Home Physical Sciences Crystal structure of poly[hexaqua-pentakis(μ4-2,2′-bipyridine-4,4′-dicarboxylato-κ4 O:O′:O″:O‴)-(μ2-2,2′-bipyridine-4,4′-dicarboxylato-κ2 O:O)tetraytterbium(III)] hydrate, C36H26N6O16Yb2
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Crystal structure of poly[hexaqua-pentakis(μ4-2,2′-bipyridine-4,4′-dicarboxylato-κ4 O:O′:O″:O‴)-(μ2-2,2′-bipyridine-4,4′-dicarboxylato-κ2 O:O)tetraytterbium(III)] hydrate, C36H26N6O16Yb2

  • Zheng Cheng , Xiao-Yu Zhang ORCID logo EMAIL logo , Xu Liu and Xiao-rui Yang
Published/Copyright: October 31, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 1

Abstract

C36H26N6O16Yb2, triclinic, P 1 ‾ (no. 2), a = 11.3387(3) Å, b = 12.1820(4) Å, c = 14.1433(4) Å, α = 95.090(2)°, β = 103.517(3)°, γ = 101.762(2)°, V = 1840.41(10) Å3, Z = 2, Rgt (F) = 0.0282, wRref (F 2) = 0.0576, T = 150 K.

CCDC no.: 2366863

A part of the molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.20 × 0.19 × 0.18 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 5.14 mm−1
Diffractometer, scan mode: SuperNova, ω
θ max, completeness: 28.4°, >99 %
N(hkl)measured, N(hkl)unique, R int: 26,819, 7,969, 0.043
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 6,913
N(param)refined: 547
Programs: CrysAlisPRO, 1 Olex2, 2 SHELX 34
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
Yb1 0.39387 (2) 0.83407 (2) 0.36524 (2) 0.01324 (5)
Yb2 −0.20611 (2) 0.36514 (2) 0.88971 (2) 0.01646 (5)
O1 −0.3433 (3) 0.3780 (2) 0.7482 (2) 0.0297 (7)
O2 −0.3998 (3) 0.3477 (2) 0.5874 (2) 0.0280 (7)
O3 −0.3981 (3) 0.3573 (3) 0.9160 (2) 0.0500 (10)
H3A −0.407438 0.360905 0.974050 0.075*
H3B −0.460853 0.307063 0.882111 0.075*
O4 0.4402 (2) 0.8629 (2) 0.52661 (19) 0.0212 (6)
O5 −0.1004 (3) 0.3635 (3) 0.7723 (2) 0.0306 (7)
O6 −0.1967 (2) 0.2439 (2) 0.6343 (2) 0.0217 (6)
O7 0.5991 (3) 0.7861 (4) 0.2037 (3) 0.0704 (14)
O8 0.2921 (2) 0.9808 (2) 0.3956 (2) 0.0222 (6)
H8A 0.213803 0.956274 0.372306 0.033*
H8B 0.305293 1.046184 0.382026 0.033*
O9 −0.1422 (3) 0.5525 (2) 0.8976 (2) 0.0289 (7)
O10 −0.2969 (2) 1.1659 (2) 0.80136 (19) 0.0201 (6)
O11 −0.2384 (3) 1.1979 (2) 0.9623 (2) 0.0314 (7)
O12 0.5827 (2) 0.8078 (2) 0.3563 (2) 0.0259 (7)
O13 −0.1737 (3) 0.4302 (3) 1.0591 (2) 0.0321 (7)
H13A −0.125488 0.491814 1.090910 0.048*
H13B −0.200348 0.395944 1.102569 0.048*
O14 0.4892 (2) 0.9989 (2) 0.6544 (2) 0.0217 (6)
O16 −0.0015 (2) 0.6250 (2) 1.0399 (2) 0.0238 (7)
N1 1.0404 (3) 0.9518 (3) 0.3897 (2) 0.0215 (8)
N2 −0.3752 (4) 0.7737 (3) 0.8986 (3) 0.0327 (9)
N3 −0.0002 (4) 0.9642 (3) 0.8731 (3) 0.0337 (9)
N4 −0.3424 (3) 0.7689 (3) 0.6514 (2) 0.0224 (8)
N5 0.2319 (3) 0.6854 (3) 0.7716 (3) 0.0345 (10)
N6 0.1716 (3) 0.4843 (3) 0.5539 (3) 0.0316 (9)
C1 −0.2823 (4) 1.1295 (3) 0.8844 (3) 0.0201 (9)
C2 −0.0168 (5) 0.8719 (4) 0.8087 (4) 0.0412 (13)
H2 −0.011184 0.881718 0.743844 0.049*
C3 0.8388 (4) 0.9229 (4) 0.4214 (3) 0.0250 (10)
H3 0.788922 0.933519 0.465330 0.030*
C4 −0.3690 (3) 0.4139 (3) 0.6663 (3) 0.0197 (9)
C5 −0.3486 (4) 0.6952 (4) 0.5742 (3) 0.0247 (10)
H5 −0.345743 0.723275 0.514028 0.030*
C6 −0.1112 (3) 0.3245 (3) 0.6851 (3) 0.0184 (9)
C7 −0.3589 (4) 0.5803 (3) 0.5756 (3) 0.0228 (9)
H7 −0.362887 0.531481 0.518112 0.027*
C8 0.4348 (3) 0.9008 (3) 0.6105 (3) 0.0148 (8)
C9 −0.3451 (4) 0.8125 (3) 0.8192 (3) 0.0211 (9)
C10 −0.0644 (4) 0.6331 (3) 0.9560 (3) 0.0209 (9)
C11 −0.3499 (4) 0.7266 (3) 0.7352 (3) 0.0201 (9)
C12 −0.0464 (4) 0.7471 (3) 0.9246 (3) 0.0213 (9)
C13 0.9671 (4) 0.9676 (3) 0.4507 (3) 0.0214 (9)
C14 −0.0120 (3) 0.3773 (3) 0.6378 (3) 0.0171 (9)
C15 0.3568 (4) 0.8646 (4) 0.7585 (3) 0.0312 (11)
H15 0.396871 0.940439 0.787395 0.037*
C16 −0.3632 (3) 0.5380 (3) 0.6629 (3) 0.0184 (9)
C17 0.0952 (4) 0.3833 (4) 0.5130 (3) 0.0341 (12)
H17 0.106008 0.347787 0.454043 0.041*
C18 −0.3146 (4) 1.0059 (3) 0.8899 (3) 0.0220 (9)
C19 0.0019 (4) 0.3277 (4) 0.5512 (3) 0.0243 (10)
H19 −0.051118 0.257218 0.518428 0.029*
C20 −0.0415 (4) 0.7635 (4) 0.8310 (3) 0.0313 (11)
H20 −0.055159 0.700516 0.781866 0.038*
C21 0.2925 (5) 0.7922 (4) 0.8090 (4) 0.0445 (14)
H21 0.291247 0.819810 0.873665 0.053*
C22 0.6434 (4) 0.8145 (4) 0.2926 (3) 0.0298 (11)
C23 −0.0086 (4) 0.9477 (3) 0.9647 (3) 0.0232 (10)
C24 0.3621 (3) 0.8248 (3) 0.6651 (3) 0.0198 (9)
C25 0.1550 (4) 0.5325 (3) 0.6371 (3) 0.0238 (10)
C26 0.2997 (3) 0.7140 (3) 0.6249 (3) 0.0196 (9)
H26 0.302121 0.683691 0.561295 0.024*
C27 0.0657 (4) 0.4815 (3) 0.6815 (3) 0.0222 (9)
H27 0.057700 0.517563 0.741300 0.027*
C28 −0.0294 (4) 0.8422 (3) 0.9930 (3) 0.0257 (10)
H28 −0.032131 0.834101 1.058708 0.031*
C29 0.8589 (4) 0.8491 (4) 0.2653 (3) 0.0269 (10)
H29 0.824196 0.809806 0.200431 0.032*
C30 −0.3593 (3) 0.6132 (3) 0.7434 (3) 0.0214 (9)
H30 −0.363202 0.586950 0.804156 0.026*
C31 0.9860 (4) 0.8942 (4) 0.3004 (3) 0.0244 (10)
H31 1.037667 0.883407 0.257989 0.029*
C32 −0.3136 (4) 0.9278 (3) 0.8138 (3) 0.0211 (9)
H32 −0.291314 0.952754 0.757207 0.025*
C33 −0.3721 (5) 0.8510 (4) 0.9732 (3) 0.0432 (13)
H33 −0.391467 0.824542 1.030194 0.052*
C34 0.7838 (4) 0.8632 (4) 0.3285 (3) 0.0236 (10)
C35 −0.3431 (5) 0.9651 (4) 0.9726 (3) 0.0380 (12)
H35 −0.342295 1.016006 1.027856 0.046*
C36 0.2339 (4) 0.6487 (4) 0.6796 (3) 0.0242 (10)
O15 −0.4598 (5) 0.4209 (4) 1.0785 (4) 0.0941 (17)
H15A −0.510080 0.370121 1.096450 0.141*
H15B −0.495080 0.476151 1.074100 0.141*

1 Source of materials

A mixture of Yb(NO3)3·5H2O (0.0452 g, 0.1 mmol) and 2,2′-bipyridine-4,4′-dicarboxylic acid (0.0366 g, 0.15 mmol) was dissolved in 8 mL of deionized water. The mixture was sealed in a 25 mL Teflon-lined steel autoclave after ultrasound treatment for 15 min and heated at 140 °C for 72 h. The mixture was cooled to room temperature at a rate of 3 °C/h, and colorless block crystals were isolated by filtration, washed with distilled water and dried in air.

2 Experimental details

CrysAlisPro 1.171.39.46 (Rigaku Oxford Diffraction, 2018). 1 Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Using Olex2, 2 the structure was solved with the ShelXT 3 structure solution program and refined with the ShelXL 4 refinement package.

The carbon bound hydrogen atoms were placed in calculated positions and refined using a riding model on attached atoms.

3 Comment

In recent years, ytterbium(III) metal-organic frameworks (Yb–MOFs) have attracted considerable attentions due to their structural diversity and potential applications in various fields such as adsorption, catalysis, detection, degradation, etc. 5 , 6 , 7 , 8 . Nitrogen-containing carboxylic acids are widely used as ligands in the synthesis of Yb–MOFs. 5 , 8 , 9 Among these ligands, 2,2′-bipyridine-4,4′-dicarboxylic acid (H2BPDC) has garnered considerable interest due to its potential as a bridging ligand and abundant coordination modes. 10 In this study, a new Yb–MOF was constructed using H2BPDC as ligand and water as solvent.

The asymmetric unit contains two Yb(III) ions, three deprotonated BPDC2− ligands (with two different coordination modes), three coordinated water molecules, and one lattice water (see figure). Yb1 and Yb2 are both 8-coordinated. Yb1 coordinates with six oxygen atoms from five deprotonated BPDC2− ligands (O1; O5; O9; O10D, O11D; O16E; D: x, −1 + y, z; E: −x, 1 − y, 2 − z), and two oxygen atoms from coordinated water molecules (O3, O13). Yb2 coordinates with seven oxygen atoms from six deprotonated BPDC2− ligands (O1A, O2A; O4; O6A; O10B; O12; O14C; A: −x, 1 − y, 1 − z; B: −x, 2 − y, 1 − z; C: 1 − x, 2 − y, 1 − z), and one oxygen atom from a water molecule (O8). The bond distances of Yb–O range from 2.198(3) to 2.795(3) Å, which are in agreement with distances found in similar Yb compound. 8 , 9 Yb1 and Yb2 are linked by a bridging BPDC2− ligand, and the title compound was connected into a three-dimensional MOF structure through alternating bridging ligands and Yb(III) centers. 11 The crystal structure of the title compound is further stablized by multiple hydrogen bonds.

Corresponding author: Xiao-Yu Zhang, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471022, P.R. China, E-mail:

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by the National Natural Science Foundation of China (No. 22371110), the Program for Science & Technology Innovation Research Team in Universities of Henan Province, China (No. 21IRTSTHN004).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2024-07-01
Accepted: 2024-10-18
Published Online: 2024-10-31
Published in Print: 2025-02-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/ncrs-2024-0278
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  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of the co-crystal 2,4,6-triamino-1,3,5-triazine-1,3-dioxide — acetic acid (1/2) C7H14N6O6
  4. Crystal structure of the dinuclear mercury(II) complex bis(μ2-bromido)-dibromido-bis{1-[(benzotriazol-1-yl)methyl]-1-H-1,3-(2-ethyl-5-methyl-imidazol)-κ1 N} dimercury(II), C26H30N10Hg2Br4
  5. Crystal structure of poly[hexaqua-pentakis(μ4-2,2′-bipyridine-4,4′-dicarboxylato-κ4 O:O′:O″:O‴)-(μ2-2,2′-bipyridine-4,4′-dicarboxylato-κ2 O:O)tetraytterbium(III)] hydrate, C36H26N6O16Yb2
  6. Hydrothermal synthesis and crystal structure of catena-poly[(1,10-phenanthroline-κ 2 N,N′)-bis(μ 2-nitroisophthalato-κ 3 O,O′:O″)nickel(II)], C20H13NiN3O7
  7. Crystal structure of 72,73,75,76-tetrafluoro-25,44-dimethyl-31,33,36,38-tetraoxo-31,32,33,36,37,38-hexahydro-3(2,7)-benzo[lmn][3,8]phenanthrolina-1,5(4,1)-dipyridin-1-iuma-2,4(1,2),7(1,4)-tribenzenacyclooctaphane-11,51-diium hexafluoridophosphate, [C46H28F4N4O4][PF6]2, a dicationic cyclophane
  8. Crystal structure of (E)-2-(4-(1H-imidazol-1-yl)benzylidene)-7-fluoro-3,4-dihydronaphthalen-1(2H)-one, C20H15FN2O
  9. The salt crystal structure of etoricoxib hydrochloride, C18H16Cl2N2O2S
  10. The structure of t-butyl 7-[2-(4-fluorophenyl)-3-phenyl-4-(phenylcarbamoyl)-5-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoate, C37H43FN2O5
  11. The crystal structure of (μ4-oxo)-tri(μ4-2,2′-bipyridine-6,6′-bis(olato)-κ5 O,O′:N:N′:O″)tetrazinc(II) – methylformamide (1/1), C33H25N7O8Zn4
  12. The co-crystal structure of 4-chlorobenzophenone–salicylhydrazide(1/1), C20H17ClN2O3
  13. Crystal structure of 9-fluoro-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O
  14. The crystal structure of the co-crystal composed of benzhydrazide and 5-aminoisophthalic acid, C8H7NO4⋅C7H8N2O
  15. The cocrystal structure of praziquantel-hesperetin (1/1), C35H38N2O8
  16. Crystal structure of new barium manganese fluorides dihydrates, Ba10Mn2F25·2H2O
  17. The crystal structure of bis[μ2-(3-(3-(pyridin-2-yl)-1H-pyrazol-1-yl)propanoate-κ2O:N)-bis(2,2′-bipyridine-κ2 N, N′)dicopper(II)]dinitrate, C42H36Cu2N12O10
  18. Crystal structure of (3,6-di(2-pyridyl)-4-phenylaminopyridazine-κ2N,N′)-bis(2-(p-toluene)pyridinyl-κ2C,N)-iridium(III) hexafluorophosphate –dichloromethane (1/1), C45H37Cl2F6IrN7P
  19. The crystal structure of 2-(2′-carboxybenzyl)benzoic acid, C15H12O5
  20. The crystal structure of dichlorido-[(E)-N′,N″-bis((2E,3E)-3-(hydroxyimino)butan-2-ylidene)-2-((E)-3-(hydroxyimino)butan-2-ylidene)hydrazine-1-carbohydrazonhydrazide-κ 4 N 4]cobalt(II), C13H22N9O3Cl2Co
  21. Crystal structure of (−)-flavesine H, C15H22N2O2
  22. Crystal structure of 3-methoxybenzyl 2-(6-methoxynaphthalen-2-yl)propanoate, C22H22O4
  23. Crystal structure of dicarbonyl(2-oxopyridin-1(2H)-olato-κ 2 O,O)iridium(I), C7H4IrNO4
  24. The crystal structure of 4-(3-(triphenylphosphonio)propyl)piperazin-1-ium dibromide trihydrate, C25H37Br2N2O3P
  25. The crystal structure of ethyl 5,6-dihydroxybenzofuran-3-carboxylate, C11H10O5
  26. Crystal structure of 14-(R)-(2′-cyano-phenoxy)-3,19-diacetyl andrographolide, C31H37NO7
  27. The twinned crystal structure of 10-(4-methyl benzoate)-2,8-diethyl-5,5-difluoro-1,3,7,9-tetramethyl-5H-di-pyrrolo[1,2-c:2′,1′-f] [1,3,2]diazaborinin-4-ium-5-uide, C25H29BF2N2O2
  28. The crystal structure of (9H-thioxanthen-9- ylidene)hydrazine monohydrate, C13H11N2SO0.5
  29. The crystal structure of pyridinium diaqua-{1,2-phenylenebis((carboxylatocarbonyl)amido-κ4 N,N′,O,O′)manganese(III), C15H14MnN3O8
  30. Crystal structure of the hydrogen storage active high entropy phase Tb0.82Sm0.18Ni0.83Co0.17Mg
  31. Crystal structure of diaqua-bis[5-methyl-1-(1H-pyrazol-3-yl)-1H-1,2,3-triazole-4-carboxylato-κ 2 N,O)]manganese(II), C14H16MnN10O6
  32. Crystal structures of diiodido-3-((pyridin-2-ylmethylene)amino)-2-(pyridin-3-yl)-2,3-dihydroquinazolin-4(1H)-one-cadmium(II)
  33. Synthesis and crystal structure of methyl 4-(2-ethoxy-2-oxoethoxy)-3,5-dimethoxybenzoate, C14H18O7
  34. Crystal structure of isoxazolo[4,5-b]pyridin-3-amine, C6H5N3O
  35. Crystal structure of 4-chloro-1-isobutyl-1H-imidazo, C14H14ClN3
  36. The crystal structure of 1,1,1,2,2,2-hexakis(2-methyl-2-phenylpropyl)distannane,C60H78Sn2
  37. The crystal structure of (2,7-dimethoxynaphthalene-1,8-diyl)bis((3-nitrophenyl)methanone), C26H18N2O8
  38. Crystal structure of diaqua-tetra((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ 1 N)zinc(II) dinitrate dihydrate, C60H76Cl8N14O14Zn
  39. The crystal structure of diphenyl bis(2-((diphenoxyphosphoryl)amino)ethyl)phosphoramidate monohydrate C40H42N3O10P3
  40. Crystal structure of 4,4′-bis(dibromomethyl)-1,1′-biphenyl, C14H10Br4
  41. Crystal structure of CaPtZn
  42. Crystal structure of 3-chloro-5-(trifluoromethyl)pyridine-2-carboxylic acid, C7H3ClF3NO2
  43. The crystal structure of (3′-(2-bromophenyl)-2-phenyl-[2,2′-bioxiran]-3-yl)(phenyl)methanone, C92H68O12Br4
  44. Crystal structure of ethyl 4-(4-benzylpiperazin-1-yl)benzoate, C20H24N2O2
  45. The crystal structure of bis(selenocyanato-κ1 N)-bis(methanol)-bis((1E,2E)-1,2-bis (1-(pyridin-4-yl)ethylidene)-hydrazine)iron(II) methanol solvate, C34H44FeN10O4Se2
  46. Crystal structure of (E)-1-(5-bromo-2-hydroxyphenyl)-3-(5-(4-methoxyphenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl)prop-2-en-1-one, C26H21BrN2O4
  47. The crystal structure of methyl 4-(4-(methylsulfonyl)phenyl)-2-methyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C19H21NO5S
  48. Crystal structure of 1′,3′-dihydro-2,2′-spirobi[indene]-1,3-dione, C17H12O2
  49. Crystal structure of (E)-2,2′,3,3′-tetrahydro-[1,1′-biindenylidene]-4,4′-diol, C18H16O2
  50. Crystal structure of di-glycylglycinium squarate dihydrate, C12H22N4O12, at 105 K
  51. Crystal structure of {[(4-fluorophenyl)methyl]triphenylphosphonium}dibromocopper(I), [C25H21FP]+[CuBr2]−
  52. Crystal structure of poly[diaqua-bis(μ2-5-((pyridin-4-yl-methyl)amino)benzene-1,3-dicarboxylato-κ 2 N:O)cadmium(II)], C28H26CdN4O10
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