Synthesis and structure of ammonium bis­(malonato)borate

Govindharajan, G.; Chidambaram, R.R.; Uthamaselvan, G.; Iyathurai, K.; Karthikeyan, K.; Natarajan, S.

doi:10.1107/S2056989025007169

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ISSN: 2056-9890

Volume 81| Part 9| September 2025| Pages 849-852

https://doi.org/10.1107/S2056989025007169

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Synthesis and structure of ammonium bis(malonato)borate

Gokila Govindharajan,^a Ramachandra Raja Chidambaram,^b Gnanasheela Uthamaselvan,^c Kalaiarasi Iyathurai,^c Kamatchi Karthikeyan ^d and Sampath Natarajan ^e ^*

^aGovernment College for Women (Affiliated to Bharathidasan University), Kumbakonam,Thanjavur, Tamilnadu-612001, India, ^bDepartment of Physics, D. G. Government Arts College for Women (Affiliated to Annamalai University), Mayiladuthurai, Taminadu-609 001, India, ^cDepartment of Physics, Government College for Women (Affiliated to Bharathidasan University), Kumbakonam, Thanjavur, Tamilnadu-612001, India, ^dDepartment of Physics, Srinivasa Ramanujan Centre, SASTRA Deemed University, Kumbakonam, Thanjavur, Tamilnadu-612001, India, and ^eDepartment of Chemistry, Chemical Biology Lab., School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
^*Correspondence e-mail: [email protected]

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 16 July 2025; accepted 9 August 2025; online 19 August 2025)

In the title salt, NH₄⁺·[B(C₃H₂O₄)₂]⁻, the boron atom is chelated by two malonate ligands in a bidentate fashion, resulting in a BO₄ tetrahedron with both chelate rings adopting shallow boat conformations. The extended structure features five N—H⋯O and three C—H⋯O hydrogen bonds, accounting for approximately 69.9% of the total intermolecular interactions.

Keywords: crystal structure; ammonium; bis(malonato)borate; Hirshfeld surface.

CCDC reference: 2455003

1. Chemical context

The bis(malonate)borate anion, [B(C₃H₂O₄)₂]⁻, is a tetrahedral boron-centred complex in which two malonate ligands are bidentately coordinated via their carboxylate oxygen atoms. This chelation results in a stable, symmetrical anion capable of forming extended hydrogen-bonded or ionic frameworks when paired with alkali metal cations such as sodium or potassium (Zviedre & Belyakov, 2007 ; Selvi et al., 2024 ). In materials science, bis(malonate)borate derivatives have attracted attention for their role in energy storage technologies. The lithium and sodium salts of this anion have been explored as polymeric ion conductors and electrolyte additives in lithium ion and sodium ion batteries, where their borate anions contribute to enhanced electrochemical stability and ionic conductivity (Mahanthappa & Weber, 2015 ).

In tribological applications, bis(malonate)borate-based ionic liquids have shown excellent thermal stability and antiwear performance, making them environmentally friendly alternatives to halogenated lubricants (Gusain & Khatri, 2015 ). In biological contexts, although less studied, the malonate ligands mimic natural chelators, suggesting potential applications in metal detoxification and enzyme inhibition. Furthermore, the aqueous solubility and biocompatibility of boron-containing compounds, including bis(malonate)borates, position them as potential boron delivery agents in boron neutron capture therapy (BNCT) for cancer treatment (Järvinen et al., 2023 ; Li et al., 2025 ; Dymova et al., 2020 ). These multifaceted properties underscore the growing interest in bis(malonate)borate anions at the intersection of green chemistry, energy materials and biomedical innovation. As part of our work in this area, we now describe the synthesis and structure of the title compound, NH₄⁺[B(C₃H₂O₄)₂]⁻, (I).

2. Structural commentary

Compound (I) features a presumed sp³-hybridized tetrahedral B atom coordinated by two chelating malonate ligands, each binding through two carboxylate O atoms (Fig. 1). Selected geometrical data are given in Table 1. In the B—O tetrahedron, the mean B—O bond length of 1.465 Å is in good agreement with the already reported structure of sodium bis(malonate)borate (Selvi et al. 2024) and also agrees with the expected value for a Bsp³—O bond length (1.468 Å; Allen et al., 1987 ). The largest O—B—O bond angles are the intracyclic angles: O1—B1—O3 = 112.4 (2)° and O5—B1—O6 = 112.5 (2)°. The six-membered boro–malonate rings B1/O5/C4/C5/C6/O6 (Fig. 2a) and B1/O1/C1/C2/C3/O3 (Fig. 2b) both adopt shallow boat conformations with puckering amplitudes Q_T = 0.457 (2) and 0.414 (2) Å, respectively. In the boat conformations of the boro-malonate rings (Fig. 2), atoms B1 and C2 deviate from the near planarity of other atoms (O3, C3, C1, and O1) by −0.413 (2) and −0.378 (2) Å, respectively. In the other ring, atoms B1 and C5 deviate from the mean plane of the other atoms (O5, C4, C6 and O6) by 0.386 (2) and 0.330 (2) Å, respectively. The dihedral angle between the boro-malonate rings is 76.5 (1)°, i.e., they are oriented almost perpendicular to each other. The [B(C₃H₂O₄)₂]⁻ anion is charge balanced by NH₄⁺ cations, which participate in an extensive hydrogen-bonded network.

Table 1
Selected geometric parameters (Å, °)

B1—O1	1.457 (3)	B1—O5	1.474 (3)
B1—O3	1.472 (3)	B1—O6	1.454 (3)

O1—B1—O3	112.42 (17)	O6—B1—O1	105.67 (17)
O1—B1—O5	108.36 (18)	O6—B1—O3	108.43 (18)
O3—B1—O5	109.46 (18)	O6—B1—O5	112.51 (17)

Figure 1
The molecular structure of (I) showing 50% displacement ellipsoids.

Figure 2
Side views of the chelate rings in (I) with torsion angles indicated.

3. Supramolecular features

The structural integrity of the extended structure of (I) is maintained by a network of N—H⋯O and C—H⋯O interactions (Fig. 3), as detailed in Table 2. Each [B(C₃H₂O₄)₂]⁻ anion accepts hydrogen bonds from five neighbouring NH₄⁺ cations (Fig. 4a). Conversely, every NH₄⁺ cation participates in analogous interactions with five adjacent [B(C₃H₂O₄)₂]⁻ anions (Fig. 4b). This results in the formation of a triangular-shaped supramolecular assembly (Fig. 4c).

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O2ⁱ	0.88 (2)	2.41 (2)	3.103 (3)	137 (2)
N1—H1A⋯O4ⁱⁱ	0.88 (2)	2.43 (2)	3.166 (3)	142 (2)
N1—H1B⋯O4ⁱⁱⁱ	0.83 (2)	2.32 (2)	2.970 (3)	136 (3)
N1—H1C⋯O7	0.86 (2)	2.03 (2)	2.864 (3)	165 (3)
N1—H1D⋯O8^iv	0.87 (2)	2.13 (2)	2.985 (3)	168 (3)
C2—H2A⋯O7^v	0.97	2.33	3.218 (3)	153
C2—H2B⋯O2^vi	0.97	2.48	3.181 (3)	129
C5—H5B⋯O6^vii	0.97	2.48	3.289 (3)	140
Symmetry codes: (i) ; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[x+1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iv) ; (v) ; (vi) ; (vii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 3
Packing diagram for (I) viewed down the a-axis direction. The dotted lines indicate the hydrogen bonds.

Figure 4
The environments of (a) the cation, (b) the anion and (c) the triangular supramolecular motif in (I); (d) the Hirshfeld surface for (I).

Hirshfeld surface analysis of (I) was performed using Crystal Explorer (Version 21.5; Spackman et al., 2021 ). Fig. 4d shows the d_norm surface for the [B(C₃H₂O₄)₂]⁻ anion where the intense red spots signify the shortest contacts (indicative of strong hydrogen bonds) and blue regions denote longer distances (suggesting weak van der Waals or repulsive interactions). Fig. 5 shows the two-dimensional fingerprint plots, with the overall interaction in Fig. 5a and the decomposed contributions and their percentages in Fig. 5b–5g. The hydrogen bonds are distinctly marked by sharp, symmetrical wings in the H⋯O/O⋯H plot (Fig. 5b), which dominates the Hirshfeld surface (69.9%).

Figure 5
Fingerprint plots for (I).

4. Database survey

A search of the Cambridge Structural Database (CSD 2025; Groom et al., 2016 ) using CCDC CONQUEST revealed two related bis(malonate)borate complexes, CSD refcode PODHAV (Selvi et al., 2024) and PITQUF (Zviedre & Belyakov, 2007), featuring Na⁺ and K⁺ counter-ions, respectively. While these exhibit malanato-borate coordination geometries very similar to (I), they differ fundamentally through their alkali metal coordination spheres as opposed to our ammonium variant. Notably, the potassium centre in PITQUF adopts an irregular nine-coordinate geometry with oxygen donors from seven distinct anions, whereas the sodium centre in PODHAV displays an intermediate coordination state – primarily square pyramidal (five O-donors) but transitioning to a distorted octahedron upon inclusion of a sixth, more weakly bound oxygen atom.

5. Synthesis and crystallization

A mixture of malonic acid, boric acid, and ammonium carbonate in a molar ratio of 4:2:1 was dissolved in double-distilled water while continuously stirring. The solution was gently heated to a temperature of 313–323 K to ensure complete dissolution, resulting in a clear, homogeneous mixture. It was then allowed to cool to room temperature and was filtered to remove any particulate impurities. The filtrate was transferred to a clean glass vessel, which was covered with a perforated lid to control evaporation, and placed in a draft-free environment maintained at a temperature of 298–303 K. Over a period of 60 days, slow evaporation of the solvent led to the growth of well-defined colourless blocks of (I). These were carefully extracted, rinsed with cold distilled water to eliminate surface impurities, and air-dried at room temperature.

6. Refinement

Crystal data, data collection and structure refinement details are summarised in Table 3. The carbon-bound hydrogen atoms were positioned based on calculated values (C—H = 0.96 Å) and were refined as riding atoms, with U_iso(H) set to 1.2 U_eq(C). For the NH₄⁺ ion, the hydrogen atoms were refined using DFIX restraints, maintaining an N—H distance of 0.86 Å and setting U_iso(H) to 1.4U_eq(N).

Table 3
Experimental details

Crystal data
Chemical formula	NH₄⁺·C₆H₄BO₈⁻
M_r	232.94
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	9.1825 (7), 7.6234 (6), 13.6905 (10)
β (°)	102.201 (2)
V (Å³)	936.71 (12)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	1.36
Crystal size (mm)	0.23 × 0.16 × 0.13

Data collection
Diffractometer	Bruker D8 VENTURE
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.526, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	14514, 1771, 1631
R_int	0.060
(sin θ/λ)_max (Å⁻¹)	0.610

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.066, 0.211, 1.15
No. of reflections	1771
No. of parameters	158
No. of restraints	10
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.27
Computer programs: APEX4 and SAINT (Bruker, 2021 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2455003

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989025007169/hb8150sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989025007169/hb8150Isup2.hkl

checkCIF report

Computing details top

Ammonium bis(malonato)borate top

Crystal data top

NH₄⁺·C₆H₄BO₈⁻	F(000) = 480
M_r = 232.94	D_x = 1.652 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 9.1825 (7) Å	Cell parameters from 9961 reflections
b = 7.6234 (6) Å	θ = 4.9–70.2°
c = 13.6905 (10) Å	µ = 1.36 mm⁻¹
β = 102.201 (2)°	T = 298 K
V = 936.71 (12) Å³	Block, colourless
Z = 4	0.23 × 0.16 × 0.13 mm

Data collection top

Bruker D8 VENTURE diffractometer	1631 reflections with I > 2σ(I)
ω and phi scans	R_int = 0.060
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 70.2°, θ_min = 4.9°
T_min = 0.526, T_max = 0.753	h = −11→10
14514 measured reflections	k = −9→9
1771 independent reflections	l = −16→16

Refinement top

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)] = 0.066	w = 1/[σ²(F_o²) + (0.1464P)² + 0.136P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.211	(Δ/σ)_max < 0.001
S = 1.15	Δρ_max = 0.22 e Å⁻³
1771 reflections	Δρ_min = −0.27 e Å⁻³
158 parameters	Extinction correction: SHELXL2019/3 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
10 restraints	Extinction coefficient: 0.027 (5)
Primary atom site location: dual

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
B1	0.3161 (3)	0.5528 (3)	0.36828 (18)	0.0533 (6)
C1	0.0934 (2)	0.6346 (3)	0.42603 (16)	0.0555 (6)
C2	0.0119 (3)	0.5359 (3)	0.33643 (18)	0.0613 (6)
H2A	−0.088477	0.582327	0.317487	0.074*
H2B	0.004154	0.414022	0.354991	0.074*
C3	0.0825 (2)	0.5434 (3)	0.24711 (16)	0.0558 (6)
C4	0.4578 (2)	0.2814 (3)	0.37743 (15)	0.0557 (6)
C5	0.5646 (3)	0.3847 (3)	0.33053 (17)	0.0577 (6)
H5A	0.663211	0.334372	0.352036	0.069*
H5B	0.536011	0.370650	0.258602	0.069*
C6	0.5738 (2)	0.5760 (3)	0.35371 (15)	0.0540 (6)
O1	0.24075 (17)	0.6373 (2)	0.43926 (11)	0.0607 (5)
O2	0.0333 (2)	0.7096 (2)	0.48443 (13)	0.0699 (6)
O3	0.22873 (16)	0.5613 (2)	0.26507 (10)	0.0567 (5)
O4	0.0112 (2)	0.5335 (3)	0.16249 (13)	0.0808 (7)
O5	0.34322 (16)	0.3679 (2)	0.39802 (11)	0.0580 (5)
O6	0.45349 (16)	0.6506 (2)	0.37350 (12)	0.0587 (5)
O7	0.68341 (18)	0.6631 (2)	0.35204 (15)	0.0691 (6)
O8	0.47475 (19)	0.1267 (2)	0.39622 (13)	0.0702 (6)
N1	0.7675 (2)	0.9580 (2)	0.48129 (16)	0.0622 (6)
H1A	0.833 (3)	1.024 (3)	0.461 (2)	0.093*
H1B	0.792 (3)	0.944 (4)	0.5427 (12)	0.093*
H1C	0.759 (3)	0.863 (3)	0.4469 (19)	0.093*
H1D	0.683 (2)	1.013 (3)	0.465 (2)	0.093*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
B1	0.0510 (12)	0.0578 (13)	0.0505 (12)	0.0042 (9)	0.0090 (9)	−0.0001 (9)
C1	0.0598 (12)	0.0537 (11)	0.0550 (12)	0.0032 (8)	0.0166 (9)	0.0023 (8)
C2	0.0538 (12)	0.0726 (14)	0.0583 (13)	−0.0037 (9)	0.0138 (10)	−0.0060 (9)
C3	0.0547 (11)	0.0614 (13)	0.0482 (11)	0.0031 (8)	0.0042 (9)	−0.0001 (8)
C4	0.0569 (12)	0.0572 (12)	0.0500 (11)	0.0025 (8)	0.0046 (8)	0.0003 (8)
C5	0.0611 (12)	0.0578 (12)	0.0553 (12)	0.0022 (9)	0.0145 (9)	−0.0041 (9)
C6	0.0519 (11)	0.0608 (12)	0.0470 (10)	0.0009 (9)	0.0053 (8)	−0.0031 (8)
O1	0.0577 (9)	0.0739 (11)	0.0494 (9)	0.0029 (7)	0.0088 (7)	−0.0083 (6)
O2	0.0768 (11)	0.0700 (11)	0.0693 (11)	0.0040 (8)	0.0301 (9)	−0.0108 (7)
O3	0.0542 (9)	0.0702 (10)	0.0463 (9)	0.0030 (6)	0.0117 (6)	0.0019 (6)
O4	0.0700 (11)	0.1141 (16)	0.0515 (10)	−0.0003 (10)	−0.0026 (8)	−0.0018 (9)
O5	0.0552 (9)	0.0586 (9)	0.0601 (9)	0.0022 (6)	0.0121 (7)	0.0055 (6)
O6	0.0523 (9)	0.0552 (9)	0.0675 (10)	0.0009 (6)	0.0103 (7)	−0.0031 (6)
O7	0.0554 (10)	0.0697 (11)	0.0822 (12)	−0.0094 (7)	0.0150 (8)	−0.0105 (8)
O8	0.0737 (11)	0.0561 (10)	0.0786 (12)	0.0055 (7)	0.0110 (9)	0.0073 (7)
N1	0.0591 (11)	0.0613 (11)	0.0629 (12)	0.0001 (8)	0.0058 (9)	−0.0016 (8)

Geometric parameters (Å, º) top

B1—O1	1.457 (3)	C4—C5	1.503 (3)
B1—O3	1.472 (3)	C4—O5	1.321 (3)
B1—O5	1.474 (3)	C4—O8	1.211 (3)
B1—O6	1.454 (3)	C5—H5A	0.9700
C1—C2	1.497 (3)	C5—H5B	0.9700
C1—O1	1.327 (3)	C5—C6	1.491 (3)
C1—O2	1.207 (3)	C6—O6	1.321 (3)
C2—H2A	0.9700	C6—O7	1.210 (3)
C2—H2B	0.9700	N1—H1A	0.875 (15)
C2—C3	1.502 (3)	N1—H1B	0.830 (15)
C3—O3	1.320 (3)	N1—H1C	0.859 (15)
C3—O4	1.207 (3)	N1—H1D	0.867 (15)

O1—B1—O3	112.42 (17)	O8—C4—O5	120.9 (2)
O1—B1—O5	108.36 (18)	C4—C5—H5A	108.3
O3—B1—O5	109.46 (18)	C4—C5—H5B	108.3
O6—B1—O1	105.67 (17)	H5A—C5—H5B	107.4
O6—B1—O3	108.43 (18)	C6—C5—C4	115.73 (19)
O6—B1—O5	112.51 (17)	C6—C5—H5A	108.3
O1—C1—C2	116.00 (18)	C6—C5—H5B	108.3
O2—C1—C2	124.1 (2)	O6—C6—C5	116.89 (19)
O2—C1—O1	119.9 (2)	O7—C6—C5	122.9 (2)
C1—C2—H2A	108.5	O7—C6—O6	120.2 (2)
C1—C2—H2B	108.5	C1—O1—B1	121.11 (17)
C1—C2—C3	114.89 (19)	C3—O3—B1	120.08 (17)
H2A—C2—H2B	107.5	C4—O5—B1	120.90 (18)
C3—C2—H2A	108.5	C6—O6—B1	121.61 (18)
C3—C2—H2B	108.5	H1A—N1—H1B	110 (2)
O3—C3—C2	116.73 (18)	H1A—N1—H1C	108 (2)
O4—C3—C2	122.6 (2)	H1A—N1—H1D	106 (2)
O4—C3—O3	120.6 (2)	H1B—N1—H1C	115 (2)
O5—C4—C5	116.80 (19)	H1B—N1—H1D	111 (2)
O8—C4—C5	122.3 (2)	H1C—N1—H1D	107 (2)

C1—C2—C3—O3	29.3 (3)	O3—B1—O1—C1	33.4 (3)
C1—C2—C3—O4	−150.8 (2)	O3—B1—O5—C4	86.0 (2)
C2—C1—O1—B1	1.7 (3)	O3—B1—O6—C6	−87.6 (2)
C2—C3—O3—B1	6.9 (3)	O4—C3—O3—B1	−172.9 (2)
C4—C5—C6—O6	−28.2 (3)	O5—B1—O1—C1	−87.7 (2)
C4—C5—C6—O7	154.0 (2)	O5—B1—O3—C3	82.4 (2)
C5—C4—O5—B1	5.0 (3)	O5—B1—O6—C6	33.6 (3)
C5—C6—O6—B1	−2.9 (3)	O5—C4—C5—C6	26.9 (3)
O1—B1—O3—C3	−38.1 (3)	O6—B1—O1—C1	151.48 (19)
O1—B1—O5—C4	−151.11 (17)	O6—B1—O3—C3	−154.56 (18)
O1—B1—O6—C6	151.66 (19)	O6—B1—O5—C4	−34.7 (3)
O1—C1—C2—C3	−33.8 (3)	O7—C6—O6—B1	175.0 (2)
O2—C1—C2—C3	145.9 (2)	O8—C4—C5—C6	−152.8 (2)
O2—C1—O1—B1	−178.0 (2)	O8—C4—O5—B1	−175.3 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2ⁱ	0.88 (2)	2.41 (2)	3.103 (3)	137 (2)
N1—H1A···O4ⁱⁱ	0.88 (2)	2.43 (2)	3.166 (3)	142 (2)
N1—H1B···O4ⁱⁱⁱ	0.83 (2)	2.32 (2)	2.970 (3)	136 (3)
N1—H1C···O7	0.86 (2)	2.03 (2)	2.864 (3)	165 (3)
N1—H1D···O8^iv	0.87 (2)	2.13 (2)	2.985 (3)	168 (3)
C2—H2A···O7^v	0.97	2.33	3.218 (3)	153
C2—H2B···O2^vi	0.97	2.48	3.181 (3)	129
C5—H5B···O6^vii	0.97	2.48	3.289 (3)	140

Symmetry codes: (i) −x+1, −y+2, −z+1; (ii) −x+1, y+1/2, −z+1/2; (iii) x+1, −y+3/2, z+1/2; (iv) x, y+1, z; (v) x−1, y, z; (vi) −x, −y+1, −z+1; (vii) −x+1, y−1/2, −z+1/2.

Acknowledgements

The authors thank the Sophisticated Analytical Instrument Facility (SAIF), Indian Institute of Technology Madras (IITM), Chennai, Tamilnadu, India, for the single-crystal X-ray diffraction data. GG, UG and IK gratefully acknowledge the infrastructural facilities at the DST–CURIE lab (DST-CURIE–PG/2022/54).

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