The crystal structure of 1,5-dibenzyl-1H-pyrazolo­[3,4-d]pyrimidine-4(5H)-thione

El Fal, M.; Ramli, Y.; Essassi, E.M.; Saadi, M.; El Ammari, L.

doi:10.1107/S205698901402828X

organic compounds

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ISSN: 2056-9890

Volume 71| Part 2| February 2015| Pages o95-o96

doi:10.1107/S205698901402828X

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The crystal structure of 1,5-dibenzyl-1H-pyrazolo[3,4-d]pyrimidine-4(5H)-thione

Mohammed El Fal,^a Youssef Ramli,^b El Mokhtar Essassi,^a ^* Mohamed Saadi ^c and Lahcen El Ammari ^c

^aLaboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco, ^bMedicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco, and ^cLaboratoire de Chimie du Solide Appliquée, Faculté des Sciences, Université Mohammed V, Avenue Ibn Battouta, BP 1014, Rabat, Morocco
^*Correspondence e-mail: em_essassi@yahoo.fr

Edited by E. R. T. Tiekink, University of Malaya, Malaysia (Received 24 December 2014; accepted 31 December 2014; online 10 January 2015)

In the title compound, C₁₉H₁₆N₄S, the pyrazolo[3,4-d]pyrimidine ring is close to being planar, with the greatest deviation from the mean plane being 0.023 (2) Å for the C atom bearing the thione S atom. The two phenyl rings are nearly perpendicular to the fused ring system [dihedral angles = 71.4 (2) and 78.1 (2)°], but are oriented in opposite directions; the dihedral angle between the phenyl rings is 32.22 (16)°. In the crystal, linear supramolecular chains along [101] are sustained by C—H⋯S interactions.

Keywords: crystal structure; pyrazolo[3,4-d]pyrimidine; thione; C—H⋯S interactions.

CCDC reference: 1041681

1. Related literature

For pharmacological and biochemical properties of pyrazolo[1,5-a]pyrimidine, see: Orlikova et al. (2014 ); Yuan et al. (2013 ); Rashad et al. (2011 ). For related structures, see: El Fal et al. (2013 , 2014 ); Alsubari et al. (2011 ); Ramli et al. (2012 ).

2. Experimental

2.1. Crystal data

C₁₉H₁₆N₄S
M_r = 332.42
Monoclinic, P 2₁
a = 4.4953 (12) Å
b = 29.140 (8) Å
c = 6.3889 (16) Å
β = 97.860 (9)°
V = 829.0 (4) Å³
Z = 2
Mo Kα radiation
μ = 0.20 mm⁻¹
T = 296 K
0.37 × 0.34 × 0.29 mm

2.2. Data collection

Bruker X8 APEX diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ) T_min = 0.589, T_max = 0.746
9214 measured reflections
3582 independent reflections
2406 reflections with I > 2σ(I)
R_int = 0.040

2.3. Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.084
S = 0.97
3582 reflections
217 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.14 e Å⁻³
Δρ_min = −0.12 e Å⁻³
Absolute structure: Flack & Bernardinelli (2000 ), 1730 Friedel pairs
Absolute structure parameter: −0.11 (7)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C5—H5⋯S1ⁱ	0.93	2.87	3.784 (3)	167
Symmetry code: (i) x-1, y, z-1.

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ); software used to prepare material for publication: PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1041681

Crystal structure: contains datablock I. DOI: 10.1107/S205698901402828X/tk5354sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S205698901402828X/tk5354Isup2.hkl

Supporting information file. DOI: 10.1107/S205698901402828X/tk5354Isup3.cml

checkCIF report

Structural commentary top

Pyrazolo[3,4-d] pyrimidine-4-thione are intermediate sub-units useful for the development of molecules of pharmaceutical interest. They have found applications in various therapeutic areas, including anti-inflammatory, anti-tumour and anti-cancer (Orlikova et al., 2014; Yuan et al., 2013; Rashad et al., 2011). The present paper is a continuation of our research work devoted to the development of pyrazolo[3,4-d] pyrimidine derivatives with potential pharmacological activities (El Fal et al., 2013; El Fal et al., 2014; Alsubari et al., 2011; Ramli et al., 2012).

The molecule of the title compound is build up from two fused five- and six-membered heterocycles linked to two phenyl rings via two –CH₂– groups as shown in Fig. 1. The pyrazolo[3,4-d]pyrimidine system is virtually planar with the largest deviation from the mean plane being -0.023 (2) Å at C1 and makes dihedral angles of 71.4 (2)° and 78.1 (2)° with the mean plane through the first (C7 to C12) and the second (C14 to C19) phenyl rings, respectively. As a matter of fact, the two phenyl rings are oriented in opposite direction to the plane of the fused rings. No classic hydrogen bonds are observed in the present structure.

Synthesis and crystallization top

3.32 g (10 mmol) of 1,5-dibenzyl-1H, 4H, 5H-pyrazolo [3,4-d] pyrimidin-4-one is refluxed in pyridine (30 ml) with 5.55 g (25 mmol) of phosphorus pentasulfide for 4 h. Then the solvent was evaporated under reduced pressure. The precipitate that formed was washed with hot water to remove residual dimerized P₂S₅ until colourless filtrate was noted. The solid was re-crystallized from ethanol to afford the title compound as yellow crystals (yield: 85%; m.p. = 563 K).

Refinement top

The H atoms were located in a difference map and treated as riding with C—H = 0.93 Å (aromatic) and C—H = 0.97 Å (methylene). All hydrogen with U_iso(H) = 1.2 U_eq (aromatic and methylene). Two reflections, i.e. 0 -2 0 and 0 2 0, were omitted fro the final refinement owing to poor agreement.

Related literature top

For pharmacological and biochemical properties of pyrazolo[1,5-a]pyrimidine, see: Orlikova et al. (2014); Yuan et al. (2013); Rashad et al. (2011). For related structures, see: El Fal et al. (2013, 2014); Alsubari et al. (2011); Ramli et al. (2012).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top

Fig. 1. Molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.

1,5-Dibenzyl-1H-pyrazolo[3,4-d]pyrimidine-4(5H)-thione top

Crystal data top

C₁₉H₁₆N₄S	F(000) = 348
M_r = 332.42	D_x = 1.332 Mg m⁻³
Monoclinic, P2₁	Melting point: 563 K
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 4.4953 (12) Å	Cell parameters from 3582 reflections
b = 29.140 (8) Å	θ = 2.8–27.1°
c = 6.3889 (16) Å	µ = 0.20 mm⁻¹
β = 97.860 (9)°	T = 296 K
V = 829.0 (4) Å³	Block, yellow
Z = 2	0.37 × 0.34 × 0.29 mm

Data collection top

Bruker X8 APEX diffractometer	3582 independent reflections
Radiation source: fine-focus sealed tube	2406 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.040
ϕ and ω scans	θ_max = 27.1°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −5→5
T_min = 0.589, T_max = 0.746	k = −37→37
9214 measured reflections	l = −8→8

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.084	w = 1/[σ²(F_o²) + (0.0318P)²] where P = (F_o² + 2F_c²)/3
S = 0.97	(Δ/σ)_max < 0.001
3582 reflections	Δρ_max = 0.14 e Å⁻³
217 parameters	Δρ_min = −0.12 e Å⁻³
1 restraint	Absolute structure: Flack & Bernardinelli (2000), 1730 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.11 (7)

Crystal data top

C₁₉H₁₆N₄S	V = 829.0 (4) Å³
M_r = 332.42	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 4.4953 (12) Å	µ = 0.20 mm⁻¹
b = 29.140 (8) Å	T = 296 K
c = 6.3889 (16) Å	0.37 × 0.34 × 0.29 mm
β = 97.860 (9)°

Data collection top

Bruker X8 APEX diffractometer	3582 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	2406 reflections with I > 2σ(I)
T_min = 0.589, T_max = 0.746	R_int = 0.040
9214 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.084	Δρ_max = 0.14 e Å⁻³
S = 0.97	Δρ_min = −0.12 e Å⁻³
3582 reflections	Absolute structure: Flack & Bernardinelli (2000), 1730 Friedel pairs
217 parameters	Absolute structure parameter: −0.11 (7)
1 restraint

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

	x	y	z	U_iso*/U_eq
C1	0.5941 (5)	0.48633 (8)	0.9980 (3)	0.0412 (6)
C2	0.4720 (5)	0.44502 (8)	1.0570 (3)	0.0411 (6)
C3	0.5145 (7)	0.41623 (9)	1.2377 (4)	0.0586 (7)
H3	0.6506	0.4222	1.3578	0.070*
C4	0.2489 (6)	0.42310 (9)	0.9208 (4)	0.0457 (6)
C5	0.2551 (6)	0.47501 (9)	0.6716 (4)	0.0488 (6)
H5	0.1885	0.4864	0.5375	0.059*
C6	0.5892 (5)	0.54088 (9)	0.6906 (4)	0.0477 (6)
H6A	0.6197	0.5330	0.5476	0.057*
H6B	0.7826	0.5495	0.7672	0.057*
C7	0.3812 (5)	0.58142 (8)	0.6832 (4)	0.0425 (6)
C8	0.3274 (6)	0.60388 (9)	0.8650 (4)	0.0545 (7)
H8	0.4188	0.5935	0.9959	0.065*
C9	0.1404 (7)	0.64137 (10)	0.8546 (5)	0.0651 (8)
H9	0.1070	0.6563	0.9780	0.078*
C10	0.0034 (7)	0.65686 (11)	0.6635 (5)	0.0700 (8)
H10	−0.1242	0.6821	0.6569	0.084*
C11	0.0546 (7)	0.63514 (11)	0.4817 (5)	0.0701 (9)
H11	−0.0375	0.6458	0.3515	0.084*
C12	0.2421 (6)	0.59761 (9)	0.4912 (4)	0.0551 (7)
H12	0.2754	0.5830	0.3671	0.066*
C13	−0.0331 (7)	0.34855 (9)	0.9311 (5)	0.0701 (9)
H13A	−0.1746	0.3609	0.8167	0.084*
H13B	−0.1461	0.3374	1.0396	0.084*
C14	0.1353 (6)	0.30957 (9)	0.8500 (5)	0.0538 (7)
C15	0.1948 (7)	0.27009 (11)	0.9677 (5)	0.0701 (8)
H15	0.1235	0.2673	1.0970	0.084*
C16	0.3567 (8)	0.23521 (11)	0.8969 (8)	0.0926 (12)
H16	0.3946	0.2088	0.9778	0.111*
C17	0.4635 (8)	0.23889 (15)	0.7078 (9)	0.0961 (13)
H17	0.5758	0.2152	0.6605	0.115*
C18	0.4049 (8)	0.27764 (16)	0.5874 (6)	0.0898 (11)
H18	0.4766	0.2801	0.4581	0.108*
C19	0.2406 (7)	0.31279 (11)	0.6575 (5)	0.0705 (8)
H19	0.2000	0.3389	0.5748	0.085*
N1	0.3381 (6)	0.38019 (8)	1.2147 (4)	0.0633 (6)
N2	0.1709 (5)	0.38498 (7)	1.0188 (4)	0.0575 (6)
N3	0.1303 (5)	0.43742 (7)	0.7249 (3)	0.0529 (5)
N4	0.4758 (4)	0.49978 (6)	0.7928 (3)	0.0422 (5)
S1	0.85051 (15)	0.51743 (3)	1.14918 (10)	0.0571 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0382 (13)	0.0485 (15)	0.0369 (13)	0.0091 (11)	0.0049 (10)	−0.0077 (11)
C2	0.0406 (14)	0.0454 (15)	0.0366 (13)	0.0074 (11)	0.0030 (11)	−0.0022 (11)
C3	0.0693 (19)	0.0591 (18)	0.0468 (16)	0.0095 (16)	0.0061 (14)	0.0028 (14)
C4	0.0446 (15)	0.0458 (16)	0.0474 (15)	0.0080 (12)	0.0087 (13)	−0.0024 (13)
C5	0.0507 (16)	0.0561 (18)	0.0367 (13)	0.0104 (14)	−0.0046 (11)	−0.0056 (12)
C6	0.0459 (15)	0.0593 (16)	0.0395 (14)	−0.0032 (13)	0.0116 (12)	0.0003 (12)
C7	0.0424 (15)	0.0473 (14)	0.0375 (14)	−0.0095 (12)	0.0049 (11)	0.0009 (12)
C8	0.0618 (18)	0.0591 (18)	0.0412 (15)	−0.0018 (14)	0.0023 (13)	0.0010 (13)
C9	0.071 (2)	0.0571 (19)	0.069 (2)	−0.0002 (16)	0.0151 (17)	−0.0094 (15)
C10	0.071 (2)	0.0573 (19)	0.082 (2)	0.0038 (16)	0.0097 (17)	0.0114 (18)
C11	0.073 (2)	0.073 (2)	0.0607 (19)	0.0017 (18)	−0.0028 (16)	0.0207 (17)
C12	0.0593 (18)	0.0584 (18)	0.0467 (15)	−0.0083 (15)	0.0040 (13)	0.0037 (13)
C13	0.0531 (18)	0.0551 (19)	0.102 (2)	−0.0104 (15)	0.0102 (17)	−0.0024 (16)
C14	0.0479 (16)	0.0475 (16)	0.0647 (18)	−0.0101 (12)	0.0028 (14)	−0.0036 (14)
C15	0.074 (2)	0.0588 (19)	0.076 (2)	−0.0095 (17)	0.0032 (16)	0.0059 (17)
C16	0.079 (3)	0.053 (2)	0.140 (4)	0.0019 (19)	−0.006 (3)	0.003 (2)
C17	0.062 (2)	0.080 (3)	0.144 (4)	0.000 (2)	0.004 (3)	−0.041 (3)
C18	0.076 (3)	0.116 (3)	0.077 (2)	−0.014 (2)	0.0093 (19)	−0.036 (3)
C19	0.069 (2)	0.069 (2)	0.072 (2)	−0.0072 (16)	0.0068 (17)	−0.0002 (16)
N1	0.0782 (18)	0.0568 (16)	0.0564 (15)	−0.0011 (13)	0.0142 (13)	0.0070 (12)
N2	0.0550 (15)	0.0504 (14)	0.0681 (16)	0.0002 (11)	0.0118 (12)	0.0033 (13)
N3	0.0503 (13)	0.0496 (14)	0.0558 (14)	0.0029 (11)	−0.0034 (11)	−0.0043 (11)
N4	0.0406 (11)	0.0509 (12)	0.0342 (10)	0.0034 (9)	0.0021 (9)	−0.0013 (9)
S1	0.0536 (4)	0.0676 (4)	0.0463 (4)	−0.0042 (4)	−0.0073 (3)	−0.0052 (4)

Geometric parameters (Å, º) top

C1—C2	1.396 (3)	C10—C11	1.370 (4)
C1—N4	1.402 (3)	C10—H10	0.9300
C1—S1	1.667 (2)	C11—C12	1.377 (4)
C2—C4	1.390 (3)	C11—H11	0.9300
C2—C3	1.419 (3)	C12—H12	0.9300
C3—N1	1.312 (3)	C13—N2	1.463 (3)
C3—H3	0.9300	C13—C14	1.496 (4)
C4—N2	1.345 (3)	C13—H13A	0.9700
C4—N3	1.357 (3)	C13—H13B	0.9700
C5—N3	1.297 (3)	C14—C19	1.380 (4)
C5—N4	1.376 (3)	C14—C15	1.380 (4)
C5—H5	0.9300	C15—C16	1.363 (5)
C6—N4	1.487 (3)	C15—H15	0.9300
C6—C7	1.503 (3)	C16—C17	1.364 (5)
C6—H6A	0.9700	C16—H16	0.9300
C6—H6B	0.9700	C17—C18	1.371 (5)
C7—C12	1.381 (3)	C17—H17	0.9300
C7—C8	1.383 (3)	C18—C19	1.373 (5)
C8—C9	1.374 (4)	C18—H18	0.9300
C8—H8	0.9300	C19—H19	0.9300
C9—C10	1.367 (4)	N1—N2	1.376 (3)
C9—H9	0.9300

C2—C1—N4	112.4 (2)	C11—C12—C7	120.7 (3)
C2—C1—S1	125.35 (18)	C11—C12—H12	119.6
N4—C1—S1	122.28 (18)	C7—C12—H12	119.6
C4—C2—C1	120.3 (2)	N2—C13—C14	111.3 (2)
C4—C2—C3	104.1 (2)	N2—C13—H13A	109.4
C1—C2—C3	135.7 (2)	C14—C13—H13A	109.4
N1—C3—C2	111.7 (3)	N2—C13—H13B	109.4
N1—C3—H3	124.1	C14—C13—H13B	109.4
C2—C3—H3	124.1	H13A—C13—H13B	108.0
N2—C4—N3	126.1 (2)	C19—C14—C15	118.5 (3)
N2—C4—C2	107.4 (2)	C19—C14—C13	120.5 (3)
N3—C4—C2	126.5 (2)	C15—C14—C13	120.9 (3)
N3—C5—N4	126.9 (2)	C16—C15—C14	120.9 (3)
N3—C5—H5	116.6	C16—C15—H15	119.6
N4—C5—H5	116.6	C14—C15—H15	119.6
N4—C6—C7	113.42 (17)	C15—C16—C17	120.3 (4)
N4—C6—H6A	108.9	C15—C16—H16	119.9
C7—C6—H6A	108.9	C17—C16—H16	119.9
N4—C6—H6B	108.9	C16—C17—C18	119.8 (4)
C7—C6—H6B	108.9	C16—C17—H17	120.1
H6A—C6—H6B	107.7	C18—C17—H17	120.1
C12—C7—C8	118.3 (2)	C17—C18—C19	120.1 (4)
C12—C7—C6	120.0 (2)	C17—C18—H18	119.9
C8—C7—C6	121.7 (2)	C19—C18—H18	119.9
C9—C8—C7	120.7 (3)	C18—C19—C14	120.3 (3)
C9—C8—H8	119.6	C18—C19—H19	119.8
C7—C8—H8	119.6	C14—C19—H19	119.8
C10—C9—C8	120.3 (3)	C3—N1—N2	105.5 (2)
C10—C9—H9	119.9	C4—N2—N1	111.2 (2)
C8—C9—H9	119.9	C4—N2—C13	127.6 (2)
C9—C10—C11	119.8 (3)	N1—N2—C13	120.7 (2)
C9—C10—H10	120.1	C5—N3—C4	111.8 (2)
C11—C10—H10	120.1	C5—N4—C1	122.1 (2)
C10—C11—C12	120.1 (3)	C5—N4—C6	116.1 (2)
C10—C11—H11	119.9	C1—N4—C6	121.78 (19)
C12—C11—H11	119.9

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···S1ⁱ	0.93	2.87	3.784 (3)	167

Symmetry code: (i) x−1, y, z−1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···S1ⁱ	0.93	2.87	3.784 (3)	167

Symmetry code: (i) x−1, y, z−1.

Acknowledgements

The authors thank the Unit of Support for Technical and Scientific Research (UATRS, CNRST) for the X-ray measurements and the University Mohammed V, Rabat, Morocco, for financial support.

References

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Volume 71| Part 2| February 2015| Pages o95-o96

doi:10.1107/S205698901402828X

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

The crystal structure of 1,5-di­benzyl-1H-pyrazolo­[3,4-d]pyrimidine-4(5H)-thione

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

The crystal structure of 1,5-dibenzyl-1H-pyrazolo[3,4-d]pyrimidine-4(5H)-thione