Poly[guanidinium [tri-μ-formato-κ6 O:O′-formato-κ2 O,O′-yttrium(III)]]

Mark A Rodriguez; Dorina F Sava Gallis; Tina M Nenoff

doi:10.1107/S1600536814013440

. 2014 Jun 14;70(Pt 7):m261–m262. doi: 10.1107/S1600536814013440

Poly[guanidinium [tri-μ-formato-κ⁶ O:O′-formato-κ² O,O′-yttrium(III)]]

Mark A Rodriguez ^a,^*, Dorina F Sava Gallis ^a, Tina M Nenoff ^a

PMCID: PMC4120533 PMID: 25161525

Abstract

In the title coordination polymer, {(CH₆N₃)[Y(CHO₂)₄]}_n, the yttrium(III) ion is coordinated by one O,O-bidentate formate ion and six μ₂ bridging formate ions, generating a square-antiprismatic YO₈ coordination polyhedron. The bridging formate ions connect the metal ions into an anionic, three-dimensional network. Charge compensation is provided by guanidinium ions, which interact with the framework by way of N—H⋯O hydrogen bonds. The guanidine molecules reside in porous channels of 3.612 by 8.189 Å, when considering the van der Waals radii of the nearest atoms (looking down the a-axis).

Related literature

Liu et al. (2011 ▶) have published the erbium (Er) analog of the title compound, catena-(tris(μ-formato)-formato-erbium diaminomethaniminium , with nearly identical cell parameters and unit-cell volume. They also document a similar Er-based structure that employs a different solvent (1H-imidazol-3-ium). The presence of formic acid in the reaction is likely a result of the DMF hydrolysis as it is known to be a common impurity in DMF (IUPAC, 1977 ▶). The diaminomethaniminium ion was generated in situ, through 2-amino-4,6-dihydroxypyrimidine ring cleavage (Calza, et al., 2004 ▶). In regard to the observed chirality of the title compound, it has been previously documented that there is a great propensity for virtually any metal-organic framework (MOF) to crystallize in a chiral space group (Lin, 2007 ▶). graphic file with name e-70-0m261-scheme1.jpg

Experimental

Crystal data

(CH₆N₃)[Y(CHO₂)₄]
M _r = 329.07
Orthorhombic,
a = 6.6537 (13) Å
b = 8.0998 (15) Å
c = 20.179 (4) Å
V = 1087.5 (4) Å³
Z = 4
Mo Kα radiation
μ = 5.40 mm⁻¹
T = 188 K
0.35 × 0.15 × 0.12 mm

Data collection

Bruker APEX CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T _min = 0.247, T _max = 0.541
8974 measured reflections
2428 independent reflections
2219 reflections with I > 2σ(I)
R _int = 0.021

Refinement

R[F ² > 2σ(F ²)] = 0.017
wR(F ²) = 0.036
S = 0.92
2428 reflections
154 parameters
H-atom parameters constrained
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.25 e Å⁻³
Absolute structure: Flack x determined using 835 quotients [(I ⁺)−(I ⁻)]/[(I ⁺)+(I ⁻)] (Parsons & Flack, 2004 ▶)
Absolute structure parameter: 0.000 (4)

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT-Plus (Bruker, 2005 ▶); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: MaterialsStudio (Accelrys, 2013 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S1600536814013440/bv2234sup1.cif

e-70-0m261-sup1.cif^{(276.5KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814013440/bv2234Isup2.hkl

e-70-0m261-Isup2.hkl^{(133.5KB, hkl)}

CCDC reference: 1007433

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

Sandia is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the United States Department of Energy’s National Nuclear Security Administration under contract DE—AC04–94 A L85000.

supplementary crystallographic information

S1. Comment

The title compound (I) C₄H₄O₈Y . (CH₆N₃) is comprised of a yttrium (Y) atom fully coordinated by formate molecules, thereby creating a three-dimensional network structure of linked Y formate nodes. Figure 1 shows the coordination of the formate groups about Y atom. The figure shows three monodentate (bridging) formate molecules designated here by their associated C atoms (C2, C3, C4) along with a bidentate formate (C1) molecule exclusively bound to the metal center. The monodentate formate molecules bridge to neighboring metal clusters to generate the three-dimensional network. Considering the summation of charge around the Y⁺³ atom, one obtains a full -1 charge from the bidentate molecule along with a total of six monodentate formate molecules, each contributing -0.5 worth of charge for a total of -4 charge for each Y-formate cluster. This net -1 charge on the cluster is balanced by the presence of one diaminomethaniminium molecule for every cluster present. Figure 2 shows the three-dimensional network of the structure as viewed down the a axis. The plot shows Y-formate clusters as node polyhedra that are linked by formate ligands. For clarity purposes, hydrogen atoms on formate molecules as well as the diaminomethaniminium solvent molecules have been removed. The void space between the linked nodes are filled by the diaminomethaniminium ions which pack along the a axis direction. Two of the Y-formate polyhedra in Figure 2 are labeled as A and B clusters and are located near the center of the image. This has been done for reference purposes.

Figure 3 shows a smaller region of the three-dimensional network to better discuss connectivity. This figure, also viewed down the a axis, shows the location of the diaminomethaniminium molecules within the pores of the framework. Noting the polyhedra labeled A and B in Figure 3, one can compare this area back to Figure 2 and how it relates to the larger three-dimensional array. Considering the lattice shown in Figure 3, one can see that the A—B polyhedra pair (or bi-cluster) are linked by the C3 formate ligand, which exclusively bridges the A and B nodes. This A—B polyhedral bi-cluster is then bridged to neighboring A—B bi-clusters via the C4 formate ligand along the b-c plane (i.e. parallel to the plane of the image). The C1 formate is the bidentate ligand and does not link to neighboring Y-formate nodes, but instead truncates within the void space. Note that the formate ligands are plotted in Figure 3 without bound H atoms for purposes of clarity, while the diaminomethaniminium molecules are shown with H atoms present. The C2 formate ligand is not visible in this image, but links the Y-formate nodes along the a axis direction. It is worth noting in regard to the C2 formate molecule that when one considers the location of the C2 and C2A formate molecules in Figure 1; it is clear that these formate ligands (labeled as O6A—C2A—O1A and O6—C2—O1) are on nearly opposite sides of the Y metal center and thus can link the Y-formate nodes in a continuous fashion along the a axis. The O1A—Y—O6 angle is 141.34 (6)° which indicates the near opposing locations of the C2 and C2A formate ligands. This opposing orientation of the paired formate ligands does not hold true for the other formate molecules. Considering the C3 and C3A ligands, these two ligands are related through the Y metal center by the O3—Y—O8A bond angle of 74.03 (6)°. Likewise, the C4 and C4A formate ligands are related by the O2—Y1—O7A bond angle of 83.47 (6)°. In both of these cases the O—Y—O bond is close to 90° which serves to facilitate a zigzag bonding array of connectivity between adjacent Y nodes. In this arrangement the C3 formate molecules bridge the A—B bi-cluster by alternating orientation along the a axis direction; whereas, the C4 formate alternates orientation along the b axis direction in a similar zigzag fashion, as can be assessed by careful evaluation of Figure 3.

In regard to the observed chirality of (I), it has been previously documented that there is a great propensity for virtually any Metal-Organic Framework (MOF) to crystallize in a chiral space group (Lin, 2007). This is thought to be inherent to the topological variety of these materials, as there are a multitude of coordination capabilities between the metal nodes and organic ligands.

S2. Experimental

The reaction mixture containing Y(NO₃)₃^. 6H₂O (0.0166 g, 0.0433 mmol), and 2-amino-4,6-DHPm (2-amino-4,6-dihydroxypyrimidine, 0.0165 g, 0.1298 mmol) in 2 ml of N,N'-dimethylformamide (DMF) was placed in a convection oven at 90°C for 18 h, followed by subsequent heating at 115°C for 24 h. The presence of formic acid in the reaction is likely a result of the DMF hydrolysis as it is known to be a common impurity in DMF (IUPAC, 1977). The diaminomethaniminium ion was generated in situ, through 2-amino-4,6-dihydroxypyrimidine ring cleavage (Calza, et al., 2004).