User:Wayne Decatur/mof dev: Difference between revisions

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Wayne Decatur (talk | contribs)
Editor, widgeteditor
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move signifcance and add gif
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
add additional spacefill toggle
 
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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' >
<StructureSection load='' size='450' side='right' caption='A Metal–organic framework structure: the CSD entry JARMEU' scene='10/1092924/Csd_entry_jarmeu_basics/2' >
 
 
==Background==
==Background==


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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>).
Shown at the right is the building block of the network (<scene name='10/1092924/Csd_entry_jarmeu_basics/2'>restore initial scene</scene>).


<span style="font-size:200%;">{{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_N}}, '''{{Font color|#C88033|Cu}}'''</span>
<span style="font-size:200%;">{{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_N}}, '''{{Font color|#C88033|Cu}}'''</span>
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</jmol>
</jmol>


The metal here is copper.
The metal here is copper.<br/> 
A beautiful diamondoid structure appears that is a 4-connected network. <br/>


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/>   
When the repeats of this 4-connected network building block are shown connected to others, the crystalline lattice appears.<br/>
When considered this way a beautiful diamondoid structure appears that is a 4-connected network. <br/>
Viewing the <scene name='10/1092924/Csd_entry_jarmeu_1x1x3_set/4'>the CSD entry JARMEU as a 1x3x3 set of the metal organic framework</scene> illustrates this.<br/>   
The large cavities are visible as the lattice layers onto itself as the view of the structure rotates. <br/>
The large cavities are visible as the lattice layers onto itself as the view of the structure rotates. <br/>
The cavities would contain anions and solvent that are not shown in this crystal structure as they'd be freely moving and randomly distributed.
The cavities would contain anions and solvent that are not shown in this crystal structure as they'd be freely moving and randomly distributed.


The extensive crystalline nature with the large cavities becomes more apparent if we consider more of the repeated building blocks. <br/>
The extensive crystalline nature with the large cavities becomes more apparent if we consider more of the repeated building blocks. <br/>
<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/>
<scene name='10/1092924/Csd_entry_jarmeu_lattice/4'>The CSD entry JARMEU as a 1x4x6 lattice of the metal organic framework</scene>.
If you don't want to wait for it to rotate around to emphasize the cavities, scroll down...
 
<br/>
<jmol>
<br/>
<jmolCheckbox>
<br/>
  <scriptWhenChecked>hide all and not cell=555;</scriptWhenChecked>
<br/>
  <scriptWhenUnchecked>display all;</scriptWhenUnchecked>
This gif features the animation in the view of 1x3x3 plane:
  <checked>false</checked>
<table>
  <!-- <checked></checked> set it to false or delete it or comment it out as <checked>false</checked> or <checked> </checked>still show as checked-->
<td><tr>
  <text>Toggle to limit to what is in just key cell vs. current lattice network context</text>
[[Image:JARMEU plane133.gif‎]]
</jmolCheckbox>
</tr></td>
</jmol>
</table>
 
<jmol>
<jmolCheckbox>
  <scriptWhenChecked>select all; spacefill on;</scriptWhenChecked>
  <scriptWhenUnchecked>select all; spacefill 0.35; select hydrogen; spacefill 0.25;</scriptWhenUnchecked>
  <checked>false</checked>
  <!-- <checked></checked> set it to false or delete it or comment it out as <checked>false</checked> or <checked> </checked>still show as checked-->
  <text>CPK Spacefll mode</text>
</jmolCheckbox>
</jmol>


<jmol>
<jmol>
<jmolButton>
<jmolButton>
<script>load /wiki/scripts/10/1092924/Jarmeu_basics/1.spt</script>
<script>load /wiki/scripts/10/1092924/Csd_entry_jarmeu_basics/2.spt</script>
<text>Restore Default Scene</text>
<text>Restore Default Scene</text>
</jmolButton>
</jmolButton>
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<br/>
<br/>
-->
-->
</StructureSection>


==Significance==
==Significance==
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</StructureSection>
==Technical Details==
 
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].


==References==
==References==
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