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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 79| Part 7| July 2023| Pages 652-656
https://doi.org/10.1107/S2056989023005248

Crystal structure of 5-(β-D-gluco­pyran­osyl­thio)-N-(4-methyl­phen­yl)-1,3,4-thia­diazol-2-amine

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Mamdouh A. Abu-Zaied,a Ali M. S. Hebishy,b Galal H. Elgemeie,b Hagar T. Salamab and Peter G. Jonesc*

aGreen Chemistry Department, National Research Centre, Dokki, Giza, Egypt, bChemistry Department, Faculty of Science, Helwan University, Cairo, Egypt, and cInstitut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, Germany
*Correspondence e-mail: p.jones@tu-braunschweig.de

Edited by C. Schulzke, Universität Greifswald, Germany (Received 19 May 2023; accepted 12 June 2023; online 20 June 2023)

This article is part of a collection of articles to commemorate the founding of the African Crystallographic Association and the 75th anniversary of the IUCr.

In the structure of the title compound, C15H19N3O5S2, the bond lengths at the linking sulfur atom are significantly different [1.7473 (17) and 1.811 (2) Å], and the angle at the exocyclic nitro­gen atom is wide at 128.45 (18)°. The inter­planar angle between the tolyl and thia­diazole rings is 9.2 (1)°. The complex hydrogen-bonding pattern, involving five donors and five acceptors, can be broken down into a one-dimensional ribbon parallel to the b axis, involving hydrogen bonds of the sugar residues only, and a two-dimensional layer structure parallel to the ab plane, based on the N—H⋯O and O—H⋯N hydrogen bonds.

CCDC reference: 2269285

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1. Chemical context

There has been considerable recent inter­est in the chemistry of compounds involving both heterocyclic and carbohydrate moieties (Lopes et al., 2021[Lopes, J. P. B., Silva, L. & Ludtke, D. S. (2021). Med. Chem. 12, 2001-2015.]). Heterocyclic thio­glycosides are promising candidates in synthetic carbohydrate research, and some of these compounds have displayed various antagonistic activities (Abu-Zaied et al., 2011[Abu-Zaied, M. A., El-Telbani, E. M., Elgemeie, G. H. & Nawwar, G. A. (2011). Eur. J. Med. Chem. 46, 229-235.], 2019[Abu-Zaied, M. A., Elgemeie, G. H. & Jones, P. G. (2019). Acta Cryst. E75, 1820-1823.]; Khedr et al., 2022[Khedr, M. A., Zaghary, W. A., Elsherif, G. E., Azzam, R. A. & Elgemeie, G. H. (2022). Nucleosides Nucleotides Nucleic Acids, 41, 643-670.]). 1,3,4-Thia­diazo­les are an important class of heterocycles that have found diverse applications in organic synthesis, biological applications, and pharmaceuticals (Sun et al., 2011[Sun, J., Yang, Y., Li, W., Zhang, Y., Wang, X., Tang, J. & Zhu, H. (2011). Bioorg. Med. Chem. Lett. 21, 6116-6121.]), thus motivating researchers to prepare many derivatives of these compounds (Matysiak, 2015[Matysiak, J. (2015). Mini Rev. Med. Chem. 15, 762-775.]). Our inter­est in synthesizing novel active heterocycles (Khedr et al., 2022[Khedr, M. A., Zaghary, W. A., Elsherif, G. E., Azzam, R. A. & Elgemeie, G. H. (2022). Nucleosides Nucleotides Nucleic Acids, 41, 643-670.]; Hebishy et al., 2022[Hebishy, A. M. S., Elgemeie, G. H., Ali, R. A. E. & Jones, P. G. (2022). Acta Cryst. E78, 638-641.]; Abdallah et al., 2022[Abdallah, A. E. M., Elgemeie, G. H. & Jones, P. G. (2022). IUCrData, 7, x220332.]) and their glycosylic derivatives (Azzam et al., 2022a[Azzam, R. A., Elgemeie, G. H., Gad, N. M. & Jones, P. G. (2022a). IUCrData, 7, x220412.],b[Azzam, R. A., Elgemeie, G. H., Elsayed, R. E., Gad, N. M. & Jones, P. G. (2022b). Acta Cryst. E78, 369-372.]) led us to expect that 1,3,4-thia­zole compounds and their sugar-linked products could be valuable systems for designing novel cytotoxic agents (Yang et al., 2012[Yang, X., Wen, Q., Zhao, T., Sun, J., Li, X., Xing, M., Lu, X. & Zhu, H. (2012). Bioorg. Med. Chem. 20, 1181-1187.]). In our previous work, many anti­viral heterocyclic thio­glycosides, such as azole and azine thio­glycosides, were synthesized and found to display effective cytotoxicities (Elgemeie et al., 2016[Elgemeie, G. H., Abu-Zaied, M. & Azzam, R. (2016). Nucleosides Nucleotides Nucleic Acids, 35, 211-222.], 2017a[Elgemeie, G. H., Abu-Zaied, M. A. & Loutfy, S. A. (2017a). Tetrahedron, 73, 5853-5861.],b[Elgemeie, G. H., Salah, A. M., Abbas, N. S., Hussein, H. A. & Mohamed, R. A. (2017b). Nucleosides Nucleotides Nucleic Acids, 36, 139-150.], 2018[Elgemeie, G. H., Abu-Zaied, M. A. & Nawwar, G. A. (2018). Nucleosides Nucleotides Nucleic Acids, 37, 112-123.]; Elgemeie & Mohamed-Ezzat, 2022a[Elgemeie, G. H. & Mohamed-Ezzat, R. A. (2022a). New Strategies Targeting Cancer Metabolism, edited by G. H. Elgemeie & R. A. Mohamed-Ezzat, pp. 221-301. Amsterdam: Elesevier. https://doi.org/10.1016/B978-0-12-821783-2.00002-9.],b[Elgemeie, G. H. & Mohamed-Ezzat, R. A. (2022b). New Strategies Targeting Cancer Metabolism, edited by G. H. Elgemeie & R. A. Mohamed-Ezzat, pp. 303-392. Amsterdam: Elesevier. https://doi.org/10.1016/B978-0-12-821783-2.00010-8.]). We have also reported that di­hydro­pyridine thio­glycosides can be used as inhibitors of the glycosyl­ation of proteins (Scala et al., 1997[Scala, S., Akhmed, K., Rao, U. S., Paull, K., Lan, L., Dickstein, B., Lee, J., Elgemeie, G. H., Stein, W. D. & Bates, S. E. (1997). Mol. Pharmacol. 51, 1024-1033.]).

In the current study, we have designed a facile synthesis of 1,3,4-thia­diazole thio­glucosides by coupling of potassium 1,3,4-thia­diazo­lates and protected α-D-gluco­pyranosyl bromide. Our target derivative was synthesized by the reaction of the thio­semicarbazide derivative 1 with carbon di­sulfide in boiling KOH/EtOH to afford the corresponding potassium 1,3,4-thia­diazole thiol­ate 2 in good yield (Fig. 1[link]). Compound 2 was then coupled with acetyl­ated α-D-gluco­pyran­ose bromide 3 in DMF at room temperature to give a product that could in principle be either the 1,3,4-thia­diazole S-glucoside 4 or the isomeric N-glucoside 5, corresponding to two different modes of glycosyl­ation. Deprotection then provided a final product that should be either the 1,3,4-thia­diazole S-glucoside 6 or the isomeric N-glucoside 7. Spectroscopic data cannot distinguish these two structures with absolute certainty, although it had already been proposed that a simple SN2 reaction between 2 and 3 would give the β-glucoside product 4 (Masoud et al., 2017[Masoud, D. M., Hammad, S. F., Elgemeie, G. H. & Jones, P. G. (2017). Acta Cryst. E73, 1751-1754.]; Hammad et al., 2018[Hammad, S. F., Masoud, D. M., Elgemeie, G. H. & Jones, P. G. (2018). Acta Cryst. E74, 853-856.]), which would imply the final formation of 6.

[Scheme 1]
[Figure 1]
Figure 1
Reaction scheme for the synthesis of 6.

This is consistent with the spectroscopic data; thus the 1H NMR spectrum of 6 showed the signal of the anomeric proton as a doublet at δ 4.72 (J1`,2` = 10.8 Hz), strongly implying a β-D-configuration. The 13C NMR spectrum exhibited a signal at δ 86.89 corresponding to C-1′, whereas the signals at δ 61.34, 70.00, 73.07 and 78.32, 81.42 were allocated to C-6′, C-4`, C-2′, C-3′ and C-5′. The X-ray structure determination, presented here, unambiguously shows the isolated product to be the 1,3,4-thia­diazole-5-thio­glucoside 6 (Fig. 1[link]).

2. Structural commentary

The mol­ecular structure of compound 6 is shown in Fig. 2[link]. Note that the standard sugar numbering has been slightly modified (to C11–16) for the crystallographic numbering. Mol­ecular dimensions (Table 1[link]) may be regarded as normal; e.g. the bond lengths at S2 are significantly different, consistent with the different hybridization of the carbon atoms [C2—S2 = 1.7473 (17), C11—S2 = 1.811 (2) Å], and the angle C5—N1—C21 is wide at 128.45 (18)°. The inter­planar angle between the tolyl and thia­diazole rings is 9.2 (1)°. The β (equatorial) position of the substituent at the glucose ring is confirmed by the torsion angle C15—O1—C11—S2 of 177.11 (10)°. The absolute configuration was confirmed by the Flack parameter, with chiralities S,R,S,S,R at C11–15 respectively consistent with the presence of D-glucose.

Table 1
Selected geometric parameters (Å, °)

S1—C2 1.7322 (19) N4—C5 1.309 (3)
S1—C5 1.7525 (18) C5—N1 1.358 (2)
C2—N3 1.298 (2) C11—S2 1.811 (2)
C2—S2 1.7473 (17) N1—C21 1.411 (2)
N3—N4 1.397 (2)    
       
C2—S1—C5 86.59 (9) C5—N4—N3 111.44 (15)
N3—C2—S1 114.31 (13) N4—C5—N1 128.67 (17)
N3—C2—S2 119.74 (14) N4—C5—S1 114.15 (14)
S1—C2—S2 125.88 (10) N1—C5—S1 117.17 (15)
C2—N3—N4 113.29 (16) C5—N1—C21 128.45 (18)
       
S2—C11—O1—C15 177.11 (10) O1—C11—S2—C2 −55.86 (12)
N3—C2—S2—C11 −164.51 (14) C12—C11—S2—C2 −174.12 (11)
S1—C2—S2—C11 18.65 (13)    
[Figure 2]
Figure 2
The mol­ecule of compound 6 in the crystal. Ellipsoids represent 50% probability levels.

3. Supra­molecular features

With five classical hydrogen bonds (Table 2[link]), the mol­ecular packing of 6 might be expected to be three-dimensional and complex, and this is indeed the case. However, the packing may be analysed in terms of more easily assimilable substructures. One, formally one-dimensional, substructure involving the sugar residues can readily be identified (Fig. 3[link]), the hydrogen bonds O2—H02⋯O3 and O3—H03⋯O4(−x + 3, y + [{1\over 2}], −z + 1 for both) combine via the 21 screw axis to form ribbons of mol­ecules parallel to the b axis. The ribbons lie in layers roughly parallel to (105). The OH group at C16 is directed away from its layer to form contacts to the neighbouring layer.

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O2—H02⋯O3i 0.82 (2) 1.87 (2) 2.6846 (19) 174 (3)
O3—H03⋯O4i 0.84 (2) 1.93 (2) 2.7375 (18) 161 (3)
O4—H04⋯N3ii 0.81 (2) 2.06 (2) 2.848 (2) 162 (3)
O5—H05⋯N4ii 0.83 (2) 2.11 (2) 2.899 (2) 159 (3)
O5—H05⋯N3ii 0.83 (2) 2.60 (2) 3.282 (2) 141 (2)
N1—H01⋯O5iii 0.84 (3) 2.05 (3) 2.853 (2) 158 (2)
C14—H14⋯S1iv 1.00 2.74 3.7044 (18) 163
C16—H16B⋯S2v 0.99 2.71 3.570 (2) 145
Symmetry codes: (i) [-x+3, y+{\script{1\over 2}}, -z+1]; (ii) [x+1, y-1, z]; (iii) [x-1, y, z]; (iv) x+1, y, z; (v) [x, y-1, z].
[Figure 3]
Figure 3
Packing diagram of compound 6: the glucose-based substructure involving two O—H⋯O hydrogen bonds (indicated by thick dashed lines). The view direction is perpendicular to the plane (105). The labelled atom (O1) indicates the asymmetric unit.

A second, two-dimensional, substructure (Fig. 4[link]) is based on the remaining three hydrogen bonds (of the types O—H⋯N and N—H⋯O), and connects the mol­ecules first by translation (both O—H⋯N hydrogen bonds; x + 1, y − 1, z) to form chains parallel to (1[\overline{1}]0) (horizontal in the Figure), and secondly by a-axis translation (the N—H⋯O hydrogen bond; x − 1, y, z). The overall effect is to create layers parallel to the ab plane.

[Figure 4]
Figure 4
Packing diagram of compound 6: the layer substructure involving the O—H⋯N and N—H⋯O hydrogen bonds (indicated by thick dashed lines). The view direction is perpendicular to the ab plane. The labelled atom (O1) indicates the asymmetric unit.

The contact O5—H05⋯N3(x + 1, y − 1, z) may be regarded as the second, weaker, branch of a three-centre inter­action, but this contact is omitted from the packing diagrams for clarity. Similarly, the two C—H⋯S inter­actions are probably inter­pretable as `weak' hydrogen bonds, but we do not discuss their structural role in detail.

4. Database survey

The search employed the routine ConQuest (Bruno et al., 2002[Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.]), part of Version 2022.3.0 of the Cambridge Structural Database (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]). We searched for pyran­ose sugars attached by a sulfur atom to heterocycles containing more than one heteroatom (a larger subset of hits was edited by hand). The six structures thus found were derivatives of 1,2,4-triazole (refcode HEKPUL; El Ashry et al., 2018[El Ashry, E. S. H., Awad, L. F., Al Moaty, M. N. A., Ghabbour, H. A. & Barakat, A. (2018). J. Mol. Struct. 1152, 87-95.]), 1,3,4-oxa­diazole (IZAJEY; Qiu & Xu, 2004[Qiu, Z.-Z. & Xu, P.-F. (2004). Acta Cryst. E60, o1365-o1366.]), benzoxazole (JIPYUD and JIPZAK; Kamat et al., 2007[Kamat, M. N., Rath, N. P. & Demchenko, A. V. (2007). J. Org. Chem. 72, 6938-6946.]), 1,3,5-oxa­thia­zole, involving a spiro junction at the sugar C1 atom (PIWVIA; Praly et al., 1994[Praly, J.-P., Faure, R., Joseph, B., Kiss, L. & Rollin, P. (1994). Tetrahedron, 50, 6559-6568.]) and 1,3,4-thia­diazole (SASXIU; Qiu et al., 2005[Qiu, Z.-Z., Hui, X.-P. & Xu, P.-F. (2005). Acta Cryst. C61, o475-o476.]). In all except PIWVIA, the sugar OH groups were substituted with ester functions. The structure SASXIU, despite having the same heterocycle as 6, (but with a 2-phenyl substituent), has a markedly different relative orientation of the glucose and heterocyclic rings, with a torsion angle Cgluc—Sgluc—Chetero—Shetero of 78.10 (10)° compared to the value of 18.65 (13)° for 6.

5. Synthesis and crystallization

Preparation of inter­mediate 4: A solution of 2,3,4,6-tetra-O-acetyl-α-D-gluco­pyranosyl bromide (3) (10 mmol) in dry DMF (15 mL) was added dropwise over 30 min to a solution of the potassium thiol­ate 2 (10 mmol) in 20 mL of DMF. The reaction mixture was stirred at room temperature until completion (monitored by TLC), then the mixture was poured into ice–water, and the resulting precipitate was collected by filtration, dried, and crystallized from ethanol to give the acetyl­ated glucoside 4.

N·B.: The NMR data, as given here and in Section 1, refer to sugar numbering C1′–C6′, which is different from the crystallographic numbering of the glucose moiety in 6 (C11–C16).

White powder (EtOH); yield 93%; m.p. 479–481 K; IR (cm−1): υ 3360 (NH), 2949 (CH3), 1741 (C=O); 1H NMR (400 MHz, DMSO-d6): δ 1.91–2.05 (4s, 12H, 4 × OAc), 2.27 (s, 3H, CH3), 4.07–4.19 (m, 3H, H-6′, H-6′′, H-5′), 4.90–4.98 (m, 2H, H-4′, H-2′), 5.39 (t-like, 1H, J = 10.8 Hz, H-3′), 5.40 (d, 1H, J1′–2′ = 7.1 Hz, H-1′), 7.16 (d, 2H, J = 8.0 Hz, Ar-H), 7.46 (d, 2H, J = 7.2 Hz, Ar-H), 10.45 (s, D2O exchangeable, 1H, NH); 13C NMR (100 MHz, DMSO-d6): δ 20.70, 20.81, 20.90 (5 × CH3), 62.20 (C-6′), 68.23 (C-4′), 70.04 (C-2′), 73.14 (C-3′), 75.17 (C-5′), 82.99 (C-1′), 118.35 (2C, Ar-C), 130.05 (2C, Ar-C), 131.99 (Ar-C), 138.30 (Ar-C), 145.21 (C-2), 167.88 (C-5), 169.50, 169.74, 169.98, 170.48 (4C=O). Analysis calculated for C23H27N3O9S2 (553.61): C 49.90, H 4.92, N 7.59, S 11.58. Found: C 49.82, H 4.81, N 7.52, S 11.46%.

Preparation of title compound 6: In a 50 mL flask, the tetra­acetyl­ated glucoside derivative 4 (0.01 mol) was dissolved in 20 mL of dry methanol, and then ammonia gas was passed through the solution at 273 K for 10 min. The mixture was then stirred until the reaction was complete (monitored by TLC using chloro­form/methanol 9:1). The solution was concentrated under reduced pressure to afford a solid residue, which was washed several times with boiling chloro­form. The residue was dried, purified and recrystallized from ethanol to give the corresponding free glucoside 6.

Colourless crystals (EtOH); yield 62%; m.p. 472–474 K; IR (cm−1): ν 3271 (OH), 2921 (CH); 1H NMR (400 MHz, DMSO-d6): δ 2.25 (s, 3H, CH3), 3.11–3.22 (m, 2H, H-6′, H-6′′), 3.23–3.29 (m, 2H, H-5′, H-4′), 3.49–3.56 (m, 1H, H-3′), 3.71–3.76 (m, 1H, H-2′), 4.59 (t, 1H, JOH–H-6′′ = 3.6 Hz, D2O-exchangeable, 6′′-OH), 4.72 (d, 1H, J1′-2′ = 10.8 Hz, H-1′), 5.05 (d, 1H, J = 6.4 Hz, D2O-exchangeable, OH), 5.17 (d, 1H, J = 6.4 Hz, D2O-exchangeable, OH), 5.53 (d, 1H, J = 8.0 Hz, D2O-exchangeable, OH), 7.14 (d, 2H, J = 11.2 Hz, Ar-H), 7.47 (d, 2H, J = 12.4 Hz, Ar-H), 10.32 (s, D2O exch., 1H, NH); 13C NMR (100 MHz, DMSO-d6): δ 20.82 (CH3), 61.34 (C-6′), 70.00 (C-4′), 73.07 (C-2′), 78.32 (C-3′), 81.42 (C-5′), 86.89 (C-1′), 117.98 (2C, Ar-C), 129.96 (2C, Ar-C), 131.33 (Ar-C), 138.50 (Ar-C), 150.03 (C-2), 166.90 (C-5). Analysis calculated for C15H19N3O5S2 (385.08): C 46.75, H 4.94, N 10.91, S 16.62. Found: C 46.6, H 4.8, N 10.9, S 16.5%.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. Hydrogen atoms of the NH and OH groups were refined freely, the latter however with O—H distances restrained to be approximately equal (command SADI). The methyl group was included as an idealized rigid group allowed to rotate but not tip (C—H = 0.98 Å, H—C—H = 109.5°). Other hydrogen atoms were included using a riding model starting from calculated positions (C—Haromatic 0.95 Å, C—Hmethine 1.00 Å, C—Hmethyl­ene 0.99 Å). The U(H) values were fixed at 1.5 × Ueq of the parent carbon atoms for the methyl group and 1.2 × Ueq for other hydrogens. An extinction correction was performed; the extinction parameter as defined by Sheldrick (2015a[Sheldrick, G. M. (2015a). Acta Cryst. C71, 3-8.]) refined to 0.0009 (3). The absolute configuration (corresponding to D-glucose) was confirmed by the Flack parameter of −0.006 (5).

Table 3
Experimental details

Crystal data
Chemical formula C15H19N3O5S2
Mr 385.45
Crystal system, space group Monoclinic, P21
Temperature (K) 100
a, b, c (Å) 6.23840 (6), 7.4355 (1), 18.32032 (17)
β (°) 91.4183 (8)
V (Å3) 849.54 (2)
Z 2
Radiation type Cu Kα
μ (mm−1) 3.14
Crystal size (mm) 0.10 × 0.08 × 0.02
 
Data collection
Diffractometer XtaLAB Synergy
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2021[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.])
Tmin, Tmax 0.851, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 70354, 3520, 3502
Rint 0.030
(sin θ/λ)max (Å−1) 0.633
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.019, 0.050, 1.03
No. of reflections 3520
No. of parameters 248
No. of restraints 7
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.30, −0.21
Absolute structure Flack x determined using 1554 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 −0.006 (5)
Computer programs: CrysAlis PRO (Rigaku OD, 2021[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]), SHELXT (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. A71, 3-8.]), SHELXL2018/3 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. C71, 3-8.]) and XP (Siemens, 1994[Siemens (1994). XP. Siemens Analytical X-Ray Instruments, Madison, Wisconsin, USA.]).

Supporting information

CCDC reference: 2269285

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989023005248/yz2035sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023005248/yz2035Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989023005248/yz2035Isup3.cml

checkCIF report


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2021); cell refinement: CrysAlis PRO (Rigaku OD, 2021); data reduction: CrysAlis PRO (Rigaku OD, 2021); program(s) used to solve structure: SHELXT (Sheldrick, 2015b); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015a); molecular graphics: XP (Siemens, 1994); software used to prepare material for publication: SHELXL2018/3 (Sheldrick, 2015a).

5-[(β-D-Glucopyranosyl)sulfanyl]-N-(4-methylphenyl)-1,3,4-thiadiazol-2-amine top
Crystal data top
C15H19N3O5S2F(000) = 404
Mr = 385.45Dx = 1.507 Mg m−3
Monoclinic, P21Cu Kα radiation, λ = 1.54184 Å
a = 6.23840 (6) ÅCell parameters from 61296 reflections
b = 7.4355 (1) Åθ = 2.4–77.5°
c = 18.32032 (17) ŵ = 3.14 mm−1
β = 91.4183 (8)°T = 100 K
V = 849.54 (2) Å3Plate, colourless
Z = 20.10 × 0.08 × 0.02 mm
Data collection top
XtaLAB Synergy
diffractometer		3520 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source3502 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.030
Detector resolution: 10.0000 pixels mm-1θmax = 77.3°, θmin = 2.4°
ω scansh = −7→7
Absorption correction: multi-scan
(CrysAlisPro; Rigaku OD, 2021)		k = −9→8
Tmin = 0.851, Tmax = 1.000l = −23→23
70354 measured reflections
Refinement top
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0289P)2 + 0.2573P]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.019(Δ/σ)max < 0.001
wR(F2) = 0.050Δρmax = 0.30 e Å−3
S = 1.03Δρmin = −0.21 e Å−3
3520 reflectionsExtinction correction: SHELXL-2018/3 (Sheldrick, 2015a), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
248 parametersExtinction coefficient: 0.0009 (3)
7 restraintsAbsolute structure: Flack x determined using 1554 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: dualAbsolute structure parameter: −0.006 (5)
Hydrogen site location: mixed
Special details top

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.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

3.7080 (0.0039) x + 2.0545 (0.0042) y + 13.5622 (0.0105) z = 13.7691 (0.0045)

* 0.0205 (0.0007) S1 * -0.0130 (0.0010) C2 * -0.0030 (0.0011) N3 * 0.0244 (0.0010) N4 * -0.0289 (0.0010) C5 -0.1014 (0.0026) N1 0.0173 (0.0026) S2

Rms deviation of fitted atoms = 0.0201

3.4518 (0.0038) x + 1.0131 (0.0062) y + 14.7993 (0.0080) z = 13.9365 (0.0076)

Angle to previous plane (with approximate esd) = 9.200 ( 0.107 )

* 0.0048 (0.0012) C21 * -0.0074 (0.0013) C22 * 0.0034 (0.0013) C23 * 0.0035 (0.0014) C24 * -0.0062 (0.0014) C25 * 0.0020 (0.0013) C26 0.0546 (0.0026) N1 0.0234 (0.0033) C27

Rms deviation of fitted atoms = 0.0049

3.6049 (0.0167) x + 0.8656 (0.1231) y + 14.5324 (0.0137) z = 13.6402 (0.0694)

Angle to previous plane (with approximate esd) = 1.978 ( 0.397 )

* 0.0000 (0.0000) H01 * 0.0000 (0.0000) C5 * 0.0000 (0.0000) C21 0.0965 (0.0103) N1

Rms deviation of fitted atoms = 0.0000

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.68679 (6)0.56520 (6)0.74337 (2)0.01368 (10)
C20.7401 (3)0.7619 (2)0.69652 (9)0.0141 (4)
N30.6138 (2)0.8948 (2)0.71166 (8)0.0164 (3)
N40.4594 (2)0.8505 (2)0.76262 (8)0.0164 (3)
C50.4713 (3)0.6807 (3)0.78116 (9)0.0141 (3)
C111.0267 (2)0.5674 (3)0.61331 (9)0.0129 (3)
H110.9082490.5059700.5852590.015*
C121.2263 (3)0.5825 (3)0.56692 (9)0.0125 (3)
H121.3363340.6569080.5936260.015*
C131.3196 (3)0.3958 (3)0.55237 (9)0.0132 (3)
H131.2256170.3310250.5160190.016*
C141.3421 (3)0.2844 (3)0.62159 (9)0.0129 (3)
H141.4577440.3368670.6538160.015*
C151.1297 (3)0.2862 (3)0.66200 (9)0.0135 (3)
H151.0142600.2350180.6293280.016*
C161.1351 (3)0.1833 (3)0.73351 (10)0.0159 (3)
H16A1.0058900.2141600.7611850.019*
H16B1.1298970.0528140.7228610.019*
O11.07795 (19)0.47115 (17)0.67845 (7)0.0135 (3)
O21.1689 (2)0.66863 (19)0.50027 (7)0.0153 (3)
H021.264 (4)0.740 (4)0.4908 (15)0.038 (8)*
O31.52906 (19)0.41758 (19)0.52349 (7)0.0168 (3)
H031.522 (4)0.482 (4)0.4857 (13)0.029 (7)*
O41.3989 (2)0.10451 (18)0.60228 (7)0.0162 (3)
H041.471 (4)0.067 (4)0.6365 (12)0.030 (7)*
O51.3225 (2)0.22073 (19)0.77822 (7)0.0178 (3)
H051.382 (4)0.122 (3)0.7831 (14)0.032 (8)*
N10.3417 (2)0.5861 (2)0.82558 (8)0.0156 (3)
H010.353 (4)0.473 (4)0.8230 (13)0.020 (6)*
C210.1567 (3)0.6454 (3)0.86130 (9)0.0154 (3)
C220.0393 (3)0.5129 (3)0.89691 (10)0.0191 (4)
H220.0823280.3906080.8941940.023*
C23−0.1396 (3)0.5595 (3)0.93618 (10)0.0221 (4)
H23−0.2164660.4685120.9608420.027*
C24−0.2085 (3)0.7375 (3)0.94008 (11)0.0220 (4)
C25−0.0925 (3)0.8667 (3)0.90351 (11)0.0230 (4)
H25−0.1383660.9884130.9050380.028*
C260.0901 (3)0.8234 (3)0.86446 (10)0.0195 (4)
H260.1677800.9147130.8403300.023*
S20.94984 (6)0.79473 (6)0.63645 (2)0.01473 (10)
C27−0.4029 (3)0.7886 (4)0.98327 (13)0.0322 (5)
H27A−0.5332850.7659160.9537620.048*
H27B−0.3952500.9164690.9960230.048*
H27C−0.4061400.7164871.0280100.048*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.01271 (18)0.0111 (2)0.01736 (19)0.00212 (16)0.00360 (13)0.00076 (16)
C20.0134 (8)0.0129 (10)0.0161 (8)0.0005 (6)0.0007 (6)−0.0002 (7)
N30.0159 (7)0.0146 (8)0.0188 (7)0.0029 (6)0.0043 (6)0.0020 (6)
N40.0147 (7)0.0164 (8)0.0183 (7)0.0024 (6)0.0050 (6)0.0016 (6)
C50.0127 (8)0.0155 (9)0.0140 (8)0.0021 (7)0.0004 (6)−0.0013 (7)
C110.0123 (7)0.0115 (8)0.0149 (7)0.0006 (7)0.0020 (6)0.0008 (7)
C120.0122 (7)0.0120 (8)0.0133 (7)0.0005 (7)0.0016 (5)0.0015 (7)
C130.0114 (8)0.0139 (9)0.0145 (8)0.0002 (6)0.0031 (6)−0.0006 (7)
C140.0141 (7)0.0103 (8)0.0145 (7)0.0010 (7)0.0031 (6)0.0000 (7)
C150.0140 (7)0.0103 (8)0.0163 (7)0.0011 (7)0.0034 (6)−0.0013 (7)
C160.0154 (8)0.0153 (9)0.0174 (8)0.0007 (7)0.0033 (6)0.0017 (7)
O10.0160 (6)0.0102 (6)0.0144 (6)0.0027 (5)0.0040 (4)0.0010 (5)
O20.0146 (6)0.0151 (7)0.0162 (6)−0.0009 (5)0.0017 (4)0.0053 (5)
O30.0147 (6)0.0166 (7)0.0194 (6)0.0030 (5)0.0074 (5)0.0049 (5)
O40.0202 (6)0.0122 (7)0.0163 (6)0.0046 (5)0.0039 (5)0.0000 (5)
O50.0211 (7)0.0135 (7)0.0188 (6)0.0027 (5)−0.0010 (5)0.0006 (5)
N10.0149 (7)0.0127 (9)0.0193 (7)0.0012 (6)0.0035 (5)0.0009 (6)
C210.0120 (8)0.0208 (10)0.0136 (7)0.0020 (7)0.0007 (6)−0.0009 (7)
C220.0177 (8)0.0202 (10)0.0195 (8)0.0008 (7)0.0013 (7)0.0005 (7)
C230.0157 (8)0.0301 (11)0.0207 (8)−0.0037 (9)0.0038 (6)0.0027 (9)
C240.0141 (8)0.0309 (12)0.0211 (9)0.0000 (7)0.0035 (7)−0.0081 (8)
C250.0197 (9)0.0225 (11)0.0271 (10)0.0042 (8)0.0049 (8)−0.0046 (8)
C260.0177 (8)0.0194 (11)0.0217 (8)0.0012 (7)0.0046 (7)0.0001 (8)
S20.01492 (19)0.0101 (2)0.01939 (19)0.00117 (15)0.00557 (14)0.00078 (16)
C270.0195 (9)0.0386 (13)0.0389 (11)−0.0030 (10)0.0112 (8)−0.0133 (11)
Geometric parameters (Å, º) top
S1—C21.7322 (19)C16—O51.438 (2)
S1—C51.7525 (18)C16—H16A0.9900
C2—N31.298 (2)C16—H16B0.9900
C2—S21.7473 (17)O2—H020.82 (2)
N3—N41.397 (2)O3—H030.84 (2)
N4—C51.309 (3)O4—H040.81 (2)
C5—N11.358 (2)O5—H050.83 (2)
C11—O11.421 (2)N1—C211.411 (2)
C11—C121.529 (2)N1—H010.84 (3)
C11—S21.811 (2)C21—C261.389 (3)
C11—H111.0000C21—C221.398 (3)
C12—O21.417 (2)C22—C231.387 (3)
C12—C131.531 (3)C22—H220.9500
C12—H121.0000C23—C241.394 (3)
C13—O31.4311 (19)C23—H230.9500
C13—C141.518 (2)C24—C251.386 (3)
C13—H131.0000C24—C271.513 (2)
C14—O41.431 (2)C25—C261.397 (2)
C14—C151.534 (2)C25—H250.9500
C14—H141.0000C26—H260.9500
C15—O11.446 (2)C27—H27A0.9800
C15—C161.517 (2)C27—H27B0.9800
C15—H151.0000C27—H27C0.9800
C2—S1—C586.59 (9)O5—C16—C15113.27 (15)
N3—C2—S1114.31 (13)O5—C16—H16A108.9
N3—C2—S2119.74 (14)C15—C16—H16A108.9
S1—C2—S2125.88 (10)O5—C16—H16B108.9
C2—N3—N4113.29 (16)C15—C16—H16B108.9
C5—N4—N3111.44 (15)H16A—C16—H16B107.7
N4—C5—N1128.67 (17)C11—O1—C15110.51 (13)
N4—C5—S1114.15 (14)C12—O2—H02108 (2)
N1—C5—S1117.17 (15)C13—O3—H03109.9 (19)
O1—C11—C12109.56 (13)C14—O4—H04106 (2)
O1—C11—S2109.19 (11)C16—O5—H05104 (2)
C12—C11—S2106.59 (13)C5—N1—C21128.45 (18)
O1—C11—H11110.5C5—N1—H01115.6 (16)
C12—C11—H11110.5C21—N1—H01113.9 (17)
S2—C11—H11110.5C26—C21—C22119.40 (17)
O2—C12—C11108.70 (13)C26—C21—N1124.47 (17)
O2—C12—C13110.40 (13)C22—C21—N1116.11 (17)
C11—C12—C13110.38 (15)C23—C22—C21120.26 (19)
O2—C12—H12109.1C23—C22—H22119.9
C11—C12—H12109.1C21—C22—H22119.9
C13—C12—H12109.1C22—C23—C24121.12 (19)
O3—C13—C14107.70 (13)C22—C23—H23119.4
O3—C13—C12108.45 (14)C24—C23—H23119.4
C14—C13—C12112.14 (14)C25—C24—C23117.89 (17)
O3—C13—H13109.5C25—C24—C27120.9 (2)
C14—C13—H13109.5C23—C24—C27121.2 (2)
C12—C13—H13109.5C24—C25—C26122.0 (2)
O4—C14—C13108.79 (13)C24—C25—H25119.0
O4—C14—C15110.46 (15)C26—C25—H25119.0
C13—C14—C15109.59 (13)C21—C26—C25119.31 (18)
O4—C14—H14109.3C21—C26—H26120.3
C13—C14—H14109.3C25—C26—H26120.3
C15—C14—H14109.3C2—S2—C11102.94 (8)
O1—C15—C16107.46 (13)C24—C27—H27A109.5
O1—C15—C14107.97 (14)C24—C27—H27B109.5
C16—C15—C14114.29 (14)H27A—C27—H27B109.5
O1—C15—H15109.0C24—C27—H27C109.5
C16—C15—H15109.0H27A—C27—H27C109.5
C14—C15—H15109.0H27B—C27—H27C109.5
C5—S1—C2—N32.54 (14)O1—C15—C16—O5−74.18 (17)
C5—S1—C2—S2179.52 (13)C14—C15—C16—O545.6 (2)
S1—C2—N3—N4−0.4 (2)C12—C11—O1—C15−66.50 (18)
S2—C2—N3—N4−177.57 (12)S2—C11—O1—C15177.11 (10)
C2—N3—N4—C5−3.0 (2)C16—C15—O1—C11−168.02 (13)
N3—N4—C5—N1−175.82 (17)C14—C15—O1—C1168.24 (16)
N3—N4—C5—S14.95 (19)N4—C5—N1—C212.2 (3)
C2—S1—C5—N4−4.30 (14)S1—C5—N1—C21−178.54 (14)
C2—S1—C5—N1176.37 (14)C5—N1—C21—C26−9.0 (3)
O1—C11—C12—O2176.33 (14)C5—N1—C21—C22172.65 (16)
S2—C11—C12—O2−65.64 (15)C26—C21—C22—C23−1.2 (3)
O1—C11—C12—C1355.11 (18)N1—C21—C22—C23177.18 (16)
S2—C11—C12—C13173.14 (11)C21—C22—C23—C241.1 (3)
O2—C12—C13—O372.56 (16)C22—C23—C24—C25−0.1 (3)
C11—C12—C13—O3−167.24 (13)C22—C23—C24—C27−179.64 (18)
O2—C12—C13—C14−168.64 (13)C23—C24—C25—C26−0.9 (3)
C11—C12—C13—C14−48.44 (18)C27—C24—C25—C26178.71 (19)
O3—C13—C14—O4−69.37 (17)C22—C21—C26—C250.3 (3)
C12—C13—C14—O4171.39 (13)N1—C21—C26—C25−177.94 (17)
O3—C13—C14—C15169.77 (14)C24—C25—C26—C210.7 (3)
C12—C13—C14—C1550.53 (19)N3—C2—S2—C11−164.51 (14)
O4—C14—C15—O1−178.61 (13)S1—C2—S2—C1118.65 (13)
C13—C14—C15—O1−58.76 (17)O1—C11—S2—C2−55.86 (12)
O4—C14—C15—C1661.89 (19)C12—C11—S2—C2−174.12 (11)
C13—C14—C15—C16−178.26 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H02···O3i0.82 (2)1.87 (2)2.6846 (19)174 (3)
O3—H03···O4i0.84 (2)1.93 (2)2.7375 (18)161 (3)
O4—H04···N3ii0.81 (2)2.06 (2)2.848 (2)162 (3)
O5—H05···N4ii0.83 (2)2.11 (2)2.899 (2)159 (3)
O5—H05···N3ii0.83 (2)2.60 (2)3.282 (2)141 (2)
N1—H01···O5iii0.84 (3)2.05 (3)2.853 (2)158 (2)
C14—H14···S1iv1.002.743.7044 (18)163
C15—H15···O2v1.002.663.577 (2)153
C11—H11···O3iii1.002.683.652 (2)164
C16—H16B···S2vi0.992.713.570 (2)145
Symmetry codes: (i) −x+3, y+1/2, −z+1; (ii) x+1, y−1, z; (iii) x−1, y, z; (iv) x+1, y, z; (v) −x+2, y−1/2, −z+1; (vi) x, y−1, z.
 

Acknowledgements

The authors acknowledge support by the Open Access Publication Funds of the Technical University of Braunschweig.

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ISSN: 2056-9890
Volume 79| Part 7| July 2023| Pages 652-656
https://doi.org/10.1107/S2056989023005248
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