Prof M Wills 1

Organic Chemistry year 1 2008-2009

Professor Martin Wills

Email: m.wills@warwick.ac.uk Office: C504

CONTENT OF LECTURES

• Substitution reactions at saturated carbon atoms: ‘SN2 and SN1’. Mechanisms of substitution reactions, intermediates, orbital structures, implications for stereochemistry, inversion and racemisation. Clayden et al, Chapter 17.

• Formation and reactions of alkenes: ‘E2 and E1’. Methods for making alkenes, structure and selectivity. Reactions of alkenes with electrophiles and nucleophiles. Oxidation and reduction reactions. Clayden et al. Chapters 19 and 20.

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What you should know – what you will learn

What you should know by now:

-Hybridisation (sp, sp2, sp3) of carbon atoms.-Orbital structure of C-C and C=C bonds.-E/Z and R/S definition and how to assign configuration.-Electronegativity and formal charge.-Organic reaction mechanisms – ‘arrow pushing’.-Factor which influence the stability of cations and anions.-Free energy and reaction profiles.

What you will learn in this part of the course:

-The detailed mechanisms of substitution reactions at saturated carbon atoms(SN2 and SN1 mechanisms).-Factors which influence the mechanisms of substitution reactions.

-Methods for the formation of alkenes (E2 and E1 mechanisms).-Reactions of alkenes.-Reduction and oxidation reactions of alkenes.

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Nucleophilic substitution reactions – overview:

Why these reactions are important and some examples:

Substitution reaction: replacing one group with another one! Some examples:

Br

O O Br+

Br

H2N NH

HBr+

Br

H2N NH

HBr+O

Substitution at a saturated (sp3) carbon atom (M Wills section):

Substitution at a saturated (sp3) carbon atom (M Wills section):

Substitution at an unsaturated (sp2) carbon atom (discussed in G. Challis section, term 2):

What mechanisms could there be for this reaction?Can you define; the nucleophile, the electrophile, the leaving group.What is the role of the solvent? What solvents could be used?

What about the counterion?Solvent

Solvent

Solvent

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Substitution reactions – some definitions.

What is the significance of the ‘saturated carbon atom’.

Br

O O Br+H

H

sp3 hybridised carbon

What ‘shape’ do thegroups around this atom define?

Which leaving groups can be used – what ‘drives’ the reaction?

X

O O X+H

H

Leaving group

+

Key point: Good leaving groups are halides (Cl, Br, I), OSO2R, other groups which stabilise a negative charge.

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Mechanisms of substitutions reactions: SN2There are two major mechanisms of substitution reactions.

The first is called the SN2 mechanism – Substitution, Nucleophilic, Bimolecular:What do these three terms mean?

It is a single step mechanism; the nucleophilic adds and the leaving group is simultaneously displaced in the same step. A concerted mechanism.

BrO Br+H

HO

HH

Rate = k [nBuBr][nPrO-]

What happens if I double the concentration of bromide? What if I double the rate of bromide and of propoxide?

Reaction co-ordinate.

EnergyBromide(starting material) Ether (product)

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Mechanisms of substitutions reactions: SN1

The second is called the SN1 mechanism – Substitution, Nucleophilic, Unimolecular:What do these three terms mean?

It is a two step mechanism; the leaving group leaves in the first step to form a cationic intermediate and the nucleophilic adds in the second step

Br

OBr

MeMe O

HHMe

Me

INTERMEDIATEcation

first stepSLOW

second stepFAST

The first step is the rate-determining step (rds)

OO(acetate)

Rate = k [C6H13Br] i.e. [acetate (nucleophile)] is not featured

What happens if I double the concentration of bromide? What if I double the rate of bromide and of propoxide?

EnergyBromide(starting material) Acetate (product)

Cation(intermediate)

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The transition state for SN2 reactions:

The SN2 mechanism – structure of the transition state.

Br

O

Br+H

H

Br

HH

O

O

HH

What ‘shape’ do thegroups around this atom define?

*** Key point of nomenclature; it’s SN2 not SN2*** This is important ***

What is the hybridisation at this C atom?

What does this symbol mean?

Note partial bonds to nucleophile and leaving group. Nucleophile adds electron density to * antibonding orbital.

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Stereochemical consquences of SN2 reactions:

The SN2 mechanism – What happens at chiral centres:

Br

O

Br+H

Me

Br

HMe

O

O

MeH

S configuration: R configuration

H

*** Key point of nomenclature; INVERSION *** This is important ***

Key concept – inversion of configuration.

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Br

HMe

- Br

HMe

O

O

MeH

S configuration:

R configurationO

HMe

S configuration:+

50% 50%A racemic product is formed.

O

O

O

or HMe

O

O

*** Key point of nomenclature; RACEMISATION *** This is important ***

Why are there two products now?What happened to the square brackets?What is the ratio of the products?

Stereochemical consquences of SN1 reactions:

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Nucleophilic substitution reactions: Summary.

SN1 and SN2

The ‘1’ and ‘2’ refer to the molecularity of the reaction (the number of species in the rateExpression).

SN1 is a two step reaction. SN2 is a one step reaction.

SN2 mechanisms go with inversion of configuration, SN1 with racemisation.

Make sure you understand the difference between an intermediate and a transition state.

Other substitution mechanisms include the SN2’ :

Br

HMe

- Br

RNH

MeRHN

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Factors which influence SN2 and SN1 reactions:

‘If I do a substitution reaction, will it go through an SN2 or SN1 mechanism?’

i) Substrate structure. Steric hindrance and cation stability.

Br

MeMe

Br

HH

more likely to undergo SN2

more likely to undergo SN1

HH

Nu:

Nu: = nucleophile

Approach unhindered

Will not form a stable cation if Br- leaves:

Nu: Approach hinderedby two large Me groups

Will form very stable cation

MeMe

Cation stability:

Me Me

Me

Me H

Me

Me H

H

H H

H> > >

tertiary secondary primary methyl cation

Unhindered substrate:

Hindered (substituted) substrate

E2Competes?

A primary halide is more likely to undergo SN2, a tertiary SN1. A secondary halide may do both.

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Other factors that increase cation stability.

Cation stability can also be increased by an adjacent double bond or aromatic ring:

H

H

H

His more stable than

benzyl cation

Charge is delocalisedinto the aromatic ringor double bond.

H

H

H

H

allyl cation

is more stable than

However an adjacent benzyl or allyl group can also increase the rate of SN2 reactions, by stabilising the transition state:

BrMeO + OMe

Br+

via

Br

OMe

HH

Orbital overlap lowers the transition stateenergy, and makes the reaction faster.

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ii) Effect of the solvent.

Solvents which stabilise cations will tend to favour SN1. For example dipolar aprotic solvents such as dimethylformamide (DMF) and dimethylsulfoxide (DMSO).

iii) Effect of the nucleophile.

In general, more reactive nucleophiles favour the SN2 reaction. This is fairly logical.

Examples of 'reactive'nucleophiles:

Alkoxides: RO

Amides: RNH

Alkyl anions (for exampleGrignard (magnesium based)reagents:

R (RMgBr)

Examples of 'less reactive'nucleophiles:

Alcohols (not deprotonated) ROH

Amines (not deprotonated) RNH2

Stabilised nucleophiles e.g. acetate:

O

O

However some relativelyunreactive anions are good nucleophiles e.g.

Anions of thiols

Anions of phenols

Phosphines

SR

O

R3P

Factors which influence SN2 and SN1 reactions cont:

iv) Effect of the leaving group; good leaving groups are needed for both mechanisms.

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SN2 vs SN1 – all aspects must be considered:

Br HMeO +

H OMe

i.e. good nucleophile, not very hindered substrate, good leaving group, polar solvent, hence SN2.

DMSO

(DMSO=Me2SO)K

Ph

Br H

Ph

H OH

H2O Ph

HO H+

i.e. weak nucleophile, more hindered substrate, potential for stable cation, polar solvent, hence SN1.

What would be your prediction of a mechanism for:

Ph

PhPh

Cl R OH+Ph

PhPh

Clpyridine

Npyridine(mild base)

?

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Formation and use of the OTs leaving group (very common in synthesis):

OH

O

TsO

+

HH

+S

Cl

O O

(TsCl)

O

HH

SO O

OTs

HH

O

SO

O O

What is the mechanism, and why go to all this trouble, i.e. why is OHa poor leaving group? How else can it beMade into a good leaving group?

Key point; Learn what a OTs (tosyl group) is – it will come up again!

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Examples of substitution mechanisms, and applications.

Mitsunobu reaction – a modern reaction.

Real life examples and applications in synthesis?

How to make an unsymmetrical ether?

Intramolecular cyclisations - 'SN2-like' (cannot be bimolecular). Add arrows.

OO

Br

OO

O

OO

O

O

O

O

SO2

O O

SO2

O

More on epoxides in Dr Clark’s lectures.

SN2 reactions are generally more synthetically useful.

O O Ph

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Alkenes– reminder of structure and formation:

Already discussed in Prof M. Shipman’s lectures:In the case of a carbon atom attached to three other groups (by two single bonds and one double bond)the single 2s and two2p orbitals mix (rehybridise) to form three sp2 orbitals. These are all arranged at mutual 120 degree angles to each other and define a trigonal shape, the remaining p orbital projects outof the plane of the three sp2 orbitals and overlaps with an identical orbital on an adjacent atomto form the double bond:

1 x 2s 2 x 2p

which lie at mutual 120 degreesin a molecule such as etheneC2H6,whilst the remaining p orbitalforms the double bond:

combine to form 3 x sp2 orbitals:on a carbon atom

C

H

H

H

HC C

H H

HH

The resulting structure is rigid and cannot rotate about the C=C bond without breakage of thebond between the p-orbitals (the bond). The can be separated into E and Z configuration isomers.

The bond is much more reactive than the bond – the bonds are not equivalent to each other.

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Alkynes – reminder of structure and formation:

In the case of a carbon atom attached to two other groups (by one single bonds and one triple bond)the single 2s and one 2p orbitals mix (rehybridise) to form two sp orbitals. These are all arranged at mutual 180 degree angles to each other and define a linear shape, the remaining p orbitals projecting outfrom the sp orbital to overlap with identical orbitals on an adjacent atom to form the triple bond:

1 x 2s 1 x 2p

which lie at 180 degreesin a molecule such as ethyneC2H4,whilst the remaining p orbitalsform the triple bond:

combine to form 2 x sp2 orbitals:on a carbon atom

C

H HC C HH

Both bonds in an alkyne are much more reactive than the bond.

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Alkenes – formation:

Most (but not all) alkene formation reactions involve an ELIMINATION reaction.

Alkyne reduction is also important (see later).

Br

PhPh

HH

H

- HBr

H

PhPh

H

Ph

HPh

H

and/or

E-alkene Z-alkene

Key point – H from one carbon atom and a leaving group (typically a halide) from the adjacent carbon atom.

Recap on alkene structure.Do you recall the orbital structure of an alkene?Can you use the Cahn-Ingold-Prelog rules to determine the configuration?

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Mechanisms for the formation of alkenes: E1 and E2:

Most elimination reactions, to form alkenes, involve an E2 or E1 elimination.

E2 = Elimination, bimolecular. It is a one-step reaction. A strong base is needed - why is this?

MeO

(This is a base)

H

BrH

H

H

H

Reaction co-ordinate.

EnergyBromide(starting material) Alkene (product)

Rate = k [Cyclohexylbromide][MeO-]

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E2 elimination – stereochemical implications: The ‘anti periplanar’ requirement.

E2 reactions require correct orbital alignment in order to work. The optimal arrangement is ‘anti periplanar’, where the ‘H’ and ‘Br’ (in an alkyl bromide) are anti to each other.

PhH

H

Br

PhH

PhHPh H

PhH

Ph H

E- alkene.

PhPh

H

Br

HH

PhPhH H

PhPh

H H

Z- alkene.

PhPh

Brcan form a E- or Z-alkene upon elimination:

Which base would you use?

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E2 elimination – stereochemical implications: orbital alignment:

Orbital alignment in E2 elimination reactions:

PhH

H

Br

Ph HPhH

Ph H

PhH

Ph H

E- alkene.

PhPh

H

Br

H H

PhPhH H

PhPh

H H

Z- alkene.

Substrate

PhH

Br

Ph H

PhPh

Br

H H

H

HtBuOK(base)

tBuOK(base)

OBut

OBut

-

-

-

-

tBuOH

Br

Br

tBuOH

The alignment of and * orbitals in the substrate leads to a smooth transition to a bond in the product. Which is the most likely product?

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The E1 elimination mechanism:

E1 = Elimination, unimolecular. It is a two-step reaction. It proceeds via a cationic intermediate.

-BrH

BrMe

H

Me

HH

Me

HEt3N:

Reaction co-ordinate.

EnergyBromide(starting material) Alkene (product)

Rate = k [Methylcyclohexylbromide]

Cation(intermediate)

Why does the substrate now have an extra methyl group?

Why was a weak base used in this reaction?

Triethylamine (Et3N)is a weak base.

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Nature of the intermediate in an E1 reaction:

E1 reactions proceed through a ‘flat’, i.e. trigonal, cation (like SN1 reactions).

-BrH

BrMe

H

Me

HH

Me

H

Me

H

H

sp2 carbon

sp3 carbon

BrMe

Me

Et3N (mild base)

E1

?

Sometimes multiple products are formed (irrespective of mechanism)–What products would you predict from this reaction (more than one is possible)?

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Formation of alkenes by elimination of alcohols:

See if you can write the mechanism for the following (E1) reaction:

HO

MeMe

H

?

HCl (strong acid)MeOH (solvent)

Why is acid needed when the alcohol is the leaving group – why can’t we rely on a base?What other alkene product can be formed, and how?

What would be the effect of using a base and an acid in the following?

Br?

NaOH

Br?

KOtBu

K O

HO?

H2SO4

E1cb ‘conjugate base’ is less common mechanism, but important.

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Some alternatives to ‘simple’ elimination – the Wittig reaction:

The Wittig reaction is one of a number of reaction that provide a means for controlling where the double bond ends up.

O H2CPh3P CH2

Phosphonium ylid

the isomer, H3C

is not formed

This is how the ylid is formed:

Ph3P CH2Ph3P CH3

basePPh3 + CH3Br

+ Ph3P O

Key point: this is important – learn it

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Some alternatives to ‘simple’ elimination – the Wittig reaction(this is important – learn it)

Here is the mechanism of the Wittig reaction (you need to complete it).

O

H2C

Ph3P CH2

+ Ph3P O

You sometimes see an alternative mechanism:

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Substitution vs elimination, base vs nucleophile:

Sometimes a particular substrate can undergo a substitution or an elimination reaction.

The outcome depends on all the factors involved in the reaction;

The ‘is an alkoxide a nucleophile or a base?’ question. Answer - depends what it does:.

Br MeO Na MeO

Br MeO Na

Alkoxide is a nucleophile.

Alkoxide is a base.

The most important factor is probably the substrate structure – deprotonation may outpace nucleophilic addition when a substrate is very hindered. Certain substrates cannot undergo elimination reactions.

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Reactions of alkenes with electrophilic reagents - bromine:

Alkenes are electron rich (in the system) and react with electrophilic reagents:

R

Br2R

R R

Br

Br

The mechanism is as follows, the intermediate is a bromonium ion:

RR

R R

Br

BrBr Br

RR

Br

Br

what about?

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Further additions of electrophiles to double bonds - HBr:

Hydrogen halides (HCl, HBr) also add across double bonds.

R

HBrR

R R

Br

HR

RR

R

The mechanism involves the addition of a proton first (with the electron-rich alkene), then the bromide. This is logical, because the alkene is electron rich.

R RR R

Br

HH

RR

H

Br

R

R

R

R

RR

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Regioselectivity of electrophilic additions to alkenes:

Addition of HCl and HBr (and other acids) across unsymmetric alkenes results in formation of the more substituted halide (via the more substituted cation).

H

HBrH

H3C H3C

H

Br

H

H

H

HMajor

HH3C

Br

H

H

H

Minor

The mechanism involves the addition of a proton first, as before, but in this case the unsymmetricalintermediate has a larger density of positive charge at one end.

H

H

H3C

H3C

H

Br

H

HH3C

H

Br

H

H H

H

HH

more stablecation

major

HH3C

Br

H

H

H3CH

Br

H

HH

less stablecation minorH

What aboutPh

Prof M Wills 32

Acid catalysed hydration (addition of water) to alkenes:

Acid catalysed hydration (addition of water) is a very important reaction of alkenes:

H

H2OH

H3C H3C

H

OH

H

H

H

HMajor

HH3C

OH

H

H

H

Minor

+

H+ catalysis

The mechanism involves the addition of a proton first, as before, followed by addition of water, the regioselectivity is the same as for addition of HCl:

HHH3C

H3C

H

O

H

HH3C

H

OH2

H

H

H

HH H

acid

HH

H2O HH3C

H

O

H H

H(H )

regenera-tion of H

This mode of addition of H2O is referred to as ‘Markonikov’ selectivity (i.e. formation of the MOST substituted alcohol via the MOST substituted cation.

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Oxymercuration of alkenes with Hg(OAc)2 gives Markovnikov product.

?Hg(OAc)2

H2ONaBH4

OHMechanism…

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Radical reactions of alkenes: HBr in diethylether containing peroxides.

HBr, peroxides in ether BrH

anti Markovnikovaddition.

Mechanism (Clayden et al p 1033-1035)

RO OR 2 RO . (radical)

HO.

H Br

BrH

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Radical reactions of alkenes - intramolecular radical cyclisation reactions:

Intramolecular radical reactions :

N

AIBN =

?

Br AIBN

nBu3SnHNSO2Ph

Br AIBN

nBu3SnHNSO2Ph

N

CN

NC

Initiation:

Br

Propagation:

H nBu3+

then..

. .

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Nucleophilic additions to C=C bonds – require nearby electron withdrawing groups (‘ewg’).

The polar effects of C=O bonds can be transmitted through adjacent C=C bonds, e.g.

The oxygen atom drives the reaction- it is more likely to gain a negative charge because it is more electronegative than adjacent atoms.

An enone: (a compound with a directly linked C=C and C=O double bond) can react with a nucleophile at either the C of the C=O bond or at the C at the end of the C=C bond. This is calledconjugate addition, 1,4-addition and/or ‘Michael’ addition.

H

C O

CC

H

H

H

H

C O

CC

H

H

H

R

R (a nucleophile)

H

Add acid at endof reaction.

H

C O

CC

H

H

H

R H

More on this from Prof Challis later in course.

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Polymerisation of alkenes/reactions of alkynes.

Alkenes/Alkynes

Another important reaction of alkenes is polymerisation, which is often radical-initiated:

H3Cn polymerisation

CH3 CH3 CH3 CH3

Br2

Br

Br Br2

Br

Br

Br

Br

Alkynes are capable of many of the same reactions as alkenes, but twice if enoughreagent is used, e.g. addition of bromine:

More on polymerisation later in the course (Professor Haddleton).

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Cycloaddition reactions of alkenes: The Diels-Alder reaction.

Alkene(dienophile)

Reaction is concerted i.e. all bonds are formed and broken at the same time:

a conjugated diene

O

O

O

+

O

O

O

O

O

O

Complete the diagram below:

Stereochemistry: Bonds are formed on one face of the alkene, hence there is a high degree of stereocontrol.

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Alkene hydroboration reaction (important)!

What happens if you carry out acid-catalysed hydration (addition of water).

Overall reaction (reagents to be added):

OH

H , H2O?

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Hydroboration mechanism – to be completed in lecture:

Concerted addition of B-H bond across the alkene -boron adds to least hindered end:

OH

BH3

All the B-H bondsare utilised.Three alkenes addto one borane.

HO-OB B

O

OB

+ B(OH)3

i) BH3

ii) H2O2, HO

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Reduction reactions of alkenes: and alkynes, stereochemistry – formation of cis alkenes by hydrogenation.

H HNH2

HNaNH2

HEtI

I

i) NaNH2

ii)Br

R1 R2

First you need to make a substituted alkyne:

Why do you need to use NH2? Can you use EtO or Et3N?

This is the key reduction reaction:

H2 (gas), Pd/C, quinoline

or H2 (gas), Lindlar catalyst

R1 R2

catalyst surface

H H

Why is the quinoline added to the catalyst? What happens if you do not add it?

The reduction takes place on a surface, and the hydrogen is transferred to one side of the alkyne.

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trans Alkenes can also be formed from alkynes:

R1 R2Na, NH3, then H

This is commonly known as ‘reducing metal’ reduction. It works by a mechanism in which‘electrons’ are generated from the metal. Li, K and Mg are also sometimes used.

Here is the mechanism:

tBuOH is often used as a source of protons.

R1 R2

Na +

R1

R2

R1

R2

R1

R2

R1

R2

R1R2

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Reduction of alkenes to alkanes – hydrogenation most commonly used:

Relative rate of hydrogenation:

fast reductionslow reduction

Commonly usedMetals:

Commonly usedSupports:

Stereochemistry:

Why use a support, how does the reaction work?

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Hydrogenation of alkenes to make margarine:

CO2H Linolenic acid mp -11 oC

H2 / Ni

CO2H Linoleic acid mp -5 oC

H2 / Ni

CO2H Oleic acid mp 16 oC

H2 / Ni

CO2H Stearic acid mp 71 oC

Polyunsaturated vegetable oil.

Fully saturated fatty acid.

Saturated fats have high melting points because they pack more efficiently.

Polyunsaturated fats are regarded as healthier than saturated ones but tend to be liquids so They are partially hydrogenated to make margarine – solid but still with double bonds in..

Prof M Wills 45

Alkene oxidation reactions:

H R2

R1 H

RO

O OHH R2

R1 H

peracid

Epoxide

H R2

R1 HThe bond in alkenesis very reactive.

OsO4

osmium tetroxide

H R2

R1 H

diolO3

R2

H

H

R1

+

Alkene oxidation reactions can give epoxides, diols, or even ketones from complete cleavage of the alkene.

What is the structure of ozone? Why might these products be useful?

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Epoxidation of alkenes using peracids:

H R2

R1 H

ArO

O O

mCPBA

H

H

R2R1

HAr

O

O O

mCPBA

H

trans (E) alkene cis (Z) alkene

O

O O

H

Cl

This is mCPBA, (meta-chloroperbenzoic acid)which is a commonly used peracid

ArO

O O

H

Learn the mechanism:Ar

OO

OH

H R2

R1 H

H R2

R1 H

This is one of the best mechanisms!

Prof M Wills 47

Ozonolysis of alkenes cleaves the double bond:

H R2

R1 H

H

R1

R2

H

i) O3

ii) reducing agent(e.g. Zn metal, Ph3P, Me2S

H R2

R1 H

H

R1

R2

H

H

R1

R2

H

ozonide

reducing agent

+

Predict the products from:

i) O3

ii) reducing agent(e.g. Zn metal, Ph3P, Me2S

OMe i) O3

ii) reducing agent(e.g. Zn metal, Ph3P, Me2S

Prof M Wills 48

Alkene dihydroxylation:

Potassium permanganate (KMnO4)

Mn

O

O

O

O

Os

O

O

O

O

2 H2O

2 H2O

What products are formed usingthe following alkenes and OsO4?

i) OsO4

ii) 2 H2O

i) OsO4

ii) 2 H2O

Note – OsO4 is expensive and very toxic. Better to use it catalytically (how would you do this?).

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The Wacker Oxidation:

R1

catalytic PdCl2, H2O, O2, CuCl2

R1

O

+

This is a commercial reaction used on a large scale in industry.The CuCl2 and O2 reoxidise the PdCl2 (Pd is expensive).

Prof M Wills 50

What you should understand and know:

• MECHANISM OF REACTIONS AT SATURATED CARBON ATOMSThe mechanisms and stereochemical implications of SN2 and SN1 reactions. Inversion with SN2, racemisation with SN1. Factors which determine the likely pathway. Alternative leaving groups. Examples of applications in synthesis.

• SYNTHESIS AND REACTIONS OF ALKENES (C=C)E1 and E2 elimination mechanisms. Stereoselective alkene synthesis from alkynes by hydrogenation and dissolving metal reduction; Wittig reaction including ylid formation and mechanism; hydrogenation of alkenes; epoxidation, dihydroxylation and ozonolysis of alkenes; hydration and hydroboration of alkenes; Wacker oxidation; Diels-Alder cycloaddition.