Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807029686/lx2012sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807029686/lx2012Isup2.hkl |
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (u-O) = 0.008 Å
- Disorder in main residue
- R factor = 0.025
- wR factor = 0.022
- Data-to-parameter ratio = 28.8
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT112_ALERT_2_B ADDSYM Detects Additional (Pseudo) Symm. Elem... m PLAT112_ALERT_2_B ADDSYM Detects Additional (Pseudo) Symm. Elem... m PLAT115_ALERT_5_B ADDSYM Detects Noncrystallographic Inversion ... 80 PerFi
Alert level C STRVA01_ALERT_4_C Flack test results are ambiguous. From the CIF: _refine_ls_abs_structure_Flack 0.510 From the CIF: _refine_ls_abs_structure_Flack_su 0.030 PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.97 PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............ 0.50 Ratio PLAT127_ALERT_1_C Implicit Hall Symbol Inconsistent with Explicit P -2bc 21 PLAT128_ALERT_4_C Non-standard setting of Space group Pna21 .... P21nb PLAT161_ALERT_4_C Missing or Zero su (esd) on x-coordinate for ... RU1 PLAT301_ALERT_3_C Main Residue Disorder ......................... 8.00 Perc.
Alert level G REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values From the CIF: _diffrn_reflns_theta_max 61.68 From the CIF: _reflns_number_total 17319 From the CIF: _diffrn_reflns_limit_ max hkl 25. 35. 16. From the CIF: _diffrn_reflns_limit_ min hkl -25. -35. -16. TEST1: Expected hkl limits for theta max Calculated maximum hkl 26. 36. 18. Calculated minimum hkl -26. -36. -18. REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 61.68 From the CIF: _reflns_number_total 17319 Count of symmetry unique reflns 9188 Completeness (_total/calc) 188.50% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 8131 Fraction of Friedel pairs measured 0.885 Are heavy atom types Z>Si present yes PLAT033_ALERT_2_G Flack Parameter Value Deviates 2 * su from zero. 0.51 PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature . 293 K
0 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 8 ALERT level C = Check and explain 4 ALERT level G = General alerts; check 5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check
The refinement was carried out based on the starting parameters imported from the P21nb modification of Tb3RuO7 (Ishizawa et al., 2007), employing anisotropic atomic displacement parameters for metal atoms and isotropic ones for O atoms. The non-split atom model indicated Δρ peaks of 10 e Å-3 near Dy5 and Dy6 atom sites in a similar manner to Tb3RuO7. The peak heights are smaller than 33 e Å-3 observed in Tb3RuO7 under approximately the same resolution level of d>0.42 Å. The split pairs of Dy5a and Dy5b, and Dy6a and Dy6b were constrained to have the same anisotropic atomic displacement parameters in the further refinements. The Flack parameter of ~0.5 (Flack, 1983) suggested an existence of inversion related twins as is common for the P21nb modifications of Ln3RuO7 (Ln=Gd, Tb).
The room temperature structure of the title compound, (I), has been confirmed as the P21nb modification of Ln3MO7 family composed of trivalent lanthanide (Ln) and pentavalent transition metal (M=Ru, Os) oxides (Figs. 1 and 2). The family is so far known to have two orthorhombic modifications Cmcm and P21nb modifications related by the phase transition (Bontchev et al., 2000, Harada & Hinatsu, 2003, Gemmill et al., 2004, 2005).
A positional disorder at two Ln atom sites, i.e., Ln5 and Ln6, was first suspected for Gd3RuO7 and confirmed in Tb3RuO7 (Ishizawa et al., 2006, 2007). A similar but faint disorder has also been detected in Dy3RuO7 in the present study using single-crystal diffraction data collected with relatively high resolution level (d>0.42 Å). The split atom sites at Dy5b and Dy6b are populated 3.0 (7) and 2.2 (8) % by the Dy atoms. The coordination numbers of Dy1, 2, 3, 4, 5a and 6a are 7 in the range 2.17–2.62 Å, whereas those of Dy5b and Dy6b are 5 in the range 2.10–2.53 Å. The mean Ru···Ru interatomic distance and Ru—O—Ru angle along the [RuO5] ∞ octahedral chain are 3.667 (4) Å and 141.4 (5)°.
For related literature, see: Bontchev et al. (2000); Gemmill et al. (2004, 2005); Harada & Hinatsu (2001 or 2003??); Ishizawa et al. (2006, 2007).
Data collection: APEX2 (Bruker, 2006); cell refinement: APEX2; data reduction: DIFDAT, SORTRF and ADDREF in Xtal3.7 (Hall et al., 2003); program(s) used to solve structure: Xtal3.7; program(s) used to refine structure: CRYLSQ in Xtal3.7; molecular graphics: ATOMS (Dowty, 2005); software used to prepare material for publication: BONDLA and CIFIO in Xtal3.7.
Dy3RuO7 | F(000) = 2384 |
Mr = 700.57 | Dx = 8.289 Mg m−3 |
Orthorhombic, P21nb | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: p -2bc 21 | Cell parameters from 12 reflections |
a = 10.516 (2) Å | θ = 23–29° |
b = 14.560 (3) Å | µ = 42.09 mm−1 |
c = 7.333 (2) Å | T = 295 K |
V = 1122.8 (4) Å3 | Prism, black |
Z = 8 | 0.06 × 0.04 × 0.03 mm |
Bruker SMART APEX II diffractometer | 7765 reflections with F > 3σ(F) |
Detector resolution: 67 pixels mm-1 | Rint = 0.098 |
ω and φ scans | θmax = 61.7°, θmin = 2.8° |
Absorption correction: numerical (SMART APEXII XPREP; Bruker, 2006) | h = −25→25 |
Tmin = 0.272, Tmax = 0.530 | k = −35→35 |
158509 measured reflections | l = −16→16 |
17319 independent reflections |
Refinement on F | Weighting scheme based on measured s.u.'s w = 1/[σ2(Fo)] |
Least-squares matrix: full | (Δ/σ)max < 0.001 |
R[F2 > 2σ(F2)] = 0.025 | Δρmax = 3.91 e Å−3 |
wR(F2) = 0.022 | Δρmin = −3.33 e Å−3 |
S = 1.43 | Extinction correction: Becker & Coppens (1974). Acta Cryst. A30,148–153 |
3980 reflections | Extinction coefficient: 196 (5) |
138 parameters | Absolute structure: Flack (1983), 8131 Friedel pairs |
0 restraints | Absolute structure parameter: 0.51 (3) |
0 constraints |
Dy3RuO7 | V = 1122.8 (4) Å3 |
Mr = 700.57 | Z = 8 |
Orthorhombic, P21nb | Mo Kα radiation |
a = 10.516 (2) Å | µ = 42.09 mm−1 |
b = 14.560 (3) Å | T = 295 K |
c = 7.333 (2) Å | 0.06 × 0.04 × 0.03 mm |
Bruker SMART APEX II diffractometer | 17319 independent reflections |
Absorption correction: numerical (SMART APEXII XPREP; Bruker, 2006) | 7765 reflections with F > 3σ(F) |
Tmin = 0.272, Tmax = 0.530 | Rint = 0.098 |
158509 measured reflections |
R[F2 > 2σ(F2)] = 0.025 | 0 restraints |
wR(F2) = 0.022 | Δρmax = 3.91 e Å−3 |
S = 1.43 | Δρmin = −3.33 e Å−3 |
3980 reflections | Absolute structure: Flack (1983), 8131 Friedel pairs |
138 parameters | Absolute structure parameter: 0.51 (3) |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Dy1 | −0.2206 (3) | 0.02169 (10) | −0.23588 (8) | 0.0052 (2) | |
Dy2 | −0.2325 (3) | 0.22160 (12) | 0.24493 (7) | 0.0049 (4) | |
Dy3 | −0.2815 (3) | 0.27324 (10) | −0.25774 (7) | 0.0048 (2) | |
Dy4 | −0.2691 (3) | −0.02693 (12) | 0.25048 (5) | 0.0047 (4) | |
Dy5a | 0.0061 (3) | 0.38826 (8) | 0.00271 (13) | 0.00570 (17) | .970 (7) |
Dy5b | −0.010 (3) | 0.363 (3) | −0.002 (3) | 0.00570 (17) | .030 (7) |
Dy6a | −0.0095 (3) | 0.36200 (8) | −0.49762 (11) | 0.00519 (17) | .978 (8) |
Dy6b | −0.010 (4) | 0.387 (4) | −0.507 (4) | 0.00519 (17) | .022 (8) |
Ru1 | 0.00000 | 0.1261 (2) | −0.0007 (4) | 0.00357 (16) | |
Ru2 | −0.00179 (8) | 0.1246 (2) | −0.5036 (3) | 0.00306 (17) | |
O1 | 0.0125 (9) | 0.0843 (6) | −0.2517 (7) | 0.0047 (13)* | |
O2 | −0.0051 (11) | 0.1712 (7) | 0.2485 (7) | 0.0067 (14)* | |
O3 | 0.1231 (8) | 0.2211 (7) | −0.4660 (9) | 0.0052 (11)* | |
O4 | −0.3634 (11) | 0.1056 (7) | 0.2322 (12) | 0.0061 (12)* | |
O5 | 0.1269 (8) | 0.0327 (7) | −0.5443 (10) | 0.0065 (10)* | |
O6 | −0.1342 (11) | 0.3808 (8) | −0.2338 (12) | 0.0070 (14)* | |
O7 | −0.1339 (8) | 0.2192 (7) | −0.4651 (10) | 0.0067 (11)* | |
O8 | −0.1343 (10) | −0.1446 (7) | 0.2649 (11) | 0.0054 (12)* | |
O9 | −0.1299 (9) | 0.0309 (7) | −0.5342 (10) | 0.0072 (12)* | |
O10 | −0.3736 (11) | 0.1313 (8) | −0.2432 (10) | 0.0067 (14)* | |
O11 | −0.1009 (9) | 0.0138 (6) | 0.0410 (10) | 0.0073 (11)* | |
O12 | 0.1044 (8) | 0.2378 (6) | −0.0407 (10) | 0.0071 (11)* | |
O13 | 0.1604 (8) | 0.0652 (5) | 0.0454 (10) | 0.0094 (10)* | |
O14 | −0.1516 (9) | 0.1925 (6) | −0.0490 (11) | 0.0112 (12)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Dy1 | 0.0045 (3) | 0.0057 (3) | 0.00540 (14) | 0.0006 (2) | 0.00020 (19) | 0.00136 (17) |
Dy2 | 0.0045 (5) | 0.0044 (3) | 0.0058 (3) | −0.0009 (3) | −0.00010 (13) | −0.00035 (12) |
Dy3 | 0.0044 (3) | 0.0048 (3) | 0.00531 (18) | −0.0007 (2) | 0.00082 (16) | −0.00004 (13) |
Dy4 | 0.0050 (5) | 0.0044 (4) | 0.0046 (3) | 0.0006 (3) | −0.00046 (9) | −0.00034 (11) |
Dy5a | 0.00470 (19) | 0.0084 (2) | 0.00403 (11) | 0.00042 (17) | −0.00019 (16) | 0.0007 (2) |
Dy5b | 0.00470 (19) | 0.0084 (2) | 0.00403 (11) | 0.00042 (17) | −0.00019 (16) | 0.0007 (2) |
Dy6a | 0.00399 (19) | 0.0073 (2) | 0.00427 (11) | 0.00025 (17) | −0.00004 (17) | −0.0002 (2) |
Dy6b | 0.00399 (19) | 0.0073 (2) | 0.00427 (11) | 0.00025 (17) | −0.00004 (17) | −0.0002 (2) |
Ru1 | 0.0029 (2) | 0.00453 (16) | 0.00325 (12) | −0.0001 (2) | 0.0000 (2) | −0.00049 (16) |
Ru2 | 0.0033 (2) | 0.00344 (12) | 0.00242 (17) | −0.0003 (2) | −0.0003 (2) | −0.00005 (16) |
Dy1i—O6 | 2.25 (1) | Dy5b—O8ii | 2.18 (3) |
Dy1i—O13ii | 2.263 (8) | Dy5b—O12 | 2.20 (4) |
Dy1i—O10i | 2.266 (12) | Dy5b—O10i | 2.38 (3) |
Dy1i—O9i | 2.391 (8) | Dy5b—O4 | 2.53 (3) |
Dy1i—O11i | 2.392 (8) | Dy5b—O9 | 2.77 (4) |
Dy1i—O5 | 2.408 (8) | Dy5b—O5 | 2.88 (4) |
Dy1i—O1i | 2.617 (10) | Dy5b—O14 | 2.91 (4) |
Dy2—O4 | 2.181 (11) | Dy6a—Dy6b | 0.37 (5) |
Dy2—O8i | 2.206 (10) | Dy6a—O10i | 2.301 (9) |
Dy2—O3ii | 2.323 (8) | Dy6a—O4i | 2.329 (10) |
Dy2—O14 | 2.356 (8) | Dy6a—O6 | 2.353 (10) |
Dy2—O7 | 2.366 (8) | Dy6a—O8ii | 2.361 (9) |
Dy2—O12ii | 2.401 (8) | Dy6a—O11ii | 2.431 (9) |
Dy2—O2 | 2.501 (12) | Dy6a—O7 | 2.468 (10) |
Dy3—O6 | 2.210 (12) | Dy6a—O3 | 2.492 (10) |
Dy3—O10 | 2.285 (12) | Dy6b—O11ii | 2.10 (5) |
Dy3—O7 | 2.311 (9) | Dy6b—O10i | 2.26 (4) |
Dy3—O3 | 2.365 (7) | Dy6b—O8ii | 2.34 (4) |
Dy3—O14 | 2.365 (9) | Dy6b—O4i | 2.34 (4) |
Dy3—O12ii | 2.403 (8) | Dy6b—O6 | 2.39 (4) |
Dy3—O2ii | 2.486 (11) | Dy6b—O7 | 2.78 (5) |
Dy4—O4 | 2.174 (11) | Dy6b—O3 | 2.81 (5) |
Dy4—O8 | 2.226 (11) | Ru1—O14 | 1.897 (9) |
Dy4—O9 | 2.312 (9) | Ru1—O13 | 1.935 (8) |
Dy4—O13i | 2.360 (7) | Ru1—O1 | 1.943 (6) |
Dy4—O11 | 2.417 (9) | Ru1—O2 | 1.943 (7) |
Dy4—O5i | 2.418 (8) | Ru1—O11 | 1.973 (9) |
Dy4—O1i | 2.444 (10) | Ru1—O12 | 1.984 (9) |
Dy5a—Dy5b | 0.41 (4) | Ru1—Ru2 | 3.646 (4) |
Dy5a—O10i | 2.270 (9) | Ru1—Ru2 | 3.688 (4) |
Dy5a—O6 | 2.279 (10) | Ru2—O5 | 1.926 (9) |
Dy5a—O8ii | 2.305 (9) | Ru2—O9 | 1.930 (10) |
Dy5a—O4 | 2.414 (10) | Ru2—O2 | 1.940 (7) |
Dy5a—O12 | 2.442 (9) | Ru2—O3 | 1.943 (10) |
Dy5a—O5 | 2.476 (10) | Ru2—O1 | 1.944 (6) |
Dy5a—O9 | 2.532 (10) | Ru2—O7 | 1.976 (9) |
Dy5b—O6 | 2.16 (3) | ||
Ru1i—O1i—Ru2i | 143.1 (5) | Ru2—O2—Ru1 | 139.7 (6) |
Symmetry codes: (i) x+1/2, −y+1/2, z+1/2; (ii) x, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | Dy3RuO7 |
Mr | 700.57 |
Crystal system, space group | Orthorhombic, P21nb |
Temperature (K) | 295 |
a, b, c (Å) | 10.516 (2), 14.560 (3), 7.333 (2) |
V (Å3) | 1122.8 (4) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 42.09 |
Crystal size (mm) | 0.06 × 0.04 × 0.03 |
Data collection | |
Diffractometer | Bruker SMART APEX II |
Absorption correction | Numerical (SMART APEXII XPREP; Bruker, 2006) |
Tmin, Tmax | 0.272, 0.530 |
No. of measured, independent and observed [F > 3σ(F)] reflections | 158509, 17319, 7765 |
Rint | 0.098 |
(sin θ/λ)max (Å−1) | 1.239 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.025, 0.022, 1.43 |
No. of reflections | 3980 |
No. of parameters | 138 |
Δρmax, Δρmin (e Å−3) | 3.91, −3.33 |
Absolute structure | Flack (1983), 8131 Friedel pairs |
Absolute structure parameter | 0.51 (3) |
Computer programs: APEX2 (Bruker, 2006), APEX2, DIFDAT, SORTRF and ADDREF in Xtal3.7 (Hall et al., 2003), CRYLSQ in Xtal3.7, ATOMS (Dowty, 2005), BONDLA and CIFIO in Xtal3.7.
The room temperature structure of the title compound, (I), has been confirmed as the P21nb modification of Ln3MO7 family composed of trivalent lanthanide (Ln) and pentavalent transition metal (M=Ru, Os) oxides (Figs. 1 and 2). The family is so far known to have two orthorhombic modifications Cmcm and P21nb modifications related by the phase transition (Bontchev et al., 2000, Harada & Hinatsu, 2003, Gemmill et al., 2004, 2005).
A positional disorder at two Ln atom sites, i.e., Ln5 and Ln6, was first suspected for Gd3RuO7 and confirmed in Tb3RuO7 (Ishizawa et al., 2006, 2007). A similar but faint disorder has also been detected in Dy3RuO7 in the present study using single-crystal diffraction data collected with relatively high resolution level (d>0.42 Å). The split atom sites at Dy5b and Dy6b are populated 3.0 (7) and 2.2 (8) % by the Dy atoms. The coordination numbers of Dy1, 2, 3, 4, 5a and 6a are 7 in the range 2.17–2.62 Å, whereas those of Dy5b and Dy6b are 5 in the range 2.10–2.53 Å. The mean Ru···Ru interatomic distance and Ru—O—Ru angle along the [RuO5] ∞ octahedral chain are 3.667 (4) Å and 141.4 (5)°.