Sandbox testing Sn2 for Veronika: 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='Sn2_for_Veronika_rotated_try2.xyz' size='340' side='right' caption='Caption for this structure' scene=''>
+<StructureSection load='Rot_Sn2.xyz' size='340' side='right' caption='Caption for this structure' scene=''>
-This is a default text for your page '''Sandbox testing Sn2 for Veronika'''. 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> stands for nulceophilic Substitution, the number 2 stands for bimolecular, with 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. On the other side, SN2 reactions are characterized by exchanging substituents. The substituent that leaves the molecule is called leaving group.
-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 ==
+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 is 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, with both educts comeing 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.
+[[Image:reaction_scheme_sn2.jpg|550px]] <br>
+The S<sub>N</sub>2 reaction has a very interesting stereochemistry inversion of the stereocenter<ref>PMID: 27505286 </ref> with an animated example of the substitution of chloride and methanol shown. Please click on the buttons below to '''animate''' the reaction with different representations. Use the '''popup''' button to enlarge the view and the '''quality''' button to turn on anti-aliasing.
-== Disease ==
-== Relevance ==
+<jmol>
-== Structural highlights ==
+<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>
-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.
 </StructureSection>
+The animation was originally done by [[User:Verena Pietzner | Prof. Dr. Verena Pietzner]]; for details, see her web site ChiLe<ref>[http://www.chemieunterricht-interaktiv.de/en/index.html ChiLe Web Site]</ref>. The implementation into Proteopedia was done by [[User:Jaime Prilusky | Prof. Jaime Prilusky]], [[User:Joel L. Sussman | Prof. Joel L. Sussman ]]
+and [[User:Veronika Pelekhov | Veronika Pelekhov]].
+===See also===
+[[SN1_reaction|S<sub>N</sub>1 reaction: Substitution of Cl<sup>&minus;</sup> and ''tert''-Butanol ]]
 == References ==
 <references/>