Literature DB >> 22090971

5-(Pyridin-4-ylmeth-yl)-1H-pyrazolo-[3,4-d]pyrimidin-4(5H)-one.

Abdulsalam Alsubari, Youssef Ramli, El Mokhtar Essassi, Hafid Zouihri.

Abstract

In the title compound, C(11)H(9)N(5)O, the pyrazolo-pyrimidin-4-one ring system is almost planar, with a maximum deviation of 0.0546 (13) Å for the O atom. The crystal packing is stabilized by inter-molecular N-H⋯N, C-H⋯O and C-H⋯N hydrogen bonds. In addition, π-π stacking is found between the pyridine ring and the pyrazolo-pyrimidin-4-one ring systems, with centroid-centroid distances in the range 3.9627 (12)-4.6781 (12) Å.

Entities: Chemical Disease Species

Year: 2011 PMID： 22090971 PMCID： PMC3212314 DOI： 10.1107/S1600536811025025

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

Related literature

For a related structure, see: Al Subari et al. (2010 ▶). For the biological activity of pyrazolopyrimidinone derivatives, see: Kim et al. (2001 ▶); Ali et al. (2009 ▶).

Experimental

Crystal data

C11H9N5O M = 227.23 Monoclinic, a = 4.6371 (3) Å b = 19.2731 (10) Å c = 5.8593 (3) Å β = 102.498 (2)° V = 511.24 (5) Å3 Z = 2 Mo Kα radiation μ = 0.10 mm−1 T = 296 K 0.25 × 0.22 × 0.17 mm

Data collection

Bruker APEXII CCD detector diffractometer 6285 measured reflections 2603 independent reflections 2201 reflections with I > 2σ(I) R int = 0.030

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.085 S = 1.05 2603 reflections 158 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.16 e Å−3 Δρmin = −0.22 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811025025/fj2436sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811025025/fj2436Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811025025/fj2436Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₁H₉N₅O	F(000) = 236
M_r = 227.23	D_x = 1.476 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 342 reflections
a = 4.6371 (3) Å	θ = 2.4–25.6°
b = 19.2731 (10) Å	µ = 0.10 mm⁻¹
c = 5.8593 (3) Å	T = 296 K
β = 102.498 (2)°	Prism, colourless
V = 511.24 (5) Å³	0.25 × 0.22 × 0.17 mm
Z = 2

Bruker APEXII CCD detector diffractometer	2201 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.030
graphite	θ_max = 28.9°, θ_min = 2.1°
ω and φ scans	h = −6→6
6285 measured reflections	k = −26→26
2603 independent reflections	l = −7→7

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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.085	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0427P)² + 0.0014P] where P = (F_o² + 2F_c²)/3
2603 reflections	(Δ/σ)_max = 0.001
158 parameters	Δρ_max = 0.16 e Å⁻³
2 restraints	Δρ_min = −0.22 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	U_iso*/U_eq
N2	0.7680 (3)	1.03978 (7)	0.5859 (2)	0.0280 (3)
N1	0.3899 (3)	0.95388 (6)	0.5329 (2)	0.0242 (3)
N3	0.7129 (3)	1.11511 (7)	0.2529 (2)	0.0275 (3)
N5	0.8324 (3)	0.71619 (7)	0.6387 (3)	0.0326 (3)
N4	0.5292 (3)	1.12382 (7)	0.0394 (2)	0.0312 (3)
O1	0.0403 (3)	0.93783 (6)	0.1944 (2)	0.0343 (3)
C8	0.3807 (3)	1.03227 (8)	0.2246 (3)	0.0233 (3)
C11	0.6365 (3)	0.98760 (8)	0.6577 (3)	0.0257 (3)
H11	0.7155	0.9713	0.8075	0.031*
C10	0.6293 (3)	1.06125 (8)	0.3675 (3)	0.0235 (3)
C7	0.2488 (4)	0.97246 (8)	0.3022 (3)	0.0242 (3)
C1	0.4678 (3)	0.83113 (8)	0.6455 (3)	0.0250 (3)
C6	0.2764 (4)	0.89454 (8)	0.6453 (3)	0.0289 (4)
H6A	0.0764	0.8842	0.5626	0.035*
H6B	0.2708	0.9066	0.8050	0.035*
C2	0.6726 (4)	0.81124 (9)	0.8437 (3)	0.0298 (4)
H2	0.6926	0.8360	0.9825	0.036*
C5	0.4487 (4)	0.79196 (8)	0.4448 (3)	0.0322 (4)
H5	0.3130	0.8036	0.3087	0.039*
C4	0.6333 (4)	0.73540 (8)	0.4486 (3)	0.0351 (4)
H4	0.6181	0.7095	0.3125	0.042*
C9	0.3281 (4)	1.07419 (8)	0.0210 (3)	0.0286 (3)
H9	0.1735	1.0677	−0.1078	0.034*
C3	0.8469 (4)	0.75365 (9)	0.8304 (3)	0.0332 (4)
H3	0.9827	0.7404	0.9646	0.040*
H3N	0.869 (4)	1.1429 (12)	0.304 (4)	0.060 (7)*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N2	0.0245 (7)	0.0290 (7)	0.0283 (7)	0.0012 (6)	0.0011 (6)	−0.0026 (6)
N1	0.0251 (6)	0.0209 (6)	0.0264 (7)	0.0009 (5)	0.0052 (5)	0.0002 (5)
N3	0.0274 (7)	0.0252 (7)	0.0290 (8)	−0.0025 (6)	0.0042 (6)	−0.0006 (6)
N5	0.0329 (8)	0.0251 (7)	0.0411 (9)	0.0029 (6)	0.0108 (7)	0.0017 (6)
N4	0.0343 (8)	0.0293 (7)	0.0288 (8)	0.0020 (6)	0.0045 (6)	0.0010 (6)
O1	0.0323 (6)	0.0308 (6)	0.0355 (7)	−0.0077 (5)	−0.0025 (5)	−0.0025 (5)
C8	0.0213 (7)	0.0222 (7)	0.0252 (8)	0.0027 (6)	0.0020 (6)	−0.0028 (6)
C11	0.0259 (8)	0.0267 (8)	0.0222 (8)	0.0053 (6)	0.0003 (6)	−0.0015 (6)
C10	0.0227 (7)	0.0215 (7)	0.0263 (8)	0.0017 (6)	0.0050 (6)	−0.0034 (6)
C7	0.0225 (7)	0.0223 (7)	0.0268 (8)	0.0032 (6)	0.0032 (6)	−0.0039 (6)
C1	0.0264 (8)	0.0221 (7)	0.0280 (8)	−0.0036 (6)	0.0096 (7)	0.0014 (6)
C6	0.0298 (9)	0.0261 (8)	0.0334 (10)	0.0017 (7)	0.0130 (8)	0.0010 (6)
C2	0.0357 (9)	0.0269 (8)	0.0256 (8)	−0.0006 (7)	0.0041 (7)	0.0001 (6)
C5	0.0360 (10)	0.0319 (9)	0.0264 (9)	0.0023 (7)	0.0019 (7)	−0.0006 (7)
C4	0.0448 (11)	0.0282 (9)	0.0337 (10)	0.0017 (8)	0.0114 (9)	−0.0033 (7)
C9	0.0296 (8)	0.0289 (8)	0.0252 (8)	0.0009 (7)	0.0015 (7)	−0.0023 (6)
C3	0.0317 (9)	0.0289 (8)	0.0360 (11)	−0.0002 (7)	0.0006 (8)	0.0058 (7)

N2—C11	1.293 (2)	C8—C7	1.425 (2)
N2—C10	1.366 (2)	C11—H11	0.9300
N1—C11	1.379 (2)	C1—C5	1.384 (2)
N1—C7	1.415 (2)	C1—C2	1.386 (2)
N1—C6	1.4725 (19)	C1—C6	1.510 (2)
N3—C10	1.339 (2)	C6—H6A	0.9700
N3—N4	1.363 (2)	C6—H6B	0.9700
N3—H3N	0.897 (16)	C2—C3	1.385 (3)
N5—C3	1.325 (2)	C2—H2	0.9300
N5—C4	1.336 (2)	C5—C4	1.383 (2)
N4—C9	1.324 (2)	C5—H5	0.9300
O1—C7	1.231 (2)	C4—H4	0.9300
C8—C10	1.387 (2)	C9—H9	0.9300
C8—C9	1.418 (2)	C3—H3	0.9300

C11—N2—C10	112.37 (14)	C2—C1—C6	121.35 (15)
C11—N1—C7	123.10 (13)	N1—C6—C1	111.23 (11)
C11—N1—C6	117.67 (14)	N1—C6—H6A	109.4
C7—N1—C6	119.20 (13)	C1—C6—H6A	109.4
C10—N3—N4	111.39 (14)	N1—C6—H6B	109.4
C10—N3—H3N	126.6 (15)	C1—C6—H6B	109.4
N4—N3—H3N	122.0 (15)	H6A—C6—H6B	108.0
C3—N5—C4	117.08 (15)	C3—C2—C1	118.49 (16)
C9—N4—N3	105.96 (13)	C3—C2—H2	120.8
C10—C8—C9	104.34 (14)	C1—C2—H2	120.8
C10—C8—C7	119.42 (14)	C4—C5—C1	119.39 (16)
C9—C8—C7	136.22 (15)	C4—C5—H5	120.3
N2—C11—N1	126.12 (15)	C1—C5—H5	120.3
N2—C11—H11	116.9	N5—C4—C5	123.05 (16)
N1—C11—H11	116.9	N5—C4—H4	118.5
N3—C10—N2	125.17 (14)	C5—C4—H4	118.5
N3—C10—C8	107.61 (13)	N4—C9—C8	110.70 (15)
N2—C10—C8	127.23 (14)	N4—C9—H9	124.7
O1—C7—N1	120.18 (14)	C8—C9—H9	124.7
O1—C7—C8	128.22 (16)	N5—C3—C2	124.12 (17)
N1—C7—C8	111.59 (14)	N5—C3—H3	117.9
C5—C1—C2	117.87 (15)	C2—C3—H3	117.9
C5—C1—C6	120.77 (15)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N5ⁱ	0.90 (2)	1.96 (2)	2.840 (2)	168 (2)
C4—H4···N4ⁱⁱ	0.93	2.61	3.526 (2)	167
C9—H9···N2ⁱⁱⁱ	0.93	2.36	3.289 (2)	174
C11—H11···O1^iv	0.93	2.52	3.430 (2)	167

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N5ⁱ	0.90 (2)	1.96 (2)	2.840 (2)	168 (2)
C4—H4⋯N4ⁱⁱ	0.93	2.61	3.526 (2)	167
C9—H9⋯N2ⁱⁱⁱ	0.93	2.36	3.289 (2)	174
C11—H11⋯O1^iv	0.93	2.52	3.430 (2)	167

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

5 in total

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2. A short history of SHELX.

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

3. 3-[2-(2,3-Dioxoindolin-1-yl)eth-yl]-1,3-oxazolidin-2-one.

Authors: Abdusalam Al Subari; Rachid Bouhfid; Hafid Zouihri; El Mokhtar Essassi; Seik Weng Ng
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2010-01-27

4. Synthesis of some novel pyrazolo[3,4-b]pyridine and pyrazolo[3,4-d]pyrimidine derivatives bearing 5,6-diphenyl-1,2,4-triazine moiety as potential antimicrobial agents.

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5. Structure validation in chemical crystallography.

Authors: Anthony L Spek
Journal: Acta Crystallogr D Biol Crystallogr Date: 2009-01-20