Literature DB >> 21201614

(2,4-Dioxo-1,2,3,4-tetra-hydro-pyrimi-dine-5-carboxyl-ato-κO,O)(4-oxido-2-oxo-1,2-dihydro-pyrimidine-5-carboxyl-ato-κO,O)bis-(1,10-phenanthroline-κN,N')yttrium(III) dihydrate.

Wei Xiong1, Huihui Xing, Yan Su, Zilu Chen.   

Abstract

In the title compound, [Y(C(5)H(2)N(2)O(4))(C(5)H(3)N(2)O(4))(C(12)H(8)N(2))(2)]·2H(2)O, the Y(III) ion lies on a twofold rotation axis and exhibits a distorted square-anti-prismatic coordination geometry. It is chelated by two 1,10-phenanthroline ligands, a 2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate mono-anion and a 4-oxido-2-oxo-1,2-dihydro-pyrimidine-5-carboxyl-ate dianion. The H atom involved in an N-H⋯N hydrogen bond between the 1,2-dihydro-pyrimidine units has half occupancy and is disordered around a twofold rotation axis.

Entities:  

Year:  2008        PMID： 21201614      PMCID： PMC2960551          DOI： 10.1107/S1600536808025701

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For the crystal structures of the isostructural Er, Eu, Tb and Yb complexes, see: Sun & Jin (2004 ▶); Xing et al. (2008 ▶). For other related literature, see: Tobiki et al. (1980 ▶); Castan et al. (1990 ▶).

Experimental

Crystal data

[Y(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2O M = 794.53 Monoclinic, a = 17.1740 (13) Å b = 14.4385 (11) Å c = 13.2365 (10) Å β = 100.881 (1)° V = 3223.2 (4) Å3 Z = 4 Mo Kα radiation μ = 1.89 mm−1 T = 295 (2) K 0.24 × 0.08 × 0.06 mm

Data collection

Bruker APEXII diffractometer Absorption correction: multi-scan (SADABS; Bruker, 1998 ▶) T min = 0.660, T max = 0.895 12035 measured reflections 3152 independent reflections 2986 reflections with I > 2σ(I) R int = 0.035

Refinement

R[F 2 > 2σ(F 2)] = 0.045 wR(F 2) = 0.096 S = 1.21 3152 reflections 240 parameters H-atom parameters constrained Δρmax = 0.41 e Å−3 Δρmin = −0.51 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808025701/gk2161sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808025701/gk2161Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
[Y(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2OF000 = 1616
Mr = 794.53Dx = 1.637 Mg m−3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 7855 reflections
a = 17.1740 (13) Åθ = 2.3–27.9º
b = 14.4385 (11) ŵ = 1.89 mm−1
c = 13.2365 (10) ÅT = 295 (2) K
β = 100.8810 (10)ºPrism, colourless
V = 3223.2 (4) Å30.24 × 0.08 × 0.06 mm
Z = 4
Bruker APEXII diffractometer3152 independent reflections
Radiation source: fine-focus sealed tube2986 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.035
T = 295(2) Kθmax = 26.0º
φ and ω scansθmin = 1.9º
Absorption correction: multi-scan(SADABS; Bruker, 1998)h = −21→21
Tmin = 0.660, Tmax = 0.895k = −17→17
12035 measured reflectionsl = −16→16
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.096  w = 1/[σ2(Fo2) + (0.0141P)2 + 9.88P] where P = (Fo2 + 2Fc2)/3
S = 1.21(Δ/σ)max < 0.001
3152 reflectionsΔρmax = 0.41 e Å−3
240 parametersΔρmin = −0.51 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
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.
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 > 2sigma(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.
xyzUiso*/UeqOcc. (<1)
Y11.00000.88802 (3)0.25000.02339 (12)
N10.90591 (16)0.75076 (19)0.2117 (2)0.0324 (6)
N20.96510 (16)0.80446 (19)0.4073 (2)0.0304 (6)
N30.83326 (16)1.02589 (19)−0.0065 (2)0.0297 (6)
H30.83790.9842−0.05140.036*
N40.78240 (19)1.1684 (2)0.0310 (2)0.0387 (7)
H40.75851.21990.01310.046*0.50
O10.90470 (14)0.93356 (15)0.11247 (17)0.0329 (6)
O20.93006 (14)0.99886 (16)0.31195 (17)0.0337 (6)
O30.84729 (15)1.10907 (17)0.34049 (17)0.0371 (6)
O40.76917 (16)1.11986 (18)−0.13684 (19)0.0451 (7)
C10.8770 (2)1.0594 (2)0.2805 (2)0.0272 (7)
C20.84980 (19)1.0723 (2)0.1678 (2)0.0269 (7)
C30.86584 (18)1.0066 (2)0.0941 (2)0.0248 (7)
C40.7937 (2)1.1063 (2)−0.0423 (3)0.0324 (7)
C50.8085 (2)1.1498 (2)0.1311 (3)0.0358 (8)
H50.79761.19280.17880.043*
C60.9900 (2)0.8317 (3)0.5036 (3)0.0386 (8)
H61.00890.89200.51480.046*
C70.9896 (3)0.7758 (3)0.5890 (3)0.0512 (11)
H71.00740.79820.65520.061*
C80.9624 (3)0.6872 (3)0.5735 (3)0.0599 (12)
H80.96260.64830.62960.072*
C90.9342 (2)0.6545 (3)0.4735 (3)0.0463 (10)
C100.9355 (2)0.7169 (2)0.3922 (3)0.0327 (8)
C110.9042 (2)0.6886 (2)0.2883 (3)0.0325 (8)
C120.8716 (2)0.5993 (2)0.2699 (3)0.0419 (9)
C130.8735 (3)0.5372 (3)0.3546 (4)0.0607 (13)
H130.85340.47760.34230.073*
C140.9036 (3)0.5634 (3)0.4513 (4)0.0618 (13)
H140.90450.52150.50480.074*
C150.8370 (2)0.5768 (3)0.1686 (4)0.0510 (11)
H150.81480.51850.15330.061*
C160.8357 (2)0.6401 (3)0.0926 (3)0.0490 (10)
H160.81190.62620.02520.059*
C170.8707 (2)0.7264 (3)0.1173 (3)0.0397 (9)
H170.86930.76930.06470.048*
O50.6925 (3)0.1887 (2)0.6600 (3)0.0956 (14)
H510.67930.24540.66440.143*
H520.70820.16810.72080.143*
U11U22U33U12U13U23
Y10.0287 (2)0.0187 (2)0.0207 (2)0.000−0.00062 (16)0.000
N10.0322 (16)0.0288 (15)0.0352 (16)−0.0037 (12)0.0040 (12)−0.0035 (12)
N20.0318 (15)0.0294 (15)0.0297 (15)−0.0002 (12)0.0051 (12)0.0008 (12)
N30.0389 (16)0.0276 (15)0.0204 (13)0.0051 (12)0.0001 (12)−0.0021 (11)
N40.057 (2)0.0273 (15)0.0278 (15)0.0107 (14)−0.0016 (14)0.0018 (12)
O10.0421 (14)0.0265 (12)0.0255 (12)0.0100 (10)−0.0052 (10)−0.0034 (9)
O20.0441 (14)0.0324 (13)0.0226 (12)0.0133 (11)0.0011 (10)0.0006 (10)
O30.0510 (15)0.0374 (14)0.0227 (12)0.0125 (12)0.0064 (11)−0.0021 (10)
O40.0562 (17)0.0369 (15)0.0358 (14)0.0044 (13)−0.0074 (12)0.0002 (12)
C10.0345 (18)0.0240 (16)0.0224 (16)−0.0025 (14)0.0032 (13)0.0017 (13)
C20.0328 (17)0.0263 (16)0.0207 (16)0.0053 (14)0.0031 (13)0.0002 (13)
C30.0284 (16)0.0237 (16)0.0209 (15)−0.0008 (13)0.0014 (13)0.0007 (12)
C40.0373 (19)0.0291 (18)0.0280 (17)−0.0006 (15)−0.0012 (14)0.0021 (14)
C50.050 (2)0.0292 (18)0.0263 (18)0.0094 (16)0.0031 (16)−0.0026 (14)
C60.039 (2)0.042 (2)0.0339 (19)−0.0026 (17)0.0042 (16)−0.0029 (16)
C70.056 (3)0.070 (3)0.028 (2)−0.010 (2)0.0082 (18)0.0061 (19)
C80.066 (3)0.069 (3)0.044 (2)−0.008 (2)0.009 (2)0.024 (2)
C90.048 (2)0.043 (2)0.048 (2)−0.0034 (19)0.0101 (19)0.0158 (19)
C100.0306 (18)0.0296 (18)0.0384 (19)−0.0007 (14)0.0078 (15)0.0034 (15)
C110.0311 (18)0.0269 (17)0.0399 (19)−0.0005 (14)0.0072 (15)−0.0017 (15)
C120.042 (2)0.0279 (19)0.058 (2)−0.0074 (16)0.0137 (19)−0.0027 (17)
C130.074 (3)0.030 (2)0.080 (3)−0.018 (2)0.017 (3)0.004 (2)
C140.076 (3)0.042 (3)0.068 (3)−0.017 (2)0.016 (3)0.021 (2)
C150.051 (2)0.035 (2)0.069 (3)−0.0161 (19)0.016 (2)−0.018 (2)
C160.047 (2)0.050 (2)0.049 (2)−0.0137 (19)0.0063 (19)−0.022 (2)
C170.039 (2)0.039 (2)0.040 (2)−0.0064 (17)0.0052 (16)−0.0062 (16)
O50.145 (4)0.059 (2)0.067 (2)0.004 (2)−0.017 (2)−0.0089 (19)
Y1—O2i2.247 (2)C2—C31.423 (4)
Y1—O22.247 (2)C5—H50.9300
Y1—O1i2.302 (2)C6—C71.391 (5)
Y1—O12.302 (2)C6—H60.9300
Y1—N12.547 (3)C7—C81.362 (6)
Y1—N1i2.547 (3)C7—H70.9300
Y1—N2i2.573 (3)C8—C91.403 (6)
Y1—N22.573 (3)C8—H80.9300
N1—C171.329 (4)C9—C101.407 (5)
N1—C111.358 (4)C9—C141.426 (6)
N2—C61.326 (4)C10—C111.439 (5)
N2—C101.363 (4)C11—C121.408 (5)
N3—C31.373 (4)C12—C151.399 (6)
N3—C41.383 (4)C12—C131.431 (6)
N3—H30.8600C13—C141.342 (6)
N4—C51.343 (4)C13—H130.9300
N4—C41.362 (4)C14—H140.9300
N4—H40.8600C15—C161.355 (6)
O1—C31.247 (4)C15—H150.9300
O2—C11.275 (4)C16—C171.395 (5)
O3—C11.248 (4)C16—H160.9300
O4—C41.258 (4)C17—H170.9300
C1—C21.489 (4)O5—H510.8533
C2—C51.364 (4)O5—H520.8518
O2i—Y1—O289.15 (13)C3—C2—C1122.6 (3)
O2i—Y1—O1i74.69 (8)O1—C3—N3117.7 (3)
O2—Y1—O1i81.79 (9)O1—C3—C2126.6 (3)
O2i—Y1—O181.79 (8)N3—C3—C2115.7 (3)
O2—Y1—O174.69 (8)O4—C4—N4122.7 (3)
O1i—Y1—O1146.81 (11)O4—C4—N3121.5 (3)
O2i—Y1—N1147.62 (8)N4—C4—N3115.8 (3)
O2—Y1—N1105.31 (9)N4—C5—C2124.8 (3)
O1i—Y1—N1135.17 (8)N4—C5—H5117.6
O1—Y1—N174.65 (9)C2—C5—H5117.6
O2i—Y1—N1i105.31 (9)N2—C6—C7124.0 (4)
O2—Y1—N1i147.62 (8)N2—C6—H6118.0
O1i—Y1—N1i74.65 (9)C7—C6—H6118.0
O1—Y1—N1i135.17 (8)C8—C7—C6118.5 (4)
N1—Y1—N1i77.82 (13)C8—C7—H7120.7
O2i—Y1—N2i79.43 (8)C6—C7—H7120.7
O2—Y1—N2i148.38 (8)C7—C8—C9120.4 (4)
O1i—Y1—N2i122.30 (9)C7—C8—H8119.8
O1—Y1—N2i74.55 (8)C9—C8—H8119.8
N1—Y1—N2i73.15 (9)C8—C9—C10117.0 (4)
N1i—Y1—N2i63.90 (9)C8—C9—C14123.6 (4)
O2i—Y1—N2148.38 (8)C10—C9—C14119.4 (4)
O2—Y1—N279.43 (9)N2—C10—C9122.8 (3)
O1i—Y1—N274.55 (8)N2—C10—C11117.7 (3)
O1—Y1—N2122.30 (9)C9—C10—C11119.5 (3)
N1—Y1—N263.90 (9)N1—C11—C12122.7 (3)
N1i—Y1—N273.15 (9)N1—C11—C10118.0 (3)
N2i—Y1—N2124.07 (12)C12—C11—C10119.3 (3)
C17—N1—C11117.1 (3)C15—C12—C11117.5 (4)
C17—N1—Y1123.5 (2)C15—C12—C13123.2 (4)
C11—N1—Y1117.9 (2)C11—C12—C13119.3 (4)
C6—N2—C10117.4 (3)C14—C13—C12121.2 (4)
C6—N2—Y1123.8 (2)C14—C13—H13119.4
C10—N2—Y1117.0 (2)C12—C13—H13119.4
C3—N3—C4125.9 (3)C13—C14—C9121.2 (4)
C3—N3—H3117.0C13—C14—H14119.4
C4—N3—H3117.0C9—C14—H14119.4
C5—N4—C4120.3 (3)C16—C15—C12119.9 (4)
C5—N4—H4119.9C16—C15—H15120.0
C4—N4—H4119.9C12—C15—H15120.0
C3—O1—Y1132.1 (2)C15—C16—C17118.8 (4)
C1—O2—Y1140.2 (2)C15—C16—H16120.6
O3—C1—O2122.6 (3)C17—C16—H16120.6
O3—C1—C2118.5 (3)N1—C17—C16123.9 (4)
O2—C1—C2118.8 (3)N1—C17—H17118.1
C5—C2—C3117.2 (3)C16—C17—H17118.1
C5—C2—C1120.2 (3)H51—O5—H52108.2
O2i—Y1—N1—C17−8.9 (4)C4—N3—C3—O1−174.8 (3)
O2—Y1—N1—C17104.9 (3)C4—N3—C3—C26.6 (5)
O1i—Y1—N1—C17−161.4 (3)C5—C2—C3—O1177.5 (3)
O1—Y1—N1—C1735.9 (3)C1—C2—C3—O1−1.8 (5)
N1i—Y1—N1—C17−108.3 (3)C5—C2—C3—N3−4.0 (5)
N2i—Y1—N1—C17−42.2 (3)C1—C2—C3—N3176.7 (3)
N2—Y1—N1—C17174.6 (3)C5—N4—C4—O4178.8 (4)
O2i—Y1—N1—C11157.1 (2)C5—N4—C4—N3−0.5 (5)
O2—Y1—N1—C11−89.1 (2)C3—N3—C4—O4176.4 (3)
O1i—Y1—N1—C114.6 (3)C3—N3—C4—N4−4.3 (5)
O1—Y1—N1—C11−158.1 (3)C4—N4—C5—C22.7 (6)
N1i—Y1—N1—C1157.7 (2)C3—C2—C5—N4−0.3 (6)
N2i—Y1—N1—C11123.8 (3)C1—C2—C5—N4179.0 (3)
N2—Y1—N1—C11−19.3 (2)C10—N2—C6—C71.8 (5)
O2i—Y1—N2—C67.0 (4)Y1—N2—C6—C7−162.4 (3)
O2—Y1—N2—C6−63.6 (3)N2—C6—C7—C80.4 (6)
O1i—Y1—N2—C620.7 (3)C6—C7—C8—C9−1.3 (7)
O1—Y1—N2—C6−127.8 (3)C7—C8—C9—C100.0 (7)
N1—Y1—N2—C6−176.6 (3)C7—C8—C9—C14−178.8 (5)
N1i—Y1—N2—C699.0 (3)C6—N2—C10—C9−3.2 (5)
N2i—Y1—N2—C6139.5 (3)Y1—N2—C10—C9162.2 (3)
O2i—Y1—N2—C10−157.3 (2)C6—N2—C10—C11176.5 (3)
O2—Y1—N2—C10132.1 (2)Y1—N2—C10—C11−18.1 (4)
O1i—Y1—N2—C10−143.6 (2)C8—C9—C10—N22.3 (6)
O1—Y1—N2—C1067.9 (2)C14—C9—C10—N2−178.8 (4)
N1—Y1—N2—C1019.1 (2)C8—C9—C10—C11−177.4 (4)
N1i—Y1—N2—C10−65.3 (2)C14—C9—C10—C111.5 (6)
N2i—Y1—N2—C10−24.8 (2)C17—N1—C11—C124.1 (5)
O2i—Y1—O1—C3−68.1 (3)Y1—N1—C11—C12−162.8 (3)
O2—Y1—O1—C323.3 (3)C17—N1—C11—C10−174.4 (3)
O1i—Y1—O1—C3−23.2 (3)Y1—N1—C11—C1018.7 (4)
N1—Y1—O1—C3134.3 (3)N2—C10—C11—N1−0.2 (5)
N1i—Y1—O1—C3−171.6 (3)C9—C10—C11—N1179.6 (3)
N2i—Y1—O1—C3−149.3 (3)N2—C10—C11—C12−178.7 (3)
N2—Y1—O1—C389.8 (3)C9—C10—C11—C121.1 (5)
O2i—Y1—O2—C172.0 (3)N1—C11—C12—C15−2.7 (6)
O1i—Y1—O2—C1146.7 (4)C10—C11—C12—C15175.7 (3)
O1—Y1—O2—C1−9.7 (3)N1—C11—C12—C13178.8 (4)
N1—Y1—O2—C1−78.6 (3)C10—C11—C12—C13−2.8 (6)
N1i—Y1—O2—C1−170.0 (3)C15—C12—C13—C14−176.4 (5)
N2i—Y1—O2—C14.0 (4)C11—C12—C13—C142.0 (7)
N2—Y1—O2—C1−137.6 (4)C12—C13—C14—C90.6 (8)
Y1—O2—C1—O3176.0 (2)C8—C9—C14—C13176.5 (5)
Y1—O2—C1—C2−4.6 (5)C10—C9—C14—C13−2.3 (7)
O3—C1—C2—C515.4 (5)C11—C12—C15—C16−0.1 (6)
O2—C1—C2—C5−164.0 (3)C13—C12—C15—C16178.4 (4)
O3—C1—C2—C3−165.3 (3)C12—C15—C16—C171.3 (6)
O2—C1—C2—C315.2 (5)C11—N1—C17—C16−2.8 (5)
Y1—O1—C3—N3158.7 (2)Y1—N1—C17—C16163.3 (3)
Y1—O1—C3—C2−22.8 (5)C15—C16—C17—N10.2 (6)
D—H···AD—HH···AD···AD—H···A
N3—H3···O3ii0.861.992.853 (4)178
N3—H3···O2ii0.862.633.189 (4)124
N4—H4···N4iii0.861.812.667 (6)174
O5—H51···O3iv0.852.152.998 (4)173
O5—H52···O4v0.852.102.935 (4)169
Y1—O22.247 (2)
Y1—O12.302 (2)
Y1—N12.547 (3)
Y1—N22.573 (3)
O2i—Y1—O289.15 (13)
O2—Y1—O1i81.79 (9)
O2—Y1—O174.69 (8)
O1i—Y1—O1146.81 (11)
O2i—Y1—N1147.62 (8)
O2—Y1—N1105.31 (9)
O1i—Y1—N1135.17 (8)
O1—Y1—N174.65 (9)
N1—Y1—N1i77.82 (13)
O2—Y1—N2i148.38 (8)
O1—Y1—N2i74.55 (8)
N1—Y1—N2i73.15 (9)
O2—Y1—N279.43 (9)
O1—Y1—N2122.30 (9)
N1—Y1—N263.90 (9)
N2i—Y1—N2124.07 (12)

Symmetry code: (i) .

Table 2

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N1—H1⋯O2ii0.862.042.898 (3)178
N1—H1⋯O1ii0.862.603.160 (4)124
N2—H2⋯N2iii0.861.812.669 (5)174
O5—H5A⋯O4iv0.852.142.970 (4)164
O5—H5B⋯O2v0.852.142.985 (4)173

Symmetry codes: (ii) ; (iii) ; (iv) ; (v) .

  4 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  [Studies on beta-lactam antibiotics. III. Synthesis of 6-[D(--)-alpha-(acylamino)-phenylacetamido]penicillanic acids and antibacterial activity (author's transl)].

Authors:  H Tobiki; H Yamada; I Nakatsuka; K Shimago; Y Eda; H Noguchi; T Komatsu; T Nakagome
Journal:  Yakugaku Zasshi       Date:  1980-01       Impact factor: 0.302

3.  (6-Oxido-2-oxo-1,2-dihydropyrimidine-5-carboxylato-κO,O)(4-oxido-2-oxo-1,2-dihydropyrimidin-3-ium-5-carboxyl-ato-κO,O)bis(1,10-phenanthroline-κN,N')erbium(III) dihydrate.

Authors:  Hui-Hui Xing; Zi-Lu Chen; Seik Weng Ng
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-01-25

4.  Platinum and palladium complexes of 3-methyl orotic acid: a route toward palladium complexes with good antitumor activity.

Authors:  P Castan; E Colacio-Rodriguez; A L Beauchamp; S Cros; S Wimmer
Journal:  J Inorg Biochem       Date:  1990-03       Impact factor: 4.155
  4 in total
  1 in total

1.  Bis[4-oxido-2-oxo-2,3-di-hydro-pyrimidin-1-ium-5-carboxyl-ato(1.5-)-κO,O]bis-(1,10-phenanthroline-κN,N')dysprosium(III) dihydrate.

Authors:  Xianlin Liu; Huihui Xing; Jing Miao; Maomao Jia; Zilu Chen
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-09-19
  1 in total

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