Role of X-Ray Crystallography in Structural Studies of Pyridyl-Ruthenium Complexes

This on X-ray Crystallography is a compilation of current trends in the use of X-ray crystallography and related structural determination methods in various fields. The methods covered here include single crystal small-molecule X-ray crystallography, macromolecular (protein) single crystal X-ray crystallography, and scattering and spectroscopic complimentary methods. The fields range from simple organic compounds, metal complexes to proteins, and also cover the meta-analyses of the database for weak interactions.


Introduction
It is extremely important for chemists to establish the structure of new compounds. A more accurate understanding of the structure leads to the construction of appropriate reaction systems. For example, although the well-known platinum complex, [PtCl 2 (NH 3 ) 2 ], has two geometrical isomers (cis and trans in Fig. 1), only the cis-isomer (so-called cisplatin) exhibits prominent antitumor activity (Reedijk, 1996;Rosenberg et al., 1969). Characterization of most structures of simple organic compounds is usually carried out by various spectroscopic measurements including NMR, IR and MS. On the other hand, detailed structural characterization of coordination compounds is achieved by X-ray diffraction methods, which can provide not only information on the geometrical structures, but also full bond parameters. In particular, single crystal X-ray diffraction is the most powerful tool for the detailed structural analysis of crystalline coordination compounds. The aim of this chapter is to demonstrate particular advantages of X-ray structural analysis when compared with other techniques on coordination compounds. Herein, X-ray analysis of a variety of mononuclear ruthenium complexes containing pyridyl substituents is mainly described.

Coordination geometries and coordination modes
Some isomeric pairs of [Ru(tpy)(L)Cl] n+ type complexes (tpy = 2,2':6',2''-terpyridine, L = asymmetrical pyridyl-based bidentate ligands in Fig. 2) have been prepared and structurally characterized as precatalysts to investigate the effect of isomeric structural features on the catalytic epoxidation process (Chowdhury et al., 2011;Dakkach et al., 2010). In the complex [Ru(tpy)(1)(OH 2 )] 2+ , the distal isomer exhibits better activity because it contains a pyridine C-H bond nearly parallel to the Ru-O bond, whereas for the proximal isomer this position is occupied by a C-CH 3 group and thus exerts a much stronger steric effect (Dakkach et al., 2010). In the complex [Ru(tpy)(2)(OH 2 )] + , on the other hand, the proximal isomer has been established to be an excellent catalyst for the chemoselective epoxidation though limited differences in electronic structural features exist between the isomeric pair (Chowdhury et al., 2011). These examples indicate that it is important to clearly distinguish the molecular structures of the compounds. In this section, representative examples of ruthenium complexes which possess asymmetrical multidentate ligands or multiple donor atoms are surveyed.

Coordination geometries of azopyridyl complexes
2-Azopyridyl derivatives (Fig. 3) behave as mono-, bi-and tridentate ligands, thus a wide variety of mononuclear complexes can be prepared. For example, 2-phenylazopyridine (3), which represents the most fundamental azopyridyl compound, is a bidentate ligand that can coordinate to a metal ion through the lone pairs on the pyridine and the azo nitrogen atoms, thereby forming a stable chelating 5-membered ring. Since the bidentate ligand (3) lacks a two-fold symmetry axis, there are five possible isomers in [Ru(3) 2 Cl 2 ] (Fig. 4) (Bao, K. Krause & R. A. Krause, 1988;Goswami, Chakravarty & Chakravorty, 1981;R. A. Krause & K. Krause, 1982Velders et al., 2004). Among them, α, β and ε adopt the cis-geometry with respect to the two chlorido ligands, whereas γ and δ are the trans-geometry. Besides the ε isomer, the structures have been determined by X-ray crystallography: the molecular structures of two [Ru(3) 2 Cl 2 ] isomers (α-and βisomers) were published in 1984 (Seal & Ray, 1984), the third (γ) and the fourth (δ) isomers were reported in 2000 and 2004, respectively (Velders et al., 2004. Ruthenium(II) complexes containing both Ru-C bonds and 3 as supporting ligands were synthesized by substituting chlorido ligand(s) in [Ru(3) 2 Cl 2 ] with CO or CN - (Oyama, Takatsuki & Fujita, 2010). The molecular structure of [Ru(3) 2 (CO)Cl] + determined by X-ray crystallography is shown in Fig. 5(a). The geometry of the complex corresponds to the αisomer shown in Fig. 4. The carbonyl C-O and Ru-Cl bond distances, and the Ru-C-O bond angle are consistent with those observed for closely related complexes ([RuL 2 (CO)Cl] + : L = bidentate pyridine-based ligands), whereas the Ru-C bond distance is longer than those in similar complexes (Clear et al., 1980;Kepert et al., 2004). This is because of the presence of two 3 ligands with azo moieties. In general, the Ru-N(azo) bond distances are shorter than those of the Ru-N(pyridine) bonds in 3 in the ruthenium complexes (Velders et al., 2004). However, one of the Ru-N(azo) bonds is very long; even longer than the distances of the Ru-N(pyridine) bonds. This is caused by the trans influence of the CO ligand. The crystal structure of [Ru(3) 2 (CN) 2 ] is shown in Fig. 5(b). Unexpectedly, the two CN groups are trans t o e a c h o t h e r , a n d t h e δ-form (shown in Fig. 4) is observed. A δ arrangement is very rare, and was only recently reported for δ-[Ru(3) 2 Cl 2 ] (Velders et al., 2004). In the δ-isomer, the two azo bonds (in mutual trans positions) should compete with each other for the Ru(II) 4d electron density, resulting in relatively long Ru-N(azo) bonds in [Ru(3) 2 (CN) 2 ] with respect to the equivalent bonds in γ-[Ru(3) 2 Cl 2 ] (Velders et al., 2004). This confirms that the Ru-N(azo) bond order decreases in [Ru(3) 2 (CN) 2 ].

Coordination geometries of other pyridyl-based complexes
The naphthyridines consist of a group of diazanaphthalenes with one nitrogen in each ring. In particular, the bidentate naphthyridine, 2-(2-pyridyl)-1,8-naphthyridine (pynp; 10), is a useful ligand for mononuclear systems (Fig. 11). For complexes with ligand 10; however, there is a stereochemical question with regard to the binding of ligand 10 because it has an asymmetrical structure. Consequently, it would be very interesting to study complexes involving 10 in an effort to understand the relationship between the coordination geometries of these complexes and their reactivities. The [Ru(tpy)(10)Cl] + complex acts as a catalyst for water oxidation: it shows excellent catalytic activity with turnover numbers (TNs) of 1,170 (Tseng et al., 2008). This value is the highest in the analogous [Ru(tpy)(L)Cl] + type complexes (L = bidentate polypyridyl ligands) whose TNs are in the range of 0-570. The ligand 10 differs from all of the other bidentate (L) because it is asymmetric. Although there are two possible isomers in [Ru(tpy)(10)Cl] + (Fig.  12), only one isomer ( Fig. 12(b)) is isolated and its structure has been determined by X-ray crystallography (Tseng et al., 2008). Two isomeric mixtures of [Ru(tpy)(10)Cl] + exist in solution (approximately 1:1), both of which can be separated by column chromatography. Alternatively, irradiation of visible light to isomeric mixtures of [Ru(tpy)(10)L] 2+ (L = OH 2 or CH 3 CN) leads the formation of only one isomer in particular organic solvents (Oyama, www.intechopen.com Yuzuriya & Takase, 2011). The resulting complex ([Ru(tpy)(10)(OH 2 )] 2+ ) is the proximal configuration ( Fig. 12(a)), which differs from the corresponding chlorido complex. In contrast, particular stereoisomers could be selectively prepared in the cis-[Ru(bpy)(10)(CO)Cl] + system (Oyama, Hamada & Takase, 2011). As shown in Fig. 13, although there are four possible geometries in the complex, only two types of the complex could be selectively synthesized. Although the prepared complexes are all single species as determined from the spectroscopic measurements, their structures cannot be assigned because of their spectral resemblance. Consequently, X-ray analysis was required to determine their detailed structures. The molecular structures of two [Ru(bpy)(10)(CO)Cl] + isomers are shown in Fig. 14. One isomer corresponds to (a) in Fig. 13 (the pyridyl ring of 10 is situated trans to the CO ligand), the another isomer corresponds to (b) in Fig. 13 (the pyridyl ring of 10 is situated cis to the CO ligand).  www.intechopen.com Picolinato (pic; 11) can also coordinate to a metal ion as an asymmetrical bidentate ligand (Fig. 15). The mono-pic complex, [Ru(11)(CO) 2 Cl 2 ] -, has been prepared and fully characterized, including X-ray analysis . Although three geometrical isomers are expected for [Ru(11)(CO) 2 Cl 2 ] -( Fig. 16(a)), only form (i) in Fig. 16(a) was confirmed, and neither form (ii) nor (iii) was detected in the solid state and in solutions. The asymmetrical chelate of 11 gives substantially different effects to the two Ru-CO bonds of [Ru(11)(CO) 2 Cl 2 ] -. The Ru-C bond distance trans to the oxygen atom is shorter than another Ru-C bond trans to the nitrogen atom ( Fig. 17(a)). The complex containing mono-11, cis-[Ru(bpy)(11)(CO) 2 ] + was also prepared by the reaction of Hpic with [Ru(bpy)(CO) 2 Cl 2 ], and only the type (iv) of the two possible isomers (iv) and (v) was obtained ( Fig. 16(b) and Fig.  17(b)) .  Two geometrical isomers (Fig. 18) of [Ru(tpy)(bpyO)(CO)] + (bpyO = 2,2'-bipyridin-6-onato; 12) were selectively synthesized by different synthetic routes . These isomers bearing 12 were determined by X-ray crystal structure analysis. Based on their pK a 's, redox potentials and IR spectra, the electron density at the ruthenium center of the distal isomer in Fig. 18 is higher than that of the proximal isomer. Such a difference is associated with the stronger trans influence of CO compared with the central pyridine of tpy, because the electron-withdrawing ability of CO induces the pyridonato structure of the resonance between ruthenium-pyridionate (Ru-bpyO -) and -pyridonato (Ru-bpyO) forms. The two-electron reductions of the distal isomer are followed by a partial Ru-CO bond cleavage, whereas the 12-based reduction of the proximal isomer causes cyclometallation by www.intechopen.com an attack of the pyridonato oxygen at the carbonyl carbon. Thus, cyclometallation caused by 12-based reduction effectively suppresses the reductive cleavage of a Ru-CO bond. [Ru(bpy)(11)(CO) 2 ] + (isomer (iv) in Fig. 16(b)). Fig. 18. Chemical structure of 2,2'-bipyridin-6-onato (bpyO) and two geometrical isomers in [Ru(tpy)(12)(CO)] + .

Coordination modes
It is known that not only some acido anions such as NO 3 -, CO 2 Rand CO 3 2-, but also organic ligands having multi donor atoms, can coordinate to metals as monodentates, chelating bidentates, or bridging bidentate ligands. In this section, such examples are presented. In coordination compounds, the NO 3 -ion can be noncoordinating (counter ion), or it can coordinate in a monodentate (NO 3 -O) or bidentate (NO 3 -O,O') fashion. The N-O stretching vibrations, for example, are observed at 1475, 1272 and 991 cm -1 in the IR spectrum of cis-[Ru(bpy) 2 (CO)(NO 3 )]PF 6 . It is rather difficult to differentiate between these structures by vibrational spectroscopy because the symmetry of the NO 3 -ion differs very little between them (C s vs. C 2v symmetry) (Nakamoto, 1986). However, X-ray data clearly indicates the monodentate coordination of the NO 3 -ion. The sums of the three O-N-O bond angles in the nitrato ligand are 360.0°, indicating that the nitrato moiety has a planar structure. Extensive studies have been made on metal complexes of carboxylic acids. The carboxylate ion may also coordinate to a metal in a monodentate (CO 2 R-O) or bidentate (CO 2 R-O,O') mode. In general, the coordination mode of the carboxylate ion is distinguishable using vibrational spectroscopy (Deacon & Phillips, 1980). Monodentate complexes exhibit ∆ν values (ν as (CO 2 -)-ν s (CO 2 -)) which are much greater than the ionic compounds, whereas chelating (bidentate) complexes exhibit ∆ν values which are significantly less than the ionic values. For example, the cis-[Ru(bpy) 2 (CO)(CO 2 H)] + complex shows the large formato ∆ν value of 339 cm -1 (Gibson et al., 1999), and this value is clearly greater than the ionic value (∆ν = 201 cm -1 ) (Ito & Bernstein, 1956). X-ray structural data for this complex clearly identified the monodentate formato ligand (CO 2 H-O) bound to an octahedral ruthenium center (Gibson et al., 1999). As stated above, the azopyridine ligand (3) generally coordinates to a metal ion through both pyridyl and azo nitrogens (bidentate chelate fashion). However, the crystal structure of a ruthenium complex containing 3 as a monodentate ligand ([Ru(bpy) 2 (3-N)(CO)] 2+ ) has been reported ( Fig. 19(a)) (Oyama, Fujita & Yui, 2008). The ligand 3 coordinates to the ruthenium center through only the pyridyl nitrogen atom. The remarkable feature in the structure of this complex concerns the azo moiety of 3, which is directed toward the adjacent terminal carbonyl ligand. Taking into account the fact that the nitrogen atom of the azo group is located just to the side of the carbonyl carbon, the existence of the CO ligand could influence the orientation of the azo moiety of 3. The redox reactions of [Ru(bpy) 2 (3-N)(CO)] 2+ using solution IR spectra under electrolysis conditions revealed a nucleophilic attack of the azo nitrogen atom of 3 on the carbonyl carbon ( Fig. 20(a)), because of the short interatomic distance between the azo nitrogen and the carbonyl carbon atoms (2.865 Å). In contrast, the dissociation of CO from the two-electron reduced species easily occurs in the analogue with the bidentate 3 ([Ru(tpy)(3-N,N')(CO)] 2+ ; Fig. 19(b)), because the ligand is unable to interact with CO ( Fig. 20(b)). The diphenyl-2-phosphinopyridine ligand (dppy; 13) has been used to construct interesting metal complexes because it possesses both the soft (P) and hard (N) donor atoms (Newkome, 1993). Although both the P-mono and P,N-bidentate coordination modes have been known for mononuclear systems (Fig. 21) (Moldes et al., 1998), 13 coordinates to the ruthenium center through only the P atom in [Ru(bpy)(13)(CO) 2 Cl] + (Ooyama & Sato, 2003). A prominent feature of the structure is that the pyridyl nitrogen atom of 13 directs toward the plane that includes two carbonyl ligands (Fig. 22(a)). The existence of carbonyl ligands may influence the orientation of the aromatic rings of 13 because relatively short distances between the noncoordinating nitrogen atom of 13 and the carbonyl carbons are observed (3.068 Å): the analogous complex situating two 13 moieties in mutually trans positions also exhibits a similar trend as shown in Fig. 22(b) (Ooyama & Sato, 2004).

Comparison of the structures and structural parameters
When chemists simply recognize the molecular structure of a compound, they usually pay particular attention to the points described above. However, it is also very helpful for chemists to understand how intermolecular forces (packing forces) act between molecules in crystals when they investigate the constructions of materials and medicines. In addition, various chemical and physical properties can be predicted by comparing bond parameters (e.g., bond distances, angles or torsion angles) in a compound.

Comparison of structures
Almost all structurally characterized coordination compounds of azopyridines have the ligand bonded to one metal center via the azoimine (N=N-C=N) chelate arrangement. In the case of 3 and 4, formation of a chelate complex creates the free aromatic ring (phenyl for 3 or 2-pyridyl for 4). The orientation of the pendant aromatic ring is dependent on its coordination environment: the dihedral angle between the two aromatic rings of [Ru(3)(CO) 2 Cl 2 ] is 35.29° (Fig. 23(a)) whereas the dihedral angle between the two pyridyl rings in [Ru(4)(CO) 2 Cl 2 ] is 7.99° ( Fig. 23(b)), which shows planarity of the coordinated 4 ). The distinction observed in solid state can be explained on the basis of a possible weak interaction between the noncoordinating nitrogen atom and the adjacent carbonyl carbon in [Ru(4)(CO) 2 Cl 2 ] rather than a different bulkiness between the CH in phenyl ring of 3 and the N in pyridyl ring of 4, because the interatomic distance between the N atom and the adjacent C atom in [Ru(4)(CO) 2 Cl 2 ] is fairly short (2.682(3) Å). This weak interaction has often been observed in ruthenium carbonyl complexes with noncoordinating pyridyl moieties (Mizukawa et al., 1999;, which contain both a pyridyl nitrogen (δ-) and a carbonyl carbon (δ+). The X-ray structures of terpyridyl complexes with the dimethoxyphenyl pendant have been determined. In the metal-free ligand 14 (Fig. 24), the three pyridyl rings are approximately coplanar, whereas the dimethoxyphenyl substituent in 14 is not coplanar with the terpyridyl moiety, making an angle of 50.2° with the central pyridyl ring (Storrier, Colbran & Craig, 1998). The dihedral angle between the central pyridyl ring and the dimethoxyphenyl ring in the ruthenium complexes with 14 are in the range of 43 to 56°, which are close to that of metal-free ligand 14 . Interestingly, the OCH 3 orientation of two methoxy moieties are different in two types of habits (yellow needles and red blocks) of [Ru(14)(bpy)(CO)](PF 6 ) 2 . As shown in Fig. 25, two OCH 3 moieties point in the same orientation in the yellow crystal ( Fig. 25(a)), whereas in the red crystal they point in opposite directions (Fig. 25(b)) . The former structure is identical to the corresponding chlorido and acetonitrile complexes. On the other hand, the latter form is consistent with that observed in the metal-free 14. These differences are most likely due to different packing or intermolecular effects on the orientation of methoxy groups of 14.

Comparison of structural parameters
Physical data of terminal carbonyl groups are generally useful indicators for electronic states around metal centers in metal complexes. In particular, bond distances and vibrational spectra are considered important (Cotton et al., 1999). In order to distinguish the electron states in the ruthenium mono carbonyl complexes with polypyridyl ligands, the stretching force constants of the CO group using IR spectral data were calculated in addition to bond distances and stretching frequencies of the {Ru-CO} 2+ moiety . Although obvious characteristics about the bond distances (Ru-C and C-O) are not shown in the complexes, the force constant (k) and the stretching frequencies of the CO groups can clearly be divided into two groups (Table 1): the k values of the azocontaining complexes are higher ca. 0.4-1.1 N cm -1 than of the values for the complexes without azopyridines. It is presumed that the electron density of the ruthenium center considerably decreases when an azo group (which has greater π-acidity) coordinates to the ruthenium atom, because the decrease of the k value caused by ligand-based oneelectron reduction corresponds to 0.56 N cm -1 in [Ru(bpy) 2 (CO)(quinoline)] 2+ (Wada et al., 2004). Thus, it can be concluded that complex formation with azopyridyl ligands induces relatively high k values. This observation can be ascribed to the decrease of the π backdonation from the ruthenium center to the CO group. As a result, this suggests that the azopyridyl ligands serve as prominent electron reservoirs compared with other polypyridyl ligands such as bpy. * 4,4'-Me2bpy = 4,4'-dimethyl-2,2'-bipyridine; 5,5'-Me2bpy = 5,5'-dimethyl-2,2'-bipyridine; 5,6'-Me2phen = 5,6'-dimethyl-1,10-phenanthroline; 4,7'-Me2phen = 4,7'-dimethyl-1,10-phenanthroline; dpk = di(2pyridyl)ketone; dpa = di(2-pyridyl)amine; phen = 1,10-phenanthroline; biq = 2,2'-biquinoline. The N-N bond distance in an azo moiety is an excellent indicator of the charge on an azo group (Kaim, 2001). The values for unreduced azo N-N bonds are 1.22-1.31 Å in metal complexes (1.23-1.26 Å for metal-free ligands). The one-electron reduced (anion radical) ligands have a bond distances of 1.31-1.41 Å, whereas the two-electron reduced (hydrazido) forms have single bonds with 1.41-1.50 Å distances (Fig. 26) (Sarkar et al., 2008). As shown in Table 2, the azo N-N bond distance of [Ru(bpy) 2 (CO)(3-N)] 2+ is dramatically shorter than those of other complexes: the distance (1.188(4) Å) is shorter than that of a typical N=N double bond (1.23 Å) (Oyama, Fujita & Yui, 2008 In the case of bis-azopyridyl complexes, bivalent azopyridine properties are observed by the different azo N-N bond distances. For example, the structure of the monoradical [Ru(4)(4 •-)(CO)(PPh 3 )] + has been determined (Shivakumar et al., 2000). The most remarkable feature of the structure is the difference in the two N-N bond distances: one is 1.284(6) Å, the other N-N bond is 1.336(6) Å. Accordingly, both unreduced and one-electron reduced (anion radical) types are present within the same molecule, which represents a model case of ground-state radical localization in one of the two ligands. The stabilization of radical on one ligand might be supported by the trans ligand. A similar example is also reported in [Ru(7 2-) 2 ] (Samanta et al., 2008). The [Ru(7) 2 ] molecule has longer N-N bond distances (1.324(7) and 1.327(6) Å), clearly suggesting the radical dianion form of the ligand (one charge from the deprotonation and another charge from the one-electron reduction centered on the azo group). This diamagnetic molecule may thus be viewed as a singlet diradical species. In this situation, the electrons from a d 4 configuration at the metal couple with the singly occupied ligand molecular orbitals to create a spin-paired entity. This situation has been confirmed by DFT (density functional theory) calculations.

Conclusion
Single crystal X-ray diffraction studies provide a valuable probe to visualize molecules.
Although some problems such as disorder and twining exist in measurements and analyses, it still represents the most important analytical method for coordination chemists. The author believes that advances in this technology will lead to an increase in the use of single crystal X-ray diffraction, including the X-ray snapshot technique which enables the capture of frame-by-frame movies of chemical reactions as they proceed in situ, now ubiquitous in NMR (Inokuma, Kawano & Fujita, 2011).

Acknowledgment
The endeavors of past and present co-workers from my research group in obtaining the results presented in this chapter are gratefully acknowledged, their names appear in the reference list. The Institute for Molecular Science, Bruker AXS Japan and Rigaku Corporation are gratefully acknowledged for performing X-ray measurements of some complexes. Finally, I thank Mr. Takashi Yamanaka for his contribution in writing this chapter.