#Pymol tutorial reactions how to

Scenarios for docking - how to make use of MS data in HADDOCK.The tautomerization is essentially irreversible, pulling the entire reaction equilibrium towards completion.This tutorial consists of the following sections: The carbonyl formed will actually tautomerize into enol form to regain aromaticity in phenol form. Rearrangement can be effective even with an aromatic 'double' bond. Note: Aromatic Claisen sigmatropic rearrangement. Rearrangement yields a more favorable product with a strong C=O double bond. This reliably drives the equilibrium towards the product. Rearrangement yields an enol product which tautomerizes into a more stable keto form. Note: Oxy-Cope sigmatropic rearrangement. In this case, the product side is preferred due to conjugation with the aromatic ring. sigma bonds, so there will generally be an equilibrium between the two configurations unless a driving force exists. Under thermal (non-photochemically excited) conditions, 4n+2 electrocyclic systems react with disrotatory stereospecificty. Note: Electrocyclization with 6 electrons. Equilibrium will generally favor the closed form with a relatively stable 6-membered ring and net exchange of a pi bond for a stronger sigma bond. Under thermal (non-photochemically excited) conditions, 4n electrocyclic systems react with conrotatory stereospecificty. Note: Electrocycle opening with 4 electrons. Equilibrium will generally favor the open form due to the 4-membered ring strain. Warning: Depending on the configurations, cyclic dienes may not allow Diels-Alder reactions at all when they 'lock' the diene out of s-cis conformation This results in a bicyclic product.ДISFAVORED: The exo products are still disfavored compared to the endo products. Note: Cyclic dienes can be very effective reactants when they are 'locked' into s-cis conformation. Refer to previous reaction examples for more instances where only the endo products are shown, not the exo products Note the relative orientations of the methyl and carbonyl substituents in the product.ДISFAVORED: The results of an exo reaction are only minor products. Note: Stereoselectivity: Kinetic preference for the endo product is commonly observed.

Note that the result is an alkene which could in turn be another dienophile. Note: Alkyne ПЂ bonds work as dienophiles. Note: Regioselectivity: In the absense of a strong electron donating group, alkyl substituents can direct the reaction with electron donating character With the EDG in 'position 2' the resulting product will have the EDG and EWG 'para' with respect to each other. Note: Regioselectivity: Diene and dienophile have complementary electron donating (methoxy) and electron withdrawing (carbonyl) groups. Note: Try drawing resonance structures for the reactants and matching partial charges to explain the regioselectivity. With the EDG in 'position 1' the resulting product will have the EDG and EWG 'ortho' with respect to each other.

Note: Stereospecificity: Trans dienophile results in anti substituents Note: Stereospecificity: Cis dienophile results in syn substituents Note: Stereospecificity: Note that the E,Z diene yields a product with the methyl groups at the 1,4 positions anti with respect to each otherДISFAVORED: Z,Z dienes are unreactive in Diels-Alder reactions because steric occlusion blocks the s-cis conformation necessary for reaction. Note: Stereospecificity: Note that the E,E diene yields a product with the methyl groups at the 1,4 positions syn with respect to each other Note: Cyclic dienophiles like maleic anhydride work for Diels-Alder reactions as well Dienophiles are commonly adjacent to electron withdrawing groups (like these carbonyls) to facilitate the reaction Note: Diels-Alder Cycloaddition between a conjugated diene and an alkene dienophile.