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Crystal structure, Hirshfeld surface analysis and DFT calculations of ethyl 2-[4-(methyl­sulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidin-1-yl]acetate

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aLaboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco, bLaboratory of Organic Chemistry and Physical Chemistry, Research Team: Molecular, Modeling, Materials and Environment, Department of Chemistry, Faculty of, Sciences, University Ibn Zohr in Agadir, BP 8106 Agadir, Morocco, cLaboratory of Spectroscopy, Molecular Modeling, Materials, Nanomaterials, Water, and Environment, CERNE2D, Faculty of Sciences, Mohammed V University in Rabat, Av. Ibn Battouta, BP 1014, Rabat, Morocco, dDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, eDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Türkiye, and fLaboratory of Heterocyclic Organic Chemistry, Medicines Science Research Center, Pharmacochemistry Competence Center, Mohammed V University in Rabat, Faculty of Sciences, Morocco
*Correspondence e-mail: n.sebbar@uiz.ac.ma

Edited by M. Weil, Vienna University of Technology, Austria (Received 10 October 2022; accepted 20 November 2022; online 30 November 2022)

The asymmetric unit of the title compound, C10H12N4O2S, contains two mol­ecules differing slightly in the orientations of the methyl groups. In the crystal, a sandwich-type structure extending parallel to the ab plane is formed by weak C—H⋯O and C—H⋯N hydrogen bonds together with slipped π-stacking inter­actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (43.5%), H⋯O/O⋯H (17.9%) and H⋯N/N⋯H (17.4%) inter­actions. The mol­ecular structure optimized by density functional theory (DFT) at the B3LYP/ 6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. Further calculations include the HOMO–LUMO energies and mol­ecular electrostatic potential (MEP) surfaces.

1. Chemical context

Pyrazolo­[3,4-d]pyrimidine derivatives are an important class of nitro­gen-containing compounds because of their pharmacological properties and their use as anti­tumor agents (Tintori et al., 2015[Tintori, C., Fallacara, A. L., Radi, M., Zamperini, C., Dreassi, E., Crespan, E., Maga, G., Schenone, S., Musumeci, F., Brullo, C., Richters, A., Gasparrini, F., Angelucci, A., Festuccia, C., Delle Monache, S., Rauh, D. & Botta, M. (2015). J. Med. Chem. 58, 347-361.]). They are also applied as protein kinase inhibitors (Schenone et al., 2014[Schenone, S., Radi, M., Musumeci, F., Brullo, C. & Botta, M. (2014). Chem. Rev. 114, 7189-7238.]; Rao & Chanda, 2020[Rao, R. N. & Chanda, K. (2020). Bioorg. Chem. 99, 103801.]), and have anti-HSV (Moukha-Chafiq et al., 2007[Moukha-chafiq, O., Taha, M. L. & Mouna, A. (2007). Nucleosides Nucleotides Nucleic Acids, 26, 1107-1110.]), anti­viral (Moukha-Chafiq et al., 2006[Moukha-Chafiq, O., Taha, M. L., Lazrek, H. B., Vasseur, J. J. & Clercq, E. D. (2006). Nucleosides Nucleotides Nucleic Acids, 25, 849-860.]; Rashad et al., 2008[Rashad, A. E., Hegab, M. I., Abdel-Megeid, R. E., Micky, J. A. & Abdel-Megeid, F. M. (2008). Bioorg. Med. Chem. 16, 7102-7106.]), anti-avian influenza virus (H5N1) (Rashad et al., 2010[Rashad, A. E., Shamroukh, A. H., Abdel-Megeid, R. E., Mostafa, A., Ali, M. A. & Banert, K. (2010). Nucleosides Nucleotides Nucleic Acids, 29, 809-820.]), anti-inflammatory (Atatreh et al., 2019[Atatreh, N., Youssef, A. M., Ghattas, M. A., Al Sorkhy, M., Alrawashdeh, S., Al-Harbi, K. B., El-Ashmawy, I. M., Almundarij, T. I., Abdelghani, A. A. & Abd-El-Aziz, A. S. (2019). Bioorg. Chem. 86, 393-400.]), anti-leishmanial (Jorda et al., 2011[Jorda, R., Sacerdoti-Sierra, N., Voller, J., Havlíček, L., Kráčalíková, K., Nowicki, M. W., Nasereddin, A., Kryštof, V., Strnad, M., Walkinshaw, M. D. & Jaffe, C. L. (2011). Bioorg. Med. Chem. Lett. 21, 4233-4237.]; Llanos-Cuentas et al., 1997[Llanos-Cuentas, A., Echevarria, J., Cruz, M., La Rosa, A., Campos, P., Campos, M., Franke, E., Berman, J., Modabber, F. & Marr, J. (1997). Clin. Infect. Dis. 25, 677-684.]), anti­cancer (Chauhan & Kumar, 2013[Chauhan, M. & Kumar, R. (2013). Bioorg. Med. Chem. 21, 5657-5668.]), and anti­bacterial activity (Rostamizadeh et al., 2013[Rostamizadeh, S., Nojavan, M., Aryan, R., Sadeghian, H. & Davoodnejad, M. (2013). Chin. Chem. Lett. 24, 629-632.]).

[Scheme 1]

As a continuation of our research on the development of N-substituted pyrazolo­[3,4-d]pyrimidine derivatives and the evaluation of their potential pharmacological activities, the title compound, C10H12N4O2S, I, was synthesized by the reaction of ethyl 2-bromo­acetate with 4-(methyl­sulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidine and potassium carbonate in the presence of potassium chloride and tetra-n-butyl­ammonium bromide as catalysts. We report herein the synthesis, mol­ecular and crystal structures, Hirshfeld surface analysis, and density functional theory (DFT) computational calculations carried out at the B3LYP/6–311 G(d,p) level along with calculation of the mol­ecular electrostatic potential (MEP) surfaces of I.

2. Structural commentary

The asymmetric unit of I contains two mol­ecules (Fig. 1[link]), differing slightly in the rotational orientations of the methyl groups (Fig. 2[link]). For the mol­ecule containing S1, the pyrazolo­pyrimidine moiety is planar to within 0.023 (2) Å (r.m.s. deviation = 0.0115) with N4 being the most distant atom from the mean plane. For the mol­ecule containing S2, the bicyclic unit is planar to within 0.020 (3) Å (r.m.s. deviation = 0.0115) with C11 being the most distant atom from the mean plane. The dihedral angle between the mean planes of the bicyclic units is 2.16 (2)°.

[Figure 1]
Figure 1
The asymmetric unit with the labeling scheme and displacement ellipsoids drawn at the 50% probability level. The π-stacking inter­actions are shown by dashed lines.
[Figure 2]
Figure 2
Overlay of the two independent mol­ecules (yellow = mol­ecule containing S1, green = mol­ecule containing S2).

3. Supra­molecular features

In the crystal, chains extending parallel to the a axis are formed by mol­ecules containing S1 through weak C3—H3⋯N4 hydrogen bonds and parallel chains by mol­ecules containing S2 through C13—H13⋯N8 hydrogen bonds (Table 1[link]). The chains containing S1 are linked into sheets parallel to the ab plane by C5—H5⋯O2 hydrogen bonds while the chains containing S2 are inter­spersed between these layers and connect them by C19—H19A⋯O1 hydrogen bonds. In addition, the different mol­ecules are associated through complementary π-stacking inter­actions between five- and six-membered rings [centroid–centroid distance = 3.422 (2) Å; slippage 1.034 Å] (Figs. 1[link] and 3[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C3—H3⋯N4i 0.95 2.55 3.450 (4) 158
C5—H5⋯O2ii 0.95 2.57 3.314 (4) 136
C13—H13⋯N8iii 0.95 2.56 3.470 (4) 159
C19—H19A⋯O1iv 0.99 2.52 3.490 (5) 166
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (ii) x, y+1, z; (iii) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (iv) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z-{\script{1\over 2}}].
[Figure 3]
Figure 3
Packing of the mol­ecules viewed along the b-axis direction with C—H⋯O and C—H⋯N hydrogen bonds shown, respectively, by black and light-blue dashed lines. The π-stacking inter­actions are shown by orange dashed lines.

4. Hirshfeld surface analysis

In order to visualize the inter­molecular inter­actions in the crystal of the title compound, a Hirshfeld surface (HS) analysis (Hirshfeld, 1977[Hirshfeld, H. L. (1977). Theor. Chim. Acta, 44, 129-138.]) was carried out by using Crystal Explorer 17.5 (Spackman et al., 2021[Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006-1011.]). In the HS plotted over dnorm (Fig. 4[link]a), the white surface indicates contacts with distances equal to the sum of van der Waals radii, and the red and blue colors indicate distances shorter or longer than the van der Waals radii, respectively (Venkatesan et al., 2016[Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H. & Sundius, T. (2016). Spectrochim. Acta A Mol. Biomol. Spectrosc. 153, 625-636.]). The shape-index of the HS is a tool to visualize the ππ stacking by the presence of adjacent red and blue triangles. If there are no adjacent red and/or blue triangles, then there are no ππ inter­actions. However, Fig. 4[link]b clearly suggests that there are ππ inter­actions in I.

[Figure 4]
Figure 4
(a) View of the three-dimensional Hirshfeld surface of the title compound, plotted over dnorm in the range −0.7208 to 1.5611 a.u. and (b) Hirshfeld surface of the title compound plotted over shape-index.

The overall two-dimensional fingerprint plot, Fig. 5[link]a, and those delineated into H⋯H, H⋯O/O⋯H, H⋯N/N⋯H, H⋯C/C⋯H, H⋯S/S⋯H, N⋯S/S⋯N, C⋯S/S⋯C, O⋯S/S⋯O and O⋯O contacts (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) are illustrated in Fig. 5[link]bj, respectively, together with their relative contributions to the Hirshfeld surface. The most important inter­action is H⋯H, contributing 43.5% to the overall crystal packing, which is reflected in Fig. 5[link]b as widely scattered points of high density due to the large hydrogen content of the mol­ecule with the tip at de = di = 1.08 Å. The pair of the scattered points of spikes in the H⋯O/O⋯H fingerprint plot (17.9% contribution to the HS, Fig. 5[link]c), has a symmetric distribution of points with the tips at de + di = 2.40 Å. The H⋯N/N⋯H contacts, Fig. 5[link]d, contribute 17.4% to the HS, and the distribution of points also has the tips at de + di = 2.40 Å. The large number of H⋯H, H⋯O/O⋯H and H⋯N/N ⋯ H inter­actions suggest that van der Waals inter­actions play the major role in the crystal packing (Hathwar et al., 2015[Hathwar, V. R., Sist, M., Jørgensen, M. R. V., Mamakhel, A. H., Wang, X., Hoffmann, C. M., Sugimoto, K., Overgaard, J. & Iversen, B. B. (2015). IUCrJ, 2, 563-574.]). In the absence of C—H⋯π inter­actions, the pair of characteristic wings resulting in the fingerprint plot delineated into H⋯C/C⋯H contacts, Fig. 5[link]e, the 9.5% contribution to the HS is viewed with the tips at de + di = 2.67 Å. The H⋯S/S⋯H contacts, Fig. 5[link]f, with a 8.9% contribution to the HS are viewed with the pair of the scattered points of spikes at de + di = 2.85 Å. The symmetric distribution of points of the N⋯S/S⋯N contacts, Fig. 5[link]g, with a 1.7% contribution to the HS appear as a pair of spikes of scattered points with the tips at de + di = 3.33 Å. Finally, the contributions of the remaining C⋯S/S⋯C, O⋯S/S⋯O and O⋯O contacts (Fig. 5[link]hj) are smaller than 1.0% to the HS with low densities of points.

[Figure 5]
Figure 5
The full two-dimensional fingerprint plots for the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) H⋯O/O⋯H, (d) H⋯N/N⋯H, (e) H⋯C/C⋯H, (f) H⋯S/S⋯H, (g) N⋯S/S⋯N, (h) C⋯S/S⋯C, (i) O⋯S/S⋯O and (j) O⋯O inter­actions. The di and de values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface.

The Hirshfeld surface representations with the function dnorm plotted onto the surface are shown for the H⋯H, H⋯O/O⋯H, H⋯N/N⋯H and H⋯C/C⋯H inter­actions in Fig. 6[link]ad, respectively.

[Figure 6]
Figure 6
The Hirshfeld surface representations with the function dnorm plotted onto the surface for (a) H⋯H, (b) H⋯O/O⋯H and (c) H⋯C/C⋯H inter­actions.

5. DFT calculations

The structure of I in the gas phase was optimized by means of density functional theory (DFT) using the hybrid B3LYP method and the 6–311 G(d,p) basis-set, which is based on Becke's model (Becke, 1993[Becke, A. D. (1993). J. Chem. Phys. 98, 5648-5652.]). It considers a mixture of the exact (Hartree–Fock) and density functional theory exchange utilizing the B3 functional, together with the LYP correlation functional (Lee et al., 1988[Lee, C., Yang, W. & Parr, R. G. (1988). Phys. Rev. B, 37, 785-789.]). After obtaining the optimized mol­ecular structure, the harmonic vibrational frequencies were calculated at the same theoretical level to confirm that the number of imaginary frequencies is zero for the stationary point. Both the structure optimization and harmonic vibrational frequency analysis of I were computed with the Gaussian 09 program (Frisch et al., 2009[Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A. Jr, Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, O., Foresman, J. B., Ortiz, J. V., Cioslowski, J. & Fox, D. J. (2009). GAUSSIAN09. Gaussian Inc., Wallingford, CT, US]). Theoretical and experimental results related to bond lengths and angles are in good agreement and are summarized in Table 2[link]. The DFT calculations provide some important information on the reactivity and site selectivity of the mol­ecular framework. Numerical values for EHOMO and ELUMO (Fig. 7[link]), electronegativity (χ), hardness (η), potential (μ), electrophilicity (ω) and softness (σ) are compiled in Table 3[link]. The electron transition from the HOMO to the LUMO energy level is shown in Fig. 7[link]. The HOMO and LUMO are localized in the plane extending from the entire ethyl 2-(4-(methyl­sulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidin-1-yl)acetate system. The energy band gap [ΔE = ELUMO - EHOMO] of the mol­ecule is 4.84 eV, and the frontier mol­ecular orbital energies, EHOMO and ELUMO are −6.55 and −1.71 eV, respectively.

Table 2
Comparison of the selected (X-ray and DFT) geometric data (Å, °)

Bonds/angles X-ray B3LYP/6–311G(d,p)
S1—C2 1.740 (3) 1.765
S1—C6 1.804 (3) 1.824
O1—C8 1.196 (4) 1.204
O2—C8 1.332 (4) 1.337
O2—C9 1.463 (5) 1.453
N1—C2 1.332 (3) 1.329
N1—C3 1.356 (4) 1.350
N2—C3 1.325 (4) 1.325
N2—C4 1.344 (4) 1.339
N3—C4 1.353 (4) 1.359
N3—N4 1.370 (3) 1.363
N3—C7 1.440 (4) 1.443
N4—C5 1.319 (4) 1.318
     
C2—S1—C6 101.68 (14) 101.324
C8—O2—C9 117.3 (3) 117.442
C2—N1—C3 117.5 (2) 117.378
C3—N2—C4 111.9 (3) 112.041
C4—N3—N4 111.2 (2) 111.358
C4—N3—C7 127.2 (3) 127.628
N4—N3—C7 120.5 (2) 120.828
C5—N4—N3 106.4 (2) 106.802
C4—C1—C2 116.0 (2) 115.050
C4—C1—C5 104.5 (2) 104.373
C2—C1—C5 139.6 (2) 140.577
N1—C2—C1 119.9 (2) 120.011
N1—C2—S1 121.86 (19) 119.923
     
C4—N3—N4—C5 1.9 (4) 1.710
C7—N3—N4—C5 170.6 (3) 171.115
C3—N1—C2—C1 0.9 (5) 0.715
C3—N1—C2—S1 −178.6 (3) −179.843
C4—N2—C3—N1 0.9 (6) 0.563
C2—N1—C3—N2 −1.3 (6) −1.149

Table 3
Calculated energies

Mol­ecular Energy (a.u.) (eV) Compound I
Total Energy TE (eV) −31458.99
EHOMO (eV) −6.55
ELUMO (eV) −1.71
Gap ΔE (eV) 4.84
Dipole moment, μ (Debye) 2.79
Ionization potential, I (eV) 6.55
Electron affinity, A 1.71
Electronegativity, χ 3.13
Hardness, η 2.42
Electrophilicity index, ω 3.53
Softness, σ 0.41
Fraction of electron transferred, ΔN 0.59
[Figure 7]
Figure 7
The energy band gap of I.

6. Mol­ecular electrostatic (MEP)

Mol­ecular electrostatic potential (MEP) surfaces can be used to predict reactive sites for electrophilic and nucleophilic attack. The calculation of MEP surfaces was carried out on the basis of B3LYP/6-31G-optimized structures using the program Gauss View. The total electron density onto which the electrostatic potential surface has been mapped is shown in Fig. 8[link]. This figure provides a visual representation of the chemically active sites and comparative reactivity of atoms where the red regions denote the most negative electrostatic potential, blue represents regions with the most positive electrostatic potential, and green represents the region of zero potential. Fig. 8[link] confirms the existence of inter­molecular C—H⋯O and C—H⋯N hydrogen-bonding inter­actions.

[Figure 8]
Figure 8
MEP surfaces of I calculated at the B3LYP/6–311 G level.

7. Database survey

A search of the Cambridge Structural Database (CSD: Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]; updated to March 2022) with the search fragment II (Fig. 9[link]) gave 18 hits of which III (XOVRUX; El Fal et al., 2014[El Fal, M., Ramli, Y., Essassi, E. M., Saadi, M. & El Ammari, L. (2014). Acta Cryst. E70, o1281.]) is the closest to I. All the others contain an additional methyl­sulfanyl substituent at the 6-position on the pyrimidine ring and a three-carbon chain attached to the nitro­gen at the 1-position with various aromatic groups on the end of the chain including a second bis­(methyl­sulfan­yl)pyrazolo­pyrimidine moiety. These were designed to study possible intra­molecular π-stacking inter­actions and are not considered close analogs of I. One other close analog is IV (El Hafi et al., 2017[El Hafi, M., Boulhaoua, M., Ramli, Y., Benchidmi, M., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x171526.]). In III, the mol­ecule lies on a mirror plane and so is rigorously planar. There is only one mol­ecule in the asymmetric unit and the packing consists of head-to-tail π-stacking of the mol­ecules along the c axis direction with a centroid-to-centroid distance of 3.6062 (8) Å. In IV, Z′ = 2 as in I but the two independent mol­ecules do not have the pyrazolo­pyrimidine moieties approximately parallel to one another as in I. Instead of chains, a self-dimer is formed by each independent mol­ecule, and each type of dimer is π-stacked in a head-to-tail fashion, forming stepped stacks inclined by ca ±51° to the bc plane.

[Figure 9]
Figure 9
4-(Methyl­sulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidine analogues.

8. Synthesis and crystallization

To a solution of 4-(methyl­sulfan­yl)-1H-pyrazolo­[3,4-d]pyrimidine (10 mmol), ethyl 2-bromo­acetate (10 mmol) and potassium carbonate (6.51 mmol) in di­methyl­formamide (DMF; 40 ml) a catalytic amount of tetra-n-butyl­ammonium bromide (0.33 mmol) was added. The mixture was stirred for 24 h. The solid material was removed by filtration and the solvent evaporated in vacuo. The resulting solid product was purified by recrystallization from ethanol to afford colorless crystals in 82% yield. 1H NMR (300 MHz, CDCl3): 1.23 (t, 3H, CH3); 2.69 (s, 3H, CH3); 4.20 (q, 2H, CH2); 5.20 (s, 2H, CH2); 8.08 (s,1H, H3); 8.70 (s, 1H, H6).

9. Refinement

Crystal, data collection and refinement details are given in Table 4[link]. Although intensity statistics indicated the centrosymmetric space group Pbca, structure solution by direct and Patterson methods revealed serious disorder. The use of dual space methods (SHELXT; Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]) gave an ordered solution in the non-centrosymmetric space group Pca21 as the only option. The model refined smoothly and gave a reasonable value for the Flack parameter. H atoms attached to carbon were placed in calculated positions (C—H = 0.95–0.99 Å using isotropic displacement parameters 1.2–1.5 times those of the parent atoms).

Table 4
Experimental details

Crystal data
Chemical formula C10H12N4O2S
Mr 252.30
Crystal system, space group Orthorhombic, Pna21
Temperature (K) 150
a, b, c (Å) 15.207 (2), 7.9249 (11), 19.540 (3)
V3) 2354.9 (6)
Z 8
Radiation type Mo Kα
μ (mm−1) 0.27
Crystal size (mm) 0.40 × 0.17 × 0.17
 
Data collection
Diffractometer Bruker Smart APEX CCD
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.86, 0.96
No. of measured, independent and observed [I > 2σ(I)] reflections 43340, 6339, 5436
Rint 0.034
(sin θ/λ)max−1) 0.687
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.122, 1.09
No. of reflections 6339
No. of parameters 311
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.57, −0.47
Absolute structure Flack x determined using 2355 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.08 (4)
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3 and SAINT. Bruker AXS, Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2018/1 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


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: SHELXL2018/1 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: publCIF (Westrip, 2010).

Ethyl 2-[4-(methylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]acetate top
Crystal data top
C10H12N4O2SDx = 1.423 Mg m3
Mr = 252.30Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna21Cell parameters from 9868 reflections
a = 15.207 (2) Åθ = 2.8–29.2°
b = 7.9249 (11) ŵ = 0.27 mm1
c = 19.540 (3) ÅT = 150 K
V = 2354.9 (6) Å3Column, colourless
Z = 80.40 × 0.17 × 0.17 mm
F(000) = 1056
Data collection top
Bruker Smart APEX CCD
diffractometer
6339 independent reflections
Radiation source: fine-focus sealed tube5436 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
Detector resolution: 8.3333 pixels mm-1θmax = 29.2°, θmin = 2.1°
φ and ω scansh = 2020
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)
k = 1010
Tmin = 0.86, Tmax = 0.96l = 2626
43340 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.043H-atom parameters constrained
wR(F2) = 0.122 w = 1/[σ2(Fo2) + (0.0807P)2 + 0.1629P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
6339 reflectionsΔρmax = 0.57 e Å3
311 parametersΔρmin = 0.47 e Å3
1 restraintAbsolute structure: Flack x determined using 2355 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: dualAbsolute structure parameter: 0.08 (4)
Special details top

Experimental. The diffraction data were obtained from 3 sets of 400 frames, each of width 0.5° in ω, collected at φ = 0.00, 90.00 and 180.00° and 2 sets of 800 frames, each of width 0.45° in φ, collected at ω = –30.00 and 210.00°. The scan time was 20 sec/frame.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.99 Å). All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. Although intensity statistics indicated a centric space group, solution in the centric space group by direct and Patterson methods indicated serious disorder while use of dual space methods (SHELXT, Sheldrick, 2015a) gave an ordered solution in the non-centric space group as the only option. Inspection of the resulting two independent molecules indicated slight differences in the rotational orientations of the methyl groups.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.74531 (5)1.26019 (8)0.57534 (6)0.0250 (2)
O10.59288 (18)0.5947 (3)0.71430 (14)0.0419 (6)
O20.54002 (17)0.3444 (3)0.67778 (13)0.0348 (5)
N10.81795 (14)0.9505 (3)0.57177 (13)0.0203 (4)
N20.73831 (15)0.6863 (3)0.57468 (14)0.0204 (5)
N30.58118 (17)0.7265 (3)0.58391 (18)0.0197 (6)
N40.52384 (15)0.8591 (3)0.58972 (14)0.0231 (5)
C10.66249 (16)0.9581 (3)0.57980 (16)0.0184 (5)
C20.74420 (16)1.0407 (3)0.57571 (17)0.0188 (5)
C30.8103 (2)0.7801 (4)0.5709 (2)0.0212 (6)
H30.8639350.7195250.5670690.025*
C40.66523 (19)0.7812 (4)0.57899 (19)0.0180 (5)
C50.57179 (18)0.9976 (4)0.58628 (16)0.0216 (6)
H50.5486981.1088760.5879100.026*
C60.86041 (19)1.3043 (5)0.5889 (2)0.0373 (8)
H6A0.8959831.2262100.5615630.056*
H6B0.8746051.2900780.6374580.056*
H6C0.8731591.4205550.5749580.056*
C70.55178 (19)0.5563 (4)0.59599 (17)0.0232 (6)
H7A0.5848170.4782460.5659400.028*
H7B0.4886590.5472920.5841540.028*
C80.56492 (19)0.5045 (4)0.67034 (17)0.0257 (6)
C90.5480 (4)0.2701 (5)0.7460 (3)0.0477 (12)
H9A0.5424990.3599000.7809770.057*
H9B0.4997920.1881640.7532790.057*
C100.6321 (4)0.1852 (10)0.7541 (3)0.090 (2)
H10A0.6313970.0788660.7285080.135*
H10B0.6423870.1618320.8026870.135*
H10C0.6791720.2577020.7365330.135*
S20.50616 (5)1.26544 (10)0.41974 (6)0.0261 (3)
O30.64984 (17)0.5962 (3)0.28477 (13)0.0395 (6)
O40.71465 (15)0.3538 (3)0.31719 (13)0.0300 (5)
N50.43223 (15)0.9564 (3)0.42506 (13)0.0213 (5)
N60.51119 (14)0.6911 (3)0.42374 (14)0.0201 (5)
N70.66818 (17)0.7297 (3)0.4129 (2)0.0209 (6)
N80.72609 (15)0.8609 (3)0.40662 (15)0.0232 (5)
C110.58765 (16)0.9615 (3)0.41661 (15)0.0184 (5)
C120.50642 (16)1.0450 (3)0.42037 (17)0.0200 (5)
C130.4397 (2)0.7853 (4)0.4266 (2)0.0213 (6)
H130.3858100.7251870.4302080.026*
C140.58423 (18)0.7855 (4)0.41793 (19)0.0174 (5)
C150.67840 (18)1.0008 (4)0.40924 (17)0.0220 (6)
H150.7016351.1118680.4065610.026*
C160.3923 (2)1.3134 (4)0.4044 (2)0.0348 (8)
H16A0.3844361.4360920.4024630.052*
H16B0.3563911.2670270.4415740.052*
H16C0.3739221.2633630.3608310.052*
C170.69686 (19)0.5584 (4)0.40147 (17)0.0207 (6)
H17A0.6631590.4810250.4313500.025*
H17B0.7598990.5480070.4133950.025*
C180.68337 (19)0.5091 (4)0.32713 (16)0.0248 (6)
C190.7050 (3)0.2858 (6)0.2481 (2)0.0409 (9)
H19A0.7560350.2130660.2372110.049*
H19B0.7037350.3796620.2146710.049*
C200.6230 (3)0.1864 (8)0.2426 (2)0.0609 (13)
H20A0.5721890.2620940.2461370.091*
H20B0.6207770.1030870.2795870.091*
H20C0.6215490.1282630.1983270.091*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0147 (4)0.0169 (3)0.0433 (6)0.0013 (2)0.0009 (4)0.0005 (3)
O10.0495 (14)0.0413 (14)0.0348 (13)0.0087 (12)0.0086 (11)0.0026 (11)
O20.0448 (14)0.0269 (12)0.0328 (11)0.0026 (10)0.0048 (10)0.0066 (10)
N10.0137 (10)0.0205 (11)0.0267 (11)0.0007 (9)0.0008 (8)0.0002 (10)
N20.0162 (11)0.0167 (11)0.0283 (12)0.0011 (8)0.0018 (8)0.0012 (12)
N30.0109 (11)0.0192 (10)0.0290 (16)0.0011 (9)0.0001 (11)0.0014 (11)
N40.0156 (10)0.0194 (12)0.0342 (14)0.0013 (9)0.0003 (9)0.0021 (10)
C10.0118 (11)0.0186 (12)0.0249 (12)0.0001 (10)0.0005 (9)0.0009 (11)
C20.0133 (11)0.0192 (11)0.0239 (12)0.0006 (10)0.0011 (9)0.0011 (12)
C30.0143 (13)0.0228 (12)0.0264 (15)0.0022 (12)0.0011 (12)0.0004 (15)
C40.0135 (12)0.0188 (11)0.0216 (14)0.0000 (11)0.0012 (11)0.0014 (14)
C50.0133 (13)0.0198 (14)0.0316 (16)0.0005 (10)0.0006 (11)0.0001 (12)
C60.0180 (14)0.0295 (18)0.064 (2)0.0067 (13)0.0016 (14)0.0057 (16)
C70.0158 (13)0.0197 (14)0.0340 (17)0.0043 (11)0.0011 (11)0.0016 (12)
C80.0196 (14)0.0269 (15)0.0305 (14)0.0007 (11)0.0017 (11)0.0002 (11)
C90.070 (3)0.036 (2)0.036 (2)0.009 (2)0.015 (2)0.0150 (17)
C100.086 (4)0.136 (5)0.048 (3)0.075 (4)0.008 (3)0.024 (3)
S20.0150 (4)0.0169 (4)0.0464 (7)0.0009 (2)0.0005 (4)0.0014 (4)
O30.0493 (14)0.0362 (13)0.0329 (12)0.0118 (12)0.0063 (11)0.0024 (10)
O40.0330 (11)0.0229 (11)0.0341 (11)0.0074 (9)0.0022 (9)0.0045 (9)
N50.0146 (10)0.0183 (11)0.0310 (12)0.0003 (9)0.0015 (9)0.0011 (10)
N60.0145 (10)0.0201 (12)0.0258 (12)0.0028 (9)0.0001 (8)0.0012 (11)
N70.0135 (12)0.0165 (11)0.0326 (17)0.0007 (9)0.0013 (12)0.0025 (11)
N80.0138 (10)0.0239 (13)0.0318 (13)0.0030 (9)0.0014 (9)0.0005 (11)
C110.0128 (11)0.0185 (12)0.0240 (12)0.0008 (10)0.0015 (9)0.0010 (11)
C120.0165 (12)0.0182 (12)0.0252 (12)0.0001 (10)0.0000 (9)0.0019 (13)
C130.0149 (13)0.0196 (12)0.0293 (16)0.0023 (12)0.0011 (12)0.0007 (15)
C140.0127 (12)0.0184 (11)0.0211 (14)0.0002 (11)0.0005 (10)0.0004 (14)
C150.0137 (12)0.0195 (14)0.0328 (17)0.0035 (10)0.0020 (11)0.0012 (12)
C160.0188 (14)0.0225 (17)0.063 (2)0.0052 (12)0.0030 (14)0.0021 (15)
C170.0160 (13)0.0160 (13)0.0299 (15)0.0021 (11)0.0005 (11)0.0006 (12)
C180.0189 (13)0.0234 (15)0.0321 (15)0.0017 (11)0.0022 (11)0.0006 (12)
C190.043 (2)0.047 (2)0.033 (2)0.0027 (19)0.0083 (18)0.0131 (19)
C200.073 (3)0.082 (3)0.028 (2)0.012 (3)0.003 (2)0.007 (2)
Geometric parameters (Å, º) top
S1—C21.740 (3)S2—C121.747 (3)
S1—C61.804 (3)S2—C161.798 (3)
O1—C81.196 (4)O3—C181.192 (4)
O2—C81.332 (4)O4—C181.334 (3)
O2—C91.463 (5)O4—C191.461 (5)
N1—C21.332 (3)N5—C121.332 (3)
N1—C31.356 (4)N5—C131.361 (4)
N2—C31.325 (4)N6—C131.320 (4)
N2—C41.344 (4)N6—C141.344 (4)
N3—C41.353 (4)N7—C141.355 (4)
N3—N41.370 (3)N7—N81.368 (3)
N3—C71.440 (4)N7—C171.443 (4)
N4—C51.319 (4)N8—C151.326 (4)
C1—C41.403 (4)C11—C141.396 (4)
C1—C21.406 (3)C11—C121.403 (3)
C1—C51.420 (4)C11—C151.422 (4)
C3—H30.9500C13—H130.9500
C5—H50.9500C15—H150.9500
C6—H6A0.9800C16—H16A0.9800
C6—H6B0.9800C16—H16B0.9800
C6—H6C0.9800C16—H16C0.9800
C7—C81.523 (4)C17—C181.518 (4)
C7—H7A0.9900C17—H17A0.9900
C7—H7B0.9900C17—H17B0.9900
C9—C101.453 (6)C19—C201.480 (6)
C9—H9A0.9900C19—H19A0.9900
C9—H9B0.9900C19—H19B0.9900
C10—H10A0.9800C20—H20A0.9800
C10—H10B0.9800C20—H20B0.9800
C10—H10C0.9800C20—H20C0.9800
C2—S1—C6101.68 (14)C12—S2—C16102.41 (14)
C8—O2—C9117.3 (3)C18—O4—C19116.0 (3)
C2—N1—C3117.5 (2)C12—N5—C13117.1 (2)
C3—N2—C4111.9 (3)C13—N6—C14111.7 (3)
C4—N3—N4111.2 (2)C14—N7—N8111.4 (2)
C4—N3—C7127.2 (3)C14—N7—C17127.1 (3)
N4—N3—C7120.5 (2)N8—N7—C17120.4 (2)
C5—N4—N3106.4 (2)C15—N8—N7106.3 (2)
C4—C1—C2116.0 (2)C14—C11—C12115.9 (2)
C4—C1—C5104.5 (2)C14—C11—C15104.9 (2)
C2—C1—C5139.6 (2)C12—C11—C15139.2 (2)
N1—C2—C1119.9 (2)N5—C12—C11120.1 (2)
N1—C2—S1121.86 (19)N5—C12—S2121.70 (19)
C1—C2—S1118.28 (19)C11—C12—S2118.22 (19)
N2—C3—N1129.0 (3)N6—C13—N5129.1 (3)
N2—C3—H3115.5N6—C13—H13115.5
N1—C3—H3115.5N5—C13—H13115.5
N2—C4—N3127.3 (3)N6—C14—N7127.1 (3)
N2—C4—C1125.7 (3)N6—C14—C11126.0 (3)
N3—C4—C1106.9 (2)N7—C14—C11106.8 (2)
N4—C5—C1111.0 (2)N8—C15—C11110.6 (2)
N4—C5—H5124.5N8—C15—H15124.7
C1—C5—H5124.5C11—C15—H15124.7
S1—C6—H6A109.5S2—C16—H16A109.5
S1—C6—H6B109.5S2—C16—H16B109.5
H6A—C6—H6B109.5H16A—C16—H16B109.5
S1—C6—H6C109.5S2—C16—H16C109.5
H6A—C6—H6C109.5H16A—C16—H16C109.5
H6B—C6—H6C109.5H16B—C16—H16C109.5
N3—C7—C8111.6 (3)N7—C17—C18110.5 (3)
N3—C7—H7A109.3N7—C17—H17A109.6
C8—C7—H7A109.3C18—C17—H17A109.6
N3—C7—H7B109.3N7—C17—H17B109.6
C8—C7—H7B109.3C18—C17—H17B109.6
H7A—C7—H7B108.0H17A—C17—H17B108.1
O1—C8—O2126.3 (3)O3—C18—O4125.8 (3)
O1—C8—C7124.8 (3)O3—C18—C17125.0 (3)
O2—C8—C7108.9 (3)O4—C18—C17109.2 (3)
C10—C9—O2111.0 (4)O4—C19—C20110.4 (3)
C10—C9—H9A109.4O4—C19—H19A109.6
O2—C9—H9A109.4C20—C19—H19A109.6
C10—C9—H9B109.4O4—C19—H19B109.6
O2—C9—H9B109.4C20—C19—H19B109.6
H9A—C9—H9B108.0H19A—C19—H19B108.1
C9—C10—H10A109.5C19—C20—H20A109.5
C9—C10—H10B109.5C19—C20—H20B109.5
H10A—C10—H10B109.5H20A—C20—H20B109.5
C9—C10—H10C109.5C19—C20—H20C109.5
H10A—C10—H10C109.5H20A—C20—H20C109.5
H10B—C10—H10C109.5H20B—C20—H20C109.5
C4—N3—N4—C51.9 (4)C14—N7—N8—C151.4 (5)
C7—N3—N4—C5170.6 (3)C17—N7—N8—C15170.3 (3)
C3—N1—C2—C10.9 (5)C13—N5—C12—C110.6 (5)
C3—N1—C2—S1178.6 (3)C13—N5—C12—S2178.6 (3)
C4—C1—C2—N10.4 (4)C14—C11—C12—N50.2 (5)
C5—C1—C2—N1177.9 (3)C15—C11—C12—N5177.4 (3)
C4—C1—C2—S1179.2 (3)C14—C11—C12—S2179.4 (3)
C5—C1—C2—S12.6 (6)C15—C11—C12—S23.4 (6)
C6—S1—C2—N112.7 (3)C16—S2—C12—N514.1 (3)
C6—S1—C2—C1167.8 (3)C16—S2—C12—C11166.6 (3)
C4—N2—C3—N10.9 (6)C14—N6—C13—N50.7 (6)
C2—N1—C3—N21.3 (6)C12—N5—C13—N60.3 (5)
C3—N2—C4—N3179.6 (4)C13—N6—C14—N7179.2 (4)
C3—N2—C4—C10.2 (5)C13—N6—C14—C111.6 (5)
N4—N3—C4—N2177.9 (3)N8—N7—C14—N6179.0 (3)
C7—N3—C4—N210.2 (7)C17—N7—C14—N611.1 (7)
N4—N3—C4—C11.6 (5)N8—N7—C14—C111.6 (5)
C7—N3—C4—C1169.3 (3)C17—N7—C14—C11169.5 (3)
C2—C1—C4—N20.0 (5)C12—C11—C14—N61.4 (5)
C5—C1—C4—N2178.8 (3)C15—C11—C14—N6179.5 (3)
C2—C1—C4—N3179.5 (3)C12—C11—C14—N7179.2 (3)
C5—C1—C4—N30.7 (4)C15—C11—C14—N71.1 (4)
N3—N4—C5—C11.5 (4)N7—N8—C15—C110.7 (4)
C4—C1—C5—N40.5 (4)C14—C11—C15—N80.3 (4)
C2—C1—C5—N4177.9 (4)C12—C11—C15—N8177.7 (4)
C4—N3—C7—C874.9 (5)C14—N7—C17—C1875.6 (5)
N4—N3—C7—C891.8 (4)N8—N7—C17—C1891.4 (4)
C9—O2—C8—O10.5 (5)C19—O4—C18—O31.0 (5)
C9—O2—C8—C7179.7 (3)C19—O4—C18—C17178.8 (3)
N3—C7—C8—O12.7 (4)N7—C17—C18—O33.4 (4)
N3—C7—C8—O2177.5 (2)N7—C17—C18—O4176.7 (2)
C8—O2—C9—C1092.6 (5)C18—O4—C19—C2093.3 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···N4i0.952.553.450 (4)158
C5—H5···O2ii0.952.573.314 (4)136
C13—H13···N8iii0.952.563.470 (4)159
C19—H19A···O1iv0.992.523.490 (5)166
Symmetry codes: (i) x+1/2, y+3/2, z; (ii) x, y+1, z; (iii) x1/2, y+3/2, z; (iv) x+3/2, y1/2, z1/2.
Comparison of the selected (X-ray and DFT) geometric data (Å, °) top
Bonds/anglesX-rayB3LYP/6-311G(d,p)
S1—C21.740 (3)1.765
S1—C61.804 (3)1.824
O1—C81.196 (4)1.204
O2—C81.332 (4)1.337
O2—C91.463 (5)1.453
N1—C21.332 (3)1.329
N1—C31.356 (4)1.350
N2—C31.325 (4)1.325
N2—C41.344 (4)1.339
N3—C41.353 (4)1.359
N3—N41.370 (3)1.363
N3—C71.440 (4)1.443
N4—C51.319 (4)1.318
C2—S1—C6101.68 (14)101.324
C8—O2—C9117.3 (3)117.442
C2—N1—C3117.5 (2)117.378
C3—N2—C4111.9 (3)112.041
C4—N3—N4111.2 (2)111.358
C4—N3—C7127.2 (3)127.628
N4—N3—C7120.5 (2)120.828
C5—N4—N3106.4 (2)106.802
C4—C1—C2116.0 (2)115.050
C4—C1—C5104.5 (2)104.373
C2—C1—C5139.6 (2)140.577
N1—C2—C1119.9 (2)120.011
N1—C2—S1121.86 (19)119.923
C4—N3—N4—C51.9 (4)1.710
C7—N3—N4—C5170.6 (3)171.115
C3—N1—C2—C10.9 (5)0.715
C3—N1—C2—S1-178.6 (3)-179.843
C4—N2—C3—N10.9 (6)0.563
C2—N1—C3—N2-1.3 (6)-1.149
Calculated energies top
Molecular Energy (a.u.) (eV)Compound I
Total Energy TE (eV)-31458.99
EHOMO (eV)-6.55
ELUMO (eV)-1.71
Gap ΔE (eV)4.84
Dipole moment, µ (Debye)2.79
Ionisation potential, I (eV)6.55
Electron affinity, A1.71
Electronegativity, χ3.13
Hardness, η2.42
Electrophilicity index, ω3.53
Softness, σ0.41
Fraction of electron transferred, ΔN0.59
 

Funding information

JTM thanks Tulane University for support of the Tulane Crystallography Laboratory. TH is grateful to Hacettepe University Scientific Research Project Unit (grant No. 013 D04 602 004).

References

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