Aqua­(4-carb­oxy­pyridine-2,6-dicarboxyl­ato-κ3O2,N,O6)(1,10-phenanthroline-κ2N,N′)nickel(II)

Zou, Q.; Wang, J.; Lin, J.

doi:10.1107/S1600536811026055

Aqua(4-carboxypyridine-2,6-dicarboxylato-κ³O²,N,O⁶)(1,10-phenanthroline-κ²N,N′)nickel(II)

The title compound, [Ni(C₈H₃NO₆)(C₁₂H₈N₂)(H₂O)], contains an Ni^II ion, a 1,10-phenanthroline (phen) ligand, a 4-carboxypyridine-2,6-dicarboxylate (Hptc²⁻) anion and a coordinated water molecule. The Ni^II atom exhibits a distorted octahedral N₃O₃ environment. O—H

O hydrogen bonding between coordinated water and carboxylate O atoms, as well as π–π stacking interactions [interplanar distances between phen rings = 3.293 (2) Å] lead to a supermolecular assembly.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536811026055/pv2419sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536811026055/pv2419Isup2.hkl Contains datablock I

CCDC reference: 841006

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.008 Å
R factor = 0.044
wR factor = 0.142
Data-to-parameter ratio = 14.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT314_ALERT_2_C Check Small Angle for H2O: Metal-O7     -H7B          93.97 Deg.
PLAT341_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0077 Ang
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          4
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600         23
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600         41

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details in CIF ....          ?
PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT Unusually Large.       8.15
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   5 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   4 ALERT level G = General information/check it is not something unexpected

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

Comment top

The asymmetric unit of the title compound contains a Ni^II ion, a 1,10-phenanthroline ligand, a 4-carboxypyridine-2,6-dicarboxylate (Hptc^2-) anion and a coordinated molecule of water. The Hptc^2- anion adopts a η³µ₁ coordination mode and chelates the Ni^II atom through the pyridine N atom and two neighboring carboxylate O atoms. The Ni^II atoms is six-coordinated by two N atoms from phen, one nitrogen from Hptc^2-, two oxygen atoms from Hptc^2- and one oxygen from coordinated water, in a octahedral N₃O₃ environment. The π–π stacking interactions between the parallel phen rings with the interplanar distance of 3.293 (2)Å interlink the [Ni(Hptc)(phen)(H₂O)] units to form one-dimensional chains, which further grow into three-dimensional supramolecular construction by hydrogen bonding O—H···O interactions between coordinated water molecules and carboxylate groups.

Related literature top

For the synthesis of pyridine-2,4,6-tricarboxylic acid, see: Syper et al. (1980). For related structures, see: Ma et al. (2002); Ramadevi et al. (2006); Harrison et al. (2006).

Experimental top

The ligand (H₃ptc) was synthesized by oxidization of pyridine-2,4,6-trimethyl with potassium permanganate as reported in the literature (Syper et al., 1980). A solution of Ni(ClO₄)₂.6H₂O (0.0731 g, 0.2 mmol), H₃ptc (0.0425 g, 0.2 mmol), phen (0.0396 g, 0.2 mmol) in H₂O (8.0 ml) wasy sealed in a 23 ml Teflon-lined stainless-steel autoclave, which was heated to 413 K and kept at this temperature for 3 days, then the reactor was slow cooled to room temperature at a rate of 5 K/h, green crystals were collected after filtration.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. ORTEP view of the title compound. The dispalcement ellipsoids are drawn at 35% probability level.
	Fig. 2. Packing diagram of the title crystal structure viewed along [100]. O—H···O hydrogen bonds are shown as dashed line.

Aqua(4-carboxypyridine-2,6-dicarboxylato- κ³O²,N,O⁶)(1,10-phenanthroline- κ²N,N')nickel(II) top

Crystal data top

[Ni(C₈H₃NO₆)(C₁₂H₈N₂)(H₂O)]	F(000) = 952
M_r = 466.04	D_x = 1.715 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 10705 reflections
a = 6.8387 (14) Å	θ = 3.0–27.4°
b = 13.421 (3) Å	µ = 1.13 mm⁻¹
c = 19.676 (4) Å	T = 293 K
β = 91.87 (3)°	Chip, green
V = 1805.0 (6) Å³	0.24 × 0.22 × 0.10 mm
Z = 4

Data collection top

Rigaku R-AXIS RAPID diffractometer	4058 independent reflections
Radiation source: fine-focus sealed tube	2573 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.054
Detector resolution: 0 pixels mm^-1	θ_max = 27.5°, θ_min = 3.0°
ω scan	h = −8→7
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −17→17
T_min = 0.763, T_max = 0.893	l = −25→24
17250 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.142	H-atom parameters constrained
S = 1.19	w = 1/[σ²(F_o²) + (0.0123P)² + 8.1487P] where P = (F_o² + 2F_c²)/3
4058 reflections	(Δ/σ)_max < 0.001
280 parameters	Δρ_max = 1.34 e Å⁻³
0 restraints	Δρ_min = −1.52 e Å⁻³

Crystal data top

[Ni(C₈H₃NO₆)(C₁₂H₈N₂)(H₂O)]	V = 1805.0 (6) Å³
M_r = 466.04	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.8387 (14) Å	µ = 1.13 mm⁻¹
b = 13.421 (3) Å	T = 293 K
c = 19.676 (4) Å	0.24 × 0.22 × 0.10 mm
β = 91.87 (3)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	4058 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	2573 reflections with I > 2σ(I)
T_min = 0.763, T_max = 0.893	R_int = 0.054
17250 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.044	0 restraints
wR(F²) = 0.142	H-atom parameters constrained
S = 1.19	Δρ_max = 1.34 e Å⁻³
4058 reflections	Δρ_min = −1.52 e Å⁻³
280 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
Ni1	0.26648 (9)	0.77711 (4)	0.53877 (3)	0.02863 (18)
N1	0.2227 (6)	0.8906 (3)	0.60244 (19)	0.0268 (9)
C1	0.3686 (7)	0.9196 (3)	0.6443 (2)	0.0309 (11)
C2	0.3585 (7)	1.0087 (3)	0.6793 (2)	0.0304 (11)
H2A	0.4603	1.0289	0.7086	0.036*
C3	0.1919 (7)	1.0673 (3)	0.6695 (2)	0.0286 (10)
C4	0.0397 (7)	1.0350 (3)	0.6258 (2)	0.0297 (10)
H4A	−0.0730	1.0730	0.6191	0.036*
C5	0.0617 (7)	0.9450 (3)	0.5930 (2)	0.0260 (10)
C6	0.5378 (7)	0.8459 (3)	0.6473 (2)	0.0291 (10)
O1	0.5323 (5)	0.7781 (3)	0.60344 (17)	0.0341 (8)
O2	0.6618 (5)	0.8555 (3)	0.69549 (19)	0.0418 (9)
C7	0.1719 (8)	1.1668 (4)	0.7044 (2)	0.0343 (11)
O3	0.3151 (6)	1.1847 (3)	0.7480 (2)	0.0595 (13)
H3A	0.3243	1.2410	0.7678	0.071*
O4	0.0343 (6)	1.2209 (3)	0.6934 (2)	0.0495 (10)
C8	−0.0789 (7)	0.9010 (3)	0.5395 (2)	0.0275 (10)
O5	−0.2403 (5)	0.9434 (2)	0.52867 (18)	0.0337 (8)
O6	−0.0182 (5)	0.8251 (2)	0.50894 (17)	0.0339 (8)
N2	0.2834 (6)	0.6679 (3)	0.4662 (2)	0.0322 (9)
C9	0.3157 (8)	0.6781 (4)	0.4005 (3)	0.0422 (13)
H9A	0.3303	0.7417	0.3828	0.051*
C10	0.3286 (9)	0.5957 (5)	0.3570 (3)	0.0497 (15)
H10A	0.3494	0.6053	0.3109	0.060*
C11	0.3106 (8)	0.5023 (5)	0.3821 (3)	0.0498 (16)
H11A	0.3230	0.4474	0.3537	0.060*
C12	0.2735 (7)	0.4888 (4)	0.4508 (3)	0.0404 (13)
C13	0.2495 (8)	0.3931 (4)	0.4819 (4)	0.0489 (16)
H13A	0.2571	0.3358	0.4556	0.059*
C14	0.2159 (8)	0.3851 (4)	0.5490 (4)	0.0494 (16)
H14A	0.2020	0.3223	0.5681	0.059*
C15	0.2011 (7)	0.4721 (4)	0.5916 (3)	0.0375 (12)
C16	0.1738 (8)	0.4681 (4)	0.6613 (3)	0.0463 (15)
H16A	0.1622	0.4071	0.6832	0.056*
C17	0.1642 (9)	0.5552 (5)	0.6972 (3)	0.0507 (15)
H17A	0.1518	0.5538	0.7441	0.061*
C18	0.1734 (8)	0.6465 (4)	0.6628 (3)	0.0422 (13)
H18A	0.1594	0.7050	0.6875	0.051*
C19	0.2191 (7)	0.5668 (4)	0.5611 (3)	0.0317 (11)
C20	0.2586 (7)	0.5750 (4)	0.4907 (3)	0.0324 (11)
N3	0.2010 (6)	0.6526 (3)	0.5969 (2)	0.0324 (9)
O7	0.4073 (5)	0.8742 (2)	0.47182 (17)	0.0345 (8)
H7A	0.3512	0.9298	0.4780	0.041*
H7B	0.5130	0.8761	0.4958	0.041*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Ni1	0.0348 (3)	0.0194 (3)	0.0314 (3)	0.0007 (3)	−0.0033 (2)	−0.0022 (3)
N1	0.034 (2)	0.0173 (18)	0.028 (2)	0.0010 (16)	−0.0053 (17)	−0.0006 (15)
C1	0.040 (3)	0.020 (2)	0.033 (3)	0.001 (2)	−0.005 (2)	0.0031 (19)
C2	0.034 (3)	0.023 (2)	0.034 (3)	0.000 (2)	−0.008 (2)	−0.001 (2)
C3	0.036 (3)	0.021 (2)	0.028 (2)	−0.002 (2)	−0.002 (2)	−0.0005 (19)
C4	0.038 (3)	0.022 (2)	0.028 (2)	0.002 (2)	−0.005 (2)	0.0019 (19)
C5	0.030 (2)	0.020 (2)	0.028 (2)	0.0004 (18)	−0.0018 (19)	0.0029 (18)
C6	0.037 (3)	0.019 (2)	0.031 (3)	−0.0007 (19)	−0.007 (2)	0.0048 (19)
O1	0.0378 (19)	0.0238 (17)	0.040 (2)	0.0042 (15)	−0.0057 (15)	−0.0025 (15)
O2	0.049 (2)	0.0286 (19)	0.046 (2)	0.0032 (17)	−0.0203 (18)	0.0017 (16)
C7	0.047 (3)	0.025 (2)	0.030 (3)	−0.002 (2)	−0.005 (2)	−0.003 (2)
O3	0.068 (3)	0.039 (2)	0.069 (3)	0.011 (2)	−0.035 (2)	−0.028 (2)
O4	0.057 (3)	0.031 (2)	0.059 (3)	0.0141 (19)	−0.021 (2)	−0.0126 (19)
C8	0.036 (3)	0.021 (2)	0.025 (2)	−0.003 (2)	−0.003 (2)	0.0037 (18)
O5	0.0275 (18)	0.0263 (18)	0.047 (2)	0.0016 (15)	−0.0073 (15)	−0.0007 (15)
O6	0.038 (2)	0.0237 (17)	0.039 (2)	0.0017 (15)	−0.0099 (15)	−0.0071 (15)
N2	0.033 (2)	0.028 (2)	0.036 (2)	0.0024 (17)	−0.0039 (18)	−0.0058 (18)
C9	0.043 (3)	0.042 (3)	0.041 (3)	0.003 (3)	−0.001 (2)	−0.008 (3)
C10	0.052 (4)	0.058 (4)	0.038 (3)	0.008 (3)	−0.009 (3)	−0.014 (3)
C11	0.043 (3)	0.046 (4)	0.060 (4)	0.008 (3)	−0.008 (3)	−0.029 (3)
C12	0.028 (3)	0.033 (3)	0.060 (4)	0.005 (2)	−0.011 (2)	−0.015 (3)
C13	0.034 (3)	0.028 (3)	0.083 (5)	0.005 (2)	−0.011 (3)	−0.015 (3)
C14	0.038 (3)	0.020 (3)	0.090 (5)	0.000 (2)	−0.004 (3)	0.000 (3)
C15	0.026 (3)	0.030 (3)	0.057 (3)	0.001 (2)	−0.003 (2)	0.006 (2)
C16	0.033 (3)	0.035 (3)	0.070 (4)	−0.001 (2)	0.004 (3)	0.019 (3)
C17	0.050 (4)	0.052 (4)	0.050 (4)	0.001 (3)	0.005 (3)	0.018 (3)
C18	0.048 (3)	0.040 (3)	0.039 (3)	0.001 (3)	0.007 (2)	0.001 (2)
C19	0.026 (2)	0.025 (2)	0.044 (3)	−0.0004 (19)	−0.008 (2)	−0.003 (2)
C20	0.029 (3)	0.024 (2)	0.043 (3)	0.003 (2)	−0.010 (2)	−0.006 (2)
N3	0.040 (2)	0.024 (2)	0.034 (2)	−0.0017 (18)	−0.0001 (18)	0.0019 (17)
O7	0.039 (2)	0.0264 (18)	0.0378 (19)	0.0009 (15)	−0.0046 (15)	−0.0006 (15)

Geometric parameters (Å, º) top

Ni1—N1	2.001 (4)	N2—C20	1.349 (6)
Ni1—N2	2.053 (4)	C9—C10	1.403 (8)
Ni1—N3	2.081 (4)	C9—H9A	0.9300
Ni1—O7	2.108 (4)	C10—C11	1.355 (9)
Ni1—O6	2.115 (3)	C10—H10A	0.9300
Ni1—O1	2.184 (3)	C11—C12	1.395 (8)
N1—C5	1.329 (6)	C11—H11A	0.9300
N1—C1	1.331 (6)	C12—C20	1.402 (7)
C1—C2	1.381 (6)	C12—C13	1.435 (8)
C1—C6	1.522 (7)	C13—C14	1.352 (9)
C2—C3	1.393 (7)	C13—H13A	0.9300
C2—H2A	0.9300	C14—C15	1.442 (8)
C3—C4	1.398 (6)	C14—H14A	0.9300
C3—C7	1.510 (7)	C15—C16	1.391 (8)
C4—C5	1.380 (6)	C15—C19	1.413 (7)
C4—H4A	0.9300	C16—C17	1.368 (9)
C5—C8	1.522 (6)	C16—H16A	0.9300
C6—O1	1.254 (6)	C17—C18	1.401 (8)
C6—O2	1.258 (6)	C17—H17A	0.9300
C7—O4	1.203 (6)	C18—N3	1.320 (6)
C7—O3	1.302 (6)	C18—H18A	0.9300
O3—H3A	0.8512	C19—N3	1.358 (6)
C8—O5	1.253 (6)	C19—C20	1.425 (7)
C8—O6	1.261 (6)	O7—H7A	0.8502
N2—C9	1.325 (7)	O7—H7B	0.8498

N1—Ni1—N2	172.90 (16)	C9—N2—C20	118.0 (4)
N1—Ni1—N3	103.18 (16)	C9—N2—Ni1	128.3 (4)
N2—Ni1—N3	80.03 (17)	C20—N2—Ni1	113.7 (3)
N1—Ni1—O7	90.09 (15)	N2—C9—C10	122.0 (6)
N2—Ni1—O7	88.24 (15)	N2—C9—H9A	119.0
N3—Ni1—O7	161.85 (15)	C10—C9—H9A	119.0
N1—Ni1—O6	77.69 (14)	C11—C10—C9	119.8 (6)
N2—Ni1—O6	95.55 (14)	C11—C10—H10A	120.1
N3—Ni1—O6	100.60 (16)	C9—C10—H10A	120.1
O7—Ni1—O6	94.23 (14)	C10—C11—C12	119.7 (5)
N1—Ni1—O1	76.68 (14)	C10—C11—H11A	120.2
N2—Ni1—O1	110.16 (15)	C12—C11—H11A	120.2
N3—Ni1—O1	82.81 (15)	C11—C12—C20	117.0 (5)
O7—Ni1—O1	88.39 (13)	C11—C12—C13	123.8 (5)
O6—Ni1—O1	154.24 (13)	C20—C12—C13	119.2 (5)
C5—N1—C1	121.8 (4)	C14—C13—C12	120.8 (5)
C5—N1—Ni1	118.1 (3)	C14—C13—H13A	119.6
C1—N1—Ni1	119.1 (3)	C12—C13—H13A	119.6
N1—C1—C2	120.8 (4)	C13—C14—C15	121.4 (5)
N1—C1—C6	112.8 (4)	C13—C14—H14A	119.3
C2—C1—C6	126.4 (4)	C15—C14—H14A	119.3
C1—C2—C3	118.3 (4)	C16—C15—C19	118.0 (5)
C1—C2—H2A	120.8	C16—C15—C14	123.8 (5)
C3—C2—H2A	120.8	C19—C15—C14	118.2 (5)
C2—C3—C4	119.9 (4)	C17—C16—C15	119.1 (5)
C2—C3—C7	121.6 (4)	C17—C16—H16A	120.5
C4—C3—C7	118.5 (4)	C15—C16—H16A	120.5
C5—C4—C3	118.0 (4)	C16—C17—C18	119.6 (6)
C5—C4—H4A	121.0	C16—C17—H17A	120.2
C3—C4—H4A	121.0	C18—C17—H17A	120.2
N1—C5—C4	121.2 (4)	N3—C18—C17	122.6 (5)
N1—C5—C8	112.7 (4)	N3—C18—H18A	118.7
C4—C5—C8	126.0 (4)	C17—C18—H18A	118.7
O1—C6—O2	126.7 (5)	N3—C19—C15	122.2 (5)
O1—C6—C1	116.1 (4)	N3—C19—C20	117.5 (4)
O2—C6—C1	117.1 (4)	C15—C19—C20	120.3 (5)
C6—O1—Ni1	114.3 (3)	N2—C20—C12	123.4 (5)
O4—C7—O3	125.1 (5)	N2—C20—C19	116.6 (4)
O4—C7—C3	122.3 (5)	C12—C20—C19	120.0 (5)
O3—C7—C3	112.6 (4)	C18—N3—C19	118.4 (5)
C7—O3—H3A	120.5	C18—N3—Ni1	129.1 (4)
O5—C8—O6	126.0 (4)	C19—N3—Ni1	111.8 (3)
O5—C8—C5	118.3 (4)	Ni1—O7—H7A	103.6
O6—C8—C5	115.7 (4)	Ni1—O7—H7B	94.0
C8—O6—Ni1	115.4 (3)	H7A—O7—H7B	105.9

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3A···O2ⁱ	0.85	1.70	2.550 (5)	178
O7—H7A···O5ⁱⁱ	0.85	1.87	2.702 (5)	167
O7—H7B···O5ⁱⁱⁱ	0.85	2.00	2.783 (5)	152

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

Experimental details

Crystal data
Chemical formula	[Ni(C₈H₃NO₆)(C₁₂H₈N₂)(H₂O)]
M_r	466.04
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	6.8387 (14), 13.421 (3), 19.676 (4)
β (°)	91.87 (3)
V (Å³)	1805.0 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	1.13
Crystal size (mm)	0.24 × 0.22 × 0.10

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.763, 0.893
No. of measured, independent and observed [I > 2σ(I)] reflections	17250, 4058, 2573
R_int	0.054
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.044, 0.142, 1.19
No. of reflections	4058
No. of parameters	280
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.34, −1.52

Computer programs: RAPID-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).