4-(Prop-2-yn-1-ylsulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidine

El Hafi, M.; Boulhaoua, M.; Ramli, Y.; Benchidmi, M.; Essassi, E.M.; Mague, J.T.

doi:10.1107/S2414314617015267

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 10| October 2017| x171526

https://doi.org/10.1107/S2414314617015267

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4-(Prop-2-yn-1-ylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidine

Mohamed El Hafi,^a ^* Mohammed Boulhaoua,^a Youssef Ramli,^b Mohammed Benchidmi,^a El Mokhtar Essassi ^a and Joel T. Mague ^c

^aLaboratoire de Chimie Organique Hétérocyclique, Centre de Recherche Des Sciences des Médicaments, Pôle de Compétence Pharmacochimie, Av Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco, ^bLaboratory of Medicinal Chemistry, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco, and ^cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA
^*Correspondence e-mail: elhafi.mohamed1@gmail.com

Edited by S. Bernès, Benemérita Universidad Autónoma de Puebla, México (Received 24 August 2017; accepted 19 October 2017; online 24 October 2017)

The asymmetric unit of the title compound, C₈H₆N₄S, consists of two independent molecules differing in the orientation of the side chain. In the crystal, molecules form dimers through N—H⋯N hydrogen bonds. The dimers stack along the a-axis direction with weak π–π stacking interactions [centroid–centroid distances of 3.898 (2) and 3.908 (2) Å]. The crystal studied was refined as a two-component twin.

Keywords: crystal structure; hydrogen bond; π-stacking; pyrimidine.

CCDC reference: 1581006

Structure description

As a continuation of our research work devoted to the development of S-substituted pyrazolo[3,4-d]pyrimidine derivatives (El Fal et al., 2014 ), we have studied the action of propargyl bromide towards 1H-pyrazolo[3,4-d]pyrimidine-4(5H)-thione, using ethanol as solvent and potassium hydroxide as base. The title compound was isolated and its structure was established.

The asymmetric unit of the title compound consists of two independent molecules differing to a small extent in the orientation of the side chain with respect to the bicyclic core (Fig. 1). Thus, the dihedral angle between the mean plane of the N1–N4/C1–C5 unit and that defined by S1/C6–C8 is 79.3 (2)°, while the corresponding angle in the second molecule is 76.4 (2)°. The bicyclic cores are planar with the maximum deviation from the mean plane being 0.016 (3) Å (C5) in the first molecule (r.m.s. deviation = 0.0094 Å) and −0.015 (3) Å (C13) in the second (r.m.s. deviation = 0.0086 Å). The dihedral angle between the bicyclic units is 76.42 (7)°.

Figure 1
The asymmetric unit with the atom-labelling scheme and 50% probability ellipsoids for non-H atoms

In the crystal, each independent molecule forms a dimer with an inversion-related counterpart through pairwise N—H⋯N hydrogen bonds (Table 1). The dimers stack along the a-axis direction with the aid of head-to-tail π–π-stacking interactions (Fig. 2). For the molecules containing S1, the centroid–centroid distance is 3.898 (2) Å, while for those containing S2, the distance is 3.908 (2) Å. In both instances, the dihedral angle between the associated planes is 1.2 (2)°.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯N2ⁱ	0.90 (6)	2.10 (6)	2.972 (4)	165 (5)
N7—H7⋯N6ⁱⁱ	0.81 (6)	2.18 (6)	2.965 (5)	163 (5)
Symmetry codes: (i) -x+3, -y, -z+1; (ii) -x+2, -y, -z.

Figure 2
Oblique view of the packing with N—H⋯N hydrogen bonds and π–π-stacking interactions shown, respectively, as blue and orange dashed lines.

Synthesis and crystallization

To a solution of 1H-pyrazolo[3,4-d]pyrimidine-4-thione (0.5 g, 3.3 mmol) in EtOH (15 ml) was added propargyl bromide (0.25 ml, 3.3 mmol) and potassium hydroxide (0.19 g, 3.3 mmol). The mixture was refluxed for 8 h, and after cooling, the reaction mixture was poured slowly into an ice bath under stirring to homogenize the whole. The solid product was precipitated and filtered. The residue was purified by recrystallization from ethanol to afford the title compound as colourless crystals (65% yield; m.p. 398–400 K).

Refinement

Crystal data, data collection and structure refinement details are summarize in Table 2. The studied crystal was found to be twinned by a 180° rotation about the b* axis, and the model was refined as a two-component twin using CELL_NOW (Sheldrick, 2008b ).

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₆N₄S
M_r	190.23
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	150
a, b, c (Å)	4.8851 (1), 9.8472 (3), 17.4428 (5)
α, β, γ (°)	86.380 (1), 89.606 (1), 81.027 (1)
V (Å³)	827.15 (4)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	3.09
Crystal size (mm)	0.29 × 0.09 × 0.03

Data collection
Diffractometer	Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction	Multi-scan (TWINABS; Sheldrick, 2009 )
T_min, T_max	0.46, 0.91
No. of measured, independent and observed [I > 2σ(I)] reflections	11085, 11079, 9249
R_int	0.039
(sin θ/λ)_max (Å⁻¹)	0.618

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.059, 0.163, 1.09
No. of reflections	11079
No. of parameters	284
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.67, −0.31
Computer programs: APEX3 and SAINT (Bruker, 2016 ), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008a ).

Structural data

CCDC reference: 1581006

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314617015267/bh4028sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617015267/bh4028Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314617015267/bh4028Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314617015267/bh4028Isup4.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008a).

4-(Prop-2-yn-1-ylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidine top

Crystal data top

C₈H₆N₄S	F(000) = 392
M_r = 190.23	D_x = 1.528 Mg m⁻³
Triclinic, P1	Melting point: 398 K
a = 4.8851 (1) Å	Cu Kα radiation, λ = 1.54178 Å
b = 9.8472 (3) Å	Cell parameters from 7441 reflections
c = 17.4428 (5) Å	θ = 5.1–72.4°
α = 86.380 (1)°	µ = 3.09 mm⁻¹
β = 89.606 (1)°	T = 150 K
γ = 81.027 (1)°	Plate, colourless
V = 827.15 (4) Å³	0.29 × 0.09 × 0.03 mm
Z = 4

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	11079 independent reflections
Radiation source: INCOATEC IµS micro-focus source	9249 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.039
Detector resolution: 10.4167 pixels mm^-1	θ_max = 72.4°, θ_min = 2.5°
ω scans	h = −6→6
Absorption correction: multi-scan (TWINABS; Sheldrick, 2009)	k = −12→11
T_min = 0.46, T_max = 0.91	l = −21→21
11085 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)] = 0.059	Hydrogen site location: difference Fourier map
wR(F²) = 0.163	All H-atom parameters refined
S = 1.09	w = 1/[σ²(F_o²) + (0.072P)² + 0.6596P] where P = (F_o² + 2F_c²)/3
11079 reflections	(Δ/σ)_max < 0.001
284 parameters	Δρ_max = 0.67 e Å⁻³
0 restraints	Δρ_min = −0.31 e Å⁻³
0 constraints

Special details top

Experimental. Analysis of 887 reflections having I/σ(I) > 12 and chosen from the full data set with CELL_NOW (Sheldrick, 2008) showed the crystal to belong to the triclinic system and to be twinned by a 180° rotation about the b* axis. The raw data were processed using the multi-component version ofSAINT under control of the two-component orientation file generated by CELL_NOW.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.5206 (2)	0.33776 (10)	0.33099 (5)	0.0286 (3)
N1	0.8655 (7)	0.3466 (3)	0.44900 (18)	0.0270 (7)
N2	1.2403 (7)	0.1661 (3)	0.49127 (18)	0.0263 (7)
N3	1.2790 (7)	−0.0317 (3)	0.41350 (19)	0.0272 (7)
H3	1.421 (13)	−0.086 (6)	0.438 (3)	0.054 (16)*
N4	1.1421 (7)	−0.0703 (4)	0.3524 (2)	0.0304 (8)
C1	0.7945 (8)	0.2734 (4)	0.3936 (2)	0.0233 (8)
C2	1.0831 (8)	0.2892 (4)	0.4948 (2)	0.0274 (9)
H2	1.127 (9)	0.343 (4)	0.534 (3)	0.026 (11)*
C3	1.1622 (8)	0.0951 (4)	0.4342 (2)	0.0223 (8)
C4	0.9406 (8)	0.0320 (4)	0.3344 (2)	0.0294 (9)
H4	0.814 (11)	0.013 (5)	0.291 (3)	0.046 (14)*
C5	0.9395 (8)	0.1406 (4)	0.3835 (2)	0.0230 (8)
C6	0.4067 (9)	0.5068 (4)	0.3667 (2)	0.0315 (9)
H6A	0.398 (9)	0.498 (4)	0.423 (3)	0.027 (11)*
H6B	0.212 (11)	0.525 (5)	0.347 (3)	0.042 (13)*
C7	0.5835 (9)	0.6066 (4)	0.3404 (2)	0.0308 (9)
C8	0.7249 (10)	0.6887 (5)	0.3172 (3)	0.0363 (10)
H8	0.851 (11)	0.744 (5)	0.304 (3)	0.039 (14)*
S2	0.0250 (2)	0.29312 (10)	0.17167 (5)	0.0281 (3)
N5	0.3598 (7)	0.3327 (3)	0.05226 (18)	0.0287 (7)
N6	0.7361 (7)	0.1642 (3)	0.00878 (18)	0.0265 (7)
N7	0.7867 (7)	−0.0506 (4)	0.08603 (19)	0.0272 (7)
H7	0.910 (12)	−0.098 (5)	0.064 (3)	0.044 (15)*
N8	0.6605 (7)	−0.1054 (4)	0.1483 (2)	0.0321 (8)
C9	0.2964 (8)	0.2445 (4)	0.1088 (2)	0.0249 (8)
C10	0.5752 (8)	0.2867 (4)	0.0059 (2)	0.0289 (9)
H10	0.620 (9)	0.355 (4)	−0.034 (3)	0.027 (11)*
C11	0.6642 (8)	0.0790 (4)	0.0663 (2)	0.0237 (8)
C12	0.4571 (9)	−0.0095 (4)	0.1677 (2)	0.0294 (9)
H12	0.336 (11)	−0.019 (5)	0.209 (3)	0.038 (13)*
C13	0.4474 (8)	0.1111 (4)	0.1182 (2)	0.0238 (8)
C14	−0.0920 (9)	0.4710 (5)	0.1372 (3)	0.0310 (9)
H14A	−0.112 (12)	0.476 (5)	0.080 (3)	0.051 (15)*
H14B	−0.260 (11)	0.490 (5)	0.160 (3)	0.039 (13)*
C15	0.0894 (9)	0.5647 (4)	0.1597 (2)	0.0313 (9)
C16	0.2341 (10)	0.6432 (5)	0.1784 (3)	0.0357 (10)
H16	0.356 (13)	0.705 (6)	0.189 (4)	0.060 (17)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0232 (5)	0.0360 (6)	0.0253 (5)	−0.0025 (4)	−0.0072 (3)	0.0030 (4)
N1	0.0268 (17)	0.0316 (17)	0.0214 (16)	−0.0022 (14)	−0.0024 (12)	0.0023 (13)
N2	0.0234 (17)	0.0315 (18)	0.0235 (16)	−0.0043 (14)	−0.0059 (12)	0.0021 (13)
N3	0.0244 (17)	0.0297 (18)	0.0267 (17)	−0.0026 (15)	−0.0030 (13)	0.0011 (14)
N4	0.0275 (18)	0.0326 (18)	0.0310 (18)	−0.0032 (15)	−0.0040 (14)	−0.0034 (14)
C1	0.0187 (18)	0.031 (2)	0.0200 (18)	−0.0064 (16)	−0.0005 (13)	0.0033 (15)
C2	0.026 (2)	0.033 (2)	0.0231 (19)	−0.0034 (17)	−0.0054 (15)	−0.0001 (16)
C3	0.0193 (18)	0.0276 (19)	0.0202 (17)	−0.0059 (16)	−0.0001 (13)	0.0025 (15)
C4	0.025 (2)	0.036 (2)	0.028 (2)	−0.0055 (18)	−0.0035 (15)	−0.0031 (17)
C5	0.0206 (19)	0.0297 (19)	0.0189 (18)	−0.0066 (16)	−0.0008 (13)	0.0031 (14)
C6	0.022 (2)	0.039 (2)	0.030 (2)	0.0018 (18)	−0.0016 (15)	0.0022 (18)
C7	0.030 (2)	0.032 (2)	0.027 (2)	0.0064 (19)	−0.0069 (16)	0.0002 (17)
C8	0.038 (3)	0.035 (2)	0.034 (2)	−0.001 (2)	−0.0024 (18)	0.0028 (19)
S2	0.0228 (5)	0.0348 (5)	0.0265 (5)	−0.0032 (4)	0.0031 (3)	−0.0024 (4)
N5	0.0277 (18)	0.0336 (18)	0.0238 (16)	−0.0024 (15)	0.0009 (13)	0.0002 (14)
N6	0.0227 (17)	0.0336 (18)	0.0236 (16)	−0.0058 (14)	0.0002 (12)	−0.0021 (13)
N7	0.0226 (17)	0.0315 (18)	0.0263 (17)	−0.0009 (15)	0.0033 (13)	0.0002 (14)
N8	0.0298 (19)	0.0361 (19)	0.0286 (18)	−0.0011 (16)	0.0017 (13)	0.0023 (14)
C9	0.0211 (19)	0.034 (2)	0.0209 (18)	−0.0072 (16)	−0.0016 (14)	−0.0046 (15)
C10	0.028 (2)	0.033 (2)	0.025 (2)	−0.0047 (18)	0.0021 (15)	0.0029 (17)
C11	0.0201 (18)	0.031 (2)	0.0213 (18)	−0.0057 (16)	−0.0013 (14)	−0.0047 (15)
C12	0.027 (2)	0.035 (2)	0.026 (2)	−0.0049 (18)	0.0033 (16)	−0.0009 (17)
C13	0.0183 (18)	0.031 (2)	0.0233 (18)	−0.0063 (16)	−0.0008 (14)	−0.0037 (15)
C14	0.019 (2)	0.040 (2)	0.032 (2)	0.0006 (18)	0.0009 (16)	−0.0032 (18)
C15	0.033 (2)	0.034 (2)	0.0223 (19)	0.0065 (19)	0.0027 (15)	−0.0002 (16)
C16	0.041 (3)	0.032 (2)	0.033 (2)	−0.003 (2)	−0.0040 (19)	−0.0017 (18)

Geometric parameters (Å, º) top

S1—C1	1.747 (4)	S2—C9	1.743 (4)
S1—C6	1.818 (4)	S2—C14	1.821 (4)
N1—C1	1.322 (5)	N5—C9	1.339 (5)
N1—C2	1.362 (5)	N5—C10	1.361 (5)
N2—C2	1.334 (5)	N6—C10	1.331 (5)
N2—C3	1.343 (5)	N6—C11	1.348 (5)
N3—C3	1.359 (5)	N7—C11	1.347 (5)
N3—N4	1.366 (5)	N7—N8	1.368 (5)
N3—H3	0.90 (6)	N7—H7	0.81 (6)
N4—C4	1.318 (5)	N8—C12	1.317 (6)
C1—C5	1.407 (5)	C9—C13	1.403 (5)
C2—H2	0.95 (5)	C10—H10	0.98 (5)
C3—C5	1.406 (5)	C11—C13	1.399 (5)
C4—C5	1.411 (6)	C12—C13	1.418 (6)
C4—H4	1.03 (6)	C12—H12	0.93 (6)
C6—C7	1.457 (6)	C14—C15	1.448 (6)
C6—H6A	0.98 (5)	C14—H14A	1.00 (6)
C6—H6B	1.00 (5)	C14—H14B	0.91 (5)
C7—C8	1.194 (7)	C15—C16	1.187 (7)
C8—H8	0.90 (5)	C16—H16	0.94 (6)

C1—S1—C6	101.40 (19)	C9—S2—C14	101.5 (2)
C1—N1—C2	117.5 (3)	C9—N5—C10	116.9 (3)
C2—N2—C3	112.2 (3)	C10—N6—C11	112.1 (3)
C3—N3—N4	110.9 (3)	C11—N7—N8	111.3 (3)
C3—N3—H3	125 (4)	C11—N7—H7	128 (4)
N4—N3—H3	124 (4)	N8—N7—H7	120 (4)
C4—N4—N3	106.5 (3)	C12—N8—N7	106.3 (3)
N1—C1—C5	120.4 (3)	N5—C9—C13	120.4 (4)
N1—C1—S1	121.3 (3)	N5—C9—S2	120.7 (3)
C5—C1—S1	118.2 (3)	C13—C9—S2	118.9 (3)
N2—C2—N1	128.4 (4)	N6—C10—N5	128.8 (4)
N2—C2—H2	116 (3)	N6—C10—H10	116 (3)
N1—C2—H2	116 (3)	N5—C10—H10	115 (3)
N2—C3—N3	127.8 (3)	N7—C11—N6	127.4 (4)
N2—C3—C5	125.4 (3)	N7—C11—C13	107.0 (3)
N3—C3—C5	106.8 (3)	N6—C11—C13	125.6 (4)
N4—C4—C5	111.3 (3)	N8—C12—C13	110.9 (4)
N4—C4—H4	114 (3)	N8—C12—H12	125 (3)
C5—C4—H4	134 (3)	C13—C12—H12	124 (3)
C3—C5—C1	115.9 (3)	C11—C13—C9	116.1 (3)
C3—C5—C4	104.4 (3)	C11—C13—C12	104.5 (3)
C1—C5—C4	139.6 (3)	C9—C13—C12	139.4 (4)
C7—C6—S1	112.2 (3)	C15—C14—S2	113.1 (3)
C7—C6—H6A	112 (3)	C15—C14—H14A	110 (3)
S1—C6—H6A	109 (2)	S2—C14—H14A	109 (3)
C7—C6—H6B	116 (3)	C15—C14—H14B	111 (3)
S1—C6—H6B	100 (3)	S2—C14—H14B	103 (3)
H6A—C6—H6B	108 (4)	H14A—C14—H14B	110 (4)
C8—C7—C6	178.5 (4)	C16—C15—C14	178.8 (5)
C7—C8—H8	172 (3)	C15—C16—H16	175 (4)

C3—N3—N4—C4	0.2 (4)	C11—N7—N8—C12	0.1 (4)
C2—N1—C1—C5	0.5 (6)	C10—N5—C9—C13	−0.4 (5)
C2—N1—C1—S1	−179.4 (3)	C10—N5—C9—S2	179.8 (3)
C6—S1—C1—N1	0.1 (4)	C14—S2—C9—N5	−1.6 (3)
C6—S1—C1—C5	−179.8 (3)	C14—S2—C9—C13	178.6 (3)
C3—N2—C2—N1	−0.2 (6)	C11—N6—C10—N5	0.4 (6)
C1—N1—C2—N2	0.4 (6)	C9—N5—C10—N6	−0.2 (6)
C2—N2—C3—N3	178.8 (4)	N8—N7—C11—N6	179.0 (3)
C2—N2—C3—C5	−0.9 (5)	N8—N7—C11—C13	0.1 (4)
N4—N3—C3—N2	−180.0 (4)	C10—N6—C11—N7	−178.7 (4)
N4—N3—C3—C5	−0.3 (4)	C10—N6—C11—C13	0.1 (5)
N3—N4—C4—C5	−0.1 (5)	N7—N8—C12—C13	−0.3 (4)
N2—C3—C5—C1	1.7 (6)	N7—C11—C13—C9	178.3 (3)
N3—C3—C5—C1	−178.0 (3)	N6—C11—C13—C9	−0.7 (5)
N2—C3—C5—C4	179.9 (4)	N7—C11—C13—C12	−0.3 (4)
N3—C3—C5—C4	0.2 (4)	N6—C11—C13—C12	−179.2 (3)
N1—C1—C5—C3	−1.4 (5)	N5—C9—C13—C11	0.8 (5)
S1—C1—C5—C3	178.5 (3)	S2—C9—C13—C11	−179.4 (3)
N1—C1—C5—C4	−178.7 (5)	N5—C9—C13—C12	178.7 (4)
S1—C1—C5—C4	1.1 (7)	S2—C9—C13—C12	−1.5 (6)
N4—C4—C5—C3	−0.1 (5)	N8—C12—C13—C11	0.4 (4)
N4—C4—C5—C1	177.5 (5)	N8—C12—C13—C9	−177.7 (4)
C1—S1—C6—C7	79.3 (3)	C9—S2—C14—C15	−76.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···N2ⁱ	0.90 (6)	2.10 (6)	2.972 (4)	165 (5)
N7—H7···N6ⁱⁱ	0.81 (6)	2.18 (6)	2.965 (5)	163 (5)

Symmetry codes: (i) −x+3, −y, −z+1; (ii) −x+2, −y, −z.

Acknowledgements

The support of NSF–MRI Grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

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