The three-dimensional inter­molecular network formed via water mol­ecules in trans-bis­(nitrito-κN)tetra­kis(pyridine-κN)ruthenium(II) dihydrate

The mol­ecular geometry of the tetra­gonal crystal structure of the title compound, [Ru(NO₂)₂(C₅H₅N)₄]·2H₂O, differs from that previously determined by powder diffraction [Schaniel et al. (2010). Phys. Chem. Chem. Phys. 12, 6171–6178]. In the [Ru(NO₂)(C₅H₅N)₄] molecule, the Ru atom lies at the intersection of three twofold axes (Wyckoff position 8b). It is coordinated by four N atoms of the pyridine rings, as well as by two N atoms of N-nitrite groups. The last two N atoms are located on a twofold axis (Wyckoff position 16f). The O atoms of the water molecules are situated on a twofold axis (Wyckoff position 16e). Short inter­molecular contacts are observed in the crystal structure, viz. N—O...OW and N—O...H—OW contacts between nitrite and water, and weak C—H...OW hydrogen bonds between pyridine and water. Thus, the inter­calated water mol­ecules act as bridges connecting the trans-[Ru(NO₂)₂(py)₄] mol­ecules into a three-dimensional network.

S1. Comment

Nitrosyl complexes have attracted a great interest over the past ten years because they present a reversible linkage isomerization under light irradiation between M—N—O and M—O—N forms, where M is a metallic atom (Fe, Co, Ru, Ni etc.) (Coppens et al., 2002, and references therein). The prototype compound is Na₂[Fe(CN)₅NO].2H₂O (Hauser et al., 1977). Another kind of reversible photochemical transformation is reported between N-nitrite (M—NO₂) and O-nitrite (M—ONO) molecules. The N-nitrite form of the molecule can usually be obtained during the synthesis of the corresponding nitrosyl complex M—N—O. The prototype compound of N-nitrite to O-nitrite linkage isomerization is [Co(NO₂)(NH₃)₅]Cl₂ (Grenthe & Nordin, 1979). Detailed crystallographic studies of these two kinds of materials are, however, still limited because of both difficulties in obtaining good single crystals and partial photochemical transformations (Coppens et al., 2002). A notable exception now exists in the family of nitrosyl complexes: trans-[RuCl(py)₄(NO)](PF₆)₂.0.5H₂O recently became a model system for the structural analysis of the two isomeric configurations of the NO ligand (Cormary et al., 2009), since the phototransformation from linear Ru—N—O (the so-called GS state) to linear Ru—O—N (the so-called MS1 state) is complete or quasi-complete in the single-crystal structure of the complex.

We report here the crystal structure of the N-nitrite form of trans-[Ru(NO₂)₂(py)₄].2H₂O, (I), which is an intermediate product obtained during the synthesis of trans-[RuCl(py)₄(NO)](PF₆)₂.0.5H₂O (Schaniel et al., 2007). High-quality yellow single crystals of (I) were obtained and the tetragonal space group I4₁/acd (Z = 8) was determined. This crystal structure differs from the powder structure previously determined in the orthorhombic space group Pna2₁, Z = 4 (Schaniel et al., 2010). In that work, the trans-[Ru(NO₂)₂(py)₄] molecular geometry showed discrepancies with parameters derived from density functional theory (DFT) (Delley, 2006), which was discussed alongside the powder structure. Analysis of the single-crystal data reported here leads to a geometry for trans-[Ru(NO₂)₂(py)₄] that is in good agreement with the DFT calculations performed for the free molecule. In addition, the single-crystal data enable discussion of the intermolecular interactions between trans-[Ru(NO₂)₂(py)₄] and intercalated water.

The molecular geometry of trans-[Ru(NO₂)₂(py)₄] differs significantly from that previously determined from powder data. The Ru atom lies at the intersection of three twofold axis (8b Wyckoff position) and is coordinated by four N atoms (labeled N1) of the pyridine rings as well as by two N atoms (labeled N2) of N-nitrite groups. The last two N atoms are located on a twofold screw axis (16f Wyckoff position). Thus, there is only one symmetry-independent pyridine ring and consequently an unique value for Ru1—N1 bond length. The two O atoms of the N-nitrite group are symmetry-equivalent and there are unique values for both Ru1—N2 and N2—O1 bond lengths (Fig. 1 and Table 1). Differences between the single-crystal structure and the previous powder structure are also clear from both bond lengths and angles values. In particular, the pyridine N—Ru distance (Ru1—N1) is longer than the nitrite N—Ru distance (Ru1—N2), while the powder structure led to the opposite conclusion (see Table 1). As mentioned above, DFT calculations are in agreement with the single-crystal structure (Table 1). Moreover, the Ru1—N2 bond length reported here [2.050 (2) Å] is not surprising when compared with values obtained from other nitro compounds of ruthenium, for example 2.033 (4) Å at 293 K in [Ru(tpy)(dpk)(NO₂)]ClO₄ (tpy is 2,2':6',2''-terpyridine? and dpk is ?; Sarkar et al., 2005), and 2.088 (1) and 2.091 (2) Å at 90 and 200 K, respectively, in [Ru(bpy)(NO)(NO₂)](PF₆)₂ (bpy is ?,?'-bipyridine?; Kovalevsky et al., 2005). Another significant difference between the present single-crystal structure and the previous powder structure concerns the angular values involving the NO₂ group. The Ru1—N2—O1 and O1—N2—O1ⁱ [symmetry code: (i) -y + 1/4, -x + 1/4, -z + 1/4] angles differ by between ca 5 and 18° (Table 1 and Fig. 1). In contrast, comparison between the trans-[Ru(NO₂)₂(py)₄] molecular geometry determined here from single-crystal data (Table 1, column 1) and that calculated from DFT (Table 1, column 2) (Schaniel et al., 2010) again shows good agreement. Thus, the present single-crystal structure validates the DFT calculations.

Analysis of the intermolecular interactions in (I) shows that the solvent water molecules act as bridges connecting the trans-[Ru(NO₂)₂(py)₄] complexes into a three-dimensional supramolecular network via (i) short O—H···O hydrogen bonds connecting the NO₂ group and water, and (ii) weak C—H···O hydrogen bonds between pyridine rings and intercalated water (Table 2, and Figs. 1 and 2). Until now, the role of such close intermolecular contacts has not been discussed in the N-nitrite to O-nitrite photochemical process. One reason is that high-quality single-crystal data for such materials is largely missing and therefore DFT studies are usually limited to the intramolecular level (Schaniel et al., 2010). The single-crystal structure presented here could be used to undertake calculations beyond this level for a deeper understanding of the photochemical reaction. Indeed, IR spectroscopic investigations on powder samples (Schaniel et al., 2010) showed that, using light of wavelength 325 nm, about 50% of the trans-[Ru(NO₂)₂(py)₄] molecules can be switched from the N-bound Ru—NO₂ to the O-bound Ru-ONO configuration below T = 250 K. The reverse transformation is also observed with light in the wavelength range 405–442 nm. Further investigation of these photochemical reactions will be performed on the single crystals.

Related literature

For related literature, see: Coppens et al. (2002); Cormary et al. (2009); Delley (2006); Grenthe & Nordin (1979); Hauser et al. (1977); Kovalevsky et al. (2005); Sarkar et al. (2005); Schaniel et al. (2007, 2010).

S2. Experimental

trans-[Ru(NO₂)₂(py)₄].2H₂O powder was prepared as described previously (Schaniel et al., 2007, and references therein). The pale-yellow powder was dissolved in ethanol (2.10 τimes 10 ^-5 mol in 10 ml) and a few drops of water were added. Good yellow needle-like single crystals of (I) were obtained after slow evaporation over a period of a few days.

S3. Refinement

All H atoms were located in a difference Fourier synthesis, but those attached to C atoms were treated as riding on their parent C atoms, with C—H = 0.93 Å and U_iso(H) = 1.2U_eq(C). The H atoms of the water molecule were refined semi-freely by introducing a distance restraint of 0.84 (2) Å while constraining U_iso(H) to 1.5U_eq(O).

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

	Fig. 1. The structure of one trans-[Ru(NO2)2(py)4] molecule and symmetry-equivalent neighbouring water molecules, showing the atom-numbering scheme (see also Table 2). Displacement ellipsoids are drawn at the 50% probability level. [Symmetry codes: (i) -y + 1/4, -x + 1/4, -z + 1/4; (ii) -x, -y + 1/2, z; (iii) x - 1/2, -y, z; (iv) y - 1/4, x + 1/4, z + 1/4.]
	Fig. 2. A projection of the trans-[Ru(NO2)2(py)4] and H2O molecules in the ab plane, showing the three-dimensional supramolecular network.

trans-bis(nitrito-κN)tetrakis(pyridine-κN)ruthenium(II) dihydrate

Crystal data

[Ru(NO2)2(C5H5N)4]·2H2O	Dx = 1.630 Mg m^−3
Mr = 545.52	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I41/acd	Cell parameters from 3452 reflections
Hall symbol: -I 4bd 2c	θ = 2.0–27.1°
a = 16.3418 (2) Å	µ = 0.76 mm^−1
c = 16.6448 (2) Å	T = 120 K
V = 4445.07 (9) Å^3	Prism, yellow
Z = 8	0.21 × 0.11 × 0.09 mm
F(000) = 2224

Data collection

Oxford Xcalibur diffractometer with Sapphire 3 CCD area detector	1221 independent reflections
Radiation source: fine-focus sealed tube	907 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
Detector resolution: 19.64 pixels mm^-1	θmax = 27.0°, θmin = 3.0°
ω scans	h = −20→20
Absorption correction: analytical (PLATON; Spek, 2009)	k = −20→20
Tmin = 0.886, Tmax = 0.941	l = −20→21
17299 measured reflections

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)] = 0.018	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.049	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0301P)^2] where P = (Fo^2 + 2Fc^2)/3
1221 reflections	(Δ/σ)max < 0.001
80 parameters	Δρmax = 0.26 e Å^−3
1 restraint	Δρmin = −0.39 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
O2	0.16048 (10)	0.0000	0.2500	0.0329 (4)
H2A	0.1273 (10)	0.0223 (11)	0.2141 (11)	0.049*
Ru1	0.0000	0.2500	0.1250	0.01115 (9)
N1	−0.05987 (7)	0.18279 (7)	0.21495 (7)	0.0143 (3)
N2	0.08869 (7)	0.16131 (7)	0.1250	0.0170 (4)
O1	0.07118 (7)	0.08656 (6)	0.13059 (6)	0.0244 (3)
C1	−0.14074 (9)	0.16593 (9)	0.21282 (9)	0.0180 (3)
H1	−0.1728	0.1890	0.1709	0.022*
C2	−0.17878 (10)	0.11683 (10)	0.26858 (9)	0.0229 (4)
H2	−0.2359	0.1067	0.2650	0.028*
C3	−0.13324 (11)	0.08240 (10)	0.32987 (9)	0.0257 (4)
H3	−0.1582	0.0479	0.3688	0.031*
C4	−0.05066 (10)	0.09936 (9)	0.33311 (9)	0.0226 (4)
H4	−0.0176	0.0767	0.3745	0.027*
C5	−0.01667 (9)	0.14948 (9)	0.27567 (9)	0.0184 (3)
H5	0.0402	0.1612	0.2790	0.022*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O2	0.0242 (9)	0.0358 (10)	0.0386 (10)	0.000	0.000	0.0094 (9)
Ru1	0.01104 (10)	0.01104 (10)	0.01136 (13)	−0.00021 (9)	0.000	0.000
N1	0.0151 (6)	0.0143 (6)	0.0133 (6)	−0.0009 (5)	0.0009 (5)	−0.0018 (5)
N2	0.0181 (6)	0.0181 (6)	0.0147 (9)	0.0014 (7)	−0.0013 (5)	−0.0013 (5)
O1	0.0280 (6)	0.0137 (6)	0.0314 (7)	0.0039 (5)	−0.0034 (5)	0.0007 (5)
C1	0.0168 (8)	0.0189 (8)	0.0184 (8)	−0.0010 (7)	0.0006 (6)	−0.0033 (7)
C2	0.0209 (8)	0.0249 (9)	0.0231 (9)	−0.0074 (7)	0.0048 (7)	−0.0048 (7)
C3	0.0362 (10)	0.0221 (9)	0.0187 (9)	−0.0079 (7)	0.0074 (8)	0.0018 (7)
C4	0.0302 (9)	0.0220 (8)	0.0154 (8)	−0.0002 (7)	−0.0014 (7)	0.0031 (7)
C5	0.0197 (8)	0.0185 (8)	0.0171 (8)	−0.0001 (6)	−0.0021 (6)	−0.0007 (7)

Geometric parameters (Å, º)

O2—H2A	0.885 (14)	N2—O1	1.2582 (13)
Ru1—N2	2.0496 (17)	C1—C2	1.375 (2)
Ru1—N2^i	2.0496 (17)	C1—H1	0.9500
Ru1—N1^ii	2.0989 (12)	C2—C3	1.382 (2)
Ru1—N1^i	2.0989 (12)	C2—H2	0.9500
Ru1—N1^iii	2.0989 (12)	C3—C4	1.379 (2)
Ru1—N1	2.0989 (12)	C3—H3	0.9500
N1—C5	1.3476 (18)	C4—C5	1.376 (2)
N1—C1	1.3503 (18)	C4—H4	0.9500
N2—O1^iii	1.2582 (13)	C5—H5	0.9500
N2—Ru1—N2^i	180.0	O1^iii—N2—O1	116.56 (17)
N2—Ru1—N1^ii	92.31 (3)	O1^iii—N2—Ru1	121.72 (9)
N2^i—Ru1—N1^ii	87.69 (3)	O1—N2—Ru1	121.72 (9)
N2—Ru1—N1^i	92.31 (3)	N1—C1—C2	122.92 (14)
N2^i—Ru1—N1^i	87.68 (3)	N1—C1—H1	118.5
N1^ii—Ru1—N1^i	175.37 (6)	C2—C1—H1	118.5
N2—Ru1—N1^iii	87.69 (3)	C1—C2—C3	119.48 (15)
N2^i—Ru1—N1^iii	92.31 (3)	C1—C2—H2	120.3
N1^ii—Ru1—N1^iii	88.99 (6)	C3—C2—H2	120.3
N1^i—Ru1—N1^iii	91.20 (6)	C4—C3—C2	118.29 (15)
N2—Ru1—N1	87.68 (3)	C4—C3—H3	120.9
N2^i—Ru1—N1	92.32 (3)	C2—C3—H3	120.9
N1^ii—Ru1—N1	91.20 (6)	C5—C4—C3	119.18 (15)
N1^i—Ru1—N1	88.99 (6)	C5—C4—H4	120.4
N1^iii—Ru1—N1	175.37 (6)	C3—C4—H4	120.4
C5—N1—C1	116.75 (13)	N1—C5—C4	123.36 (14)
C5—N1—Ru1	120.14 (10)	N1—C5—H5	118.3
C1—N1—Ru1	122.97 (10)	C4—C5—H5	118.3
N2—Ru1—N1—C5	42.63 (10)	N1^ii—Ru1—N2—O1	−50.54 (6)
N2^i—Ru1—N1—C5	−137.37 (10)	N1^i—Ru1—N2—O1	129.46 (6)
N1^ii—Ru1—N1—C5	134.90 (12)	N1^iii—Ru1—N2—O1	−139.43 (6)
N1^i—Ru1—N1—C5	−49.72 (10)	N1—Ru1—N2—O1	40.57 (6)
N2—Ru1—N1—C1	−132.82 (11)	C5—N1—C1—C2	−0.6 (2)
N2^i—Ru1—N1—C1	47.18 (11)	Ru1—N1—C1—C2	175.03 (11)
N1^ii—Ru1—N1—C1	−40.55 (10)	N1—C1—C2—C3	−0.2 (2)
N1^i—Ru1—N1—C1	134.82 (13)	C1—C2—C3—C4	0.5 (2)
N1^ii—Ru1—N2—O1^iii	129.46 (6)	C2—C3—C4—C5	−0.1 (2)
N1^i—Ru1—N2—O1^iii	−50.54 (6)	C1—N1—C5—C4	1.1 (2)
N1^iii—Ru1—N2—O1^iii	40.56 (6)	Ru1—N1—C5—C4	−174.67 (12)
N1—Ru1—N2—O1^iii	−139.43 (6)	C3—C4—C5—N1	−0.8 (2)

Symmetry codes: (i) −x, −y+1/2, z; (ii) y−1/4, x+1/4, −z+1/4; (iii) −y+1/4, −x+1/4, −z+1/4.