

research communications
H-imidazole-κN3)[N-(2-oxidobenzylidene)threonato-κ3O,N,O′]zinc(II)
and Hirshfeld surface analysis of aqua(1aDepartment of Chemistry, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
*Correspondence e-mail: akitsu2@rs.tus.ac.jp
The title complex, [Zn(C11H11NO4)(C3H4N2)(H2O)], which includes a tridentate ligand, was synthesized from L-threonine and salicylaldehyde. One water molecule and one imidazole molecule additionally coordinate the zinc(II) center in a distorted trigonal–bipyramidal geometry. The features N—H⋯O and O—H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H/H⋯H (50.7%) and O⋯H/H⋯O (25.0%) contacts.
Keywords: Schiff base ligand; zinc(II) complex; amino acid; Hirshfeld surface analysis; crystal structure.
CCDC reference: 2431599
1. Chemical context
Amino acid et al., 2020; Hirotsu et al., 2022
; Gozdas et al., 2024
; Bowman et al., 2021
). According to a review on the synthesis of amino acid Schiff base–metal complexes (Akitsu et al., 2022
), in general, and their metal complexes are versatile compounds and are widely used in many research and industrial applications. For example, supramolecular encapsulation of nanocrystalline in β-cyclodextrin (Mahato et al., 2022
), photoreaction with titanium dioxide (Takeshita & Akitsu, 2015
), photocatalytic reduction of hexavalent chromium (Nakagame et al., 2019
; Miyagawa et al., 2020
), Schiff base ligand–SPCE (screen-printed carbon electrode) sensors (Bressi et al., 2022
), and flexible ruthenium(II) Schiff base complexes, which have been shown to play a key role in drug activity upon photoirradiation (Gillard et al., 2020
).
Furthermore, Schiff base complexes are considered an important class of organic compounds with a wide range of biological properties, including free-radical-scavenging activity, antibacterial activity, and antitumor activity (Kumar, 2022). In our laboratory, we synthesized novel mono-chlorinated Schiff base copper(II) complexes and tested their antibacterial activity against Gram-positive and Gram-negative bacteria. The most active compounds were then tested for antioxidant activity, and it was found that E. coli absorbed these compounds with very high affinity (Otani et al., 2022
). We are also conducting research using microfluidic devices to efficiently synthesize amino acid Schiff base copper(II) complexes (Kobayashi et al., 2023
), and synthesis of amino acid Schiff base copper(II) complexes containing azobenzene moiety (Kaneda et al., 2024
). Our goal is to evaluate the SOD activity of artificial metalloproteins made by conjugating these Schiff base copper(II) complexes with proteins such as lysozyme (Furuya et al., 2023
; Nakane et al., 2024
).
Therefore, we have been studying the bioactivity of Schiff base complexes derived from amino acids and decided to synthesize a zinc complex of this ligand to compare its bioactivity with that of the copper complex. In this report, we describe the
and intermolecular interactions of the zinc(II) complex, coordinated with imidazole as a model for histidine residues in proteins.2. Structural commentary
The molecular structure of the title compound consists of one imidazole molecule, one water molecule and a tridentate ligand, which is synthesized from L-threonine and salicylaldehyde, coordinating to a zinc(II) center in distorted trigonal–bipyramidal geometry (Fig. 1). The two largest coordination angles O1—Zn01—O2 and N1—Zn01—O5 are 166.60 (11), 130.65 (13)°, and the τ value derived from them, which is five-coordinated geometry index, is 0.599 (Addison et al., 1984
). The C7—N1 distance is 1.276 (5) Å, which is close to a typical C=N double-bond length for an imine (Katsuumi et al., 2020
). The Zn01—O1, Zn01—O2 and Zn01—O5 coordination lengths are 2.061 (2), 2.117 (3) and 1.996 (3) Å, respectively, close to a typical Zn—O bond length (Noor et al., 2021
). The Zn01—N1 and Zn1—N2 bonds of 2.038 (3) and 2.015 (3) Å corresponds to a typical Zn—N bond length (Noor et al., 2021
). These five atoms coordinating to Zn1 have similar bond distances.
![]() | Figure 1 The molecular structure of the title compound with ellipsoids drawn at the 50% probability level. |
3. Supramolecular features
Four intermolecular hydrogen bonds are observed in the crystal (Fig. 2); two hydrogen bonds (O5—H16A⋯O1 and O5H—H16B⋯O3) lead to the formation of a chain structure along the a-axis direction. One hydrogen bond (O4—H15⋯O2) is formed along the c-axis direction (Table 1
). In addition, an intermolecular N3—H17⋯O1 interaction is found (symmetry codes given in Table 1
).
|
![]() | Figure 2 A view of the O—H⋯O and N—H⋯O hydrogen bonds, shown as dashed lines. [Symmetry codes: (i) −x + |
A Hirshfeld surface analysis (McKinnon et al., 2007; Spackman & Jayatilaka, 2009
) was performed to further investigate the intermolecular interactions and contacts. The intermolecular O—H⋯O hydrogen bonds are indicated by bright red spots appearing near O 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 fingerprint plots (Fig. 3
).
![]() | Figure 3 Hirshfeld surfaces mapped over dnorm and the two-dimensional fingerprint plots. |
The contributions to the packing from H⋯H, C⋯C, C⋯H/H⋯C, N⋯H/H⋯N, and H⋯O/O⋯H contacts are 50.7, 3.3, 14.9, 4.3 and 25.0%, respectively. The structure is characterized by high proportion of H⋯H interactions, where H⋯H are van der Waals interactions. The high value of C⋯H/H⋯C is thought to arise from C—H⋯π interactions due to the presence of aromatic rings in the compound. The low value of 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 5.43, update of November 2021; Groom et al., 2016) for similar structures returned four relevant entries: aqua-[N-{[2-oxyphenyl]methylidene}threoninato]-(methanol)copper(II) (YUYFUW; Katsuumi et al., 2020
), oxonium bis{2-[(tetrahydrofuran-2-ylmethyl)carbonoimidoyl]phenolato}zinc(II) perchlorate (KOVRAQ; Mandal et al., 2014
), (3-(4-hydroxyphenyl)-2-{[(2-oxidophenyl)methylidene]amino}propanoato)(1H-imidazole)copper(II) (GIQWUC; Suzuki et al., 2023
), mono/bis(aqua-κO)[N-(2-oxidobenzylidene)valinato-κ3O,N,O′]copper(II) (VEXZIL; Akiyama et al., 2023
).
5. Synthesis and crystallization
L-threonine (11.912 mg, 0.10 mmol) was reacted with salicylaldehyde (12.212 mg, 0.10 mmol) in methanol (5 mL) and water (2 mL), and the resulting mixture was stirred at 313 K for 1 h to afford a yellow solution. To this solution, zinc(II) acetate dihydrate (21.951 mg, 0.100 mmol) was added and it was stirred at 313 K for 1 h. Then imidazole (6.808 mg, 0.10 mmol) was added, yielding a pale-yellow solution. For crystallization, the solution was placed in air at 300 K for several days, and the title complex was obtained as pale yellow columnar-shaped single crystals suitable for single-crystal X-ray diffraction structure analysis. All reagents are commercially available, but L-threonine moiety may partially racemize during synthesis. IR (ATR): 1070 cm−1(w), 1284 cm−1(m), 1376 cm−1(m), 1473 cm−1(m), 1475 cm−1(m), 1548 cm−1(w, C=C double bond), 1622 cm−1(s, C=O double bond), 1634 cm−1(s, C=N double bond), 3251 cm−1(br, O—H). UV-vis (H2O): 270 nm (ɛ = 38000 L mol−1 cm−1, π–π*); 359 nm (ɛ = 18000 L mol−1 cm−1, n–π*).
6. Refinement
Crystal data, data collection and structure . All C-bound H atoms were placed in geometrically calculated positions (C—H = 0.94–1.00 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 N-bound H atom H17 was constrained using a riding model with Uiso(H) = 1.2Ueq(N), and the O-bound H atoms H15, H16A, H16B were located based on a difference-Fourier map and refined freely.
|
Supporting information
CCDC reference: 2431599
https://doi.org/10.1107/S2056989025002385/ox2014sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989025002385/ox2014Isup2.hkl
[Zn(C11H11NO4)(C3H4N2)(H2O)] | F(000) = 768 |
Mr = 372.67 | Dx = 1.570 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
a = 18.3835 (7) Å | Cell parameters from 6515 reflections |
b = 7.7141 (3) Å | θ = 3.0–25.0° |
c = 13.3800 (5) Å | µ = 1.59 mm−1 |
β = 123.787 (1)° | T = 173 K |
V = 1576.99 (11) Å3 | Prism, yellow |
Z = 4 | 0.10 × 0.10 × 0.10 mm |
Bruker-AXS D8 QUEST diffractometer | 2701 reflections with I > 2σ(I) |
Detector resolution: 7.3910 pixels mm-1 | Rint = 0.073 |
profile data from θ/2θ scans | θmax = 25.1°, θmin = 3.0° |
Absorption correction: multi-scan | h = −21→21 |
Tmin = 0.64, Tmax = 0.86 | k = −9→9 |
10846 measured reflections | l = −15→15 |
2752 independent reflections |
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)] = 0.032 | w = 1/[σ2(Fo2) + (0.0364P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.074 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.35 e Å−3 |
2752 reflections | Δρmin = −0.29 e Å−3 |
218 parameters | Absolute structure: Flack x determined using 1180 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
1 restraint | Absolute structure parameter: 0.143 (11) |
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 | ||
Zn01 | 0.65438 (2) | 0.42759 (7) | 0.11898 (3) | 0.01670 (17) | |
O1 | 0.59603 (16) | 0.2984 (3) | 0.1916 (2) | 0.0174 (5) | |
O2 | 0.74153 (18) | 0.5370 (4) | 0.0799 (3) | 0.0323 (7) | |
O3 | 0.8834 (2) | 0.5634 (5) | 0.1533 (3) | 0.0391 (8) | |
O4 | 0.7676 (2) | 0.1327 (5) | 0.1191 (3) | 0.0372 (8) | |
O5 | 0.5804 (2) | 0.3045 (4) | −0.0380 (3) | 0.0276 (7) | |
H16A | 0.529 (5) | 0.302 (8) | −0.085 (6) | 0.041000* | |
N1 | 0.7722 (2) | 0.3625 (4) | 0.2698 (3) | 0.0196 (7) | |
N2 | 0.6124 (2) | 0.6638 (4) | 0.1298 (3) | 0.0241 (7) | |
N3 | 0.6028 (3) | 0.9438 (6) | 0.1430 (3) | 0.0420 (10) | |
H17 | 0.611949 | 1.055498 | 0.141612 | 0.050000* | |
H15 | 0.768 (5) | 0.115 (10) | 0.061 (6) | 0.063000* | |
C1 | 0.6293 (2) | 0.2935 (5) | 0.3089 (3) | 0.0187 (7) | |
C2 | 0.5734 (3) | 0.2624 (6) | 0.3481 (4) | 0.0273 (9) | |
H2 | 0.512602 | 0.246220 | 0.290352 | 0.033000* | |
C3 | 0.6056 (3) | 0.2549 (7) | 0.4692 (4) | 0.0365 (11) | |
H3 | 0.566229 | 0.235803 | 0.492934 | 0.044000* | |
C4 | 0.6946 (3) | 0.2747 (7) | 0.5573 (4) | 0.0372 (11) | |
H4 | 0.716190 | 0.269067 | 0.640331 | 0.045000* | |
C5 | 0.7501 (3) | 0.3026 (7) | 0.5208 (4) | 0.0339 (10) | |
H5 | 0.810969 | 0.314747 | 0.580187 | 0.041000* | |
C6 | 0.7204 (3) | 0.3139 (5) | 0.3988 (3) | 0.0221 (8) | |
C7 | 0.7866 (3) | 0.3359 (6) | 0.3735 (3) | 0.0230 (8) | |
H7 | 0.845966 | 0.330118 | 0.439697 | 0.028000* | |
C8 | 0.8438 (2) | 0.3703 (5) | 0.2529 (3) | 0.0225 (8) | |
H8 | 0.899618 | 0.402041 | 0.330026 | 0.027000* | |
C9 | 0.8220 (3) | 0.5031 (6) | 0.1559 (4) | 0.0268 (9) | |
C10 | 0.8523 (3) | 0.1890 (6) | 0.2094 (4) | 0.0297 (9) | |
H10 | 0.887625 | 0.201059 | 0.173851 | 0.036000* | |
C11 | 0.8964 (4) | 0.0585 (8) | 0.3105 (6) | 0.0507 (14) | |
H11A | 0.955393 | 0.099246 | 0.372280 | 0.076000* | |
H11B | 0.900354 | −0.053288 | 0.279021 | 0.076000* | |
H11C | 0.862170 | 0.045004 | 0.345727 | 0.076000* | |
C12 | 0.5546 (3) | 0.6991 (6) | 0.1608 (4) | 0.0295 (9) | |
H12 | 0.523720 | 0.613729 | 0.174295 | 0.035000* | |
C13 | 0.5472 (3) | 0.8718 (6) | 0.1695 (4) | 0.0381 (11) | |
H13 | 0.511549 | 0.930343 | 0.189603 | 0.046000* | |
C14 | 0.6408 (3) | 0.8169 (7) | 0.1196 (4) | 0.0346 (10) | |
H14 | 0.681965 | 0.833681 | 0.098842 | 0.041000* | |
H16B | 0.599 (5) | 0.243 (10) | −0.059 (6) | 0.052000* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Zn01 | 0.0144 (2) | 0.0149 (2) | 0.0197 (2) | −0.00040 (18) | 0.00884 (17) | 0.00248 (17) |
O1 | 0.0165 (12) | 0.0172 (13) | 0.0178 (11) | −0.0024 (11) | 0.0091 (10) | −0.0005 (10) |
O2 | 0.0171 (14) | 0.0431 (19) | 0.0350 (15) | 0.0022 (13) | 0.0133 (12) | 0.0193 (14) |
O3 | 0.0215 (15) | 0.045 (2) | 0.0486 (18) | −0.0046 (14) | 0.0184 (13) | 0.0176 (16) |
O4 | 0.0358 (17) | 0.045 (2) | 0.0399 (17) | −0.0091 (15) | 0.0269 (15) | −0.0134 (16) |
O5 | 0.0164 (14) | 0.0383 (19) | 0.0231 (14) | 0.0040 (14) | 0.0080 (12) | −0.0115 (13) |
N1 | 0.0190 (15) | 0.0173 (14) | 0.0238 (15) | 0.0012 (13) | 0.0127 (13) | 0.0015 (12) |
N2 | 0.0222 (16) | 0.0146 (17) | 0.0257 (16) | −0.0017 (13) | 0.0073 (13) | 0.0010 (13) |
N3 | 0.048 (2) | 0.0124 (18) | 0.0373 (18) | 0.0022 (19) | 0.0066 (16) | −0.0011 (18) |
C1 | 0.0222 (18) | 0.0121 (17) | 0.0214 (17) | 0.0030 (15) | 0.0119 (15) | −0.0014 (14) |
C2 | 0.025 (2) | 0.034 (2) | 0.029 (2) | 0.0011 (18) | 0.0186 (17) | −0.0006 (18) |
C3 | 0.037 (2) | 0.050 (3) | 0.034 (2) | 0.002 (2) | 0.027 (2) | 0.001 (2) |
C4 | 0.038 (2) | 0.057 (3) | 0.0196 (19) | 0.007 (2) | 0.0182 (18) | 0.002 (2) |
C5 | 0.030 (2) | 0.045 (3) | 0.0198 (19) | 0.004 (2) | 0.0099 (17) | 0.0006 (19) |
C6 | 0.0226 (18) | 0.024 (2) | 0.0195 (17) | 0.0026 (16) | 0.0113 (15) | −0.0012 (15) |
C7 | 0.0178 (17) | 0.024 (2) | 0.0192 (18) | 0.0008 (15) | 0.0053 (15) | 0.0020 (15) |
C8 | 0.0116 (16) | 0.027 (2) | 0.0259 (18) | −0.0022 (15) | 0.0085 (15) | 0.0012 (15) |
C9 | 0.022 (2) | 0.026 (2) | 0.034 (2) | −0.0045 (18) | 0.0170 (18) | 0.0028 (18) |
C10 | 0.025 (2) | 0.033 (2) | 0.039 (2) | 0.0010 (18) | 0.0230 (19) | 0.0036 (19) |
C11 | 0.062 (3) | 0.036 (3) | 0.066 (3) | 0.023 (3) | 0.042 (3) | 0.018 (3) |
C12 | 0.024 (2) | 0.021 (2) | 0.033 (2) | 0.0022 (17) | 0.0095 (18) | −0.0052 (17) |
C13 | 0.035 (2) | 0.026 (2) | 0.039 (2) | 0.0076 (18) | 0.0116 (19) | −0.0052 (18) |
C14 | 0.036 (2) | 0.023 (3) | 0.030 (2) | −0.003 (2) | 0.0088 (19) | 0.0024 (17) |
Zn01—O5 | 1.996 (3) | N3—C14 | 1.337 (7) |
Zn01—N2 | 2.015 (3) | N3—C13 | 1.371 (7) |
Zn01—N1 | 2.038 (3) | C1—C2 | 1.410 (6) |
Zn01—O1 | 2.060 (2) | C1—C6 | 1.427 (5) |
Zn01—O2 | 2.117 (3) | C2—C3 | 1.383 (6) |
O1—C1 | 1.331 (4) | C3—C4 | 1.394 (7) |
O2—C9 | 1.272 (5) | C4—C5 | 1.371 (7) |
O3—C9 | 1.238 (5) | C5—C6 | 1.407 (6) |
O4—C10 | 1.408 (6) | C6—C7 | 1.443 (6) |
N1—C7 | 1.276 (5) | C8—C9 | 1.522 (6) |
N1—C8 | 1.456 (5) | C8—C10 | 1.556 (6) |
N2—C14 | 1.327 (6) | C10—C11 | 1.509 (7) |
N2—C12 | 1.366 (6) | C12—C13 | 1.351 (7) |
O5—Zn01—N2 | 116.22 (13) | C2—C1—C6 | 117.4 (3) |
O5—Zn01—N1 | 130.65 (13) | C3—C2—C1 | 121.2 (4) |
N2—Zn01—N1 | 112.96 (13) | C2—C3—C4 | 121.5 (4) |
O5—Zn01—O1 | 92.14 (12) | C5—C4—C3 | 118.1 (4) |
N2—Zn01—O1 | 94.77 (12) | C4—C5—C6 | 122.5 (4) |
N1—Zn01—O1 | 87.64 (11) | C5—C6—C1 | 119.2 (4) |
O5—Zn01—O2 | 95.52 (13) | C5—C6—C7 | 116.4 (4) |
N2—Zn01—O2 | 91.69 (14) | C1—C6—C7 | 124.2 (3) |
N1—Zn01—O2 | 79.03 (12) | N1—C7—C6 | 125.5 (4) |
O1—Zn01—O2 | 166.60 (11) | N1—C8—C9 | 109.2 (3) |
C1—O1—Zn01 | 123.4 (2) | N1—C8—C10 | 108.0 (3) |
C9—O2—Zn01 | 115.1 (3) | C9—C8—C10 | 108.7 (3) |
C7—N1—C8 | 121.1 (3) | O3—C9—O2 | 124.9 (4) |
C7—N1—Zn01 | 125.5 (3) | O3—C9—C8 | 117.8 (4) |
C8—N1—Zn01 | 113.0 (2) | O2—C9—C8 | 117.2 (3) |
C14—N2—C12 | 105.7 (4) | O4—C10—C11 | 110.5 (4) |
C14—N2—Zn01 | 127.5 (3) | O4—C10—C8 | 107.7 (3) |
C12—N2—Zn01 | 126.5 (3) | C11—C10—C8 | 112.3 (4) |
C14—N3—C13 | 108.9 (5) | C13—C12—N2 | 110.8 (5) |
O1—C1—C2 | 119.4 (3) | C12—C13—N3 | 104.6 (5) |
O1—C1—C6 | 123.1 (3) | N2—C14—N3 | 110.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H15···O2i | 0.79 (7) | 1.89 (7) | 2.678 (4) | 170 (8) |
O5—H16A···O1ii | 0.79 (7) | 1.91 (7) | 2.708 (4) | 178 (6) |
O5—H16B···O3i | 0.72 (8) | 2.02 (8) | 2.724 (4) | 165 (7) |
N3—H17···O1iii | 0.88 | 2.06 | 2.830 (6) | 145 |
C14—H14···O2 | 0.95 | 2.61 | 3.077 (6) | 111 |
C13—H13···O3iv | 0.95 | 2.36 | 3.253 (6) | 156 |
C2—H2···O3v | 0.95 | 2.48 | 3.351 (5) | 152 |
Symmetry codes: (i) −x+3/2, y−1/2, −z; (ii) −x+1, y, −z; (iii) x, y+1, z; (iv) x−1/2, y+1/2, z; (v) x−1/2, y−1/2, z. |
Funding information
Funding for this research was provided by: Grant-in-Aid for Scientific Research (B) KAKENHI (24K00912).
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