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research papers\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296
Volume 73| Part 1| January 2017| Pages 47-51
https://doi.org/10.1107/S2053229616019422

Polymeric structure of a coproporphyrin I ruthenium(II) complex: a powder diffraction study

CROSSMARK_Color_square_no_text.svg
Sergey V. Andreev,a,b Sergey A. Zverev,a,c Ilya A. Zamilatskov,a,c Nadezhda M. Kurochkina,a Gelii V. Ponomarev,d Andrew N. Fitche and Vladimir V. Chernysheva,f*

aA. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky prospect, 31, 119071 Moscow, Russian Federation, bScientific Research Disinfectology Institute, Nauchnyi proezd 18, 117246 Moscow, Russian Federation, cMoscow Technological University, 78 Vernadsky Avenue, 119454 Moscow, Russian Federation, dV. N. Orekhovich Institute of Biomedical Chemistry, RAMS 10 build. 8, Pogodinskaya Street, 119121 Moscow, Russian Federation, eEuropean Synchrotron Radiation Facility, BP 220, F-38043 Grenoble Cedex, France, and fDepartment of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation
*Correspondence e-mail: vladimir@struct.chem.msu.ru

Edited by L. R. Falvello, Universidad de Zaragoza, Spain (Received 12 November 2016; accepted 4 December 2016; online 1 January 2017)

Porphyrin complexes of ruthenium are widely used as models for the heme protein system, for modelling naturally occurring iron–porphyrin systems and as catalysts in epoxidation reactions. The structural diversity of ruthenium complexes offers an opportunity to use them in the design of multifunctional supra­molecular assemblies. Coproporphyrins and metallocoproporphyrins are used as sensors in bioassay and the potential use of derivatives as multiparametric sensors for oxygen and H+ is one of the main factors driving a growing inter­est in the synthesis of new porphyrin derivatives. In the co­proporphyrin I RuII complex catena-poly[[carbonyl­ruthenium(II)]-μ-2,7,12,17-tetra­kis­[2-(eth­oxy­carbon­yl)eth­yl]-3,8,13,18-tetra­methyl­porphyrinato-κ5N,N′,N′′,N′′′:O], [Ru(C44H52N4O8)(CO)]n, the RuII centre is coordinated by four N atoms in the basal plane, and by axial C (carbonyl ligand) and O (eth­oxy­carbonyl­ethyl arm from a neighbouring complex) atoms. The complex adopts a distorted octa­hedral geometry. Self-assembly of the mol­ecules during crystallization from a methyl­ene chloride–ethanol (1:10 v/v) solution at room temperature gives one-dimensional polymeric chains.

CCDC reference: 1520660

Similar articles

1. Introduction

Porphyrin complexes of ruthenium have been studied actively in recent decades because of their many useful applications. They are widely used as models for the heme protein system (Masuda et al., 1982[Masuda, H., Taga, T., Osaki, K., Sugimoto, H., Mori, M. & Ogoshi, H. (1982). Bull. Chem. Soc. Jpn, 55, 3887-3890.]), for modelling naturally occurring iron–porphyrin systems involved in oxidation processes of the mono- and di­oxy­genase type (James et al., 1988[James, B. R., Pacheco, A., Rettig, S. J. & Ibers, R. G. (1988). Inorg. Chem. 27, 2414-2421.]) and as catalysts in epoxidation reactions (Barona-Castano et al., 2016[Barona-Castano, J. C., Carmona-Vargas, C. C., Brocksom, T. J. & de Oliveira, K. T. (2016). Molecules, 21, 310-337.]), including aerobic oxidation tandem epoxidation–isomerization (Jiang et al., 2008[Jiang, G., Chen, J., Thu, H.-Y., Huang, J.-S., Zhu, N. & Che, C.-M. (2008). Angew. Chem. Int. Ed. 47, 6638-6642.]). Ruthenium in porphyrinates can exist in a variety of oxidation states, viz. RuII (Ariel et al., 1984[Ariel, S., Dolphin, D., Donazetis, G., James, B. R., Leung, T. W., Rettig, S. J., Trotter, J. & Williams, G. M. (1984). Can. J. Chem. 62, 755-762.]), RuIII (James et al., 1984[James, B. R., Dolphin, D., Leung, T. W., Einstein, F. W. B. & Willis, A. C. (1984). Can. J. Chem. 62, 1238-1245.]), RuIV (Maeda et al., 2015[Maeda, K., Terada, T., Iwamoto, T., Kurahashi, T. & Matsubara, S. (2015). Org. Lett. 17, 5284-5287.]) or RuVI (Katsunori et al., 2012[Katsunori, T., Mazumder, K., Siwu, E. R. O., Nozaki, S., Watanabe, Ya. & Fukase, K. (2012). Tetrahedron Lett. 53, 1756-1759.]), and it is able to coordinate one or two small axial ligands, such as aqua, hydroxide, di­nitro­gen, nitrite, nitrosyl, carbonyl, methanol, ethanol, tetra­hydro­furan, pyridine and many others, as can be found from a search in the Cambridge Structural Database (ConQuest, Version 1.18 with updates; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]), which gave 225 hits. The structural diversity of ruthenium complexes, which can also form metal–metal bonds (Collman et al., 1984[Collman, J. P., Barnes, C. E., Swepston, P. N. & Ibers, J. A. (1984). J. Am. Chem. Soc. 106, 3500-3510.]), offers an opportunity to use them in the design of multifunctional supra­molecular assemblies (Mamardashvili et al., 2013[Mamardashvili, G. M., Mamardashvili, N. Zh. & Koifman, O. I. (2013). Macroheterocycles, 6, 67-73.]).

Due to their unique photophysical and photochemical pro­perties, coproporphyrins and metallocoproporphyrins have also been used as sensors in bioassay (Papkovsky & O'Riordan, 2005[Papkovsky, D. B. & O'Riordan, T. C. (2005). J. Fluoresc. 15, 569-584.]; Dmitriev et al., 2012[Dmitriev, R. I., Zhdanov, A. V., Jasionek, G. & Papkovsky, D. B. (2012). Anal. Chem. 84, 2930-2938.]; Burke et al., 2007[Burke, M., O'Sullivan, P. J., Ponomarev, G. V., Yashunsky, D. V. & Papkovsky, D. B. (2007). Anal. Chim. Acta, 585, 139-146.]). The potential use of derivatives of coproporphyrins as multiparametric sensors for oxygen and H+ is one of the main factors driving a growing inter­est in the synthesis of new porphyrin derivatives (Borchert et al., 2011[Borchert, N. B., Ponomarev, G. V., Kerry, J. P. & Papkovsky, D. B. (2011). Anal. Chem. 83, 18-22.]). Recently, we reported synthetic and crystallographic studies of the coproporphyrin I mol­ecular complexes with PdII (Volov et al., 2014[Volov, A. N., Zamilatskov, I. A., Mikhel, I. S., Erzina, D. R., Ponomarev, G. V., Koifman, O. I. & Tsivadze, A. Yu. (2014). Macroheterocycles, 7, 256-261.]; Tyurin et al., 2015[Tyurin, V. S., Erzina, D. R., Zamilatskov, I. A., Chernyadyev, A. Yu., Ponomarev, G. V., Yashunskiy, D. V., Maksimova, A. V., Krasnovskiy, A. A. & Tsivadze, A. Yu. (2015). Macroheterocycles, 8, 376-383.]). We report herein the synthesis and structural characterization of the novel ruthenium(II) complex of coproporphyrin I tetra­ethyl ester, (1), namely catena-poly[[carbonyl­ruthenium(II)]-μ-2,7,12,17-tetra­kis­[2-(eth­oxy­carbon­yl)eth­yl]-3,8,13,18-tetra­methyl­porphyrinato-κ5N,N′,N′′,N′′′:O], (2), which crystallizes with the formation of one-dimensional polymeric chains.

[Scheme 1]

2. Experimental

Commercial reagents were used without purification. Solvents were purified according to standard procedures: CH2Cl2 was distilled over calcium hydride under an argon atmosphere and toluene was dried over magnesium chloride and then distilled over sodium. Coproporphyrin I, (1), was prepared according to a literature procedure (Smith, 1972[Smith, K. M. (1972). J. Chem. Soc. Perkin Trans. 1, pp. 1471-1475.]). Silica gel 40/60 (Merck) was used for column and flash chromatography. For preparative thin-layer chromatography (TLC), silica gel 60 (Merck) 20 × 20 cm plates with a 1 mm layer thickness were used. A mixture of methyl­ene chloride–ethanol was used as solvent for elution. Electronic absorption, NMR and mass spectra for the final product are presented in the Supporting information.

2.1. Synthesis and crystallization

To a solution of (1) (50 mg, 0.065 mmol) in dry toluene (15 ml) was added Ru3(CO)12 (83.5 mg, 0.13 mmol). The resulting mixture was refluxed for 24 h. After completion of the reaction, the solvent was evaporated. Purification was carried out by preparative chromatography using an ethanol–di­chloro­methane (100:1 v/v) mixture. A powder sample suitable for crystal structure determination was obtained by crystallization from the methyl­ene chloride–ethanol (1:10 v/v) solvent system at room temperature over a period of 7 d.

2.2. Refinement

X-ray powder diffraction measurements were carried out at room temperature at beamline ID22 of the European Synchrotron Radiation Facility (ESRF, Grenoble, France). The instrument is equipped with a cryogenically cooled double-crystal Si 111 monochromator and Si 111 analyzers. The powder was loaded into a 1 mm diameter borosilicate thin-walled glass capillary which was rotated during measurements at a rate of 1200 rpm to improve the powder averaging. Calibration of the instrument and refinement of the X-ray wavelength [0.399927 (3) Å] were performed using NIST silicon standard 640c.

The monoclinic cell dimensions were determined using three indexing programs: TREOR90 (Werner et al., 1985[Werner, P.-E., Eriksson, L. & Westdahl, M. (1985). J. Appl. Cryst. 18, 367-370.]), ITO (Visser, 1969[Visser, J. W. (1969). J. Appl. Cryst. 2, 89-95.]) and AUTOX (Zlokazov, 1992[Zlokazov, V. B. (1992). J. Appl. Cryst. 25, 69-72.], 1995[Zlokazov, V. B. (1995). Comput. Phys. Commun. 85, 415-422.]). Based on systematic extinctions and other considerations, the space group was determined as C2/c. The unit-cell parameters and space group were further tested using a Pawley fit (Pawley, 1981[Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361.]) and confirmed by crystal structure solution. The geometry of the initial mol­ecular model of (2) with the Ru centre coordinated by the four N atoms only, i.e. without the carbonyl ligand, was optimized by density functional theory (DFT) calculations in vacuo using the quantum-chemical program PRIRODA (Laikov, 1997[Laikov, D. N. (1997). Chem. Phys. Lett. 281, 151-154.], 2004[Laikov, D. N. (2004). PRIRODA. Moscow State University.], 2005[Laikov, D. N. (2005). Chem. Phys. Lett. 416, 116-120.]; Laikov & Ustynyuk, 2005[Laikov, D. N. & Ustynyuk, Y. A. (2005). Russ. Chem. Bull. 54, 820-826.]), employing the generalized gradient approximation (GGA) and the PBE exchange-correlation function (Perdew et al., 1996[Perdew, J. P. S., Burke, S. & Ernzerhof, M. (1996). Phys. Rev. Lett. 77, 3865-3868.]). This fragment was used in the crystal structure determination. The crystal structure was solved using two techniques, viz. simulated annealing (Zhukov et al., 2001[Zhukov, S. G., Chernyshev, V. V., Babaev, E. V., Sonneveld, E. J. & Schenk, H. (2001). Z. Kristallogr. 216, 5-9.]) using the program MRIA (Zlokazov & Chernyshev, 1992[Zlokazov, V. B. & Chernyshev, V. V. (1992). J. Appl. Cryst. 25, 447-451.]) and parallel tempering (Favre-Nicolin & Cerný, 2002[Favre-Nicolin, V. & Cerný, R. (2002). J. Appl. Cryst. 35, 734-743.]) using the program FOX (Favre-Nicolin & Cerný, 2002[Favre-Nicolin, V. & Cerný, R. (2002). J. Appl. Cryst. 35, 734-743.], 2004[Favre-Nicolin, V. & Cerný, R. (2004). Z. Kristallogr. 219, 847-856.]). The carbonyl group was added to the model after the analysis of a difference Fourier map, where axial positive residual electron density was observed at 1.9 Å from the Ru centre. The final Rietveld refinement was performed with the program MRIA following the procedure described by us previously (Dorokhov et al., 2007[Dorokhov, A. V., Chernyshov, D. Y., Burlov, A. S., Garnovskii, A. D., Ivanova, I. S., Pyatova, E. N., Tsivadze, A. Y., Aslanov, L. A. & Chernyshev, V. V. (2007). Acta Cryst. B63, 402-410.]; Logacheva et al., 2009[Logacheva, N. M., Baulin, V. E., Tsivadze, A. Y., Pyatova, E. N., Ivanova, I. S., Velikodny, Y. A. & Chernyshev, V. V. (2009). Dalton Trans. pp. 2482-2489.]; Chernyshev et al., 2013[Chernyshev, V. V., Petkune, S., Actins, A., Auzins, R., Davlyatshin, D. I., Nosyrev, P. V. & Velikodny, Y. A. (2013). Acta Cryst. C69, 299-302.]). In the refinement, anisotropic line broadening was taken into account with the use of nine variables (Popa, 1998[Popa, N. C. (1998). J. Appl. Cryst. 31, 176-180.]). All non-H atoms were refined isotropically. One common Uiso parameter was varied for 32 atoms, i.e. 24 atoms of the porphyrin core and eight C atoms attached to the core. The maximum difference peak and hole at the end of refinement had densities of 0.61 and −0.89 e Å−3, respectively. Crystal data, data collection and structure refinement details are summarized in Table 1[link] and the diffraction profiles after the final bond-restrained Rietveld refinement are shown in Fig. 1[link].

Table 1
Experimental details

Crystal data
Chemical formula [Ru(C44H52N4O8)(CO)]
Mr 893.98
Crystal system, space group Monoclinic, C2/c
Temperature (K) 295
a, b, c (Å) 39.3876 (19), 9.6153 (8), 29.5299 (16)
β (°) 130.719 (7)
V (Å3) 8476.3 (9)
Z 8
Radiation type Synchrotron, λ = 0.399927(2) Å
μ (mm−1) 0.09
Specimen shape, size (mm) Cylinder, 15 × 1.0
 
Data collection
Diffractometer ESRF powder diffractometer ID22
Specimen mounting Specimen was sealed in a 1.0 mm diameter borosilicate glass capillary
Data collection mode Transmission
Scan method Continuous
2θ values (°) 2θmin = 1.000, 2θmax = 20.000, 2θstep = 0.002
 
Refinement
R factors and goodness of fit Rp = 0.031, Rwp = 0.040, Rexp = 0.013, RBragg = 0.070, χ2 = 9.566
No. of parameters 247
No. of restraints 193
H-atom treatment H-atom parameters not refined
Computer programs: MRIA (Zlokazov & Chernyshev, 1992[Zlokazov, V. B. & Chernyshev, V. V. (1992). J. Appl. Cryst. 25, 447-451.]), FOX (Favre-Nicolin & Cerný, 2004[Favre-Nicolin, V. & Cerný, R. (2004). Z. Kristallogr. 219, 847-856.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]), SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).
[Figure 1]
Figure 1
Rietveld plot showing the experimental (black) and difference (red) profiles for (2). The vertical bars (blue) correspond to the positions of the Bragg peaks.

3. Results and discussion

In the title compound, the RuII centre is coordinated by four N atoms [Ru—N = 2.025 (17)–2.055 (12) Å] in the basal plane and by an axial carbonyl ligand [Ru—C = 1.871 (19) Å]. A carbonyl O atom (O5) of the eth­oxy­carbonyl­ethyl arm [Ru—O = 2.194 (12) Å] from a neighbouring asymmetric unit completes the distorted octa­hedral coordination geometry. The metal atom is displaced by 0.11 (1) Å from the mean plane of the porphyrin core, toward the carbonyl ligand. As seen in Fig. 2[link], just one of four ethyl ester arms serves as a connector between neighbouring mol­ecules via the aforementioned axially coordinating atom O5, mediating the formation of polymeric chains running along [010] (Fig. 3[link]). The porphyrin cores of neighbouring links in the chain are inclined to one another by 74.3 (2)°. Examples of metal–porphyrin complexes in which the carbonyl groups of lateral substituents coordinate neighbouring metal centres have been observed, though they are rare; our search in the Cambridge Structural Database (CSD) resulted in just three hits, namely catena-(bis­{μ3-5,10,15,20-tetra­kis­[3′,5′-bis­(eth­oxy­carbon­yl)phen­yl]porphyrinato}dizinc(II)) (CSD refcode LUBKOI; Bhyrappa et al., 2002[Bhyrappa, P., Vaijayanthimala, G. & Verghese, B. (2002). Tetrahedron Lett. 43, 6427-6429.]), bis­{μ2-diethyl-2,2′-[(porphyrin-5,15-di­yl)bis­(naphthalene-1,2-di­yloxy)]diacetatato}dizinc(II) di­chloro­methane solvate (MUVQAW; Amaya et al., 2010[Amaya, T., Ueda, T. & Hirao, T. (2010). Tetrahedron Lett. 51, 3376-3379.]) and catena-[bis­{μ-5-tert-butyl-N,N′-bis­[2-(10,15,20-tri­phenyl­por­phy­rin-21,23-diyl-5-yl)phen­yl]isophthalamide}­tetra­zinc unknown solvate] (OGUFIH; Fang et al., 2015[Fang, X. S., Han, Z., Xu, C. L., Li, X. H., Wang, Y. & Hu, C. J. (2015). Dalton Trans. 44, 12511-12515.]).

[Figure 2]
Figure 2
View of (2) showing the atomic numbering and 50% probability displacement spheres. H atoms have been omitted for clarity. [Symmetry codes: (i) −x + [{3\over 2}], y + [{1\over 2}], −z + [{3\over 2}]; (ii) −x + [{3\over 2}], y − [{1\over 2}], −z + [{3\over 2}].]
[Figure 3]
Figure 3
A portion of the polymeric chain in the crystal structure of (2).

The most inter­esting feature of the crystal structure of (2) is the formation of a mol­ecular cavity, as the four eth­oxy­carbonyl­ethyl substituents are located on the same side of the porphyrin plane, like the petals of a tulip. The CSD contains no examples of tetra­methyl metalloporphyrins with four eth­oxy­carbonyl­ethyl branches, and a search for metalloporphyrins with similar substituents yielded the following four structures: {2,7,12,17-tetra­kis­[2-(iso­propyl­oxycarbon­yl)eth­yl]-3,8,13,18-tetra­methyl­porphyrinato}platinum(II) and -palladium(II) (KILQIH and KILQON, respectively; Zamilatskov et al., 2012[Zamilatskov, I. A., Savinkina, E. V., Volov, A. N., Grigoriev, M. S., Lonin, I. S., Obolenskaya, L. N., Ponomarev, G. V., Koifman, O. I., Kuzovlev, A. S., Kuzmicheva, G. M. & Tsivadze, A. Yu. (2012). Macroheterocycles, 5, 308-314.]), and chlorido- and (acetato-κ2O,O′)(tetra­methyl-3,8,13,18-tetra­methyl­porphyrin-2,7,12,17-tetra­propionato-κ4N,N′,N′′,N′′′)thallium(III) di­chloro­methane solvate (WECSIG and WECTAZ, respectively; Senge et al., 1993[Senge, M. O., Ruhlandt-Senge, K., Regli, K. J. & Smith, K. M. (1993). J. Chem. Soc. Dalton Trans. pp. 3519-3538.]); none of these structures has a mol­ecular cavity. Surprisingly, to provide the axial coordination of the RuII atom in (2), the flexible eth­oxy­carbonyl­ethyl branch from the neighbouring segment of the polymer positions its O atom (O5) within the `tulip petals'. This fragment of the neighbouring porphyrin core thus penetrates into the `tulip bowl' of the mol­ecule (Fig. 3[link]).

The aforementioned features of the crystal packing of (2) demonstrate its potential for self-assembling in various modes depending on crystallization and environmental conditions, as has been observed for [tetra­kis­(pyridin-4-yl)porphyrin]zinc, [Zn(tpyp)]. Several coordination polymers were obtained for [Zn(tpyp)], viz. a one-dimensional chain structure (Krupitsky et al., 1994[Krupitsky, H., Stein, Z., Goldberg, I. & Strouse, C. E. (1994). J. Inclusion Phenom. Mol. Recogn. Chem. 18, 177-192.]), a one-dimensional ladder structure (Diskin-Posner et al., 2001[Diskin-Posner, Y., Patra, G. K. & Goldberg, I. (2001). J. Chem. Soc. Dalton Trans. pp. 2775-2782.]), a one-dimensional ribbon structure (Ring et al., 2005[Ring, D. J., Aragoni, M. C., Champness, N. R. & Wilson, C. (2005). CrystEngComm, 7, 621-623.]) and a three-dimensional framework (Krupitsky et al., 1994[Krupitsky, H., Stein, Z., Goldberg, I. & Strouse, C. E. (1994). J. Inclusion Phenom. Mol. Recogn. Chem. 18, 177-192.]). For compound (2), we hope to remove the carbonyl fragments either from the solution before crystallization or directly from the solid-state sample to explore other possibilities for self-assembly of the coproporphyrin I tetra­ethyl ester ruthenium(II) complex.

Supporting information

CCDC reference: 1520660

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2053229616019422/fa3396sup1.cif

Rietveld powder data: contains datablock I. DOI: https://doi.org/10.1107/S2053229616019422/fa3396Isup2.rtv

Absorption electronic, NMR and mass spectra for the final product. DOI: https://doi.org/10.1107/S2053229616019422/fa3396sup3.pdf


Computing details top

Cell refinement: MRIA (Zlokazov & Chernyshev, 1992); program(s) used to solve structure: MRIA (Zlokazov & Chernyshev, 1992) and FOX (Favre-Nicolin & Cerný, 2004); program(s) used to refine structure: MRIA (Zlokazov & Chernyshev, 1992); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

catena-Poly[[carbonylruthenium(II)]-µ-2,7,12,17-tetrakis[2-(ethoxycarbonyl)ethyl]-3,8,13,18-tetramethylporphyrinato-κ5N,N',N'',N''':O] top
Crystal data top
[Ru(C44H52N4O8)(CO)]F(000) = 3728
Mr = 893.98Dx = 1.401 Mg m−3
Monoclinic, C2/cSynchrotron radiation, λ = 0.399927(2) Å
Hall symbol: -C 2ycµ = 0.09 mm−1
a = 39.3876 (19) ÅT = 295 K
b = 9.6153 (8) ÅParticle morphology: no specific habit
c = 29.5299 (16) Åcolorless
β = 130.719 (7)°cylinder, 15 × 1.0 mm
V = 8476.3 (9) Å3Specimen preparation: Prepared at 295 K and 101 kPa
Z = 8
Data collection top
ESRF powder
diffractometer ID22		Data collection mode: transmission
Radiation source: ID22 bending magnet at ESRF, synchrotron radiationScan method: continuous
Si 111 double crystal monochromator2θmin = 1.000°, 2θmax = 20.000°, 2θstep = 0.002°
Specimen mounting: Specimen was sealed in a 1.0 mm diameter borosilicate glass capillary
Refinement top
Refinement on Inet247 parameters
Least-squares matrix: full with fixed elements per cycle193 restraints
Rp = 0.03121 constraints
Rwp = 0.040H-atom parameters not refined
Rexp = 0.013Weighting scheme based on measured s.u.'s
RBragg = 0.070(Δ/σ)max = 0.003
9501 data pointsBackground function: Chebyshev polynomial up to the 5th order
Profile function: split-type pseudo-VoigtPreferred orientation correction: none
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Ru10.88520 (4)0.5249 (2)0.82080 (6)0.0170 (12)*
N10.9371 (3)0.3887 (14)0.8584 (5)0.034 (10)*
N20.8917 (3)0.5230 (13)0.8947 (5)0.034 (10)*
N30.8290 (3)0.6456 (15)0.7803 (5)0.034 (10)*
N40.8732 (3)0.5119 (13)0.7428 (5)0.034 (10)*
C10.9549 (4)0.3341 (19)0.8342 (6)0.034 (10)*
C20.9928 (4)0.2503 (19)0.8768 (6)0.034 (10)*
C30.9990 (4)0.2549 (18)0.9290 (7)0.034 (10)*
C40.9652 (4)0.3374 (19)0.9178 (6)0.034 (10)*
C50.9575 (4)0.3725 (18)0.9559 (5)0.034 (10)*
H50.97760.33340.99380.041*
C60.9254 (4)0.4549 (18)0.9473 (6)0.034 (10)*
C70.9209 (4)0.4849 (18)0.9914 (6)0.034 (10)*
C80.8857 (4)0.5682 (17)0.9663 (6)0.034 (10)*
C90.8675 (4)0.5963 (19)0.9058 (6)0.034 (10)*
C100.8307 (4)0.6775 (19)0.8638 (6)0.034 (10)*
H100.81670.72260.87560.041*
C110.8129 (4)0.6974 (17)0.8053 (6)0.034 (10)*
C120.7734 (4)0.7848 (19)0.7630 (6)0.034 (10)*
C130.7672 (4)0.7845 (18)0.7121 (6)0.034 (10)*
C140.8005 (4)0.6945 (18)0.7212 (6)0.034 (10)*
C150.8070 (4)0.6615 (19)0.6821 (5)0.034 (10)*
H150.78660.70080.64430.041*
C160.8397 (4)0.5778 (19)0.6906 (6)0.034 (10)*
C170.8442 (4)0.5503 (17)0.6468 (6)0.034 (10)*
C180.8800 (4)0.4628 (17)0.6723 (6)0.034 (10)*
C190.8980 (4)0.4395 (19)0.7331 (6)0.034 (10)*
C200.9356 (4)0.3604 (19)0.7753 (6)0.034 (10)*
H200.94970.31980.76280.041*
C211.0222 (5)0.1708 (18)0.8744 (7)0.034 (10)*
H21A1.02970.08740.89780.041*
H21B1.04970.22400.89540.041*
C221.0099 (4)0.126 (2)0.8183 (6)0.049 (10)*
H22A1.00480.20780.79520.059*
H22B0.98210.07440.79560.059*
C231.0462 (4)0.0347 (18)0.8273 (7)0.055 (11)*
C241.0564 (5)−0.214 (2)0.8123 (6)0.069 (10)*
H24A1.0360−0.29200.79660.083*
H24B1.0856−0.24520.84780.083*
C251.0596 (5)−0.168 (2)0.7667 (7)0.089 (11)*
H25A1.0699−0.24470.75750.134*
H25B1.0803−0.09250.78230.134*
H25C1.0306−0.13920.73110.134*
C261.0361 (4)0.1737 (18)0.9841 (6)0.034 (10)*
H26A1.05380.12750.97700.051*
H26B1.02330.10580.99300.051*
H26C1.05470.23621.01730.051*
C270.9516 (4)0.4256 (18)1.0535 (6)0.034 (10)*
H27A0.94720.47491.07800.041*
H27B0.98250.43901.07100.041*
C280.9429 (4)0.2704 (18)1.0533 (6)0.051 (10)*
H28A0.94470.22431.02570.061*
H28B0.96690.23371.09280.061*
C290.8992 (4)0.2311 (19)1.0369 (6)0.059 (11)*
C300.8427 (5)0.0444 (18)1.0068 (7)0.071 (11)*
H30A0.82620.11761.00780.085*
H30B0.8528−0.02221.03810.085*
C310.8128 (4)−0.0275 (16)0.9454 (5)0.091 (12)*
H31A0.78950.03500.91580.136*
H31B0.7997−0.10950.94700.136*
H31C0.8306−0.05290.93500.136*
C320.8667 (4)0.6283 (19)0.9920 (6)0.034 (10)*
H32A0.84110.68450.96240.051*
H32B0.88890.68481.02600.051*
H32C0.85780.55451.00420.051*
C330.7508 (4)0.859 (2)0.7794 (6)0.034 (10)*
H33A0.73110.92670.74820.041*
H33B0.77340.91120.81550.041*
C340.7244 (5)0.7836 (17)0.7898 (7)0.046 (10)*
H34A0.72000.84110.81260.055*
H34B0.74020.70010.81270.055*
C350.6781 (4)0.7437 (17)0.7289 (6)0.050 (10)*
C360.6421 (4)0.5757 (18)0.6487 (7)0.058 (10)*
H36A0.63470.66070.62620.070*
H36B0.65690.51290.64060.070*
C370.6008 (4)0.5101 (18)0.6313 (7)0.068 (12)*
H37A0.58070.48860.58940.102*
H37B0.58650.57330.63950.102*
H37C0.60860.42610.65380.102*
C380.7278 (4)0.8624 (18)0.6580 (6)0.034 (10)*
H38A0.72790.85260.62580.051*
H38B0.73000.95910.66770.051*
H38C0.70040.82500.64620.051*
C390.8137 (4)0.6012 (19)0.5812 (6)0.034 (10)*
H39A0.79970.68870.57710.041*
H39B0.83130.61550.56930.041*
C400.7777 (4)0.4897 (18)0.5414 (6)0.052 (12)*
H40A0.79210.39960.55150.062*
H40B0.75760.48660.54980.062*
C410.7509 (5)0.5157 (17)0.4762 (7)0.058 (11)*
C420.6974 (4)0.4449 (19)0.3694 (7)0.071 (11)*
H42A0.69460.54370.36090.085*
H42B0.71140.40200.35550.085*
C430.6524 (4)0.384 (2)0.3371 (6)0.094 (11)*
H43A0.63450.39920.29500.141*
H43B0.63830.42760.35040.141*
H43C0.65520.28600.34490.141*
C440.8932 (4)0.4175 (19)0.6362 (6)0.034 (10)*
H44A0.91870.35680.66000.051*
H44B0.90060.49790.62490.051*
H44C0.86860.36920.60100.051*
O11.0781 (3)0.0868 (13)0.8400 (4)0.058 (7)*
O21.0411 (3)−0.1050 (14)0.8286 (4)0.063 (7)*
O30.8775 (3)0.3143 (12)1.0409 (4)0.054 (7)*
O40.8818 (3)0.1038 (13)1.0157 (4)0.058 (7)*
O50.6509 (3)0.8273 (12)0.7038 (4)0.042 (6)*
O60.6724 (3)0.6071 (13)0.7148 (4)0.053 (6)*
O70.7559 (3)0.6281 (14)0.4631 (4)0.054 (6)*
O80.7260 (3)0.4236 (13)0.4346 (4)0.060 (7)*
O90.9432 (3)0.7812 (12)0.8590 (4)0.074 (7)*
C450.9192 (5)0.6859 (19)0.8412 (6)0.074 (10)*
Geometric parameters (Å, º) top
Ru1—C451.871 (19)C25—H25C0.9600
Ru1—N22.025 (17)C26—H26A0.9601
Ru1—N42.031 (16)C26—H26B0.9599
Ru1—N12.041 (12)C26—H26C0.9600
Ru1—N32.055 (12)C27—C281.53 (2)
Ru1—O5i2.194 (12)C27—H27A0.9700
N1—C11.39 (3)C27—H27B0.9700
N1—C41.418 (18)C28—C291.50 (3)
N2—C61.383 (17)C28—H28A0.9700
N2—C91.39 (3)C28—H28B0.9700
N3—C111.34 (3)C29—O31.23 (2)
N3—C141.404 (18)C29—O41.34 (2)
N4—C161.366 (16)C30—O41.50 (2)
N4—C191.37 (3)C30—C311.54 (2)
C1—C201.39 (2)C30—H30A0.9701
C1—C21.418 (19)C30—H30B0.9699
C2—C31.40 (3)C31—H31A0.9600
C2—C211.43 (3)C31—H31B0.9600
C3—C41.39 (3)C31—H31C0.9600
C3—C261.513 (18)C32—H32A0.9600
C4—C51.38 (3)C32—H32B0.9600
C5—C61.37 (2)C32—H32C0.9603
C5—H50.9300C33—C341.46 (3)
C6—C71.45 (3)C33—H33A0.9699
C7—C81.33 (2)C33—H33B0.9700
C7—C271.50 (2)C34—C351.558 (16)
C8—C91.45 (2)C34—H34A0.9702
C8—C321.49 (3)C34—H34B0.9700
C9—C101.380 (19)C35—O51.143 (17)
C10—C111.39 (2)C35—O61.35 (2)
C10—H100.9299C36—C371.49 (3)
C11—C121.467 (19)C36—O61.512 (19)
C12—C131.36 (3)C36—H36A0.9700
C12—C331.45 (3)C36—H36B0.9701
C13—C141.44 (3)C37—H37A0.9601
C13—C381.512 (17)C37—H37B0.9599
C14—C151.37 (3)C37—H37C0.9602
C15—C161.40 (3)C38—H38A0.9600
C15—H150.9300C38—H38B0.9599
C16—C171.44 (3)C38—H38C0.9601
C17—C181.37 (2)C39—C401.54 (2)
C17—C391.55 (2)C39—H39A0.9701
C18—C191.45 (3)C39—H39B0.9699
C18—C441.52 (3)C40—C411.49 (2)
C19—C201.385 (18)C40—H40A0.9701
C20—H200.9299C40—H40B0.9699
C21—C221.45 (3)C41—O71.21 (2)
C21—H21A0.9699C41—O81.297 (18)
C21—H21B0.9701C42—C431.48 (2)
C22—C231.55 (3)C42—O81.48 (2)
C22—H22A0.9700C42—H42A0.9700
C22—H22B0.9700C42—H42B0.9699
C23—O11.16 (2)C43—H43A0.9601
C23—O21.36 (2)C43—H43B0.9599
C24—O21.44 (3)C43—H43C0.9600
C24—C251.50 (3)C44—H44A0.9600
C24—H24A0.9700C44—H44B0.9600
C24—H24B0.9700C44—H44C0.9600
C25—H25A0.9601O5—Ru1ii2.194 (11)
C25—H25B0.9599O9—C451.17 (2)
C45—Ru1—N295.7 (7)H25B—C25—H25C109.5
C45—Ru1—N490.2 (7)C3—C26—H26A109.5
N2—Ru1—N4173.8 (5)C3—C26—H26B109.5
C45—Ru1—N195.9 (7)H26A—C26—H26B109.5
N2—Ru1—N191.7 (6)C3—C26—H26C109.5
N4—Ru1—N189.3 (5)H26A—C26—H26C109.5
C45—Ru1—N389.6 (7)H26B—C26—H26C109.5
N2—Ru1—N387.9 (6)C7—C27—C28111.4 (12)
N4—Ru1—N390.5 (5)C7—C27—H27A109.3
N1—Ru1—N3174.5 (5)C28—C27—H27A109.3
C45—Ru1—O5i175.2 (8)C7—C27—H27B109.3
N2—Ru1—O5i87.0 (5)C28—C27—H27B109.3
N4—Ru1—O5i87.1 (5)H27A—C27—H27B108.0
N1—Ru1—O5i80.0 (5)C29—C28—C27117.0 (15)
N3—Ru1—O5i94.4 (5)C29—C28—H28A108.1
C1—N1—C4104.8 (12)C27—C28—H28A108.0
C1—N1—Ru1128.7 (10)C29—C28—H28B108.1
C4—N1—Ru1126.3 (13)C27—C28—H28B108.0
C6—N2—C9106.2 (15)H28A—C28—H28B107.3
C6—N2—Ru1124.7 (14)O3—C29—O4117.5 (16)
C9—N2—Ru1128.9 (9)O3—C29—C28121.8 (16)
C11—N3—C14106.1 (13)O4—C29—C28120.6 (17)
C11—N3—Ru1127.2 (9)O4—C30—C31106.7 (17)
C14—N3—Ru1126.6 (13)O4—C30—H30A110.4
C16—N4—C19107.1 (15)C31—C30—H30A110.4
C16—N4—Ru1126.2 (13)O4—C30—H30B110.4
C19—N4—Ru1126.6 (8)C31—C30—H30B110.4
N1—C1—C20121.7 (13)H30A—C30—H30B108.6
N1—C1—C2110.5 (15)C30—C31—H31A109.5
C20—C1—C2127.7 (19)C30—C31—H31B109.5
C3—C2—C1106.7 (17)H31A—C31—H31B109.5
C3—C2—C21120.6 (13)C30—C31—H31C109.5
C1—C2—C21132.8 (18)H31A—C31—H31C109.5
C4—C3—C2107.7 (13)H31B—C31—H31C109.5
C4—C3—C26130.7 (19)C8—C32—H32A109.5
C2—C3—C26121.5 (17)C8—C32—H32B109.5
C5—C4—C3128.9 (13)H32A—C32—H32B109.5
C5—C4—N1120.8 (14)C8—C32—H32C109.5
C3—C4—N1110.2 (17)H32A—C32—H32C109.4
C6—C5—C4131.0 (13)H32B—C32—H32C109.4
C6—C5—H5114.5C12—C33—C34120.2 (18)
C4—C5—H5114.5C12—C33—H33A107.3
C5—C6—N2125.2 (18)C34—C33—H33A107.3
C5—C6—C7125.9 (13)C12—C33—H33B107.3
N2—C6—C7108.9 (15)C34—C33—H33B107.3
C8—C7—C6108.2 (15)H33A—C33—H33B106.9
C8—C7—C27129 (2)C33—C34—C35109.8 (15)
C6—C7—C27123.2 (15)C33—C34—H34A109.7
C7—C8—C9107.2 (19)C35—C34—H34A109.7
C7—C8—C32129.6 (16)C33—C34—H34B109.7
C9—C8—C32123.2 (13)C35—C34—H34B109.7
C10—C9—N2123.8 (16)H34A—C34—H34B108.2
C10—C9—C8126.7 (18)O5—C35—O6125.9 (11)
N2—C9—C8109.4 (13)O5—C35—C34118.1 (14)
C9—C10—C11125.3 (19)O6—C35—C34115.4 (11)
C9—C10—H10117.4C37—C36—O6107.1 (17)
C11—C10—H10117.4C37—C36—H36A110.3
N3—C11—C10126.5 (14)O6—C36—H36A110.3
N3—C11—C12111.3 (14)C37—C36—H36B110.3
C10—C11—C12122.1 (18)O6—C36—H36B110.3
C13—C12—C33131.7 (13)H36A—C36—H36B108.5
C13—C12—C11105.5 (16)C36—C37—H37A109.5
C33—C12—C11122.6 (15)C36—C37—H37B109.5
C12—C13—C14108.1 (13)H37A—C37—H37B109.5
C12—C13—C38119.2 (17)C36—C37—H37C109.5
C14—C13—C38132.5 (17)H37A—C37—H37C109.5
C15—C14—N3122.1 (15)H37B—C37—H37C109.5
C15—C14—C13128.9 (13)C13—C38—H38A109.5
N3—C14—C13109.0 (17)C13—C38—H38B109.5
C14—C15—C16129.7 (13)H38A—C38—H38B109.5
C14—C15—H15115.2C13—C38—H38C109.5
C16—C15—H15115.2H38A—C38—H38C109.5
N4—C16—C15124.7 (18)H38B—C38—H38C109.5
N4—C16—C17109.5 (15)C40—C39—C17108.2 (14)
C15—C16—C17125.7 (13)C40—C39—H39A110.1
C18—C17—C16107.7 (14)C17—C39—H39A110.1
C18—C17—C39124.2 (19)C40—C39—H39B110.1
C16—C17—C39128.0 (15)C17—C39—H39B110.1
C17—C18—C19105.7 (18)H39A—C39—H39B108.4
C17—C18—C44119.3 (15)C41—C40—C39113.1 (15)
C19—C18—C44134.9 (13)C41—C40—H40A109.0
N4—C19—C20125.4 (17)C39—C40—H40A109.0
N4—C19—C18109.8 (12)C41—C40—H40B109.0
C20—C19—C18124.7 (19)C39—C40—H40B109.0
C19—C20—C1128.0 (19)H40A—C40—H40B107.8
C19—C20—H20116.0O7—C41—O8119.2 (16)
C1—C20—H20116.0O7—C41—C40115.9 (13)
C2—C21—C22122.4 (11)O8—C41—C40124.6 (16)
C2—C21—H21A106.7C43—C42—O8111.1 (17)
C22—C21—H21A106.7C43—C42—H42A109.4
C2—C21—H21B106.7O8—C42—H42A109.4
C22—C21—H21B106.7C43—C42—H42B109.4
H21A—C21—H21B106.6O8—C42—H42B109.4
C21—C22—C23112.8 (11)H42A—C42—H42B108.0
C21—C22—H22A109.0C42—C43—H43A109.5
C23—C22—H22A109.0C42—C43—H43B109.5
C21—C22—H22B109.0H43A—C43—H43B109.5
C23—C22—H22B109.0C42—C43—H43C109.5
H22A—C22—H22B107.8H43A—C43—H43C109.5
O1—C23—O2124.3 (16)H43B—C43—H43C109.5
O1—C23—C22119.5 (16)C18—C44—H44A109.5
O2—C23—C22115.4 (16)C18—C44—H44B109.5
O2—C24—C25112.9 (15)H44A—C44—H44B109.5
O2—C24—H24A109.0C18—C44—H44C109.5
C25—C24—H24A109.0H44A—C44—H44C109.5
O2—C24—H24B109.0H44B—C44—H44C109.5
C25—C24—H24B109.0C23—O2—C24127.3 (17)
H24A—C24—H24B107.8C29—O4—C30125.7 (15)
C24—C25—H25A109.5C35—O5—Ru1ii162.6 (10)
C24—C25—H25B109.5C35—O6—C36115.1 (12)
H25A—C25—H25B109.5C41—O8—C42127.0 (14)
C24—C25—H25C109.5O9—C45—Ru1173.9 (13)
H25A—C25—H25C109.5
Symmetry codes: (i) −x+3/2, y−1/2, −z+3/2; (ii) −x+3/2, y+1/2, −z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C25—H25C···O2iii0.962.173.08 (2)157
C37—H37C···O9i0.962.292.93 (2)123
C39—H39A···O7iv0.972.433.37 (2)161
C39—H39B···O3v0.972.543.51 (2)173
C43—H43B···O1vi0.962.193.00 (2)141
C44—H44A···O1iii0.962.603.29 (2)129
Symmetry codes: (i) −x+3/2, y−1/2, −z+3/2; (iii) −x+2, y, −z+3/2; (iv) −x+3/2, −y+3/2, −z+1; (v) x, −y+1, z−1/2; (vi) x−1/2, −y+1/2, z−1/2.
 

Acknowledgements

This research was supported by the Russian Ministry of Science and Education (grant No. RFMEFI61616X0069). We also thank ESRF for the access to ID22 station, experiment MA-3313.

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ISSN: 2053-2296
Volume 73| Part 1| January 2017| Pages 47-51
https://doi.org/10.1107/S2053229616019422
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