research communications
κO)(methanol-κO)[N-(2-oxidobenzylidene)threoninato-κ3O,N,O′]copper(II)
and Hirshfeld surface analysis of (aqua-aDepartment of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan, and bChemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700-064, India
*Correspondence e-mail: akitsu2@rs.tus.ac.jp
In the title complex molecule, [Cu(C11H11NO4)(CH4O)(H2O)], the Cu atom is coordinated in a distorted square-pyramidal geometry by a tridentate ligand synthesized from L-threonine and salicylaldehyde, one methanol molecule and one water molecule. In the crystal, the molecules show intra- and intermolecular O—H⋯O hydrogen bonds. The Hirshfeld surface analysis indicates that the most important contributions to the packing are H⋯H (49.4%) and H⋯O/O⋯H (31.3%) contacts.
Keywords: Schiff base complex; copper; amino acid; Hirshfeld analysis; crystal structure.
CCDC reference: 2025511
1. Chemical context
Amino acid et al., 2008; Li et al., 2010; Xue et al., 2009). On the other hand, copper has various oxidation states, of which the +2 is the most stable. Copper ions readily form complexes and produce abundant coordination chemistry, while Schiff base–copper(II) complexes are known to increase the catalytic efficiency of redox reactions (Cozzi, 2004; Roy & Manassero, 2010).
which can be easily synthesized by condensation of primary with carbonyl components, are organic ligands having an azomethine (>C=N–) group. They play an important and diverse role in coordination chemistry (QiuOne method of reducing highly toxic CrVI compounds to less toxic CrIII compounds is the use of titanium(IV) oxide, a heterogeneous photocatalyst. Although useful for such redox reactions (Kitano et al., 2007; Sun et al., 2006; Tuprakay & Liengcharernsit, 2005), it is only active under UV illumination (Schneider et al., 2014). In our laboratory, a heterogeneous titanium (IV) oxide photocatalyst was combined with a Schiff base–CuII complex and irradiated with visible light. The presence of a π-conjugated ligand system increases the efficiency (Yoshida et al., 2017; Nakagame et al., 2019). It can be said that the Schiff base–copper complex has a photocatalytic effect. In the present study, the title Schiff base–copper complex was synthesized by microwave irradiation in order to shorten the synthesis time and to obtain high purity. The is reported here.
2. Structural commentary
The molecular structure of the title compound consists of a tridentate ligand synthesized from L-threonine and salicylaldehyde, one methanol molecule, and one water molecule coordinating to copper (Fig. 1) in a distorted square-pyramidal coordination geometry. The C8=N1 double-bond distance is 1.286 (5) Å, close to a typical C=N double-bond length for an imine. The Cu1—O2, Cu1—O3 and Cu1—O4 bond lengths are 1.968 (3), 1.937 (3) and 1.910 (3) Å, respectively, which are close to a typical Cu—O single bond length. The Cu1—N1 bond length of 1.922 (3) Å corresponds to the typical Cu—N single-bond length. These four atoms coordinated to Cu1 have similar bond-distance values, and the contribution degree of the electron cloud is almost the same. The Cu1—O6 bond [2.471 (3) Å] has been lengthened by a pseudo Jahn–Teller effect. One intramolecular O—H⋯O hydrogen bond (O5—H5⋯O6; Table 1) is observed between the methoxy function and the amino acid side chain (Fig. 2).
3. Supramolecular features
Three intermolecular O—H⋯O hydrogen bonds (Table 1 and Fig. 2) are observed in the crystal; one hydrogen bond (O6—H4⋯O1iii; symmetry code given in Table 1) forms a chain along the a-axis direction and while the other two hydrogen bonds (O3—H2⋯O4i and O3—H3⋯O2ii; Table 1) form a hydrogen-bonded O2/Cu1/O3/H2/O4i/Cu1i/O3i/H3i ring with an R22(8) motif (Table 1 and Fig. 2). The molecules are stacked in a double-column along the a-axis direction via these three hydrogen bonds.
Hirshfeld surface analysis (Spackman & Jayatilaka, 2009; McKinnon et al., 2007) was performed to better understand the intermolecular interactions and contacts. The O—H⋯O hydrogen bonds are indicated by bright-red spots appearing near O1, O2, O4 and water H atoms 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 and H⋯O/O⋯H contacts are 49.4 and 31.3%, respectively. The calculated atomic charge on the surface is shown in Fig. 4. There are negative charge distributions around the O atoms of hydrogen-bond acceptors; this and other features of the intermolecular interactions are in agreement with the of atoms in the crystal structure.
4. Database survey
A search in the Cambridge Structural Database (CSD, Version 5.41, update of November 2019; Groom et al., 2016) for similar structures returned three relevant entries: (2,2′-bipyridine-N,N′)[N-(2-oxido-1-naphthylidene)threoninato-N,O,O′]copper(II) (refcode BIZGIB; Qiu et al., 2008), diaqua(N-salicylidene-L-threoninato)copper(II) (SLCDCU; Korhonen & Hämäläinen, 1981) and {N-[2-(hydroxy)-3-methoxybenzylidene]threoninato}(1,10-phenanthroline)copper hemihydrate (UQUYUB; Jing et al., 2011). In the crystal of BIZGIB, a two-dimensional network is formed by a combination of intermolecular O—H⋯O and C—H⋯O hydrogen bonds. In the crystal of SLCDCU, two molecules form square planes by two intermolecular hydrogen bonds. In the crystal of UQUYUB, intermolecular O—H⋯O hydrogen bonds form a one-dimensional left-handed helical structure running along [001].
5. Synthesis and crystallization
L-Threonine (0.0234 g, 0.196 mmol) and salicylaldehyde (0.0295 g, 0.242 mmol) were dissolved in methanol (15 ml), which was treated for 5 min with microwave irradiation at 358 K to yield a transparent yellow ligand solution. To this solution, copper(II) acetate dihydrate (0.0421 g, 0.211 mmol) was added and treated for 5 min while being irradiated with microwaves at 358 K. The solution was placed in the air, and the solvent was removed. The title compound (0.0533 g, 0.169 mmol, yield 85.9%) was obtained as a green solid. IR (KBr, cm−1): 1633 (C=N double bond). A part of the obtained solid was dissolved in a small amount of methanol and left in air, and single crystals suitable for X-ray diffraction were obtained after several days.
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 H atoms were located based on a difference-Fourier map. Atoms H4 and H5 of the terminal OH group were constrained using a riding model with O—H = 0.82 Å. H5 was assigned Uiso(H) = 1.2Ueq(O), while the Uiso of H4 (attached to O6 was refined. Atoms H2 and H3 of the water molecule were refined freely.
details are summarized in Table 2Supporting information
CCDC reference: 2025511
https://doi.org/10.1107/S2056989020011706/is5551sup1.cif
contains datablocks General, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020011706/is5551Isup3.hkl
Data collection: APEX3 (Bruker, 2017); cell
APEX3 (Bruker, 2017); data reduction: SAINT (Bruker, 2017); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).[Cu(C11H11NO4)(CH4O)(H2O)] | Dx = 1.611 Mg m−3 |
Mr = 334.80 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 3748 reflections |
a = 7.0614 (4) Å | θ = 3.5–27.2° |
b = 11.0738 (6) Å | µ = 1.61 mm−1 |
c = 17.6541 (10) Å | T = 173 K |
V = 1380.49 (13) Å3 | Prism, green |
Z = 4 | 0.58 × 0.25 × 0.11 mm |
F(000) = 692 |
Bruker APEXIII CCD diffractometer | 3706 independent reflections |
Radiation source: fine-focus sealed tube | 2981 reflections with I > 2σ(I) |
Detector resolution: 7.3910 pixels mm-1 | Rint = 0.078 |
φ and ω scans | θmax = 31.2°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2017) | h = −10→10 |
Tmin = 0.65, Tmax = 0.70 | k = −15→14 |
21250 measured reflections | l = −24→24 |
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
Least-squares matrix: full | w = 1/[σ2(Fo2) + (0.0366P)2 + 0.3357P] where P = (Fo2 + 2Fc2)/3 |
R[F2 > 2σ(F2)] = 0.028 | (Δ/σ)max = 0.001 |
wR(F2) = 0.097 | Δρmax = 1.40 e Å−3 |
S = 1.33 | Δρmin = −2.47 e Å−3 |
3706 reflections | Extinction correction: SHELXL-2016/6 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
195 parameters | Extinction coefficient: 0.0061 (19) |
0 restraints | Absolute structure: Flack x determined using 1080 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Hydrogen site location: mixed | Absolute structure parameter: 0.013 (6) |
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 | ||
Cu1 | 0.61538 (6) | 0.62966 (4) | 0.57142 (2) | 0.01921 (15) | |
N1 | 0.5954 (4) | 0.5019 (3) | 0.64462 (16) | 0.0182 (6) | |
O1 | 0.1357 (4) | 0.6119 (3) | 0.68853 (17) | 0.0321 (7) | |
C1 | 0.2945 (5) | 0.6045 (4) | 0.6605 (2) | 0.0213 (8) | |
O2 | 0.3562 (4) | 0.6679 (3) | 0.60469 (15) | 0.0236 (6) | |
C2 | 0.9302 (5) | 0.4684 (4) | 0.5454 (2) | 0.0226 (8) | |
O3 | 0.5999 (5) | 0.7596 (3) | 0.49822 (19) | 0.0312 (7) | |
H3 | 0.681 (8) | 0.770 (5) | 0.467 (3) | 0.030 (14)* | |
H2 | 0.510 (9) | 0.813 (6) | 0.497 (4) | 0.043 (16)* | |
C3 | 1.1020 (7) | 0.4402 (4) | 0.5083 (2) | 0.0305 (9) | |
H3A | 1.143887 | 0.489273 | 0.468909 | 0.037* | |
O4 | 0.8381 (4) | 0.5673 (3) | 0.52418 (16) | 0.0238 (6) | |
C4 | 1.2084 (6) | 0.3414 (5) | 0.5293 (3) | 0.0357 (11) | |
H4A | 1.321203 | 0.325388 | 0.504001 | 0.043* | |
C5 | 1.1509 (7) | 0.2654 (4) | 0.5873 (3) | 0.0359 (11) | |
H5A | 1.225553 | 0.200181 | 0.601761 | 0.043* | |
O5 | 0.5433 (4) | 0.6871 (3) | 0.76923 (17) | 0.0270 (7) | |
H5 | 0.630851 | 0.694020 | 0.739006 | 0.040* | |
C6 | 0.9816 (7) | 0.2880 (4) | 0.6233 (3) | 0.0295 (10) | |
H6A | 0.940205 | 0.235879 | 0.661122 | 0.035* | |
O6 | 0.8220 (4) | 0.7368 (3) | 0.66221 (19) | 0.0277 (7) | |
H4 | 0.914663 | 0.694152 | 0.670341 | 0.043 (16)* | |
C7 | 0.8696 (6) | 0.3893 (3) | 0.6037 (2) | 0.0225 (8) | |
C8 | 0.7002 (5) | 0.4070 (3) | 0.6473 (2) | 0.0203 (8) | |
H7A | 0.663550 | 0.345351 | 0.679967 | 0.024* | |
C9 | 0.4331 (5) | 0.5140 (4) | 0.6951 (2) | 0.0205 (8) | |
H8A | 0.370634 | 0.435523 | 0.700865 | 0.025* | |
C10 | 0.4885 (6) | 0.5637 (4) | 0.7740 (2) | 0.0224 (8) | |
H10A | 0.373683 | 0.561185 | 0.805101 | 0.027* | |
C11 | 0.6344 (7) | 0.4869 (4) | 0.8141 (2) | 0.0310 (9) | |
H11A | 0.597899 | 0.403518 | 0.811274 | 0.046* | |
H11B | 0.642361 | 0.510986 | 0.866273 | 0.046* | |
H11C | 0.755515 | 0.497466 | 0.790346 | 0.046* | |
C12 | 0.8794 (7) | 0.8592 (4) | 0.6574 (3) | 0.0387 (10) | |
H12A | 0.990908 | 0.865077 | 0.626517 | 0.058* | |
H12B | 0.906569 | 0.889230 | 0.707250 | 0.058* | |
H12C | 0.779612 | 0.906256 | 0.635190 | 0.058* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0168 (2) | 0.0205 (2) | 0.0203 (2) | 0.00153 (18) | 0.00096 (18) | 0.00462 (17) |
N1 | 0.0179 (14) | 0.0197 (16) | 0.0170 (14) | 0.0001 (13) | −0.0011 (13) | 0.0003 (11) |
O1 | 0.0178 (12) | 0.0454 (18) | 0.0330 (15) | 0.0048 (13) | 0.0040 (12) | 0.0103 (13) |
C1 | 0.0173 (16) | 0.025 (2) | 0.0212 (19) | −0.0012 (14) | −0.0032 (15) | 0.0023 (15) |
O2 | 0.0177 (12) | 0.0286 (15) | 0.0246 (14) | 0.0036 (11) | 0.0010 (12) | 0.0074 (11) |
C2 | 0.0219 (18) | 0.025 (2) | 0.0209 (18) | 0.0039 (15) | −0.0024 (15) | −0.0038 (15) |
O3 | 0.0224 (15) | 0.0358 (17) | 0.0354 (16) | 0.0069 (14) | 0.0069 (15) | 0.0201 (13) |
C3 | 0.027 (2) | 0.037 (2) | 0.028 (2) | 0.003 (2) | 0.006 (2) | −0.0015 (16) |
O4 | 0.0224 (13) | 0.0229 (14) | 0.0261 (15) | 0.0020 (11) | 0.0049 (12) | 0.0036 (11) |
C4 | 0.025 (2) | 0.046 (3) | 0.036 (3) | 0.0113 (19) | 0.0019 (18) | −0.011 (2) |
C5 | 0.036 (2) | 0.037 (3) | 0.034 (2) | 0.018 (2) | −0.006 (2) | −0.0042 (19) |
O5 | 0.0306 (16) | 0.0244 (16) | 0.0260 (16) | 0.0016 (12) | 0.0025 (13) | −0.0043 (12) |
C6 | 0.036 (2) | 0.025 (2) | 0.028 (2) | 0.0063 (18) | −0.0023 (19) | 0.0003 (17) |
O6 | 0.0183 (13) | 0.0266 (16) | 0.0384 (17) | 0.0004 (11) | −0.0019 (13) | −0.0006 (13) |
C7 | 0.0235 (17) | 0.022 (2) | 0.0225 (17) | 0.0017 (16) | −0.0028 (16) | −0.0054 (14) |
C8 | 0.0249 (18) | 0.0161 (19) | 0.0198 (18) | −0.0005 (14) | −0.0011 (15) | 0.0001 (14) |
C9 | 0.0175 (16) | 0.022 (2) | 0.0219 (18) | −0.0005 (13) | 0.0023 (15) | 0.0028 (14) |
C10 | 0.0246 (19) | 0.023 (2) | 0.0193 (19) | −0.0008 (15) | 0.0016 (16) | 0.0007 (15) |
C11 | 0.039 (2) | 0.030 (2) | 0.0239 (19) | 0.005 (2) | −0.0079 (19) | 0.0002 (16) |
C12 | 0.042 (2) | 0.031 (2) | 0.043 (2) | −0.005 (2) | 0.004 (2) | −0.0045 (19) |
Cu1—O6 | 2.471 (3) | C5—H5A | 0.9300 |
Cu1—O4 | 1.910 (3) | O5—C10 | 1.423 (5) |
Cu1—N1 | 1.922 (3) | O5—H5 | 0.8200 |
Cu1—O3 | 1.937 (3) | C6—C7 | 1.415 (6) |
Cu1—O2 | 1.968 (3) | C6—H6A | 0.9300 |
N1—C8 | 1.286 (5) | O6—C12 | 1.417 (5) |
N1—C9 | 1.458 (5) | O6—H4 | 0.8200 |
O1—C1 | 1.228 (5) | C7—C8 | 1.436 (6) |
C1—O2 | 1.286 (5) | C8—H7A | 0.9300 |
C1—C9 | 1.528 (5) | C9—C10 | 1.548 (6) |
C2—O4 | 1.327 (5) | C9—H8A | 0.9800 |
C2—C3 | 1.414 (6) | C10—C11 | 1.512 (6) |
C2—C7 | 1.418 (6) | C10—H10A | 0.9800 |
O3—H3 | 0.81 (6) | C11—H11A | 0.9600 |
O3—H2 | 0.87 (7) | C11—H11B | 0.9600 |
C3—C4 | 1.378 (7) | C11—H11C | 0.9600 |
C3—H3A | 0.9300 | C12—H12A | 0.9600 |
C4—C5 | 1.387 (7) | C12—H12B | 0.9600 |
C4—H4A | 0.9300 | C12—H12C | 0.9600 |
C5—C6 | 1.376 (7) | ||
O4—Cu1—N1 | 95.03 (13) | C7—C6—H6A | 119.4 |
O4—Cu1—O3 | 91.37 (14) | C12—O6—H4 | 109.5 |
N1—Cu1—O3 | 172.54 (15) | C6—C7—C2 | 119.9 (4) |
O4—Cu1—O2 | 166.91 (13) | C6—C7—C8 | 116.3 (4) |
N1—Cu1—O2 | 83.64 (13) | C2—C7—C8 | 123.8 (4) |
O3—Cu1—O2 | 89.26 (13) | N1—C8—C7 | 124.8 (4) |
C8—N1—C9 | 120.3 (3) | N1—C8—H7A | 117.6 |
C8—N1—Cu1 | 125.8 (3) | C7—C8—H7A | 117.6 |
C9—N1—Cu1 | 113.6 (2) | N1—C9—C1 | 108.7 (3) |
O1—C1—O2 | 125.6 (4) | N1—C9—C10 | 112.6 (3) |
O1—C1—C9 | 117.9 (4) | C1—C9—C10 | 106.8 (3) |
O2—C1—C9 | 116.6 (3) | N1—C9—H8A | 109.6 |
C1—O2—Cu1 | 115.3 (2) | C1—C9—H8A | 109.6 |
O4—C2—C3 | 118.1 (4) | C10—C9—H8A | 109.6 |
O4—C2—C7 | 124.5 (4) | O5—C10—C11 | 112.5 (3) |
C3—C2—C7 | 117.4 (4) | O5—C10—C9 | 110.9 (3) |
Cu1—O3—H3 | 122 (4) | C11—C10—C9 | 113.2 (3) |
Cu1—O3—H2 | 124 (4) | O5—C10—H10A | 106.6 |
H3—O3—H2 | 114 (5) | C11—C10—H10A | 106.6 |
C4—C3—C2 | 121.2 (4) | C9—C10—H10A | 106.6 |
C4—C3—H3A | 119.4 | C10—C11—H11A | 109.5 |
C2—C3—H3A | 119.4 | C10—C11—H11B | 109.5 |
C2—O4—Cu1 | 125.3 (3) | H11A—C11—H11B | 109.5 |
C3—C4—C5 | 121.4 (4) | C10—C11—H11C | 109.5 |
C3—C4—H4A | 119.3 | H11A—C11—H11C | 109.5 |
C5—C4—H4A | 119.3 | H11B—C11—H11C | 109.5 |
C6—C5—C4 | 119.0 (4) | O6—C12—H12A | 109.5 |
C6—C5—H5A | 120.5 | O6—C12—H12B | 109.5 |
C4—C5—H5A | 120.5 | H12A—C12—H12B | 109.5 |
C10—O5—H5 | 109.5 | O6—C12—H12C | 109.5 |
C5—C6—C7 | 121.1 (4) | H12A—C12—H12C | 109.5 |
C5—C6—H6A | 119.4 | H12B—C12—H12C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H2···O4i | 0.87 (7) | 1.84 (7) | 2.692 (4) | 169 (6) |
O3—H3···O2ii | 0.81 (6) | 1.89 (6) | 2.687 (4) | 167 (6) |
O5—H5···O6 | 0.82 | 1.97 | 2.783 (4) | 171 |
O6—H4···O1iii | 0.82 | 1.84 | 2.653 (4) | 175 |
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) x+1/2, −y+3/2, −z+1; (iii) x+1, y, z. |
Funding information
This work was supported by a Grant-in-Aid for Scientific Research (A) KAKENHI (20H00336).
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