Dy₃RuO₇ with partial structural disorder

The flux-grown single crystals of tridysprosium ruthenium hepta­oxide, Dy₃RuO₇, have a noncentrosymmetric ortho­rhom­bic structure composed of infinite single chains of corner-linked RuO₆ octa­hedra embedded in a Dy₃O matrix. Partial disorder of Dy atoms was faintly observed. Two Dy atom sites out of the six crystallographically independent Dy sites split into two positions, which are separated by approximately 0.3-0.5 Å and have different coordination environments. The investigated crystal was an inversion twin.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](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

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S1. Comment

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)°.

Related literature

For related literature, see: Bontchev et al. (2000); Gemmill et al. (2004, 2005); Harada & Hinatsu (2001 or 2003??); Ishizawa et al. (2006, 2007).

S2. Refinement

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).

Computing details

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.

Figures

	Fig. 1. The structure of Dy3RuO7 projected along a, containing Ru1O6 (blue) and Ru2O6 (purple) octahedral chains in the Tb (red) and O (light blue) matrix. The less populated Dy5b and Dy6b are drawn in yellow. The ADP ellipsoids are drawn at the 97% probability level.
	Fig. 2. The structure of Dy3RuO7 projected along c with the same colour scheme and probability level of the ADP ellipsoid as in Fig. 1. The Dy—O bonds except for Dy5b and Dy6b are given in black thin lines.

tridysprosium ruthenium heptaoxide

Crystal data

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) Å^3	Prism, black
Z = 8	0.06 × 0.04 × 0.03 mm

Data collection

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

Refinement on F	Weighting scheme based on measured s.u.'s w = 1/[σ^2(Fo)]
Least-squares matrix: full	(Δ/σ)max < 0.001
R[F^2 > 2σ(F^2)] = 0.025	Δρmax = 3.91 e Å^−3
wR(F^2) = 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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

Dy1^i—O6	2.25 (1)	Dy5b—O8^ii	2.18 (3)
Dy1^i—O13^ii	2.263 (8)	Dy5b—O12	2.20 (4)
Dy1^i—O10^i	2.266 (12)	Dy5b—O10^i	2.38 (3)
Dy1^i—O9^i	2.391 (8)	Dy5b—O4	2.53 (3)
Dy1^i—O11^i	2.392 (8)	Dy5b—O9	2.77 (4)
Dy1^i—O5	2.408 (8)	Dy5b—O5	2.88 (4)
Dy1^i—O1^i	2.617 (10)	Dy5b—O14	2.91 (4)
Dy2—O4	2.181 (11)	Dy6a—Dy6b	0.37 (5)
Dy2—O8^i	2.206 (10)	Dy6a—O10^i	2.301 (9)
Dy2—O3^ii	2.323 (8)	Dy6a—O4^i	2.329 (10)
Dy2—O14	2.356 (8)	Dy6a—O6	2.353 (10)
Dy2—O7	2.366 (8)	Dy6a—O8^ii	2.361 (9)
Dy2—O12^ii	2.401 (8)	Dy6a—O11^ii	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—O11^ii	2.10 (5)
Dy3—O7	2.311 (9)	Dy6b—O10^i	2.26 (4)
Dy3—O3	2.365 (7)	Dy6b—O8^ii	2.34 (4)
Dy3—O14	2.365 (9)	Dy6b—O4^i	2.34 (4)
Dy3—O12^ii	2.403 (8)	Dy6b—O6	2.39 (4)
Dy3—O2^ii	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—O13^i	2.360 (7)	Ru1—O1	1.943 (6)
Dy4—O11	2.417 (9)	Ru1—O2	1.943 (7)
Dy4—O5^i	2.418 (8)	Ru1—O11	1.973 (9)
Dy4—O1^i	2.444 (10)	Ru1—O12	1.984 (9)
Dy5a—Dy5b	0.41 (4)	Ru1—Ru2	3.646 (4)
Dy5a—O10^i	2.270 (9)	Ru1—Ru2	3.688 (4)
Dy5a—O6	2.279 (10)	Ru2—O5	1.926 (9)
Dy5a—O8^ii	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)
Ru1^i—O1^i—Ru2^i	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.