Metal-Ligand Polyhedra: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Alexander Berchansky

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 <StructureSection load='' size='450' side='right' scene='40/405708/Polyhedron_main_chains/11' caption=''>
-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" />.
+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>.
 ==M24L48 Polyhedron (26 Faces)==
-Shown at right (<scene name='40/405708/Polyhedron_main_chains/11'>restore initial scene</scene>) is the "main chain" of a crystallographic model for the largest metal-ligand polyhedron reported as of May, 2010<ref name="sun-fujita-2010" >PMID: 20430973</ref>. <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.
+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.
+<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>
 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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 **[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/a/ad/M24L48_main_chains.pdb View in FirstGlance in Jmol]
 *M24L48 all atoms: [[Image:M24l48-single-polyhedron.pdb]] (This is actually in the XYZ atomic coordinate file format.)
-**[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/b/ba/M24l48-single-polyhedron.pdb View in FirstGlance in Jmol] To clean up the view:
+**[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/b/ba/M24l48-single-polyhedron.pdb View in FirstGlance in Jmol], then:
-# Hide the many "?" by unchecking [http://firstglance.jmol.org/notes.htm#labels Labels].
+** Views tab, Vines/Sticks.
 *M12L24 all atoms: [[Image:M12L24-single-polyhedron.pdb]]
 **[http://firstglance.jmol.org/fg.htm?mol=https://proteopedia.org/wiki/images/d/d5/M12L24-single-polyhedron.pdb View in FirstGlance in Jmol]