Ethyl 5-amino-1-(5-bromo­pyrimidin-2-yl)-1H-pyrazole-4-carboxyl­ate

Subramanyam, M.; Lingappa, B.; Thiruvalluvar, A.; Kalluraya, B.; Butcher, R.J.

doi:10.1107/S1600536807054554

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Ethyl 5-amino-1-(5-bromopyrimidin-2-yl)-1H-pyrazole-4-carboxylate

M. Subramanyam, B. Lingappa, A. Thiruvalluvar, B. Kalluraya and R. J. Butcher

The molecule of the title compound, C₁₀H₁₀BrN₅O₂, is planar, except for the amino and carboxylate groups. The molecules are linked by intermolecular C—H

O and N—H

N hydrogen bonds, and by slipped π–π stacking between symmetry-related pyrazole and pyrimidine rings [centroid-to-centroid distance 3.512 (1) Å, interplanar distance 3.391 Å and offset angle 15.1°]. Intramolecular N—H

N and N—H

O hydrogen bonds stabilize the planar conformation.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807054554/dn2257sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807054554/dn2257Isup2.hkl Contains datablock I

CCDC reference: 672811

checkCIF report

Key indicators

Single-crystal X-ray study
T = 200 K
Mean (C-C) = 0.003 Å
R factor = 0.030
wR factor = 0.077
Data-to-parameter ratio = 22.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.98

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

Thiruvalluvar et al., (2007a,b,c) have reported the crystal structures of pyrimidine derivatives. The title compound, C₁₀H₁₀BrN₅O₂, is planar, except the amino and carboxylate group (Fig. 1). The molecules are linked by intermolecular C—H···O and N—H···N hydrogen bonds forming ribbons parallel to the a axis (Fig. 2, Table 1). These ribbons are further interconnected through weak slippest π-π stacking between the N1—N2—C3—C4—C5 and the symmetry related (2 - x, -y, 1 - z) N12—C11—N16—C15—C14—C13 rings(centroid-to-centroid distance of 3.512 (1) Å, interplanar distance of 3.391 Å and offset angle of 15.1°). Intramolecular N—H···N and N—H···O hydrogen bonds (Table 1) stabilize the planar conformation

Related literature top

For related crystal structures, see Thiruvalluvar et al. (2007a,b,c).

Experimental top

Ethoxymethylenecyanoacetate (1.7 g, 0.01 mol) was added in small portion to a solution of 2-hydrazino-5-bromo-pyrimidine (1.9.0 g, 0.01 mol) in ethanol (17 ml). The reaction mass was refluxed for 1 h on a water bath, the completion of the reaction was monitored by TLC. The contents were cooled to room temperature and distilled mineral water (17 ml) was added, stirred for 2 h, the solid obtained was filtered, washed with DM water and dried. Recrystallization from ethyl acetate gave the title compound as pinkish crystals, yield (2.0 g, 64%).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: PLATON (Spek, 2003).

Figures top

	Fig. 1. The molecular structure of the title compound, showing the atom-numbering scheme and displacement ellipsoids drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. Partial packing view of the title compound, showing the formation of ribbon through N—H···N and C—H···O hydrogen bonds. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted·[Symmetry codes: (i) x - 1, y, z; (ii) x + 1, y, z]

Ethyl 5-amino-1-(5-bromopyrimidin-2-yl)-1H-pyrazole-4-carboxylate top

Crystal data top

C₁₀H₁₀BrN₅O₂	F(000) = 624
M_r = 312.13	D_x = 1.731 Mg m⁻³
Monoclinic, P2₁/n	Melting point: 484(1) K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.7107 Å
a = 6.3433 (3) Å	Cell parameters from 4274 reflections
b = 28.9030 (8) Å	θ = 4.7–32.4°
c = 6.9439 (3) Å	µ = 3.44 mm⁻¹
β = 109.821 (5)°	T = 200 K
V = 1197.68 (9) Å³	Rectangular-plate, colourless
Z = 4	0.52 × 0.39 × 0.14 mm

Data collection top

Oxford Diffraction Gemini diffractometer	3933 independent reflections
Radiation source: Enhance (Mo) X-ray Source	2361 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
Detector resolution: 10.5081 pixels mm^-1	θ_max = 32.4°, θ_min = 4.7°
ϕ and ω scans	h = −9→8
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)	k = −42→41
T_min = 0.221, T_max = 0.633	l = −10→10
12255 measured reflections

Refinement top

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)] = 0.030	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.077	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0342P)²] where P = (F_o² + 2F_c²)/3
3933 reflections	(Δ/σ)_max < 0.001
172 parameters	Δρ_max = 0.37 e Å⁻³
0 restraints	Δρ_min = −0.48 e Å⁻³

Crystal data top

C₁₀H₁₀BrN₅O₂	V = 1197.68 (9) Å³
M_r = 312.13	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 6.3433 (3) Å	µ = 3.44 mm⁻¹
b = 28.9030 (8) Å	T = 200 K
c = 6.9439 (3) Å	0.52 × 0.39 × 0.14 mm
β = 109.821 (5)°

Data collection top

Oxford Diffraction Gemini diffractometer	3933 independent reflections
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)	2361 reflections with I > 2σ(I)
T_min = 0.221, T_max = 0.633	R_int = 0.030
12255 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.030	0 restraints
wR(F²) = 0.077	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.37 e Å⁻³
3933 reflections	Δρ_min = −0.48 e Å⁻³
172 parameters

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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

	x	y	z	U_iso*/U_eq
Br1	1.22590 (4)	−0.15293 (1)	0.84262 (3)	0.0432 (1)
O41	0.4802 (2)	0.14654 (5)	0.5849 (2)	0.0374 (5)
O42	0.7778 (2)	0.19419 (5)	0.6487 (2)	0.0294 (4)
N1	1.0031 (2)	0.04632 (5)	0.7293 (2)	0.0222 (5)
N2	1.1764 (3)	0.07781 (5)	0.7447 (3)	0.0282 (5)
N5	0.6064 (3)	0.04722 (6)	0.6635 (3)	0.0309 (6)
N12	0.8851 (3)	−0.02943 (5)	0.7405 (3)	0.0308 (5)
N16	1.2688 (3)	−0.01193 (6)	0.8024 (3)	0.0338 (5)
C3	1.0773 (3)	0.11816 (7)	0.7149 (3)	0.0263 (6)
C4	0.8460 (3)	0.11555 (7)	0.6794 (3)	0.0233 (5)
C5	0.7997 (3)	0.06879 (6)	0.6884 (3)	0.0213 (5)
C11	1.0544 (3)	−0.00088 (6)	0.7589 (3)	0.0228 (5)
C13	0.9366 (3)	−0.07441 (7)	0.7638 (3)	0.0331 (6)
C14	1.1527 (3)	−0.08978 (7)	0.8098 (3)	0.0290 (6)
C15	1.3162 (4)	−0.05673 (7)	0.8309 (3)	0.0366 (7)
C41	0.6802 (3)	0.15228 (6)	0.6332 (3)	0.0240 (5)
C43	0.6324 (4)	0.23428 (7)	0.6071 (3)	0.0373 (7)
C44	0.7478 (4)	0.27217 (8)	0.5359 (4)	0.0509 (8)
H3	1.15424	0.14647	0.71703	0.0316*
H5A	0.498 (4)	0.0619 (7)	0.668 (3)	0.028 (6)*
H5B	0.603 (3)	0.0169 (8)	0.685 (3)	0.034 (6)*
H13	0.82039	−0.09633	0.74809	0.0397*
H15	1.46789	−0.06636	0.86713	0.0439*
H43A	0.60326	0.24388	0.73262	0.0448*
H43B	0.48727	0.22693	0.50016	0.0448*
H44A	0.77406	0.26244	0.41075	0.0764*
H44B	0.65362	0.29995	0.50771	0.0764*
H44C	0.89149	0.27902	0.64250	0.0764*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0682 (2)	0.0255 (1)	0.0432 (1)	0.0145 (1)	0.0284 (1)	0.0065 (1)
O41	0.0204 (7)	0.0319 (9)	0.0607 (10)	0.0011 (6)	0.0149 (7)	0.0077 (7)
O42	0.0253 (7)	0.0196 (7)	0.0429 (8)	0.0022 (5)	0.0110 (6)	0.0031 (6)
N1	0.0182 (8)	0.0186 (8)	0.0315 (8)	−0.0016 (6)	0.0108 (6)	−0.0030 (6)
N2	0.0215 (8)	0.0208 (8)	0.0443 (9)	−0.0053 (7)	0.0138 (7)	−0.0045 (7)
N5	0.0184 (9)	0.0236 (10)	0.0535 (11)	−0.0001 (7)	0.0160 (8)	0.0010 (8)
N12	0.0238 (8)	0.0218 (9)	0.0472 (10)	−0.0022 (7)	0.0124 (7)	−0.0002 (8)
N16	0.0223 (8)	0.0278 (9)	0.0508 (10)	0.0024 (7)	0.0117 (8)	0.0043 (8)
C3	0.0232 (10)	0.0213 (10)	0.0356 (10)	−0.0053 (7)	0.0115 (8)	−0.0042 (8)
C4	0.0215 (9)	0.0246 (10)	0.0255 (9)	−0.0013 (7)	0.0104 (8)	−0.0001 (8)
C5	0.0190 (9)	0.0237 (9)	0.0230 (9)	0.0003 (7)	0.0095 (7)	−0.0030 (7)
C11	0.0237 (9)	0.0229 (10)	0.0222 (9)	0.0009 (7)	0.0083 (7)	−0.0019 (7)
C13	0.0343 (11)	0.0204 (10)	0.0460 (12)	−0.0034 (8)	0.0154 (10)	−0.0019 (9)
C14	0.0385 (11)	0.0238 (10)	0.0268 (10)	0.0038 (8)	0.0138 (9)	0.0000 (8)
C15	0.0280 (11)	0.0310 (12)	0.0512 (13)	0.0102 (9)	0.0140 (10)	0.0071 (10)
C41	0.0250 (9)	0.0229 (9)	0.0268 (9)	0.0023 (8)	0.0124 (7)	0.0020 (8)
C43	0.0345 (11)	0.0254 (11)	0.0517 (13)	0.0074 (9)	0.0144 (10)	0.0055 (10)
C44	0.0477 (14)	0.0328 (13)	0.0672 (16)	0.0024 (11)	0.0131 (12)	0.0200 (12)

Geometric parameters (Å, º) top

Br1—C14	1.878 (2)	C3—C4	1.405 (3)
O41—C41	1.209 (2)	C4—C41	1.452 (3)
O42—C41	1.348 (2)	C4—C5	1.389 (3)
O42—C43	1.448 (3)	C13—C14	1.372 (3)
N1—N2	1.403 (2)	C14—C15	1.381 (3)
N1—C5	1.385 (2)	C43—C44	1.492 (3)
N1—C11	1.401 (2)	C3—H3	0.9500
N2—C3	1.308 (3)	C13—H13	0.9500
N5—C5	1.334 (3)	C15—H15	0.9500
N12—C11	1.326 (3)	C43—H43A	0.9900
N12—C13	1.337 (3)	C43—H43B	0.9900
N16—C11	1.328 (3)	C44—H44A	0.9800
N16—C15	1.329 (3)	C44—H44B	0.9800
N5—H5B	0.89 (2)	C44—H44C	0.9800
N5—H5A	0.82 (2)

Br1···C4ⁱ	3.663 (2)	C11···C11ⁱⁱ	3.424 (3)
Br1···C41ⁱⁱ	3.551 (2)	C13···C3ⁱⁱ	3.530 (3)
Br1···C4ⁱⁱ	3.660 (2)	C13···N2ⁱⁱ	3.358 (3)
Br1···C41ⁱ	3.483 (2)	C14···C3ⁱⁱ	3.532 (3)
Br1···H44Bⁱⁱⁱ	3.2300	C14···C5ⁱ	3.448 (3)
Br1···H44C^iv	3.1000	C14···C4ⁱⁱ	3.480 (3)
O41···N2^v	3.216 (2)	C15···C5ⁱⁱ	3.445 (3)
O41···N5	2.980 (2)	C15···N5ⁱ	3.387 (3)
O41···C3^v	3.096 (2)	C41···Br1ⁱⁱ	3.551 (2)
O42···C44^vi	3.410 (3)	C41···Br1ⁱ	3.483 (2)
O41···H3^v	2.5300	C44···O42^x	3.410 (3)
O41···H5A	2.51 (2)	C3···H44B^vi	3.0500
O41···H13^vii	2.8500	C11···H5B	2.78 (2)
O41···H43B	2.4000	C41···H5A	2.90 (2)
O42···H3	2.6600	C43···H43B^vi	3.1000
O42···H44B^vi	2.8100	C43···H44C^x	3.0900
N2···O41^viii	3.216 (2)	C44···H43B^vi	3.0600
N2···N5^viii	3.096 (3)	H3···O41^viii	2.5300
N2···N16	2.659 (2)	H3···O42	2.6600
N2···C13ⁱⁱ	3.358 (3)	H3···H44B^vi	2.5500
N5···C15ⁱ	3.387 (3)	H5A···O41	2.51 (2)
N5···N12	2.771 (2)	H5A···N2^v	2.32 (3)
N5···O41	2.980 (2)	H5A···N16^v	2.91 (2)
N5···N2^v	3.096 (3)	H5A···C41	2.90 (2)
N5···N16^v	3.137 (3)	H5B···N12	2.16 (2)
N12···N5	2.771 (2)	H5B···N16^v	2.65 (2)
N16···N2	2.659 (2)	H5B···C11	2.78 (2)
N16···N5^viii	3.137 (3)	H13···O41^vii	2.8500
N2···H5A^viii	2.32 (3)	H15···N2^ix	2.8900
N2···H15^ix	2.8900	H43B···O41	2.4000
N12···H5B	2.16 (2)	H43B···C43^x	3.1000
N16···H5A^viii	2.91 (2)	H43B···C44^x	3.0600
N16···H5B^viii	2.65 (2)	H43B···H44C^x	2.3500
C3···O41^viii	3.096 (2)	H44B···Br1^xi	3.2300
C3···C13ⁱⁱ	3.530 (3)	H44B···O42^x	2.8100
C3···C14ⁱⁱ	3.532 (3)	H44B···C3^x	3.0500
C4···C14ⁱⁱ	3.480 (3)	H44B···H3^x	2.5500
C4···Br1ⁱⁱ	3.660 (2)	H44C···Br1^xii	3.1000
C4···Br1ⁱ	3.663 (2)	H44C···C43^vi	3.0900
C5···C14ⁱ	3.448 (3)	H44C···H43B^vi	2.3500
C5···C15ⁱⁱ	3.445 (3)

C41—O42—C43	117.32 (16)	C13—C14—C15	117.13 (19)
N2—N1—C5	111.27 (14)	N16—C15—C14	122.3 (2)
N2—N1—C11	118.90 (14)	O41—C41—O42	123.78 (17)
C5—N1—C11	129.82 (15)	O41—C41—C4	125.07 (17)
N1—N2—C3	104.14 (17)	O42—C41—C4	111.15 (17)
C11—N12—C13	115.91 (19)	O42—C43—C44	107.6 (2)
C11—N16—C15	115.51 (19)	N2—C3—H3	123.00
H5A—N5—H5B	116 (2)	C4—C3—H3	123.00
C5—N5—H5A	120.1 (16)	N12—C13—H13	119.00
C5—N5—H5B	120.8 (13)	C14—C13—H13	119.00
N2—C3—C4	113.41 (19)	N16—C15—H15	119.00
C3—C4—C5	105.58 (18)	C14—C15—H15	119.00
C3—C4—C41	129.40 (18)	O42—C43—H43A	110.00
C5—C4—C41	124.97 (18)	O42—C43—H43B	110.00
N5—C5—C4	130.41 (19)	C44—C43—H43A	110.00
N1—C5—N5	123.99 (16)	C44—C43—H43B	110.00
N1—C5—C4	105.60 (17)	H43A—C43—H43B	108.00
N1—C11—N16	115.87 (16)	C43—C44—H44A	109.00
N1—C11—N12	116.85 (17)	C43—C44—H44B	109.00
N12—C11—N16	127.28 (17)	C43—C44—H44C	109.00
N12—C13—C14	121.81 (19)	H44A—C44—H44B	109.00
Br1—C14—C13	121.97 (15)	H44A—C44—H44C	109.00
Br1—C14—C15	120.90 (16)	H44B—C44—H44C	109.00

C43—O42—C41—O41	0.8 (3)	C15—N16—C11—N1	179.79 (17)
C43—O42—C41—C4	−179.89 (16)	C15—N16—C11—N12	−0.3 (3)
C41—O42—C43—C44	−153.54 (18)	C11—N16—C15—C14	2.2 (3)
N2—N1—C5—C4	−0.5 (2)	N2—C3—C4—C41	−177.5 (2)
C11—N1—C5—N5	−2.1 (3)	N2—C3—C4—C5	−0.1 (2)
C11—N1—C5—C4	178.32 (17)	C3—C4—C5—N5	−179.2 (2)
N2—N1—C11—N12	−179.22 (17)	C3—C4—C41—O41	172.3 (2)
N2—N1—C11—N16	0.8 (2)	C41—C4—C5—N1	177.91 (18)
C5—N1—C11—N12	2.1 (3)	C41—C4—C5—N5	−1.6 (4)
C5—N1—C11—N16	−177.97 (18)	C3—C4—C5—N1	0.3 (2)
C11—N1—N2—C3	−178.50 (16)	C5—C4—C41—O42	176.03 (18)
N2—N1—C5—N5	179.11 (19)	C3—C4—C41—O42	−7.0 (3)
C5—N1—N2—C3	0.4 (2)	C5—C4—C41—O41	−4.7 (3)
N1—N2—C3—C4	−0.2 (2)	N12—C13—C14—Br1	−180.00 (17)
C13—N12—C11—N16	−1.7 (3)	N12—C13—C14—C15	−0.1 (3)
C13—N12—C11—N1	178.25 (17)	Br1—C14—C15—N16	177.87 (16)
C11—N12—C13—C14	1.8 (3)	C13—C14—C15—N16	−2.0 (3)

Symmetry codes: (i) −x+2, −y, −z+2; (ii) −x+2, −y, −z+1; (iii) −x+3/2, y−1/2, −z+3/2; (iv) −x+5/2, y−1/2, −z+3/2; (v) x−1, y, z; (vi) x+1/2, −y+1/2, z+1/2; (vii) −x+1, −y, −z+1; (viii) x+1, y, z; (ix) −x+3, −y, −z+2; (x) x−1/2, −y+1/2, z−1/2; (xi) −x+3/2, y+1/2, −z+3/2; (xii) −x+5/2, y+1/2, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5A···O41	0.82 (2)	2.51 (2)	2.980 (2)	118 (2)
N5—H5A···N2^v	0.82 (2)	2.32 (3)	3.096 (3)	158.0 (19)
N5—H5B···N12	0.89 (2)	2.16 (2)	2.771 (2)	125.0 (17)
C3—H3···O41^viii	0.95	2.53	3.096 (2)	118.0

Symmetry codes: (v) x−1, y, z; (viii) x+1, y, z.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₀BrN₅O₂
M_r	312.13
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	200
a, b, c (Å)	6.3433 (3), 28.9030 (8), 6.9439 (3)
β (°)	109.821 (5)
V (Å³)	1197.68 (9)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	3.44
Crystal size (mm)	0.52 × 0.39 × 0.14

Data collection
Diffractometer	Oxford Diffraction Gemini diffractometer
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2007)
T_min, T_max	0.221, 0.633
No. of measured, independent and observed [I > 2σ(I)] reflections	12255, 3933, 2361
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.754

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.030, 0.077, 1.03
No. of reflections	3933
No. of parameters	172
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.37, −0.48

Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5A···O41	0.82 (2)	2.51 (2)	2.980 (2)	118 (2)
N5—H5A···N2ⁱ	0.82 (2)	2.32 (3)	3.096 (3)	158.0 (19)
N5—H5B···N12	0.89 (2)	2.16 (2)	2.771 (2)	125.0 (17)
C3—H3···O41ⁱⁱ	0.95	2.53	3.096 (2)	118.0

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

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