organic compounds
(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
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).
Experimental
Crystal data
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Data collection: APEX2 (Bruker–Nonius, 2004); cell 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).
Supporting information
10.1107/S1600536809006369/tk2375sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809006369/tk2375Isup2.hkl
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 α]D20 was measured in methanol solution and yielded the values of -191.4° and +224.1°, respectively. The collected as Peak 1 was recrystallized from EtOAc/hexane to yield single crystals.
using 20–50% EtOAc in hexane to afford 5.85 g (67%) of yellow solid. The racemic product thus obtained was subjected to chiral on Chiralpak AS—H 21.2 x 250 mm column with 15% IPA in CO2 at 140 bar as (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 [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
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.Data collection: SMART (Bruker, 1997); cell
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).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. |
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 monochromator | 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 | Absolute structure parameter: 0.061 (12) |
C13H17N5OS | V = 1368.02 (15) Å3 |
Mr = 291.38 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 6.6209 (4) Å | µ = 2.14 mm−1 |
b = 14.0757 (9) Å | T = 100 K |
c = 14.6793 (10) Å | 0.12 × 0.10 × 0.06 mm |
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 = 0.882 | Rint = 0.021 |
9765 measured reflections |
R[F2 > 2σ(F2)] = 0.021 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.057 | Δρmax = 0.22 e Å−3 |
S = 1.06 | Δρmin = −0.16 e Å−3 |
2419 reflections | Absolute structure: Flack (1983), 964 Friedel pairs |
187 parameters | Absolute structure parameter: 0.061 (12) |
0 restraints |
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) |
Experimental details
Crystal data | |
Chemical formula | C13H17N5OS |
Mr | 291.38 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 6.6209 (4), 14.0757 (9), 14.6793 (10) |
V (Å3) | 1368.02 (15) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 2.14 |
Crystal size (mm) | 0.12 × 0.10 × 0.06 |
Data collection | |
Diffractometer | Bruker Kappa APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.783, 0.882 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9765, 2419, 2388 |
Rint | 0.021 |
(sin θ/λ)max (Å−1) | 0.601 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.021, 0.057, 1.06 |
No. of reflections | 2419 |
No. of parameters | 187 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.22, −0.16 |
Absolute structure | Flack (1983), 964 Friedel pairs |
Absolute structure parameter | 0.061 (12) |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008), ORTEP-32 (Farrugia, 1997), WinGX (Farrugia, 1999).
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) |
References
Bruker–Nonius (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
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Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838. CrossRef CAS IUCr Journals Google Scholar
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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).