research communications
H-pyrrol-2-yl)prop-2-en-1-one hemihydrate
and Hirshfeld surface analysis of 3-(3-hydroxyphenyl)-1-(1aSchool of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand, bDepartment of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia, cCentre for Drug Research, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia, and dNatural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
*Correspondence e-mail: sitimunirah@upm.edu.my
High-quality single crystals of the title compound, 2C13H11NO2·H2O, were grown and a structural analysis was performed. The comprises one molecule of 3-(3-hydroxyphenyl)-1-(1H-pyrrol-2-yl)prop-2-en-1-one (3HPPP), which was recently discovered to be a promising anti-MRSA candidate, and a half-molecule of water. The compound crystallizes in the monoclinic P2/c. The features intermolecular pyrrole-N—H⋯O (water), carbonyl/keto-C—O⋯H—O-phenol and phenol-C—O⋯H (water) hydrogen bonds, which help to consolidate the crystal packing. A Hirshfeld surface analysis for the components in the showed that H⋯H (40.9%) and H⋯C/C⋯H (32.4%) contacts make the largest contributions to the intermolecular interactions of 3HPPP. Considering the presence of water, in its vicinity H⋯O/O⋯H and H⋯C/C⋯H are the most significant contacts, contributing 48.7 and 29.8%, respectively.
Keywords: chalcone; pyrrole-derived chalcone; pyrrole; crystal structure; SCXRD.
CCDC reference: 2233979
1. Chemical context
α,β-unsaturated carbonyl system in between two aromatic rings (Zhuang et al., 2017; Attarde et al., 2010). are widely used as precursors for the biosynthesis of compounds in the flavonoid class, and can be chemically synthesized by various reactions such as aldol condensation, and Suzuki and Wittig reactions (Zhuang et al., 2017). To date, have continued to attract great interest from researchers because of their simple chemistry and diverse applications in medicinal and synthetic chemistry (Zhuang et al., 2017), analytical chemistry (Sun et al., 2012), materials chemistry and lighting technology (Anandkumar et al., 2017; Danko et al., 2012).
are 1,3-diphenyl-2-propen-1-ones with anChalcone analogues have been reported with a wide range of biological activities, including anti-inflammatory, antimicrobial, and anticancer properties (Kar Mahapatra et al., 2019; Lin et al., 2002; Nowakowska, 2007). Recently, we discovered a new promising anti-microbial candidate, 3-(3-hydroxyphenyl)-1-(1H-pyrrol-2-yl)prop-2-en-1-one (3HPPP), which showed remarkable inhibitory activity on methicillin-resistant Staphylococcus aureus (MRSA, ATCC 700699) with MIC and MBC values of 0.23 mg ml−1 and 0.47 mg ml−1, respectively (Gunasekharan et al., 2021). However, as yet the of this compound has remained elusive. The molecular structure of its hydrate is analysed and discussed herein.
2. Structural commentary
The molecular structure of the 3HPPP plus the symmetry-completed water molecule are shown in Fig. 1. The consists of a molecule of 3HPPP in a neutral state plus half a water molecule of crystallization. The investigated bioactive compound crystallized in the monoclinic P2/c, with the containing four molecules of 3HPPP together with two molecules of water. Four water molecules reside on four of the cell edges on the crystallographic c-axis and are shared between the unit and adjacent cells. Further analysis of the metrical parameters of the molecule showed no anomalies compared to the available literature data for related compounds. The planarity of 3HPPP is confirmed as both the aromatic pyrrole (N1/C1–C4) and phenyl (C8–C13) rings are aligned in the plane of the aliphatic α,β-unsaturated ketone linker, making dihedral angles of 0.91 (7) and 5.98 (7)°, respectively with the linker.
of3. Supramolecular features
Fig. 2 illustrates the of 3HPPP viewed along the crystallographic b-axis and the supramolecular association within and around it. In the crystal, molecules are linked into dimers via multiple intermolecular hydrogen bonds (Table 1). The dimers are arranged in planes with two distinct orientations and at an angle of roughly 61° to each other, while the water molecules act as hinges. This represents a zigzag pattern when viewed along the the ac diagonal. Furthermore, the 3HPPP dimers are arranged in a stair-like fashion, which ascends/descends roughly in the b-axis direction. Intermolecular hydrogen bonds C13—H13⋯O1i [symmetry code: (i) −x + 1, −y + 1, −z + 1) between two molecules of 3HPPP can be observed connecting these non-covalently. Molecules of 3HPPP are linked into inversion dimer–dimer chains through these weak interactions. Moreover, the lattice water molecules act as donors and acceptors in hydrogen bonds with the phenol and pyrrole moieties of 3HPPP [O3—H3O⋯O2ii and N1—H1N⋯O3; symmetry code: (ii) x − 1, −y + 1, z − ; Table 2]. All hydrogen atoms and all lone pairs of the water molecule are engaged in hydrogen bonding (Fig. 2). These hydrogen bonds connect two of the 3HPPP dimers in different planes comparably strongly and further consolidate the crystal packing.
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4. Database survey
A database survey of the Cambridge Structural Database (WEBCSD version 1.9.32, updated September 2022; Groom et al., 2016) revealed that no structure of a compound with a close similarity to the entire 3HPPP molecule as been reported. However, focusing on the pyrrole ene-one side yielded three [refcodes HIXGAW (Norsten et al., 1999); RICFEP (Camarillo et al., 2007) and RICFEP01 (Jones, 2013)] similar compounds with a 77–88% similarity score relative to the title compound. The title compound differs from those at the substituted ethyl-phenol (C6–C13) side. The overall conformation of the title compound and HIXGAW are very nearly planar and the other two (RICFEP and RICFEP01) are planar. A notable difference relates to the substitution on the keto side. The respective dihedral angles in the studied compound and in HIXGAW are in the range of 5.49–24.65°.
5. Hirshfeld surface analysis
Crystal Explorer 21 (Spackman et al., 2021) was used to calculate the Hirshfeld surfaces to obtain further insight into the intermolecular interactions in the of the title compound. The three-dimensional Hirshfeld surfaces plotted over dnorm ranging from −0.667 to 1.118 a.u. are shown in Fig. 3. For compound 3HPPP (Fig. 3a), the most prominent interactions in the crystal packing are the hydrogen bonds, which are represented by four bright-red spots on the mapped dnorm surface. The bright-red spots around O1 and O2 correspond to the hydrogen bonding between hydroxyl and carbonyl/keto functional groups of two molecules of 3HPPP. The other two bright-red spots are due to hydrogen bonding between the pyrrole-N—H and the water molecule, and between the water molecule and the hydroxyl group of 3HPPP. In addition to these four spots, two faint-red spots appear around O1 and H13, representing the non-classical hydrogen-bond interaction of an aromatic C–H and the carbonyl/keto The intensities of all these red spots indicate the relative strengths of the interactions, as well as the distances of the contacts. The dnorm Hirshfeld surface for the water molecules present in the was also calculated and mapped (Fig. 3b). Four bright-red spots are observed, which are due to the pyrrole-to-water and water-to-hydroxyl hydrogen bonds and are thereby mirrors of the interactions involving water described above.
The overall two-dimensional fingerprint plots of both molecules, water and 3HPPP, and those delineated into H⋯H, H⋯O/O⋯H, H⋯C/C⋯H and H⋯N/N⋯H interactions are shown in Fig. 4, while the percentage contributions are listed in Table 2. The two-dimensional fingerprint plots for compound 3HPPP show that H⋯H and H⋯ C/C⋯ H are the most significant interatomic interactions in the crystal packing, contributing 40.9 and 32.4%, respectively, to the Hirshfeld surface. The H⋯O/O⋯H (19.4%) and other minor contacts (H⋯N/N⋯H = 2.0%) further contribute to the Hirshfeld surfaces. On the other hand, the most prominent interatomic contacts for the water molecule are H⋯O/O⋯H, as expected, with a 48.7% contribution while H⋯H and H⋯C/C⋯H contacts contribute 16.2 and 29.8%, respectively.
6. Synthesis and crystallization
The 3-hydroxypyrrolylated chalcone 3HPPP was synthesized by a Claisen–Schmidt condensation reaction between 2-acetylpyrrole (2 mmol) and 3-hydroxybenzaldehyde (2 mmol) under ethanolic (10 ml) conditions. The resulting mixture was stirred for 5 min followed by the dropwise addition of 3 ml of a 40% aqueous NaOH solution (Fig. 5). The mixture was stirred overnight at room temperature. After the reaction was essentially complete, it was quenched by pouring the resultant solution onto crushed ice and extraction with ethyl acetate (3 × 10 ml). The organic layer was washed with distilled water (3 × 10 ml), filtered, dried over anhydrous MgSO4 and concentrated in vacuo. Finally, the collected crudes were purified by gravity using hexane:ethyl acetate (ratio of 7:3) as solvent system. Multiple spectroscopic analyses confirmed the chemical structure (Mohd Faudzi et al., 2020). The obtained pure 3HPPP was then recrystallized by slow evaporation of an ethanol solution, giving crystals suitable for X-ray diffraction analysis.
7. Refinement
Crystal data, data collection and structure . The hydrogen atoms bound to oxygen or nitrogen were found in difference maps and refined freely. The carbon-bound hydrogen atoms, which are all aromatic, were geometrically placed and refined using a riding model with C—H = 0.95 Å and Uiso(H) = 1.2Ueq(C).
details are summarized in Table 3
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Supporting information
CCDC reference: 2233979
https://doi.org/10.1107/S2056989023001925/yz2023sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023001925/yz2023Isup2.hkl
Data collection: CrysAlis PRO 1.171.41.121a (Rigaku OD, 2021); cell
CrysAlis PRO 1.171.41.121a (Rigaku OD, 2021); data reduction: CrysAlis PRO 1.171.41.121a (Rigaku OD, 2021); program(s) used to solve structure: SHELXT2018/2 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: Olex2 1.3 (Dolomanov et al., 2009); software used to prepare material for publication: publCIF (Westrip, 2010).2C13H11NO2·H2O | F(000) = 468 |
Mr = 444.47 | Dx = 1.369 Mg m−3 |
Monoclinic, P2/c | Cu Kα radiation, λ = 1.54184 Å |
a = 11.9096 (1) Å | Cell parameters from 9119 reflections |
b = 5.5836 (1) Å | θ = 3.8–76.1° |
c = 16.8121 (2) Å | µ = 0.78 mm−1 |
β = 105.356 (1)° | T = 100 K |
V = 1078.07 (3) Å3 | Prism, colourless |
Z = 2 | 0.18 × 0.17 × 0.13 mm |
XtaLAB Synergy, Dualflex, AtlasS2 diffractometer | 2067 reflections with I > 2σ(I) |
Radiation source: micro-focus sealed X-ray tube | Rint = 0.028 |
ω scans | θmax = 75.2°, θmin = 3.9° |
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2021) | h = −14→14 |
Tmin = 0.676, Tmax = 1.000 | k = −6→7 |
13888 measured reflections | l = −18→21 |
2221 independent reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.034 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.095 | w = 1/[σ2(Fo2) + (0.0512P)2 + 0.3933P] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max < 0.001 |
2221 reflections | Δρmax = 0.30 e Å−3 |
163 parameters | Δρmin = −0.19 e Å−3 |
0 restraints | Extinction correction: SHELXL2018/3 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: dual | Extinction coefficient: 0.0039 (5) |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.27900 (7) | 0.42189 (15) | 0.33951 (5) | 0.0268 (2) | |
O2 | 0.81284 (7) | 0.95369 (15) | 0.59533 (5) | 0.0215 (2) | |
O3 | 0.000000 | 0.0526 (2) | 0.250000 | 0.0208 (3) | |
N1 | 0.10566 (8) | 0.45548 (17) | 0.19188 (5) | 0.0186 (2) | |
C1 | 0.17738 (9) | 0.7925 (2) | 0.15408 (6) | 0.0178 (2) | |
H1A | 0.225141 | 0.928386 | 0.153517 | 0.021* | |
C2 | 0.07695 (9) | 0.7278 (2) | 0.09255 (6) | 0.0222 (3) | |
H2A | 0.044033 | 0.812012 | 0.042726 | 0.027* | |
C3 | 0.03512 (9) | 0.5190 (2) | 0.11809 (6) | 0.0222 (3) | |
H3 | −0.032172 | 0.434067 | 0.088590 | 0.027* | |
C4 | 0.19382 (9) | 0.62052 (19) | 0.21594 (6) | 0.0159 (2) | |
C5 | 0.28203 (9) | 0.59293 (19) | 0.29291 (6) | 0.0177 (2) | |
C6 | 0.37555 (9) | 0.7736 (2) | 0.31381 (6) | 0.0179 (2) | |
H6 | 0.376212 | 0.901776 | 0.276763 | 0.021* | |
C7 | 0.45937 (9) | 0.75864 (19) | 0.38443 (6) | 0.0173 (2) | |
H7 | 0.455306 | 0.624717 | 0.418413 | 0.021* | |
C8 | 0.55672 (9) | 0.92326 (19) | 0.41588 (6) | 0.0155 (2) | |
C9 | 0.56928 (9) | 1.14020 (19) | 0.37719 (6) | 0.0174 (2) | |
H9 | 0.513693 | 1.186081 | 0.327786 | 0.021* | |
C10 | 0.66350 (9) | 1.28752 (19) | 0.41156 (6) | 0.0184 (2) | |
H10 | 0.672229 | 1.433834 | 0.384975 | 0.022* | |
C11 | 0.74552 (9) | 1.22472 (19) | 0.48433 (6) | 0.0181 (2) | |
H11 | 0.809769 | 1.326921 | 0.507080 | 0.022* | |
C12 | 0.73238 (9) | 1.0110 (2) | 0.52331 (6) | 0.0166 (2) | |
C13 | 0.63891 (9) | 0.86102 (19) | 0.48899 (6) | 0.0161 (2) | |
H13 | 0.630823 | 0.714363 | 0.515581 | 0.019* | |
H2O | 0.7856 (15) | 0.832 (3) | 0.6202 (11) | 0.050 (5)* | |
H1N | 0.0948 (13) | 0.324 (3) | 0.2186 (9) | 0.034 (4)* | |
H3O | −0.0335 (16) | −0.039 (4) | 0.2091 (11) | 0.062 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0251 (4) | 0.0272 (5) | 0.0228 (4) | −0.0081 (3) | −0.0032 (3) | 0.0089 (3) |
O2 | 0.0178 (4) | 0.0239 (4) | 0.0194 (4) | −0.0044 (3) | −0.0012 (3) | 0.0032 (3) |
O3 | 0.0218 (5) | 0.0193 (6) | 0.0208 (5) | 0.000 | 0.0046 (4) | 0.000 |
N1 | 0.0170 (4) | 0.0199 (5) | 0.0176 (4) | −0.0025 (4) | 0.0025 (3) | 0.0010 (4) |
C1 | 0.0176 (5) | 0.0187 (5) | 0.0171 (5) | 0.0015 (4) | 0.0044 (4) | 0.0011 (4) |
C2 | 0.0214 (5) | 0.0256 (6) | 0.0167 (5) | 0.0024 (4) | 0.0000 (4) | 0.0025 (4) |
C3 | 0.0172 (5) | 0.0277 (6) | 0.0182 (5) | −0.0011 (4) | −0.0015 (4) | −0.0008 (4) |
C4 | 0.0145 (5) | 0.0173 (5) | 0.0163 (5) | −0.0006 (4) | 0.0045 (4) | −0.0010 (4) |
C5 | 0.0173 (5) | 0.0189 (5) | 0.0167 (5) | 0.0002 (4) | 0.0043 (4) | 0.0013 (4) |
C6 | 0.0183 (5) | 0.0185 (5) | 0.0166 (5) | −0.0009 (4) | 0.0040 (4) | 0.0019 (4) |
C7 | 0.0176 (5) | 0.0170 (5) | 0.0176 (5) | 0.0003 (4) | 0.0051 (4) | 0.0014 (4) |
C8 | 0.0153 (5) | 0.0165 (5) | 0.0156 (5) | 0.0011 (4) | 0.0056 (4) | −0.0016 (4) |
C9 | 0.0190 (5) | 0.0180 (5) | 0.0150 (5) | 0.0017 (4) | 0.0043 (4) | 0.0002 (4) |
C10 | 0.0232 (5) | 0.0144 (5) | 0.0191 (5) | −0.0002 (4) | 0.0083 (4) | 0.0007 (4) |
C11 | 0.0176 (5) | 0.0176 (5) | 0.0195 (5) | −0.0038 (4) | 0.0055 (4) | −0.0030 (4) |
C12 | 0.0150 (5) | 0.0196 (5) | 0.0147 (5) | 0.0017 (4) | 0.0034 (4) | −0.0014 (4) |
C13 | 0.0172 (5) | 0.0147 (5) | 0.0170 (5) | 0.0005 (4) | 0.0059 (4) | 0.0008 (4) |
O1—C5 | 1.2417 (13) | C5—C6 | 1.4748 (14) |
O2—C12 | 1.3683 (12) | C6—C7 | 1.3362 (14) |
O2—H2O | 0.901 (19) | C6—H6 | 0.9500 |
O3—H3O | 0.864 (18) | C7—C8 | 1.4642 (14) |
O3—H3Oi | 0.864 (18) | C7—H7 | 0.9500 |
N1—C3 | 1.3484 (13) | C8—C13 | 1.3973 (14) |
N1—C4 | 1.3749 (13) | C8—C9 | 1.4015 (15) |
N1—H1N | 0.888 (17) | C9—C10 | 1.3879 (15) |
C1—C4 | 1.3906 (14) | C9—H9 | 0.9500 |
C1—C2 | 1.4056 (14) | C10—C11 | 1.3932 (14) |
C1—H1A | 0.9500 | C10—H10 | 0.9500 |
C2—C3 | 1.3804 (17) | C11—C12 | 1.3902 (15) |
C2—H2A | 0.9500 | C11—H11 | 0.9500 |
C3—H3 | 0.9500 | C12—C13 | 1.3903 (15) |
C4—C5 | 1.4429 (14) | C13—H13 | 0.9500 |
C12—O2—H2O | 109.4 (11) | C5—C6—H6 | 119.7 |
H3O—O3—H3Oi | 108 (3) | C6—C7—C8 | 127.97 (10) |
C3—N1—C4 | 109.61 (9) | C6—C7—H7 | 116.0 |
C3—N1—H1N | 122.9 (10) | C8—C7—H7 | 116.0 |
C4—N1—H1N | 127.4 (10) | C13—C8—C9 | 119.15 (9) |
C4—C1—C2 | 107.27 (10) | C13—C8—C7 | 117.69 (9) |
C4—C1—H1A | 126.4 | C9—C8—C7 | 123.14 (9) |
C2—C1—H1A | 126.4 | C10—C9—C8 | 119.53 (9) |
C3—C2—C1 | 107.15 (9) | C10—C9—H9 | 120.2 |
C3—C2—H2A | 126.4 | C8—C9—H9 | 120.2 |
C1—C2—H2A | 126.4 | C9—C10—C11 | 121.19 (10) |
N1—C3—C2 | 108.67 (10) | C9—C10—H10 | 119.4 |
N1—C3—H3 | 125.7 | C11—C10—H10 | 119.4 |
C2—C3—H3 | 125.7 | C12—C11—C10 | 119.33 (10) |
N1—C4—C1 | 107.30 (9) | C12—C11—H11 | 120.3 |
N1—C4—C5 | 120.68 (9) | C10—C11—H11 | 120.3 |
C1—C4—C5 | 132.01 (10) | O2—C12—C11 | 118.55 (9) |
O1—C5—C4 | 120.80 (10) | O2—C12—C13 | 121.51 (10) |
O1—C5—C6 | 121.48 (9) | C11—C12—C13 | 119.94 (9) |
C4—C5—C6 | 117.73 (9) | C12—C13—C8 | 120.84 (10) |
C7—C6—C5 | 120.54 (10) | C12—C13—H13 | 119.6 |
C7—C6—H6 | 119.7 | C8—C13—H13 | 119.6 |
C4—C1—C2—C3 | −0.20 (12) | C5—C6—C7—C8 | −178.53 (9) |
C4—N1—C3—C2 | 0.25 (13) | C6—C7—C8—C13 | −175.38 (10) |
C1—C2—C3—N1 | −0.03 (13) | C6—C7—C8—C9 | 6.06 (17) |
C3—N1—C4—C1 | −0.38 (12) | C13—C8—C9—C10 | 0.72 (14) |
C3—N1—C4—C5 | −179.58 (9) | C7—C8—C9—C10 | 179.26 (9) |
C2—C1—C4—N1 | 0.35 (12) | C8—C9—C10—C11 | −0.54 (15) |
C2—C1—C4—C5 | 179.42 (11) | C9—C10—C11—C12 | −0.24 (16) |
N1—C4—C5—O1 | −1.17 (16) | C10—C11—C12—O2 | −179.10 (9) |
C1—C4—C5—O1 | 179.86 (11) | C10—C11—C12—C13 | 0.84 (15) |
N1—C4—C5—C6 | 178.55 (9) | O2—C12—C13—C8 | 179.27 (9) |
C1—C4—C5—C6 | −0.42 (17) | C11—C12—C13—C8 | −0.67 (15) |
O1—C5—C6—C7 | −0.66 (16) | C9—C8—C13—C12 | −0.12 (15) |
C4—C5—C6—C7 | 179.62 (10) | C7—C8—C13—C12 | −178.74 (9) |
Symmetry code: (i) −x, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O1ii | 0.901 (19) | 1.828 (19) | 2.7257 (11) | 174.2 (16) |
N1—H1N···O3 | 0.888 (17) | 2.041 (17) | 2.8722 (13) | 155.4 (14) |
C13—H13···O1ii | 0.95 | 2.51 | 3.2050 (13) | 130 |
O3—H3O···O2iii | 0.864 (18) | 2.320 (18) | 2.9430 (7) | 129.2 (16) |
Symmetry codes: (ii) −x+1, −y+1, −z+1; (iii) x−1, −y+1, z−1/2. |
Contact | Percentage contribution | |
3HPPP | Water | |
H···H | 40.9 | 16.2 |
H···O/O···H | 19.4 | 48.7 |
H···C/C···H | 32.4 | 29.8 |
H···N/N···H | 2.0 | 4.6 |
Funding information
The authors acknowledge the Ministry of Higher Education, Malaysia under the Fundamental Research Grant Scheme (FRGS) (grant No. FRGS/1/2018/STG01/UPM/02/8; vote number of 55401477) and Universiti Putra Malaysia under the Putra grant – Putra Graduates Initiative (IPS)(GP-IPS/2018/9618500) for their financial support.
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