trans-Di­chloro­tetrakis(4-methylpyrimidine-N¹)­ruthenium(II)

The title compound, trans-[Ru^IICl₂(N¹-mepym)₄] (mepym is 4-methylpyrimidine, C₅H₆N₂), obtained from the reaction of trans,cis,cis-[Ru^IICl₂(N¹-mepym)₂(SbPh₃)₂] (Ph is phenyl) with excess mepym in ethanol, has fourfold crystallographic symmetry and has the four pyrimidine bases coordinated through N¹ and arranged in a propeller-like orientation. The Ru—N and Ru—Cl bond distances are 2.082 (2) and 2.400 (4) Å, respectively. The methyl group, and the N³ and Cl atoms are involved in intermolecular C—H...N and C—­H...Cl hydrogen-bond interactions.

S1. Comment

The structural characterization of ruthenium complexes with pyrimidine and purine bases is an important preliminary step to understand the molecular mechanism for the cytostatic effects exerted by certain ruthenium compounds (Clarke et al., 1999, and references therein).

As part of a project from this laboratory devoted to the synthesis and the structural characterization of new ruthenium complexes which contain pyrimidine and purine bases (see for instance previously published papers by this group: Cini & Pifferi, 2000; Bellucci & Cini, 1999; Pifferi & Cini, 1998; Cini et al., 1993) we wish to report here on the X-ray diffraction analysis of the crystal and molecular structure of trans-[RuCl₂(mepym)₄], (I). \sch

The complex molecule contains the 4-methyl-1,3-pyrimidine ligand which can be considered a model of the nucleic acid pyrimidine bases. It has a pseudo-octahedral coordination sphere (see Fig. 1) in which the metal atom is linked to two Cl^- anions (at apical positions) and to four N¹ atoms from the mepym ligands. The Ru and Cl atoms are located on the fourfold crystallographic axis.

The Ru—Cl bond distances [average, 2.400 (4) Å] are in agreement with the corresponding values for other Ru^II-complexes (Bellucci & Cini, 1999; Pifferi & Cini, 1998). The Ru—N bond distances are 2.082 (2) Å, a value somewhat shorter than the Ru—N(mepym) lengths [2.131 (5) Å] found for trans,cis,cis-[RuCl₂(mepym)₂(SbPh₃)₂] (Cini et al., 2001). This fact is understandable on the basis of the larger trans influence exerted by triphenylstibine when compared to mepyn as well as on the high steric hindrance due to two cis SbPh₃ ligands. Other Ru—N bond lengths for substituted pyrimidine agree well with the value found in this work and are 2.036 (3) Å (average) for cis,trans, cis-dichloro-bis(2-phenylazo)pyrimidine)ruthenium(II) (Santra et al., 1999) and 2.081 (2) Å (average) for trans,cis,cis,-dichloro-bis(2-phenylazo) pyrimidine)ruthenium(II) (Santra et al., 1999). The bond angles around the metal center have almost the idealized values of 90 and 180°.

The bond distances and angles within the mepym ligand have normal values when compared to other metal complexes, see for instance, trans-dichloro (phenyl)-bis(pyridine)(N¹-4-methyl-1,3-pyrimidine)rhodium(III) (Cini et al., 1999) and catena[(µ²-N,S-thiocyanato)-(N-4-methylpyrimidine) copper(I)] (Teichert & Sheldrick, 1999). The orientation of the mepym planes with respect to the Ru—Cl vectors is almost exactly staggered, the C2—N1—Ru—Cl2 torsion angle being -39.3 (3)°. As a consequence, the arrangement of the four mepym ligands in the equatorial plane of the complex molecule can be described as propeller-like.

The existence of two C—H···Cl intramolecular hydrogen-bond type interactions per mepym ligand is not excluded on the basis of the contact distances and angles (see Table 2), even though an eclipsed conformation would bring to stronger C—H···Cl interactions.

The analysis of the crystal packing shows the existence of short intermolecular C—H···Cl and C—H···N contacts which involve the methyl group, and the chloride ligands and the N3 atoms. The selected contact distances and angles are quoted in Table 2. It has to be emphasized that interactions of the type C—H···X (X = O, N, halogen) attract increasing interest in the community of structural and bioinorganic chemists (see for instance: Taylor & Kennard, 1982; Sigel et al., 1998; Lippert et al., 2001; Huang et al., 1998; Cini & Cavaglioni, 1999).

S2. Experimental

The crystals of the title compound as red prisms were obtained on mixing a suspension of trans,cis,cis-[Ru^IICl₂(N¹-mepym)₂(SbPh₃)₂] (Cini et al., 2001) in absolute ethanol with a hundred excess mepym and refluxing the mixture under an atmosphere of ultra-pure nitrogen for 30 min. The deaerated clear solution was then stored at 278 K; single crystals formed within 48 h.

Computing details

Data collection: XSCANS (Siemens, 1994); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: ORTEP-32/ORTEPIII (Farrugia, 1998); software used to prepare material for publication: CIFTAB (Sheldrick, 1997b).

Figures

Fig. 1. Molecular structure showing 30% probability displacement ellipsoids.

Trans-dichloro-tetrakis(N¹-4-methyl-1,3-pyrimidine- ruthenium(II)

Crystal data

[RuCl2(C5H6N2)4]	Dx = 1.552 Mg m^−3
Mr = 548.44	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I4	Cell parameters from 24 reflections
a = 11.295 (1) Å	θ = 6–16°
c = 9.200 (1) Å	µ = 0.92 mm^−1
V = 1173.7 (2) Å^3	T = 293 K
Z = 2	Prism, red
F(000) = 556	0.30 × 0.20 × 0.10 mm

Data collection

Siemens P4 diffractometer	898 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.028
Graphite monochromator	θmax = 25.0°, θmin = 2.6°
ω scans	h = −10→12
Absorption correction: empirical (using intensity measurements) via ψ scan (North et al., 1968)	k = −13→11
Tmin = 0.872, Tmax = 0.912	l = −9→10
2354 measured reflections	3 standard reflections every 97 reflections
990 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.029	H-atom parameters constrained
wR(F^2) = 0.059	Calculated w = 1/[σ^2(Fo^2) + (0.0304P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.05	(Δ/σ)max < 0.001
990 reflections	Δρmax = 0.29 e Å^−3
73 parameters	Δρmin = −0.17 e Å^−3
1 restraint	Absolute structure: Flack, 1983
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.19 (5)

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. The assignment of the positions for the N3 and C5 atoms was based on the smallest values for the agreement factors and on the analysis of the intermolecular contacts. All the H atoms were set in calculated positions and allowed to ride on the respective C atoms during refinement. All the non-hydrogen atoms were treated anisotropically; whereas all the H atoms were considered isotropic and their displacement parameters were restrained to 1.2U(eq) of the atoms to which they are bound.

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
Ru	0.0000	0.0000	−0.04177 (17)	0.04569 (19)
Cl1	0.0000	0.0000	−0.3025 (3)	0.0622 (14)
Cl2	0.0000	0.0000	0.2192 (3)	0.0617 (14)
N1	−0.1701 (2)	0.0712 (2)	−0.0401 (8)	0.0498 (6)
C2	−0.2521 (4)	0.0367 (4)	0.0557 (5)	0.0608 (12)
H2	−0.2315	−0.0228	0.1209	0.073*
N3	−0.3626 (3)	0.0815 (4)	0.0651 (5)	0.0738 (11)
C4	−0.3924 (3)	0.1682 (3)	−0.0325 (15)	0.0569 (11)
C5	−0.3127 (4)	0.2042 (3)	−0.1335 (5)	0.0549 (11)
H5	−0.3329	0.2614	−0.2018	0.066*
C6	−0.2050 (4)	0.1559 (4)	−0.1332 (5)	0.0589 (11)
H6	−0.1506	0.1826	−0.2017	0.071*
C7	−0.5139 (4)	0.2197 (4)	−0.0248 (10)	0.0805 (15)
H7A	−0.5569	0.1833	0.0534	0.121*
H7B	−0.5546	0.2055	−0.1148	0.121*
H7C	−0.5085	0.3034	−0.0080	0.121*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Ru	0.0442 (2)	0.0442 (2)	0.0487 (3)	0.000	0.000	0.000
Cl1	0.069 (2)	0.069 (2)	0.049 (3)	0.000	0.000	0.000
Cl2	0.066 (2)	0.066 (2)	0.053 (3)	0.000	0.000	0.000
N1	0.0470 (15)	0.0466 (14)	0.0557 (15)	−0.0008 (11)	−0.007 (5)	0.000 (5)
C2	0.048 (2)	0.063 (3)	0.071 (3)	−0.0005 (19)	−0.001 (2)	0.011 (2)
N3	0.056 (2)	0.077 (3)	0.088 (3)	−0.0004 (18)	0.004 (2)	0.005 (2)
C4	0.0551 (19)	0.0463 (18)	0.069 (3)	0.0036 (14)	−0.004 (4)	0.001 (5)
C5	0.055 (3)	0.048 (2)	0.062 (3)	0.0088 (19)	−0.007 (2)	0.0125 (19)
C6	0.061 (3)	0.053 (3)	0.062 (3)	−0.0004 (19)	0.003 (2)	0.006 (2)
C7	0.059 (2)	0.083 (3)	0.100 (5)	0.0124 (19)	−0.001 (4)	0.012 (4)

Geometric parameters (Å, º)

Ru—N1^i	2.082 (2)	N3—C4	1.371 (10)
Ru—N1^ii	2.082 (2)	C4—C5	1.356 (11)
Ru—N1	2.082 (2)	C4—C7	1.492 (5)
Ru—N1^iii	2.082 (2)	C5—C6	1.333 (5)
Ru—Cl1	2.398 (4)	C5—H5	0.9300
Ru—Cl2	2.400 (4)	C6—H6	0.9300
N1—C2	1.337 (6)	C7—H7A	0.9600
N1—C6	1.343 (7)	C7—H7B	0.9600
C2—N3	1.349 (5)	C7—H7C	0.9600
C2—H2	0.9300
N1^i—Ru—N1^ii	179.2 (4)	N1—C2—H2	117.5
N1^i—Ru—N1	89.997 (3)	N3—C2—H2	117.5
N1^ii—Ru—N1	89.997 (3)	C2—N3—C4	117.0 (4)
N1^i—Ru—N1^iii	89.997 (3)	C5—C4—N3	120.0 (3)
N1^ii—Ru—N1^iii	89.997 (3)	C5—C4—C7	121.8 (7)
N1—Ru—N1^iii	179.2 (4)	N3—C4—C7	118.3 (8)
N1^i—Ru—Cl1	90.4 (2)	C6—C5—C4	118.8 (4)
N1^ii—Ru—Cl1	90.4 (2)	C6—C5—H5	120.6
N1—Ru—Cl1	90.4 (2)	C4—C5—H5	120.6
N1^iii—Ru—Cl1	90.4 (2)	C5—C6—N1	124.1 (4)
N1^i—Ru—Cl2	89.6 (2)	C5—C6—H6	117.9
N1^ii—Ru—Cl2	89.6 (2)	N1—C6—H6	117.9
N1—Ru—Cl2	89.6 (2)	C4—C7—H7A	109.5
N1^iii—Ru—Cl2	89.6 (2)	C4—C7—H7B	109.5
Cl1—Ru—Cl2	180.0	H7A—C7—H7B	109.5
C2—N1—C6	115.1 (3)	C4—C7—H7C	109.5
C2—N1—Ru	122.1 (4)	H7A—C7—H7C	109.5
C6—N1—Ru	122.8 (4)	H7B—C7—H7C	109.5
N1—C2—N3	125.0 (4)

Symmetry codes: (i) −y, x, z; (ii) y, −x, z; (iii) −x, −y, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···Cl2	0.93	2.78	3.247 (5)	112
C6—H6···Cl1	0.93	2.83	3.300 (5)	113
C7—H7C···Cl1^iv	0.96	2.92	3.772 (6)	149

Symmetry code: (iv) x−1/2, y+1/2, z+1/2.