Metal-Ligand Polyhedra

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<StructureSection load='' size='450' side='right' scene='40/405708/Polyhedron_main_chains/11' caption=''>
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<StructureSection load='' size='450' side='right' caption='A Metal–organic framework structure: the CSD entry JARMEU' scene='10/1092924/Jarmeu_basics/1' >
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Metal ions with square planar coordination, when mixed with bent bidentate ligands, can self-assemble into polyhedra of various sizes. Geometrical constraints limit the number of metal ions (vertices) to 6, 12, 24, 30, or 60 for entropically favored regular or semiregular polyhedra<ref>Coxeter, H. S. M., ''Regular Polytopes'', Dover Publications, New York, 3rd ed., 1973.</ref>. In 2010 was reported self-assembly of a "giant" polyhedron with 24 metal ions, and a hollow spherical interior 36 &Aring; in diameter<ref name="sun-fujita-2010" />. The self-assembly process demonstrates emergent behavior, and is reminiscent of the self-assembly of large biological structures, such as virus capsids. Such nano-spheres can also be functionalized to create, among other possibilities, synthetic receptors and nanoreactors<ref name="news-and-views" />. A 2022 extensive review<ref name="2022rev">McTernan, Charlie T., Jack A. Davies, and Jonathan R. Nitschke, [https://pubs.acs.org/doi/10.1021/acs.chemrev.1c00763 Beyond Platonic: How to Build Metal–Organic Polyhedra Capable of Binding Low-Symmetry, Information-Rich Molecular Cargoes], Chem. Rev. 2022, 122, 10393−10437.</ref> cites potential applications in sensing, catalysis, and drug delivery<ref name="2015apps">PMID: 25319756</ref><ref name="2021biomed">PMID: 32255835</ref>.
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==M24L48 Polyhedron (26 Faces)==
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==Background==
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Shown at right (<scene name='40/405708/Polyhedron_main_chains/11'>restore initial scene</scene>) is a crystallographic model for the largest metal-ligand polyhedron reported as of May, 2010<ref name="sun-fujita-2010" >PMID: 20430973</ref>. It has an interior cavity about 32 &Aring; in diameter. <scene name='Metal-Ligand_Polyhedra/Polyhedron_main_chains/10'>24 palladium ions</scene> form the vertices of a 26-face polyhedron<ref>M24L48 forms a 26-faced ''rhombicubooctahedron'' with 18 square faces and 8 triangular faces. In this instance, the rectangular faces are very close to squares 13.35 &Aring;ngstroms on a side.</ref>. Three square faces and one triangular face meet at each vertex.
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Synthesized metal-organic frameworks have been shown to have a wide range of applications, as [[Proteopedia:Hot_News|highlighted three chemists doing seminal work in this field being awarded the Nobel Prize in Chemistry in 2025]].
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<span style="font-size:200%;">{{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_N}}, '''<span style="background-color:black;color:yellow;">&nbsp;S&nbsp;</span>, {{Font color|#00b000|Pd}}'''</span>
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Here the crystal structure of a cubic diamond metal-organic framework is featured; [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=JARMEU&DatabaseToSearch=CSD the CSD entry JARMEU]<ref>B.F. Hoskins and R. Robson. 1989. Infinite polymeric frameworks consisting of three dimensionally linked rod-like segments. Journal of the American Chemical Society, v111, pg. 5962-5964, [https://pubs.acs.org/doi/abs/10.1021/ja00197a079 |DOI: 10.1021/ja00197a079]</ref>. <br/>
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This is the structure that revealed that a crystalline, diamondoid, extended framework was formed that had large cavities, establishing this class of solid polymeric materials.
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Each palladium ion is coordinated by <scene name='Metal-Ligand_Polyhedra/Polyhedron_main_chains/9'>four nitrogens</scene>. The nitrogens are bridged by a <scene name='Metal-Ligand_Polyhedra/Single_main_chain_ligand/2'>dipyridylthiophene</scene> ("ligand"). There are two ligand molecules (L) per metal ion (M); hence, this structure is called '''M24L48'''.
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==A cubic diamond lattice metal-organic framework==
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The models shown thus far are simplified, including only the "main chain". The actual M24L48 complex analyzed crystallographically contained a substituent of -OCH<sub>2</sub>CH<sub>2</sub>O- on each thiophene ring, PF<sub>6</sub><sup>-</sup> counterions bound to the surface of the polyhedron, and hydrogen atoms. Here is the <scene name='Metal-Ligand_Polyhedra/M2l1_with_och2ch2o_h_pf6/3'>chemically complete M2L1 subunit</scene> (but lacking the three additional nitrogens coordinating each palladium, and water, which was not resolved crystallographically). Here is the <scene name='Metal-Ligand_Polyhedra/Full_polyhedron/5'>complete M24L48 polyhedron</scene> (but lacking PF<sub>6</sub><sup>-</sup> and water).
 
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The diameter of this M24L48 polyhedron is 40 &Aring; (Pd to farthest Pd). A sphere of 50 &Aring; circumscribes the molecular shell, and a sphere of 36 &Aring; can be inscribed in the interior. In comparison, the diameter of the M12L24 polyhedron (see below) is 26 &Aring; (Pd to farthest Pd).
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Shown at the right is the building block of the network(<scene name='10/1092924/Jarmeu_basics/1'>restore initial scene</scene>).
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<span style="font-size:200%;">{{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_N}}, '''{{Font color|#C88033|Cu}}'''</span>
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<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select all; spacefill on;</scriptWhenChecked>
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<scriptWhenUnchecked>select all; spacefill 0.35; select hydrogen; spacefill 0.25;</scriptWhenUnchecked>
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<checked>false</checked>
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<text>CPK Spacefll mode</text>
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</jmol>
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The metal here is copper.
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When the repeats of this building block are shown connected to others, the crystalline lattice appears. Viewing the <scene name='10/1092924/Csd_entry_jarmeu_1x1x3_set/4'>the CSD entry JARMEU as a 1x1x3 set of the metal organic framework</scene> illustrates this.<br/>
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When considered this way a beautiful diamondoid structure appears that is a 4-connected network. <br/>
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The large cavities are visible as the lattice layers onto itself as the view of the structure rotates. <br/>
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The cavities would contain anions and solvent that are not shown in this crystal structure as they'd be freely moving and randomly distributed.
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The extensive crystalline nature with the large cavities becomes more apparent if we consider more of the repeated building blocks. <br/>
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<scene name='10/1092924/Csd_entry_jarmeu_1x3x3_plane/3'>The CSD entry JARMEU as a 1x3x3 plane of the metal organic framework</scene>. (Substantial patience required when loading this scene; it is suggested to only do that after you have examined the others.)<br/>
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If you don't want to wait for it to rotate around to emphasize the cavities, scroll down...
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This gif features the animation in the view of 1x3x3 plane:
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<table>
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<td><tr>
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[[Image:JARMEU plane133.gif‎]]
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</tr></td>
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</table>
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<jmol>
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<script>load /wiki/scripts/10/1092924/Jarmeu_basics/1.spt</script>
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<text>Restore Default Scene</text>
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==Ligand Angle vs. Polyhedron Size==
 
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* '''149<sup>o</sup>: M24L48.''' The dipyridylthiphene ligand described above, in the M24L48 polyhedron, has a bend angle of 149<sup>o</sup><ref name="sun-fujita-2010" />.
 
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* '''127<sup>o</sup>: M12L24.''' A ligand with a sharper bend of 127<sup>o</sup> (dipyridylfuran<ref>Dipyridylfuran differs from dipyridylthiophene in that oxygen replaces the sulfur.</ref>) forms a <scene name='Metal-Ligand_Polyhedra/M12l24_single_polyhedron/2'>smaller polyhedron, M12L24</scene><ref name="tominaga-fujita-2004">PMID: 15455450</ref>.
 
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Interestingly, mixtures of the two ligands (149 and 127 degrees) form only one size of polygon: a 3:7 mixture respectively (and up to 10:0) forms only M24L48, while a 2:8 mixture (and down to 0:10) forms only M12L24<ref name="sun-fujita-2010" />.
 
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* '''90<sup>o</sup>: M6L12.''' A ligand with an even sharper bend of 90<sup>o</sup> forms M6L12<ref name="suzuki-fujita-2009">PMID: 19294246</ref>.
 
==Significance==
==Significance==
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Metal-ligand polyhedra could serve as nanoreactors containing a chemically defined nano-environment. Similar polyhedra have been constructed from ligands with covalent adducts facing the interior: "endohedral functionalization". In one case, 24 perfluoroalkyl chains were caged in an M12L24 polyhedron, forming a fluorous phase potentially useful for separation, purification, or reaction control in organic syntheses<ref>PMID: 16946067</ref>. In addition, the surfaces of such polyhedra have been decorated with attached groups. Photoresponsive nanoparticles and other functionalizations have been demonstrated<ref name="news-and-views">PMID: 20508119</ref>.
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Since the proposal of this class of materials, metal-organic framework have been proven to support many roles. Applications to gas storage, analytical chemistry and (bio)sensors, batteries and fuel cell technology, separation science, synthesis and catalysis, harvesting of water from dry (low humidity) air, water purification and environmental remediation, capture/destruction of harmful agents, energy conversion and storage, hydrogen generation, food
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safety, and drug delivery & diagnostics/therapy have been demonstrated<ref>https://www.nobelprize.org/uploads/2025/10/advanced-chemistryprize2025.pdf</ref>.
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More generally, self-assembly of metal-ligand polyhedra demonstrates emergent behavior, in which microscopic differences (such as ligand angles) lead to macroscopic differences (such as polyhedron size). Such self-assembly is reminiscent of the assembly of virus capsids and other biological structures.
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Highlighting the significance is the fact [[Proteopedia:Hot_News| three chemists doing seminal work in this field were awarded the Nobel Prize in Chemistry in 2025]]. The structure featured here played a key role in establishing this field.
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==Models==
 
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Models shown in this article were kindly provided by Makoto Fujita, who gave permission for their display here. In [[FirstGlance in Jmol]], click '''Vines''' to display the molecule as sticks.
 
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*M24L48 main chain atoms only: [[Image:M24L48_main_chains.pdb]]
 
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**[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/a/ad/M24L48_main_chains.pdb View in FirstGlance in Jmol]
 
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*M24L48 all atoms: [[Image:M24l48-single-polyhedron.pdb]] (This is actually in the XYZ atomic coordinate file format.)
 
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**[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/b/ba/M24l48-single-polyhedron.pdb View in FirstGlance in Jmol], then:
 
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** Views tab, Vines/Sticks.
 
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*M12L24 all atoms: [[Image:M12L24-single-polyhedron.pdb]]
 
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**[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/d/d5/M12L24-single-polyhedron.pdb View in FirstGlance in Jmol]
 
</StructureSection>
</StructureSection>
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==References and Notes==
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==Technical Details==
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The views featuring the 1x1x3 set and the plane were built using [https://chemapps.stolaf.edu/jmol/jsmol/jcse/explore.htm the Jmol Crystal Symmetry Explorer] to examine [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=JARMEU&DatabaseToSearch=CSD CSD Entry: JARMEU].
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==References==
<references/>
<references/>
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==See also==
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* [[Catalytic Molybdenum Metal-Organic Framework]]
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* [[Metal-Ligand Polyhedra]]

Revision as of 20:59, 10 October 2025

A Metal–organic framework structure: the CSD entry JARMEU

Drag the structure with the mouse to rotate

Technical Details

The views featuring the 1x1x3 set and the plane were built using the Jmol Crystal Symmetry Explorer to examine CSD Entry: JARMEU.

References

  1. ↑ B.F. Hoskins and R. Robson. 1989. Infinite polymeric frameworks consisting of three dimensionally linked rod-like segments. Journal of the American Chemical Society, v111, pg. 5962-5964, |DOI: 10.1021/ja00197a079
  2. ↑ https://www.nobelprize.org/uploads/2025/10/advanced-chemistryprize2025.pdf

See also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Alexander Berchansky

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