Doc Brown's Chemistry
Revising Advanced Organic Chemistry
PART 14 ORGANIC ISOMERISM and Stereochemistry Revision Notes
Part 14.2 Organic Stereoisomerism - Introduction and E/Z isomerism
(was called cis-trans geometric/geometrical isomerism)
E/Z stereoisomerism is explained and examples of E/Z isomers fully described including how to name them and assign the E or Z prefix to the specific isomer name. A few details of differences in physical and chemical properties are pointed out where it seems appropriate. Note for simple cases modern E = old trans isomers AND modern Z = old cis isomers. cis and trans are still to be found in older textbooks and even some contemporary literature.
Case studies are discussed concerning structure, naming, formation, properties and stereochemical consequences of optical/geometrical isomerism
ORGANIC CHEMISTRY PART 14 ISOMERISM INDEX: 14.1 ISOMERISM general introduction-definition * STRUCTURAL ISOMERISM general definition * 14.1a Chain isomerism * 14.1b Positional isomerism * 14.1c Functional group isomerism * 14.1d Tautomerism * 14.2 STEREOISOMERISM general definition * 14.2 E/Z ('ex' Geometric/Geometrical cis/trans) Isomerism * 14.3 R/S Optical Isomerism and chiral auxiliary synthesis * 14.4 Protein-enzyme structure, function and inhibition * 14.5 Combinatorial chemistry 14.6 Stereoregular polymers - isotactic/atactic/syndiotactic poly(propene) and also Isomerism in Transition metal complexes
14.2 to 14.6 Stereoisomerism-Stereochemistry - Definition and Introduction
Stereoisomerism occurs when two or more molecules have identical molecular formula AND the same structural formula (i.e. the atoms are arranged in the same order), BUT differ in their 2D or 3D spatial arrangements of their bonds - which means different spatial arrangement of the atoms - even though they are bonded in the same order!
There are two main sub-divisions of stereoisomerism, (a) E/Z (cis/trans geometrical) isomerism and (b) R/S optical isomerism. A 3rd section (c), looks at other stereochemical examples which do not readily fit into (a) or (b). However, before these sections, you need to read to know about 'priority rules' to assign the correct nomenclature to any absolute stereoisomer configuration.
Priority Rules for designating the precise isomer configuration in stereoisomerism
In order to specify exactly which stereoisomer you are referring to in e.g. E/Z (geometrical/geometric isomerism) and R/S optical isomerism (molecules exhibiting chirality) you need rules to account for the different groups of atoms. These are known as the Cahn-Ingold-Prelog priority sequence rules and their importance can only be fully understood when dealing the isomerisms described in sections (2a) E/Z Isomerism and (2b) R/S optical Isomerism. A brief description of the first two rules are given below, which is all you need for pre-university courses. When dealing with a C-X bond grouping, the priority of X is given by ....
Sequence priority Rule 1: The higher the atomic number of an atom the higher the priority it is assigned.
Sequence priority Rule 2: If the relative priority of two groups cannot be decided by Rule 1, it shall be determined by applying Rule 1 to the next atom or sequence of atoms in the group 'X'.
These two rules will be applied below in the case of geometrical isomers (E/Z notation) and optical isomers (R/S notation for enantiomers) and this rules section will be referred back to as examples of these isomerisms are described. Please note that for UK pre-university chemistry courses, no detailed knowledge of the Cahn-Ingold-Prelog priority sequence rules is expected and in many cases just knowing -H has the lowest priority is sufficient to assign the E or Z isomer in E/Z stereoisomerism and I don't think the R/S notation for optical stereoisomerism is needed for any UK based pre-university course except Cambridge pre-U chemistry?
14.2(a) E/Z Stereoisomerism (Geometrical/Geometric cis/trans Isomerism)
NOTE: The IUPAC recommend that the term geometrical/geometric isomerism is NOT used but to use the stereoisomerism classification E/Z stereoisomerism or E-Z isomerism. The E/Z notation is replacing the limited cis/trans notation in assigning names to a particular stereoisomer. However cis/trans nomenclature is in widespread use so it will be acknowledged in parallel with the E/Z convention where appropriate.
In molecules of the same molecular formula, exhibit E/Z stereoisomerism, spatially different molecules (E/Z isomers) exist because of the inhibited/restricted rotation about at least one bond due to too high an energy requirement (don't say rotation is impossible, its the energy barrier that causes the existence of two distinct isomers!).
A simple example: but-2-ene
The E (trans) , and the
Z (cis) , , forms of but-2-ene
However, in order for E/Z stereoisomers to exist there must be two different atoms/groups attached to both carbon atoms of the C=C carbon carbon double bond (see diagram below) or two adjacent carbons in a substituted cycloalkane.
The three most common situations you are likely to encounter are >C=C< or a >C=N- double bond and around a C-C single bond in cycloalkanes. In both cases the energy required is too high to allow free rotation around the double bond BUT free rotation is possible around single bonds (C-C, C-O etc.) e.g. alkyl groups around the C-C single bonds in non-cyclo linear/branched alkanes.
If two identical atoms/groups are attached to the same carbon, you cannot have geometrical isomers e.g. those with R2C=C< or R2C=N- where R = R. See the diagram below.
The 'old' nomenclature term cis often means the same substituents are on the same side of the double bond and trans when they are on opposite sides. Under the E/Z notation cis is now Z and trans is now E. In a sense cis/trans isomers were a special case of a substituent and a hydrogen atom on each carbon of the C=C double bond. E/Z configuration assignment is absolutely necessary when there 3 or 4 different substituents on the C=C group (again, see the diagram below)
Introductory exemplar diagrams to illustrate whether E-Z isomers can exist or not and how to use the modern E/Z isomerism notation-designation-assignment of absolute configuration.
Lower right example: E-3-methylpent-2-ene and Z-3-methylpent-2-ene
To understand the two lower left and right examples apply the Priority Rules to alkenes for E/Z ('geometrical') isomerism:
For each carbon of the double bond the higher priority atom/group is worked out.
The Z isomer is where both highest priority groups are on the same side of the double bond (includes all cis configurations of the old convention).
The E isomer is where the two highest priority atoms/groups are diagonally opposite each other on different sides of the plane of the double bond system (includes all trans isomers of the old convention).
(Note: In terms of the two highest priority atoms or groups, E, 'on opposite sides', comes from the German word entgegen, meaning 'opposite' and the Z 'on the same side' comes from the German word zusammen meaning 'together')
the E/Z isomers of
Z-hep-2-ene and E-hep-2-ene (cis and trans 2-heptene)
and the E/Z isomers of
Z-3-methylhex-3-ene and E-3-methylhex-3-ene (cis & trans 3-methyl-3-hexene)
Case study 2a.1 Isomers of C4H8, cis/trans or Z/E-but-2-ene
Priority order: -CH3 > H (since at. no. of 6 > 1 for hydrogen)
(1) Z-but-2-ene (cis) (bpt 4oC) , , (Z-2-butene)
(2) E-but-2-ene (trans) (bpt 1oC), , (E-2-butene)
(1) and (2) are very similar physically (e.g. colourless gases and very low bpt) and chemically (e.g. alkene electrophilic addition reactions).
Note that there are four other physically similar isomers of C4H8 namely, (3) 2-methylpropene (bpt -7oC, chain isomer), (4) but-1-ene (bpt -6oC, position of C=C isomer), (5) methylcyclopropane and (6) cyclobutane (bpts 5oC and 13oC, 5 and 6 are alkane functional group isomers of alkenes 1 to 4), BUT non of (3) to (6) can form geometrical isomers. (3) and (4) would be chemically similar to (1) and (2) being alkenes, but (5) and (6) have no 'alkene' chemistry but just the limited chemistry of alkanes e.g. uv chlorination as well as the combustion, which they all readily undergo!
, , E-3-methylpent-2-ene (trans)
and , Z-3-methylpent-2-ene (cis)
BUT , 2-methyl-2-pentene does NOT exhibit E/Z isomerism because two identical groups are attached to one of the carbon atoms of the double bond.
4,4-dimethylpent-2-ene, has two E/Z (trans/cis) isomers:
Z-4,4-dimethylpent-2-ene , and E-4,4-dimethylpent-2-ene
Case study 2a.2 trans/cis or Z/E-but-2-ene-1,4-dioic acid, HOOC-CH=CH-COOH
(butenedioic acids, old names given below). Substituent group priority -COOH > H
On heating the trans form (1) fumaric acid) now called E-but-2-ene-1,4-dioc acid, it proves difficult to change it into the cyclic anhydride (3) below.
Z-but-2-ene-1,4-dioc acid (2)cis form, maleic acid (3) + H2O
However, if the Z(cis) form (2) is heated, it readily changes into the cyclic acid anhydride (3). Not only does the restricted rotation about the C=C bond cause the existence of geometrical isomers, but in this case you can only readily get the elimination of water when the two -OH groups are on the same side of the planar >C=C< system, as in the cis form (2). In the trans form (1) the elimination reaction is stereochemically hindered because the -OH so far apart. However, both (1) and (2) undergo the same electrophilic addition reactions of the 'alkene' double bond, >C=C< and the same reactions of the carboxylic acid group -COOH.
Some physical differences.
*Sometimes the trans isomer has the higher symmetry and packs more closely into a crystal lattice, increasing the intermolecular forces, and this tends to increase melting points and density but decrease solubility as solvation is not as energetically favourable. (* unfortunately, there seem to be many exceptions to this 'rough rule of thumb', so beware).
(1) The trans form: d = 1.64 gcm-3, solubility in water 0.7g/100 cm3 at 25 oC, melting point 287 oC,
(2) The cis form: d = 1.59 gcm-3, solubility in water 78.8g/100 cm3 at 25 oC, melting point 130 oC,
Case study 2a.3 Physical properties of cis/trans or Z/E-1,2-dichloroethene
The Cd+-Cld- bond is polar due to the difference in electronegativity between carbon and chlorine (Cl > C).
(1) Z-1,2-dichloroethene (cis) d = 1.265cm-3, mpt -80 oC, bpt 60 oC, dipole moment 1.89D, with both Cl's on the same side of the C=C bond, the combined effect of the two polar C-Cl bonds makes it a much more polar molecule and raises the bpt compared to (2), but not the mpt.
(2) E-1,2-dichloroethene (trans) d = 1.259cm-3, mpt -50 oC, bpt 48 oC, dipole moment 0.00D, the effect of the C-Cl polar bonds cancel each other out giving a relatively non-polar molecule, this
and there is positional isomer (3) shown below.
(3) d = 1.218 cm-3, mpt -? oC, bpt 32 oC, dipole moment 1.30D?, 1,1-dichloroethene, is a positional isomer of the two geometrical isomers and cannot exhibit geometrical isomerism because two identical groups (H's or Cl's) are attached to the same carbon of the double bond.
All three isomers are chemically similar e.g. the electrophilic addition reactions of alkenes.
Case study 2a.4 Di-substituted cycloalkanes
Cis and trans isomers can exist in 1,2-disubstituted cyclopropanes* and cyclobutanes* because the -C-C- ring structure inhibits rotation about the C-C bonds. If the 1,2-substituents are on the same side of the plane of the triangle/square of carbon atoms you get the Z (cis) form, if the are on opposite sides you get the E (trans) form. * Alicyclic compounds (means cyclo-aliphatic)
(1) 1,2-dichlorocyclopropane can give E/Z isomers and the group priority is Cl > H
(2) 1,1-dichlorocyclopropane is a positional isomer of C3H4Cl2, and cannot exhibit geometrical isomerism.
(3) 1,2-dibromocyclobutane, likewise can give ...
(4) or (9) 1,1-dibromocyclobutane, is a positional isomer of C4H6Br2 and cannot exhibit E/Z (geometrical) isomerism because the two bromine atoms are attached to the same carbon.
(5) 1,3-dibromocyclobutane is also positional isomer of C4H6Br2 and can exhibit E/Z (geometric) isomerism.
Note: The molecular formulae C3H4Cl2 and C4H6Br2 can theoretically give rise to other functional group/positional/E/Z (trans/cis geometric) isomers in the form of non-cyclic alkenes e.g.
Case study 2a.5 Isomerism in azo (-N=N-) and R2C=N-X compounds
Organic (or inorganic) compounds of the structure R-N=N-R' (e.g. aromatic azo dyes) can exist as cis and trans isomers in just the same way as alkenes, where R or R' = H, alkyl, aryl group etc. R can be different or the same as R'. Stereochemically, the lone pairs on the nitrogen effectively behave as an atom bonding pair of electrons in determining the trigonal planar orientation of the -N= bonds and the lone pair of electrons on the nitrogen. Three groups of electrons around an atom X, always give a trigonal planar arrangement around the central atom >X-. The double bond, N=N or C=N, ensures that too high an energy is required for ready rotation about the double bond. The cis and trans forms will have different physical properties such as melting/boiling points.
Examples of -N=N- systems:
(1) (Z/cis) and (2) (E/trans)
(3) (Z/cis) and (4) (E/trans)
Case Study 2a.6 Dienes can also exhibit E/Z stereoisomerism
, Z-buta-1,3-diene (cis)
, E-buta-1,3-diene (trans)
ORGANIC CHEMISTRY PART 14 ISOMERISM INDEX: 14.1 ISOMERISM general introduction-definition * STRUCTURAL ISOMERISM general definition * 14.1a Chain isomerism * 14.1b Positional isomerism * 14.1c Functional group isomerism * 14.1d isomerism1.htm * 14.2 STEREOISOMERISM general definition * 14.2 E/Z ('ex' Geometric/Geometrical cis/trans) Isomerism * 14.3 R/S Optical Isomerism and chiral auxiliary synthesis * 14.4 Protein-enzyme structure, function and inhibition * 14.5 Combinatorial chemistry 14.6 Stereoregular polymers - isotactic/atactic/syndiotactic poly(propene) and also Isomerism in Transition metal complexes
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