research communications
H-imidazole-κN3)[N-(2-oxidobenzylidene)tyrosinato-κ3O,N,O′]copper(II)
and Hirshfeld surface analysis of (1aDepartment of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
*Correspondence e-mail: [email protected]
The title copper(II) complex, [Cu(C16H13NO4)(C3H4N2)], consists of a tridentate ligand synthesized from L-tyrosine and salicylaldehyde. One imidazole molecule is additionally coordinating to the copper(II) ion. The features N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds. The Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (37.9%), C⋯H (28.2%) and O⋯H/H⋯O (21.2%) contacts.
Keywords: Schiff base complex; copper; amino acid; Hirshfeld analysis; crystal structure.
CCDC reference: 2266335
1. Chemical context
Amino acid et al., 2008; Li et al., 2010; Xue et al., 2009; Katsuumi et al., 2020; Akiyama et al., 2023). On the other hand, copper has various oxidation states, of which the divalent is the most stable. Copper(II) ions readily form complexes and produce abundant coordination chemistry, while amino acid Schiff base–copper(II) complexes have been studied in terms of photoreaction with titanium dioxide (Takeshita et al., 2015), photocatalytic reduction of hexavalent chromium (Nakagame et al., 2019), and antibacterial activity (Otani et al., 2022). The ligand forms a tridentate chelate, but the introduction of a hydroxyl group is effective in increasing solubility in aqueous solvents (Miyagawa et al., 2020). On the other hand, many similar metal complexes with an amino acid having a hydroxyl group, L-tyrosine, have been reported (Pu et al., 2011; Wang et al., 2005; Tan et al., 2008).
which can be easily synthesized by mixing primary and carbonyl components, are organic ligands having an azomethine (C=N) group. They play an important and diverse role in coordination chemistry (QiuIn this report we describe the
and intermolecular interactions of the copper(II) complex coordinated by a tyrosine derivative and imidazole, which serves as a model for histidine residues in proteins and is effective for photoreactions with titanium dioxide. To obtain the product in higher yield than from conventional synthesis, microwave radiation was employed, although conventional synthesis may also give the same product.2. Structural commentary
The molecular structure of the title compound consists of a tridentate ligand occupying the equatorial plane synthesized from L-tyrosine, salicylaldehyde and one imidazole molecule coordinating to the copper(II) center (Fig. 1). The C10—N2 distance is 1.322 (4) Å, close to a typical C=N double-bond length for an imine (Katsuumi et al., 2020). The Cu1—O1 and Cu1—O2 bond lengths are 1.892 (2) and 1.947 (2) Å, respectively, close to a typical Cu—O single-bond length (Katsuumi et al., 2020). The Cu1—N2 and Cu1—N3 bonds of 1.958 (2) and 1.932 (2) Å corresponds to the typical Cu—N single-bond length (Katsuumi et al., 2020). These four atoms coordinating to Cu1 have similar bond distances.
3. Supramolecular features
Four intermolecular O—H⋯O, N—H⋯O, C—H⋯O hydrogen bonds (Table 1 and Fig. 2) are observed in the crystal; one hydrogen bond (O2—H11⋯N1i; symmetry code given in Table 1) forms a chain structure along the b-axis direction. The other hydrogen bonds (O4—H11⋯N1ii, O3—H4A⋯O4iii and O4—H13A⋯C13iv) link the molecules (Fig. 2).
Hirshfeld surface analysis (Spackman & Jayatilaka, 2009; McKinnon et al., 2007) was performed to better understand the intermolecular interactions and contacts. The intermolecular O—H⋯O hydrogen bonds are indicated by bright-red spots appearing near O3 and O4 on the Hirshfeld surfaces mapped over dnorm and by two sharp spikes of almost the same length in the region 1.6 Å < (de + di) < 2.0 Å in the 2D finger plots (Fig. 3). The contributions to the packing from H⋯H, C⋯C, C⋯H/H⋯C, O⋯H/H⋯O and N⋯H/H⋯N contacts are 37.9, 0.4, 28.2, 21.2, and 5.2%, respectively. This structure is characterized by high proportions of H⋯H and C⋯H/H⋯C interactions, where H⋯H are van der Waals interactions. The force effect, C⋯H/H⋯C, is thought to arise from C—H⋯π interactions due to the presence of aromatic rings in the structure. The low value of C⋯C/C⋯C is the result of the low contribution of π–π stacking due to non-overlapping aromatic rings in the structure.
4. Database survey
A search in the Cambridge Structural Database (CSD, Version 5.41, update of March 2022; Groom et al., 2016) for similar structures returned three relevant entries: {2-(4-hydroxyphenyl)-2-[(3-methoxy-2-oxidobenzylidene)amino-κ2O2,N]- propanoato-κO}(1,10-phenanthroline-κ2N,N)copper(II) dihydrate (UNOSIA; Pu et al., 2011), 2,2-bipyridine N-salicylidenetyrosinatocopper(II) (QAJTAX01; Wang et al., 2005) and [(2S)-2-(3,5-dichloro-2-oxidobenzyl-ideneamino)-3-(4-hydroxyphenyl)-propionato-κ3O,N,O](dimethylformamide-κO)copper(II) (YIXKUM; Tan et al., 2008).
5. Synthesis and crystallization
L-tyrosine (181.3 mg, 1.00 mmol) reacted with salicylaldehyde (125.5 mg, 1.03 mmol) in methanol (20 mL), which was treated with microwave irradiation at 358 K for 5 min to yield a yellow ligand solution. Copper(II) acetate monohydrate (200.9 mg, 1.01 mmol) was added to the ligand solution and treated with microwave irradiation at 358 K for 5 min to yield a green solution. To this green solution, imidazole (70.0 mg, 1.02 mmol) was added and treated with microwave irradiation at 358 K for 5 min to yield a dark-green solution.
For recrystallization, the solution was placed in the air at room temperature for several days, and the title complex was obtained (80.9 mg 0.195 mmol, yield 19.5%) as black needle-shaped crystals suitable for single-crystal X-ray diffraction experiments.
Elementary analysis: found: C, 54.48; H, 4.15; N, 10.11%. Calculated: C19H18CuN3O4, C, 55.00; H, 4.13; N, 10.13%. IR (KBr): 1059 cm−1 (m), 1085 cm−1 (w), 1128 cm−1 (w), 1149 cm−1 (m), 1225 cm−1 (w), 1271 cm−1 (m), 1370 cm−1 (w), 1372 cm−1 (w), 1378 cm−1 (m), 1384 cm−1 (w), 1448 cm−1 (s, C=C double bond), 1516 cm−1 (m), 1610 cm−1 (s, C=O double bond), 1625 cm−1(s, C=N double bond), 3159 cm−1 (br), 3214 cm−1 (br), 3297 cm−1 (br, O⋯H). UV–vis (MeOH): 269 nm (ɛ= 13636 L mol−1 cm−1, π–π*); 368 nm (ɛ = 5636 L mol−1 cm−1, n–π*); 618 nm (ɛ = 135 L mol−1 cm−1, d–d).
6. Refinement
Crystal data, data collection and structure . All C-bound H atoms were placed on geometrically calculated positions (C—H = 0.93–0.98 Å) and were constrained using a riding model with Uiso(H) = 1.2Ueq(C) for R2CH and R3CH H atoms and 1.5Ueq(C) for the methyl H atoms. The O-bound H14 atom was located based on a difference-Fourier map and refined freely as an isotropic atom. The N-bound H atoms were located in a difference-Fourier map. Atom H11 of the imidazole ring was refined freely as an isotropic atom.
details are summarized in Table 2
|
Supporting information
CCDC reference: 2266335
https://doi.org/10.1107/S2056989023004735/ex2071sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023004735/ex2071Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989023004735/ex2071sup3.tif
Data collection: APEX2 (Bruker, 2019); cell
SAINT V8.40B (Bruker, 2019); data reduction: SAINT V8.40B (Bruker, 2019); program(s) used to solve structure: SHELXT2018/2 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: ShelXle (Hübschle et al., 2011).[Cu(C16H13NO4)(C3H4N2)] | Dx = 1.579 Mg m−3 |
Mr = 414.89 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 9965 reflections |
a = 5.5005 (2) Å | θ = 2.9–26.4° |
b = 12.1363 (5) Å | µ = 1.28 mm−1 |
c = 26.147 (1) Å | T = 173 K |
V = 1745.46 (12) Å3 | Prism, black |
Z = 4 | 0.50 × 0.30 × 0.20 mm |
F(000) = 852 |
Bruker D8 QUEST diffractometer | 3501 reflections with I > 2σ(I) |
Detector resolution: 7.3910 pixels mm-1 | Rint = 0.047 |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | θmax = 26.4°, θmin = 1.9° |
Tmin = 0.55, Tmax = 0.78 | h = −6→6 |
19853 measured reflections | k = −15→15 |
3571 independent reflections | l = −32→32 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.025 | w = 1/[σ2(Fo2) + (0.0276P)2 + 0.2834P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.062 | (Δ/σ)max = 0.001 |
S = 1.06 | Δρmax = 0.33 e Å−3 |
3571 reflections | Δρmin = −0.21 e Å−3 |
251 parameters | Absolute structure: Refined as an inversion twin |
0 restraints | Absolute structure parameter: 0.017 (12) |
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. Refined as a 2-component inversion twin. |
x | y | z | Uiso*/Ueq | ||
Cu1 | 0.67468 (5) | 0.46981 (2) | 0.56047 (2) | 0.02401 (11) | |
O1 | 0.8939 (3) | 0.35005 (15) | 0.55615 (7) | 0.0334 (4) | |
N1 | 0.9329 (6) | 0.6643 (2) | 0.44552 (9) | 0.0420 (6) | |
H11 | 0.951 (6) | 0.717 (3) | 0.4317 (12) | 0.031 (8)* | |
C1 | 0.5421 (5) | 0.3165 (2) | 0.63934 (9) | 0.0263 (5) | |
H1 | 0.429138 | 0.291841 | 0.664328 | 0.032* | |
O2 | 0.4294 (3) | 0.58526 (14) | 0.56409 (7) | 0.0287 (4) | |
N2 | 0.8346 (4) | 0.54082 (17) | 0.50227 (7) | 0.0288 (4) | |
C2 | 0.7397 (5) | 0.2446 (2) | 0.62716 (9) | 0.0266 (5) | |
N3 | 0.5042 (4) | 0.41212 (17) | 0.61927 (8) | 0.0247 (4) | |
O3 | 0.1144 (4) | 0.64649 (19) | 0.60736 (8) | 0.0437 (5) | |
C3 | 0.7677 (6) | 0.1496 (2) | 0.65788 (10) | 0.0327 (6) | |
H3 | 0.654313 | 0.13602 | 0.684559 | 0.039* | |
O4 | 0.3089 (4) | 0.22066 (16) | 0.85680 (7) | 0.0341 (4) | |
H4A | 0.191 (7) | 0.191 (3) | 0.8583 (9) | 0.051* | |
C4 | 0.9544 (6) | 0.0768 (2) | 0.65012 (11) | 0.0355 (6) | |
H4 | 0.973698 | 0.014587 | 0.671828 | 0.043* | |
C5 | 1.1151 (5) | 0.0952 (2) | 0.60999 (11) | 0.0350 (6) | |
H5 | 1.244308 | 0.044786 | 0.604282 | 0.042* | |
C6 | 1.0904 (5) | 0.1854 (2) | 0.57830 (11) | 0.0337 (6) | |
H6 | 1.200419 | 0.194846 | 0.550635 | 0.04* | |
C7 | 0.9050 (5) | 0.2637 (2) | 0.58620 (9) | 0.0271 (5) | |
C8 | 1.0473 (5) | 0.5091 (2) | 0.47797 (9) | 0.0317 (6) | |
H8 | 1.136848 | 0.443916 | 0.484952 | 0.038* | |
C9 | 1.1065 (5) | 0.5856 (2) | 0.44292 (10) | 0.0373 (6) | |
H9 | 1.243185 | 0.584623 | 0.420719 | 0.045* | |
C10 | 0.7719 (6) | 0.6358 (2) | 0.48134 (10) | 0.0372 (7) | |
H10 | 0.632492 | 0.677619 | 0.490455 | 0.045* | |
C11 | 0.2751 (5) | 0.5780 (2) | 0.60006 (9) | 0.0280 (5) | |
C12 | 0.2973 (5) | 0.4790 (2) | 0.63643 (8) | 0.0262 (5) | |
H12 | 0.145376 | 0.433906 | 0.634481 | 0.031* | |
C13 | 0.3284 (5) | 0.5233 (2) | 0.69154 (8) | 0.0301 (5) | |
H13A | 0.485063 | 0.563191 | 0.693498 | 0.036* | |
H13B | 0.197503 | 0.577417 | 0.698212 | 0.036* | |
C14 | 0.3233 (5) | 0.43791 (19) | 0.73347 (8) | 0.0248 (5) | |
C15 | 0.5135 (5) | 0.4309 (2) | 0.76836 (10) | 0.0290 (6) | |
H15 | 0.651326 | 0.477154 | 0.764186 | 0.035* | |
C16 | 0.5065 (5) | 0.3581 (2) | 0.80895 (10) | 0.0305 (5) | |
H16 | 0.638341 | 0.354933 | 0.832366 | 0.037* | |
C17 | 0.3077 (5) | 0.28973 (19) | 0.81552 (8) | 0.0251 (5) | |
C18 | 0.1184 (5) | 0.2928 (2) | 0.78049 (9) | 0.0276 (5) | |
H18 | −0.016298 | 0.244436 | 0.784071 | 0.033* | |
C19 | 0.1271 (5) | 0.3673 (2) | 0.74005 (9) | 0.0275 (5) | |
H19 | −0.004041 | 0.36992 | 0.716438 | 0.033* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.03258 (17) | 0.02037 (15) | 0.01908 (14) | 0.00257 (12) | 0.00109 (11) | 0.00198 (11) |
O1 | 0.0418 (10) | 0.0297 (9) | 0.0287 (9) | 0.0086 (8) | 0.0108 (8) | 0.0089 (8) |
N1 | 0.0750 (19) | 0.0271 (12) | 0.0239 (11) | −0.0099 (12) | 0.0061 (12) | 0.0052 (10) |
C1 | 0.0339 (14) | 0.0223 (12) | 0.0227 (11) | 0.0004 (11) | 0.0033 (10) | −0.0008 (9) |
O2 | 0.0396 (9) | 0.0256 (8) | 0.0207 (8) | 0.0061 (7) | −0.0004 (8) | 0.0028 (7) |
N2 | 0.0411 (12) | 0.0236 (10) | 0.0217 (9) | −0.0016 (11) | −0.0006 (9) | 0.0013 (8) |
C2 | 0.0361 (14) | 0.0201 (11) | 0.0236 (11) | 0.0016 (10) | −0.0001 (9) | −0.0002 (9) |
N3 | 0.0295 (11) | 0.0218 (10) | 0.0228 (9) | 0.0034 (9) | 0.0013 (8) | 0.0001 (8) |
O3 | 0.0537 (14) | 0.0427 (11) | 0.0346 (10) | 0.0245 (11) | 0.0055 (9) | 0.0059 (9) |
C3 | 0.0434 (16) | 0.0243 (12) | 0.0304 (13) | 0.0023 (12) | 0.0035 (11) | 0.0046 (10) |
O4 | 0.0361 (10) | 0.0364 (10) | 0.0297 (9) | 0.0009 (9) | 0.0002 (9) | 0.0098 (8) |
C4 | 0.0489 (17) | 0.0218 (12) | 0.0359 (14) | 0.0042 (12) | −0.0023 (13) | 0.0059 (11) |
C5 | 0.0378 (15) | 0.0242 (13) | 0.0429 (15) | 0.0090 (12) | −0.0013 (12) | −0.0003 (11) |
C6 | 0.0377 (15) | 0.0296 (14) | 0.0340 (13) | 0.0036 (12) | 0.0068 (11) | 0.0019 (11) |
C7 | 0.0338 (13) | 0.0208 (12) | 0.0268 (12) | 0.0019 (10) | −0.0011 (10) | −0.0007 (10) |
C8 | 0.0332 (14) | 0.0357 (14) | 0.0261 (12) | −0.0030 (11) | −0.0010 (10) | 0.0016 (10) |
C9 | 0.0435 (15) | 0.0423 (15) | 0.0261 (12) | −0.0105 (13) | 0.0031 (12) | −0.0006 (12) |
C10 | 0.0593 (19) | 0.0252 (12) | 0.0272 (12) | 0.0028 (13) | 0.0049 (12) | 0.0005 (10) |
C11 | 0.0359 (14) | 0.0252 (12) | 0.0229 (11) | 0.0050 (11) | −0.0043 (10) | −0.0033 (9) |
C12 | 0.0316 (12) | 0.0231 (11) | 0.0239 (11) | 0.0035 (12) | 0.0029 (9) | −0.0017 (9) |
C13 | 0.0444 (14) | 0.0223 (11) | 0.0236 (11) | 0.0016 (13) | 0.0054 (11) | −0.0008 (10) |
C14 | 0.0296 (13) | 0.0230 (11) | 0.0216 (10) | 0.0025 (10) | 0.0044 (10) | −0.0027 (8) |
C15 | 0.0257 (13) | 0.0326 (13) | 0.0288 (12) | −0.0034 (11) | 0.0045 (10) | −0.0022 (10) |
C16 | 0.0259 (12) | 0.0395 (14) | 0.0261 (12) | 0.0004 (12) | −0.0008 (10) | 0.0011 (11) |
C17 | 0.0297 (12) | 0.0236 (11) | 0.0220 (10) | 0.0035 (11) | 0.0027 (10) | 0.0002 (9) |
C18 | 0.0279 (13) | 0.0255 (12) | 0.0296 (12) | −0.0043 (10) | 0.0016 (10) | 0.0001 (10) |
C19 | 0.0279 (14) | 0.0307 (13) | 0.0239 (11) | −0.0010 (11) | −0.0035 (9) | −0.0007 (10) |
Cu1—O1 | 1.8919 (18) | C3—C4 | 1.371 (4) |
Cu1—N3 | 1.932 (2) | O4—C17 | 1.367 (3) |
Cu1—O2 | 1.9473 (17) | C4—C5 | 1.390 (4) |
Cu1—N2 | 1.958 (2) | C5—C6 | 1.379 (4) |
O1—C7 | 1.311 (3) | C6—C7 | 1.410 (4) |
N1—C10 | 1.335 (4) | C8—C9 | 1.345 (4) |
N1—C9 | 1.352 (4) | C11—C12 | 1.537 (3) |
C1—N3 | 1.290 (3) | C12—C13 | 1.547 (3) |
C1—C2 | 1.430 (4) | C13—C14 | 1.509 (3) |
O2—C11 | 1.270 (3) | C14—C19 | 1.389 (4) |
N2—C10 | 1.322 (4) | C14—C15 | 1.390 (4) |
N2—C8 | 1.386 (4) | C15—C16 | 1.381 (4) |
C2—C3 | 1.413 (3) | C16—C17 | 1.383 (4) |
C2—C7 | 1.424 (4) | C17—C18 | 1.388 (4) |
N3—C12 | 1.468 (3) | C18—C19 | 1.392 (4) |
O3—C11 | 1.228 (3) | ||
O1—Cu1—N3 | 94.49 (8) | O1—C7—C6 | 119.0 (2) |
O1—Cu1—O2 | 175.72 (8) | O1—C7—C2 | 123.5 (2) |
N3—Cu1—O2 | 83.45 (8) | C6—C7—C2 | 117.5 (2) |
O1—Cu1—N2 | 90.31 (8) | C9—C8—N2 | 109.0 (3) |
N3—Cu1—N2 | 174.98 (9) | C8—C9—N1 | 106.4 (3) |
O2—Cu1—N2 | 91.86 (8) | N2—C10—N1 | 110.1 (3) |
C7—O1—Cu1 | 127.44 (16) | O3—C11—O2 | 123.3 (2) |
C10—N1—C9 | 108.7 (2) | O3—C11—C12 | 119.3 (2) |
N3—C1—C2 | 125.5 (2) | O2—C11—C12 | 117.3 (2) |
C11—O2—Cu1 | 116.69 (16) | N3—C12—C11 | 107.73 (19) |
C10—N2—C8 | 105.8 (2) | N3—C12—C13 | 113.0 (2) |
C10—N2—Cu1 | 126.0 (2) | C11—C12—C13 | 108.25 (19) |
C8—N2—Cu1 | 127.85 (18) | C14—C13—C12 | 115.8 (2) |
C3—C2—C7 | 119.4 (2) | C19—C14—C15 | 117.7 (2) |
C3—C2—C1 | 117.0 (2) | C19—C14—C13 | 121.9 (2) |
C7—C2—C1 | 123.6 (2) | C15—C14—C13 | 120.3 (2) |
C1—N3—C12 | 119.8 (2) | C16—C15—C14 | 121.5 (3) |
C1—N3—Cu1 | 124.84 (18) | C15—C16—C17 | 120.1 (3) |
C12—N3—Cu1 | 114.78 (15) | O4—C17—C16 | 117.5 (2) |
C4—C3—C2 | 121.6 (3) | O4—C17—C18 | 122.8 (2) |
C3—C4—C5 | 118.9 (2) | C16—C17—C18 | 119.7 (2) |
C6—C5—C4 | 121.3 (3) | C17—C18—C19 | 119.6 (2) |
C5—C6—C7 | 121.2 (2) | C14—C19—C18 | 121.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H11···O2i | 0.75 (4) | 2.40 (4) | 3.050 (3) | 147 (3) |
N1—H11···O4ii | 0.75 (4) | 2.48 (3) | 3.058 (3) | 136 (3) |
O4—H4A···O3iii | 0.74 | 1.98 | 2.666 (3) | 154 |
C13—H13A···O4iv | 0.99 | 2.58 | 3.364 (3) | 136 |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+3/2, −y+1, z−1/2; (iii) −x, y−1/2, −z+3/2; (iv) −x+1, y+1/2, −z+3/2. |
Funding information
This work was supported by a Grant-in-Aid for Scientific Research (A) KAKENHI (20H00336).
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