Sandbox new: Difference between revisions

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

Joel L. Sussman

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 ==Your Heading Here (maybe something like 'Structure')==
-<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene='88/887580/Sn2_for_veronika/1'>
+<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene='88/887580/Sn2_for_veronika/2'>
-This is a default text for your page '''Sandbox new'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
+SN2 reaction is a basic reaction type in organic chemistry. The letter S<sub>N</sub> stand for nulceophilic Substitution, the number 2 stands for bimolecular. This means that both reactions partners are involved in the reaction rate determining step. It also exists an S<sub>N</sub>1 reaction; here, only one reaction partner is involved in this step.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
-== Function ==
+On the other side, SN2 reactions are characterised for exchanging substituents. The substituent that leaves the molecule is called leaving group.
-== Disease ==
+Typically, alkanes with a substituent in primary position undergo S<sub>N</sub>2 reactions. In contrast to a S<sub>N</sub>1 reaction, no stable carbo cation can be formed. Therefore, another way will be taken.
+The S<sub>N</sub>2 <jmol><jmolLink><script>anim mode once; frame range 1 10; delay 0.5; frame play</script><text>reaction starts</text></jmolLink></jmol> by establishing a so called intermediate state.  This means that both educts come close to each other. By this, the bond of the leaving group is partly broken, and the bond to the new group is partly formed. The formation of this intermediate state is the rate determining step of the reaction.
+In the <jmol><jmolLink><script>anim mode once; frame range 11 20; delay 0.5; frame play</script><text>second step</text></jmolLink></jmol>, the bond of the leaving group is completely broken, and at the same time the bond to the new substituent is completely formed.
-== Relevance ==
+[[Image:reaction_scheme_sn2.jpg|500px]]
-== Structural highlights ==
+The S<sub>N</sub>2 reaction has a very interesting stereochemistry.
+inversion of the stereocenter...
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+<jmol>
+<jmolButton><script>frame 1</script><text>First</text></jmolButton>
+<jmolButton><script>frame prev</script><text>Previous</text></jmolButton>
+<jmolButton><script>anim mode once; frame 1; delay 0.5; anim on</script><text>Play</text></jmolButton>
+<jmolButton><script>frame next</script><text>Next</text></jmolButton>
+</jmol>
+<jmol>
+<jmolButton><script>frame all</script><text>All frames</text></jmolButton>
+<jmolButton><script>animation mode palindrome 0.5 0.2; anim on</script><text>Loop backwards and forward</text></jmolButton>
+<jmolButton><script>if(_animating);anim off;else;frame play;endif</script><text>Toggle animation</text></jmolButton>
+</jmol>
+<jmol>
+<jmolButton><script>spacefill 90; dots on; wireframe 30;</script><text>translucent atoms</text></jmolButton>
+<jmolButton><script>spacefill on; dots off;</script><text>spacefilling atoms</text></jmolButton>
+<jmolButton><script>spacefill 90; dots off; wireframe 30;</script><text>backbone</text></jmolButton>
+</jmol>
+===See also===
+[[SN1_reaction|S<sub>N</sub>1 reaction: Substitution of Cl<sup>&minus;</sup> and ''tert''-Butanol ]]
+== References ==
+This demo was adapted from http://www.chemieunterricht-interaktiv.de/en/animations/sn2_substitution/sn2_substitution_3d.html by Dr. V. Pietzner, part of the ChiLe project
 </StructureSection>
 == References ==
 <references/>
+[[Category: BioMolViz]]
+[[Category: Chemical Reactions]]