electronic reprint Acta Crystallographica Section C
Crystal Structure Communications ISSN 0108-2701
Positional and compositional disorder in a ruthenium(II) piano-stool complex Ilia A. Guzei, Brian S. Dolinar, Nozipho Khumalo and James Darkwa
Acta Cryst. (2013). C69, 847–850
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Crystallography Journals Online is available from journals.iucr.org Acta Cryst. (2013). C69, 847–850
Ilia Guzei et al. · [Ru(PO2 F2 )(C10 H14 )(C9 H9 N3 )](PF6 )0.85 (BF4 )0.15
metal-organic compounds Acta Crystallographica Section C
[(p-cymene)Ru(L)](PF6)2 {L is 2-[(1H-pyrazol-1-yl)methyl]pyridine}.
Crystal Structure Communications ISSN 0108-2701
Positional and compositional disorder in a ruthenium(II) piano-stool complex Ilia A. Guzei,a* Brian S. Dolinar,a Nozipho Khumalob and James Darkwab a
Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706, USA, and bDepartment of Chemistry, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa Correspondence e-mail:
[email protected] Received 4 June 2013 Accepted 26 June 2013
In (6-p-cymene)(difluorophosphinato-O){2-[(1H-pyrazol1-yl)methyl-N2]pyridine-N}ruthenium(II) 0.85-hexafluorophosphate 0.15-tetrafluoroborate, [Ru(PO2F2)(C10H14)(C9H9N3)](PF6)0.85(BF4)0.15, (I), the [PO2F2] ligand exhibits positional disorder due to one F atom and one O atom sharing the same two positions related by a mirror reflection across the O—P—F plane. The correct composition of this coordinated anion was successfully determined to be [PO2F2] by refining the complex with various tetrahedral anions in which terminal atoms have similar atomic form factors. The noncoordinated counter-ion is compositionally disordered between [PF6] and [BF4] . The difficulty in determining the correct composition of this anion illustrates the importance of a crystallographer remaining impartial and open to encountering unexpected moieties in the process of elucidating a structure. Keywords: crystal structure; compositional disorder; idealized geometry.
Whereas the geometrical parameters of the structure are rather typical (see below), the process of the structural refinement and ion identification is instructive and our detailed description of these processes can be useful to young crystallographers in training. Currently, independent scientists and single-crystal X-ray instrument manufacturers offer software packages capable of solving and refining small-molecule structures automatically: SHELXT (Sheldrick, 2013), PLATON/SYSTEM-S (Spek, 2009), STANDARD (Fuller et al., 2010), Autostructure by Bruker (Ruf, 2009; Bruker, 2013a,b), AutoChem by Agilent Technologies (Agilent, 2012), and CrystalClear by Rigaku Americas (Rigaku Americas Corporation, 2013). Unfortunately, chemically reasonable structures are not always produced by automated structure solution and refinement packages due to unexpected compositions, disorder, twinning and other problems, in which cases human intervention becomes necessary. However, even a chemist trained in crystallography can occasionally be mystified by a structure with an unforeseen composition when his or her expectation of seeing a certain result is not met, and when the structure fails to conform (as it should in such cases) to the expected result. Thus, it is critical to remain objective during the structural refinement and recognize that undesirable and
1. Discussion Arene–ruthenium(II) complexes are known for their cytotoxic effect against human ovarian and lung cancer cell lines (Bugarcic et al., 2009). This has led to a number of new areneruthenium(II) nitrogen-donor complexes (Govindaswamy et al., 2004; Marchetti et al., 2008; Mishra & Mukherjee, 2010). We have previously prepared a number of [(p-cymene)Ru{2[(pyrazol-1-yl)methyl]pyridine}Cl]X and [(p-cymene)Ru{2[(pyrazol-1-yl)methyl]pyridine}2]X2 (X = [PF6] or [BF4] ) complexes as potential antimalarial agents (Khumalo, 2013). In one of these reactions, carried out using [(p-cymene)RuCl2]2, 2-[(1H-pyrazol-1-yl)methyl]pyridine and AgPF6 as starting materials, we unexpectedly isolated (6-p-cymene)(difluorophosphinato-O){2-[(1H-pyrazol-1-yl)methyl-N2]pyridine-N}ruthenium(II) 0.85-hexafluorophosphate 0.15tetrafluoroborate, (I), a product formed as a result of partial hydrolysis of the [PF6] counter-ion of the expected product Acta Cryst. (2013). C69, 847–850
Figure 1 The RuII cation of (I), shown with 50% probability displacement ellipsoids. All H atoms have been omitted for clarity. Atoms F2A and O2A represent the overall ligand composition, but each site is occupied half of the time by an F atom and half of the time by an O atom.
doi:10.1107/S0108270113017605
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metal-organic compounds Table 1 Experimental details. Crystal data Chemical formula
[Ru(PO2F2)(C10H14)(C9H9N3)](PF6)0.85(BF4)0.15 631.81 Monoclinic, P21/n 100 15.6531 (17), 8.7619 (9), 17.4895 (18) 106.316 (5) 2302.1 (4) 4 Cu K 7.54 0.16 0.10 0.06
Mr Crystal system, space group Temperature (K) ˚) a, b, c (A ( ) ˚ 3) V (A Z Radiation type (mm 1) Crystal size (mm) Data collection Diffractometer Absorption correction Tmin, Tmax No. of measured, independent and observed [I > 2(I)] reflections Rint ˚ 1) (sin /)max (A Refinement R[F 2 > 2(F 2)], wR(F 2), S No. of reflections No. of parameters No. of restraints H-atom treatment ˚ 3) max, min (e A
Bruker SMART APEXII area-detector Analytical (SADABS; Bruker, 2012) 0.429, 0.735 32 407, 4479, 4065 0.039 0.618
0.024, 0.057, 1.02 4479 327 0 H-atom parameters constrained 0.47, 0.33
Computer programs: APEX2 and SAINT-Plus (Bruker, 2013), SHELXTL (Sheldrick, 2013) and OLEX2 (Dolomanov et al., 2009).
chemically unexpected structures can ensue from a ‘routine’ structural characterization. ‘Desire’ is a dangerous concept in science – whereas one may want something to happen, he/she cannot assume it will happen and must accept what does happen. Compound (I) is such an example. In this case, the data-set quality was good and the structure could readily be solved; however, chemical knowledge and proficiency in advanced refinement techniques were necessary to identify one of the ligands, model its disorder, model compositional disorder in the counter-ion, and complete the refinement. We describe herein the resolution of these challenges. The initial structure solution of (I) produced most of the non-H atoms in the RuII complex and the position of the [PF6] anion (Figs. 1 and 2a). It was easy to recognize the L and p-cymene ligands in the RuII complex, however, the presence of a third ligand was unexpected. Several reasonable possibilities existed for an anion with a tetrahedral geometry and similar atomic form factors for the terminal atoms, viz. [PO4]3 , [SO4]2 , [ClO4] , and even rare [PO3F]2 , and [PO2F2] . In general, the overall ligand geometry, bond lengths and angles, and atomic scattering power must be taken into consideration during ligand identification. Differentiating among these five anions was important in establishing the charge on the Ru atom in the complex. The phosphate was rejected due to its high negative charge that would require the Ru atom to have a formal charge of +4. The structure was refined sequentially with [SO4]2 , [ClO4] and [PO3F]2 , and when these models proved to be unsatisfactory, [PO2F2] was chosen. The formation of [PO2F2] could be expected from a
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known reagent, but this requires knowledge of the chemistry and is a result of one of those undesirable side reactions when water and air found their way into the reaction vessel. In each case, the Fourier difference map was examined graphically using OLEX2 (Dolomanov et al., 2009) after refining the model to convergence. The difference Fourier maps for [SO4]2 and [ClO4] (Figs. 3a and 3b) show a large negative region of residual electron density around the S and Cl atoms, respectively, indicating that both S and Cl are too electron-rich to be the correct atom for the site. At the same time, there were regions of positive electron density around the O atoms of the anion suggesting that they are electron-deficient, and that heavier atoms should be present at their positions. In the case of [PO3F]2 , there were no peaks or holes near the P atom, indicating that P is the correct atom for the site, but there were regions of positive electron density near the uncoordinated O atoms (Fig. 3c). In Fig. 3(d), the Fourier difference map for [PO2F2] has no prominent features around any of the five atoms, indicating the correct composition. At this point we searched the Cambridge Structural Database (CSD, Version 5.34, February 2013; Allen, 2002) for instances of ruthenium complexes with [PO2F2] and found three: [{6-p-MeC6H4(i-Pr)}Ru(OPF2O){PN(i-Pr)}]PF6, (II) (Carmona et al., 2006), [{Ru[P(OMe)3]2(PFO3)}2(-S)(PF2O2)2] (Matsumoto et al., 1997) and [Ru(mes){2P,O-(t-Bu)P[CH2C(O)OMe](CH2CO2Me)}(O-O2PF2)]PF6 (mes is mesityl; Werner et al., 2001). Among these three complexes, the [PO2F2] anion is monodentate and well refined only in ˚ , a value in (II), with an Ru—O bond length of 2.117 (3) A excellent agreement with the corresponding distance of ˚ in (I). When [PO2F2] was refined as an ordered 2.1130 (15) A moiety, the difference Fourier map showed no features for atom F1, indicating its correct identity and occupancy, but revealed negative regions of electron density about the other F atom and a positive region for the O atom, regardless of which atom was assigned to each of the two positions. Thus, the difluorophosphinate ligand in (I) is disordered by a mirror reflection about the O1—P1—F1 plane, effectively placing atoms F2 and O2 on each side of the plane 50% of the time. Indeed, when the disordered F and O atoms were modelled as having half-occupancy at each position the best refinement was obtained. The positions and anisotropic displacement
Figure 2 The anion of (I), with (a) the minor disorder components omitted and (b) the [PF6] /[BF4] disorder [in a 0.854 (3):0.146 (3) ratio] illustrated; atoms B1 and P2 share the same position. The [BF4] anion was refined isotropically.
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Acta Cryst. (2013). C69, 847–850
metal-organic compounds parameters of the two disordered atoms were constrained to be the same. The asymmetric unit contains one molecule of the [(pcymene)Ru(L)(PO2F2)]+ complex (Fig. 1) and a noncoordi˚ 3) nating anion (Fig. 2). There were small peaks (0.6–1.3 e A of additional electron density forming a tetrahedron within the noncoordinating [PF6] anion, with P-to-peak distances in ˚ range, indicating compositional disorder the 1.10–1.49 A between [PF6] and another moiety. The latter proved to be [BF4] , as we initially proposed based on the geometry and charge, and later confirmed this possibility with the chemist (Figs. 2a and 2b). The [PF6] was the desired noncoordinating anion, whereas [BF4] was believed to have been carried over from a previous synthetic step. Monoanions [PF6] and [BF4] share the same site in the lattice in a 0.854 (3):0.146 (3) ratio (Fig. 2b). The tetrahedral geometry and isotropic displacement parameters of the [BF4] anion were constrained to achieve a computationally stable refinement (Guzei, 2013). The Ru complex has a typical piano-stool geometry with an 6-coordinated arene and three additional sites of ligation
occupied by a bidentate L ligand and the disordered difluorophosphinate ligand. The Ru–(arene centroid) distance ˚ , is noticeably shorter than in (I), calculated to be 1.6787 (9) A ˚ computed from 1763 Ru– the average value of 1.71 (5) A centroid(6-C6) bond distances in 1412 relevant complexes reported in the CSD. The Ru—Npy bond distance of ˚ in (I) is slightly longer than the average Ru— 2.1163 (18) A ˚ obtained by averaging 3695 bond Npy distance of 2.09 (6) A distances in 1494 structures. The Ru—Npz distance of ˚ in (I) is somewhat shorter than the average 2.0809 (18) A ˚ calculated from 543 relevant Ru—Npz distance of 2.09 (6) A bond lengths in 171 Ru complexes. The folding angle of the L ligand defined as the dihedral angle between the Ru1—N1— C5—C6 and Ru1—N3—N2—C6 planes is 125.41 (12) . Relevant values for CoII (Benade et al., 2011), NiII (Ojwach, Guzei, Benade et al., 2009) and PdII complexes (Ojwach et al., 2009; Segapelo et al., 2009; Spencer et al., 2012) averaged 121 (6) . In none of the four comparisons is the difference statistically significant and the geometrical parameters are therefore typical.
Figure 3 The difference Fourier maps of compound (I) refined with the (a) [SO4]2 , (b) [ClO4] , (c) [PO3F]2 and (d) [PO2F2] ligand. The regions of negative electron density are lighter (red in the electronic version of the paper) and the regions of positive electron density are darker (blue). All atoms are drawn as 50% probability displacement ellipsoids. All H atoms and the anions have been omitted for clarity. Acta Cryst. (2013). C69, 847–850
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metal-organic compounds This study is an example of an expectedly straightforward structural characterization becoming nonroutine. It illustrates the importance of being impartial regarding the outcome and being receptive to the possibility of encountering unexpected moieties in the structure as well as being able to account for the residual electron density. Additionally, this structural study supports the postulate that good quality data sets yield good quality structures.
2. Experimental Crystal data, data collection and structure refinement details are summarized in Table 1. To a Schlenk tube wrapped in aluminium foil was added [(p-cymene)RuCl2]2 (50 mg, 0.08 mmol), 2-[(1H-pyrazol-1-yl)methyl]pyridine (30 mg, 0.16 mmol) and AgPF6 (50 mg, 0.20 mmol) in a glove-box. Dichloromethane (40 ml) was added to the Schlenk tube and the reaction was run for 18 h with vigorous stirring. The silver chloride precipitate was removed using a 0.45 mm glass fiber filter. The filtrate was then concentrated to ca 5 ml after which diethyl ether and hexane were added dropwise one after the other while shaking vigorously to obtain a precipitate. Slow evaporation of a dichloromethane–diethyl ether solution of the product gave orange sheet-like crystals of (I). We thank Professor T. Andrew Mobley (Grinnell College, Iowa, USA) for his review of the manuscript, and an anonymous reviewer for very helpful comments. Supplementary data for this paper are available from the IUCr electronic archives (Reference: WQ3041). Services for accessing these data are described at the back of the journal.
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