0.0007 (6)0.0027 (6)
C20.0218 (7)0.0245 (7)0.0178 (7)0.0019 (6)0.0048 (6)0.0038 (6)
C30.0195 (6)0.0169 (6)0.0136 (6)0.0011 (6)0.0012 (6)0.0028 (5)
C40.0232 (7)0.0236 (7)0.0173 (7)0.0037 (6)0.0020 (6)0.0017 (6)
C50.0144 (6)0.0143 (6)0.0160 (6)0.0004 (6)0.0003 (6)0.0005 (5)
C60.0117 (6)0.0151 (6)0.0146 (6)0.0003 (5)0.0006 (6)0.0005 (5)
C70.0099 (5)0.0168 (6)0.0139 (6)0.0004 (5)0.0020 (6)0.0000 (5)
C80.0249 (8)0.0185 (6)0.0212 (7)0.0053 (6)0.0008 (6)0.0003 (5)
C90.0082 (6)0.0170 (6)0.0154 (6)0.0009 (5)0.0003 (6)0.0002 (5)
C100.0150 (6)0.0153 (6)0.0183 (6)0.0006 (6)0.0001 (6)0.0003 (5)
C110.0131 (6)0.0156 (6)0.0190 (6)0.0003 (5)0.0002 (6)0.0036 (5)
C120.0096 (6)0.0158 (6)0.0154 (6)0.0008 (6)0.0005 (6)0.0004 (5)
C130.0287 (8)0.0208 (7)0.0137 (6)0.0034 (6)0.0004 (6)0.0009 (5)
N10.0183 (5)0.0138 (5)0.0122 (5)0.0015 (5)0.0001 (5)0.0010 (4)
N20.0186 (5)0.0137 (5)0.0176 (5)0.0017 (5)0.0003 (5)0.0018 (4)
N30.0240 (6)0.0136 (5)0.0137 (5)0.0014 (5)0.0036 (5)0.0002 (4)
N40.0135 (5)0.0160 (5)0.0164 (5)0.0004 (5)0.0007 (5)0.0017 (4)
N50.0136 (5)0.0149 (5)0.0141 (5)0.0005 (5)0.0010 (5)0.0013 (4)
O10.0363 (6)0.0441 (7)0.0152 (5)0.0122 (5)0.0067 (5)0.0030 (5)
S10.02089 (16)0.01483 (15)0.01383 (15)0.00088 (14)0.00033 (14)0.00007 (12)
Geometric parameters (Å, º) top
C1—O11.4369 (18)C8—N31.4639 (17)
C1—C21.515 (2)C8—H8A0.9800
C1—H1A0.9900C8—H8B0.9800
C1—H1B0.9900C8—H8C0.9800
C2—C31.5373 (19)C9—N51.3525 (17)
C2—H2A0.9900C9—C101.4066 (18)
C2—H2B0.9900C10—C111.3710 (18)
C3—N11.4652 (15)C10—H100.9500
C3—C41.5484 (19)C11—N41.3479 (17)
C3—H31.0000C11—H110.9500
C4—O11.4262 (18)C12—N41.3282 (16)
C4—H4A0.9900C12—N51.3375 (16)
C4—H4B0.9900C12—S11.7644 (13)
C5—N21.3162 (16)C13—S11.7990 (13)
C5—C61.4119 (17)C13—H13A0.9800
C5—H50.9500C13—H13B0.9800
C6—C71.4080 (17)C13—H13C0.9800
C6—C91.4425 (17)N1—N21.3811 (14)
C7—N11.3545 (16)N3—H3N0.858 (15)
C7—N31.3700 (16)
O1—C1—C2103.83 (12)N3—C8—H8B109.5
O1—C1—H1A111.0H8A—C8—H8B109.5
C2—C1—H1A111.0N3—C8—H8C109.5
O1—C1—H1B111.0H8A—C8—H8C109.5
C2—C1—H1B111.0H8B—C8—H8C109.5
H1A—C1—H1B109.0N5—C9—C10120.10 (12)
C1—C2—C3102.56 (12)N5—C9—C6117.54 (11)
C1—C2—H2A111.3C10—C9—C6122.36 (12)
C3—C2—H2A111.3C11—C10—C9117.16 (12)
C1—C2—H2B111.3C11—C10—H10121.4
C3—C2—H2B111.3C9—C10—H10121.4
H2A—C2—H2B109.2N4—C11—C10123.96 (12)
N1—C3—C2111.96 (11)N4—C11—H11118.0
N1—C3—C4111.79 (11)C10—C11—H11118.0
C2—C3—C4103.48 (10)N4—C12—N5128.31 (12)
N1—C3—H3109.8N4—C12—S1118.95 (9)
C2—C3—H3109.8N5—C12—S1112.74 (9)
C4—C3—H3109.8S1—C13—H13A109.5
O1—C4—C3106.78 (12)S1—C13—H13B109.5
O1—C4—H4A110.4H13A—C13—H13B109.5
C3—C4—H4A110.4S1—C13—H13C109.5
O1—C4—H4B110.4H13A—C13—H13C109.5
C3—C4—H4B110.4H13B—C13—H13C109.5
H4A—C4—H4B108.6C7—N1—N2112.13 (10)
N2—C5—C6113.04 (11)C7—N1—C3129.90 (11)
N2—C5—H5123.5N2—N1—C3117.75 (10)
C6—C5—H5123.5C5—N2—N1104.45 (10)
C7—C6—C5103.86 (11)C7—N3—C8123.02 (12)
C7—C6—C9127.08 (12)C7—N3—H3N109.4 (10)
C5—C6—C9129.03 (12)C8—N3—H3N111.1 (11)
N1—C7—N3125.53 (11)C12—N4—C11113.97 (11)
N1—C7—C6106.50 (11)C12—N5—C9116.49 (11)
N3—C7—C6127.87 (11)C4—O1—C1106.25 (11)
N3—C8—H8A109.5C12—S1—C13101.21 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3N···N50.858 (15)2.157 (15)2.8510 (14)137.9 (14)

Experimental details

Crystal data
Chemical formulaC13H17N5OS
Mr291.38
Crystal system, space groupOrthorhombic, P212121
Temperature (K)100
a, b, c (Å)6.6209 (4), 14.0757 (9), 14.6793 (10)
V3)1368.02 (15)
Z4
Radiation typeCu Kα
µ (mm1)2.14
Crystal size (mm)0.12 × 0.10 × 0.06
Data collection
DiffractometerBruker Kappa APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.783, 0.882
No. of measured, independent and
observed [I > 2σ(I)] reflections
9765, 2419, 2388
Rint0.021
(sin θ/λ)max1)0.601
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.057, 1.06
No. of reflections2419
No. of parameters187
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.16
Absolute structureFlack (1983), 964 Friedel pairs
Absolute structure parameter0.061 (12)

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008), ORTEP-32 (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3N···N50.858 (15)2.157 (15)2.8510 (14)137.9 (14)
 

References

First citationBruker–Nonius (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBurla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381–388.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationGolic, L., Sinur, A. & Tisler, M. (1993). Acta Chim. Slov. 40, 281–288.  CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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