Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536810046556/bg2373sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536810046556/bg2373Isup2.hkl |
CCDC reference: 802992
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.005 Å
- R factor = 0.045
- wR factor = 0.078
- Data-to-parameter ratio = 20.7
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT934_ALERT_3_B Number of (Iobs-Icalc)/SigmaW .gt. 10 Outliers . 1
Alert level C PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X) Ru1 -- S2 .. 5.72 su PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) ..... 10 PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 3 PLAT973_ALERT_2_C Large Calcd. Positive Residual Density on Ru1 1.01 eA-3 PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L= 0.600 98
Alert level G PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 3 PLAT794_ALERT_5_G Note: Tentative Bond Valency for Ru1 ....... 3.80
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 2 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check
The RuII precursor [Ru([9]aneS3)(bpy)Cl]Cl was prepared according to reported methods (Goodfellow et al., 1997). Remaining chemicals were purchased from commercial sources and used as received without further purification. [Ru([9]aneS3)(bpy)Cl]Cl (105.6 mg; 0.21 mmol) was treated with AgNO3 (53.0 mg; 0.31 mmol) in order to produce an intermediate labile species by exchanging the coordinated Cl- ligand by a solvent molecule (20 minutes stirring at room temperature in 50 ml of commercial grade ethanol). A white precipitate (AgCl) was filtered off through Celite, and the volume of the remaining red-orange solution was reduced to half by evaporation at 50 °C in a rotatory evaporator. After one month at -18 °C, the title compound was isolated as orange crystals.
Hydrogen atoms bound to carbon were located at their idealized positions and were included in the final structural model in riding approximation with C—H = 0.95 Å (aromatic C—H) and 0.99 Å (—CH2). The isotropic thermal displacement parameters for these atoms were fixed at 1.2 times Ueq of the respective parent carbon atom.
Hydrogen atoms associated with the water molecule of crystallization have been directly located from difference Fourier maps and were included in the final structural model with the distances restrained to 0.95 (1) Å and Uiso=1.5×Ueq of the respective parent oxygen atom.
The ruthenium coordination complexes containing 1,4,7-trithiacyclonane ([9]aneS3) have been studied for their activity as antitumoral agents (Bratsos et al., 2008; Serli et al., 2005). Some members of this family of compounds have been tested as cytotoxic (Marques, Santos et al., 2009) and antimicrobial (Marques, Braga et al., 2009) agents, or as catalysts (Sala et al., 2004). We have also studied the solid-state properties of the inclusion compounds of a number of these ruthenium compounds in cyclodextrins (Marques et al., 2008). While reacting the RuII precursor [Ru([9]aneS3)(bpy)Cl]Cl with AgNO3 we isolated the title compound as a secondary product.
The asymmetric unit of the title compound (see Scheme) comprises a whole [Ru([9]aneS3)(bpy)Cl]+ cation, a charge-balancing nitrate anion and a water molecule of crystallization (Figure 1). A survey in the Cambridge Structural Database revealed that this RuII cation has already been described by other groups while co-crystallizing with different anions, namely chloride and trifluoromethanesulfonate (Serli et al., 2005; Goodfellow et al., 1997). This cation has an octahedral coordination environment for RuII with the tricoordinating [9]aneS3 molecule occupying one of the faces of the polyhedron [Ru—S distances ranging from 2.2800 (9) to 2.4379 (8) Å]. The remaining three coordination sites are occupied by a chelating 2,2'-bipyridine (bpy) [Ru—N distances of 2.088 (3) and 2.093 (3) Å], and a chlorido anion [Ru—Cl distance of 2.4379 (8) Å]. The octahedral angles of the coordination polyhedron fall within a short range of the ideal values: while the cis angles range from 77.86 (10) to 98.04 (7)°, the trans angles are in the 174.02 (8)–177.46 (3)° range.
The water molecule of crystallization and the charge-balancing nitrate anion interact via strong hydrogen bonds (Table 1), leading to a polymeric H1Y—{O1W—H1X···O3—N3—O2···H1Y}∞ chain running parallel to the c-axis (dashed pink lines in Figure 2), which can be described by a C22 graph set motif (Grell et al., 1999). Noteworthy, these hydrogen bonds are of strong nature [O···O distances of 3.037 (4) and 2.839 (4) Å] and highly directional [O—H···O angles of 169 (4) and 166 (4)°].
The title compound, based on the [Ru([9]aneS3)(bpy)Cl]+ cation, is considerably different from the two previously related structures: while in our structure the charge-balancing nitrate co-crystallizes with one water molecule, the chloride and trifluoromethanesulfonate structures contain three and none of these entities, respectively (Goodfellow et al., 1997; Serli et al., 2005). Noteworthy, in the former structure (having three water molecules) the crystal packing exhibits a supramolecular two-dimensional network of hydrogen bonding interactions. In the title compound the presence of a single water molecule in the composition promotes the formation of only a one-dimensional supramolecular chain (see above). In summary, it is feasible to consider the title compound as an intermediary case between the two already known structures.
For general background to the cytotoxic activity of compounds with the (Ru[9]aneS3) unit, see: Bratsos et al. (2008); Serli et al. (2005). For related compounds, see: Sala et al. (2004); Marques, Braga et al. (2009); Marques, Santos et al. (2009); Marques et al. (2008). For compounds with the same cation as the title compound, see: Serli et al. (2005); Goodfellow et al. (1997). For graph-set notation for hydrogen-bonded aggregates, see: Grell et al. (1999)
Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT-Plus (Bruker, 2005); data reduction: SAINT-Plus (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
[RuCl(C10H8N2)(C6H12S3)]NO3·H2O | F(000) = 1120 |
Mr = 553.07 | Dx = 1.808 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5581 reflections |
a = 7.6523 (4) Å | θ = 2.5–30.4° |
b = 25.1887 (12) Å | µ = 1.24 mm−1 |
c = 11.1099 (5) Å | T = 150 K |
β = 108.438 (2)° | Block, orange |
V = 2031.52 (17) Å3 | 0.05 × 0.04 × 0.02 mm |
Z = 4 |
Bruker X8 Kappa CCD APEXII diffractometer | 5360 independent reflections |
Radiation source: fine-focus sealed tube | 4179 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.048 |
ω and φ scans | θmax = 29.1°, θmin = 3.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1998) | h = −10→9 |
Tmin = 0.941, Tmax = 0.976 | k = −34→29 |
21232 measured reflections | l = −15→15 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.078 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | w = 1/[σ2(Fo2) + (0.026P)2 + 1.766P] where P = (Fo2 + 2Fc2)/3 |
5360 reflections | (Δ/σ)max = 0.002 |
259 parameters | Δρmax = 0.74 e Å−3 |
3 restraints | Δρmin = −0.60 e Å−3 |
[RuCl(C10H8N2)(C6H12S3)]NO3·H2O | V = 2031.52 (17) Å3 |
Mr = 553.07 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.6523 (4) Å | µ = 1.24 mm−1 |
b = 25.1887 (12) Å | T = 150 K |
c = 11.1099 (5) Å | 0.05 × 0.04 × 0.02 mm |
β = 108.438 (2)° |
Bruker X8 Kappa CCD APEXII diffractometer | 5360 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1998) | 4179 reflections with I > 2σ(I) |
Tmin = 0.941, Tmax = 0.976 | Rint = 0.048 |
21232 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 3 restraints |
wR(F2) = 0.078 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | Δρmax = 0.74 e Å−3 |
5360 reflections | Δρmin = −0.60 e Å−3 |
259 parameters |
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. 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. |
x | y | z | Uiso*/Ueq | ||
Ru1 | 0.57746 (4) | 0.910714 (10) | 0.22233 (2) | 0.01142 (7) | |
S1 | 0.38460 (11) | 0.90192 (3) | 0.01591 (7) | 0.01507 (17) | |
S2 | 0.68086 (11) | 0.82613 (3) | 0.20539 (7) | 0.01433 (17) | |
S3 | 0.35078 (11) | 0.87415 (3) | 0.28829 (7) | 0.01582 (17) | |
Cl1 | 0.81988 (11) | 0.94626 (3) | 0.14642 (7) | 0.01768 (17) | |
N1 | 0.5087 (4) | 0.98857 (10) | 0.2537 (2) | 0.0143 (6) | |
N2 | 0.7509 (4) | 0.92503 (10) | 0.4070 (2) | 0.0147 (6) | |
N3 | 0.9073 (4) | 0.70605 (11) | 0.2395 (3) | 0.0225 (7) | |
O1 | 0.7828 (3) | 0.70188 (10) | 0.1357 (2) | 0.0280 (6) | |
O2 | 1.0661 (4) | 0.71932 (12) | 0.2423 (2) | 0.0385 (7) | |
O3 | 0.8748 (4) | 0.69717 (11) | 0.3408 (2) | 0.0355 (7) | |
C1 | 0.3886 (5) | 1.02027 (13) | 0.1688 (3) | 0.0189 (7) | |
H1 | 0.3243 | 1.0063 | 0.0874 | 0.023* | |
C2 | 0.3555 (5) | 1.07204 (13) | 0.1954 (3) | 0.0206 (7) | |
H2 | 0.2682 | 1.0928 | 0.1335 | 0.025* | |
C3 | 0.4493 (5) | 1.09354 (14) | 0.3120 (3) | 0.0233 (8) | |
H3 | 0.4284 | 1.1292 | 0.3317 | 0.028* | |
C4 | 0.5749 (5) | 1.06186 (14) | 0.3996 (3) | 0.0199 (7) | |
H4 | 0.6424 | 1.0758 | 0.4804 | 0.024* | |
C5 | 0.6021 (4) | 1.00952 (13) | 0.3691 (3) | 0.0143 (7) | |
C6 | 0.7357 (4) | 0.97384 (13) | 0.4554 (3) | 0.0153 (7) | |
C7 | 0.8451 (5) | 0.98784 (14) | 0.5772 (3) | 0.0187 (7) | |
H7 | 0.8325 | 1.0219 | 0.6104 | 0.022* | |
C8 | 0.9720 (5) | 0.95207 (15) | 0.6495 (3) | 0.0224 (8) | |
H8 | 1.0458 | 0.9610 | 0.7332 | 0.027* | |
C9 | 0.9903 (5) | 0.90346 (14) | 0.5989 (3) | 0.0214 (8) | |
H9 | 1.0786 | 0.8786 | 0.6464 | 0.026* | |
C10 | 0.8781 (5) | 0.89129 (14) | 0.4777 (3) | 0.0185 (7) | |
H10 | 0.8917 | 0.8577 | 0.4430 | 0.022* | |
C11 | 0.4255 (5) | 0.83499 (13) | −0.0368 (3) | 0.0179 (7) | |
H11A | 0.3333 | 0.8101 | −0.0234 | 0.021* | |
H11B | 0.4098 | 0.8358 | −0.1287 | 0.021* | |
C12 | 0.6176 (5) | 0.81530 (13) | 0.0351 (3) | 0.0172 (7) | |
H12A | 0.7076 | 0.8337 | 0.0024 | 0.021* | |
H12B | 0.6248 | 0.7769 | 0.0189 | 0.021* | |
C13 | 0.5226 (5) | 0.78117 (13) | 0.2499 (3) | 0.0169 (7) | |
H13A | 0.4228 | 0.7702 | 0.1727 | 0.020* | |
H13B | 0.5901 | 0.7489 | 0.2900 | 0.020* | |
C14 | 0.4398 (5) | 0.80803 (13) | 0.3412 (3) | 0.0179 (7) | |
H14A | 0.5350 | 0.8109 | 0.4255 | 0.022* | |
H14B | 0.3385 | 0.7857 | 0.3508 | 0.022* | |
C15 | 0.1622 (4) | 0.85625 (14) | 0.1442 (3) | 0.0191 (7) | |
H15A | 0.1780 | 0.8190 | 0.1211 | 0.023* | |
H15B | 0.0433 | 0.8589 | 0.1614 | 0.023* | |
C16 | 0.1581 (4) | 0.89212 (14) | 0.0344 (3) | 0.0189 (7) | |
H16A | 0.1075 | 0.9271 | 0.0472 | 0.023* | |
H16B | 0.0743 | 0.8767 | −0.0448 | 0.023* | |
O1W | 0.1468 (4) | 0.72516 (12) | 0.0102 (3) | 0.0371 (7) | |
H1X | 0.058 (4) | 0.7458 (15) | −0.051 (3) | 0.056* | |
H1Y | 0.106 (5) | 0.7187 (17) | 0.080 (2) | 0.056* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Ru1 | 0.01225 (13) | 0.01040 (12) | 0.01162 (11) | −0.00014 (11) | 0.00379 (9) | −0.00145 (10) |
S1 | 0.0154 (4) | 0.0154 (4) | 0.0138 (3) | 0.0000 (3) | 0.0038 (3) | −0.0017 (3) |
S2 | 0.0147 (4) | 0.0127 (4) | 0.0161 (4) | −0.0002 (3) | 0.0057 (3) | −0.0014 (3) |
S3 | 0.0167 (4) | 0.0155 (4) | 0.0169 (4) | −0.0006 (4) | 0.0077 (3) | −0.0015 (3) |
Cl1 | 0.0169 (4) | 0.0177 (4) | 0.0201 (4) | −0.0022 (3) | 0.0082 (3) | −0.0017 (3) |
N1 | 0.0150 (14) | 0.0133 (14) | 0.0166 (12) | 0.0005 (12) | 0.0078 (11) | −0.0011 (10) |
N2 | 0.0174 (15) | 0.0122 (14) | 0.0152 (12) | −0.0022 (12) | 0.0062 (11) | 0.0004 (10) |
N3 | 0.0270 (18) | 0.0167 (15) | 0.0242 (15) | 0.0051 (14) | 0.0085 (13) | 0.0028 (12) |
O1 | 0.0273 (15) | 0.0213 (14) | 0.0292 (14) | 0.0035 (12) | 0.0002 (11) | −0.0024 (11) |
O2 | 0.0268 (16) | 0.0520 (19) | 0.0373 (16) | −0.0106 (15) | 0.0109 (12) | −0.0049 (14) |
O3 | 0.0439 (18) | 0.0402 (17) | 0.0278 (14) | 0.0133 (15) | 0.0187 (13) | 0.0132 (12) |
C1 | 0.0197 (18) | 0.0180 (18) | 0.0209 (16) | 0.0022 (15) | 0.0094 (14) | 0.0007 (13) |
C2 | 0.0216 (19) | 0.0142 (17) | 0.0294 (18) | 0.0067 (15) | 0.0126 (15) | 0.0052 (14) |
C3 | 0.029 (2) | 0.0152 (17) | 0.0317 (18) | −0.0002 (17) | 0.0179 (16) | −0.0038 (14) |
C4 | 0.0220 (19) | 0.0204 (18) | 0.0211 (16) | −0.0023 (16) | 0.0124 (14) | −0.0053 (14) |
C5 | 0.0139 (16) | 0.0161 (17) | 0.0173 (15) | −0.0035 (14) | 0.0114 (13) | −0.0020 (12) |
C6 | 0.0155 (17) | 0.0163 (17) | 0.0163 (15) | −0.0073 (14) | 0.0080 (13) | −0.0025 (12) |
C7 | 0.0206 (18) | 0.0195 (18) | 0.0167 (15) | −0.0086 (15) | 0.0078 (13) | −0.0065 (13) |
C8 | 0.0209 (19) | 0.031 (2) | 0.0132 (15) | −0.0135 (17) | 0.0025 (13) | −0.0018 (14) |
C9 | 0.0181 (18) | 0.0226 (19) | 0.0202 (16) | −0.0038 (16) | 0.0019 (13) | 0.0050 (14) |
C10 | 0.0184 (18) | 0.0172 (17) | 0.0181 (15) | −0.0027 (15) | 0.0028 (13) | 0.0002 (13) |
C11 | 0.0224 (18) | 0.0160 (17) | 0.0147 (15) | −0.0014 (15) | 0.0053 (13) | −0.0066 (12) |
C12 | 0.0242 (19) | 0.0137 (16) | 0.0162 (15) | 0.0012 (15) | 0.0096 (13) | −0.0034 (12) |
C13 | 0.0205 (18) | 0.0113 (15) | 0.0204 (16) | 0.0001 (14) | 0.0085 (13) | 0.0027 (13) |
C14 | 0.0217 (18) | 0.0162 (17) | 0.0180 (16) | −0.0017 (15) | 0.0095 (14) | 0.0031 (13) |
C15 | 0.0111 (17) | 0.0217 (18) | 0.0237 (17) | −0.0013 (15) | 0.0046 (13) | −0.0044 (14) |
C16 | 0.0123 (17) | 0.0213 (18) | 0.0215 (16) | −0.0006 (15) | 0.0031 (13) | −0.0016 (13) |
O1W | 0.0376 (17) | 0.0435 (18) | 0.0324 (15) | −0.0048 (15) | 0.0139 (13) | 0.0038 (13) |
Ru1—N1 | 2.088 (3) | C5—C6 | 1.467 (5) |
Ru1—N2 | 2.093 (3) | C6—C7 | 1.392 (4) |
Ru1—S3 | 2.2800 (9) | C7—C8 | 1.381 (5) |
Ru1—S2 | 2.3012 (8) | C7—H7 | 0.9500 |
Ru1—S1 | 2.3120 (8) | C8—C9 | 1.372 (5) |
Ru1—Cl1 | 2.4379 (8) | C8—H8 | 0.9500 |
S1—C16 | 1.825 (3) | C9—C10 | 1.382 (4) |
S1—C11 | 1.843 (3) | C9—H9 | 0.9500 |
S2—C12 | 1.819 (3) | C10—H10 | 0.9500 |
S2—C13 | 1.836 (3) | C11—C12 | 1.517 (5) |
S3—C14 | 1.825 (3) | C11—H11A | 0.9900 |
S3—C15 | 1.841 (3) | C11—H11B | 0.9900 |
N1—C1 | 1.350 (4) | C12—H12A | 0.9900 |
N1—C5 | 1.361 (4) | C12—H12B | 0.9900 |
N2—C10 | 1.343 (4) | C13—C14 | 1.515 (4) |
N2—C6 | 1.361 (4) | C13—H13A | 0.9900 |
N3—O1 | 1.247 (4) | C13—H13B | 0.9900 |
N3—O3 | 1.247 (4) | C14—H14A | 0.9900 |
N3—O2 | 1.251 (4) | C14—H14B | 0.9900 |
C1—C2 | 1.378 (5) | C15—C16 | 1.510 (5) |
C1—H1 | 0.9500 | C15—H15A | 0.9900 |
C2—C3 | 1.378 (5) | C15—H15B | 0.9900 |
C2—H2 | 0.9500 | C16—H16A | 0.9900 |
C3—C4 | 1.385 (5) | C16—H16B | 0.9900 |
C3—H3 | 0.9500 | O1W—H1X | 0.95 (3) |
C4—C5 | 1.393 (4) | O1W—H1Y | 0.94 (3) |
C4—H4 | 0.9500 | ||
N1—Ru1—N2 | 77.86 (10) | C7—C6—C5 | 124.1 (3) |
N1—Ru1—S3 | 93.92 (8) | C8—C7—C6 | 119.8 (3) |
N2—Ru1—S3 | 93.76 (8) | C8—C7—H7 | 120.1 |
N1—Ru1—S2 | 174.02 (8) | C6—C7—H7 | 120.1 |
N2—Ru1—S2 | 96.43 (8) | C9—C8—C7 | 119.2 (3) |
S3—Ru1—S2 | 88.19 (3) | C9—C8—H8 | 120.4 |
N1—Ru1—S1 | 98.04 (7) | C7—C8—H8 | 120.4 |
N2—Ru1—S1 | 175.57 (8) | C8—C9—C10 | 119.0 (3) |
S3—Ru1—S1 | 88.18 (3) | C8—C9—H9 | 120.5 |
S2—Ru1—S1 | 87.61 (3) | C10—C9—H9 | 120.5 |
N1—Ru1—Cl1 | 88.41 (8) | N2—C10—C9 | 122.7 (3) |
N2—Ru1—Cl1 | 87.70 (8) | N2—C10—H10 | 118.6 |
S3—Ru1—Cl1 | 177.46 (3) | C9—C10—H10 | 118.6 |
S2—Ru1—Cl1 | 89.59 (3) | C12—C11—S1 | 111.4 (2) |
S1—Ru1—Cl1 | 90.51 (3) | C12—C11—H11A | 109.3 |
C16—S1—C11 | 100.05 (16) | S1—C11—H11A | 109.3 |
C16—S1—Ru1 | 103.44 (11) | C12—C11—H11B | 109.3 |
C11—S1—Ru1 | 106.47 (10) | S1—C11—H11B | 109.3 |
C12—S2—C13 | 101.89 (15) | H11A—C11—H11B | 108.0 |
C12—S2—Ru1 | 103.80 (11) | C11—C12—S2 | 113.2 (2) |
C13—S2—Ru1 | 106.02 (11) | C11—C12—H12A | 108.9 |
C14—S3—C15 | 99.61 (16) | S2—C12—H12A | 108.9 |
C14—S3—Ru1 | 103.17 (11) | C11—C12—H12B | 108.9 |
C15—S3—Ru1 | 106.61 (11) | S2—C12—H12B | 108.9 |
C1—N1—C5 | 117.8 (3) | H12A—C12—H12B | 107.8 |
C1—N1—Ru1 | 126.2 (2) | C14—C13—S2 | 110.8 (2) |
C5—N1—Ru1 | 115.9 (2) | C14—C13—H13A | 109.5 |
C10—N2—C6 | 118.5 (3) | S2—C13—H13A | 109.5 |
C10—N2—Ru1 | 125.6 (2) | C14—C13—H13B | 109.5 |
C6—N2—Ru1 | 115.8 (2) | S2—C13—H13B | 109.5 |
O1—N3—O3 | 120.4 (3) | H13A—C13—H13B | 108.1 |
O1—N3—O2 | 119.8 (3) | C13—C14—S3 | 112.6 (2) |
O3—N3—O2 | 119.7 (3) | C13—C14—H14A | 109.1 |
N1—C1—C2 | 122.8 (3) | S3—C14—H14A | 109.1 |
N1—C1—H1 | 118.6 | C13—C14—H14B | 109.1 |
C2—C1—H1 | 118.6 | S3—C14—H14B | 109.1 |
C3—C2—C1 | 119.7 (3) | H14A—C14—H14B | 107.8 |
C3—C2—H2 | 120.1 | C16—C15—S3 | 111.5 (2) |
C1—C2—H2 | 120.1 | C16—C15—H15A | 109.3 |
C2—C3—C4 | 118.3 (3) | S3—C15—H15A | 109.3 |
C2—C3—H3 | 120.8 | C16—C15—H15B | 109.3 |
C4—C3—H3 | 120.8 | S3—C15—H15B | 109.3 |
C3—C4—C5 | 119.9 (3) | H15A—C15—H15B | 108.0 |
C3—C4—H4 | 120.1 | C15—C16—S1 | 113.2 (2) |
C5—C4—H4 | 120.1 | C15—C16—H16A | 108.9 |
N1—C5—C4 | 121.5 (3) | S1—C16—H16A | 108.9 |
N1—C5—C6 | 115.3 (3) | C15—C16—H16B | 108.9 |
C4—C5—C6 | 123.2 (3) | S1—C16—H16B | 108.9 |
N2—C6—C7 | 120.8 (3) | H16A—C16—H16B | 107.8 |
N2—C6—C5 | 115.1 (3) | H1X—O1W—H1Y | 109.6 (15) |
N1—Ru1—S1—C16 | −76.63 (14) | Ru1—N1—C1—C2 | −177.6 (2) |
S3—Ru1—S1—C16 | 17.07 (12) | N1—C1—C2—C3 | 1.1 (5) |
S2—Ru1—S1—C16 | 105.33 (12) | C1—C2—C3—C4 | −0.2 (5) |
Cl1—Ru1—S1—C16 | −165.10 (12) | C2—C3—C4—C5 | −0.6 (5) |
N1—Ru1—S1—C11 | 178.43 (14) | C1—N1—C5—C4 | 0.3 (4) |
S3—Ru1—S1—C11 | −87.87 (12) | Ru1—N1—C5—C4 | 177.1 (2) |
S2—Ru1—S1—C11 | 0.39 (12) | C1—N1—C5—C6 | −177.7 (3) |
Cl1—Ru1—S1—C11 | 89.96 (12) | Ru1—N1—C5—C6 | −1.0 (3) |
N2—Ru1—S2—C12 | −158.31 (14) | C3—C4—C5—N1 | 0.6 (5) |
S3—Ru1—S2—C12 | 108.11 (12) | C3—C4—C5—C6 | 178.5 (3) |
S1—Ru1—S2—C12 | 19.86 (12) | C10—N2—C6—C7 | −2.2 (4) |
Cl1—Ru1—S2—C12 | −70.67 (12) | Ru1—N2—C6—C7 | −179.6 (2) |
N2—Ru1—S2—C13 | 94.76 (13) | C10—N2—C6—C5 | 176.1 (3) |
S3—Ru1—S2—C13 | 1.18 (11) | Ru1—N2—C6—C5 | −1.3 (3) |
S1—Ru1—S2—C13 | −87.07 (11) | N1—C5—C6—N2 | 1.5 (4) |
Cl1—Ru1—S2—C13 | −177.60 (11) | C4—C5—C6—N2 | −176.5 (3) |
N1—Ru1—S3—C14 | −154.39 (13) | N1—C5—C6—C7 | 179.7 (3) |
N2—Ru1—S3—C14 | −76.32 (13) | C4—C5—C6—C7 | 1.7 (5) |
S2—Ru1—S3—C14 | 20.01 (11) | N2—C6—C7—C8 | 0.6 (5) |
S1—Ru1—S3—C14 | 107.67 (11) | C5—C6—C7—C8 | −177.5 (3) |
N1—Ru1—S3—C15 | 101.21 (14) | C6—C7—C8—C9 | 1.2 (5) |
N2—Ru1—S3—C15 | 179.28 (14) | C7—C8—C9—C10 | −1.3 (5) |
S2—Ru1—S3—C15 | −84.39 (12) | C6—N2—C10—C9 | 2.1 (5) |
S1—Ru1—S3—C15 | 3.27 (12) | Ru1—N2—C10—C9 | 179.2 (2) |
N2—Ru1—N1—C1 | 176.7 (3) | C8—C9—C10—N2 | −0.3 (5) |
S3—Ru1—N1—C1 | −90.3 (3) | C16—S1—C11—C12 | −133.3 (2) |
S1—Ru1—N1—C1 | −1.6 (3) | Ru1—S1—C11—C12 | −26.0 (2) |
Cl1—Ru1—N1—C1 | 88.7 (3) | S1—C11—C12—S2 | 45.9 (3) |
N2—Ru1—N1—C5 | 0.2 (2) | C13—S2—C12—C11 | 67.2 (3) |
S3—Ru1—N1—C5 | 93.2 (2) | Ru1—S2—C12—C11 | −42.9 (2) |
S1—Ru1—N1—C5 | −178.1 (2) | C12—S2—C13—C14 | −136.2 (2) |
Cl1—Ru1—N1—C5 | −87.8 (2) | Ru1—S2—C13—C14 | −27.9 (2) |
N1—Ru1—N2—C10 | −176.6 (3) | S2—C13—C14—S3 | 48.1 (3) |
S3—Ru1—N2—C10 | 90.2 (3) | C15—S3—C14—C13 | 65.5 (3) |
S2—Ru1—N2—C10 | 1.6 (3) | Ru1—S3—C14—C13 | −44.2 (3) |
Cl1—Ru1—N2—C10 | −87.7 (3) | C14—S3—C15—C16 | −135.6 (2) |
N1—Ru1—N2—C6 | 0.6 (2) | Ru1—S3—C15—C16 | −28.6 (3) |
S3—Ru1—N2—C6 | −92.6 (2) | S3—C15—C16—S1 | 46.3 (3) |
S2—Ru1—N2—C6 | 178.8 (2) | C11—S1—C16—C15 | 69.2 (3) |
Cl1—Ru1—N2—C6 | 89.5 (2) | Ru1—S1—C16—C15 | −40.6 (3) |
C5—N1—C1—C2 | −1.2 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1W—H1X···O3i | 0.95 (3) | 2.10 (3) | 3.037 (4) | 169 (4) |
O1W—H1Y···O2ii | 0.94 (3) | 1.92 (2) | 2.839 (4) | 166 (4) |
Symmetry codes: (i) x−1, −y+3/2, z−1/2; (ii) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | [RuCl(C10H8N2)(C6H12S3)]NO3·H2O |
Mr | 553.07 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 150 |
a, b, c (Å) | 7.6523 (4), 25.1887 (12), 11.1099 (5) |
β (°) | 108.438 (2) |
V (Å3) | 2031.52 (17) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.24 |
Crystal size (mm) | 0.05 × 0.04 × 0.02 |
Data collection | |
Diffractometer | Bruker X8 Kappa CCD APEXII |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1998) |
Tmin, Tmax | 0.941, 0.976 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 21232, 5360, 4179 |
Rint | 0.048 |
(sin θ/λ)max (Å−1) | 0.685 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.078, 1.08 |
No. of reflections | 5360 |
No. of parameters | 259 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.74, −0.60 |
Computer programs: APEX2 (Bruker, 2006), SAINT-Plus (Bruker, 2005), SHELXTL (Sheldrick, 2008), DIAMOND (Brandenburg, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O1W—H1X···O3i | 0.95 (3) | 2.10 (3) | 3.037 (4) | 169 (4) |
O1W—H1Y···O2ii | 0.94 (3) | 1.916 (15) | 2.839 (4) | 166 (4) |
Symmetry codes: (i) x−1, −y+3/2, z−1/2; (ii) x−1, y, z. |
The ruthenium coordination complexes containing 1,4,7-trithiacyclonane ([9]aneS3) have been studied for their activity as antitumoral agents (Bratsos et al., 2008; Serli et al., 2005). Some members of this family of compounds have been tested as cytotoxic (Marques, Santos et al., 2009) and antimicrobial (Marques, Braga et al., 2009) agents, or as catalysts (Sala et al., 2004). We have also studied the solid-state properties of the inclusion compounds of a number of these ruthenium compounds in cyclodextrins (Marques et al., 2008). While reacting the RuII precursor [Ru([9]aneS3)(bpy)Cl]Cl with AgNO3 we isolated the title compound as a secondary product.
The asymmetric unit of the title compound (see Scheme) comprises a whole [Ru([9]aneS3)(bpy)Cl]+ cation, a charge-balancing nitrate anion and a water molecule of crystallization (Figure 1). A survey in the Cambridge Structural Database revealed that this RuII cation has already been described by other groups while co-crystallizing with different anions, namely chloride and trifluoromethanesulfonate (Serli et al., 2005; Goodfellow et al., 1997). This cation has an octahedral coordination environment for RuII with the tricoordinating [9]aneS3 molecule occupying one of the faces of the polyhedron [Ru—S distances ranging from 2.2800 (9) to 2.4379 (8) Å]. The remaining three coordination sites are occupied by a chelating 2,2'-bipyridine (bpy) [Ru—N distances of 2.088 (3) and 2.093 (3) Å], and a chlorido anion [Ru—Cl distance of 2.4379 (8) Å]. The octahedral angles of the coordination polyhedron fall within a short range of the ideal values: while the cis angles range from 77.86 (10) to 98.04 (7)°, the trans angles are in the 174.02 (8)–177.46 (3)° range.
The water molecule of crystallization and the charge-balancing nitrate anion interact via strong hydrogen bonds (Table 1), leading to a polymeric H1Y—{O1W—H1X···O3—N3—O2···H1Y}∞ chain running parallel to the c-axis (dashed pink lines in Figure 2), which can be described by a C22 graph set motif (Grell et al., 1999). Noteworthy, these hydrogen bonds are of strong nature [O···O distances of 3.037 (4) and 2.839 (4) Å] and highly directional [O—H···O angles of 169 (4) and 166 (4)°].
The title compound, based on the [Ru([9]aneS3)(bpy)Cl]+ cation, is considerably different from the two previously related structures: while in our structure the charge-balancing nitrate co-crystallizes with one water molecule, the chloride and trifluoromethanesulfonate structures contain three and none of these entities, respectively (Goodfellow et al., 1997; Serli et al., 2005). Noteworthy, in the former structure (having three water molecules) the crystal packing exhibits a supramolecular two-dimensional network of hydrogen bonding interactions. In the title compound the presence of a single water molecule in the composition promotes the formation of only a one-dimensional supramolecular chain (see above). In summary, it is feasible to consider the title compound as an intermediary case between the two already known structures.