Synthesis and crystal structure of ethyl 2-(1,3-benzo­thia­zol-2-yl)-1-oxo-1H-pyrido[2,1-b][1,3]benzo­thia­zole-4-carboxyl­ate

Elboshi, H.A.; Azzam, R.A.; Elgemeie, G.H.; Jones, P.G.

doi:10.1107/S2056989026000204

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ISSN: 2056-9890

Volume 82| Part 2| February 2026| Pages 182-186

https://doi.org/10.1107/S2056989026000204

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Synthesis and crystal structure of ethyl 2-(1,3-benzothiazol-2-yl)-1-oxo-1H-pyrido[2,1-b][1,3]benzothiazole-4-carboxylate

Heba A. Elboshi,^a Rasha A. Azzam,^a Galal H. Elgemeie ^a and Peter G. Jones ^b ^*

^aChemistry Department, Faculty of Science, Helwan University, Cairo, Egypt, and ^bInstitut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, Germany
^*Correspondence e-mail: [email protected]

Edited by M. Weil, Vienna University of Technology, Austria (Received 5 December 2025; accepted 9 January 2026; online 20 January 2026)

The molecule of the title compound, C₂₁H₁₄N₂O₃S₂, is approximately planar except for the terminal carbon atom of the ethyl group. The planarity is promoted by two short intramolecular S⋯O=C contacts and one intramolecular ‘weak' C—H⋯O=C hydrogen bond. The two thiazole rings show some appreciable differences in bond lengths and angles, associated with their different annelation patterns. The molecular packing involves one ‘weak' hydrogen bond of the type C—H⋯O=C, which links the molecules in zigzag chains via a 2₁ screw axis along [010]. Additionally, ‘stacked' pairs of molecules, necessarily with parallel ring systems, are related by an inversion operator, and two π contacts C—H⋯π and C=O⋯π are observed.

Keywords: crystal structure; benzothiazole; hydrogen bonds; π stacking.

CCDC reference: 2521548

1. Chemical context

A central objective in the field of medicinal chemistry is the design and development of novel therapeutic molecules to treat infections (Desai et al., 2013 ; Li et al., 2000 ). Numerous patents and scientific studies have shown that benzothiazole scaffolds have exceptional biological properties (Gill et al., 2015 ), and several medications with such heterocyclic rings have been found to have a wide range of pharmaceutical applications and biological activities (Catalano et al., 2021 ). In particular, antibacterial, antiviral, antifungal, and anti-inflammatory properties have been established for benzothiazole compounds (Azzam et al., 2020 ).

It is important to note that the biological actions of benzothiazole derivatives depend on their exact molecular structure, functional groups, and the biochemical path or enzyme they interact with (Kamal et al., 2015 ). Furthermore, the pharmacokinetic and pharmacodynamic characteristics of benzothiazole-based medications must be carefully taken into account throughout development (Al-Tel et al., 2011 ). To maximize their biological activity and minimize any related toxicity, researchers are still investigating and altering the molecular and crystal structures of benzothiazole derivatives (Keri et al., 2015 ).

We have recently synthesized some novel heterocyclic compounds with significant biological activities by incorporating a benzothiazole moiety (Elgemeie et al., 2022 ). One such compound, with both beneficial optical properties and biological activity, was a benzothiazole with substituted coumarin residues (Abdallah et al., 2023 ). Novel coumarin-benzothiazole compounds, discovered by us, are now being utilized as laser dyes for medical purposes (Elgemeie, 1989 ). Additionally, we have synthesized novel benzothiazole-based heterocycles that had noteworthy fluorescence properties and biological significance (Azzam et al., 2022 ). In this paper, we provide a novel approach to the synthesis of a condensed benzothiazole-pyridine derivative by reacting ethyl 2-benzothiazolyl acetate 1 with 2-(benzo[d]thiazole-2-yl)-3-(dimethylamino)prop-2-enoate 2 in refluxing KOH/dioxane for two hours; the product, ethyl 2-(1,3-benzothiazol-2-yl)-1-oxo-1H-pyrido[2,1-b][1,3]benzothiazole-4-carboxylate 5, was produced in acceptable yield (Fig. 1). To establish the molecular structure of 5 unambiguously, its crystal structure was determined and is presented here.

Figure 1
The synthesis of compound 5.

2. Structural commentary

The molecular structure of compound 5 is shown in Fig. 2; selected bond lengths and angles are collated in Table 1. Both the bicyclic and tricyclic ring systems contain a five-membered thiazole ring, but these show some significant differences in bond lengths and angles, some associated with the additional annelated ring in the tricyclic system. Thus the largest difference in bond lengths is for the bonds C4A—N9B = 1.3750 (11) Å, cf. C2′—N3′ = 1.3106 (11) Å, the former bond being annelated but the latter non-annelated and thus formally closer to a double bond. Similarly, the angle S5—C4A—N9B = 112.92 (8)° is appreciably narrower than S1′—C2′—N3′ = 115.89 (6)° (but in fact all related pairs of angles differ by some 1.5–3.5°). The bond length C2—C2′ between the ring systems is 1.4619 (11) Å. The exocyclic S—C—C bond angles of the ring systems are all appreciably greater than 120°, the largest being S1′—C7A′—C7′ = 128.87 (7)°, but this is normal for such systems. The angle S1′—C2′—C2, not constrained by being within a ring system, is much smaller at 122.73 (6)°.

Table 1
Selected geometric parameters (Å, °)

C1—O1	1.2292 (10)	C9A—N9B	1.4168 (11)
C2—C2′	1.4619 (11)	S1′—C7A′	1.7287 (9)
C4A—N9B	1.3750 (11)	S1′—C2′	1.7553 (8)
C4A—S5	1.7250 (8)	C2′—N3′	1.3106 (11)
S5—C5A	1.7403 (10)	N3′—C3A′	1.3831 (12)
C5A—C9A	1.3994 (12)	C3A′—C7A′	1.4067 (13)

N9B—C4A—S5	112.92 (6)	C7A′—S1′—C2′	88.77 (4)
C4—C4A—S5	126.17 (6)	N3′—C2′—S1′	115.89 (6)
C4A—S5—C5A	90.34 (4)	C2—C2′—S1′	122.73 (6)
C6—C5A—S5	125.86 (7)	C2′—N3′—C3A′	110.29 (7)
C9A—C5A—S5	112.64 (6)	N3′—C3A′—C7A′	115.21 (7)
C5A—C9A—N9B	110.92 (7)	C7′—C7A′—S1′	128.87 (7)
C4A—N9B—C9A	113.15 (7)	C3A′—C7A′—S1′	109.83 (6)

Figure 2
The molecular structure of compound 5 in the crystal; ellipsoids correspond to 50% probability levels.

Both ring systems are planar to a good approximation (r.m.s. deviations 0.008 Å for the bicyclic and 0.024 Å for the tricyclic system), and, despite the apparent possibility of free rotation about the formally single bond C2—C2′, the interplanar angle between the ring systems is only 3.12 (3)°, meaning that much of the molecule is planar (Fig. 3). Associated with this are the short contacts S1′⋯O1 2.7241 (7), S5⋯O2 2.7146 (9) and H9⋯O1 2.24 Å. We have noted such short intramolecular S⋯O contacts before in related heterocyclic systems, and in one recent paper presented a brief database review of such contacts (Elgemeie et al., 2025 ).

Figure 3
The molecule of 5 viewed ‘edge-on'. Hydrogen atoms are omitted; radii are arbitrary.

3. Supramolecular features

The molecular packing involves just one hydrogen bond, the ‘weak' contact H7⋯O1 via a 2₁ screw axis (Fig. 4, Table 2). Apart from this, there are several short contacts between ring centres of gravity (Cg) of pairs of molecules, necessarily with parallel ring systems, related by the inversion operator 1 − x, 1 − y, 1 − z (Fig. 5). Denoting the rings from left to right in Fig. 2 as A–E, the contacts are: CgA⋯CgC = 3.5077 (5), CgA⋯CgD = 3.6392 (5) and CgB⋯CgC = 3.6371 (5) Å, with slippages of 0.98, 1.37 and 1.33 Å, respectively. The other two short contacts are the probable C—H⋯π interaction C6—H6⋯CgA = 2.49 Å (via the glide plane operator − $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z and with angle 151° at H6) and O2⋯CgD = 3.3684 (10) Å (1 − x, 2 − y, 1 − z, with C10—O2⋯CgD 89.4°). Attempts to combine more than one set of these contacts in one figure lead to complex three-dimensional diagrams that are difficult to interpret.

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C9—H9⋯O1	0.95	2.24	2.8116 (11)	118
C7—H7⋯O1ⁱ	0.95	2.42	3.3470 (12)	164
Symmetry code: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 4
Two zigzag chains of compound 5 parallel to the b axis, centred on the region y ≃ 0.75. The view direction is approximately perpendicular to the bc plane. The molecules are linked via a 2₁ screw axis by a ‘weak' hydrogen bond (Table 2

). Hydrogen atoms not involved in hydrogen bonding are omitted.

Figure 5
Two neighbouring molecules of compound 5 related by the inversion operator 1 − x, 1 − y, 1 − z. Short contacts between ring centroids are indicated by thick dashed lines (see text). Hydrogen atoms are omitted.

4. Database survey

The search of version 6.00 of the Cambridge Database (Groom et al., 2016 ) employed the routine ConQuest (Bruno et al., 2002 ; version 2025.1.1). Structures with the same tricyclic ring system as compound 5 were sought (any bond orders, coordination numbers 2 for the sulfur atom and 3 for all other atoms). Seven hits were found, two of which were closely related to 5, namely 2-(1,3-benzothiazol-2-yl)-4-(furan-2-carbonyl)-1-oxo-1H-pyrido[2,1-b][1,3]benzothiazol-3-yl furan-2-carboxylate toluene solvate and 2-(1,3-benzothiazol-2-yl)-4-benzoyl-1-oxo-1H-pyrido[2,1-b][1,3]benzothiazol-3-yl benzoate (refcodes NOTKAM and NOTKEQ; Lystsova et al., 2023 ). Both of these (room temperature) structures have oxo functions and 1,3-benzothiazol-2-yl substituents at the same atoms as 5; they also have closely similar bond lengths between the ring systems [1.463 (3) and 1.464 (5), 1.465 (5) Å] and similar intramolecular S⋯O contacts that again lead to approximate coplanarity of the ring systems. The structure of the ionic compound 1-amino-2-(1,3-benzothiazol-2-yl)-3H-pyrido[2,1-b][1,3]benzothiazol-3-iminium chloride methanol solvate (REZVUQ; Chen et al., 2018 ) also contains analogously linked bi- and tricyclic systems, but no C=O function corresponding to that of 5.

5. Synthesis and crystallization

Ethyl 2-benzothiazolyl acetate 1 (10 mmol) was added to a stirred solution of 2-(benzo[d]thiazole-2-yl)-3-(dimethylamino)prop-2-enoate 2 (10 mmol) in dry dioxane (30 ml) containing potassium hydroxide (10 mmol) and the reaction mixture was refluxed for 2 h. The precipitate of 5 thus formed was filtered off from the hot solution and recrystallized from ethanol.

Yellow solid (yield 50%), m.p. > 603 K; IR (KBr, cm⁻¹): υ 3061 (Ar—CH), 1665, 1639 (2C=O); ¹H NMR (400 MHz, DMSO-d₆): δ = 1.42 (t, J = 8.0 Hz, 3H, CH₃-CH₂), 4.14 (q, J = 7.2 Hz, 2H, CH₃-CH₂), 7.45 (t, J = 7.2 Hz, 1H, benzothiazole-H), 7.56 (t, J = 7.2 Hz, 1H, benzothiazole-H), 7.70 (m, 2H, benzothiazole-H), 8.08 (d, J = 10.0 Hz, 1H, benzothiazole-H), 8.15 (d, J = 10.8 Hz, 1H, benzothiazole-H), 8.26 (d, J = 7.0 Hz, 1H, benzothiazole-H), 9.28 (s, 1H, CH-pyridine), 9.34 (d, J = 9.2 Hz, 1H, benzothiazole-H); Analysis: calculated for C₂₁H₁₄N₂O₃S₂ (406.48): C 62.05, H 3.47, N 6.89. Found: C 61.99, H 3.44, N 6.88%.

6. Refinement

Details of data collection and structure refinement are summarized in Table 3. Data were collected at 110 K because the crystals cracked at the standard temperature of 100 K, presumably because of a phase change.

Table 3
Experimental details

Crystal data
Chemical formula	C₂₁H₁₄N₂O₃S₂
M_r	406.46
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	110
a, b, c (Å)	8.7402 (2), 12.0342 (3), 17.2069 (4)
β (°)	100.847 (2)
V (Å³)	1777.51 (7)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.33
Crystal size (mm)	0.17 × 0.13 × 0.04

Data collection
Diffractometer	XtaLAB Synergy
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2024 )
T_min, T_max	0.717, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	138468, 9507, 7763
R_int	0.041
θ values (°)	θ_max = 38.3, θ_min = 2.4
(sin θ/λ)_max (Å⁻¹)	0.873

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.114, 1.04
No. of reflections	9507
No. of parameters	254
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.62, −0.48
Computer programs: CrysAlis PRO (Rigaku OD, 2024), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), XP (Bruker, 1998 ) and publCIF (Westrip, 2010 ).

The tricyclic ring system was assigned the standard IUPAC numbering; the benzothiazole system bonded to it was also numbered in the standard fashion, but with added primes ('). The methyl group was refined as an idealized rigid group with C—H = 0.98 Å, H—C—H = 109.5°, allowed to rotate but not tip (AFIX 137). Other hydrogen atoms were included using a riding model starting from calculated positions (C—H_arom = 0.95, C—H_methylene = 0.98 Å). The U(H) values were fixed at 1.5 × U_eq of the parent carbon atoms for the methyl group and 1.2 × U_eq for the other hydrogen atoms.

There is one significant peak of residual electron density, namely 1.62 e Å⁻³ near S5. We speculate that it may represent a small amount of contamination by a compound containing a different, but unidentified, heterocyclic system. We note that the peak size is only 0.75 e Å⁻³ if the data are cut to the IUCr limit of 0.84 Å resolution; one cosmetic disadvantage of structures determined to higher resolution is that the sizes of anomalous features in the residual density are magnified, because the Fourier syntheses are summed over a much larger number of reflections.

Supporting information

CCDC reference: 2521548

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989026000204/wm5782sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989026000204/wm5782Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989026000204/wm5782Isup3.cml

checkCIF report

Computing details top

Ethyl 2-(1,3-benzothiazol-2-yl)-1-oxo-1H-pyrido[2,1-b][1,3]benzothiazole-4-carboxylate top

Crystal data top

C₂₁H₁₄N₂O₃S₂	F(000) = 840
M_r = 406.46	D_x = 1.519 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 8.7402 (2) Å	Cell parameters from 74718 reflections
b = 12.0342 (3) Å	θ = 2.4–38.4°
c = 17.2069 (4) Å	µ = 0.33 mm⁻¹
β = 100.847 (2)°	T = 110 K
V = 1777.51 (7) Å³	Tablet, yellow
Z = 4	0.17 × 0.13 × 0.04 mm

Data collection top

XtaLAB Synergy diffractometer	9507 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Mo) X-ray Source	7763 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.041
Detector resolution: 10.0000 pixels mm^-1	θ_max = 38.3°, θ_min = 2.4°
ω scans	h = −15→14
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2024)	k = −20→20
T_min = 0.717, T_max = 1.000	l = −29→29
138468 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.114	w = 1/[σ²(F_o²) + (0.0599P)² + 0.650P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.002
9507 reflections	Δρ_max = 1.62 e Å⁻³
254 parameters	Δρ_min = −0.48 e Å⁻³
0 restraints

Special details top

Experimental. Data were collected at 110 K because the crystals cracked at 100K (presumably because of a phase change).

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

	x	y	z	U_iso*/U_eq
C1	0.65788 (10)	0.69830 (7)	0.44909 (5)	0.01536 (12)
O1	0.76314 (9)	0.65176 (6)	0.42328 (4)	0.02042 (12)
C2	0.59709 (9)	0.66342 (7)	0.51720 (5)	0.01495 (12)
C3	0.47917 (10)	0.72150 (7)	0.54192 (5)	0.01638 (13)
H3	0.440918	0.695749	0.586835	0.020*
C4	0.41390 (10)	0.81725 (7)	0.50297 (5)	0.01657 (13)
C4A	0.47129 (10)	0.85341 (7)	0.43754 (5)	0.01602 (13)
S5	0.41018 (3)	0.96920 (2)	0.38107 (2)	0.01898 (5)
C5A	0.54333 (11)	0.94027 (7)	0.32026 (5)	0.01838 (14)
C6	0.56482 (12)	1.00226 (8)	0.25492 (6)	0.02274 (16)
H6	0.507318	1.068571	0.240780	0.027*
C7	0.67208 (14)	0.96498 (9)	0.21098 (6)	0.02596 (18)
H7	0.688512	1.005776	0.165996	0.031*
C8	0.75624 (13)	0.86739 (9)	0.23270 (6)	0.02592 (18)
H8	0.828854	0.842816	0.201681	0.031*
C9	0.73690 (12)	0.80524 (8)	0.29827 (5)	0.02112 (15)
H9	0.794908	0.739144	0.312423	0.025*
C9A	0.62904 (10)	0.84346 (7)	0.34264 (5)	0.01668 (13)
N9B	0.58738 (9)	0.79589 (6)	0.41105 (4)	0.01527 (11)
C10	0.28474 (10)	0.87873 (8)	0.52649 (6)	0.01966 (14)
O2	0.22737 (10)	0.96137 (7)	0.49221 (5)	0.02754 (15)
O3	0.23929 (9)	0.83336 (6)	0.58949 (5)	0.02420 (14)
C11	0.10238 (12)	0.88120 (9)	0.61358 (7)	0.02589 (18)
H11A	0.091902	0.960214	0.597449	0.031*
H11B	0.114066	0.877614	0.671879	0.031*
C12	−0.03956 (13)	0.81867 (11)	0.57590 (8)	0.0330 (2)
H12A	−0.055028	0.826992	0.518296	0.049*
H12B	−0.130465	0.848089	0.594846	0.049*
H12C	−0.026483	0.739813	0.589797	0.049*
S1'	0.79989 (3)	0.47864 (2)	0.52878 (2)	0.01664 (5)
C2'	0.65958 (10)	0.56342 (7)	0.55998 (5)	0.01534 (12)
N3'	0.61155 (9)	0.53095 (6)	0.62404 (5)	0.01790 (12)
C3A'	0.68446 (10)	0.43293 (7)	0.65194 (5)	0.01778 (13)
C4'	0.66015 (12)	0.37627 (9)	0.72000 (6)	0.02291 (16)
H4'	0.589405	0.404375	0.750868	0.027*
C5'	0.74142 (12)	0.27854 (8)	0.74125 (6)	0.02500 (18)
H5'	0.726025	0.239428	0.787114	0.030*
C6'	0.84629 (12)	0.23661 (8)	0.69577 (6)	0.02418 (17)
H6'	0.900282	0.169307	0.711295	0.029*
C7'	0.87240 (12)	0.29179 (8)	0.62857 (6)	0.02156 (16)
H7'	0.943451	0.263331	0.598000	0.026*
C7A'	0.79064 (10)	0.39078 (7)	0.60724 (5)	0.01730 (13)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0185 (3)	0.0135 (3)	0.0143 (3)	0.0008 (2)	0.0034 (2)	0.0003 (2)
O1	0.0255 (3)	0.0185 (3)	0.0195 (3)	0.0057 (2)	0.0101 (2)	0.0022 (2)
C2	0.0164 (3)	0.0142 (3)	0.0145 (3)	0.0006 (2)	0.0037 (2)	0.0006 (2)
C3	0.0168 (3)	0.0163 (3)	0.0164 (3)	0.0004 (2)	0.0041 (2)	−0.0007 (2)
C4	0.0165 (3)	0.0153 (3)	0.0183 (3)	0.0010 (2)	0.0044 (2)	−0.0011 (2)
C4A	0.0167 (3)	0.0137 (3)	0.0175 (3)	0.0004 (2)	0.0027 (2)	−0.0007 (2)
S5	0.01982 (9)	0.01425 (8)	0.02237 (10)	0.00197 (6)	0.00266 (7)	0.00199 (6)
C5A	0.0204 (3)	0.0157 (3)	0.0182 (3)	−0.0009 (3)	0.0013 (3)	0.0020 (2)
C6	0.0265 (4)	0.0202 (4)	0.0202 (4)	−0.0012 (3)	0.0009 (3)	0.0060 (3)
C7	0.0330 (5)	0.0264 (4)	0.0182 (4)	−0.0024 (4)	0.0043 (3)	0.0068 (3)
C8	0.0328 (5)	0.0287 (4)	0.0178 (4)	0.0013 (4)	0.0088 (3)	0.0043 (3)
C9	0.0262 (4)	0.0218 (4)	0.0167 (3)	0.0022 (3)	0.0075 (3)	0.0027 (3)
C9A	0.0196 (3)	0.0158 (3)	0.0143 (3)	−0.0005 (2)	0.0024 (2)	0.0019 (2)
N9B	0.0177 (3)	0.0137 (3)	0.0146 (3)	0.0007 (2)	0.0036 (2)	0.0008 (2)
C10	0.0182 (3)	0.0187 (3)	0.0228 (4)	0.0012 (3)	0.0058 (3)	−0.0027 (3)
O2	0.0267 (3)	0.0243 (3)	0.0333 (4)	0.0094 (3)	0.0098 (3)	0.0033 (3)
O3	0.0225 (3)	0.0251 (3)	0.0283 (3)	0.0042 (2)	0.0130 (3)	0.0003 (3)
C11	0.0224 (4)	0.0283 (4)	0.0296 (5)	0.0026 (3)	0.0117 (3)	−0.0054 (4)
C12	0.0230 (4)	0.0314 (5)	0.0455 (6)	0.0005 (4)	0.0089 (4)	−0.0060 (5)
S1'	0.01858 (9)	0.01580 (8)	0.01603 (9)	0.00217 (6)	0.00447 (6)	0.00049 (6)
C2'	0.0165 (3)	0.0148 (3)	0.0150 (3)	0.0004 (2)	0.0034 (2)	0.0006 (2)
N3'	0.0191 (3)	0.0188 (3)	0.0166 (3)	0.0008 (2)	0.0054 (2)	0.0031 (2)
C3A'	0.0184 (3)	0.0178 (3)	0.0168 (3)	−0.0015 (3)	0.0023 (3)	0.0029 (2)
C4'	0.0245 (4)	0.0246 (4)	0.0196 (4)	−0.0026 (3)	0.0040 (3)	0.0064 (3)
C5'	0.0279 (4)	0.0224 (4)	0.0228 (4)	−0.0044 (3)	0.0000 (3)	0.0077 (3)
C6'	0.0276 (4)	0.0168 (3)	0.0247 (4)	−0.0015 (3)	−0.0038 (3)	0.0039 (3)
C7'	0.0240 (4)	0.0160 (3)	0.0223 (4)	0.0012 (3)	−0.0016 (3)	−0.0004 (3)
C7A'	0.0188 (3)	0.0153 (3)	0.0168 (3)	−0.0006 (2)	0.0008 (3)	0.0007 (2)

Geometric parameters (Å, º) top

C1—O1	1.2292 (10)	S1'—C2'	1.7553 (8)
C1—N9B	1.4267 (11)	C2'—N3'	1.3106 (11)
C1—C2	1.4374 (11)	N3'—C3A'	1.3831 (12)
C2—C3	1.3772 (11)	C3A'—C4'	1.4054 (12)
C2—C2'	1.4619 (11)	C3A'—C7A'	1.4067 (13)
C3—C4	1.3995 (12)	C4'—C5'	1.3869 (14)
C4—C4A	1.3859 (12)	C5'—C6'	1.4061 (16)
C4—C10	1.4688 (12)	C6'—C7'	1.3891 (14)
C4A—N9B	1.3750 (11)	C7'—C7A'	1.4021 (12)
C4A—S5	1.7250 (8)	C3—H3	0.9500
S5—C5A	1.7403 (10)	C6—H6	0.9500
C5A—C6	1.3912 (13)	C7—H7	0.9500
C5A—C9A	1.3994 (12)	C8—H8	0.9500
C6—C7	1.3851 (16)	C9—H9	0.9500
C7—C8	1.3988 (15)	C11—H11A	0.9900
C8—C9	1.3904 (13)	C11—H11B	0.9900
C9—C9A	1.3978 (13)	C12—H12A	0.9800
C9A—N9B	1.4168 (11)	C12—H12B	0.9800
C10—O2	1.2154 (12)	C12—H12C	0.9800
C10—O3	1.3392 (12)	C4'—H4'	0.9500
O3—C11	1.4566 (12)	C5'—H5'	0.9500
C11—C12	1.4909 (16)	C6'—H6'	0.9500
S1'—C7A'	1.7287 (9)	C7'—H7'	0.9500

O1—C1—N9B	119.82 (7)	N3'—C3A'—C7A'	115.21 (7)
O1—C1—C2	125.31 (7)	C4'—C3A'—C7A'	119.96 (8)
N9B—C1—C2	114.86 (7)	C5'—C4'—C3A'	118.74 (9)
C3—C2—C1	121.10 (7)	C4'—C5'—C6'	120.85 (9)
C3—C2—C2'	119.51 (7)	C7'—C6'—C5'	121.21 (9)
C1—C2—C2'	119.38 (7)	C6'—C7'—C7A'	117.94 (9)
C2—C3—C4	122.10 (8)	C7'—C7A'—C3A'	121.30 (8)
C4A—C4—C3	118.05 (7)	C7'—C7A'—S1'	128.87 (7)
C4A—C4—C10	118.69 (8)	C3A'—C7A'—S1'	109.83 (6)
C3—C4—C10	123.22 (8)	C2—C3—H3	119.0
N9B—C4A—C4	120.91 (7)	C4—C3—H3	119.0
N9B—C4A—S5	112.92 (6)	C7—C6—H6	120.8
C4—C4A—S5	126.17 (6)	C5A—C6—H6	120.8
C4A—S5—C5A	90.34 (4)	C6—C7—H7	119.9
C6—C5A—C9A	121.48 (9)	C8—C7—H7	119.9
C6—C5A—S5	125.86 (7)	C9—C8—H8	119.0
C9A—C5A—S5	112.64 (6)	C7—C8—H8	119.0
C7—C6—C5A	118.40 (9)	C8—C9—H9	121.2
C6—C7—C8	120.13 (9)	C9A—C9—H9	121.2
C9—C8—C7	122.03 (10)	O3—C11—H11A	109.7
C8—C9—C9A	117.63 (9)	C12—C11—H11A	109.7
C9—C9A—C5A	120.32 (8)	O3—C11—H11B	109.7
C9—C9A—N9B	128.75 (8)	C12—C11—H11B	109.7
C5A—C9A—N9B	110.92 (7)	H11A—C11—H11B	108.2
C4A—N9B—C9A	113.15 (7)	C11—C12—H12A	109.5
C4A—N9B—C1	122.97 (7)	C11—C12—H12B	109.5
C9A—N9B—C1	123.88 (7)	H12A—C12—H12B	109.5
O2—C10—O3	124.64 (9)	C11—C12—H12C	109.5
O2—C10—C4	123.14 (9)	H12A—C12—H12C	109.5
O3—C10—C4	112.22 (8)	H12B—C12—H12C	109.5
C10—O3—C11	117.00 (8)	C5'—C4'—H4'	120.6
O3—C11—C12	109.74 (9)	C3A'—C4'—H4'	120.6
C7A'—S1'—C2'	88.77 (4)	C4'—C5'—H5'	119.6
N3'—C2'—C2	121.37 (7)	C6'—C5'—H5'	119.6
N3'—C2'—S1'	115.89 (6)	C7'—C6'—H6'	119.4
C2—C2'—S1'	122.73 (6)	C5'—C6'—H6'	119.4
C2'—N3'—C3A'	110.29 (7)	C6'—C7'—H7'	121.0
N3'—C3A'—C4'	124.83 (9)	C7A'—C7'—H7'	121.0

O1—C1—C2—C3	179.64 (9)	O1—C1—N9B—C4A	−178.70 (8)
N9B—C1—C2—C3	0.31 (12)	C2—C1—N9B—C4A	0.66 (11)
O1—C1—C2—C2'	−1.53 (13)	O1—C1—N9B—C9A	1.28 (13)
N9B—C1—C2—C2'	179.14 (7)	C2—C1—N9B—C9A	−179.35 (7)
C1—C2—C3—C4	−0.66 (13)	C4A—C4—C10—O2	−1.47 (14)
C2'—C2—C3—C4	−179.49 (8)	C3—C4—C10—O2	−179.40 (9)
C2—C3—C4—C4A	0.03 (13)	C4A—C4—C10—O3	178.76 (8)
C2—C3—C4—C10	177.97 (8)	C3—C4—C10—O3	0.83 (13)
C3—C4—C4A—N9B	0.94 (12)	O2—C10—O3—C11	5.83 (15)
C10—C4—C4A—N9B	−177.10 (8)	C4—C10—O3—C11	−174.39 (8)
C3—C4—C4A—S5	−179.45 (7)	C10—O3—C11—C12	93.40 (12)
C10—C4—C4A—S5	2.51 (12)	C3—C2—C2'—N3'	−3.68 (13)
N9B—C4A—S5—C5A	−0.03 (7)	C1—C2—C2'—N3'	177.47 (8)
C4—C4A—S5—C5A	−179.66 (8)	C3—C2—C2'—S1'	175.35 (6)
C4A—S5—C5A—C6	179.73 (9)	C1—C2—C2'—S1'	−3.50 (11)
C4A—S5—C5A—C9A	1.02 (7)	C7A'—S1'—C2'—N3'	1.15 (7)
C9A—C5A—C6—C7	1.11 (14)	C7A'—S1'—C2'—C2	−177.93 (7)
S5—C5A—C6—C7	−177.50 (8)	C2—C2'—N3'—C3A'	178.20 (8)
C5A—C6—C7—C8	−0.21 (16)	S1'—C2'—N3'—C3A'	−0.89 (10)
C6—C7—C8—C9	−0.38 (17)	C2'—N3'—C3A'—C4'	179.46 (9)
C7—C8—C9—C9A	0.09 (16)	C2'—N3'—C3A'—C7A'	0.04 (11)
C8—C9—C9A—C5A	0.79 (14)	N3'—C3A'—C4'—C5'	−179.96 (9)
C8—C9—C9A—N9B	179.69 (9)	C7A'—C3A'—C4'—C5'	−0.57 (14)
C6—C5A—C9A—C9	−1.42 (14)	C3A'—C4'—C5'—C6'	0.02 (15)
S5—C5A—C9A—C9	177.36 (7)	C4'—C5'—C6'—C7'	0.33 (15)
C6—C5A—C9A—N9B	179.50 (8)	C5'—C6'—C7'—C7A'	−0.10 (14)
S5—C5A—C9A—N9B	−1.72 (9)	C6'—C7'—C7A'—C3A'	−0.46 (13)
C4—C4A—N9B—C9A	178.69 (8)	C6'—C7'—C7A'—S1'	178.88 (7)
S5—C4A—N9B—C9A	−0.96 (9)	N3'—C3A'—C7A'—C7'	−179.75 (8)
C4—C4A—N9B—C1	−1.32 (12)	C4'—C3A'—C7A'—C7'	0.80 (13)
S5—C4A—N9B—C1	179.02 (6)	N3'—C3A'—C7A'—S1'	0.80 (10)
C9—C9A—N9B—C4A	−177.26 (9)	C4'—C3A'—C7A'—S1'	−178.65 (7)
C5A—C9A—N9B—C4A	1.71 (10)	C2'—S1'—C7A'—C7'	179.58 (9)
C9—C9A—N9B—C1	2.75 (14)	C2'—S1'—C7A'—C3A'	−1.02 (7)
C5A—C9A—N9B—C1	−178.28 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9···O1	0.95	2.24	2.8116 (11)	118
C7—H7···O1ⁱ	0.95	2.42	3.3470 (12)	164

Symmetry code: (i) −x+3/2, y+1/2, −z+1/2.

Acknowledgements

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

References

Abdallah, A. E. M., Abdel-Latif, S. A. & Elgemeie, G. H. (2023). ACS Omega 8, 19587–19602. CrossRef PubMed Google Scholar
Al-Tel, T. H., Al-Qawasmeh, R. A. & Zaarour, R. (2011). Eur. J. Med. Chem. 46, 1874–1881. PubMed Google Scholar
Azzam, R. A., Elboshi, H. A. & Elgemeie, G. H. (2022). Antibiotics 11, 1799. CrossRef PubMed Google Scholar
Azzam, R. A., Elgemeie, G. H. & Osman, R. R. (2020). J. Mol. Struct. 1201, 127194. Web of Science CSD CrossRef Google Scholar
Bruker (1998). XP. Bruker Analytical X–Ray Instruments, Madison, Wisconsin, USA. Google Scholar
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. Web of Science CrossRef CAS IUCr Journals Google Scholar
Catalano, A., Rosato, A., Salvagno, L., Iacopetta, D., Ceramella, J., Fracchiolla, G., Sinicropi, M. S. & Franchini, C. (2021). Antibiotics 10, 803. CrossRef PubMed Google Scholar
Chen, Y., Zhang, W., Zhao, Z., Cai, Y., Gong, J., Kwok, R. T. K., Lam, J. W. Y., Sung, H. H. Y., Williams, I. D. & Tang, B. D. (2018). Angew. Chem. Int. Ed. 57, 5011–5015. CrossRef Google Scholar
Desai, N. C., Rajpara, K. M. & Joshi, V. V. (2013). Bioorg. Med. Chem. Lett. 23, 2714–2717. CrossRef PubMed Google Scholar
Elgemeie, G. H. (1989). Chem. Ind. 19, 653–654. Google Scholar
Elgemeie, G. H., Azzam, R. A., Zaghary, W. A., Khedr, M. A. & Elsherif, G. E. (2022). Curr. Pharm. Des. 28, 3374–3403. Web of Science CrossRef CAS PubMed Google Scholar
Elgemeie, G. H., Metwally, N. H., Abd Al-latif, E. S. M. & Jones, P. G. (2025). Acta Cryst. E81, 827–831. CSD CrossRef IUCr Journals Google Scholar
Gill, R. K., Rawal, R. K. & Bariwal, J. (2015). Arch. Pharm. 348, 155–178. Web of Science CrossRef CAS Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CrossRef IUCr Journals Google Scholar
Kamal, A., Syed, M. A. H. & Mohammed, S. M. (2015). Expert Opin. Ther. Pat. 25, 335–349. CrossRef PubMed Google Scholar
Keri, R. S., Patil, M. R., Patil, S. A. & Budagumpi, S. (2015). Eur. J. Med. Chem. 89, 207–251. Web of Science CrossRef CAS PubMed Google Scholar
Li, Q., Mitscher, L. A. & Shen, L. L. (2000). Med. Res. Rev. 20, 231–293. Web of Science CrossRef PubMed CAS Google Scholar
Lystsova, E. A., Novikov, A. S., Dmitriev, M. V., Maslivets, A. N. & Khramtsova, E. E. (2023). Molecules 28, 5495. CSD CrossRef PubMed Google Scholar
Rigaku OD (2024). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England. Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar

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