Crystal structure of aqua-trans-bis­(dimethyl sulfoxide-κO)(pyridine-2,6-di­carboxyl­ato-κ3O2,N,O6)nickel(II)

Liu, C.; Felts, A.C.; Takahashi, D.; Kinden, W.; Abboud, K.A.

doi:10.1107/S2056989017006090

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Volume 73| Part 5| May 2017| Pages 777-779

https://doi.org/10.1107/S2056989017006090

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Crystal structure of aqua-trans-bis(dimethyl sulfoxide-κO)(pyridine-2,6-dicarboxylato-κ³O²,N,O⁶)nickel(II)

Chen Liu,^a ^* Ashley C. Felts,^b Daisuke Takahashi,^b Wynnry Kinden ^a and Khalil A. Abboud ^b

^aDepartment of Chemistry and Environmental Science, Grenfell Campus, Memorial University of Newfoundland, Corner Brook, NL, A2H 5G4, Canada, and ^bDepartment of Chemistry, University of Florida, Gainesville, FL, 32611-7200, USA
^*Correspondence e-mail: cliu@grenfell.mun.ca

Edited by M. Weil, Vienna University of Technology, Austria (Received 29 March 2017; accepted 22 April 2017; online 28 April 2017)

In the title complex, [Ni(C₇H₃NO₄)(C₂H₆OS)₂(H₂O)], the Ni^II cation is situated on a twofold rotation axis and exhibits a distorted octahedral NO₅ coordination environment defined by a tridentate pyridine-2,6-dicarboxylic acid dianion (dpa²⁻), two dimethyl sulfoxide (DMSO) molecules, and a water molecule. In the crystal, the complex molecules are linked by O—H⋯O and C—H⋯O hydrogen bonds into a three-dimensional network whereby DMSO molecules from neighboring complexes overlap to form layers parallel to (001), alternating with layers of Ni^II–dpa²⁻ moieties. The title complex is isotypic with its cobalt(II) analogue.

Keywords: crystal structure; pyridine-2,6-dicarboxylic acid dianion; dimethyl sulfoxide; nickel(II); hydrogen bonding.

CCDC reference: 1545417

1. Chemical context

Crystal engineering plays an important role in the research of molecule-based functional materials by providing an effective approach towards the rational design and preparation of compounds with special structural features (Robin & Fromm, 2006 ; Cook et al., 2013 ; Wang et al., 2013 ). The crystallization of coordination polymers involves both the formation of a local coordination geometry and the propagation and packing of extended polymeric structures in the three-dimensional space. The competition among various types of intermolecular interactions plays a critical role in this process and is strongly influenced by synthetic conditions such as the choice of solvent, temperature, and the molecular features of the starting materials (Li & Du, 2011 ; Du et al., 2013 ). Although much has been learned about how the synthetic conditions affect intermolecular interactions and the final crystal structures, the targeted synthesis of a coordination polymer with a particular crystal structure is still a challenge. We recently reported an Ni^II-containing one-dimensional coordination polymer based on the tridentate 2,6-pyridine dicarboxylic acid dianion (dpa²⁻) and bridging pyrazine molecules that was prepared by using DMSO as the solvent (Liu et al., 2016 ). The one-dimensional polymeric structure exhibits π–π interactions that were not previously observed when water was used as the solvent under the same preparation conditions. In order to explore the bridging effect of substituted pyrazine, we have repeated this preparation using 2-chloropyrazine to replace pyrazine under the same synthetic conditions. We report herein the synthesis and crystal structure of the resulting title compound for which incorporation of 2-chloropyrazine was not observed.

2. Structural commentary

The title complex crystallizes in the monoclinic space group C2/c with half of the molecule in the asymmetric unit, the other half being generated by twofold rotation symmetry. The tridentate 2,6-pyridine dicarboxylic acid dianion coordinates to the Ni^II cation in a meridional fashion via the pyridine nitrogen atom and two carboxylate oxygen atoms (Fig. 1). The reactant 2-chloropyrazine is not found in the structure of the title complex. Instead, the Ni^II cation is further coordinated by two trans-positioned DMSO molecules and a water molecule through their oxygen atoms. Water molecules may have been produced as a result of the reaction between 2,6-pyridine dicarboxylic acid and nickel carbonate. The two Ni1—O1_dpa bonds have the same length 2.1130 (7) Å] and the two Ni1—O4_DMSO bonds have the same length [2.0934 (7) Å]. The Ni1—N1 bond length is 1.9613 (12) Å and the Ni1—O3_water bond length is 2.0040 (11) Å, both being significantly shorter than the other four bonds, resulting in a distorted octahedral NO₅ coordination environment of the Ni^II cation. These bond lengths are very similar to those observed in the pyrazine-bridged one-dimensional structure reported previously (Liu et al., 2016).

Figure 1
The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level. Unlabeled atoms are related by the symmetry transformation −x, y, $[{1\over 2}]$ − z.

3. Supramolecular features

In the crystal, the mononuclear complexes are linked via an extensive network of C—H⋯O and O—H⋯O hydrogen bonds where the hydrogen-bond donors are the C—H groups of DMSO molecules and the O—H groups of the coordinating water molecules and the hydrogen-bond acceptors are the non-coordinating O2 atoms of the 2,6-pyridine dicarboxylic acid dianion and the O4 atoms of the DMSO molecules (Table 1, Fig. 2). In the crystal packing, layers of the Ni^II–dpa²⁻ complexes alternating with layers of DMSO molecules are formed parallel to (001) (Fig. 2).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3⋯O2ⁱ	0.790 (17)	1.867 (17)	2.6555 (10)	176.3 (18)
C5—H5B⋯O2ⁱ	0.98	2.58	3.3650 (14)	137
C6—H6A⋯O2ⁱⁱ	0.98	2.62	3.3504 (13)	132
C6—H6B⋯O4ⁱⁱⁱ	0.98	2.38	3.3302 (14)	162
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (iii) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Figure 2
The crystal packing of the title compound, showing hydrogen bonds as dashed lines.

4. Database survey

A search of the Cambridge Structural Database (Groom et al., 2016 ) returned eight structures that are related to the title complex. These structures incorporate some or all of the ligands in the title complex and include mononuclear and binuclear complexes, as well as coordination polymers. One of the structures is mer-aqua-bis(dimethylsulfoxide-O)(pyridine-2,6-dicarboxylato-N,O,O′)cobalt(II) (Felloni et al., 2010 ) that crystallizes isotypically with the title complex. Therefore bond lengths and bond angles surrounding the Co^II are very similar to those in the title complex. Another mononuclear complex is aquachlorido(dimethyl sulfoxide-O)(pyridine-2,6-dicarboxylato-N,O,O′)iron(III) (Rafizadeh et al., 2006 ). In the crystal, this complex also forms alternating layers parallel to (001) due to the interdigitation of DMSO molecules. Other complexes in the search results involve either coordinating or non-coordinating DMSO molecules and one or more 2,6-pyridine dicarboxylate dianions coordinating to a metal ion.

5. Synthesis and crystallization

Anhydrous NiCO₃ (0.33 mmol, 39.56 mg), 2,6-pyridine dicarboxylic acid (0.33 mmol, 55.71 mg), and 2-chloropyrazine (0.50 mmol, 57.26 mg) were mixed in 10 ml dimethyl sulfoxide under stirring for 30 minutes. The resulting mixture was placed in a stainless steel autoclave. The autoclave was then sealed and heated to 373 K for 24 h and cooled to room temperature at a rate of 0.1 K per minute. The resulting green crystals were collected by filtration (yield 30.0%). Selected IR bands (KBr, cm⁻¹): 3134.9 (O—H), 1613.1 (C=O), 1365.8 (C—O), 999.6 (S=O).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The title complex is located on a twofold rotation axis, thus half of it occupies the asymmetric unit. The coordinating water molecule lies on the symmetry axis which requires one hydrogen atom to be located while the other is related by symmetry. This hydrogen atom was obtained from a difference-Fourier map and was refined freely. The other hydrogen atoms were positioned geometrically (C—H = 0.93/1.00 Å) and allowed to ride with U_iso(H)= 1.2/1.5U_eq(C). Methyl hydrogen atoms were allowed to rotate but not to tip.

Table 2
Experimental details

Crystal data
Chemical formula	[Ni(C₇H₃NO₄)(C₂H₆OS)₂(H₂O)]
M_r	398.08
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	9.8767 (5), 11.4597 (5), 14.3166 (7)
β (°)	104.4577 (7)
V (Å³)	1569.09 (13)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	1.53
Crystal size (mm)	0.46 × 0.17 × 0.11

Data collection
Diffractometer	Bruker APEXII DUO CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )
T_min, T_max	0.678, 0.910
No. of measured, independent and observed [I > 2σ(I)] reflections	18746, 1936, 1907
R_int	0.011
(sin θ/λ)_max (Å⁻¹)	0.666

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.016, 0.043, 1.06
No. of reflections	1936
No. of parameters	108
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.46, −0.24
Computer programs: APEX2 and SAINT (Bruker, 2014), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), XP in SHELXTL-Plus (Sheldrick, 2008 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1545417

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017006090/wm5380sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017006090/wm5380Isup2.hkl

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL-Plus (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Aqua-trans-bis(dimethyl sulfoxide-κO)(pyridine-2,6-dicarboxylato-κ³O²,N,O⁶)nickel(II) top

Crystal data top

[Ni(C₇H₃NO₄)(C₂H₆OS)₂(H₂O)]	F(000) = 824
M_r = 398.08	D_x = 1.685 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 9.8767 (5) Å	Cell parameters from 9953 reflections
b = 11.4597 (5) Å	θ = 2.0–28.0°
c = 14.3166 (7) Å	µ = 1.53 mm⁻¹
β = 104.4577 (7)°	T = 100 K
V = 1569.09 (13) Å³	Block, green
Z = 4	0.46 × 0.17 × 0.11 mm

Data collection top

Bruker APEXII DUO CCD diffractometer	1907 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.011
phi and ω scans	θ_max = 28.3°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −13→13
T_min = 0.678, T_max = 0.910	k = −15→15
18746 measured reflections	l = −19→19
1936 independent 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)] = 0.016	Hydrogen site location: mixed
wR(F²) = 0.043	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0225P)² + 1.5829P] where P = (F_o² + 2F_c²)/3
1936 reflections	(Δ/σ)_max = 0.001
108 parameters	Δρ_max = 0.46 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Special details top

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.

Refinement. All H atoms were positioned geometrically ( C—H = 0.93/1.00 Å) and allowed to ride with U_iso(H)= 1.2/1.5U_eq(C). Methyl ones were allowed to rotate around the corresponding C—C.

The Ni complex is located on a 2-fold rotational axis of symmetry thus half of it occupies the asymmetric unit. The coordinated water molecule lies on the symmetry axis which requires one proton to be located while the other is related by the symmetry. The water proton was obtained from a Difference Fourier map and refined freely.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Ni1	0.0000	0.32387 (2)	0.2500	0.00867 (6)
S1	0.08818 (3)	0.40008 (2)	0.46249 (2)	0.01346 (7)
O1	0.16898 (7)	0.28806 (6)	0.18844 (5)	0.01235 (14)
O2	0.29613 (8)	0.13796 (7)	0.15626 (6)	0.01647 (15)
O3	0.0000	0.49874 (10)	0.2500	0.0186 (2)
H3	0.0626 (17)	0.5376 (15)	0.2789 (12)	0.033 (4)*
O4	0.13764 (8)	0.32772 (6)	0.38736 (5)	0.01257 (14)
N1	0.0000	0.15272 (10)	0.2500	0.0095 (2)
C1	0.0000	−0.08533 (12)	0.2500	0.0151 (3)
H1A	0.0000	−0.1682	0.2500	0.018*
C2	0.10055 (10)	−0.02463 (9)	0.21553 (7)	0.01328 (18)
H2A	0.1691	−0.0650	0.1919	0.016*
C3	0.09697 (10)	0.09684 (8)	0.21703 (7)	0.01026 (17)
C4	0.19693 (10)	0.18040 (9)	0.18444 (7)	0.01114 (18)
C5	0.24415 (12)	0.46192 (10)	0.53687 (8)	0.0204 (2)
H5A	0.2213	0.5058	0.5897	0.031*
H5B	0.2865	0.5145	0.4982	0.031*
H5C	0.3102	0.3994	0.5636	0.031*
C6	0.04879 (12)	0.29765 (11)	0.54609 (8)	0.0213 (2)
H6A	0.0278	0.3397	0.6004	0.032*
H6B	0.1294	0.2463	0.5699	0.032*
H6C	−0.0324	0.2508	0.5138	0.032*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Ni1	0.00926 (9)	0.00735 (9)	0.00927 (9)	0.000	0.00206 (6)	0.000
S1	0.01554 (12)	0.01458 (12)	0.00942 (12)	0.00621 (9)	0.00155 (9)	−0.00145 (8)
O1	0.0122 (3)	0.0109 (3)	0.0147 (3)	−0.0010 (3)	0.0048 (3)	−0.0004 (3)
O2	0.0138 (3)	0.0181 (4)	0.0196 (4)	0.0040 (3)	0.0081 (3)	0.0023 (3)
O3	0.0178 (5)	0.0085 (5)	0.0237 (6)	0.000	−0.0057 (4)	0.000
O4	0.0131 (3)	0.0143 (3)	0.0099 (3)	0.0037 (3)	0.0021 (3)	−0.0030 (2)
N1	0.0102 (5)	0.0094 (5)	0.0083 (5)	0.000	0.0011 (4)	0.000
C1	0.0189 (7)	0.0091 (6)	0.0170 (7)	0.000	0.0038 (5)	0.000
C2	0.0143 (4)	0.0116 (4)	0.0136 (4)	0.0025 (4)	0.0028 (3)	−0.0008 (3)
C3	0.0103 (4)	0.0114 (4)	0.0085 (4)	0.0005 (3)	0.0012 (3)	0.0001 (3)
C4	0.0099 (4)	0.0140 (5)	0.0088 (4)	−0.0002 (3)	0.0009 (3)	0.0006 (3)
C5	0.0233 (5)	0.0204 (5)	0.0137 (5)	0.0012 (4)	−0.0022 (4)	−0.0044 (4)
C6	0.0227 (5)	0.0259 (6)	0.0180 (5)	0.0069 (4)	0.0105 (4)	0.0038 (4)

Geometric parameters (Å, º) top

Ni1—N1	1.9613 (12)	N1—C3ⁱ	1.3327 (11)
Ni1—O3	2.0040 (11)	C1—C2ⁱ	1.3994 (12)
Ni1—O4	2.0934 (7)	C1—C2	1.3995 (12)
Ni1—O4ⁱ	2.0934 (7)	C1—H1A	0.9500
Ni1—O1ⁱ	2.1130 (7)	C2—C3	1.3927 (14)
Ni1—O1	2.1130 (7)	C2—H2A	0.9500
S1—O4	1.5316 (7)	C3—C4	1.5296 (13)
S1—C5	1.7860 (11)	C5—H5A	0.9800
S1—C6	1.7872 (12)	C5—H5B	0.9800
O1—C4	1.2686 (12)	C5—H5C	0.9800
O2—C4	1.2476 (12)	C6—H6A	0.9800
O3—H3	0.790 (17)	C6—H6B	0.9800
N1—C3	1.3326 (11)	C6—H6C	0.9800

N1—Ni1—O3	180.0	C2ⁱ—C1—C2	120.38 (13)
N1—Ni1—O4	91.21 (2)	C2ⁱ—C1—H1A	119.8
O3—Ni1—O4	88.79 (2)	C2—C1—H1A	119.8
N1—Ni1—O4ⁱ	91.21 (2)	C3—C2—C1	117.93 (10)
O3—Ni1—O4ⁱ	88.79 (2)	C3—C2—H2A	121.0
O4—Ni1—O4ⁱ	177.58 (4)	C1—C2—H2A	121.0
N1—Ni1—O1ⁱ	78.80 (2)	N1—C3—C2	120.60 (9)
O3—Ni1—O1ⁱ	101.20 (2)	N1—C3—C4	112.51 (9)
O4—Ni1—O1ⁱ	90.43 (3)	C2—C3—C4	126.88 (9)
O4ⁱ—Ni1—O1ⁱ	90.04 (3)	O2—C4—O1	126.23 (9)
N1—Ni1—O1	78.80 (2)	O2—C4—C3	118.26 (9)
O3—Ni1—O1	101.20 (2)	O1—C4—C3	115.51 (9)
O4—Ni1—O1	90.04 (3)	S1—C5—H5A	109.5
O4ⁱ—Ni1—O1	90.43 (3)	S1—C5—H5B	109.5
O1ⁱ—Ni1—O1	157.60 (4)	H5A—C5—H5B	109.5
O4—S1—C5	104.76 (5)	S1—C5—H5C	109.5
O4—S1—C6	106.00 (5)	H5A—C5—H5C	109.5
C5—S1—C6	99.26 (6)	H5B—C5—H5C	109.5
C4—O1—Ni1	114.28 (6)	S1—C6—H6A	109.5
Ni1—O3—H3	124.3 (13)	S1—C6—H6B	109.5
S1—O4—Ni1	115.15 (4)	H6A—C6—H6B	109.5
C3—N1—C3ⁱ	122.56 (12)	S1—C6—H6C	109.5
C3—N1—Ni1	118.72 (6)	H6A—C6—H6C	109.5
C3ⁱ—N1—Ni1	118.72 (6)	H6B—C6—H6C	109.5

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O2ⁱⁱ	0.790 (17)	1.867 (17)	2.6555 (10)	176.3 (18)
C5—H5B···O2ⁱⁱ	0.98	2.58	3.3650 (14)	137
C6—H6A···O2ⁱⁱⁱ	0.98	2.62	3.3504 (13)	132
C6—H6B···O4^iv	0.98	2.38	3.3302 (14)	162

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

Acknowledgements

CL wishes to acknowledge the financial support of the Vice President Research Fund, Grenfell Campus, Memorial University of Newfoundland. KAA wishes to acknowledge the National Science Foundation and the University of Florida for funding of the purchase of the X-ray equipment.

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