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

The title compound, C(12)H(13)ClN(6), was prepared by reaction of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine with 2-(1H-imid-azol-4-yl)-N-methyl-ethanamine, 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 mol-ecules into layers parallel to (03).

Related literature

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

Crystal data

C12H13ClN6

M = 276.73

Monoclinic,

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 ▶) T min = 0.953, T max = 0.976

8932 measured reflections

2669 independent reflections

2223 reflections with I > 2σ(I)

R int = 0.029

Refinement

R[F 2 > 2σ(F 2)] = 0.043

wR(F 2) = 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

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

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

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

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

C12H13ClN6	F(000) = 576
Mr = 276.73	Dx = 1.476 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 4149 reflections
a = 4.4673 (5) Å	θ = 2.3–27.6°
b = 15.8855 (17) Å	µ = 0.30 mm−1
c = 17.6544 (19) Å	T = 208 K
β = 96.244 (2)°	Rod, colorless
V = 1245.4 (2) Å3	0.16 × 0.08 × 0.08 mm
Z = 4

Bruker SMART CCD area-detector diffractometer	2669 independent reflections
Radiation source: fine-focus sealed tube	2223 reflections with I > 2σ(I)
graphite	Rint = 0.029
phi and ω scans	θmax = 27.7°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −5→2
Tmin = 0.953, Tmax = 0.976	k = −20→19
8932 measured reflections	l = −22→22

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.123	H-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 parameters	Δρmax = 0.38 e Å−3
0 restraints	Δρmin = −0.55 e Å−3

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	−0.0192 (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	−0.4315	0.3165	0.2638	0.043*
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	−0.3424	0.6876	0.1634	0.042*
C7	0.2759 (5)	0.53923 (14)	0.41905 (14)	0.0525 (6)
H7A	0.0959	0.5146	0.4359	0.079*
H7B	0.3892	0.5680	0.4614	0.079*
H7C	0.3992	0.4952	0.4004	0.079*
C8	0.3331 (4)	0.68204 (12)	0.36897 (11)	0.0346 (4)
H8A	0.3273	0.7100	0.3194	0.042*
H8B	0.5448	0.6750	0.3891	0.042*
C9	0.1773 (4)	0.73809 (12)	0.42332 (11)	0.0339 (4)
H9A	−0.0034	0.7630	0.3957	0.041*
H9B	0.1139	0.7035	0.4647	0.041*
C10	0.3803 (4)	0.80697 (11)	0.45646 (10)	0.0297 (4)
C11	0.5339 (4)	0.81184 (12)	0.52734 (11)	0.0344 (4)
H11	0.5279	0.7730	0.5673	0.041*
C12	0.6424 (4)	0.92068 (12)	0.45984 (11)	0.0354 (4)
H12	0.7291	0.9715	0.4459	0.042*
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	−0.6479	0.4145	0.1688	0.040*
N3	−0.4509 (3)	0.57078 (10)	0.17064 (9)	0.0340 (3)
N4	0.1919 (3)	0.59882 (10)	0.35853 (9)	0.0351 (4)
N5	0.4505 (3)	0.87609 (10)	0.41396 (9)	0.0325 (3)
N6	0.6992 (3)	0.88485 (10)	0.52872 (9)	0.0357 (4)
H6A	0.8182	0.9042	0.5670	0.043*
Cl1	0.02168 (14)	0.36102 (3)	0.38240 (3)	0.0529 (2)

	U11	U22	U33	U12	U13	U23
C1	0.0312 (8)	0.0258 (8)	0.0273 (9)	0.0014 (6)	0.0001 (6)	−0.0027 (7)
C2	0.0335 (8)	0.0243 (8)	0.0244 (9)	0.0013 (6)	−0.0012 (6)	−0.0004 (6)
C3	0.0414 (9)	0.0262 (9)	0.0291 (9)	−0.0002 (7)	−0.0047 (7)	0.0041 (7)
C4	0.0457 (10)	0.0258 (9)	0.0344 (10)	−0.0026 (7)	−0.0026 (7)	0.0009 (7)
C5	0.0339 (8)	0.0264 (9)	0.0277 (9)	0.0022 (7)	−0.0018 (6)	−0.0023 (7)
C6	0.0470 (10)	0.0275 (9)	0.0297 (10)	0.0045 (7)	−0.0016 (7)	0.0042 (7)
C7	0.0680 (13)	0.0322 (11)	0.0498 (14)	0.0004 (10)	−0.0272 (10)	0.0014 (9)
C8	0.0321 (8)	0.0318 (9)	0.0389 (10)	−0.0054 (7)	−0.0013 (7)	−0.0069 (8)
C9	0.0321 (8)	0.0321 (9)	0.0366 (10)	−0.0037 (7)	−0.0003 (7)	−0.0046 (8)
C10	0.0294 (7)	0.0277 (9)	0.0311 (9)	0.0024 (6)	−0.0005 (6)	−0.0029 (7)
C11	0.0395 (9)	0.0298 (9)	0.0323 (10)	0.0011 (7)	−0.0025 (7)	0.0004 (7)
C12	0.0386 (9)	0.0283 (9)	0.0376 (11)	−0.0030 (7)	−0.0036 (7)	−0.0024 (8)
N1	0.0408 (8)	0.0250 (7)	0.0327 (9)	0.0002 (6)	0.0004 (6)	−0.0001 (6)
N2	0.0387 (7)	0.0285 (8)	0.0312 (8)	−0.0022 (6)	−0.0069 (6)	−0.0021 (6)
N3	0.0415 (8)	0.0282 (8)	0.0301 (8)	0.0048 (6)	−0.0060 (6)	0.0008 (6)
N4	0.0407 (8)	0.0257 (8)	0.0359 (9)	−0.0009 (6)	−0.0090 (6)	−0.0031 (6)
N5	0.0349 (7)	0.0303 (8)	0.0305 (8)	−0.0009 (6)	−0.0048 (6)	−0.0002 (6)
N6	0.0390 (8)	0.0320 (8)	0.0331 (9)	−0.0011 (6)	−0.0094 (6)	−0.0062 (7)
Cl1	0.0763 (4)	0.0314 (3)	0.0444 (3)	−0.0069 (2)	−0.0233 (3)	0.0115 (2)

C1—N1	1.355 (2)	C7—H7C	0.9700
C1—N4	1.355 (2)	C8—N4	1.468 (2)
C1—C2	1.434 (2)	C8—C9	1.531 (3)
C2—C5	1.427 (2)	C8—H8A	0.9800
C2—C3	1.457 (2)	C8—H8B	0.9800
C3—C4	1.359 (3)	C9—C10	1.499 (2)
C3—Cl1	1.7360 (18)	C9—H9A	0.9800
C4—N2	1.363 (2)	C9—H9B	0.9800
C4—H4	0.9400	C10—C11	1.362 (2)
C5—N3	1.349 (2)	C10—N5	1.385 (2)
C5—N2	1.355 (2)	C11—N6	1.374 (2)
C6—N3	1.321 (2)	C11—H11	0.9400
C6—N1	1.331 (2)	C12—N5	1.320 (2)
C6—H6	0.9400	C12—N6	1.342 (2)
C7—N4	1.446 (3)	C12—H12	0.9400
C7—H7A	0.9700	N2—H2	0.8700
C7—H7B	0.9700	N6—H6A	0.8700
N1—C1—N4	114.64 (15)	H8A—C8—H8B	107.8
N1—C1—C2	119.20 (15)	C10—C9—C8	111.87 (14)
N4—C1—C2	126.15 (16)	C10—C9—H9A	109.2
C5—C2—C1	113.83 (15)	C8—C9—H9A	109.2
C5—C2—C3	102.77 (14)	C10—C9—H9B	109.2
C1—C2—C3	143.40 (16)	C8—C9—H9B	109.2
C4—C3—C2	108.69 (15)	H9A—C9—H9B	107.9
C4—C3—Cl1	118.73 (14)	C11—C10—N5	109.35 (16)
C2—C3—Cl1	132.58 (14)	C11—C10—C9	128.54 (17)
C3—C4—N2	109.48 (16)	N5—C10—C9	122.03 (16)
C3—C4—H4	125.3	C10—C11—N6	106.29 (16)
N2—C4—H4	125.3	C10—C11—H11	126.9
N3—C5—N2	123.13 (15)	N6—C11—H11	126.9
N3—C5—C2	126.66 (16)	N5—C12—N6	112.00 (17)
N2—C5—C2	110.21 (15)	N5—C12—H12	124.0
N3—C6—N1	128.55 (17)	N6—C12—H12	124.0
N3—C6—H6	115.7	C6—N1—C1	119.29 (15)
N1—C6—H6	115.7	C5—N2—C4	108.84 (15)
N4—C7—H7A	109.5	C5—N2—H2	125.6
N4—C7—H7B	109.5	C4—N2—H2	125.6
H7A—C7—H7B	109.5	C6—N3—C5	112.45 (15)
N4—C7—H7C	109.5	C1—N4—C7	123.13 (16)
H7A—C7—H7C	109.5	C1—N4—C8	121.64 (15)
H7B—C7—H7C	109.5	C7—N4—C8	115.03 (15)
N4—C8—C9	112.60 (15)	C12—N5—C10	105.27 (16)
N4—C8—H8A	109.1	C12—N6—C11	107.09 (15)
C9—C8—H8A	109.1	C12—N6—H6A	126.5
N4—C8—H8B	109.1	C11—N6—H6A	126.5
C9—C8—H8B	109.1

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

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) ; (ii) .