Diaqua­bis(1,10-phenanthroline-κ²N,N′)­nickel(II) diperchlorate 0.4-hydrate

The title complex, [Ni(C₁₂H₈N₂)₂(H₂O)₂](ClO₄)₂·0.4H₂O, possesses crystallographically imposed C₂ symmetry. The Ni^II atom is coordinated by four N atoms from two 1,10-phenanthroline ligands and two water mol­ecules in a distorted octa­hedral coordination geometry. The packing is governed by inter­molecular hydrogen bonds and a π–π stacking inter­action with a centroid-to-centroid distance of 3.650 (2) Å.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.012 Å
• H-atom completeness 97%
• Disorder in solvent or counterion
• R factor = 0.071
• wR factor = 0.262
• Data-to-parameter ratio = 14.5

checkCIF/PLATON results

No syntax errors found



Alert level C
RFACR01_ALERT_3_C  The value of the weighted R factor is > 0.25
            Weighted R factor given   0.262
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT084_ALERT_2_C High R2 Value ..................................       0.26
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C5
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C6
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for       Cl1A
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for       Cl1B
PLAT302_ALERT_4_C Anion/Solvent Disorder .........................      45.00 Perc.
PLAT341_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...         12
PLAT432_ALERT_2_C Short Inter X...Y Contact  C10    ..  O2B     ..       2.98 Ang.
PLAT601_ALERT_2_C Structure Contains Solvent Accessible VOIDS of .      55.00 A   3 

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C24 H20.8 Cl2 N4 Ni1 O10.4
            Atom count from the _atom_site data:  C24 H20 Cl2 N4 Ni1 O10.4
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    4
           From the CIF: _chemical_formula_sum  C24 H20.80 Cl2 N4 Ni O10.40
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         96.00     96.00    0.00
           H         83.20     80.00    3.20
           Cl         8.00      8.00    0.00
           N         16.00     16.00    0.00
           Ni         4.00      4.00    0.00
           O         41.60     41.60    0.00
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......         97

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

   7 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 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
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

We have been recently interested in the nature of π-π stacking as it plays an important role in some biological processes (Deisenhofer & Michel, 1989). A series of metal complexes incorporating different aromatic ligands has been prepared and their crystal structures provide useful information about π-π stacking (Wu et al., 2003; Pan & Xu, 2004; Li et al., 2005). As part of ongoing investigations, the title complex, incorporating 1,10-phenanthroline, (I), has been prepared.

As illustrated in Fig. 1, the Ni^II atom lies on a C₂ symmetry position and has a distorted octahedral geometry with six coordinating atoms: four N atoms from two 1,10-phenanthroline ligands, two O from two water molecules (Table 1). A depleted hydration water molecule (occupation: 1/5) completes the structure. Intermolecular O—H···O hydrogen bonding involving the coordinating water molecules as donors and the perchlorate O atoms as acceptors forms chains, which are further assembled via π-π stacking interactions between adjacent phen rings, thus forming a supramolecular network structure (Fig. 2; Table 2). The centroid-centroid distance of adjacent phen rings (at 1/2 - x,1/2 - y,1 - z) is 3.650 (2) Å, indicating a normal π-π interaction.

Related literature

For related literature, see: Deisenhofer & Michel (1989); Li et al. (2005); Pan & Xu (2004); Wu et al. (2003).

S2. Experimental

The title complex was prepared by addition of a stoichiometric amount of 1,10-phenanthroline (2 mmol) to warm aqueous solution of nickel perchlorate (2 mmol) (about 333–343 K). The PH was then adjusted from 5.5 to 6.5 with NaOH (10 mmol). The resulting solution was put into a 30 ml stainless steel reaction bottle with the gather four fluorine ethylene inner pad, sealed up completely and stored at 443 K for 144 h. Cyan single crystals were obtained after cooling to room temperature.

S3. Refinement

The occupation factor of a depleted hydration water molecule (O2W) was refined in the initial stages, and kept fixed at the latest cycles of refinement; the corresponding H atoms were disregarded from the model. The disorder of perchlorate unit was refined and split into two positions with an occupancy ratio of (0.721 (1):0.279 (1)). The Cl—O distances were restrained to be 1.44 Å, both within a standard deviation of 0.01 Å. Carbon-bound H atoms were placed at calculated positions and were treated as riding on the parent C atoms with C—H = 0.93 Å and with U_iso(H) = 1.2 U_eq(C). Water H atoms were tentatively located in difference Fourier maps and were refined with distance restraints of O–H = 0.82 Å and H···H = 1.29 Å, each within a standard deviation of 0.01 Å.

Computing details

Data collection: APEX2 (Bruker, 1998); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1998); software used to prepare material for publication: SHELXTL (Bruker, 1998).

Figures

	Fig. 1. The structure of (I), showing the atomic numbering scheme. Non-H atoms are shown as 30% probability displacement ellipsoids. The disordered perchlorate ions were omitted for clarity. Symmetry code: as in Table 1.
	Fig. 2. A packing view of (I), showing the intermolecular hydrogen bonds and the π-π interaction as broken lines. For clarity, H atoms and disordered perchlorate ions are not shown.

Diaquabis(1,10-phenanthroline-κ2 N,N')nickel(II) diperchlorate 0.4-hydrate

Crystal data

[Ni(C12H8N2)2(H2O)2](ClO4)2·0.4H2O	F(000) = 1352
Mr = 661.26	Dx = 1.377 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1167 reflections
a = 18.2558 (6) Å	θ = 1.4–28°
b = 15.9362 (6) Å	µ = 0.83 mm^−1
c = 11.7096 (4) Å	T = 293 K
β = 110.591 (2)°	Block, green
V = 3189.02 (19) Å^3	0.26 × 0.20 × 0.18 mm
Z = 4

Data collection

Bruker APEX II area-detector diffractometer	3488 independent reflections
Radiation source: fine-focus sealed tube	1861 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.071
φ and ω scan	θmax = 27.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −23→23
Tmin = 0.827, Tmax = 0.867	k = −20→16
13780 measured reflections	l = −14→14

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.071	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.262	H-atom parameters constrained
S = 1.08	w = 1/[σ^2(Fo^2) + (0.144P)^2] where P = (Fo^2 + 2Fc^2)/3
3488 reflections	(Δ/σ)max < 0.001
241 parameters	Δρmax = 0.64 e Å^−3
97 restraints	Δρmin = −0.37 e Å^−3

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)
Ni1	0.5000	0.33437 (6)	0.7500	0.0538 (4)
O1W	0.5725 (2)	0.4330 (3)	0.7362 (4)	0.0714 (11)
H1W	0.6100	0.4324	0.7126	0.107*
H2W	0.5883	0.4636	0.7969	0.107*
N1	0.5844 (3)	0.2437 (3)	0.7589 (4)	0.0625 (12)
N2	0.5543 (3)	0.3252 (3)	0.9371 (4)	0.0601 (12)
C1	0.5407 (4)	0.3668 (4)	1.0251 (6)	0.0703 (16)
H1	0.5059	0.4117	1.0042	0.084*
C2	0.5761 (5)	0.3464 (5)	1.1478 (7)	0.089 (2)
H2	0.5646	0.3770	1.2070	0.107*
C3	0.6264 (5)	0.2828 (6)	1.1799 (6)	0.095 (2)
H3	0.6495	0.2685	1.2618	0.114*
C4	0.6447 (4)	0.2375 (5)	1.0923 (6)	0.083 (2)
C5	0.6995 (6)	0.1692 (6)	1.1172 (10)	0.120 (3)
H5	0.7241	0.1517	1.1973	0.144*
C6	0.7164 (5)	0.1298 (7)	1.0269 (9)	0.119 (3)
H6	0.7529	0.0865	1.0463	0.143*
C7	0.6789 (4)	0.1538 (5)	0.9025 (8)	0.087 (2)
C8	0.6946 (5)	0.1164 (6)	0.8020 (10)	0.106 (3)
H8	0.7304	0.0727	0.8154	0.128*
C9	0.6579 (5)	0.1443 (5)	0.6911 (9)	0.100 (3)
H9	0.6691	0.1214	0.6260	0.120*
C10	0.6021 (4)	0.2082 (4)	0.6696 (6)	0.0759 (18)
H10	0.5765	0.2264	0.5900	0.091*
C11	0.6231 (3)	0.2178 (4)	0.8737 (6)	0.0674 (16)
C12	0.6059 (3)	0.2614 (4)	0.9702 (5)	0.0634 (15)
O2W	0.501 (2)	0.023 (2)	0.449 (3)	0.134 (11)	0.20
Cl1A	0.8269 (3)	0.0925 (3)	0.4969 (4)	0.0610 (12)	0.720 (11)
O1A	0.8132 (5)	0.0811 (7)	0.3699 (6)	0.109 (3)	0.720 (11)
O2A	0.8634 (8)	0.1706 (5)	0.5390 (10)	0.124 (4)	0.720 (11)
O3A	0.7595 (5)	0.0778 (7)	0.5247 (11)	0.131 (4)	0.720 (11)
O4A	0.8859 (5)	0.0327 (6)	0.5610 (8)	0.132 (3)	0.720 (11)
Cl1B	0.8131 (10)	0.0938 (11)	0.4849 (14)	0.103 (6)	0.280 (11)
O1B	0.8366 (14)	0.0403 (15)	0.405 (2)	0.113 (7)	0.280 (11)
O2B	0.8446 (18)	0.1755 (13)	0.485 (3)	0.136 (9)	0.280 (11)
O3B	0.7289 (9)	0.1023 (18)	0.432 (2)	0.140 (8)	0.280 (11)
O4B	0.8293 (15)	0.0550 (14)	0.6000 (14)	0.116 (8)	0.280 (11)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Ni1	0.0576 (6)	0.0605 (7)	0.0444 (7)	0.000	0.0195 (4)	0.000
O1W	0.078 (3)	0.074 (3)	0.070 (3)	−0.018 (2)	0.036 (2)	−0.013 (2)
N1	0.065 (3)	0.071 (3)	0.056 (3)	0.003 (2)	0.026 (2)	−0.008 (2)
N2	0.062 (3)	0.071 (3)	0.049 (3)	0.001 (2)	0.022 (2)	0.000 (2)
C1	0.078 (4)	0.081 (4)	0.053 (4)	0.000 (3)	0.025 (3)	−0.007 (3)
C2	0.104 (5)	0.107 (6)	0.057 (4)	−0.012 (5)	0.028 (4)	−0.019 (4)
C3	0.107 (6)	0.124 (7)	0.043 (4)	0.006 (5)	0.013 (4)	0.009 (4)
C4	0.086 (4)	0.093 (5)	0.054 (4)	0.004 (4)	0.006 (3)	0.007 (4)
C5	0.126 (7)	0.120 (7)	0.084 (6)	0.039 (6)	0.000 (5)	0.032 (5)
C6	0.111 (7)	0.118 (7)	0.103 (8)	0.054 (6)	0.007 (5)	0.016 (6)
C7	0.081 (4)	0.083 (5)	0.093 (6)	0.026 (4)	0.025 (4)	0.002 (4)
C8	0.100 (6)	0.097 (6)	0.127 (8)	0.037 (5)	0.045 (5)	0.002 (6)
C9	0.098 (6)	0.101 (6)	0.115 (8)	0.015 (5)	0.054 (5)	−0.015 (5)
C10	0.082 (4)	0.080 (4)	0.075 (5)	0.005 (4)	0.040 (3)	−0.009 (4)
C11	0.067 (4)	0.071 (4)	0.065 (4)	0.007 (3)	0.024 (3)	0.006 (3)
C12	0.058 (3)	0.074 (4)	0.051 (3)	0.000 (3)	0.010 (2)	−0.002 (3)
O2W	0.124 (13)	0.130 (14)	0.135 (14)	−0.002 (10)	0.030 (9)	−0.020 (10)
Cl1A	0.0745 (18)	0.069 (2)	0.048 (2)	0.0005 (14)	0.0329 (15)	0.0057 (15)
O1A	0.103 (6)	0.175 (9)	0.048 (4)	0.019 (6)	0.024 (3)	−0.002 (4)
O2A	0.191 (10)	0.104 (5)	0.091 (7)	−0.044 (5)	0.068 (7)	−0.018 (5)
O3A	0.118 (6)	0.160 (8)	0.158 (9)	−0.008 (6)	0.102 (7)	−0.009 (7)
O4A	0.144 (7)	0.154 (7)	0.115 (6)	0.063 (6)	0.065 (5)	0.075 (6)
Cl1B	0.110 (8)	0.119 (9)	0.077 (8)	−0.008 (7)	0.027 (6)	0.004 (6)
O1B	0.130 (14)	0.132 (14)	0.098 (13)	−0.020 (12)	0.066 (11)	−0.009 (11)
O2B	0.183 (16)	0.108 (12)	0.104 (17)	−0.019 (12)	0.036 (15)	0.005 (10)
O3B	0.108 (10)	0.210 (18)	0.096 (14)	0.022 (11)	0.029 (10)	0.019 (14)
O4B	0.152 (16)	0.128 (14)	0.057 (9)	−0.010 (13)	0.023 (9)	0.004 (9)

Geometric parameters (Å, º)

Ni1—N2^i	2.068 (5)	C5—H5	0.9300
Ni1—N2	2.068 (5)	C6—C7	1.427 (11)
Ni1—N1^i	2.089 (5)	C6—H6	0.9300
Ni1—N1	2.089 (5)	C7—C11	1.397 (9)
Ni1—O1W	2.098 (4)	C7—C8	1.434 (12)
Ni1—O1W^i	2.098 (4)	C8—C9	1.312 (12)
O1W—H1W	0.8234	C8—H8	0.9300
O1W—H2W	0.8268	C9—C10	1.400 (10)
N1—C10	1.323 (7)	C9—H9	0.9300
N1—C11	1.345 (7)	C10—H10	0.9300
N2—C1	1.320 (7)	C11—C12	1.453 (9)
N2—C12	1.346 (7)	O2W—O2W^ii	1.41 (6)
C1—C2	1.391 (9)	Cl1A—O3A	1.398 (6)
C1—H1	0.9300	Cl1A—O2A	1.416 (7)
C2—C3	1.331 (10)	Cl1A—O1A	1.431 (6)
C2—H2	0.9300	Cl1A—O4A	1.435 (7)
C3—C4	1.387 (11)	Cl1B—O4B	1.416 (9)
C3—H3	0.9300	Cl1B—O2B	1.423 (10)
C4—C12	1.407 (8)	Cl1B—O1B	1.441 (10)
C4—C5	1.437 (11)	Cl1B—O3B	1.449 (10)
C5—C6	1.355 (13)
N2^i—Ni1—N2	171.9 (3)	C6—C5—C4	121.8 (8)
N2^i—Ni1—N1^i	80.10 (19)	C6—C5—H5	119.1
N2—Ni1—N1^i	94.27 (18)	C4—C5—H5	119.1
N2^i—Ni1—N1	94.27 (18)	C5—C6—C7	120.9 (8)
N2—Ni1—N1	80.10 (19)	C5—C6—H6	119.6
N1^i—Ni1—N1	92.5 (3)	C7—C6—H6	119.6
N2^i—Ni1—O1W	92.95 (17)	C11—C7—C6	119.3 (8)
N2—Ni1—O1W	93.11 (17)	C11—C7—C8	116.4 (7)
N1^i—Ni1—O1W	171.63 (17)	C6—C7—C8	124.3 (7)
N1—Ni1—O1W	92.70 (18)	C9—C8—C7	119.5 (7)
N2^i—Ni1—O1W^i	93.11 (17)	C9—C8—H8	120.3
N2—Ni1—O1W^i	92.95 (17)	C7—C8—H8	120.3
N1^i—Ni1—O1W^i	92.70 (18)	C8—C9—C10	120.7 (8)
N1—Ni1—O1W^i	171.63 (17)	C8—C9—H9	119.7
O1W—Ni1—O1W^i	83.0 (2)	C10—C9—H9	119.7
Ni1—O1W—H1W	129.8	N1—C10—C9	122.2 (7)
Ni1—O1W—H2W	114.4	N1—C10—H10	118.9
H1W—O1W—H2W	102.5	C9—C10—H10	118.9
C10—N1—C11	118.1 (6)	N1—C11—C7	123.2 (6)
C10—N1—Ni1	129.5 (5)	N1—C11—C12	116.7 (5)
C11—N1—Ni1	112.4 (4)	C7—C11—C12	120.1 (6)
C1—N2—C12	117.3 (5)	N2—C12—C4	123.2 (6)
C1—N2—Ni1	129.8 (4)	N2—C12—C11	117.3 (5)
C12—N2—Ni1	112.6 (4)	C4—C12—C11	119.4 (6)
N2—C1—C2	122.9 (7)	O3A—Cl1A—O2A	114.2 (7)
N2—C1—H1	118.6	O3A—Cl1A—O1A	111.9 (7)
C2—C1—H1	118.6	O2A—Cl1A—O1A	111.3 (6)
C3—C2—C1	119.6 (7)	O3A—Cl1A—O4A	109.1 (6)
C3—C2—H2	120.2	O2A—Cl1A—O4A	103.2 (7)
C1—C2—H2	120.2	O1A—Cl1A—O4A	106.5 (6)
C2—C3—C4	120.7 (7)	O4B—Cl1B—O2B	116.6 (13)
C2—C3—H3	119.7	O4B—Cl1B—O1B	110.6 (13)
C4—C3—H3	119.7	O2B—Cl1B—O1B	109.4 (13)
C3—C4—C12	116.3 (7)	O4B—Cl1B—O3B	106.3 (12)
C3—C4—C5	125.2 (8)	O2B—Cl1B—O3B	106.4 (13)
C12—C4—C5	118.5 (7)	O1B—Cl1B—O3B	107.0 (13)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1W···O1B^iii	0.82	1.99	2.75 (2)	154
O1W—H1W···O1A^iii	0.82	1.97	2.787 (9)	169
O1W—H2W···O4A^iv	0.83	1.91	2.733 (8)	174
O1W—H2W···O4B^iv	0.83	2.14	2.87 (2)	148

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