Further refinement of di­aqua(1,7,11,17-tetraoxa-2,6,12,16-tetra­aza­cyclo­ei­cosane-N,N',N'',N''')­nickel(II) dichloride

This further refinement of [Ni(C₁₂H₂₈N₄O₄)(H₂O)₂]Cl₂ based on the original intensity data improves upon the original by modelling the element of disorder associated with two of the methyl­ene groups of the macrocyclic ligand and reduces R by about a factor of two in the process. The occupancies [0.256 (3) and 0.190 (5)] of the minor components are, however, low enough to leave the atomic parameters and geometry of the major component little changed from those described in the original publication. The mol­ecule is subject to the operation of a crystallographic mirror plane passing through Ni, O of the water mol­ecules, and two ligand methyl­ene groups.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.025
• wR factor = 0.063
• Data-to-parameter ratio = 13.8

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

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S1. Comment

A feature of the structure of the title comound, (I) (Fig. 1), as reported previously by Kuksa et al. (2000) was comparatively high residual electron density in the vicinity of C4. Modelling this and a similar but somewhat smaller feature in the vicinity of C7 in terms of disorder of the atoms concerned brought about a significant improvement in the structure determination with the reduction of R[F² > 2σ(F²)] and wR2 (all F² data) from 0.050 and 0.136, respectively, to the corresponding values given below. The introduction of disorder into the model, whereby C4 and C7 are both distributed over pairs of sites as C4/C4A and C7/C7A with occupancies of 0.744 (3) and 0.810 (5) for the major (C4 and C7) components, respectively, and with H attached to these and neighbouring atoms treated appropriately, has little effect upon the structural features of the major component such as the coordination of Ni and the internal geometry of the macrocyclic ligand (Table 1) or the hydrogen-bond parameters (Table 2).

The coordination of Ni is octahedral with equatorial N, with Ni1—N1 and Ni1—N2 2.0990 (12) and 2.1091 (12) Å, respectively, and water molecules in the axial positions, with Ni1—O1W and Ni1—O2W at 2.1299 (14) and 2.1061 (14) Å, respectively. The angles at Ni involving cis-donor atoms lie in the range 86.52 (5)–93.92 (7)°, while trans angles of 178.75 (4) and 179.93 (5)° are observed. The chloride anion does not participate in the coordination of Ni, but is heavily involved as an H-bond acceptor (see below).

A notable feature of the major component form of the macrocyclic ligand (Fig. 1) is the two-up two-down arrangement of the methylene groups at the points of the envelope flaps of the six- (C1 and C7) and eight-membered [C4 and C4ⁱ; symmetry code: (i) x, 1/2 - y, z] chelate rings relative to the plane defined by Ni and its attached N, with C4 and C4ⁱ above the plane and C1 and C7 below it. In the minor component form with C4A and C7A replacing C4 and C7, the arrangement is now three-up, one-down, with only C1 below the reference plane, and is clearly not simply a total inversion of the original two-up two-down arrangement. This further justifies the use, adopted initially on the basis of the magnitudes of the difference map peaks, of two distinct occupancy factors in modelling the disorder. As shown in Table 1, the major and minor forms of the macrocyclic ligand differ appreciably in terms of the C3—C4, C4—C5 and C6–C7 bond lengths (or their equivalent for the minor component) and also in the angles subtended by non-H atoms at C3, C5 and C6, as well as those at C4, C4A, C7 and C7A.

The hydrogen bonds listed in Table 2, all of which have Cl as acceptor, create infinite chains propagated in the direction of the a axis (Fig. 2).

S2. Experimental

The synthesis and growth of crystals of (I) have been described by Kuksa et al. (2000).

S3. Refinement

A more complete account of the data collection process is given by Darr et al. (1993). H atoms attached to C (methylene groups) were placed in calculated positions, with C—H = 0.99 Å and refined as riding atoms with U_iso = 1.2U_eq(C). H atoms attached to N and O were located in a difference map and refined isotropically.

Computing details

Data collection: MADNES (Pflugrath & Messerschmidt, 1989); cell refinement: MADNES; data reduction: ABSMAD (Karaulov, 1992); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The molecule of (I) showing the labelling scheme. Non-H atoms are shown as 50% probability ellipsoids and H as small circles. [Symmetry code: (i) x, 1/2 - y, z.]

Fig. 2. A portion of the hydrogen-bonded chain in (I). The representation is the same as that used in Fig. 1, except that H atoms other than those involved in hydrogen bonds to Cl (dashed lines) have been omitted and only selected atoms are labelled, in a generic manner. The direction of view is essentially along c with a across the page, i.e. the mirror plane running horizontally through the mid-line of the Figure is seen edge-on.

2,6,12,16-Tetraaza-1,7,11,17-tetraoxacycloicosane-diaquanickel(II) dichloride

Crystal data

[Ni(C12H28N4O4)(H2O)2]Cl2	F(000) = 484
Mr = 458.03	Dx = 1.555 Mg m^−3
Monoclinic, P21/m	Mo Kα radiation, λ = 0.71073 Å
a = 7.4288 (3) Å	Cell parameters from 15576 reflections
b = 13.1426 (5) Å	θ = 2.0–26.4°
c = 10.2527 (3) Å	µ = 1.30 mm^−1
β = 102.2480 (18)°	T = 150 K
V = 978.22 (6) Å^3	Block, light violet
Z = 2	0.60 × 0.15 × 0.15 mm

Data collection

Delft Instruments FAST area-detector diffractometer	2090 independent reflections
Radiation source: fine-focus sealed tube	1892 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.051
ϕ scans	θmax = 26.4°, θmin = 2.0°
Absorption correction: part of the refinement model (ΔF) (DIFABS; Walker & Stuart, 1983)	h = −9→9
Tmin = 0.710, Tmax = 0.823	k = −16→16
15576 measured reflections	l = −12→12

Refinement

Refinement on F^2	Primary atom site location: heavy-atom method
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.025	Hydrogen site location: geom and difmap
wR(F^2) = 0.063	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0267P)^2 + 0.4373P] where P = (Fo^2 + 2Fc^2)/3
2090 reflections	(Δ/σ)max < 0.001
152 parameters	Δρmax = 0.31 e Å^−3
0 restraints	Δρmin = −0.64 e Å^−3

Special details

Experimental. General cell determination and refinement and data collection strategy given by Darr et al., (1993). [Darr, J·A, Drake, S·R., Hursthouse, M·B. & Malik, K·M·A. (1993). Inorg. Chem. 32, 5704–5708.]

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.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

7.1501 (0.0011) x - 0.0000 (0.0000) y - 4.8119 (0.0047) z = 0.5695 (0.0015)

* 0.0000 (0.0000) O1 * 0.0000 (0.0000) O2 * 0.0000 (0.0000) O1_$1 * 0.0000 (0.0000) O2_$1 - 0.0656 (0.0006) Ni1

Rms deviation of fitted atoms = 0.0000

6.4812 (0.0022) x - 0.0000 (0.0000) y + 2.9991 (0.0059) z = 2.2657 (0.0012)

Angle to previous plane (with approximate e.s.d.) = 45.00 (0.03)

* 0.0000 (0.0000) N1 * 0.0000 (0.0000) N2 * 0.0000 (0.0000) N1_$1 * 0.0000 (0.0000) N2_$1 - 0.0214 (0.0008) Ni1

Rms deviation of fitted atoms = 0.0000

'Linear' torsion angles excluded as per PLATON element of checkcif N2 Ni1 N1 O1 154 (2) 4_565.. . ? N2 Ni1 N1 C2 - 82 (2) 4_565.. . ? N1 Ni1 N2 O2 - 20 (2) 4_565.. . ? N1 Ni1 N2 C6 104 (2) 4_565.. . ?

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.

Anisotropic displacement parameters refined for all non-H atoms. H atoms of water and N—H groups from difference maps and refined isotropically in the usual manner. All other H (methylene groups) placed in calculated positions with C—H 0.99 A and refined riding with U_iso 1.2 times Uequ of C. C4 and C7 disordered in pairs as C4/C4A and C7/C7A with sof's for major components determined prior to final refinement as 0.744 (3) and 0.810 (5) resp. applied to the pairs and to H attached both to them and neighbouring C (C3, C5 and C6).

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
Ni1	0.23391 (3)	0.2500	0.24285 (2)	0.01320 (10)
Cl1	0.73803 (4)	0.07626 (3)	0.24487 (3)	0.01941 (11)
O1W	0.51256 (19)	0.2500	0.35069 (15)	0.0182 (3)
H1W	0.568 (3)	0.2013 (14)	0.3345 (18)	0.036 (5)*
O2W	−0.04151 (19)	0.2500	0.13598 (14)	0.0180 (3)
H2W	−0.096 (3)	0.2002 (14)	0.1564 (18)	0.034 (5)*
O1	0.15440 (12)	0.05709 (8)	0.11108 (10)	0.0204 (2)
O2	0.33653 (13)	0.06625 (8)	0.38171 (10)	0.0206 (2)
N1	0.29493 (16)	0.13413 (9)	0.11811 (12)	0.0170 (2)
H1N	0.396 (2)	0.1059 (13)	0.1653 (16)	0.022 (4)*
N2	0.17873 (16)	0.13271 (9)	0.36923 (12)	0.0170 (3)
H2N	0.085 (2)	0.0976 (13)	0.3214 (15)	0.017 (4)*
C1	0.4252 (3)	0.2500	−0.0275 (2)	0.0249 (5)
H1A	0.5352	0.2500	0.0465	0.030*
H1B	0.4685	0.2500	−0.1124	0.030*
C2	0.3158 (2)	0.15393 (13)	−0.01978 (14)	0.0263 (3)
H2A	0.1924	0.1606	−0.0790	0.032*
H2B	0.3790	0.0956	−0.0515	0.032*
C3	0.2234 (2)	−0.04547 (11)	0.12978 (15)	0.0230 (3)
H3A	0.3583	−0.0467	0.1363	0.028*	0.74
H3B	0.1639	−0.0892	0.0542	0.028*	0.74
H3C	0.2953	−0.0576	0.0603	0.028*	0.26
H3D	0.1149	−0.0909	0.1087	0.028*	0.26
C4	0.1765 (3)	−0.08232 (16)	0.2592 (2)	0.0232 (4)	0.74
H4A	0.0463	−0.0650	0.2575	0.028*	0.74
H4B	0.1871	−0.1574	0.2625	0.028*	0.74
C4A	0.3383 (8)	−0.0822 (4)	0.2574 (6)	0.0224 (12)	0.26
H4C	0.4685	−0.0656	0.2580	0.027*	0.26
H4D	0.3282	−0.1573	0.2596	0.027*	0.26
C5	0.2923 (2)	−0.04018 (12)	0.38390 (15)	0.0248 (3)
H5A	0.2279	−0.0520	0.4577	0.030*	0.74
H5B	0.4091	−0.0791	0.4047	0.030*	0.74
H5C	0.1602	−0.0500	0.3839	0.030*	0.26
H5D	0.3671	−0.0738	0.4637	0.030*	0.26
C6	0.1419 (2)	0.15349 (13)	0.50294 (15)	0.0268 (3)
H6A	0.1880	0.0957	0.5627	0.032*	0.81
H6B	0.0071	0.1581	0.4957	0.032*	0.81
H6C	0.0613	0.0988	0.5244	0.032*	0.19
H6D	0.2601	0.1492	0.5689	0.032*	0.19
C7	0.2304 (4)	0.2500	0.5643 (2)	0.0237 (6)	0.81
H7A	0.3612	0.2500	0.5570	0.028*	0.81
H7B	0.2279	0.2500	0.6604	0.028*	0.81
C7A	0.0573 (15)	0.2500	0.5204 (10)	0.022 (2)	0.19
H7C	0.0343	0.2500	0.6121	0.026*	0.19
H7D	−0.0649	0.2500	0.4589	0.026*	0.19

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Ni1	0.01242 (14)	0.01446 (15)	0.01340 (15)	0.000	0.00427 (9)	0.000
Cl1	0.01442 (18)	0.0204 (2)	0.0240 (2)	0.00084 (12)	0.00530 (14)	−0.00023 (13)
O1W	0.0153 (7)	0.0164 (8)	0.0234 (8)	0.000	0.0051 (6)	0.000
O2W	0.0149 (7)	0.0172 (8)	0.0218 (8)	0.000	0.0033 (6)	0.000
O1	0.0132 (5)	0.0175 (5)	0.0294 (6)	−0.0017 (4)	0.0021 (4)	−0.0033 (4)
O2	0.0135 (5)	0.0183 (5)	0.0275 (6)	0.0021 (4)	−0.0012 (4)	0.0022 (4)
N1	0.0125 (5)	0.0202 (6)	0.0185 (6)	−0.0022 (5)	0.0035 (4)	−0.0031 (5)
N2	0.0129 (6)	0.0197 (6)	0.0182 (6)	0.0013 (5)	0.0030 (4)	0.0018 (5)
C1	0.0225 (11)	0.0354 (13)	0.0189 (10)	0.000	0.0092 (8)	0.000
C2	0.0304 (8)	0.0322 (9)	0.0184 (7)	−0.0031 (7)	0.0096 (6)	−0.0063 (6)
C3	0.0238 (7)	0.0179 (7)	0.0272 (8)	0.0018 (6)	0.0047 (6)	−0.0045 (6)
C4	0.0225 (10)	0.0163 (10)	0.0294 (11)	−0.0009 (8)	0.0026 (8)	−0.0002 (8)
C4A	0.019 (3)	0.015 (3)	0.035 (3)	−0.002 (2)	0.007 (2)	−0.001 (2)
C5	0.0288 (8)	0.0175 (8)	0.0277 (8)	0.0018 (6)	0.0048 (6)	0.0051 (6)
C6	0.0319 (8)	0.0308 (9)	0.0205 (7)	−0.0014 (7)	0.0120 (6)	0.0048 (7)
C7	0.0254 (13)	0.0318 (15)	0.0129 (12)	0.000	0.0021 (10)	0.000
C7A	0.024 (6)	0.031 (6)	0.013 (5)	0.000	0.013 (4)	0.000

Geometric parameters (Å, º)

Ni1—N1	2.0990 (12)	C3—H3B	0.990
Ni1—O2W	2.1061 (14)	C3—H3C	0.990
Ni1—N2	2.1091 (12)	C3—H3D	0.990
Ni1—O1W	2.1299 (14)	C4—C5	1.488 (2)
O1W—H1W^i	0.796 (18)	C4—H4A	0.990
O1W—H1W	0.796 (18)	C4—H4B	0.990
O2W—H2W^i	0.820 (18)	C4A—C5	1.514 (6)
O2W—H2W	0.820 (18)	C4A—H4C	0.990
O1—C3	1.4404 (17)	C4A—H4D	0.990
O1—N1	1.4451 (14)	C5—H5A	0.990
O2—C5	1.4381 (18)	C5—H5B	0.990
O2—N2	1.4457 (14)	C5—H5C	0.990
N1—C2	1.4776 (18)	C5—H5D	0.990
N1—H1N	0.883 (18)	C6—C7A	1.443 (5)
N2—C6	1.4792 (18)	C6—C7	1.504 (2)
N2—H2N	0.890 (17)	C6—H6A	0.990
C1—C2	1.5130 (19)	C6—H6B	0.990
C1—H1A	0.990	C6—H6C	0.990
C1—H1B	0.990	C6—H6D	0.990
C2—H2A	0.990	C7—H7A	0.990
C2—H2B	0.990	C7—H7B	0.990
C3—C4A	1.484 (6)	C7A—H7C	0.990
C3—C4	1.521 (2)	C7A—H7D	0.990
C3—H3A	0.990
N1—Ni1—N1^i	93.02 (7)	C4A—C3—H3C	106.6
N1—Ni1—O2W	89.69 (4)	O1—C3—H3D	106.6
N1—Ni1—N2^i	178.75 (4)	C4A—C3—H3D	106.6
N1—Ni1—N2	86.52 (5)	H3C—C3—H3D	106.6
O2W—Ni1—N2	91.47 (4)	C5—C4—C3	115.67 (16)
N2^i—Ni1—N2	93.92 (7)	C5—C4—H4A	108.4
N1—Ni1—O1W	90.26 (4)	C3—C4—H4A	108.4
O2W—Ni1—O1W	179.93 (5)	C5—C4—H4B	108.4
N2^i—Ni1—O1W	88.58 (4)	C3—C4—H4B	108.4
H1W^i—O1W—Ni1	112.2 (14)	H4A—C4—H4B	107.4
H1W^i—O1W—H1W	107 (3)	C3—C4A—C5	116.4 (4)
Ni1—O1W—H1W	112.2 (14)	C3—C4A—H4C	108.2
H2W^i—O2W—Ni1	110.1 (13)	C5—C4A—H4C	108.2
H2W^i—O2W—H2W	106 (3)	C3—C4A—H4D	108.2
Ni1—O2W—H2W	110.1 (13)	C5—C4A—H4D	108.2
C3—O1—N1	114.59 (10)	H4C—C4A—H4D	107.3
C5—O2—N2	113.93 (10)	O2—C5—C4	116.16 (13)
O1—N1—C2	107.27 (10)	O2—C5—C4A	104.3 (2)
O1—N1—Ni1	106.96 (7)	O2—C5—H5A	108.2
C2—N1—Ni1	122.35 (10)	C4—C5—H5A	108.2
O1—N1—H1N	104.7 (11)	O2—C5—H5B	108.2
C2—N1—H1N	110.4 (11)	C4—C5—H5B	108.2
Ni1—N1—H1N	103.8 (11)	H5A—C5—H5B	107.4
O2—N2—C6	109.60 (11)	O2—C5—H5C	110.9
O2—N2—Ni1	103.67 (7)	C4A—C5—H5C	110.9
C6—N2—Ni1	122.19 (10)	O2—C5—H5D	110.9
O2—N2—H2N	105.0 (10)	C4A—C5—H5D	110.9
C6—N2—H2N	109.2 (10)	H5C—C5—H5D	108.9
Ni1—N2—H2N	105.8 (10)	C7A—C6—N2	116.6 (4)
C2^i—C1—C2	113.13 (18)	N2—C6—C7	113.13 (15)
C2^i—C1—H1A	109.0	N2—C6—H6A	109.0
C2—C1—H1A	109.0	C7—C6—H6A	109.0
C2^i—C1—H1B	109.0	N2—C6—H6B	109.0
C2—C1—H1B	109.0	C7—C6—H6B	109.0
H1A—C1—H1B	107.8	H6A—C6—H6B	107.8
N1—C2—C1	111.34 (13)	C7A—C6—H6C	108.1
N1—C2—H2A	109.4	N2—C6—H6C	108.1
C1—C2—H2A	109.4	C7A—C6—H6D	108.1
N1—C2—H2B	109.4	N2—C6—H6D	108.1
C1—C2—H2B	109.4	H6C—C6—H6D	107.3
H2A—C2—H2B	108.0	C6—C7—C6^i	115.0 (2)
O1—C3—C4A	123.0 (2)	C6—C7—H7A	108.5
O1—C3—C4	105.85 (13)	C6—C7—H7B	108.5
O1—C3—H3A	110.6	H7A—C7—H7B	107.5
C4—C3—H3A	110.6	C6—C7A—C6^i	123.0 (7)
O1—C3—H3B	110.6	C6—C7A—H7C	106.6
C4—C3—H3B	110.6	C6—C7A—H7D	106.6
H3A—C3—H3B	108.7	H7C—C7A—H7D	106.5
O1—C3—H3C	106.6
C3—O1—N1—C2	94.10 (13)	C2^i—C1—C2—N1	−75.6 (2)
C3—O1—N1—Ni1	−133.00 (9)	N1—O1—C3—C4A	65.5 (3)
N1^i—Ni1—N1—O1	−137.98 (6)	N1—O1—C3—C4	114.49 (13)
O2W—Ni1—N1—O1	−48.31 (8)	O1—C3—C4—C5	−74.79 (17)
N2—Ni1—N1—O1	43.18 (8)	C4A—C3—C4—C5	45.7 (3)
O1W—Ni1—N1—O1	131.74 (8)	O1—C3—C4A—C5	36.0 (5)
N1^i—Ni1—N1—C2	−13.89 (13)	C4—C3—C4A—C5	−45.1 (3)
O2W—Ni1—N1—C2	75.78 (11)	N2—O2—C5—C4	65.48 (18)
N2—Ni1—N1—C2	167.28 (11)	N2—O2—C5—C4A	114.7 (2)
O1W—Ni1—N1—C2	−104.16 (11)	C3—C4—C5—O2	41.1 (2)
C5—O2—N2—C6	86.09 (14)	C3—C4—C5—C4A	−44.5 (3)
C5—O2—N2—Ni1	−141.95 (9)	C3—C4A—C5—O2	−66.2 (4)
N1—Ni1—N2—O2	48.24 (8)	C3—C4A—C5—C4	46.3 (3)
O2W—Ni1—N2—O2	137.84 (8)	O2—N2—C6—C7A	150.9 (5)
N2^i—Ni1—N2—O2	−130.59 (6)	Ni1—N2—C6—C7A	29.5 (5)
O1W—Ni1—N2—O2	−42.11 (8)	O2—N2—C6—C7	94.40 (16)
N1—Ni1—N2—C6	172.37 (11)	Ni1—N2—C6—C7	−26.97 (18)
O2W—Ni1—N2—C6	−98.03 (11)	C7A—C6—C7—C6^i	−33.6 (5)
N2^i—Ni1—N2—C6	−6.46 (13)	N2—C6—C7—C6^i	72.7 (2)
O1W—Ni1—N2—C6	82.02 (11)	N2—C6—C7A—C6^i	−60.6 (10)
O1—N1—C2—C1	166.45 (12)	C7—C6—C7A—C6^i	38.5 (6)
Ni1—N1—C2—C1	42.49 (17)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1W···Cl1	0.796 (18)	2.375 (18)	3.1571 (11)	167.7 (18)
O2W—H2W···Cl1^ii	0.820 (18)	2.339 (18)	3.1493 (11)	169.9 (17)
N1—H1N···Cl1	0.883 (18)	2.529 (18)	3.3597 (12)	156.9 (14)
N2—H2N···Cl1^ii	0.890 (17)	2.546 (17)	3.3351 (12)	148.0 (13)

Symmetry code: (ii) x−1, y, z.