Poly[propane-1,3-diammonium [diaqua­tetra­kis(μ₄-benzene-1,2,4,5-tetra­carboxyl­ato)nickelate(II)] hemihydrate]

The reaction of nickel(II) nitrate hexa­hydrate with the proton-transfer compound (pnH₂)₂(btc)·2H₂O (where pn = propane-1,3-diamine and btcH₄ = benzene-1,2,4,5-tetra­carboxylic acid) in aqueous solution resulted in the formation of the title compound, {(C₃H₁₂N₂)[Ni(C₁₀H₂O₈)(H₂O)₂]·0.5H₂O}_n. Each Ni²⁺ ion is situated on a crystallographic twofold rotation axis and is coordinated in a distorted octa­hedral geometry by six O atoms [Ni—O = 2.0540 (15)–2.0804 (11) Å] from two water mol­ecules and four btc⁴⁻ ligands, which also act as bridging ligands between Ni²⁺ ions. In the crystal structure, inter­molecular O—H...O, N—H...O and C—H...O hydrogen bonds and C—H...π inter­actions contribute to the formation of a three-dimensional supra­molecular structure. The crystal studied was an inversion twin.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• Disorder in solvent or counterion
• R factor = 0.028
• wR factor = 0.073
• Data-to-parameter ratio = 18.4

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT111_ALERT_2_B ADDSYM Detects (Pseudo) Centre of Symmetry .....         86 PerFi

Alert level C
STRVA01_ALERT_4_C           Flack test results are ambiguous.
           From the CIF: _refine_ls_abs_structure_Flack    0.412
           From the CIF: _refine_ls_abs_structure_Flack_su    0.017
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............       0.50 Ratio
PLAT076_ALERT_1_C Occupancy       0.50 less than 1.0 for Sp.pos  .        H6A
PLAT302_ALERT_4_C Anion/Solvent Disorder .........................       7.00 Perc.
PLAT313_ALERT_2_C Oxygen with three covalent bonds (rare) ........         O6

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           30.04
           From the CIF: _reflns_number_total               2424
           Count of symmetry unique reflns         1309
           Completeness (_total/calc)            185.18%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1115
           Fraction of Friedel pairs measured     0.852
           Are heavy atom types Z>Si present        yes
PLAT033_ALERT_2_G Flack Parameter Value Deviates 2 * su from zero.       0.41
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   7 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Just as there is a field of molecular chemistry based on the covalent bond, there is a field of supramolecular chemistry, the chemistry of molecular assemblies and intermolecular interactions. The importance of weak hydrogen bonds in the context of crystal engineering, molecular recognition and supramolecular chemistry have been well recognized in recent years. In this regard, we have reported cases in which proton transfer from pyridine-2,6-dicarboxylic acid (pydcH₂) and benzene-1,2,4,5-tetracarboxylicacid (btcH₄) to piperazine (pipz), propane-1,3-diamine and 1,10-phenanthroline (phen) resulted in the formation of novel self-assembled (pipzH₂)(pydc), (pnH₂)₂(btc).2H₂O (Aghabozorg, et al., 2007) and (phenH)₄(btcH₃)₂(btcH₂) (Aghabozorg, Ghadermazi & Gharamaleki, 2006) systems, respectively. The resulting compounds with some remaining sites as electron donors can coordinate to metallic ions (Aghabozorg, Ghasemikhah et al., 2006; Aghabozorg, Zabihi et al., 2006).

Here we report a new polymeric compound obtained from reaction of (pnH₂)₂(btc).2H₂O with nickel(II) nitrate. The crystal structure of the title polymeric compound is shown in Fig. 1. The intermolecular hydrogen bond distances are listed in the Table. The negative charge of the anionic complex is neutralized by dicationic propane-1,3-diaminium species. According to the crystal structure of (I), the coordination around Ni^II is distorted octahedral. A considerable feature of the compound (I) is the presence of C—H···π stacking interactions between C—H groups of (pnH₂)²⁺ cations and aromatic rings of (btc)^4– fragments. The C—H···π distances (measured to the centre of phenyl ring) are 2.60 Å for C8—H8A···Cg1 and 2.97 Å for C7—H7A···Cg1 with the angles of 142° and 137°, respectively [Cg1 is a centroid of C1—C4/C2ⁱ/C3ⁱ; symmetry code: (i) 1/2 + x, -1/2 + y, -1/2 + z]. The most important features of the crystal structure of (I) is a number of O—H···O, N—H···O and C—H···O hydrogen bonds between (pnH₂)²⁺ and [Ni(H₂O)₂(btc)]^2– fragments and uncoordinated water molecules with D···A distances ranging from 2.668 (2) Å to 3.242 (2) Å (Table). Ion pairing, C—H···π stacking and van der Waals forces are also effective in the stabilization of the crystal structure, resulting in the formation of an interesting supramolecular structure (Fig. 2).

Related literature

For details of the preparation of related proton-transfer compounds, see: Aghabozorg et al. (2007); Aghabozorg, Ghadermazi & Attar Gharamaleki (2006). For the crystal structures of related complexes, see: Aghabozorg, Ghasemikhah et al. (2006); Aghabozorg, Zabihi et al. (2006).

S2. Experimental

The proton-transfer compound was prepared by a reaction between propane-1,3-diamine and benzene-1,2,4,5-tetracarboxylic acid (Aghabozorg et al., 2007). Starting with a 1:1 molar ratio of the reactants in THF, a puffy white precipitate was obtained. By recrystallization in an aqueous solution, pale-yellow crystals were obtained. A solution of Ni(NO₃)₂.6H₂O (143 mg, 0.5 mmol) in water (15 ml) was added to an aqueous solution of (pnH₂)₂(btc).2H₂O (253 mg, 1.0 mmol) in water (15 ml) in a 1:2 molar ratio. Crystals of (I) suitable for X-ray characterization were obtained after a few days at room temperature.

S3. Refinement

The value of the Flack parameter of 0.412 (17) indicates that the absolute structure in this case cannot be determined unambiguously due to the specific centrosymmetric arrangement of the anionic pattern. The refinement of the structure in the centrosymmetric space group Imma gives rise to disodering of the dication.

The hydrogen atoms of coordinate water molecules and –NH3 groups were localized in difference Fourier synthesis, but placed in idealized positions (O—H 0.90 Å, N—H 0.90–0.92 Å). C-bound H atoms were placed in calculated positions (C—H 0.95–0.99 Å). The crystalline water molecule was treated as disordered between two positions related by a mirror plane with the occupancies of 0.25 (for O6) The attached H atoms were positioned geometrically (O—H 0.96, 0.97 Å). All H atoms were refined in a riding model with U_iso(H)=1.2–1.3Ueq of the parent atom.

Computing details

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The structure of (I), showing the atom-numbering scheme and displacement ellipsoids at the 50% probability level.
	Fig. 2. The crystal packing of (I). Hydrogen bonds are shown as dashed lines.

Poly[propane-1,3-diammonium [diaquatetrakis(µ₄-benzene-1,2,4,5-tetracarboxylato)nickelate(II)] hemihydrate]

Crystal data

(C3H12N2)[Ni(C10H2O8)(H2O)2]·0.5H2O	F(000) = 892
Mr = 430.01	Dx = 1.716 Mg m^−3
Orthorhombic, Ima2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: I 2 -2a	Cell parameters from 6046 reflections
a = 16.3724 (6) Å	θ = 2.5–30.0°
b = 7.1673 (4) Å	µ = 1.23 mm^−1
c = 14.1857 (8) Å	T = 100 K
V = 1664.63 (15) Å^3	Prism, colourless
Z = 4	0.30 × 0.30 × 0.20 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer	2424 independent reflections
Radiation source: fine-focus sealed tube	2353 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.022
φ and ω scans	θmax = 30.0°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −23→22
Tmin = 0.710, Tmax = 0.792	k = −10→10
10153 measured reflections	l = −19→19

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.028	H-atom parameters constrained
wR(F^2) = 0.073	w = 1/[σ^2(Fo^2) + (0.05P)^2 + 1.1P] where P = (Fo^2 + 2Fc^2)/3
S = 1.00	(Δ/σ)max < 0.001
2424 reflections	Δρmax = 0.44 e Å^−3
132 parameters	Δρmin = −0.24 e Å^−3
1 restraint	Absolute structure: Flack (1983), 1113 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.412 (17)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
N1	0.59831 (9)	0.2336 (2)	0.13471 (12)	0.0224 (3)
H1A	0.5517	0.2517	0.1007	0.027*
H1B	0.6023	0.3068	0.1862	0.027*
H1C	0.5982	0.1168	0.1618	0.027*
C7	0.67406 (11)	0.2598 (3)	0.07757 (14)	0.0223 (4)
H7A	0.6754	0.3883	0.0521	0.027*
H7B	0.6737	0.1719	0.0237	0.027*
C8	0.7500	0.2259 (4)	0.1374 (2)	0.0227 (4)
H8A	0.7500	0.0960	0.1611	0.027*
H8B	0.7500	0.3113	0.1922	0.027*
Ni1	0.5000	0.5000	0.35324 (4)	0.01460 (8)
O1	0.40867 (9)	0.4393 (2)	0.44765 (10)	0.0196 (3)
O2	0.46016 (8)	0.19013 (19)	0.52250 (10)	0.0223 (3)
O3	0.41573 (8)	0.0581 (2)	0.74825 (10)	0.0186 (3)
O4	0.43957 (8)	0.36127 (18)	0.71826 (10)	0.0217 (2)
O5	0.54310 (7)	0.22702 (15)	0.35648 (11)	0.0198 (2)
H5A	0.5196	0.1739	0.3058	0.024*
H5B	0.5204	0.1936	0.4118	0.024*
C1	0.2500	0.3097 (4)	0.50968 (18)	0.0180 (5)
H1	0.2500	0.3499	0.4459	0.022*
C2	0.32398 (11)	0.2805 (3)	0.55610 (13)	0.0166 (3)
C3	0.32397 (11)	0.2229 (2)	0.65041 (13)	0.0164 (3)
C4	0.2500	0.1941 (4)	0.69672 (17)	0.0161 (4)
H4	0.2500	0.1544	0.7606	0.019*
C5	0.40460 (11)	0.3053 (3)	0.50457 (12)	0.0179 (3)
C6	0.40005 (11)	0.2128 (2)	0.70882 (13)	0.0162 (3)
O6	0.7040 (7)	0.0338 (19)	0.3588 (14)	0.088 (4)	0.25
H6A	0.7500	−0.0326	0.3312	0.105*	0.50
H6B	0.6575	−0.0252	0.3298	0.105*	0.25

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0173 (6)	0.0238 (7)	0.0261 (7)	−0.0001 (5)	0.0008 (5)	−0.0031 (6)
C7	0.0207 (7)	0.0201 (8)	0.0261 (9)	−0.0002 (6)	0.0001 (6)	−0.0003 (7)
C8	0.0197 (10)	0.0217 (11)	0.0266 (11)	0.000	0.000	−0.0006 (9)
Ni1	0.01386 (12)	0.01624 (12)	0.01370 (12)	−0.00143 (8)	0.000	0.000
O1	0.0189 (6)	0.0204 (6)	0.0194 (6)	0.0014 (5)	0.0036 (5)	0.0037 (5)
O2	0.0193 (6)	0.0244 (6)	0.0233 (6)	0.0033 (5)	0.0031 (5)	0.0027 (5)
O3	0.0186 (6)	0.0191 (6)	0.0181 (6)	0.0010 (5)	−0.0030 (5)	0.0009 (5)
O4	0.0202 (5)	0.0209 (6)	0.0240 (6)	−0.0022 (5)	−0.0049 (5)	0.0026 (5)
O5	0.0211 (5)	0.0205 (5)	0.0177 (5)	−0.0003 (4)	−0.0020 (6)	−0.0010 (5)
C1	0.0179 (11)	0.0218 (11)	0.0145 (11)	0.000	0.000	0.0021 (9)
C2	0.0160 (7)	0.0181 (8)	0.0157 (8)	−0.0012 (6)	0.0027 (7)	0.0021 (6)
C3	0.0146 (7)	0.0164 (7)	0.0181 (8)	−0.0006 (6)	0.0001 (6)	−0.0002 (6)
C4	0.0156 (10)	0.0151 (10)	0.0175 (12)	0.000	0.000	0.0009 (8)
C5	0.0154 (7)	0.0210 (8)	0.0173 (8)	−0.0020 (6)	0.0014 (6)	−0.0016 (6)
C6	0.0144 (7)	0.0199 (8)	0.0144 (7)	0.0010 (6)	0.0013 (6)	0.0005 (6)
O6	0.071 (6)	0.137 (10)	0.055 (6)	0.048 (6)	−0.004 (8)	−0.008 (8)

Geometric parameters (Å, º)

N1—C7	1.493 (2)	O2—C5	1.254 (2)
N1—H1A	0.9121	O3—C6	1.268 (2)
N1—H1B	0.9011	O4—C6	1.253 (2)
N1—H1C	0.9210	O5—H5A	0.9000
C7—C8	1.525 (3)	O5—H5B	0.9011
C7—H7A	0.9900	C1—C2	1.394 (2)
C7—H7B	0.9900	C1—H1	0.9500
C8—C7^i	1.525 (3)	C2—C3	1.400 (2)
C8—H8A	0.9900	C2—C5	1.519 (3)
C8—H8B	0.9900	C3—C4	1.393 (2)
Ni1—O1	2.0540 (15)	C3—C6	1.498 (3)
Ni1—O3^ii	2.0724 (14)	C4—H4	0.9500
Ni1—O5	2.0804 (11)	O6—H6A	0.9729
O1—C5	1.257 (2)	O6—H6B	0.9631
C7—N1—H1A	112.9	O5^iii—Ni1—O5	177.46 (10)
C7—N1—H1B	107.8	C5—O1—Ni1	128.29 (13)
H1A—N1—H1B	114.0	C6—O3—Ni1^v	128.88 (12)
C7—N1—H1C	110.0	Ni1—O5—H5A	103.6
H1A—N1—H1C	110.4	Ni1—O5—H5B	97.4
H1B—N1—H1C	101.0	H5A—O5—H5B	114.0
N1—C7—C8	110.80 (16)	C2^vi—C1—C2	120.6 (2)
N1—C7—H7A	109.5	C2—C1—H1	119.7
C8—C7—H7A	109.5	C1—C2—C3	119.7 (2)
N1—C7—H7B	109.5	C1—C2—C5	120.65 (17)
C8—C7—H7B	109.5	C3—C2—C5	119.63 (19)
H7A—C7—H7B	108.1	C4—C3—C2	119.6 (2)
C7—C8—C7^i	109.3 (2)	C4—C3—C6	117.06 (17)
C7—C8—H8A	109.8	C2—C3—C6	122.88 (19)
C7—C8—H8B	109.8	C3^vi—C4—C3	120.8 (2)
H8A—C8—H8B	108.3	C3—C4—H4	119.6
O1^iii—Ni1—O1	98.61 (9)	O2—C5—O1	126.49 (17)
O1—Ni1—O3^ii	86.64 (5)	O2—C5—C2	117.11 (16)
O1—Ni1—O3^iv	174.74 (7)	O1—C5—C2	116.40 (17)
O3^ii—Ni1—O3^iv	88.12 (8)	O4—C6—O3	126.22 (17)
O1—Ni1—O5^iii	86.44 (6)	O4—C6—C3	116.58 (16)
O1—Ni1—O5	91.91 (6)	O3—C6—C3	117.07 (16)
O3^ii—Ni1—O5	93.02 (6)	H6A—O6—H6B	103.0
O3^iv—Ni1—O5	88.81 (6)
N1—C7—C8—C7^i	−178.27 (13)	Ni1—O1—C5—O2	8.0 (3)
O1^iii—Ni1—O1—C5	−66.36 (16)	Ni1—O1—C5—C2	−171.57 (12)
O3^ii—Ni1—O1—C5	113.24 (18)	C1—C2—C5—O2	−140.7 (2)
O5^iii—Ni1—O1—C5	−157.75 (17)	C3—C2—C5—O2	37.6 (2)
O5—Ni1—O1—C5	20.32 (17)	C1—C2—C5—O1	39.0 (3)
C2^vi—C1—C2—C3	−0.6 (4)	C3—C2—C5—O1	−142.72 (16)
C2^vi—C1—C2—C5	177.70 (17)	Ni1^v—O3—C6—O4	8.7 (3)
C1—C2—C3—C4	0.5 (2)	Ni1^v—O3—C6—C3	−166.96 (12)
C5—C2—C3—C4	−177.8 (2)	C4—C3—C6—O4	−113.8 (2)
C1—C2—C3—C6	−171.7 (2)	C2—C3—C6—O4	58.6 (2)
C5—C2—C3—C6	10.0 (2)	C4—C3—C6—O3	62.3 (2)
C2—C3—C4—C3^vi	−0.3 (3)	C2—C3—C6—O3	−125.31 (17)
C6—C3—C4—C3^vi	172.29 (15)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2^ii	0.91	1.91	2.819 (2)	174
N1—H1B···O3^iv	0.90	2.03	2.838 (2)	149
N1—H1C···O4^vii	0.92	2.09	2.985 (2)	163
O5—H5A···O4^ii	0.90	1.82	2.668 (2)	156
O5—H5B···O2	0.90	1.85	2.731 (2)	164
O6—H6B···O4^vii	0.96	2.39	3.321 (3)	164
C7—H7A···Cg(C1-C4/C2^i/C3^i)^viii	0.99	2.97	3.757 (2)	137
C8—H8A···Cg(C1-C4/C2^i/C3^i)^ix	0.99	2.60	3.433 (2)	142

Symmetry codes: (ii) x, −y+1/2, z−1/2; (iv) −x+1, y+1/2, z−1/2; (vii) −x+1, y−1/2, z−1/2; (viii) x+1/2, y+1/2, z−1/2; (ix) x+1/2, y−1/2, z−1/2.