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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2025 Aug 19;81(Pt 9):849–852. doi: 10.1107/S2056989025007169

Synthesis and structure of ammonium bis­(malonato)borate

Gokila Govindharajan a, Ramachandra Raja Chidambaram b, Gnanasheela Uthamaselvan c, Kalaiarasi Iyathurai c, Kamatchi Karthikeyan d, Sampath Natarajan e,*
Editor: W T A Harrisonf
PMCID: PMC12412698  PMID: 40918579

The title salt features BO4 tetra­hedra at the centre of [B(C3H2O4)2] anions.

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

Abstract

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.

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).1.

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 QT = 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.

Figure 1.

Figure 1

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

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 2.

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).

Figure 3.

Figure 3

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

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA 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⋯O8iv 0.87 (2) 2.13 (2) 2.985 (3) 168 (3)
C2—H2A⋯O7v 0.97 2.33 3.218 (3) 153
C2—H2B⋯O2vi 0.97 2.48 3.181 (3) 129
C5—H5B⋯O6vii 0.97 2.48 3.289 (3) 140

Symmetry codes: (i) Inline graphic; (ii) Inline graphic; (iii) Inline graphic; (iv) Inline graphic; (v) Inline graphic; (vi) Inline graphic; (vii) Inline graphic.

Figure 4.

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 dnorm 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.

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 Uiso(H) set to 1.2 Ueq(C). For the NH4+ ion, the hydrogen atoms were refined using DFIX restraints, maintaining an N—H distance of 0.86 Å and setting Uiso(H) to 1.4Ueq(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)
V3) 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)
Tmin, Tmax 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−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
Δρmax, Δρmin (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).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989025007169/hb8150sup1.cif

e-81-00849-sup1.cif (452.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989025007169/hb8150Isup2.hkl

e-81-00849-Isup2.hkl (142.6KB, hkl)

CCDC reference: 2455003

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

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).

supplementary crystallographic information

Ammonium bis(malonato)borate. Crystal data

NH4+·C6H4BO8 F(000) = 480
Mr = 232.94 Dx = 1.652 Mg m3
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 mm1
β = 102.201 (2)° T = 298 K
V = 936.71 (12) Å3 Block, colourless
Z = 4 0.23 × 0.16 × 0.13 mm

Ammonium bis(malonato)borate. Data collection

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

Ammonium bis(malonato)borate. Refinement

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(Fo2) + (0.1464P)2 + 0.136P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.211 (Δ/σ)max < 0.001
S = 1.15 Δρmax = 0.22 e Å3
1771 reflections Δρmin = −0.27 e Å3
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

Ammonium bis(malonato)borate. Special details

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.

Ammonium bis(malonato)borate. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
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*

Ammonium bis(malonato)borate. Atomic displacement parameters (Å2)

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)

Ammonium bis(malonato)borate. Geometric parameters (Å, º)

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)

Ammonium bis(malonato)borate. Hydrogen-bond geometry (Å, º)

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···O8iv 0.87 (2) 2.13 (2) 2.985 (3) 168 (3)
C2—H2A···O7v 0.97 2.33 3.218 (3) 153
C2—H2B···O2vi 0.97 2.48 3.181 (3) 129
C5—H5B···O6vii 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.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989025007169/hb8150sup1.cif

e-81-00849-sup1.cif (452.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989025007169/hb8150Isup2.hkl

e-81-00849-Isup2.hkl (142.6KB, hkl)

CCDC reference: 2455003

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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