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COMMUNICATIONS
ISSN: 2056-9890
Volume 82| Part 6| June 2026| Pages 544-550
https://doi.org/10.1107/S2056989026004755

Crystal structure determination of an FeII azo aldehyde complex [Fe(C14H11N2O3)2(H2O)2] by MicroED

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Kazuki Ishikawa,a Fumishi Yoshizawa,a Reon Aihara,a Norihito Funato,a Daisuke Nakane,a Takashiro Akitsu,a* Takanori Nakane,b,c Akihiro Kawamotob,c and Genji Kurisub,c

aDepartment of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan, bInstitute for Protein Research, The University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan, and cJEOL YOKOGUSHI Research Alliance Laboratories, The University of Osaka, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
*Correspondence e-mail: [email protected]

(Received 25 February 2026; accepted 7 May 2026; online 12 May 2026)

This article is part of the collection Early Career Scientists in Structural Science.

The title compound, di­aquabis­{2-formyl-6-meth­oxy-4-[(E)-2-phenyl­diazen-1-yl]phenolato-κ2O1,O2}iron(II), [Fe(C14H11N2O3)2(H2O)2], comprises two bi­dentate ligands derived from 2-meth­oxy-4-(phenyl­diazen­yl)-6-formyl­phenol and two coordinated water mol­ecules. The FeII center is located at a crystallographic inversion center and adopts an octa­hedral coordination geometry. Both azo-phenolate ligands coordinate in a bidentate chelating mode (κ2O,O′) through the phenolate oxygen and formyl oxygen atoms in a centrosymmetric arrangement. The crystal structure was determined at 79 K using the MicroED method (λ = 0.02508 Å). The complex crystallizes in the monoclinic space group P21/n with Z = 2. The azo groups adopt trans conformations. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (36.8%) and C⋯H/H⋯C (31.9%) contacts.

CCDC reference: 2552645

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1. Chemical context

Vanillin (4-hy­droxy-3-meth­oxy­benzaldehyde) and its derivatives are commercially available and biocompatible; because they possess both phenolic hydroxyl groups and aldehyde functional groups, they serve as versatile building blocks for the construction of multidentate ligands (Andruh, 2015View full citation). The meth­oxy substituent on the aromatic ring influences the electronic properties through electron-donating effects, thereby modulating the redox potential and coordination behaviour of the resulting metal complexes (Yamane et al., 2017View full citation; Soni et al., 2020View full citation; Kashiwagi et al., 2019View full citation). The synthesis of azo-Schiff base hybrid ligands combining azo groups with vanillin-derived moieties represents an intriguing approach for the development of compounds that unite the coordination versatility of Schiff bases with the chromophoric properties of azo functionalities.

In our laboratory, we have been investigating metal complexes with multifunctional ligands for potential applications in dye-sensitized solar cells, flame retardants in heat-stabilized materials, and artificial metalloenzymes (Yamane et al., 2017View full citation; Soni et al., 2020View full citation; Kashiwagi et al., 2019View full citation). Metal–salen complexes, particularly those incorporating azo-functionalized building blocks combined with chiral di­amine moieties such as (1R,2R)-(+)-1,2-di­phenyl­ethyl­enedi­amine, have attracted considerable inter­est due to their potential as asymmetric catalysts and chiral recognition materials.

Structural characterization of metal complexes bearing salicylaldehyde-based ligands remains limited in the literature (Akitsu et al., 2005aView full citation,bView full citation; Watanabe et al., 2009View full citation). The title compound, [Fe(C14H11N2O3)2(H2O)2], is a highly symmetric complex centred on an FeII ion, which was unexpectedly obtained as a side product of microcrystalline powder during synthesis. In this report, we describe the crystal structure of this FeII complex, whose structure was determined using microcrystal electron diffraction (MicroED).

[Scheme 1]

2. Structural commentary

The complex mol­ecule (Fig. 1[link]) crystallizes in the monoclinic space group P21/n with atom Fe1 positioned at a crystallographic inversion center, forming a symmetric pseudo-octa­hedral structure. The Fe1 center is six-coordinate with an O6 donor set, comprising oxygen atoms from two deprotonated ones (O1, O1i), two formyl groups (O3, O3i) and two coordinated water mol­ecules (O4, O4i). The resulting coordination geometry affords a trans-octa­hedral arrangement.

[Figure 1]
Figure 1
Mol­ecular structure of the title compound with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level [symmetry code: (i) −x, 1 − y, −z].

The principal Fe—O bond distances are: Fe1—O1 (phenolate) = 1.906 (3) Å, Fe1—O3 (form­yl) = 2.029 (3) Å, and Fe1—O4 (water) = 2.109 (4) Å. These bond lengths are consistent with those typically observed in six-coordinate FeII complexes with mixed oxygen donor atoms. Each 2-meth­oxy-4-(phenyl­diazen­yl)-6-formyl­phenolato ligand coordinates in a bidentate chelating mode (κ2O,O′) through the deprotonated phenolate oxygen (O1) and formyl oxygen (O3) atoms. The chelate bite angle O1—Fe1—O3 is 86.20 (14)°, indicating a small distortion from the ideal octa­hedral angle of 90° (Table 1[link]).

Table 1
Selected geometric parameters (Å, °)

Fe1—O1 1.906 (3) O1—C10 1.222 (4)
Fe1—O3 2.029 (3) O3—C13 1.147 (5)
Fe1—O4 2.109 (4) N2—N1 1.185 (6)
       
O3—Fe1—O1 86.20 (14) C14—O2—C11 116.7 (3)
O4—Fe1—O1 88.32 (15) H1b—O4—H1a 104.5
O4—Fe1—O3 90.41 (13) C7—N1—N2 116.5 (4)
C10—O1—Fe1 130.0 (3) C6—N2—N1 115.2 (3)

The azo group (N1=N2) within the ligand exhibits a bond distance of 1.185 (6) Å, characteristic of a strong double bond, and adopts a trans conformation. The conjugated ligand framework contributes to the rigidity and near-planarity of the aromatic system. Due to the centrosymmetric nature of the complex, the asymmetric unit contains exactly half of the mol­ecule, with the complete structure generated by inversion symmetry.

3. Supra­molecular features

The crystal structure of the title compound is consolidated by dense packing and diverse non-covalent inter­actions. Hydrogen bonding plays a crucial role in the supra­molecular assembly: the coordinated water mol­ecules (O4) act as hydrogen-bond donors to adjacent formyl oxygen atoms (O3) and, to a lesser extent, to meth­oxy oxygen atoms (O2) (Table 2[link]). The O4—H1b⋯O3 hydrogen bond propagates along the a-axis direction via crystallographic translation, linking the mol­ecules into a one-dimensional chain parallel to the a axis.

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O4—H1a⋯O2i 1.04 1.82 2.845 169
O4—H1b⋯O3ii 1.04 1.82 2.788 153
Hydrogen-atom positions cannot be accurately determined in kinematical refinement of MicroED datasets. Therefore, distances involving hydrogen atoms are not quantitatively reliable and s.u.'s are not estimated. Symmetry codes: (i) Mathematical equation; (ii) Mathematical equation.

Hirshfeld surface analysis (Spackman & Jayatilaka, 2009View full citation; McKinnon et al., 2007View full citation) was performed to qu­anti­tatively characterize the inter­molecular inter­actions. As shown in the Hirshfeld surface analysis, C—H⋯π inter­actions between aromatic C—H groups and the π-electron systems of neighbouring rings contribute significantly to the crystal packing efficiency. Additional weak C—H⋯O hydrogen bonds between aromatic C—H groups and coordinated oxygen atoms further consolidate the structure.

The relative contributions to the total Hirshfeld surface are: H⋯H contacts (36.8%), C⋯H/H⋯C contacts (31.9%), O⋯H/H⋯O contacts (18.7%), and C⋯C contacts (1.7%). The high proportion of H⋯H inter­actions reflects efficient van der Waals packing and space filling in the crystal structure. The substantial C⋯H/H⋯C contribution arises primarily from C—H⋯π inter­actions involving the extensive aromatic ring systems present in the ligand framework. The moderate O⋯H/H⋯O contribution (18.7%) corresponds to both O—H⋯O and C—H⋯O hydrogen bonds linking adjacent mol­ecules. The relatively low C⋯C contribution (1.7%) indicates minimal face-to-face π–π stacking, with the crystal packing instead dominated by edge-to-face or T-shaped aromatic inter­actions.

The inter­molecular C—H⋯O hydrogen bonds are visualized as red spots near O3 and O1 on the Hirshfeld surfaces mapped over dnorm (Fig. 2[link], Fig. 3[link]). The O—H⋯O hydrogen bonds are the dominant inter­molecular inter­actions, and other weak inter­actions such as C—H⋯π and C—H⋯O are of minor importance. The enrichment ratios are EHC = 1.32, ENH = 1.41, EHH = 0.83, ECC = 0.52 and EOH = 1.36 (Jelsch et al., 2014View full citation).

[Figure 2]
Figure 2
Crystal packing of the title compound viewed down from the crystallographic b axis. Lines indicate inter­molecular hydrogen bonds. [Symmetry codes: (i) −x, 1 − y, −z; (ii) −x + 1, −y + 1, −z].
[Figure 3]
Figure 3
Hirshfeld surfaces mapped over dnorm and two-dimensional fingerprint plots.

4. Database survey

A survey of the Cambridge Structural Database (CSD, Version 5.43, update November 2024; Groom et al., 2016View full citation) revealed several reported iron complexes containing azo groups with the metal ions in both +2 and +3 oxidation states. While mononuclear complexes of the general formula [Fe(L)2(H2O)2] are documented, complexes bearing azo-vanillin frameworks similar to the title compound remain relatively uncommon.

Fe—O bond distances in FeII complexes typically range from 1.95 to 2.15 Å for phenolate coordination and 2.05 to 2.25 Å for neutral oxygen donors such as water or aldehyde groups, while the corresponding distances in FeIII complexes are typically shorter at 1.85-2.00 Å for phenolate and 1.95-2.10 Å for neutral donors, reflecting the larger ionic radius of FeII compared to FeIII. The Fe—O bond lengths observed in the title complex fall within these established ranges for FeII complexes, supporting the structural validity of the determined model despite the challenges inherent in MicroED data collection and refinement. Related structures include FeII complexes with salicylaldimine ligands and azo-containing Schiff base complexes (Keypour et al., 2013View full citation), which exhibit similar octa­hedral coordination geometries with mixed O/N donor sets.

The presence of coordinated water mol­ecules in six-coordinate FeII complexes is common when the primary ligands provide fewer than six donor atoms. The trans arrangement of water ligands in the title compound represents a frequently observed configuration in octa­hedral metal complexes, providing charge balance and completing the coordination sphere.

5. Synthesis and crystallization

While the intended product was an iron–salen complex incorporating di­amine, 1H NMR and MicroED analysis revealed that the target complex was not formed. Instead, an unexpected bis-(azo-vanillinato)FeII complex [Fe(C14H11N2O3)2(H2O)2] was obtained.

The original preparation procedures are as follows. Aniline (0.311 mL, 0.3 mmol) was dissolved in 6 M of hydro­chloric acid (3 mL) and cooled in an ice bath. An aqueous solution of sodium nitrite (NaNO2, 0.023 g, 0.33 mmol in 2 mL water) was added dropwise at 273–278 K to generate the diazo­nium salt. After stirring for 30 min, o-vanillin (0.046 g, 0.3 mmol) in ethanol (5 mL) was added and stirred for 1 h at ice-bath temperature. The pH was adjusted to approximately 10 by addition of 10% aqueous sodium hydroxide solution, and the precipitated azo-vanillin was collected by suction filtration.

The azo-vanillin inter­mediate was dissolved in ethanol (10 mL), and (1R,2R)-(+)-1,2-di­phenyl­ethyl­enedi­amine (0.032 g, 0.15 mmol) in ethanol (5 mL) was added and stirred at 313 K for 3 h. FeII sulfate hepta­hydrate (FeSO4·7H2O, 0.021 g, 0.075 mmol) in water (2 mL) was added and stirred at 313 K for 2 h to give a dark-brown solution with precipitates, which were filtered, dried and subjected to MicroED

6. Refinement

Crystal data, data collection, and structure refinement details are summarized in Tables 3[link] and 4[link]. MicroED data were collected at 79 K on a Talos Arctica electron microscope equipped with a Falcon 3 direct electron detector, controlled by SerialEM (Mastronarde, 2003View full citation) (Table 7 and Fig. 4[link]). The diffraction patterns were processed with DIALS (Winter et al., 2018View full citation; Clabbers et al., 2018View full citation) and xia2.multiplex (Gildea et al., 2022View full citation), parallelized by GNU parallel (Tange, 2011View full citation). Data scaling was performed using dials.scale (Beilsten-Edmands et al., 2020View full citation). Crystallographic merging statistics are shown in Tables 5[link], 6[link] and 7[link][link]. The structure was solved by charge flipping using olex2. solve (Bourhis et al., 2015View full citation) and kinematically refined by full-matrix least-squares procedures on F2 using olex2.refine (Bourhis et al., 2015View full citation). All non-hydrogen atoms were refined anisotropically. In addition to the Fe–salen complex described in this manuscript, the grid contained two more components (see scatter plots of unit-cell parameters in Fig. 5[link]). They were separately processed and phased as in Gogoi et al. (2023View full citation). The two components turned out to be a free ligand (CCDC-2524690; COD-3000633) and an inorganic salt (supplementary Fig. S1). Because of the very low occurrences of their crystals, their completeness was limited. Moreover, the inorganic salt could not be identified due to the difficulty in element identification by MicroED. Therefore, we do not describe their structures further in this report.

Table 3
Experimental details

Crystal data
Chemical formula [Fe(C14H11N2O3)2(H2O)2]
Mr 602.38
Crystal system, space group Monoclinic, P21/n
Temperature (K) 79
a, b, c (Å) 4.7419 (4), 22.447 (6), 11.0960 (11)
β (°) 90.396 (8)
V (Å3) 1181.0 (3)
Z 2
Radiation type Electron, λ = 0.02508 Å
μ (mm−1) 0.00
Crystal size (mm) 0.02 × 0.0002 × 0.0002
 
Data collection
Diffractometer Talos Arctica electron microscope
No. of measured, independent and observed [I ≥ 2u(I)] reflections 277706, 5188, 3421
Rint 0.234
(sin θ/λ)max (Å−1) 0.807
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.218, 0.534, 2.00
No. of reflections 5188
No. of parameters 178
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin 1.68, −0.62
Density values in MicroED maps are proportional to Coulomb potential but the scale is not necessarily absolute. Computer programs: OLEX2.solve (Bourhis et al., 2015View full citation), OLEX2.refine (Bourhis et al., 2015View full citation), OLEX2 (Dolomanov et al., 2009View full citation) and publCIF (Westrip, 2010View full citation).

Table 4
Summary of MicroED data collection and processing

Microscope parameters  
Scope Talos Arctica
Acceleration voltage 200 kV (∼0.025079 Å)
Probe Nanoprobe mode
Gun lens 8
Beam convergence Parallel
Beam diameter ∼1.6 um
Fluence ∼0.055 e Å−1 sec−1
Rotation ∼0.4354°/frame
Energy filtering Not equipped
Detector Falcon 3 (integrating mode)
Pixel size 28 µm (after binning by 2)
Camera length 615.5 mm
Frame rate ∼0.35 sec / fraction
Microscope control SerialEM
Stage temperature ∼79 K
   
Data collection and processing  
Sample grid Qu­antiFoil Mo R0.6/1.0
Snapshot screening > 750 positions
Data collection 377 positions
Initial indexing success 312 crystals
Processing DIALS with GNU parallel
   
Cluster 1 (blue cluster; the Fe complex)
Indexed 241 crystals
Selected for merging  
Selection criteria CC1/[email protected]Å > 1/2, xia.multiplex, dials.scale with deltacchalf filtering
   
Cluster 2 (red cluster; the free ligand)
Indexed 5 crystals
Selected for merging 5 crystals
Selection criteria none (used all)
   
Cluster 3 (orange cluster; unknown inorganic salt)
Indexed 7 crystals
Selected for merging 7 crystals
Selection criteria none (used all)

Table 5
Merging statistics for the Fe complex

dmax dmin obs uniq mult. %comp <I/σ(I)> rpim cc1/2
6.20 1.67 11334 275 41.21 99.28 49.7 0.020 0.984*
1.67 1.33 13981 270 51.78 100.00 38.0 0.021 0.992*
1.33 1.16 13115 268 48.94 100.00 30.4 0.025 0.995*
1.16 1.06 15612 277 56.36 100.00 25.2 0.028 0.997*
1.06 0.98 12292 252 48.78 100.00 20.1 0.034 0.995*
0.98 0.93 13964 260 53.71 100.00 17.9 0.034 0.991*
0.93 0.88 16465 284 57.98 100.00 13.3 0.048 0.958*
0.88 0.84 13495 260 51.90 100.00 9.9 0.059 0.964*
0.84 0.81 11891 253 47.00 100.00 6.9 0.080 0.932*
0.81 0.78 14647 266 55.06 100.00 6.5 0.076 0.923*
0.78 0.76 16342 269 60.75 100.00 5.3 0.090 0.914*
0.76 0.73 15344 273 56.21 100.00 4.5 0.109 0.903*
0.73 0.72 13776 262 52.58 100.00 3.5 0.133 0.882*
0.72 0.70 12463 252 49.46 100.00 2.4 0.192 0.633*
0.70 0.68 12810 257 49.84 100.00 2.5 0.191 0.840*
0.68 0.67 14628 255 57.36 100.00 2.4 0.184 0.693*
0.67 0.65 17458 278 62.80 100.00 2.9 0.154 0.797*
0.65 0.64 15599 279 55.91 100.00 1.7 0.273 0.464*
0.64 0.63 14029 269 52.15 100.00 1.5 0.284 0.552*
0.63 0.62 14499 263 55.13 100.00 1.6 0.278 0.618*
6.20 0.62 283744 5322 53.32 99.96 12.4 0.033 0.995*

Table 6
Merging statistics for the free ligand

dmax dmin obs uniq mult. %comp <I/σ(I)> rpim cc1/2
5.55 1.95 181 62 2.92 80.52 27.5 0.049 0.995*
1.95 1.56 247 74 3.34 89.16 20.2 0.060 0.979*
1.56 1.36 203 59 3.44 89.39 11.2 0.105 0.920*
1.36 1.24 268 70 3.83 89.74 9.3 0.110 0.964*
1.24 1.15 204 60 3.40 90.91 9.4 0.107 0.956*
1.15 1.08 295 77 3.83 92.77 9.6 0.116 0.932*
1.08 1.03 201 58 3.47 87.88 9.5 0.112 0.956*
1.03 0.99 277 71 3.90 93.42 7.3 0.135 0.965*
0.99 0.95 254 68 3.74 86.08 4.9 0.153 0.892*
0.95 0.92 221 63 3.51 92.65 4.4 0.201 0.815*
0.92 0.89 257 64 4.02 88.89 3.5 0.215 0.693*
0.89 0.86 283 73 3.88 90.12 2.9 0.218 0.700*
0.86 0.84 242 63 3.84 92.65 2.1 0.288 0.517*
0.84 0.82 205 59 3.47 86.76 2.3 0.275 0.706*
0.82 0.80 269 70 3.84 88.61 1.8 0.388 0.665*
5.55 0.80 3607 991 3.64 89.20 8.4 0.113 0.973*

Table 7
Merging statistics for the unknown inorganic salt

dmax dmin obs uniq mult. %comp <I/σ(I)> rpim cc1/2
4.89 1.59 691 110 6.28 82.09 17.4 0.074 0.983*
1.59 1.27 719 103 6.98 89.57 12.5 0.088 0.971*
1.27 1.11 739 102 7.25 89.47 8.4 0.114 0.944*
1.11 1.01 765 96 7.97 90.57 8.2 0.120 0.973*
1.01 0.94 824 105 7.85 90.52 5.6 0.117 0.885*
0.94 0.88 662 88 7.52 88.00 3.9 0.181 0.833*
0.88 0.84 841 98 8.58 91.59 4.0 0.151 0.864*
0.84 0.80 759 99 7.67 92.52 3.5 0.167 0.684*
0.80 0.77 731 94 7.78 91.26 2.5 0.186 0.859*
0.77 0.74 815 99 8.23 91.67 2.3 0.231 0.723*
0.74 0.72 819 101 8.11 90.99 2.2 0.214 0.482*
0.72 0.70 610 80 7.62 89.89 1.9 0.340 0.763*
0.70 0.68 889 100 8.89 90.91 1.5 0.266 0.641*
0.68 0.67 777 99 7.85 92.52 1.4 0.279 0.542*
0.67 0.65 724 93 7.78 89.42 1.2 0.403 0.514*
4.89 0.65 11365 1467 7.75 90.00 5.3 0.112 0.981*
[Figure 4]
Figure 4
SerialEM square montage of the MicroED grid: The red crosses indicate positions screened for diffraction. Discontinuities in the image are due to alignment errors in the montaging process.
[Figure 5]
Figure 5
Scatter plots of unit-cell parameters: 298 crystals that diffracted to better than 1.2 Å were plotted out of 377 measured positions. This is a raw result before applying prior cell information and Bravais lattice constraints. The plot includes low-quality and/or mis-indexed crystals that were rejected in later steps of data processing. The blue cluster corresponds to the Fe complex described in this study. The red cluster was the free ligand and the orange cluster was an unknown inorganic salt.

The benzene ring (C1–C6) collapsed (long C—C) during the calculation, so we used the AFIX66 constraint. Hydrogen atoms bound to carbon and oxygen were placed at peak positions and refined using a riding model.

The final reliability indices are R1 = 0.2176 [for 3421 reflections with I ≥ 2σ(I)] and wR2 = 0.5343 (all 5188 data), with a goodness-of-fit of 2.0002. The relatively high R-factors are typical for MicroED data and are attributed to the neglect of dynamical diffraction, partial charges and bond polarization, Additionally, the equivalent reflections showed a relatively high Rint value of 0.2335. This is also common in high-multiplicity MicroED datasets. First, intensities of equivalent reflections vary due to multiple scattering. Next, Rint increases with the multiplicity of the dataset, as pointed out in Diederichs & Karplus (1997View full citation) for the case of a related metric Rmerge. Despite these refinement challenges, the structural model is chemically reasonable, with the connectivity and overall mol­ecular geometry unambiguously determined. The coordination environment of the iron center and the arrangement of the azo-vanillin ligands are clearly resolved, providing valuable insight into the coordination chemistry of this unexpected product.

Readers should be aware that the estimated standard deviations (ESDs) of refined parameters are severely underestimated in MicroED. They are calculated from the covariance matrix via error-propagation by the least square refinement engine. However, necessary assumptions (independent, zero mean, random errors with known sigmas) do not hold in MicroED. For example, we estimate up to 0.3% of errors are possible in the virtual camera distance of our scope. Neglect of dynamical scattering and partial charges introduces systematic errors. Refined parameters and ESDs in the accompanying tables were automatically extracted from the refined CIF file as is but we consider numbers beyond the second decimal place as qu­anti­tatively dubious. Indeed, recent analysis by Gemmi et al. (2026View full citation) suggested that an average accuracy of atomic positions achieved though kinematic refinement is about 0.03–0.05 Å depending on the beam sensitivity of the sample.

7. Data Availability

The refined coordinates of the Fe complex (CCDC-2552645; COD-3000632) and the free ligand (CCDC-2524690; COD-3000633) have been deposited at the Cambridge Crystallographic Data Centre and the Crystallography Open Database. The raw diffraction images have been deposited to XRDa-469(https://doi.org/10.51093/xrd-00469). Scripts and manuals for MicroED data collection and processing are available at our GitHub repository https://github.com/GKLabIPR/MicroED.

Supporting information

CCDC reference: 2552645

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989026004755/meu2001sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989026004755/meu2001Isup2.hkl

Structure of the free ligand contained in the MicroED grid. DOI: https://doi.org/10.1107/S2056989026004755/meu2001sup3.tif

Structure of an unknown salt contained in the MicroED grid. Because of limited data completeness and the difficulty of element identification in MicroED, we could not confidently identify the salt and finalize the refinement. DOI: https://doi.org/10.1107/S2056989026004755/meu2001sup4.tif

Intermolecular C---H...O hydrogen bonds as red spots. DOI: https://doi.org/10.1107/S2056989026004755/meu2001sup5.tif

checkCIF report


Computing details top

Diaquabis{2-formyl-6-methoxy-4-[(E)-2-phenyldiazen-1-yl]phenolato-κ2O1,O2}iron(II) top
Crystal data top
[Fe(C14H11N2O3)2(H2O)2]F(000) = 231.684
Mr = 602.38Dx = 1.694 Mg m−3
Monoclinic, P21/nElectron radiation, λ = 0.02508 Å
a = 4.7419 (4) ÅCell parameters from 16876 reflections
b = 22.447 (6) Åθ = 6.6–56.6°
c = 11.0960 (11) ŵ = 0.000 mm−1
β = 90.396 (8)°T = 79 K
V = 1181.0 (3) Å3Powder, orange
Z = 20.01 × 0.001 × 0.001 mm
Data collection top
Talos Arctica electron microscope
diffractometer		Rint = 0.234
Radiation source: Talos Arctica Field Emission Gunθmax = 1.2°, θmin = 0.1°
continuous rotation electron diffraction (MicroED) scansh = −7→7
277706 measured reflectionsk = −36→36
5188 independent reflectionsl = −17→17
3421 reflections with I ≥ 2u(I)
Refinement top
Refinement on F224 constraints
Least-squares matrix: fullPrimary atom site location: iterative
R[F2 > 2σ(F2)] = 0.218H-atom parameters constrained
wR(F2) = 0.534 w = 1/[σ2(Fo2) + (0.2P)2]
where P = (Fo2 + 2Fc2)/3
S = 2.00(Δ/σ)max = 0.001
5188 reflectionsΔρmax = 1.68 e Å−3
178 parametersΔρmin = −0.62 e Å−3
0 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Fe10.00.50.00.0396 (7)
O10.2119 (6)0.55697 (19)0.0903 (3)0.0427 (10)
O20.5723 (6)0.63117 (19)0.1573 (3)0.0409 (9)
O3−0.2221 (6)0.48661 (18)0.1532 (3)0.0423 (10)
O40.2951 (6)0.4348 (2)0.0538 (3)0.0448 (10)
H1a0.367 (3)0.4130 (6)−0.0228 (3)0.0673 (15)*
H1b0.476 (2)0.4423 (2)0.1053 (13)0.0673 (15)*
N10.2246 (7)0.6181 (2)0.5519 (3)0.0462 (11)
N20.3901 (7)0.6548 (2)0.5823 (3)0.0464 (11)
C10.1835 (5)0.64836 (14)0.7774 (2)0.0469 (12)
H10.0233 (5)0.61580 (14)0.7478 (2)0.0562 (14)*
C20.1866 (6)0.66845 (16)0.8959 (2)0.0587 (14)
H20.0288 (6)0.65182 (16)0.9603 (2)0.0704 (17)*
C30.3885 (6)0.70949 (16)0.93334 (18)0.0563 (14)
H30.3909 (6)0.72543 (16)1.02738 (18)0.0675 (17)*
C40.5874 (6)0.73045 (15)0.8522 (2)0.0539 (13)
H40.7476 (6)0.76301 (15)0.8819 (2)0.0647 (16)*
C50.5843 (5)0.71036 (16)0.7337 (2)0.0518 (13)
H50.7421 (5)0.72699 (16)0.6694 (2)0.0621 (16)*
C60.3824 (5)0.66932 (15)0.69635 (17)0.0433 (12)
C70.2252 (8)0.6029 (2)0.4355 (3)0.0461 (12)
C80.0401 (8)0.5627 (2)0.3995 (3)0.0461 (12)
H6−0.1088 (8)0.5436 (2)0.4650 (3)0.0553 (14)*
C90.0305 (8)0.5446 (2)0.2835 (3)0.0422 (11)
C100.2059 (7)0.5688 (2)0.1977 (3)0.0366 (10)
C110.4016 (7)0.6108 (2)0.2396 (3)0.0392 (11)
C120.4135 (8)0.6268 (2)0.3536 (3)0.0396 (10)
H70.5731 (8)0.6594 (2)0.3841 (3)0.0475 (12)*
C13−0.1757 (8)0.5049 (2)0.2477 (3)0.0414 (11)
H8−0.3149 (8)0.4887 (2)0.3198 (3)0.0497 (13)*
C140.7404 (8)0.6756 (2)0.1895 (4)0.0474 (12)
H1c0.844 (3)0.6937 (5)0.1094 (4)0.0711 (18)*
H1e0.6157 (9)0.7107 (4)0.2326 (14)0.0711 (18)*
H1d0.901 (2)0.6593 (3)0.2531 (12)0.0711 (18)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Fe10.0288 (7)0.0499 (15)0.0402 (9)0.0002 (7)0.0003 (5)−0.0078 (7)
O10.0359 (13)0.054 (3)0.0379 (14)0.0004 (15)−0.0024 (10)−0.0081 (14)
O20.0352 (13)0.051 (3)0.0367 (14)−0.0033 (14)0.0038 (10)−0.0097 (13)
O30.0350 (13)0.044 (3)0.0479 (17)−0.0031 (14)0.0005 (11)−0.0039 (14)
O40.0304 (12)0.066 (3)0.0379 (14)0.0002 (14)0.0021 (9)−0.0075 (14)
N10.0417 (16)0.064 (3)0.0330 (15)−0.0064 (18)0.0028 (11)−0.0024 (16)
N20.0407 (16)0.062 (3)0.0369 (16)−0.0085 (18)0.0059 (12)−0.0076 (17)
C10.049 (2)0.055 (3)0.0367 (19)0.001 (2)0.0072 (15)−0.0046 (18)
C20.075 (3)0.069 (4)0.0314 (18)0.017 (3)−0.0039 (18)−0.006 (2)
C30.056 (2)0.080 (4)0.0328 (19)0.009 (3)−0.0036 (16)−0.007 (2)
C40.051 (2)0.054 (4)0.057 (3)0.003 (2)−0.0093 (19)−0.001 (2)
C50.047 (2)0.073 (4)0.0352 (19)0.003 (2)−0.0075 (15)0.002 (2)
C60.0446 (18)0.058 (3)0.0271 (15)0.005 (2)0.0047 (13)−0.0007 (16)
C70.0436 (19)0.062 (4)0.0326 (17)−0.009 (2)0.0032 (14)−0.0023 (18)
C80.0409 (18)0.064 (4)0.0333 (17)−0.011 (2)0.0077 (13)−0.0089 (18)
C90.0348 (16)0.051 (3)0.0405 (19)−0.0079 (18)−0.0019 (13)−0.0087 (18)
C100.0293 (14)0.046 (3)0.0341 (16)−0.0013 (16)0.0005 (11)−0.0014 (16)
C110.0302 (14)0.055 (3)0.0320 (16)0.0014 (17)−0.0003 (11)−0.0054 (16)
C120.0387 (16)0.048 (3)0.0323 (16)−0.0010 (18)0.0021 (12)−0.0084 (16)
C130.0346 (16)0.049 (3)0.0403 (19)−0.0044 (18)−0.0014 (13)−0.0049 (17)
C140.0360 (17)0.062 (4)0.044 (2)0.000 (2)0.0002 (14)−0.008 (2)
Geometric parameters (Å, º) top
Fe1—O11.906 (3)C3—C41.3900
Fe1—O1i1.906 (3)C4—H41.1030
Fe1—O32.029 (3)C5—C41.3900
Fe1—O3i2.029 (3)C5—H51.1030
Fe1—O42.109 (4)C6—C11.3900
Fe1—O4i2.109 (4)C6—C51.3900
O1—C101.222 (4)C7—C81.319 (6)
O2—C111.307 (5)C7—C121.387 (5)
O2—C141.325 (6)C8—H61.1030
O3—C131.147 (5)C9—C81.350 (5)
O4—H1a1.0400C9—C131.378 (6)
O4—H1b1.0400C10—C91.380 (5)
N1—C71.336 (5)C10—C111.399 (6)
N2—N11.185 (6)C11—C121.316 (5)
N2—C61.308 (4)C12—H71.1030
C1—H11.1030C13—H81.1030
C1—C21.3900C14—H1c1.0970
C2—H21.1030C14—H1e1.0970
C3—C21.3900C14—H1d1.0970
C3—H31.1030
O1i—Fe1—O1180.0H4—C4—C5120.00 (8)
O3i—Fe1—O193.80 (14)C4—C5—H5120.00 (8)
O3—Fe1—O186.20 (14)C4—C5—C6120.0
O3—Fe1—O1i93.80 (14)H5—C5—C6120.00 (8)
O3i—Fe1—O1i86.20 (14)C1—C6—N2124.4
O3i—Fe1—O3180.0C5—C6—N2115.5
O4—Fe1—O188.32 (15)C5—C6—C1120.0
O4—Fe1—O1i91.68 (15)C8—C7—N1117.5 (4)
O4i—Fe1—O191.68 (15)C8—C7—C12119.8 (4)
O4i—Fe1—O1i88.32 (15)C12—C7—N1122.7 (4)
O4i—Fe1—O389.59 (13)H6—C8—C7119.6 (2)
O4—Fe1—O390.41 (13)H6—C8—C9119.6 (2)
O4—Fe1—O3i89.59 (13)C9—C8—C7120.8 (4)
O4i—Fe1—O3i90.41 (13)C8—C9—C10121.5 (4)
O4—Fe1—O4i180.0C8—C9—C13119.2 (4)
C10—O1—Fe1130.0 (3)C13—C9—C10119.0 (4)
C14—O2—C11116.7 (3)C9—C10—O1127.2 (4)
C13—O3—Fe1i128.0 (3)C9—C10—C11116.0 (3)
H1a—O4—Fe1i108.4C11—C10—O1116.8 (3)
H1b—O4—Fe1i125.9C10—C11—O2114.6 (3)
H1b—O4—H1a104.5C12—C11—O2123.6 (4)
C7—N1—N2116.5 (4)C12—C11—C10121.8 (4)
C6—N2—N1115.2 (3)C11—C12—C7120.0 (4)
H1—C1—C6120.00 (8)H7—C12—C7120.0 (2)
C2—C1—H1120.00 (8)H7—C12—C11120.0 (2)
C2—C1—C6120.0C9—C13—O3128.8 (4)
H2—C2—C1120.00 (8)H8—C13—O3115.6 (3)
H2—C2—C3120.00 (8)H8—C13—C9115.6 (2)
C3—C2—C1120.0H1c—C14—O2109.5
C2—C3—H3120.00 (8)H1e—C14—O2109.5
C2—C3—C4120.0H1e—C14—H1c109.5
C4—C3—H3120.00 (8)H1d—C14—O2109.5
C3—C4—C5120.0H1d—C14—H1c109.5
H4—C4—C3120.00 (8)H1d—C14—H1e109.5
Fe1—O1—C10—C9−2.6 (5)C1—C2—C3—C40.0 (3)
Fe1—O1—C10—C11176.1 (4)C1—C6—C5—C40.0 (3)
Fe1—O3—C13—C95.2 (5)C5—C4—C3—C20.0 (3)
O1—C10—C9—C8−178.3 (5)C5—C6—C1—C20.0 (3)
O1—C10—C9—C13−4.2 (6)C6—C1—C2—C30.0 (3)
O1—C10—C11—C12180.0 (4)C6—C5—C4—C30.0 (3)
O2—C11—C10—O1−1.5 (5)C7—N1—N2—C6179.2 (4)
O2—C11—C10—C9177.3 (4)C7—C8—C9—C13−176.5 (5)
O2—C11—C12—C7−179.7 (5)C9—C8—C7—C12−0.2 (6)
O3—C13—C9—C8176.8 (6)C9—C10—C11—C12−1.2 (5)
N1—N2—C6—C1−5.3 (6)C10—C9—C8—C7−2.4 (5)
N1—N2—C6—C5177.2 (4)C10—C9—C13—O32.6 (6)
N1—C7—C8—C9−179.2 (5)C10—C11—O2—C14172.8 (4)
N1—C7—C12—C11−179.0 (5)C10—C11—C12—C7−1.2 (5)
N2—N1—C7—C8−179.1 (5)C11—C10—C9—C83.0 (5)
N2—N1—C7—C121.9 (6)C11—C10—C9—C13177.1 (4)
N2—C6—C1—C2−177.4 (3)C11—C12—C7—C82.0 (5)
N2—C6—C5—C4177.6 (2)C12—C11—O2—C14−8.7 (5)
Symmetry code: (i) −x, −y+1, −z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H1a···O2ii1.041.822.845169
O4—H1b···O3iii1.041.822.788153
Symmetry codes: (ii) −x+1, −y+1, −z; (iii) x+1, y, z.
Summary of MicroED data collection and processing top
Microscope parameters
ScopeTalos Arctica
Acceleration voltage200 kV (~ 0.025079 Å)
ProbeNanoprobe mode
Gun lens8
Beam convergenceParallel
Beam diameter~ 1.6 um
Fluence~ 0.055 e Å-1 sec-1
Rotation~ 0.4354°/frame
Energy filteringNot equipped
DetectorFalcon 3 (integrating mode)
Pixel size28 µm (after binning by 2)
Camera length615.5 mm
Frame rate~ 0.35 sec / fraction
Microscope controlSerialEM
Stage temperature~ 79 K
Data collection and processing
Sample gridQuantiFoil Mo R0.6/1.0
Snapshot screening> 750 positions
Data collection377 positions
Initial indexing success312 crystals
ProcessingDIALS with GNU parallel
Cluster 1(blue cluster; the Fe complex)
Indexed241 crystals
Selected for merging
Selection criteriaCC1/[email protected]Å > 0.50, xia.multiplex, dials.scale with deltacchalf filtering
Cluster 2(red cluster; the free ligand)
Indexed5 crystals
Selected for merging5 crystals
Selection criterianone (used all)
Cluster 3(orange cluster; unknown inorganic salt)
Indexed7 crystals
Selected for merging7 crystals
Selection criterianone (used all)
Merging statistics for the Fe complex top
d_max_d_min_obsuniqmult.%comp<I/σ(I)>r_pim_cc1/2
6.201.671133427541.2199.2849.70.0200.984*
1.671.331398127051.78100.0038.00.0210.992*
1.331.161311526848.94100.0030.40.0250.995*
1.161.061561227756.36100.0025.20.0280.997*
1.060.981229225248.78100.0020.10.0340.995*
0.980.931396426053.71100.0017.90.0340.991*
0.930.881646528457.98100.0013.30.0480.958*
0.880.841349526051.90100.009.90.0590.964*
0.840.811189125347.00100.006.90.0800.932*
0.810.781464726655.06100.006.50.0760.923*
0.780.761634226960.75100.005.30.0900.914*
0.760.731534427356.21100.004.50.1090.903*
0.730.721377626252.58100.003.50.1330.882*
0.720.701246325249.46100.002.40.1920.633*
0.700.681281025749.84100.002.50.1910.840*
0.680.671462825557.36100.002.40.1840.693*
0.670.651745827862.80100.002.90.1540.797*
0.650.641559927955.91100.001.70.2730.464*
0.640.631402926952.15100.001.50.2840.552*
0.630.621449926355.13100.001.60.2780.618*
6.200.62283744532253.3299.9612.40.0330.995*
Merging statistics for the free ligand top
d_max_d_min_obsuniqmult.%comp<I/σ(I)>r_pim_cc1/2
5.551.95181622.9280.5227.50.0490.995*
1.951.56247743.3489.1620.20.0600.979*
1.561.36203593.4489.3911.20.1050.920*
1.361.24268703.8389.749.30.1100.964*
1.241.15204603.4090.919.40.1070.956*
1.151.08295773.8392.779.60.1160.932*
1.081.03201583.4787.889.50.1120.956*
1.030.99277713.9093.427.30.1350.965*
0.990.95254683.7486.084.90.1530.892*
0.950.92221633.5192.654.40.2010.815*
0.920.89257644.0288.893.50.2150.693*
0.890.86283733.8890.122.90.2180.700*
0.860.84242633.8492.652.10.2880.517*
0.840.82205593.4786.762.30.2750.706*
0.820.80269703.8488.611.80.3880.665*
5.550.8036079913.6489.208.40.1130.973*
Merging statistics for the unknown inorganic salt top
d_max_d_min_obsuniqmult.%comp<I/σ(I)>r_pim_cc1/2
4.891.596911106.2882.0917.40.0740.983*
1.591.277191036.9889.5712.50.0880.971*
1.271.117391027.2589.478.40.1140.944*
1.111.01765967.9790.578.20.1200.973*
1.010.948241057.8590.525.60.1170.885*
0.940.88662887.5288.003.90.1810.833*
0.880.84841988.5891.594.00.1510.864*
0.840.80759997.6792.523.50.1670.684*
0.800.77731947.7891.262.50.1860.859*
0.770.74815998.2391.672.30.2310.723*
0.740.728191018.1190.992.20.2140.482*
0.720.70610807.6289.891.90.3400.763*
0.700.688891008.8990.911.50.2660.641*
0.680.67777997.8592.521.40.2790.542*
0.670.65724937.7889.421.20.4030.514*
4.890.651136514677.7590.005.30.1120.981*
 

Acknowledgements

The authors disclose use of Claude for language translation and editing.

Funding information

This work was performed under the Collaborative Research Program (MicroED) of the Institute for Protein Research, The University of Osaka (MEDCR-25–02). The electron microscopy is partly supported by Research Support Project for Life Science and Drug Discovery (BINDS) from AMED under grant No. JP25ama121001.

References

Return to citationAkitsu, T., Takeuchi, Y. & Einaga, Y. (2005a). Acta Cryst. C61, m324–m328.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 Return to citationAkitsu, T., Takeuchi, Y. & Einaga, Y. (2005b). Acta Cryst. E61, m772–m774.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 Return to citationAndruh, M. (2015). Dalton Trans. 44, 16633–16653.  Web of Science CrossRef CAS PubMed Google Scholar
 Return to citationBeilsten-Edmands, J., Winter, G., Gildea, R., Parkhurst, J., Waterman, D. & Evans, G. (2020). Acta Cryst. D76, 385–399.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationBourhis, L. J., Dolomanov, O. V., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2015). Acta Cryst. A71, 59–75.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationClabbers, M. T. B., Gruene, T., Parkhurst, J. M., Abrahams, J. P. & Waterman, D. G. (2018). Acta Cryst. D74, 506–518.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationDiederichs & Karplus (1997). Nature Struct. Biol. 4, 269–275.  Google Scholar
 Return to citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 Return to citationGemmi, M., Palatinus, L., Boullay, P., Abrahams, J. P., Ben Meriem, A., Cordero-Oyonarte, E., Emerson Agbemeh, V., Chintakindi, H., Faye Diouf, M. D., Filipcik, P., Gemmrich Hernandéz, L., van Genderen, E., Hadermann, J., Hajizadeh, A., Jeriga, B., Kolb, U., Matinyan, S., Passuti, S., Santucci, M., Suresh, A., Pérez, O., Tai, C.-W., Vypritskaia, A., Wang, L., Xu, H. & Zou, X. (2026). IUCrJ 13, 198–210.  Web of Science CrossRef PubMed IUCr Journals Google Scholar
 Return to citationGildea, R. J., Beilsten-Edmands, J., Axford, D., Horrell, S., Aller, P., Sandy, J., Sanchez-Weatherby, J., Owen, C. D., Lukacik, P., Strain-Damerell, C., Owen, R. L., Walsh, M. A. & Winter, G. (2022). Acta Cryst. D78, 752–769.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationGogoi, D., Sasaki, T., Nakane, T., Kawamoto, A., Hojo, H., Kurisu, G. & Thakuria, R. (2023). Cryst. Growth Des. 23, 5821–5826.  Web of Science CSD CrossRef CAS Google Scholar
 Return to citationGroom, 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
 Return to citationJelsch, C., Ejsmont, K. & Huder, L. (2014). IUCrJ 1, 119–128.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
 Return to citationKashiwagi, K., Pradhan, S., Haraguchi, T. & Akitsu, T. (2019). J. Indian Chem. Soc. 96, 593–597.  CAS Google Scholar
 Return to citationKeypour, H., Shooshtari, A., Rezaeivala, M., Valencia, L., Pérez-Lourido, P. & Khavasi, H. R. (2013). Polyhedron 50, 104–110.  Google Scholar
 Return to citationMastronarde, D. N. (2003). Microsc. Microanal. 9, 1182–1183.  CrossRef Google Scholar
 Return to citationMcKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814–3816.  Web of Science CrossRef Google Scholar
 Return to citationSoni, K., Sharma, A., Akitsu, T. & Teotia, M. (2020). J. Sci. Ind. Res. 79, 582–585.  CAS Google Scholar
 Return to citationSpackman, M. A. & Jayatilaka, D. (2009). CrystEngComm 11, 19–32.  Web of Science CrossRef CAS Google Scholar
 Return to citationTange, O. (2011). ;login: The USENIX Magazine 36, pp. 42–47.  Google Scholar
 Return to citationWatanabe, Y., Aritake, Y. & Akitsu, T. (2009). Acta Cryst. E65, m1640–m1641.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 Return to citationWinter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). Acta Cryst. D74, 85–97.  Web of Science CrossRef IUCr Journals Google Scholar
 Return to citationYamane, S., Hiyoshi, Y., Tanaka, S., Ikenomoto, S., Numata, T., Takakura, K., Haraguchi, T., Palafox, M. A., Hara, M., Sugiyama, M. & Akitsu, T. (2017). J. Chem. Chem. Eng. 11, 135–151.  CAS Google Scholar

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ISSN: 2056-9890
Volume 82| Part 6| June 2026| Pages 544-550
https://doi.org/10.1107/S2056989026004755
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