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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2374.
Published online 2009 September 9. doi:  10.1107/S1600536809035533
PMCID: PMC2970313

trans-4-(2-Amino-5-bromo-6-methyl­pyrimidin-4-ylamino)-1-methyl­cyclo­hexa­nol

Abstract

The title compound, C12H19BrN4O, represents the minor component of the two products obtained in a series of transformations involving the Grignard reaction of tert-butoxy­carbonyl-protected 4-amino­cyclo­hexa­none with MeMgBr, and subsequent inter­action of the obtained amino-substituted cyclo­hexa­nol with 4-chloro-6-methyl­pyrimidin-2-amine followed by bromination with N-bromo­succinimide. The X-ray structure showed that this product represents a trans isomer with respect to the amino and hydr­oxy substituents in the cyclo­hexyl ring; the dihedral angle between the amino­pyrimidine plane and the (noncrystallographic) mirror plane of the substituted cyclo­hexyl fragment is 33.6 (3)°. Only two of the four potentially ‘active’ H atoms participate in inter­molecular N—H(...)O and O—H(...)N hydrogen bonds, linking the mol­ecules into layers parallel to the (10An external file that holds a picture, illustration, etc.
Object name is e-65-o2374-efi1.jpg) plane.

Related literature

For the structure of a similar N-pyrimidine derivative of amino­cyclo­hexane, see Melguizo et al. (2003 [triangle]).

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Object name is e-65-o2374-scheme1.jpg

Experimental

Crystal data

  • C12H19BrN4O
  • M r = 315.22
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2374-efi2.jpg
  • a = 9.9514 (18) Å
  • b = 7.1879 (11) Å
  • c = 19.566 (4) Å
  • β = 91.053 (3)°
  • V = 1399.3 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.93 mm−1
  • T = 198 K
  • 0.10 × 0.10 × 0.08 mm

Data collection

  • Siemens P4 with APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.758, T max = 0.799
  • 8853 measured reflections
  • 3251 independent reflections
  • 2500 reflections with I > 2σ(I)
  • R int = 0.030

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.114
  • S = 1.05
  • 3251 reflections
  • 166 parameters
  • H-atom parameters constrained
  • Δρmax = 0.83 e Å−3
  • Δρmin = −0.77 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809035533/bg2293sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809035533/bg2293Isup2.hkl

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

supplementary crystallographic information

Comment

The Grignard reaction of tert-butoxycarbonyl(BOC)-protected 4-aminocyclohexanone, 4-C4H9OC(O)N(H)C6H9O, with MeMgBr produced the mixture of cis- and trans- 4-BOC-amino-1-methyl-cyclohexanols, which was subsequently reacted with 4-chloro-6-methylpyrimidin-2-amine and then brominated with N-bromosuccinimide. The isomeric mixture of the products was separated by means of flash chromatography and the corresponding X-ray structural study of the minor isomer showed that the title compound represents a trans-isomer with respect to the amino and hydroxy substituents in the cyclohexane ring (Fig. 1). The plane of the diaminopyrimidine C1/C2/C3/C4/N1/N2/N4 fragment forms a dihedral angle of 33.6 (3)° with the approximate mirror plane of the cyclohexyl fragment, namely the plane passing through N4/C6/C9/C12/O1. This conformation is significantly different from that observed in the related compound described in Melguizo et al., 2003, where the dihedral angle formed by the aminopyrimidine plane and the mirror plane of the cyclohexyl ring is just 13.6°.

There are four H atoms in the molecule, which are capable of H-bond formation. However, only two of them (H1 and H3A) participate in intermolecular H-bonds (Table 1), which link the molecules into layers parallel to the (1,0,-1) plane of the crystal (Fig. 2).

Experimental

Synthesis of tert-butyl 4-hydroxy-4-methylcyclohexylcarbamate. To a cooled (0°C) solution of 4-N-boc-amino-cyclohexanone (4.79 g, 22.5 mmol) in tetrahydrofuran (190 ml) was added methylmagnesium bromide (3 M solution in diethyl ether, 22.5 ml, 67.2 mmol). The ice bath was removed and the reaction was stirred at room temperature for 6 h, and then quenched with saturated ammonia chloride and water. The reaction mixture was concentrated and residue was dissolved in ethyl acetate and washed with saturated ammonia chloride, dried (MgSO4), filtered, and concentrated again. The crude product was purified by flash chromatography eluting with hexanes/ethyl acetate (10–50%) then chloroform/methanol (10%) to afford tert-butyl 4-hydroxy-4-methylcyclohexylcarbamate as a mixture of isomers (2.72 g, 53%).

Synthesis of 4-(2-amino-6-methylpyrimidin-4-ylamino)-1-methylcyclohexanol. To a cooled (0°C) solution of tert-butyl 4-hydroxy-4-methylcyclohexylcarbamate (2.72 g, 11.9 mmol) in dichloromethane was added hydrochloric acid (2 M solution in diethyl ether, 10 eq). The ice bath was removed and the solution was stirred at room temperature for 6 hrs then concentrated to afford 4-amino-1-methylcyclohexanol hydrochloride, which was used without further purification. A solution of 2-amino-4-chloro-6-methylpyrimidine (2.20 g, 15.4 mmol), 4-amino-1-methylcyclohexanol hydrochloride, and diisopropylethyl amine (7.6 ml, 44 mmol) in dimethyl acetamide (52 ml) was heated to 160°C in a sealed tube overnight. The reaction mixture was concentrated, the solids were slurried in chloroform and the filtrate was concentrated again. The crude product was purified by flash choromatagraphy eluting with chloroform/7 N ammonia in methanol followed by SFC chromatography to afford 4-(2-amino-6-methylpyrimidin-4-ylamino)-1-methylcyclohexanol as a mixture of isomers (600 mg, 17% over 2 steps).

Synthesis of 4-(2-amino-5-bromo-6-methylpyrimidin-4-ylamino) -1-methylcyclohexanol. To a solution of 4-(2-amino-6-methylpyrimidin-4-ylamino)-1-methylcyclohexanol (600 mg, 2.54 mmol) in dichloromethane (20.0 ml) was added N-bromosuccinimide (452 mg, 2.54 mmol). After stirring for 2.5 hrs at room temperature, the solution was concentrated. The residue was dissolved in ethyl acetate (450 ml) and washed with 50% saturated sodium carbonate, brine, dried (MgSO4), filtered, and concentrated again. The crude product was purified by flash chromatography to afford major (407 mg, 51%) and minor (151 mg, 19%) isomers of 4-(2-amino-5-bromo-6-methylpyrimidin-4-ylamino)-1-methylcyclohexanol. Minor isomer (the title compound) was subjected to the X-ray study and proved to be the trans-isomer.

1H NMR spectra for major (cis) isomer: (400 MHz, DMSO-d6) δp.p.m. 1.11 (s, 3 H) 1.26 - 1.37 (m, 2 H) 1.52 - 1.61 (m, 4 H) 1.61 - 1.73 (m, 2 H) 2.17 (s, 3 H) 3.77 - 3.87 (m, 1 H) 4.06 (s, 1 H) 5.73 (d, J=8.34 Hz, 1 H) 6.08 (s, 2 H)

1H NMR spectra for minor (trans) isomer (the title compound): (400 MHz, DMSO-d6) δp.p.m. 1.16 (s, 3 H) 1.36 - 1.45 (m, 2 H) 1.45 - 1.56 (m, 4 H) 1.64 - 1.73 (m, 2 H) 2.17 (s, 3 H) 3.87 - 3.97 (m, 1 H) 4.28 (s, 1 H) 5.93 (d, J=8.59 Hz, 1 H) 6.11 (s, 2 H)

Refinement

All H atoms were placed in geometrically calculated positions (O—H 0.84 Å, N—H 0.88 Å, C—H 0.98 Å, 0.99 Å, 1.00 Å for methyl, methylene and methyne H atoms respectively) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom for methylene, methyne and amine groups, and 1.5Ueq for methyl and hydroxyl H atoms.

Figures

Fig. 1.
Molecular structure of the title compound showing 50% probability displacement ellipsoids and atom numbering scheme; H atoms are drawn as circles with arbitrary small radius.
Fig. 2.
Packing diagram for the title compound viewed approximately along the b axis. H-Bonds are shown as dashed lines; H atoms bound to carbon atoms are omitted.

Crystal data

C12H19BrN4OF(000) = 648
Mr = 315.22Dx = 1.496 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2554 reflections
a = 9.9514 (18) Åθ = 2.3–26.0°
b = 7.1879 (11) ŵ = 2.93 mm1
c = 19.566 (4) ÅT = 198 K
β = 91.053 (3)°Prism, colorless
V = 1399.3 (4) Å30.10 × 0.10 × 0.08 mm
Z = 4

Data collection

Siemens P4 with APEX CCD area-detector diffractometer3251 independent reflections
Radiation source: fine-focus sealed tube2500 reflections with I > 2σ(I)
graphiteRint = 0.030
[var phi] and ω scansθmax = 28.3°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −13→13
Tmin = 0.758, Tmax = 0.799k = −9→3
8853 measured reflectionsl = −25→25

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0567P)2 + 0.5508P] where P = (Fo2 + 2Fc2)/3
3251 reflections(Δ/σ)max < 0.001
166 parametersΔρmax = 0.83 e Å3
0 restraintsΔρmin = −0.77 e Å3

Special details

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)

xyzUiso*/Ueq
C10.5559 (2)0.1796 (4)0.70305 (12)0.0340 (5)
C20.4564 (2)0.4484 (3)0.74028 (12)0.0345 (5)
C30.3689 (2)0.4380 (4)0.68582 (12)0.0343 (5)
C40.3783 (2)0.2877 (3)0.64026 (11)0.0308 (5)
C50.4551 (4)0.6010 (4)0.79203 (16)0.0553 (8)
H5A0.52240.57530.82800.083*
H5B0.36590.60840.81230.083*
H5C0.47600.71950.76980.083*
C60.3088 (3)0.1409 (3)0.53025 (12)0.0360 (5)
H60.34510.02030.54800.043*
C70.4063 (2)0.2217 (4)0.47943 (12)0.0371 (6)
H7A0.42230.12970.44280.045*
H7B0.49340.24720.50290.045*
C80.3519 (3)0.4009 (4)0.44790 (13)0.0387 (6)
H8A0.41630.44670.41380.046*
H8B0.34520.49640.48410.046*
C90.2144 (3)0.3769 (3)0.41323 (12)0.0337 (5)
C100.1169 (2)0.2822 (4)0.46142 (13)0.0359 (5)
H10A0.03400.24930.43540.043*
H10B0.09190.37150.49760.043*
C110.1739 (3)0.1065 (3)0.49515 (14)0.0400 (6)
H11A0.10950.06030.52920.048*
H11B0.18420.00880.46000.048*
C120.1583 (3)0.5624 (4)0.38954 (16)0.0529 (7)
H12A0.22300.62330.35970.079*
H12B0.14210.64150.42930.079*
H12C0.07370.54230.36430.079*
N10.5510 (2)0.3157 (3)0.75037 (10)0.0354 (5)
N20.4744 (2)0.1602 (3)0.64825 (10)0.0334 (4)
N30.6521 (2)0.0517 (4)0.71160 (12)0.0510 (6)
H3A0.6596−0.03970.68200.061*
H3B0.70810.05880.74690.061*
N40.2904 (2)0.2682 (3)0.58727 (10)0.0355 (5)
H40.21730.33700.58720.043*
O10.23817 (18)0.2603 (3)0.35549 (9)0.0420 (4)
H10.16540.24130.33420.063*
Br10.23506 (4)0.62118 (5)0.671478 (18)0.06510 (16)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0334 (12)0.0391 (13)0.0292 (12)0.0023 (10)−0.0052 (10)−0.0036 (10)
C20.0362 (13)0.0361 (12)0.0311 (12)−0.0024 (10)0.0010 (10)−0.0052 (10)
C30.0341 (13)0.0357 (12)0.0330 (12)0.0048 (10)−0.0012 (10)−0.0026 (10)
C40.0305 (12)0.0357 (13)0.0261 (11)−0.0010 (9)−0.0015 (9)0.0012 (9)
C50.0625 (19)0.0506 (17)0.0523 (18)0.0074 (14)−0.0080 (15)−0.0204 (14)
C60.0397 (14)0.0341 (13)0.0336 (13)0.0029 (10)−0.0131 (10)−0.0028 (10)
C70.0305 (12)0.0488 (15)0.0318 (12)0.0033 (10)−0.0085 (10)−0.0130 (11)
C80.0392 (14)0.0455 (14)0.0315 (12)−0.0098 (11)0.0002 (10)−0.0048 (11)
C90.0378 (13)0.0344 (12)0.0289 (12)0.0038 (10)−0.0043 (10)−0.0023 (10)
C100.0308 (12)0.0419 (14)0.0346 (12)0.0000 (10)−0.0085 (10)0.0023 (11)
C110.0418 (14)0.0376 (14)0.0402 (14)−0.0080 (11)−0.0122 (11)0.0056 (11)
C120.070 (2)0.0410 (15)0.0473 (17)0.0115 (14)0.0002 (15)0.0079 (13)
N10.0342 (11)0.0412 (11)0.0306 (10)0.0010 (9)−0.0056 (8)−0.0077 (9)
N20.0359 (11)0.0374 (11)0.0267 (10)0.0035 (8)−0.0071 (8)−0.0059 (8)
N30.0541 (14)0.0575 (14)0.0405 (12)0.0239 (12)−0.0226 (11)−0.0177 (11)
N40.0321 (10)0.0446 (12)0.0297 (10)0.0073 (9)−0.0075 (8)−0.0030 (9)
O10.0410 (10)0.0525 (11)0.0319 (9)0.0119 (8)−0.0100 (7)−0.0119 (8)
Br10.0679 (3)0.0608 (2)0.0659 (3)0.03307 (16)−0.01891 (17)−0.01908 (15)

Geometric parameters (Å, °)

C1—N31.335 (3)C7—H7B0.9900
C1—N21.340 (3)C8—C91.526 (3)
C1—N11.349 (3)C8—H8A0.9900
C2—N11.352 (3)C8—H8B0.9900
C2—C31.366 (3)C9—O11.430 (3)
C2—C51.493 (4)C9—C121.514 (4)
C3—C41.405 (3)C9—C101.525 (3)
C3—Br11.891 (2)C10—C111.529 (3)
C4—N21.331 (3)C10—H10A0.9900
C4—N41.351 (3)C10—H10B0.9900
C5—H5A0.9800C11—H11A0.9900
C5—H5B0.9800C11—H11B0.9900
C5—H5C0.9800C12—H12A0.9800
C6—N41.457 (3)C12—H12B0.9800
C6—C111.517 (3)C12—H12C0.9800
C6—C71.518 (4)N3—H3A0.8800
C6—H61.0000N3—H3B0.8800
C7—C81.523 (4)N4—H40.8800
C7—H7A0.9900O1—H10.8400
N3—C1—N2116.8 (2)H8A—C8—H8B107.8
N3—C1—N1116.6 (2)O1—C9—C12109.9 (2)
N2—C1—N1126.6 (2)O1—C9—C10110.1 (2)
N1—C2—C3120.5 (2)C12—C9—C10110.3 (2)
N1—C2—C5115.7 (2)O1—C9—C8104.89 (19)
C3—C2—C5123.8 (2)C12—C9—C8111.0 (2)
C2—C3—C4119.2 (2)C10—C9—C8110.5 (2)
C2—C3—Br1121.01 (19)C9—C10—C11113.6 (2)
C4—C3—Br1119.76 (17)C9—C10—H10A108.8
N2—C4—N4118.2 (2)C11—C10—H10A108.8
N2—C4—C3120.7 (2)C9—C10—H10B108.8
N4—C4—C3121.1 (2)C11—C10—H10B108.8
C2—C5—H5A109.5H10A—C10—H10B107.7
C2—C5—H5B109.5C6—C11—C10112.2 (2)
H5A—C5—H5B109.5C6—C11—H11A109.2
C2—C5—H5C109.5C10—C11—H11A109.2
H5A—C5—H5C109.5C6—C11—H11B109.2
H5B—C5—H5C109.5C10—C11—H11B109.2
N4—C6—C11109.1 (2)H11A—C11—H11B107.9
N4—C6—C7110.6 (2)C9—C12—H12A109.5
C11—C6—C7109.7 (2)C9—C12—H12B109.5
N4—C6—H6109.1H12A—C12—H12B109.5
C11—C6—H6109.1C9—C12—H12C109.5
C7—C6—H6109.1H12A—C12—H12C109.5
C6—C7—C8111.2 (2)H12B—C12—H12C109.5
C6—C7—H7A109.4C1—N1—C2116.5 (2)
C8—C7—H7A109.4C4—N2—C1116.4 (2)
C6—C7—H7B109.4C1—N3—H3A120.0
C8—C7—H7B109.4C1—N3—H3B120.0
H7A—C7—H7B108.0H3A—N3—H3B120.0
C7—C8—C9113.2 (2)C4—N4—C6124.3 (2)
C7—C8—H8A108.9C4—N4—H4117.8
C9—C8—H8A108.9C6—N4—H4117.8
C7—C8—H8B108.9C9—O1—H1109.5
C9—C8—H8B108.9

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3A···O1i0.882.032.828 (3)151
O1—H1···N1ii0.842.022.803 (3)155

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x−1/2, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BG2293).

References

  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • 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.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Melguizo, M., Quesada, A., Low, J. N. & Glidewell, C. (2003). Acta Cryst. B59, 263–276. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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