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The reaction of ytterbium(III) chloride with a self-assembling pyridine-containing ligand system, [H2pyda]2+[pydc]2- [pyda is 2,6-di­amino­pyridine (C5H7N3) and pydcH2 is 2,6-pyridine­di­carboxyl­ic acid (C7H5NO4)], in water leads to the formation of the title YbIII complex, (H5O2)(Hpyda)2[Yb(pydc)3]·2H2O. The Yb atom lies on a twofold rotation axis and is nine-coordinate with a distorted tricapped trigonal-prismatic geometry. The formula unit of the complex contains one (H5O2)+ di­hydro­nium cation on a twofold rotation axis, two protonated pyda mol­ecules and two water mol­ecules.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804006415/cf6321sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536804006415/cf6321Isup2.hkl
Contains datablock I

CCDC reference: 227871

Key indicators

  • Single-crystal X-ray study
  • T = 115 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.028
  • wR factor = 0.059
  • Data-to-parameter ratio = 19.3

checkCIF/PLATON results

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Alert level A PLAT355_ALERT_3_A Long O-H Bond (0.82A) O1W - H1WC ... 1.22 Ang.
Alert level B PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low ....... 0.95 PLAT094_ALERT_2_B Ratio of Maximum / Minimum Residual Density .... 5.23 PLAT417_ALERT_2_B Short Inter D-H..H-D H1WB .. H2WA .. 2.03 Ang. PLAT420_ALERT_2_B D-H Without Acceptor O1W - H1WC ... ?
Alert level C PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT062_ALERT_4_C Rescale T(min) & T(max) by ..................... 0.96 PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT128_ALERT_4_C Non-standard setting of Space group P2/c .... P2/n PLAT313_ALERT_2_C Oxygen with three covalent bonds (rare) ........ O1W PLAT420_ALERT_2_C D-H Without Acceptor N5 - H5NA ... ? PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 9
1 ALERT level A = In general: serious problem 4 ALERT level B = Potentially serious problem 7 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 5 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

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 1998); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Dihydronium 2,6-diaminopyridinium tris(2,6-pyridinedicarboxylato)ytterbate(III) dihydrate top
Crystal data top
(H5O2)(C5H8N3)2[Yb(C7H3NO4)3]·2H2OF(000) = 962
Mr = 961.71Dx = 1.776 Mg m3
Monoclinic, P2/nMo Kα radiation, λ = 0.71073 Å
a = 9.6357 (5) ÅCell parameters from 9085 reflections
b = 10.5295 (5) Åθ = 2.3–30.0°
c = 17.7932 (9) ŵ = 2.69 mm1
β = 94.953 (1)°T = 115 K
V = 1798.54 (16) Å3Prism, yellow
Z = 20.25 × 0.20 × 0.15 mm
Data collection top
Bruker SMART 1000 CCD area-detector
diffractometer
5008 independent reflections
Radiation source: normal-focus sealed tube4154 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
φ and ω scansθmax = 30.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1998)
h = 1313
Tmin = 0.552, Tmax = 0.695k = 1114
16540 measured reflectionsl = 2424
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.028Hydrogen site location: difference Fourier map
wR(F2) = 0.059H-atom parameters constrained
S = 0.89 w = 1/[σ2(Fo2) + (0.0305P)2]
where P = (Fo2 + 2Fc2)/3
5008 reflections(Δ/σ)max < 0.001
259 parametersΔρmax = 3.83 e Å3
0 restraintsΔρmin = 0.73 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Yb10.75000.027931 (18)0.25000.01593 (5)
O10.82900 (18)0.0390 (2)0.13504 (9)0.0184 (4)
O20.8354 (2)0.0208 (2)0.01031 (10)0.0254 (4)
O30.58909 (19)0.18982 (19)0.27676 (10)0.0190 (4)
O40.4469 (2)0.35061 (19)0.23967 (11)0.0218 (4)
O50.53391 (18)0.06764 (19)0.20744 (10)0.0195 (4)
O60.4042 (2)0.2378 (2)0.17286 (12)0.0274 (5)
N10.6447 (2)0.1410 (2)0.13920 (12)0.0151 (4)
N20.75000.2062 (3)0.25000.0163 (6)
C10.6731 (3)0.1044 (3)0.07066 (14)0.0169 (5)
C20.6030 (3)0.1536 (3)0.00565 (15)0.0222 (6)
H2A0.62380.12510.04280.027*
C30.5023 (3)0.2451 (3)0.01317 (15)0.0265 (7)
H3A0.45200.28000.03030.032*
C40.4751 (3)0.2857 (3)0.08481 (15)0.0225 (6)
H4A0.40800.35000.09120.027*
C50.5482 (3)0.2298 (3)0.14642 (14)0.0164 (5)
C60.7879 (3)0.0071 (3)0.07082 (14)0.0183 (6)
C70.5245 (3)0.2606 (3)0.22722 (15)0.0165 (5)
C80.6366 (3)0.2702 (3)0.22362 (14)0.0177 (5)
C90.6330 (3)0.4014 (3)0.22093 (17)0.0253 (6)
H9A0.55250.44490.19980.030*
C100.75000.4679 (5)0.25000.0287 (9)
H10A0.75000.55810.25000.034*
C110.5127 (3)0.1876 (3)0.19887 (15)0.0184 (6)
N30.3952 (2)0.4097 (3)0.38226 (13)0.0214 (5)
H3N0.41990.39290.33540.026*
N40.4650 (3)0.2117 (3)0.42549 (14)0.0283 (6)
H4NA0.49090.20360.38040.034*
H4NB0.44350.14210.45730.034*
N50.3481 (3)0.6060 (3)0.32954 (16)0.0342 (6)
H5NA0.37350.58070.28370.041*
H5NB0.31490.67730.33100.041*
C120.4050 (3)0.3232 (3)0.43910 (15)0.0222 (6)
C130.3559 (3)0.3568 (3)0.50789 (17)0.0280 (7)
H13A0.35940.29810.54850.034*
C140.3025 (3)0.4764 (4)0.51564 (16)0.0299 (7)
H14A0.26880.49950.56240.036*
C150.2958 (3)0.5654 (3)0.45725 (18)0.0306 (7)
H15A0.25900.64800.46370.037*
C160.3452 (3)0.5287 (3)0.38924 (15)0.0236 (5)
O1W0.2911 (2)0.0459 (2)0.18735 (13)0.0344 (5)
H1WA0.35790.01490.19330.041*
H1WB0.22370.01220.16780.041*
H1WC0.25000.03540.25000.041*
O2W0.1077 (2)0.8913 (2)0.11804 (12)0.0332 (5)
H2WA0.12240.91860.07160.040*
H2WB0.02180.91050.12460.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Yb10.01515 (7)0.01487 (9)0.01804 (8)0.0000.00296 (5)0.000
O10.0187 (8)0.0180 (11)0.0190 (8)0.0037 (8)0.0041 (6)0.0008 (8)
O20.0293 (10)0.0288 (12)0.0195 (9)0.0062 (9)0.0099 (7)0.0024 (9)
O30.0219 (9)0.0172 (11)0.0183 (9)0.0038 (8)0.0036 (7)0.0002 (8)
O40.0245 (10)0.0166 (11)0.0251 (10)0.0052 (8)0.0058 (8)0.0027 (8)
O50.0153 (8)0.0166 (11)0.0264 (10)0.0003 (7)0.0007 (7)0.0005 (8)
O60.0195 (10)0.0255 (13)0.0358 (12)0.0055 (9)0.0045 (8)0.0023 (9)
N10.0152 (10)0.0132 (12)0.0171 (10)0.0014 (8)0.0030 (8)0.0006 (8)
N20.0165 (14)0.0162 (18)0.0166 (14)0.0000.0032 (11)0.000
C10.0167 (12)0.0151 (15)0.0195 (12)0.0029 (10)0.0046 (9)0.0006 (10)
C20.0219 (13)0.0276 (18)0.0172 (12)0.0002 (11)0.0031 (10)0.0001 (11)
C30.0231 (13)0.034 (2)0.0224 (15)0.0047 (12)0.0004 (11)0.0054 (13)
C40.0214 (13)0.0228 (17)0.0233 (13)0.0038 (11)0.0025 (10)0.0021 (11)
C50.0150 (11)0.0150 (15)0.0197 (12)0.0024 (10)0.0043 (9)0.0004 (10)
C60.0156 (11)0.0197 (18)0.0200 (12)0.0032 (10)0.0036 (9)0.0034 (10)
C70.0134 (11)0.0147 (15)0.0219 (13)0.0023 (10)0.0034 (9)0.0014 (11)
C80.0175 (12)0.0168 (15)0.0191 (12)0.0018 (10)0.0036 (10)0.0001 (10)
C90.0228 (14)0.0179 (17)0.0355 (16)0.0044 (12)0.0038 (11)0.0033 (13)
C100.0263 (19)0.014 (2)0.046 (2)0.0000.0041 (17)0.000
C110.0181 (12)0.0174 (16)0.0199 (13)0.0012 (11)0.0024 (10)0.0003 (11)
N30.0220 (11)0.0194 (14)0.0234 (12)0.0012 (10)0.0052 (9)0.0020 (10)
N40.0349 (14)0.0224 (15)0.0290 (13)0.0029 (11)0.0104 (11)0.0046 (11)
N50.0429 (16)0.0240 (16)0.0370 (15)0.0123 (13)0.0115 (12)0.0040 (12)
C120.0192 (13)0.0230 (17)0.0247 (14)0.0020 (12)0.0027 (10)0.0005 (12)
C130.0260 (15)0.033 (2)0.0252 (15)0.0014 (13)0.0031 (11)0.0002 (13)
C140.0253 (13)0.041 (2)0.0240 (13)0.0004 (15)0.0064 (10)0.0093 (14)
C150.0259 (14)0.031 (2)0.0355 (16)0.0046 (13)0.0078 (12)0.0104 (13)
C160.0202 (12)0.0211 (15)0.0298 (13)0.0027 (13)0.0036 (10)0.0030 (14)
O1W0.0190 (10)0.0283 (15)0.0558 (14)0.0004 (9)0.0028 (9)0.0038 (11)
O2W0.0251 (11)0.0407 (16)0.0342 (12)0.0063 (10)0.0053 (9)0.0072 (10)
Geometric parameters (Å, º) top
Yb1—O12.3513 (17)C8—C91.383 (4)
Yb1—O1i2.3513 (17)C8—C111.511 (4)
Yb1—O52.3768 (18)C9—C101.389 (4)
Yb1—O5i2.3768 (18)C9—H9A0.950
Yb1—O3i2.3799 (19)C10—C9i1.389 (4)
Yb1—O32.3799 (19)C10—H10A0.950
Yb1—N1i2.447 (2)N3—C161.352 (4)
Yb1—N12.447 (2)N3—C121.358 (4)
Yb1—N22.465 (3)N3—H3N0.905
O1—C61.273 (3)N4—C121.339 (4)
O2—C61.241 (3)N4—H4NA0.864
O3—C71.275 (3)N4—H4NB0.960
O4—C71.239 (3)N5—C161.340 (4)
O5—C111.287 (3)N5—H5NA0.911
O6—C111.225 (3)N5—H5NB0.818
N1—C11.330 (3)C12—C131.395 (4)
N1—C51.332 (3)C13—C141.372 (5)
N2—C81.334 (3)C13—H13A0.950
N2—C8i1.334 (3)C14—C151.396 (5)
C1—C21.389 (4)C14—H14A0.950
C1—C61.507 (4)C15—C161.393 (4)
C2—C31.382 (4)C15—H15A0.950
C2—H2A0.9500O1W—H1WA0.721
C3—C41.391 (4)O1W—H1WB0.937
C3—H3A0.950O1W—H1WC1.222
C4—C51.383 (4)O2W—H2WA0.898
C4—H4A0.950O2W—H2WB0.870
C5—C71.510 (4)
O1—Yb1—O1i145.14 (10)C4—C3—H3A120.2
O1—Yb1—O586.36 (6)C5—C4—C3118.2 (3)
O1i—Yb1—O579.04 (6)C5—C4—H4A120.9
O1—Yb1—O5i79.04 (6)C3—C4—H4A120.9
O1i—Yb1—O5i86.36 (6)N1—C5—C4122.3 (2)
O5—Yb1—O5i129.90 (10)N1—C5—C7114.0 (2)
O1—Yb1—O3i77.00 (7)C4—C5—C7123.7 (2)
O1i—Yb1—O3i130.85 (6)O2—C6—O1125.4 (2)
O5—Yb1—O3i143.85 (6)O2—C6—C1119.0 (2)
O5i—Yb1—O3i78.41 (7)O1—C6—C1115.6 (2)
O1—Yb1—O3130.85 (6)O4—C7—O3126.1 (2)
O1i—Yb1—O377.00 (7)O4—C7—C5118.5 (2)
O5—Yb1—O378.41 (7)O3—C7—C5115.3 (2)
O5i—Yb1—O3143.85 (6)N2—C8—C9122.3 (3)
O3i—Yb1—O388.51 (9)N2—C8—C11114.5 (3)
O1—Yb1—N1i134.72 (6)C9—C8—C11123.2 (2)
O1i—Yb1—N1i65.66 (7)C8—C9—C10118.2 (3)
O5—Yb1—N1i138.90 (7)C8—C9—H9A120.9
O5i—Yb1—N1i70.03 (7)C10—C9—H9A120.9
O3i—Yb1—N1i65.21 (7)C9i—C10—C9119.5 (4)
O3—Yb1—N1i73.88 (7)C9i—C10—H10A120.3
O1—Yb1—N165.66 (7)C9—C10—H10A120.3
O1i—Yb1—N1134.72 (6)O6—C11—O5126.1 (3)
O5—Yb1—N170.03 (7)O6—C11—C8119.3 (3)
O5i—Yb1—N1138.90 (7)O5—C11—C8114.6 (2)
O3i—Yb1—N173.88 (7)C16—N3—C12123.7 (2)
O3—Yb1—N165.21 (7)C16—N3—H3N112.9
N1i—Yb1—N1121.77 (10)C12—N3—H3N123.3
O1—Yb1—N272.57 (5)C12—N4—H4NA114.8
O1i—Yb1—N272.57 (5)C12—N4—H4NB116.4
O5—Yb1—N264.95 (5)H4NA—N4—H4NB124.4
O5i—Yb1—N264.95 (5)C16—N5—H5NA123.9
O3i—Yb1—N2135.75 (5)C16—N5—H5NB119.9
O3—Yb1—N2135.75 (5)H5NA—N5—H5NB115.6
N1i—Yb1—N2119.12 (5)N4—C12—N3117.1 (3)
N1—Yb1—N2119.12 (5)N4—C12—C13124.4 (3)
C6—O1—Yb1124.61 (16)N3—C12—C13118.4 (3)
C7—O3—Yb1124.60 (16)C14—C13—C12118.6 (3)
C11—O5—Yb1125.40 (16)C14—C13—H13A120.7
C1—N1—C5119.5 (2)C12—C13—H13A120.7
C1—N1—Yb1119.58 (17)C13—C14—C15122.3 (3)
C5—N1—Yb1120.52 (16)C13—C14—H14A118.8
C8—N2—C8i119.3 (4)C15—C14—H14A118.8
C8—N2—Yb1120.34 (18)C16—C15—C14117.6 (3)
C8i—N2—Yb1120.34 (18)C16—C15—H15A121.2
N1—C1—C2122.1 (2)C14—C15—H15A121.2
N1—C1—C6113.9 (2)N5—C16—N3117.3 (3)
C2—C1—C6124.0 (2)N5—C16—C15123.5 (3)
C3—C2—C1118.3 (2)N3—C16—C15119.2 (3)
C3—C2—H2A120.8H1WA—O1W—H1WB109.9
C1—C2—H2A120.8H1WA—O1W—H1WC100.5
C2—C3—C4119.5 (3)H1WB—O1W—H1WC90.7
C2—C3—H3A120.2H2WA—O2W—H2WB106.0
O1i—Yb1—O1—C6134.6 (2)O3—Yb1—N2—C8i139.43 (14)
O5—Yb1—O1—C669.7 (2)N1i—Yb1—N2—C8i42.76 (14)
O5i—Yb1—O1—C6158.5 (2)N1—Yb1—N2—C8i137.24 (14)
O3i—Yb1—O1—C678.0 (2)C5—N1—C1—C21.5 (4)
O3—Yb1—O1—C61.6 (2)Yb1—N1—C1—C2171.4 (2)
N1i—Yb1—O1—C6111.4 (2)C5—N1—C1—C6177.8 (2)
N1—Yb1—O1—C60.00 (19)Yb1—N1—C1—C69.2 (3)
N2—Yb1—O1—C6134.6 (2)N1—C1—C2—C31.1 (4)
O1—Yb1—O3—C70.6 (2)C6—C1—C2—C3178.2 (3)
O1i—Yb1—O3—C7155.4 (2)C1—C2—C3—C40.6 (4)
O5—Yb1—O3—C774.1 (2)C2—C3—C4—C51.7 (4)
O5i—Yb1—O3—C7139.86 (19)C1—N1—C5—C40.3 (4)
O3i—Yb1—O3—C772.0 (2)Yb1—N1—C5—C4172.6 (2)
N1i—Yb1—O3—C7136.6 (2)C1—N1—C5—C7178.9 (2)
N1—Yb1—O3—C70.93 (19)Yb1—N1—C5—C76.0 (3)
N2—Yb1—O3—C7108.03 (19)C3—C4—C5—N11.2 (4)
O1—Yb1—O5—C1168.33 (19)C3—C4—C5—C7177.2 (3)
O1i—Yb1—O5—C1179.86 (19)Yb1—O1—C6—O2174.7 (2)
O5i—Yb1—O5—C114.11 (17)Yb1—O1—C6—C14.5 (3)
O3i—Yb1—O5—C11130.36 (19)N1—C1—C6—O2170.4 (2)
O3—Yb1—O5—C11158.7 (2)C2—C1—C6—O29.0 (4)
N1i—Yb1—O5—C11110.5 (2)N1—C1—C6—O18.9 (3)
N1—Yb1—O5—C11133.7 (2)C2—C1—C6—O1171.8 (3)
N2—Yb1—O5—C114.11 (17)Yb1—O3—C7—O4175.2 (2)
O1—Yb1—N1—C15.33 (18)Yb1—O3—C7—C54.2 (3)
O1i—Yb1—N1—C1139.71 (17)N1—C5—C7—O4173.0 (2)
O5—Yb1—N1—C189.85 (19)C4—C5—C7—O48.5 (4)
O5i—Yb1—N1—C138.6 (2)N1—C5—C7—O36.5 (3)
O3i—Yb1—N1—C188.08 (19)C4—C5—C7—O3172.1 (3)
O3—Yb1—N1—C1176.0 (2)C8i—N2—C8—C91.51 (18)
N1i—Yb1—N1—C1134.3 (2)Yb1—N2—C8—C9178.49 (18)
N2—Yb1—N1—C145.7 (2)C8i—N2—C8—C11177.1 (2)
O1—Yb1—N1—C5178.2 (2)Yb1—N2—C8—C112.9 (2)
O1i—Yb1—N1—C533.2 (2)N2—C8—C9—C102.9 (4)
O5—Yb1—N1—C583.06 (19)C11—C8—C9—C10175.6 (2)
O5i—Yb1—N1—C5148.50 (17)C8—C9—C10—C9i1.39 (17)
O3i—Yb1—N1—C599.0 (2)Yb1—O5—C11—O6175.4 (2)
O3—Yb1—N1—C53.06 (18)Yb1—O5—C11—C84.2 (3)
N1i—Yb1—N1—C552.83 (18)N2—C8—C11—O6179.0 (2)
N2—Yb1—N1—C5127.17 (18)C9—C8—C11—O62.4 (4)
O1—Yb1—N2—C890.74 (13)N2—C8—C11—O50.6 (3)
O1i—Yb1—N2—C889.26 (13)C9—C8—C11—O5178.0 (2)
O5—Yb1—N2—C83.47 (13)C16—N3—C12—N4175.8 (3)
O5i—Yb1—N2—C8176.53 (13)C16—N3—C12—C132.6 (4)
O3i—Yb1—N2—C8139.43 (14)N4—C12—C13—C14177.0 (3)
O3—Yb1—N2—C840.57 (14)N3—C12—C13—C141.3 (4)
N1i—Yb1—N2—C8137.24 (14)C12—C13—C14—C150.1 (5)
N1—Yb1—N2—C842.76 (14)C13—C14—C15—C160.4 (5)
O1—Yb1—N2—C8i89.26 (13)C12—N3—C16—N5176.7 (3)
O1i—Yb1—N2—C8i90.74 (13)C12—N3—C16—C152.4 (4)
O5—Yb1—N2—C8i176.53 (13)C14—C15—C16—N5178.2 (3)
O5i—Yb1—N2—C8i3.47 (13)C14—C15—C16—N30.8 (4)
O3i—Yb1—N2—C8i40.57 (14)
Symmetry code: (i) x+3/2, y, z+1/2.
 

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