Literature DB >> 21583904

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

Zhengyu Liu, Kevin K-C Liu, Arnold L Rheingold, Antonio Dipasquale, Alex Yanovsky.   

Abstract

The title compound, C(13)H(17)N(5)OS, was obtained by cyclo-addition of 2-[2-(methyl-sulfan-yl)pyrimidin-4-yl]-3-oxo-propane-nitrile with (tetra-hydro-furan-3-yl)hydrazine dihydro-chloride and subsequent N-methyl-ation of 4-[2-(methyl-sulfan-yl)-pyrimidin-4-yl]-1-(tetra-hydro-furan-2-yl)-1H-pyrazol-5-amine with methyl iodide. The two mol-ecules in the asymmetric unit have opposite absolute configurations and are related by a noncrystallographic inversion center. Both feature intra-mol-ecular N-H⋯N hydrogen bonds. The geometry of the mol-ecules is similar to that observed in the structure of a single enanti-omer of the title compound.

Entities:  

Year:  2009        PMID: 21583904      PMCID: PMC2977768          DOI: 10.1107/S1600536809014317

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the structure of the R-enanti­omer component of the racemic title compound, see: Liu et al. (2009a ▶). For details of the synthesis of the title compound, see: Liu et al. (2009a ▶,b ▶).

Experimental

Crystal data

C13H17N5OS M = 291.38 Monoclinic, a = 15.7404 (5) Å b = 10.1515 (3) Å c = 18.9644 (6) Å β = 112.829 (1)° V = 2792.92 (15) Å3 Z = 8 Cu Kα radiation μ = 2.10 mm−1 T = 100 K 0.30 × 0.20 × 0.20 mm

Data collection

Bruker P4/APEX CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T min = 0.572, T max = 0.679 18618 measured reflections 5007 independent reflections 4521 reflections with I > 2σ(I) R int = 0.030

Refinement

R[F 2 > 2σ(F 2)] = 0.043 wR(F 2) = 0.119 S = 1.05 5007 reflections 371 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.88 e Å−3 Δρmin = −0.32 e Å−3 Data collection: SMART (Bruker, 1997 ▶); cell refinement: SAINT (Bruker, 1997 ▶); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); 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/S1600536809014317/dn2448sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809014317/dn2448Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H17N5OSF(000) = 1232
Mr = 291.38Dx = 1.386 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ynCell parameters from 1033 reflections
a = 15.7404 (5) Åθ = 4.9–54.9°
b = 10.1515 (3) ŵ = 2.10 mm1
c = 18.9644 (6) ÅT = 100 K
β = 112.829 (1)°Block, colorless
V = 2792.92 (15) Å30.30 × 0.20 × 0.20 mm
Z = 8
Bruker P4/APEX CCD diffractometer5007 independent reflections
Radiation source: fine-focus sealed tube4521 reflections with I > 2σ(I)
graphiteRint = 0.030
ω scansθmax = 68.6°, θmin = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −18→18
Tmin = 0.572, Tmax = 0.679k = −11→12
18618 measured reflectionsl = −22→21
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0596P)2 + 1.859P] where P = (Fo2 + 2Fc2)/3
5007 reflections(Δ/σ)max = 0.001
371 parametersΔρmax = 0.88 e Å3
0 restraintsΔρmin = −0.32 e Å3
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.
xyzUiso*/Ueq
C10.22461 (16)−0.1765 (2)0.31756 (13)0.0393 (5)
H1A0.1969−0.25210.28340.047*
H1B0.2861−0.15830.31700.047*
C20.16265 (14)−0.0551 (2)0.29178 (11)0.0310 (4)
H2A0.0969−0.08050.26700.037*
H2B0.1794−0.00080.25580.037*
C30.18197 (12)0.01907 (18)0.36747 (10)0.0213 (4)
H30.21910.09980.36910.026*
C40.24143 (13)−0.07910 (18)0.42835 (11)0.0249 (4)
H4A0.3068−0.05110.44890.030*
H4B0.2204−0.08360.47120.030*
C5−0.01506 (12)0.02935 (18)0.41206 (10)0.0208 (4)
H5−0.0595−0.01010.42790.025*
C6−0.01006 (12)0.16645 (17)0.40075 (10)0.0199 (4)
C70.06411 (12)0.17913 (17)0.37729 (10)0.0196 (4)
C80.11656 (13)0.29925 (19)0.28860 (11)0.0263 (4)
H8A0.18020.27260.29920.039*
H8B0.10690.38990.26930.039*
H8C0.07400.24020.25010.039*
C9−0.06565 (12)0.27261 (18)0.41090 (10)0.0203 (4)
C10−0.13890 (13)0.25167 (19)0.43403 (11)0.0256 (4)
H10−0.15660.16540.44230.031*
C11−0.18401 (13)0.3611 (2)0.44425 (11)0.0289 (4)
H11−0.23300.34850.46110.035*
C12−0.09392 (12)0.49396 (18)0.40780 (10)0.0231 (4)
C130.02328 (15)0.6340 (2)0.35791 (13)0.0331 (5)
H13A0.07310.58520.39710.050*
H13B0.04620.72010.34990.050*
H13C0.00150.58420.30990.050*
C14−0.23088 (16)0.4429 (2)0.17690 (13)0.0387 (5)
H14A−0.29200.42200.17750.046*
H14B−0.20540.52070.20980.046*
C15−0.16593 (14)0.3254 (2)0.20499 (11)0.0324 (5)
H15A−0.18160.27140.24170.039*
H15B−0.10090.35440.22950.039*
C16−0.18296 (12)0.24857 (18)0.13061 (10)0.0220 (4)
H16−0.21890.16690.12970.026*
C17−0.24264 (13)0.34274 (19)0.06774 (11)0.0271 (4)
H17A−0.21900.34840.02650.033*
H17B−0.30710.31100.04540.033*
C180.01589 (12)0.24134 (17)0.08857 (10)0.0204 (4)
H180.06010.28130.07260.025*
C190.01176 (12)0.10435 (17)0.10037 (10)0.0191 (4)
C20−0.06290 (12)0.09089 (17)0.12278 (9)0.0188 (3)
C21−0.11957 (13)−0.03136 (19)0.20869 (11)0.0262 (4)
H21A−0.08080.03120.24710.039*
H21B−0.1069−0.12100.22930.039*
H21C−0.1847−0.01030.19580.039*
C220.06828 (11)−0.00076 (18)0.09110 (9)0.0193 (4)
C230.14461 (12)0.02003 (18)0.07200 (10)0.0224 (4)
H230.16310.10630.06460.027*
C240.19188 (12)−0.08969 (19)0.06428 (11)0.0247 (4)
H240.2430−0.07720.05020.030*
C250.09580 (12)−0.22284 (18)0.09390 (10)0.0216 (4)
C26−0.03578 (16)−0.3636 (2)0.12571 (14)0.0366 (5)
H26A−0.0215−0.31330.17300.055*
H26B−0.0608−0.44980.13080.055*
H26C−0.0814−0.31550.08290.055*
N10.09784 (10)0.05689 (15)0.37756 (8)0.0199 (3)
N20.04867 (10)−0.03777 (15)0.39826 (8)0.0217 (3)
N30.09942 (11)0.29183 (15)0.35925 (9)0.0220 (3)
N4−0.16316 (11)0.48479 (16)0.43195 (10)0.0283 (4)
N5−0.04410 (10)0.39615 (15)0.39708 (8)0.0212 (3)
N6−0.09717 (10)0.21269 (14)0.12244 (8)0.0197 (3)
N7−0.04837 (10)0.30785 (14)0.10218 (8)0.0215 (3)
N8−0.09920 (11)−0.02230 (15)0.13985 (9)0.0215 (3)
N90.16958 (10)−0.21327 (16)0.07561 (9)0.0249 (3)
N100.04399 (10)−0.12520 (15)0.10180 (8)0.0200 (3)
O10.23183 (11)−0.20351 (14)0.39248 (9)0.0365 (4)
O2−0.23835 (12)0.46761 (15)0.10208 (9)0.0398 (4)
S1−0.07026 (3)0.65654 (5)0.38885 (3)0.02884 (14)
S20.06756 (3)−0.38593 (4)0.10801 (3)0.02817 (14)
H3N0.0715 (16)0.355 (2)0.3657 (13)0.034*
H8N−0.0682 (16)−0.085 (2)0.1349 (13)0.034*
U11U22U33U12U13U23
C10.0401 (12)0.0408 (13)0.0374 (12)0.0094 (10)0.0153 (9)−0.0107 (10)
C20.0277 (10)0.0418 (12)0.0246 (10)0.0030 (9)0.0113 (8)−0.0049 (8)
C30.0195 (8)0.0206 (9)0.0254 (9)0.0011 (7)0.0106 (7)0.0006 (7)
C40.0231 (9)0.0236 (9)0.0296 (10)0.0047 (7)0.0120 (8)0.0033 (7)
C50.0199 (8)0.0209 (9)0.0222 (9)−0.0021 (7)0.0087 (7)0.0011 (7)
C60.0193 (8)0.0195 (9)0.0207 (8)−0.0008 (7)0.0075 (7)0.0006 (7)
C70.0184 (8)0.0184 (8)0.0209 (8)−0.0011 (7)0.0063 (7)−0.0005 (7)
C80.0240 (9)0.0270 (10)0.0272 (9)0.0014 (8)0.0091 (7)0.0066 (8)
C90.0183 (8)0.0200 (9)0.0205 (8)0.0001 (7)0.0054 (7)0.0005 (7)
C100.0228 (9)0.0240 (10)0.0313 (10)−0.0004 (7)0.0120 (8)0.0028 (7)
C110.0230 (9)0.0306 (10)0.0366 (11)0.0020 (8)0.0153 (8)0.0025 (8)
C120.0199 (8)0.0225 (9)0.0239 (9)0.0006 (7)0.0051 (7)−0.0018 (7)
C130.0408 (11)0.0218 (10)0.0438 (12)−0.0044 (8)0.0242 (10)−0.0009 (8)
C140.0423 (12)0.0363 (12)0.0386 (12)0.0071 (10)0.0168 (10)−0.0073 (9)
C150.0290 (10)0.0423 (12)0.0265 (10)0.0078 (9)0.0114 (8)−0.0052 (9)
C160.0209 (8)0.0214 (9)0.0257 (9)0.0022 (7)0.0113 (7)0.0010 (7)
C170.0253 (9)0.0277 (10)0.0298 (10)0.0070 (8)0.0123 (8)0.0044 (8)
C180.0207 (8)0.0178 (9)0.0235 (9)−0.0015 (7)0.0092 (7)−0.0009 (7)
C190.0191 (8)0.0180 (9)0.0195 (8)−0.0013 (7)0.0066 (7)−0.0007 (6)
C200.0195 (8)0.0166 (8)0.0188 (8)−0.0008 (7)0.0057 (6)−0.0006 (6)
C210.0281 (9)0.0249 (10)0.0263 (9)0.0018 (8)0.0112 (8)0.0062 (7)
C220.0177 (8)0.0204 (9)0.0172 (8)−0.0002 (7)0.0040 (6)−0.0005 (6)
C230.0201 (8)0.0209 (9)0.0252 (9)−0.0019 (7)0.0078 (7)0.0000 (7)
C240.0174 (8)0.0267 (10)0.0295 (10)0.0019 (7)0.0084 (7)−0.0005 (7)
C250.0213 (8)0.0195 (9)0.0217 (9)0.0019 (7)0.0057 (7)−0.0009 (7)
C260.0449 (12)0.0194 (10)0.0575 (14)−0.0029 (9)0.0329 (11)0.0000 (9)
N10.0189 (7)0.0181 (7)0.0243 (7)−0.0004 (6)0.0102 (6)0.0012 (6)
N20.0231 (7)0.0177 (7)0.0251 (8)−0.0026 (6)0.0101 (6)0.0021 (6)
N30.0229 (8)0.0170 (7)0.0292 (8)−0.0001 (6)0.0134 (6)0.0018 (6)
N40.0225 (8)0.0264 (9)0.0378 (9)0.0030 (6)0.0136 (7)−0.0009 (7)
N50.0189 (7)0.0209 (8)0.0217 (7)−0.0006 (6)0.0058 (6)−0.0010 (6)
N60.0205 (7)0.0166 (7)0.0235 (7)0.0006 (6)0.0101 (6)0.0010 (6)
N70.0225 (7)0.0172 (7)0.0251 (8)−0.0016 (6)0.0098 (6)0.0006 (6)
N80.0235 (8)0.0160 (7)0.0282 (8)0.0016 (6)0.0136 (6)0.0020 (6)
N90.0192 (7)0.0231 (8)0.0311 (8)0.0031 (6)0.0085 (6)−0.0017 (6)
N100.0201 (7)0.0180 (7)0.0204 (7)−0.0002 (6)0.0063 (6)−0.0011 (6)
O10.0445 (9)0.0246 (7)0.0426 (8)0.0084 (6)0.0194 (7)−0.0002 (6)
O20.0538 (10)0.0272 (8)0.0448 (9)0.0133 (7)0.0260 (8)0.0044 (6)
S10.0310 (3)0.0180 (2)0.0391 (3)0.00095 (18)0.0152 (2)−0.00141 (18)
S20.0329 (3)0.0160 (2)0.0385 (3)0.00297 (18)0.0170 (2)0.00048 (18)
C1—O11.408 (3)C14—H14A0.9900
C1—C21.529 (3)C14—H14B0.9900
C1—H1A0.9900C15—C161.541 (3)
C1—H1B0.9900C15—H15A0.9900
C2—C31.543 (2)C15—H15B0.9900
C2—H2A0.9900C16—N61.464 (2)
C2—H2B0.9900C16—C171.533 (2)
C3—N11.461 (2)C16—H161.0000
C3—C41.537 (2)C17—O21.415 (2)
C3—H31.0000C17—H17A0.9900
C4—O11.415 (2)C17—H17B0.9900
C4—H4A0.9900C18—N71.322 (2)
C4—H4B0.9900C18—C191.414 (2)
C5—N21.320 (2)C18—H180.9500
C5—C61.415 (2)C19—C201.403 (2)
C5—H50.9500C19—C221.443 (2)
C6—C71.407 (2)C20—N61.348 (2)
C6—C91.447 (2)C20—N81.377 (2)
C7—N11.349 (2)C21—N81.463 (2)
C7—N31.372 (2)C21—H21A0.9800
C8—N31.468 (2)C21—H21B0.9800
C8—H8A0.9800C21—H21C0.9800
C8—H8B0.9800C22—N101.358 (2)
C8—H8C0.9800C22—C231.399 (2)
C9—N51.351 (2)C23—C241.378 (3)
C9—C101.400 (2)C23—H230.9500
C10—C111.372 (3)C24—N91.342 (2)
C10—H100.9500C24—H240.9500
C11—N41.341 (3)C25—N101.328 (2)
C11—H110.9500C25—N91.338 (2)
C12—N51.329 (2)C25—S21.7614 (19)
C12—N41.339 (2)C26—S21.798 (2)
C12—S11.7594 (19)C26—H26A0.9800
C13—S11.799 (2)C26—H26B0.9800
C13—H13A0.9800C26—H26C0.9800
C13—H13B0.9800N1—N21.383 (2)
C13—H13C0.9800N3—H3N0.82 (2)
C14—O21.400 (3)N6—N71.378 (2)
C14—C151.526 (3)N8—H8N0.83 (2)
O1—C1—C2105.75 (16)H15A—C15—H15B109.1
O1—C1—H1A110.6N6—C16—C17112.64 (14)
C2—C1—H1A110.6N6—C16—C15112.50 (15)
O1—C1—H1B110.6C17—C16—C15103.46 (15)
C2—C1—H1B110.6N6—C16—H16109.4
H1A—C1—H1B108.7C17—C16—H16109.4
C1—C2—C3102.99 (15)C15—C16—H16109.4
C1—C2—H2A111.2O2—C17—C16107.18 (15)
C3—C2—H2A111.2O2—C17—H17A110.3
C1—C2—H2B111.2C16—C17—H17A110.3
C3—C2—H2B111.2O2—C17—H17B110.3
H2A—C2—H2B109.1C16—C17—H17B110.3
N1—C3—C4112.99 (14)H17A—C17—H17B108.5
N1—C3—C2112.86 (14)N7—C18—C19112.69 (16)
C4—C3—C2103.01 (15)N7—C18—H18123.7
N1—C3—H3109.3C19—C18—H18123.7
C4—C3—H3109.3C20—C19—C18103.83 (15)
C2—C3—H3109.3C20—C19—C22126.39 (16)
O1—C4—C3107.29 (15)C18—C19—C22129.77 (16)
O1—C4—H4A110.3N6—C20—N8124.39 (16)
C3—C4—H4A110.3N6—C20—C19106.85 (15)
O1—C4—H4B110.3N8—C20—C19128.72 (16)
C3—C4—H4B110.3N8—C21—H21A109.5
H4A—C4—H4B108.5N8—C21—H21B109.5
N2—C5—C6112.72 (15)H21A—C21—H21B109.5
N2—C5—H5123.6N8—C21—H21C109.5
C6—C5—H5123.6H21A—C21—H21C109.5
C7—C6—C5103.87 (15)H21B—C21—H21C109.5
C7—C6—C9126.33 (16)N10—C22—C23119.94 (16)
C5—C6—C9129.80 (16)N10—C22—C19116.56 (15)
N1—C7—N3124.83 (16)C23—C22—C19123.50 (16)
N1—C7—C6106.75 (15)C24—C23—C22117.31 (17)
N3—C7—C6128.40 (16)C24—C23—H23121.3
N3—C8—H8A109.5C22—C23—H23121.3
N3—C8—H8B109.5N9—C24—C23123.55 (17)
H8A—C8—H8B109.5N9—C24—H24118.2
N3—C8—H8C109.5C23—C24—H24118.2
H8A—C8—H8C109.5N10—C25—N9127.40 (17)
H8B—C8—H8C109.5N10—C25—S2118.83 (14)
N5—C9—C10120.07 (16)N9—C25—S2113.77 (13)
N5—C9—C6117.08 (15)S2—C26—H26A109.5
C10—C9—C6122.86 (16)S2—C26—H26B109.5
C11—C10—C9117.09 (17)H26A—C26—H26B109.5
C11—C10—H10121.5S2—C26—H26C109.5
C9—C10—H10121.5H26A—C26—H26C109.5
N4—C11—C10123.96 (17)H26B—C26—H26C109.5
N4—C11—H11118.0C7—N1—N2112.18 (14)
C10—C11—H11118.0C7—N1—C3128.07 (15)
N5—C12—N4127.39 (18)N2—N1—C3119.35 (14)
N5—C12—S1119.05 (14)C5—N2—N1104.46 (14)
N4—C12—S1113.57 (14)C7—N3—C8120.42 (15)
S1—C13—H13A109.5C7—N3—H3N109.2 (17)
S1—C13—H13B109.5C8—N3—H3N113.3 (17)
H13A—C13—H13B109.5C12—N4—C11114.28 (16)
S1—C13—H13C109.5C12—N5—C9117.16 (16)
H13A—C13—H13C109.5C20—N6—N7112.26 (14)
H13B—C13—H13C109.5C20—N6—C16127.71 (15)
O2—C14—C15105.96 (16)N7—N6—C16119.47 (14)
O2—C14—H14A110.5C18—N7—N6104.35 (14)
C15—C14—H14A110.5C20—N8—C21121.13 (15)
O2—C14—H14B110.5C20—N8—H8N107.4 (17)
C15—C14—H14B110.5C21—N8—H8N113.2 (16)
H14A—C14—H14B108.7C25—N9—C24114.62 (16)
C14—C15—C16102.77 (16)C25—N10—C22117.17 (15)
C14—C15—H15A111.2C1—O1—C4105.24 (15)
C16—C15—H15A111.2C14—O2—C17106.04 (16)
C14—C15—H15B111.2C12—S1—C13102.24 (9)
C16—C15—H15B111.2C25—S2—C26102.10 (9)
D—H···AD—HH···AD···AD—H···A
N3—H3N···N50.82 (2)2.16 (2)2.828 (2)139 (2)
N8—H8N···N100.83 (2)2.13 (2)2.820 (2)140 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N3—H3N⋯N50.82 (2)2.16 (2)2.828 (2)139 (2)
N8—H8N⋯N100.83 (2)2.13 (2)2.820 (2)140 (2)
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1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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

Authors:  Zhengyu Liu; Kevin K-C Liu; Jeff Elleraas; Arnold L Rheingold; Antonio Dipasquale; Alex Yanovsky
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-02-28

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

Authors:  Zhengyu Liu; Kevin K-C Liu; Jeff Elleraas; Arnold L Rheingold; Antonio Dipasquale; Alex Yanovsky
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-03-06
  3 in total
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1.  (2-Amino-phen-yl)[(5S)-5-hydr-oxy-3,5-dimethyl-4,5-dihydro-1H-pyrazol-1-yl]methanone.

Authors:  Mohammad Arfan; M Nawaz Tahir; Rasool Khan; Sumbal Saba; Mohammad S Iqbal
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-07-11
  1 in total

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