Crystal structure of propane-1,3-diaminium squarate dihydrate

Propane-1,3-diaminium squarate dihydrate, C₃H₁₂N₂²⁺·C₄O₄²⁻·2H₂O, results from the proton-transfer reaction of propane-1,3-di­amine with squaric acid and subsequent crystallization from aqueous medium. The title compound crystallizes in the tetra­gonal crystal system (space group P4bm) with Z = 2. The squarate dianion belongs to the point group D_4h and contains a crystallographic fourfold axis. The propane-1,3-diaminium dication exhibits a C_2v-symmetric all-anti conformation and resides on a special position with mm2 site symmetry. The orientation of the propane-1,3-diaminium ions makes the crystal structure polar in the c-axis direction. The solid-state supra­molecular structure features a triperiodic network of strong hydrogen bonds of the N—H⋯O and O—H⋯O types.

1. Chemical context

Squaric acid (H₂C₄O₄; systematic name: 3,4-di­hydroxy­cyclo­but-3-ene-1,2-dione) and its derivatives have been widely studied in organic chemistry and materials science (Grus et al., 2021; Laramie et al., 2017; Wurm & Klok, 2013; Xia & Wang, 2017). Squaric acid analogues have also attracted attention in medicinal chemistry (Chasák et al., 2021; Ruseva et al., 2022). In structural chemistry, the inter­est in squaric acid and its mono- and dianions arises mainly from their planar, sym­metrical and strained mol­ecular structures and their diverse hydrogen-bonding patterns in the solid state (Allen et al., 2013; Gilli et al., 2001). As a strong diprotic organic acid with pK_a1 = 0.59 ± 0.09 and pK_a2 = 3.48 ± 0.023 at 298 K (as determined by potentiometric titrations; Schwartz & Howard, 1970), squaric acid readily forms proton-transfer compounds with nitro­gen bases and a wide variety of structurally characterized examples can be found in the Cambridge Structural Database (CSD; Groom et al., 2016). In the present contribution, we describe the crystal structure of the dihydrate of the proton-transfer compound propane-1,3-diaminium squar­ate.

2. Structural commentary

Fig. 1 shows the mol­ecular structures of the components of the title compound in the crystal. The squarate dianion exhibits D_4h point-group symmetry and contains a crystallographic fourfold rotation axis with the direction [001]. The propane-1,3-diaminium dication adopts a C_2v-symmetric all-anti conformation and is located on a special position with mm2 site symmetry in the crystal structure. The overall orientation of the mol­ecular dications renders the crystal structure polar in the c-axis direction. The water mol­ecule of crystallization sits on a crystallographic mirror plane perpendicular to the [110] direction.

Figure 1 Displacement ellipsoid plot (50% probability level) of the title compound. Hydrogen atoms are shown by small spheres of arbitrary radius. Dashed lines represent hydrogen bonds. Symmetry codes: (iv) y, −x, z; (v) −x, −y, z; (vi) −y, x, z; (vii) −x + 1, −y, z;

3. Supra­molecular features

Apart from ion–ion inter­actions between propane-1,3-diamin­ium dications and squarate dianions, hydrogen bonding dominates the solid-state structure of the title compound. The protonated amino group joins two squarate ions via N—H⋯O hydrogen bonds. The remaining hydrogen-bond donor site of the aminium group forms an N—H⋯O hydrogen bond to a water mol­ecule (Fig. 2). The water mol­ecule in turn acts as hydrogen-bond acceptor towards two squarate ions, which results in a triperiodic hydrogen-bond network (Fig. 3). Table 1 lists the corresponding hydrogen-bond parameters, which are characteristic of strong hydrogen bonds (Thakuria et al., 2017). The centroid–centroid distance between the squarate ions in the [001] direction corresponds to the c lattice parameter. A packing index of 67.8% (Kitajgorodskij, 1973), as calculated with PLATON (Spek, 2020), indicates a relatively open structure. This lends support to the view that strong hydrogen bonding governs the structure rather than van der Waals close packing.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O2	0.85 (3)	1.92 (3)	2.758 (2)	171 (3)
N1—H1B⋯O1^i	0.896 (19)	1.905 (18)	2.7887 (12)	168.4 (17)
O2—H2A⋯O1	0.84 (2)	1.91 (2)	2.7413 (13)	175 (2)
Symmetry code: (i) .

Figure 2 Section of the crystal structure of the title compound, viewed approximately along the [010] direction. Dashed lines illustrate hydrogen bonds. Symmetry codes: (i) x + , −y + , z + 1; (ii) −y + , −x + , z; (iii) y, −x, z + 1.

Figure 3 The tetra­gonal unit cell of the title compound, projected along the c-axis direction. Dashed lines illustrate hydrogen bonds. Colour scheme: C, grey; H, white; N, blue; O, red.

4. Database survey

The CSD (version 5.43 with September 2022 updates; Groom et al., 2016) contains >400 crystal structures with propane-1,3-diaminium cations and >100 crystal structures with squarate dianions. A structure closely related to the title compound is that of the homologous pentane-1,5-diaminium squarate dihydrate (CSD refcode: JARGAN; Ivanova & Spiteller, 2014). In contrast to the title compound, the crystal structure of JARGAN is centrosymmetric, although the pentane-1,5-diaminium cation likewise exhibits a polar (approximately) C_2v-symmetric all-anti conformation. A solvent-free crystal structure of propane-1,3-diaminum bis­(hydrogen squarate) has also been published (TURQEC; Mathew et al., 2002). The propane-1,3-diaminum cations in TURQEC similarly adopt an all-anti conformation with approximate C_2v point-group symmetry, but the crystal structure is centrosymmetric. Worthy of note, a low-temperature crystal structure determination of the parent free-base propane-1,3-di­amine, which is liquid at room temperature, has also been disclosed (QATVUC; Thalladi et al., 2000).

5. Synthesis and crystallization

Starting materials were obtained from commercial sources and used as received. A solution of propane-1,3-di­amine (148 mg, 2 mmol) in 25 mL of ethanol was mixed with a solution of squaric acid (228 mg, 2 mmol) in 40 mL of distilled water. After stirring at 333 K for 4 h, the mixture was left at ambient conditions. After three weeks, colourless crystalline material was collected by filtration and air-dried. Colourless crystals of the title compound suitable for single-crystal X-ray diffraction were grown from methanol/water (1:1) by the slow evaporation method.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. Hydrogen-atom positions were refined freely, and U_iso(H) values were set 1.2U_eq(C, N, O) to improve the data/parameter ratio. The direction of the polar axis was chosen to give a Flack x parameter, as calculated by Parsons' quotient method (Parsons et al., 2013), close to zero. In the absence of significant anomalous scattering, however, the polar axis direction could not be determined reliably in view of the high standard uncertainty of the Flack x parameter (Flack & Bernardinelli, 1999). For this reason, the presence of inversion twinning also cannot be excluded.

Table 2
Experimental details

Crystal data
Chemical formula	C3H12N2^2+·C4O4^2−·2H2O
Mr	224.22
Crystal system, space group	Tetragonal, P4bm
Temperature (K)	105
a, c (Å)	11.2716 (2), 4.3310 (1)
V (Å^3)	550.25 (2)
Z	2
Radiation type	Mo Kα
μ (mm^−1)	0.12
Crystal size (mm)	0.23 × 0.16 × 0.11
Data collection
Diffractometer	Oxford Diffraction Xcalibur2
Absorption correction	Multi-scan [ABSPACK in CrysAlis PRO (Rigaku OD, 2023)]
Tmin, Tmax	0.928, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	11463, 745, 721
Rint	0.027
(sin θ/λ)max (Å^−1)	0.679
Refinement
R[F^2 > 2σ(F^2)], wR(F^2), S	0.027, 0.070, 1.09
No. of reflections	745
No. of parameters	54
No. of restraints	1
H-atom treatment	Only H-atom coordinates refined
Δρmax, Δρmin (e Å^−3)	0.38, −0.13
Absolute structure	Flack x determined using 298 quotients [(I^+)−(I^−)]/[(I^+)+(I^−)] (Parsons et al., 2013)
Absolute structure parameter	0.1 (5)
Computer programs: CrysAlis system (Oxford Diffraction, 2009), CrysAlis PRO (Rigaku OD, 2023), SHELXS97 (Sheldrick, 2008), SHELXL2019/3 (Sheldrick, 2015), DIAMOND (Brandenburg, 2018) and publCIF (Westrip, 2010).

Supporting information

Computing details

Propane-1,3-diaminium 3,4-dioxocyclobutene-1,2-diolate dihydrate

Crystal data

C3H12N2^2+·C4O4^2^−·2H2O	Dx = 1.353 Mg m^−3
Mr = 224.22	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P4bm	Cell parameters from 5992 reflections
a = 11.2716 (2) Å	θ = 3.6–28.7°
c = 4.3310 (1) Å	µ = 0.12 mm^−1
V = 550.25 (2) Å^3	T = 105 K
Z = 2	Block, colourless
F(000) = 240	0.23 × 0.16 × 0.11 mm

Data collection

Oxford Diffraction Xcalibur2 diffractometer	745 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source	721 reflections with I > 2σ(I)
Detector resolution: 8.4171 pixels mm^-1	Rint = 0.027
ω scans	θmax = 28.9°, θmin = 3.6°
Absorption correction: multi-scan [ABSPACK in CrysAlisPro (Rigaku OD, 2023)]	h = −15→15
Tmin = 0.928, Tmax = 1.000	k = −15→14
11463 measured reflections	l = −5→5

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.027	Only H-atom coordinates refined
wR(F^2) = 0.070	w = 1/[σ^2(Fo^2) + (0.045P)^2 + 0.0625P] where P = (Fo^2 + 2Fc^2)/3
S = 1.09	(Δ/σ)max < 0.001
745 reflections	Δρmax = 0.38 e Å^−3
54 parameters	Δρmin = −0.13 e Å^−3
1 restraint	Absolute structure: Flack x determined using 298 quotients [(I^+)-(I^-)]/[(I^+)+(I^-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.1 (5)

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.00512 (11)	0.09200 (10)	0.0161 (4)	0.0143 (3)
C2	0.42195 (10)	0.07805 (10)	0.5294 (5)	0.0137 (4)
H2	0.4703 (15)	0.1281 (16)	0.407 (5)	0.016*
C3	0.500000	0.000000	0.7310 (7)	0.0129 (5)
H3	0.5480 (17)	0.0480 (17)	0.851 (6)	0.015*
N1	0.34377 (9)	0.15623 (9)	0.7173 (4)	0.0126 (3)
H1A	0.3011 (18)	0.1989 (18)	0.601 (7)	0.015*
H1B	0.3902 (15)	0.2026 (15)	0.834 (5)	0.015*
O1	0.01160 (8)	0.20294 (8)	0.0165 (3)	0.0188 (3)
O2	0.21736 (10)	0.28264 (10)	0.2827 (4)	0.0244 (4)
H2A	0.1556 (18)	0.2608 (18)	0.191 (5)	0.029*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0114 (5)	0.0119 (6)	0.0196 (5)	0.0002 (4)	−0.0025 (5)	0.0017 (7)
C2	0.0144 (5)	0.0144 (5)	0.0123 (7)	0.0006 (6)	−0.0005 (6)	0.0005 (6)
C3	0.0132 (7)	0.0132 (7)	0.0124 (11)	0.0005 (9)	0.000	0.000
N1	0.0117 (5)	0.0117 (5)	0.0144 (6)	0.0004 (5)	−0.0013 (5)	0.0013 (5)
O1	0.0149 (4)	0.0098 (4)	0.0316 (5)	−0.0004 (3)	−0.0064 (5)	0.0014 (5)
O2	0.0197 (5)	0.0197 (5)	0.0337 (9)	−0.0071 (6)	−0.0117 (5)	0.0117 (5)

Geometric parameters (Å, º)

C1—O1	1.2527 (14)	C3—H3	0.92 (3)
C1—C1^i	1.4687 (15)	C3—H3^iv	0.92 (3)
C1—C1^ii	1.4687 (15)	N1—H1A	0.85 (3)
C2—N1	1.488 (2)	N1—H1B	0.896 (19)
C2—C3	1.520 (3)	N1—H1B^iii	0.896 (19)
C2—H2	0.946 (19)	O2—H2A	0.84 (2)
C2—H2^iii	0.946 (19)	O2—H2A^iii	0.84 (2)
O1—C1—C1^i	135.16 (13)	C2^iv—C3—H3	108.8 (8)
O1—C1—C1^ii	134.84 (13)	C2—C3—H3^iv	108.8 (8)
C1^i—C1—C1^ii	89.999 (1)	C2^iv—C3—H3^iv	108.8 (8)
N1—C2—C3	111.80 (18)	H3—C3—H3^iv	112 (3)
N1—C2—H2	107.1 (11)	C2—N1—H1A	110 (2)
C3—C2—H2	109.4 (11)	C2—N1—H1B	108.0 (11)
N1—C2—H2^iii	107.1 (11)	H1A—N1—H1B	109.7 (14)
C3—C2—H2^iii	109.4 (11)	C2—N1—H1B^iii	108.0 (11)
H2—C2—H2^iii	112 (2)	H1A—N1—H1B^iii	109.7 (14)
C2—C3—C2^iv	109.9 (2)	H1B—N1—H1B^iii	111 (2)
C2—C3—H3	108.8 (8)	H2A—O2—H2A^iii	105 (3)
N1—C2—C3—C2^iv	180.000 (1)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1^v	0.946 (19)	2.590 (19)	3.4712 (18)	155.1 (14)
N1—H1A···O2	0.85 (3)	1.92 (3)	2.758 (2)	171 (3)
N1—H1B···O1^vi	0.896 (19)	1.905 (18)	2.7887 (12)	168.4 (17)
O2—H2A···O1	0.84 (2)	1.91 (2)	2.7413 (13)	175 (2)

Symmetry codes: (v) x+1/2, −y+1/2, z; (vi) x+1/2, −y+1/2, z+1.