Cahn-Ingold-Prelog Rules: E-Z Configurations

How to Manipulate JSmol Structures

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Index:

Introduction:

The assignment of (E) and (Z)-descriptors follows from the Cahn-Ingold-Prelog (CIP) Rules. The 2013 IUPAC Bluebook no longer recommends descriptors for double bonds in rings smaller than 8-membered.



Fig. 1

 

 

2-Hexene

Alkenes that are 1,2-disubstituted (relative to ethylene) were historically described as cis/trans isomers regardless of the nature of the substituents. Typical examples are cis- and trans-2-hexene as illustrated in Fig. 1 and 2, respectively. But what about unsymmetrical tri- and tetra-substituted double bond? This nomenclature is not unambiguous because it is unclear as to which groups would be utilized to assign cis/trans stereochemistry.
A method is required to assign unambiguously the stereochemistry of double bonds. This need is fulfilled by employing the Cahn-Ingold-Prelog (CIP) Rules. The priorities of groups in 2-hexene at C2 and C3 are determined. In both examples, a carbon and a hydrogen are attached to C2 and C3. The CIP Rule 1a requires carbon, which has the higher atomic number, to have priority over hydrogen. In the case of cis-2-hexene, both carbons are on the same side of the double bond and the name (Z)-2-hexene is applied (Ger. zusammen = together). For trans-2-hexene the designation is (E)-2-hexene (Ger. entgegen = opposite). Click on "show labels". 
Parenthetically, when one of the carbons of the double bond has exactly the same substituents, there is no stereochemical issue and, therefore, no E/Z assignment.  

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Fig. 2

 




Fig. 3a

(Z)-3-Methyl-3-heptene

Fig. 3b

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(Z)-3-Methyl-3-heptene


The left hand panel shows a double bond (Fig. 3a) bearing three alkyl groups. Click "show carbon #". It is apparent that at C3 ethyl>methyl and at C4 propyl>H. While such a technique is effective in this trivial example, in more complex examples it may not suffice.
Digraph 3b illustrates the proper method to assess priorities. The double bond is placed in the central sphere. C3 is attached to C2 and C8 in sphere 2. In sphere 3 C2 is attached to {C1, H, H} while C8 is connected to {H, H, H}. A one-to-one comparison of these locants is made looking for the first difference. In this instance C1>H. Therefore, ethyl>methyl. The priorities for C4 are made in sphere 2 where C5>H. The double bond has the (Z)-configuration,   Verify by clicking "show labels".

(E)-3-(Bromochloromethylene)-2-methylhexane
Fig. 4b provides a different way to present a digraph. Click "show carbon #" in Fig. 4a.  Sphere 1 has Br>Cl (CIP Rule 1a). C3 is attached to C2 and C4 in sphere 2. C2 is connected to {C7, C1, H} in sphere 3 while C4 leads to {C5, H, H}. Therefore, C2> C4.  Bromine and the isopropyl group have priority at C8 and C3, respectively. The double bond has the (E)-configuration. Verify by clicking "show labels".   




Fig. 4a

(E)-3-(Bromochloromethylene)-2-methylhexane



Fig. 4b

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Fig. 5a 

(Z)-3-Isopropyl-1,3-pentadiene 




Fig. 5b 




Fig. 5c 

(Z)-3-Isopropyl-1,3-pentadiene

Only the trisubstituted double bond in 5a requires E/Z configurational assignment. The monosubstituted double bond has duplicate carbons attached to C1 and C2 (Fig. 5c). That is, C2 is attached to C1 twice, once as a non-duplicate atom and once as a duplicate atom signified as (1). Duplicate atoms have the same atomic number as their non-duplicate counterpart in the nth sphere but they are bonded to three atoms of atomic number zero in the (n+1)th sphere.

This procedure is rigorous and it is usually applied in complex cases. However, the isopropyl group and the ersatz sec-butyl group of Fig. 5c only differ because of C(2), which provides a longer pathway and makes the vinyl group of higher priority than the isopropyl group. 

 

(E)-3-Ethynyl-4-methoxypenta-1,3-diene

 Fig. 6 compares the priorities of a vinyl and ethynyl group. The vinyl group is treated the same way as in Fig. 5. The ethynyl group's two carbons each have two duplicate carbon atoms, (7) and (8) (Fig. 6b). Sphere 3 in Fig. 6c shows ethynyl>vinyl because C7{8,(8),(8)>C2{1,(1),H}. in Fig. 6c hydrogens are not shown. All atoms are understood to be tetravalent, three of which lie in sphere (n+1). In sphere 2 the oxygen has priority over C5. 3-Ethynyl-4-methoxypenta-1,3-diene has the (E)-configuration.  

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Fig. 6a 


(E)-3-Ethynyl-4-methoxypenta-1,3-diene


Fig. 6b 


Fig. 6c 



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Fig. 7a 

(Z)-3-Cyano-2-(methoxycarbonyl)-4-oxobut-2-enoic acid 





Fig. 7b 

Fig. 7c 



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(Z)-3-Cyano-2-(methoxycarbonyl) -4-oxobut-2-enoic acid (Fig. 7)

This oxobutenoic acid contains four different functional groups. The ester group at C2 has priority over the carboxylic acid because C7>H in sphere 4 (Fig. 7c). The priorities at C3 have C4{O,(O),H}>C5{N,(N),(N)}. The first sign of difference is O>N. The C2,C3-double bond has the (Z)-configuration.



(4E,6Z)-2-Methyl-5-((E)-prop-1-en-1-yl)octa-2,4,6-triene


Click on "show labels" in Fig. 8a. Notice that the C2,C3-double bond has no label because it is non-stereogenic owing to the presence of two methyl groups at C2. Converting the (E)- and (Z)-double bonds to duplicate atoms would be fruitless because both entities would be the same. CIP Rule 3 is invoked, which gives priority to (Z) over (E) and both of them have priority over non-stereogenic double bonds. Consequently, the C4-C5 double bond has the (E)-configuration.

 

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Fig.8a

(4E,6Z)-2-Methyl-5-((E)-prop-1-en-1-yl)octa-2,4,6-triene




Fig. 8b


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