The title compound,
trans-[Ru
IICl
2(
N1-mepym)
4] (mepym is 4-methylpyrimidine, C
5H
6N
2), obtained from the reaction of
trans,
cis,
cis-[Ru
IICl
2(
N1-mepym)
2(SbPh
3)
2] (Ph is phenyl) with excess mepym in ethanol, has fourfold crystallographic symmetry and has the four pyrimidine bases coordinated through N
1 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 N
3 and Cl atoms are involved in intermolecular C—H
N and C—H
Cl hydrogen-bond interactions.
Supporting information
CCDC reference: 173350
The crystals of the title compound as red prisms were obtained on mixing a
suspension of
trans,cis,cis-[RuIICl2(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.
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).
Trans-dichloro-tetrakis(
N1-4-methyl-1,3-pyrimidine- ruthenium(II)
top
Crystal data top
[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) Å3 | T = 293 K |
Z = 2 | Prism, red |
F(000) = 556 | 0.30 × 0.20 × 0.10 mm |
Data collection top
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 top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.029 | H-atom parameters constrained |
wR(F2) = 0.059 | Calculated w = 1/[σ2(Fo2) + (0.0304P)2] where P = (Fo2 + 2Fc2)/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) |
Crystal data top
[RuCl2(C5H6N2)4] | Z = 2 |
Mr = 548.44 | Mo Kα radiation |
Tetragonal, I4 | µ = 0.92 mm−1 |
a = 11.295 (1) Å | T = 293 K |
c = 9.200 (1) Å | 0.30 × 0.20 × 0.10 mm |
V = 1173.7 (2) Å3 | |
Data collection top
Siemens P4 diffractometer | 898 reflections with I > 2σ(I) |
Absorption correction: empirical (using intensity measurements) via ψ scan (North et al., 1968) | Rint = 0.028 |
Tmin = 0.872, Tmax = 0.912 | 3 standard reflections every 97 reflections |
2354 measured reflections | intensity decay: none |
990 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.029 | H-atom parameters constrained |
wR(F2) = 0.059 | Δρmax = 0.29 e Å−3 |
S = 1.05 | Δρmin = −0.17 e Å−3 |
990 reflections | Absolute structure: Flack, 1983 |
73 parameters | Absolute structure parameter: 0.19 (5) |
1 restraint | |
Special details top
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 (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
Ru—N1i | 2.082 (2) | N3—C4 | 1.371 (10) |
Ru—N1ii | 2.082 (2) | C4—C5 | 1.356 (11) |
Ru—N1 | 2.082 (2) | C4—C7 | 1.492 (5) |
Ru—N1iii | 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 | | |
| | | |
N1i—Ru—N1ii | 179.2 (4) | N1—C2—H2 | 117.5 |
N1i—Ru—N1 | 89.997 (3) | N3—C2—H2 | 117.5 |
N1ii—Ru—N1 | 89.997 (3) | C2—N3—C4 | 117.0 (4) |
N1i—Ru—N1iii | 89.997 (3) | C5—C4—N3 | 120.0 (3) |
N1ii—Ru—N1iii | 89.997 (3) | C5—C4—C7 | 121.8 (7) |
N1—Ru—N1iii | 179.2 (4) | N3—C4—C7 | 118.3 (8) |
N1i—Ru—Cl1 | 90.4 (2) | C6—C5—C4 | 118.8 (4) |
N1ii—Ru—Cl1 | 90.4 (2) | C6—C5—H5 | 120.6 |
N1—Ru—Cl1 | 90.4 (2) | C4—C5—H5 | 120.6 |
N1iii—Ru—Cl1 | 90.4 (2) | C5—C6—N1 | 124.1 (4) |
N1i—Ru—Cl2 | 89.6 (2) | C5—C6—H6 | 117.9 |
N1ii—Ru—Cl2 | 89.6 (2) | N1—C6—H6 | 117.9 |
N1—Ru—Cl2 | 89.6 (2) | C4—C7—H7A | 109.5 |
N1iii—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) top
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···Cl1iv | 0.96 | 2.92 | 3.772 (6) | 149 |
Symmetry code: (iv) x−1/2, y+1/2, z+1/2. |
Experimental details
Crystal data |
Chemical formula | [RuCl2(C5H6N2)4] |
Mr | 548.44 |
Crystal system, space group | Tetragonal, I4 |
Temperature (K) | 293 |
a, c (Å) | 11.295 (1), 9.200 (1) |
V (Å3) | 1173.7 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.92 |
Crystal size (mm) | 0.30 × 0.20 × 0.10 |
|
Data collection |
Diffractometer | Siemens P4 diffractometer |
Absorption correction | Empirical (using intensity measurements) via ψ scan (North et al., 1968) |
Tmin, Tmax | 0.872, 0.912 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2354, 990, 898 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.029, 0.059, 1.05 |
No. of reflections | 990 |
No. of parameters | 73 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.29, −0.17 |
Absolute structure | Flack, 1983 |
Absolute structure parameter | 0.19 (5) |
Selected geometric parameters (Å, º) topRu—N1 | 2.082 (2) | C2—N3 | 1.349 (5) |
Ru—Cl1 | 2.398 (4) | N3—C4 | 1.371 (10) |
Ru—Cl2 | 2.400 (4) | C4—C5 | 1.356 (11) |
N1—C2 | 1.337 (6) | C4—C7 | 1.492 (5) |
N1—C6 | 1.343 (7) | C5—C6 | 1.333 (5) |
| | | |
N1i—Ru—N1 | 89.997 (3) | N1—C2—N3 | 125.0 (4) |
N1—Ru—N1ii | 179.2 (4) | C2—N3—C4 | 117.0 (4) |
N1—Ru—Cl1 | 90.4 (2) | C5—C4—N3 | 120.0 (3) |
N1—Ru—Cl2 | 89.6 (2) | C5—C4—C7 | 121.8 (7) |
Cl1—Ru—Cl2 | 180.0 | N3—C4—C7 | 118.3 (8) |
C2—N1—C6 | 115.1 (3) | C6—C5—C4 | 118.8 (4) |
C2—N1—Ru | 122.1 (4) | C5—C6—N1 | 124.1 (4) |
C6—N1—Ru | 122.8 (4) | | |
Symmetry codes: (i) −y, x, z; (ii) −x, −y, z. |
Hydrogen-bond geometry (Å, º) top
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···Cl1iii | 0.96 | 2.92 | 3.772 (6) | 149 |
Symmetry code: (iii) x−1/2, y+1/2, z+1/2. |
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 RuII-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).