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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 1| January 2010| Page o242
doi:10.1107/S1600536809054750

5-Chloro-N-[2-(1H-imidazol-4-yl)eth­yl]-N-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Daniel Richter,a John C. Kath,a Arnold L. Rheingold,b Antonio DiPasqualeb and Alex Yanovskya*

aPfizer Global Research and Development, La Jolla Labs, 10770 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 17 December 2009; accepted 19 December 2009; online 24 December 2009)

The title compound, C12H13ClN6, was prepared by reaction of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine with 2-(1H-imid­azol-4-yl)-N-methyl­ethanamine, and the X-ray study confirmed that chloro-substituent in six-membered ring was replaced in the reaction. The exocyclic N atom environment is approximately coplanar with the pyrrolo[2,3-d]pyrimidine [corresponding dihedral angle is 5.5 (1)°], whereas the mean plane of the N—C—C—C link connecting with the imidazolyl ring is almost exactly orthogonal to the plane of the bicyclic system [dihedral angle = 91.6 (2)°]. The imidazolyl plane itself, however, forms a relatively small dihedral angle of 20.8 (1)° with the pyrrolo[2,3-d]pyrimidine plane. There are two independent N—H⋯N hydrogen bonds in the structure, which link mol­ecules into layers parallel to ([\overline{1}]03).

Related literature

For the structures of related compounds with the pyrrolo[2,3-d]pyrimidin-4-amine bicyclic framework, see: Abola & Sundaralingam (1973[Abola, E. & Sundaralingam, M. (1973). Acta Cryst. B29, 697-703.]); Slauson et al. (2008[Slauson, S. R., Rimoldi, J. M. & Fronczek, F. R. (2008). Acta Cryst. E64, o1650-o1651.]); Zabel et al. (1987[Zabel, V., Saenger, W. & Seela, F. (1987). Acta Cryst. C43, 131-134.]).

[Scheme 1]

Experimental

Crystal data

  • C12H13ClN6

  • Mr = 276.73

  • Monoclinic, P 21 /n

  • a = 4.4673 (5) Å

  • b = 15.8855 (17) Å

  • c = 17.6544 (19) Å

  • β = 96.244 (2)°

  • V = 1245.4 (2) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.30 mm−1

  • T = 208 K

  • 0.16 × 0.08 × 0.08 mm
Data collection

  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.953, Tmax = 0.976

  • 8932 measured reflections

  • 2669 independent reflections

  • 2223 reflections with I > 2σ(I)

  • Rint = 0.029
Refinement

  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.123

  • S = 1.05

  • 2669 reflections

  • 173 parameters

  • H-atom parameters constrained

  • Δρmax = 0.38 e Å−3

  • Δρmin = −0.55 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N2—H2⋯N5i 0.87 1.98 2.845 (2) 175
N6—H6A⋯N3ii 0.87 2.04 2.892 (2) 167
Symmetry codes: (i) [-x-{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [x+{\script{3\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR97 (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.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809054750/dn2525sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809054750/dn2525Isup2.hkl

checkCIF report


Comment top

The title compound, C12H13ClN6, was prepared by reaction of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine with 2-(1H-imidazol-4-yl)-N-methylethanamine, and the present X-ray study confirmed that chloro-substituent in six-membered ring got replaced in this reaction (Fig. 1).

The pyrrolo[2,3-d]pyrimidine system is planar within 0.001 Å, and its least-squares plane, C1/C2/C3/C4/N2/C5/N3/C6/N1 is almost coplanar with the plane C1/N4/C7/C8, the corresponding dihedral angle being equal to 5.5 (1)° (the maximum deviation of the N4 atom from the latter plane being 0.028 (2) Å). The N4—C8—C9—C10 chain linking the bicyclic system with the imidazolyl group may be considered as approximately planar (within 0.130 Å) and its mean plane is orthogonal to the plane of pyrrolopyrimidine [91.6 (2)°]. At the same time the imidazolyl plane forms a relatively small dihedral angle of 20.8 (1)° with the bicyclic system.

The geometric parameters of pyrrolopyrimidin-4-amine system are similar to those observed in related structures (Zabel et al., 1987; Abola & Sundaralingam, 1973), although the title compound provides the first structure with no substitution at the N atom in the pyrrole part. The only other structurally studied compound with disubstituted 4-amino-group (Slauson et al., 2008) shows noticeable non-planarity of the environment of the exocyclic N atom.

There are two independent H-bonds in the structure (Table 1) which link molecules into layers parallel to (-1,0,3) plane (Fig. 2).

Related literature top

For the structures of related compounds with the pyrrolo[2,3-d]pyrimidin-4-amine bicyclic framework, see: Abola & Sundaralingam (1973); Slauson et al. (2008); Zabel et al. (1987).

Experimental top

To a mixture of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine (119 mg, 0.63 mmol) and [2-(1H-imidazol-4-yl)-ethyl]-methylamine (79 mg, 0.63 mmol) dissolved in 2-propanol (1 ml) was added di-isopropyl-ethylamine (0.12 ml, 1.1 eq). The reaction was heated at 80°C for 18 hrs. The solvent was removed and the reaction purified on Si—NH2 (6% MeOH/EtOAc); product was isolated as colorless solid, 48 mg (27%). 1H NMR (400 MHz, DMSO-d6) δ p.p.m. 2.85 - 2.91 (m, 2 H), 3.22 (s, 3 H), 3.88 (dd, J=8.56, 6.80 Hz, 2 H), 6.78 (s, 1 H), 7.41 (d, J=1.76 Hz, 1 H), 7.52 (d, J=1.01 Hz, 1 H), 8.17 (s, 1 H), 12.05 (s, 1 H).

Refinement top

All H atoms were placed in geometrically calculated positions (C—H 0.97 Å for methyl, 0.98 Å for methylene, 0.94 Å for aromatic CH-groups; N—H 0.87 Å) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom [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: SIR97 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-32 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. Partial packing view of the title compound, viewed down the a axis. Hydrogen bonds are shown as dashed lines. H atoms not involved in hydrogen bondings have been omitted for clarity. [Symmetry code: (i) -x-1/2, y-1/2, -z+1/2]
5-Chloro-N-[2-(1H-imidazol-4-yl)ethyl]-N-methyl- 7H-pyrrolo[2,3-d]pyrimidin-4-amine top
Crystal data top
C12H13ClN6F(000) = 576
Mr = 276.73Dx = 1.476 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4149 reflections
a = 4.4673 (5) Åθ = 2.3–27.6°
b = 15.8855 (17) ŵ = 0.30 mm−1
c = 17.6544 (19) ÅT = 208 K
β = 96.244 (2)°Rod, colorless
V = 1245.4 (2) Å30.16 × 0.08 × 0.08 mm
Z = 4
Data collection top
Bruker SMART CCD area-detector
diffractometer		2669 independent reflections
Radiation source: fine-focus sealed tube2223 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
phi and ω scansθmax = 27.7°, θmin = 1.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −5→2
Tmin = 0.953, Tmax = 0.976k = −20→19
8932 measured reflectionsl = −22→22
Refinement top
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) = 0.123H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0625P)2 + 0.5128P]
where P = (Fo2 + 2Fc2)/3
2669 reflections(Δ/σ)max = 0.001
173 parametersΔρmax = 0.38 e Å−3
0 restraintsΔρmin = −0.55 e Å−3
Crystal data top
C12H13ClN6V = 1245.4 (2) Å3
Mr = 276.73Z = 4
Monoclinic, P21/nMo Kα radiation
a = 4.4673 (5) ŵ = 0.30 mm−1
b = 15.8855 (17) ÅT = 208 K
c = 17.6544 (19) Å0.16 × 0.08 × 0.08 mm
β = 96.244 (2)°
Data collection top
Bruker SMART CCD area-detector
diffractometer		2669 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		2223 reflections with I > 2σ(I)
Tmin = 0.953, Tmax = 0.976Rint = 0.029
8932 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.123H-atom parameters constrained
S = 1.05Δρmax = 0.38 e Å−3
2669 reflectionsΔρmin = −0.55 e Å−3
173 parameters
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
C1−0.0192 (4)0.58232 (11)0.29931 (10)0.0283 (4)
C2−0.1622 (4)0.50275 (10)0.28217 (10)0.0277 (4)
C3−0.1729 (4)0.41555 (11)0.30729 (11)0.0328 (4)
C4−0.3817 (4)0.37368 (12)0.25972 (11)0.0358 (4)
H4−0.43150.31650.26380.043*
C5−0.3795 (4)0.50431 (11)0.21665 (10)0.0297 (4)
C6−0.2998 (4)0.63935 (11)0.19349 (11)0.0351 (4)
H6−0.34240.68760.16340.042*
C70.2759 (5)0.53923 (14)0.41905 (14)0.0525 (6)
H7A0.09590.51460.43590.079*
H7B0.38920.56800.46140.079*
H7C0.39920.49520.40040.079*
C80.3331 (4)0.68204 (12)0.36897 (11)0.0346 (4)
H8A0.32730.71000.31940.042*
H8B0.54480.67500.38910.042*
C90.1773 (4)0.73809 (12)0.42332 (11)0.0339 (4)
H9A−0.00340.76300.39570.041*
H9B0.11390.70350.46470.041*
C100.3803 (4)0.80697 (11)0.45646 (10)0.0297 (4)
C110.5339 (4)0.81184 (12)0.52734 (11)0.0344 (4)
H110.52790.77300.56730.041*
C120.6424 (4)0.92068 (12)0.45984 (11)0.0354 (4)
H120.72910.97150.44590.042*
N1−0.0952 (3)0.64914 (9)0.25352 (9)0.0331 (3)
N2−0.5079 (3)0.42744 (9)0.20513 (9)0.0336 (3)
H2−0.64790.41450.16880.040*
N3−0.4509 (3)0.57078 (10)0.17064 (9)0.0340 (3)
N40.1919 (3)0.59882 (10)0.35853 (9)0.0351 (4)
N50.4505 (3)0.87609 (10)0.41396 (9)0.0325 (3)
N60.6992 (3)0.88485 (10)0.52872 (9)0.0357 (4)
H6A0.81820.90420.56700.043*
Cl10.02168 (14)0.36102 (3)0.38240 (3)0.0529 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0312 (8)0.0258 (8)0.0273 (9)0.0014 (6)0.0001 (6)−0.0027 (7)
C20.0335 (8)0.0243 (8)0.0244 (9)0.0013 (6)−0.0012 (6)−0.0004 (6)
C30.0414 (9)0.0262 (9)0.0291 (9)−0.0002 (7)−0.0047 (7)0.0041 (7)
C40.0457 (10)0.0258 (9)0.0344 (10)−0.0026 (7)−0.0026 (7)0.0009 (7)
C50.0339 (8)0.0264 (9)0.0277 (9)0.0022 (7)−0.0018 (6)−0.0023 (7)
C60.0470 (10)0.0275 (9)0.0297 (10)0.0045 (7)−0.0016 (7)0.0042 (7)
C70.0680 (13)0.0322 (11)0.0498 (14)0.0004 (10)−0.0272 (10)0.0014 (9)
C80.0321 (8)0.0318 (9)0.0389 (10)−0.0054 (7)−0.0013 (7)−0.0069 (8)
C90.0321 (8)0.0321 (9)0.0366 (10)−0.0037 (7)−0.0003 (7)−0.0046 (8)
C100.0294 (7)0.0277 (9)0.0311 (9)0.0024 (6)−0.0005 (6)−0.0029 (7)
C110.0395 (9)0.0298 (9)0.0323 (10)0.0011 (7)−0.0025 (7)0.0004 (7)
C120.0386 (9)0.0283 (9)0.0376 (11)−0.0030 (7)−0.0036 (7)−0.0024 (8)
N10.0408 (8)0.0250 (7)0.0327 (9)0.0002 (6)0.0004 (6)−0.0001 (6)
N20.0387 (7)0.0285 (8)0.0312 (8)−0.0022 (6)−0.0069 (6)−0.0021 (6)
N30.0415 (8)0.0282 (8)0.0301 (8)0.0048 (6)−0.0060 (6)0.0008 (6)
N40.0407 (8)0.0257 (8)0.0359 (9)−0.0009 (6)−0.0090 (6)−0.0031 (6)
N50.0349 (7)0.0303 (8)0.0305 (8)−0.0009 (6)−0.0048 (6)−0.0002 (6)
N60.0390 (8)0.0320 (8)0.0331 (9)−0.0011 (6)−0.0094 (6)−0.0062 (7)
Cl10.0763 (4)0.0314 (3)0.0444 (3)−0.0069 (2)−0.0233 (3)0.0115 (2)
Geometric parameters (Å, º) top
C1—N11.355 (2)C7—H7C0.9700
C1—N41.355 (2)C8—N41.468 (2)
C1—C21.434 (2)C8—C91.531 (3)
C2—C51.427 (2)C8—H8A0.9800
C2—C31.457 (2)C8—H8B0.9800
C3—C41.359 (3)C9—C101.499 (2)
C3—Cl11.7360 (18)C9—H9A0.9800
C4—N21.363 (2)C9—H9B0.9800
C4—H40.9400C10—C111.362 (2)
C5—N31.349 (2)C10—N51.385 (2)
C5—N21.355 (2)C11—N61.374 (2)
C6—N31.321 (2)C11—H110.9400
C6—N11.331 (2)C12—N51.320 (2)
C6—H60.9400C12—N61.342 (2)
C7—N41.446 (3)C12—H120.9400
C7—H7A0.9700N2—H20.8700
C7—H7B0.9700N6—H6A0.8700
N1—C1—N4114.64 (15)H8A—C8—H8B107.8
N1—C1—C2119.20 (15)C10—C9—C8111.87 (14)
N4—C1—C2126.15 (16)C10—C9—H9A109.2
C5—C2—C1113.83 (15)C8—C9—H9A109.2
C5—C2—C3102.77 (14)C10—C9—H9B109.2
C1—C2—C3143.40 (16)C8—C9—H9B109.2
C4—C3—C2108.69 (15)H9A—C9—H9B107.9
C4—C3—Cl1118.73 (14)C11—C10—N5109.35 (16)
C2—C3—Cl1132.58 (14)C11—C10—C9128.54 (17)
C3—C4—N2109.48 (16)N5—C10—C9122.03 (16)
C3—C4—H4125.3C10—C11—N6106.29 (16)
N2—C4—H4125.3C10—C11—H11126.9
N3—C5—N2123.13 (15)N6—C11—H11126.9
N3—C5—C2126.66 (16)N5—C12—N6112.00 (17)
N2—C5—C2110.21 (15)N5—C12—H12124.0
N3—C6—N1128.55 (17)N6—C12—H12124.0
N3—C6—H6115.7C6—N1—C1119.29 (15)
N1—C6—H6115.7C5—N2—C4108.84 (15)
N4—C7—H7A109.5C5—N2—H2125.6
N4—C7—H7B109.5C4—N2—H2125.6
H7A—C7—H7B109.5C6—N3—C5112.45 (15)
N4—C7—H7C109.5C1—N4—C7123.13 (16)
H7A—C7—H7C109.5C1—N4—C8121.64 (15)
H7B—C7—H7C109.5C7—N4—C8115.03 (15)
N4—C8—C9112.60 (15)C12—N5—C10105.27 (16)
N4—C8—H8A109.1C12—N6—C11107.09 (15)
C9—C8—H8A109.1C12—N6—H6A126.5
N4—C8—H8B109.1C11—N6—H6A126.5
C9—C8—H8B109.1
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N5i0.871.982.845 (2)175
N6—H6A···N3ii0.872.042.892 (2)167
Symmetry codes: (i) −x−1/2, y−1/2, −z+1/2; (ii) x+3/2, −y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H13ClN6
Mr276.73
Crystal system, space groupMonoclinic, P21/n
Temperature (K)208
a, b, c (Å)4.4673 (5), 15.8855 (17), 17.6544 (19)
β (°) 96.244 (2)
V (Å3)1245.4 (2)
Z4
Radiation typeMo Kα
µ (mm−1)0.30
Crystal size (mm)0.16 × 0.08 × 0.08
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.953, 0.976
No. of measured, independent and
observed [I > 2σ(I)] reflections		8932, 2669, 2223
Rint0.029
(sin θ/λ)max (Å−1)0.654
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.123, 1.05
No. of reflections2669
No. of parameters173
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.38, −0.55

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SIR97 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008), ORTEP-32 (Farrugia, 1997) and PLATON (Spek, 2009), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N5i0.871.982.845 (2)175
N6—H6A···N3ii0.872.042.892 (2)167
Symmetry codes: (i) −x−1/2, y−1/2, −z+1/2; (ii) x+3/2, −y+3/2, z+1/2.
 

References

First citationAbola, E. & Sundaralingam, M. (1973). Acta Cryst. B29, 697–703.  CSD CrossRef CAS IUCr Journals Google Scholar
 First citationBruker (1997). SMART 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 citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSlauson, S. R., Rimoldi, J. M. & Fronczek, F. R. (2008). Acta Cryst. E64, o1650–o1651.  Web of Science CSD CrossRef IUCr Journals Google Scholar
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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 1| January 2010| Page o242
doi:10.1107/S1600536809054750
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