© The Royal Society of Chemistry The Basics of Organic Mechanism What is this resource and who is it for? This is an Open Educational Resource designed to summarise key concepts in organic chemistry that are required for entry to an undergraduate course. The resource is designed for 1 st year undergraduates and revisits ideas from A-level. It also begins to show how they are applied early in a University course.Open Educational Resource It is therefore anticipated that you will have some knowledge of A-level chemistry before undertaking the activity but even with good subject knowledge, there should also be some material here you are unfamiliar with. This resource is not designed to support any specific A-level specification but may also be used in schools alongside other resources where appropriate. Learning Objectives On completion of this activity you should be able to … Use the hybridisation model to explain the bonding in alkanes and alkenes in terms of  and  bonds. Use curly arrows to represent the movement of electrons in nucleophilic substitution reactions and electrophilic addition reactions. Explain the differences between the S N 1 and S N 2 mechanisms and where they occur. Appreciate some limitations of the curly arrow model Related Resources The use of curly arrows to explain the properties of organic acids and bases is discussed in the acid/base resource.     Who made it? Declan Fleming worked at the University of Bath as a Teacher Fellow as part of The Royal Society of Chemistry’s work under the National HE STEM Programme. Part of his remit was looking into ways that e-learning can be used to support students at the KS5/HE interface.National HE STEM Programme Declan’s work is copyright The Royal Society of Chemistry.

© The Royal Society of Chemistry In order to describe the orbits of electrons, we need to think of them as waves. We talk about orbitals and often represent them as shapes in which we have a high probability of finding an electron. What is a bond? (1) One property of waves is interference. Where two waves of the same phase meet, they will combine to make a larger wave (constructive interference). If they are out of phase, they will cancel each other out (destructive interference). This animation shows both types of interference occurring. Image by: JoanjocJoanjoc Image by: HaadeHaade Animation by: Oleg AlexandrovOleg Alexandrov

© The Royal Society of Chemistry A build up of electron density occurs between the nuclei when electrons are put into this kind of orbital and a bond is formed. If they are out phase they will form an “anti-bonding” molecular orbital. There are two ways atomic s-orbitals can meet. If they are in phase they will form a bonding molecular orbital. What is a bond? (2) Different colours are used to represent the phase of atomic orbitals. Often simply black and white. Sometimes you will see people include a “+” and “-” sign instead. It all means the same thing. + H H H-H + H HH This is known as a  (sigma) bond There is no electron density between the nuclei when electrons are put into this kind of orbital – this causes a bond to be broken. © The Royal Society of Chemistry

This can be used to explain why we form H 2 but not He 2 … E HH H-H   What is a bond? (3) He He-He   E 1s When H atoms combine, both electrons go into a bonding orbital – a bond results. When He atoms combine, the same number of electrons go into an anti-bonding orbital as the bonding orbital so no overall bond occurs. HOMO Highest Occupied Molecular Orbital LUMO Lowest Unoccupied Molecular Orbital © The Royal Society of Chemistry

Image by: Ben MillsBen Mills © The Royal Society of Chemistry

Although we talk about carbon as having “4 electrons in its outer shell” when we draw dot-cross diagrams to represent bonding, we know that in reality there are 2 unpaired electrons in its outermost energy level. Hybridisation E degenerate sp 3 hybrids Considering the energy payback possible from forming more covalent bonds, carbon mixes or hybridises its 2s and 2p orbitals to form 4 new degenerate (of the same energy) orbitals called sp 3 hybrids. E All at same energy: degenerate Notice characteristics of s and p orbitals The name tells us they came from an s and 3 p orbitals C: 1s 2 2s 2 2p 2 Image by: SvenSven

© The Royal Society of Chemistry Hybridisation Methane is formed from 4 sp 3 hybrids combining with the 1s orbitals on hydrogen atoms Remember this is still a model! This is known as a sigma (  ) bond because if you look down the axis of the bond, it looks like an s- orbital.  bond between carbon atoms  bond between C and H atoms  bond between carbon atoms In ethene, there are 3 sp 2 hybrids and 1 p orbital on each carbon. The bonding with H is as before but now two bonds (a  and a  ) can form between the carbon atoms  120  Why  ? Hybridisation Methane is formed from 4 sp 3 hybrids combining with the 1s orbitals on hydrogen atoms Remember this is still a model! This is known as a sigma (  ) bond because if you look down the axis of the bond, it looks like an s- orbital.  bond between carbon atoms  bond between C and H atoms  bond between carbon atoms In ethene, there are 3 sp 2 hybrids and 1 p orbital on each carbon. The bonding with H is as before but now two bonds (a  and a  ) can form between the carbon atoms  120  Why  ? © The Royal Society of Chemistry

When a bond breaks (also known as fission or dissociation), it can do so in one of two ways: Homolytic Fission or Heterolytic Fission. We can use curly arrows to represent the movement of the electrons Breaking Bonds – Heterolytic Fission H H Two electrons are needed to make a single covalent bond. One from each atom. A curly arrow with a full arrowhead is used to show the movement of two electrons. This atom has gained one electron so has a negative charge (remember one electron already belonged to it) This would be written as follows. Note that the arrow starts where the electrons have come from (the bond) and finishes where they end up (the right hand hydrogen atom)

© The Royal Society of Chemistry When a bond breaks (also known as fission or dissociation), it can do so in one of two ways: Homolytic Fission or Heterolytic Fission. We can use curly arrows to represent the movement of the electrons Breaking Bonds – Homolytic Fission HH Two electrons are needed to make a single covalent bond. One from each atom. A curly arrow with a half or fish-hook arrowhead is used to show the movement of one electron This atom has only regained the electron it was already contributing to the bond. It is neutral but has an unpaired electron so it is known as a radical. This would be written as follows. Note that the arrows start where the electrons have come from (the bond) and finish where they end up (the atoms).. The dots are optional. They represent the unpaired electrons.

© The Royal Society of Chemistry

Electronegativity (the ability of an atom to attract a pair of electrons within a covalent bond) increases across a period as nuclear charge increases and atomic radius is slightly reduced. Electronegativity decreases down a group as atomic radius increase whilst the increase in the nuclear charge is balanced by the increase in the number of shielding electrons Bond Polarity Increasing electronegativity ++ -- This colour map shows the distribution of charge in the Cl 2 molecule. Notice how the molecule is symmetrical This colour map shows the distribution of charge in the HCl molecule. Notice how there is an extra build up of charge density to the right of the Cl atom The bond is said to be polar. The Greek letter  is used to indicate a small change – in this case where the small change is in charge density, we use it to represent a partial charge. Image by: JoanjocJoanjoc © The Royal Society of Chemistry

Nucleophiles are species that have a lone pair of electrons available to form a covalent bond with electrophiles. They will be found with either a full or a partial negative charge on one atom. Nucleophiles Lone pair forming a bond Ammonia as a nucleophile reacting with chloromethane ++ -- ++ -- Both molecules are polar because of the high electronegativity of N and Cl compared to H and C respectively. This bond will break This type of reaction is known as nucleophilic substitution. A nucleophile attacks an electrophile forming a bond. The carbon atom can only support 4 bonds so another is broken and a leaving group (here Cl) is substituted out. : © The Royal Society of Chemistry

There are two major pathways a nucleophilic substitution can take… Nucleophilic Substitution: S N 2 Rate = k[H 3 CBr][OH - ] Rate determining step contains both molecules* Nucleophile Lone pair(s) Negative charge Electrophile Partial positive charge Br leaving group E Transition State S N 2 Bimolecular Nucleophilic Substitution Animation is © 2001 by Daniel J. BergerDaniel J. Berger *only one step (correctly) assuming there are no faster steps after this one !

© The Royal Society of Chemistry There are two major pathways a nucleophilic substitution can take… Nucleophilic Substitution: S N 1 Rate = k[(H 3 C) 3 CBr] Slow first step involving only (H 3 C) 3 CBr followed by fast addition of nucleophile Carbocation Positively charged carbon E S N 1 Unimolecular Nucleophilic Substitution Vacant p-orbital Compare this animation to the previous one. Which type of mechanism will produce a pure product and which could produce a mixture of products? Two steps, the first has a larger E a so happens much more slowly slowfast Animation is © 2001 by Daniel J. BergerDaniel J. Berger

© The Royal Society of Chemistry As we move from a primary to a tertiary carbon two things happen... Nucleophilic Substitution: Why does S N 1 happen? The carbon atom that is to be attacked becomes more sterically hindered by the surrounding atoms. The carbocation becomes more stable due to inductive effects and hyperconjugation Electrons in adjoining  -bonds to hydrogens that are  to the carbocation can stabilise it by forming an extended molecular orbital. This is called hyperconjugation Although not usually referred to as a polar bond, there is a difference in electronegativity between C + H which results in charge being pushed towards the vacant p-orbital to stabilise it. This is an inductive effect © The Royal Society of Chemistry

How attractive will the carbon be to the nucleophile? Bond Polarity – increases up the group What factors affect the speed of nucleophilic substitution? How easy will it be to break the carbon-halogen bond? Bond Strength – increases up the group. A simple experiment can be performed to determine which of these factors is the most important using silver nitrate solution which will form silver halide precipitates in the presence of the halide ions released in the reaction. A precipitate will be formed from the reaction of CH 3 I before it will from CH 3 Cl indicating that bond strength is more important to the rate of the reaction. AgCl precipitation i.e. how effective is our leaving group? Image by: LupoLupo Image by: Dr. TDr. T

© The Royal Society of Chemistry Electrophiles Electrophiles are species that can accept a pair of electrons from a nucleophile to form a covalent bond. ++ -- ++ -- Electrophilic Addition Markovnikov Product : Major product comes from reaction via most stable carbocation Secondary carbocation  -bond formed from the overlap of 2 p-orbitals

© The Royal Society of Chemistry Chemguide.co.uk Further Reading The hybridisation model can be used to explain the bonding in alkanes and alkenes in terms of  and  bonds. Curly arrows can be used to represent the movement of electrons in nucleophilic substitution reactions and electrophilic addition reactions. S N 1 is a mechanism that has 2 steps and happens with sterically hindered tertiary carbon centres which can be stabilised by inductive effects and hyperconjugation. S N 2 is a mechanism with 2 molecules in one step that occurs with primary carbon centres.   

© The Royal Society of Chemistry Image Credits Other images are public domain or by Declan Fleming. By Ben MillsBen Mills Thanks to David Read, Paul Wyatt and Ian Williams for their feedback on and input into this resource. By LupoLupo Copyright © Included in this resource with the kind permission of Daniel J. Berger. Daniel J. Berger By Dr. TDr. T By SvenSven By JoanjocJoanjoc By HaadeHaade By Oleg AlexandrovOleg Alexandrov By JoanjocJoanjoc This resource was created by Declan Fleming. The content of this resource, together with The Royal Society of Chemistry’s name, is subject to a Creative Commons licence on an “Attribution, Non-Commercial, Share-Alike” basis. The HE STEM Programme name and logo are the name and registered marks of the University of Birmingham. To the fullest extent permitted by law the University of Birmingham reserves its rights I its name and marks which may not be used except with its prior written permission.