Doc Brown's Chemistry Advanced Level Pre-University Organic Chemistry Revision Study Notes for UK KS5 A/AS GCE advanced level organic chemistry students US K12 grade 11 grade 12 organic chemistry mechanisms introduction definitions and examples of terms used in organic chemistry

Revising Advanced A Level Organic Chemistry Mechanism Revision Notes

PART 10 Summary of organic reaction mechanisms - a mechanistic introduction to organic synthetic chemistry and explanations of different types of organic reactions

10.1 INTRODUCTION to types of organic reactions and mechanisms

and a  broad sort of alphabetical glossary of terms used in organic chemistry

including page with links to detailed revision-information notes on organic synthesis reaction mechanisms

IMPORTANT DEFINITIONS and ORGANIC CHEMISTRY TERMINOLOGY

Technical terms explained! 

Links to revision notes that include full diagrams and explanation of the mechanisms and the 'molecular' equation and reaction conditions and other con-current reaction pathways and products are also explained. I've also included other terms that are of general importance in organic chemistry

Alphabetical list of organic chemistry terminology

DETAILED INDEX of all the mechanisms of organic synthesis reactions covered

PLEASE NOTE

• Whatever their abstract nature (and 'truthfulness'!), a study of mechanisms is important to understand how organic chemical reactions take place and why molecules react in a particular way.

  • It also allows predictions of what might happen to an organic molecule with a particular reagent.

  • They also explains why, in many cases, there is more than one expected organic product of the reaction or an unexpected product is formed.

• Many of the graphic images are quite compressed in design.

  • This is quite deliberate, so that they will fit on screen plus text lines in future quizzes.

  • I'm currently producing some larger style mechanism diagrams on various new organic chemistry pages.

• The image numbers mechanism 1, 2, 3 etc. are NOT meant to be sequential, its just the order they were drawn!

• Unless otherwise stated R or R' = H, alkyl (e.g. -CH₂CH₃) or aryl (e.g. C₆H₅),

  • and for simplicity, R₂ or R₃ does not imply that the 2 or 3 R groups have to be the same.

• abstraction: When one reacting species removes an atom/ion from another molecule, radical or ion.

  • e.g. a methyl radical abstracts a chlorine atom from a chlorine molecule

    • CH₃^. + Cl₂ ===> CH₃Cl + ^.Cl  (see mechanisms Part 10.2)

  • or a water molecule abstracting a proton from a protonated alcohol molecule

    • H₂O + CH₃CH₂OH₂⁺ ===> H₃O⁺ + CH₃CH₂OH  (see mechanisms Part 10.5)

    • Though the phrase proton transfer is more appropriate here.

• activated complex: An unstable or 'transient state' formed when two reactant particles collide with sufficient kinetic energy in a reaction mechanism step. The activated complex breaks down to give the products.   (see mechanisms Part 10.4)

• activation energy E_a: The minimum energy reacting particles must possess in order to form an 'activated complex' or transition state before forming the products.

  • Its the top of the hump on a reaction progress energy profile diagram.   (see mechanisms Part 10.4)

  • 

• acylation: The introduction of a R-C=O group into a molecule e.g. benzene (R = alkyl or aryl).  

  • C₆H₆ + CH₃COCl  ===>  C₆H₅COCH₃  +  HCl

  • (see electrophilic substitution mechanisms Part 10.8)

• acylonium ion: A type of carbocation formed in the electrophilic substitution acylation of aromatic compounds

  • e.g. CH₃-C⁺=O or CH₃CO⁺  where the positive charge is carried on the carbon of the C=O bond.

  • They are formed in e.g. the aluminium chloride catalysed acylation of aromatic compounds.   (see mechanisms Part 10.8)

• addition reaction: The adding of one molecule to another with no other product, but not necessarily in a single reaction step mechanism. Most of such reactions (you will come across at this stage) involve addition of a reagent across a double bond (e.g. C=C or C=O) with an initial single product.

  • With alkenes (and sometimes aldehydes/ketones) you are changing from an unsaturated molecule to a saturated one.

  • The molecule is usually added in two parts across e.g. a double bond

    • e.g. electrophilic addition of hydrogen halide to alkenes:

      • >C=C< + HX ==> >CH-CX<   (see mechanisms Part 10.3)

      • CH₃CH=CH₂  +  HBr  ===>  CH₃CHBrCH₃

    • or nucleophilic addition of hydrogen cyanide to aldehydes/ketones to give hydroxy-nitriles

      • >C=O + HCN ==> >C(OH)-CN   (see mechanisms Part 10.6)

      • CH₃CH₂CHO  +  HCN  ===>  CH₃CH₂CH(OH)CN

    • These reactions often involve two steps (one for each 'bit' of the reagent) in the mechanism.

• addition polymerisation  see polymerisation

• alkoxy group: An alkyl-oxygen part of a molecule e.g. CH₃CH₂-O- is an ethoxy group.

• alkyl group: A saturated section of a molecule derived from an alkane e.g.

  • -CH₃ methyl, -CH₂CH₃ ethyl, or -CH₂CH₂CH₃ propyl etc.

• alkylation: The introduction of an alkyl group into a molecule e.g. into a benzene (R = alkyl or aryl).  

  • e.g. C₆H₆  +  CH₃Cl  ===> C₆H₅CH₃  +  HCl (see electrophilic substitution mechanisms Part 10.8)

• arrows, use of curly arrows in mechanisms:

  • A half-arrow head means a single electron shift (movement) and a full arrow head shows an electron pair shift (movement) and used in the context of making or breaking bonds.

  • A full arrow can indicate:

    • Starting from an electron rich pi (π) bond and moving electrons towards an atom to form a new bond.

    • Starting from a pi (π) or sigma (σ) bond, moving an electron pair to form a negative ion.

    • Starting from an atom or ion, a pair of electrons moves towards another atom to form a bond.

  • Examples: 1. to 2. show pairs of single electron shifts and 3. to 6. show bond pair shifts.

  1. The bonding pair of electrons of the chlorine molecule is split between the two chlorine atoms/radicals on homolytic bond fission in the initiation of a free radical chain reaction.   (for 1. and 2. see mechanisms Part 10.2) This is easily achieved using uv radiation: Cl₂  == uv photon ==> 2Cl• (•is the unpaired electron)

      

  2. One electron from each radical pairs up to form a C-Cl covalent bond in a free radical chain termination step.    (for 1. and 2. see mechanisms Part 10.2)

      

  3. A bond pair from the alkene pi bond is donated to a proton on the oxonium ion, H₃O⁺, forming a C-H bond and simultaneously the H-O bond pair moves completely on to the oxygen to form a lone pair of non-bonding electrons on the negative hydroxide ion.   (see mechanisms Part 10.3)

      

  4. A hydroxide ion, OH^-, donates a lone pair of non-bonding electrons to a carbon atom to form a C-OH bond and simultaneously the C-Cl bond pair shifts to become a lone pair of electrons on the chlorine atom as a chloride ion is formed.   (see mechanisms Part 10.4)

      

  5. The cyanide ion, ^-CN, donates a lone pair of electrons to form a C-N bond and simultaneously one of the C=O bond pairs moves completely on to the oxygen to form a lone pair of non-bonding electrons and giving the oxygen atom an overall single positive charge.   (see mechanisms Part 10.6)

      

  6. The C-H bond pair shifts to complete the π (pi) electrons of the benzene ring and simultaneously a hydrogensulfate ion donates a lone pair and forms an H-O bond in forming a sulphuric acid molecule.    (see mechanisms Part 10.8)

      

• aryl group: A section of a molecule derived from aromatic compounds like benzene or methylbenzene

  • e.g. the phenyl group is the simplest, C₆H₅- or

• attacking ... : A somewhat dramatic term applied to the 'active' reagent that directly interacts with the organic 'substrate' molecule in question. You can use phrases like 'nucleophilic attack' or 'electrophilic attack'.

  • e.g. the nucleophile OH^- 'attacking' the positive carbon of the polarised C^δ+-Cl^δ- bond in a nucleophilic substitution of a halogenoalkane,

  • or the positive part of the polarised H^δ+-Br^δ- electrophile attacking the π electrons of an alkene double bond in an electrophilic addition reaction.

• 'bimolecular' in a mechanism or kinetics context e.g. in the context of a collision between two particles (molecules or ions).

  • It may infer a single step 'bimolecular' mechanism with a 2nd order kinetics rate expression see e.g. S_N2

• bond fission: This means breaking a bond between two atoms to give two 'fragments' (atoms, ions or molecules), but there are two modes of fission, depending on what happens to the original bonding pair of electrons.

  • This is illustrated below by the breaking of a C-Br (or C:Br) bond.

  • Heterolytic bond fission: The bonding pair of electrons (ox below) leaves with one of the fragments and leads to positive and negative ion formation from the original electrically neutral molecule. Typically this follows from the bond polarity e.g.  C^δ+-Cl^δ- due the difference in electronegativity (Cl > C).

    • i.e. for 2-chloro-2-methylpropane, the formation of a carbocation and chloride ion.

    • (CH₃)₃C:Cl ===> (CH₃)₃C⁺ + :Cl^-    (see mechanisms Part 10.4)

    • Left is the theoretical diagram of the heterolytic bond fission of chloromethane for comparison with its homolytic bond fission described below.

    • The 'fragment' taking the bonding pair of electrons becomes a negative and the other 'fragment' must automatically be a positive ion.

      • Only the outer electrons need to be shown in such dot and cross diagrams of ions.

    • In fact chloromethane will NOT undergo heterolytic bond fission BUT 2-chloro-2-methylpropane will, but in each case the diagrams illustrate what happens to the bonding pair of electrons (ox).

  • Homolytic bond fission: The bonding pair of electrons is 'split' between the two fragments each with an unpaired electron and leads to the formation of free radicals (initiated by heat or uv light).

    • e.g. both 'fragments' or free radicals retain one of the bonding electrons:

    •  H₃C:Cl ===> H₃C^. + Cl^.  (see mechanisms Part 10.2)

    •   Left is the theoretical diagram of the homolytic bond fission of chloromethane, and a methyl radical and chlorine atom free radicals are formed.

      • Only the outer electrons need to be shown in such dot and cross diagrams of free radical.

    • Homolytic bond fission commonly occurs with organic molecules at high temperatures (high energy thermal collisions) or subjected to uv radiation (photon quantum energy can be sufficient to break strong covalent bonds).

    • This is easily achieved for chlorine using uv radiation: Cl₂  == uv photon ==> 2Cl• (•is the unpaired electron)

      • This is the initiation step in chlorine - alkane free radical reaction to synthesise halogenoalkanes.

• bromonium ion:  A form of carbocation produced in the 1st step of the electrophilic addition of bromine to an alkene. It involves a C-Br-C bonded triangle which carries the positive charge. The addition of chlorine proceeds in the same way via a chloronium ion.   (see mechanisms Part 10.3)

• carbocation: A positive ion derived from an organic molecule where the charge is usually carried by a carbon atom e.g. the ethyl carbocation is CH₃CH₂⁺ 

  • and note that the three bonds from the carbon carrying the positive charge are in a trigonal planar configuration (2 x C-H and a C-C in this case).   (see mechanisms Part 10.3)

  • Note you will come across the same type of positive ion in mass spectrometry.

  • The stability of carbocations is usually: tertiary R₃C⁺ > secondary R₂CH⁺ > primary R-CH₂⁺

    • where R is alkyl with an ensuing inductive effect (+I) of stabilisation.

• chain reaction : Here the term is often used in the context of highly reactive free radicals, where in a reaction step, one radical brings about a chemical change and forms another reactive radical to continue the reaction.   (see mechanisms Part 10.2)

  • e.g. a chain propagation step in uv/Cl₂ chlorination of alkanes

    • CH₃^. + Cl₂ ===> CH₃Cl + ^.Cl

      • where the chlorine radical/atom ^.Cl can continue the reaction because of its unpaired electron.

• Condensation polymerisation  see polymerisation

• cracking : The thermal decomposition of alkanes into lower alkanes and alkenes by free radical or ionic mechanisms.

• curly arrows showing electron shifts and 'attacking' points on a substrate molecule: see arrows

  • Starting from an electron rich pi (π) bond and moving electrons towards an atom to form a new bond.

  • Starting from a pi (π) or sigma (σ) bond, moving an electron pair to form a negative ion.

  • Starting from an atom or ion, a pair of electrons moves towards another atom to form a bond.

• E1: Shorthand for an elimination reaction in which the rate determining step 'appears' to involve only one of the reactant molecules or intermediate (X) and the rate is independent any other reactant or intermediate.   (see mechanisms Part 10.4)

  • This results in overall 1st order reaction kinetics: e.g. rate = k₂[X]

  • However, the reaction must still go via a collision with another molecule, but it doesn't have to be a reactant molecule, so this other molecule doesn't show up in the equation e.g. it is most likely to be a solvent molecule.

• E2: Shorthand for an elimination reaction in which the rate determining step is a bimolecular collision of two reactant molecules or intermediates (X and Y) and the rate is independent any other reactant or intermediate.   (see mechanisms Part 10.4)

  • This results in overall 2nd order reaction kinetics: e.g. rate = k₂[X][Y]

• electron shift: see use of arrows in mechanisms

• electronegativity: The electron attracting power of an atom in a covalent bond situation.

  • The electronegativity difference between the two atoms of a bond is indicative of whether there is a significant electron shift towards one atom towards the other, or not as the case maybe.

    • It is an important concept in descriptions of relative reactivity and the detailed description and explanation of a reaction's mechanism.

  • One of the most common scales used is the Pauling electronegativity and a selection of values is listed.

    • e.g. Na 0.9, Al 1.5, C 2.1, H 2.1, P 2.1, S 2.5, Br 2.8, Cl 3.0, N 3.0, O 3.5, F 4.0

  • The concept is important when considering polar bonds, which arise when there is a significant electronegativity difference between two atoms in a bond. The bigger the difference, the more polar the bond. Polar bonds can determine how a molecule reacts in terms of which part of the structure of a molecule changes, how reagents react and what reagents the molecule will react with. The more electronegative atom carries the ^δ- charge e.g. ...

    • The C^δ+ in the polar bond C^δ-Cl^δ- in halogenoalkanes are susceptible to nucleophilic attack by electron pair donors.   (see mechanisms Part 10.4)

    • The C^δ+ in the polar bond >C^δ+=O^δ- in aldehydes/ketones/acyl chlorides etc. are susceptible to nucleophilic attack by electron pair donors.   (see mechanisms Part 10.6)

    • The polarised hydrogen bromide molecule, H^δ+-Br^δ-, acts as an electrophile by proton donation in which the proton (H atom) of the HBr acts as a H⁺ ion and accepts a pair of electrons to form a C-H bond.   (see mechanisms Part I)

    • Examples of electrophiles: Br⁺ (from polarised bromine molecule), H⁺ from an acid, NO₂⁺ in nitration reactions.

    • For more see electrophile notes below.

• electrophile: A 'reagent' atom, ion or molecules that can accept a pair of electrons (Lewis acids) from an 'electron rich' part of a molecule like the π electrons of an alkene/arene or a δ- carbon atom and form a covalent bond.

  • i.e. the 'electron deficient' electrophilic reagent attacks a region of high electron charge in another molecule.

  • They act as Lewis acids (and often Bronsted-Lowry acid too), i.e. electron pair acceptors when interacting with molecules such as alkenes and arenes.

  • (see alkene addition mechanisms or aromatic electrophilic substitution mechanisms)

  • Electrophiles are either positive ions, polarised molecules or electron deficient molecules - all capable of accepting a pair of electrons (see some examples in the electronegativity section above)..

  • e.g. Br₂ (on collision Br^δ+-Br^δ-), CH₃CH₂⁺, Br⁺, SO₃, H^δ+-^δ-OSO₂OH (H₂SO₄), H^δ+-Br^δ-, NO₂⁺

• electrophilic attack: The interaction of an electrophile reagent (electron pair acceptor) with an electron pair donor prior to forming the products of that mechanism step e.g. 'attacks' on .... 

  • Alkenes or or   etc.

    • above are three examples of electrophilic attack on alkenes - electron pair donors (see alkene mechanisms)

  • Arenes or or or

    • and four examples of electrophilic attack on benzene - electron pair donor, the simplest arene or aromatic hydrocarbon.  (see aromatic mechanisms)

• electrophilic addition: An electrophilic reagent adds to a molecule to give the product (without any elimination).

  • e.g. hydrogen bromide adding to an alkene >C=C<  +  H-Br  ===>  >CH-CBr<.

    • (see alkene mechanisms)

• electrophilic substitution: An electrophilic reagent replaces an atom or group of atoms in another molecule.

  • e.g. the nitration of benzene. C₆H₆  +  HNO₃  ===> C₆H₅NO₂ + H₂O

  • where a H in the benzene ring replaced by NO₂ via the electron pair accepting electrophile, the NO₂⁺ ion.

    • (see aromatic mechanisms)

• elimination reaction: A small molecules is eliminated (removed) from a larger molecule, often by combining two fragments from adjacent atoms. This is often water and an unsaturated molecule is formed e.g.

  • >CH-C(OH)< ===> >C=C< + H₂O 

    • CH₃CH₂OH  ===>   CH₂=CH₂  +  H₂O

    • e.g. loss of water, dehydration of an alcohol to give an alkene, see alcohol mechanisms)

  • >CH-C(Br)< + KOH ===> >C=C< + H₂O + KBr

    • CH₃CHBrCH₃  +  KOH  ===>  CH₃CH=CH₂  +  KBr  +  H₂O

    • e.g. loss of HBr, alkene formation from a halogenoalkane, see halogenoalkane mechanisms)

• free radical: An atom or fragment of a molecule with an unpaired electron, often shown by a dot. (see alkane mechanisms)

  • They are usually highly reactive species e.g. a chlorine atom Cl• or a methyl radical CH₃•

  • Free radicals are very reactive because the unpaired electron makes the radical unstable, and it will seek to pair up with another electron i.e. in stable covalent bond formation.

  • In reaction mechanisms they are usually formed by a homolytic bond fission.

  • e.g. in the chlorination of alkanes the 1st step is:   Cl₂ == uv ==> 2Cl•

  • but they also abstract atoms from other molecules  e.g. Cl•  +  CH₄  ===>  HCl  +  •CH₃

    • and that another free radical is formed to continue a chain reaction - in free radical mechanisms it is known as a propagation step.

• functional group: An atom or group of atoms in an organic molecule that confers on that molecule a particular set of characteristic chemical reactions. (see summary of functional groups)

• heterolytic bond fission: see bond fission

• homolytic bond fission: see bond fission

• homologous series: a series of chemically similar compounds with closely related general formulae,

  • e.g. C_nH_2n+2 for alkanes, where the only difference may be more/less -CH₂- groups in the longest carbon chain of the molecule.

  • Members of a homologous series will have the same functional group and undergo a similar set of chemical reactions AND would show similarity in reaction mechanisms. (see summary of functional groups)

• hydrolysis: A reaction, usually in aqueous media based solvent, between one molecule and water/acid/alkali which leads to the formation of at least two products e.g.

  • the tertiary halogenoalkane 2-chloro-2-methylpropane, reacts with water to form 2-methylpropan-2-ol and hydrochloric acid. (see halogenoalkane mechanisms)

    • (CH₃)₃C-Cl  +  2H₂O  ===> (CH₃)₃C-OH  +  H₃O⁺  +  Cl^- 

  • The ester methyl ethanoate forms sodium ethanoate and methanol when refluxed with aqueous sodium hydroxide.

    • CH₃COOCH₃  +  NaOH  ===>  CH₃COONa  +  CH₃OH

    • Hydrolysis of an ester with potassium/sodium hydroxide is sometimes called saponification.

  • The ester methyl ethanoate forms ethanoic acid and methanol when refluxed with dilute hydrochloric acid.

    • CH₃COOCH₃ + H₂O ===> CH₃COOH  +  CH₃OH

  • Aliphatic acid/acyl chlorides readily hydrolyse back to the parent carboxylic acid with water. (see mechanisms Part 10.7)

    • RCOCl + 2H₂O ===> RCOOH + H₃O⁺ + Cl^- 

  • These are also usually substitution reactions and usually mechanistically involve water, proton or hydroxide ion attack on the substrate organic molecule.

• initiation step: The name of the 1st step in a reaction mechanism sequence. The term is usually applied to the 1st step in free radical chain reactions, when the initial radicals are formed. (see alkane mechanisms)

  • e.g. in the chlorination of methane the 1st step is: Cl₂ ==hv==> 2^.Cl when a uv photon splits the chlorine molecule

  • or an organic peroxide splitting on heated to give two alkoxy radicals : RO-OR ==> 2RO^. 

• isomeric products: This means two or more products from the same reaction which have the same molecular formula but different molecular structure (e.g. positional isomerism). [see detailed notes on ISOMERISM]

  • This can happen when e.g. an unsymmetrical reagent like HX adds to an unsymmetrical alkene, because you can theoretically add H-X or X-H across an R₂C=CR'₂  double bond where R and R' are different.

    • e.g. adding hydrogen bromide to a non-symmetric alkene

    • R₂C=CR'₂ + HBr ===> {R₂CH-CBrR'₂ or R₂CBr-CHR'₂}

• Lewis acid: An atom, ion or molecule that can accept a pair of electrons to form a bond.

  • Electrophiles are Lewis acids - electron pair acceptors.

  • e.g. organic reaction examples include Br⁺, CH₃⁺, or the polar H^δ+-Br^δ- and H^δ+-O^δ-SO₂OH (H₂SO₄)

• Lewis base: An atom, ion or molecule that can donate a pair of electrons to form a bond.

  • Nucleophiles are Lewis bases - electron pair donors.

  • See Lewis acid - Lewis base theory (applies to both inorganic and organic chemistry contexts).

• Markownikoff Rule (Markownikov/Markovnikov): This is a rule that predicts the orientation of electrophilic addition of an electrophile like H^δ+Br^δ- or I^δ+Cl^δ+ (in general lets call it W^δ+-X^δ-) to a non-symmetrical alkene and it can be expressed in several ways (see alkene mechanisms) e.g.

  • The negative part of the addendum, W^δ+-X^δ-, attaches itself to the carbon atom of the double bond which initially has the least hydrogen atoms bonded it to it.

  • So for an non-symmetrical alkene like propene, you would expect the majority reaction to be ...

  • CH₃CH=CH₂ + W-X ==> CH₃CHX-CH₂W

    • (much less of CH₃CHW-CH₂X, as you cannot assume zero probability of forming the other isomeric product!)

    • The rule is related to the stability of carbocations: tertiary R₃C⁺ > secondary R₂CH⁺ > primary R-CH₂⁺

      • where R is alkyl with an ensuing inductive effect (+I) of stabilisation.

• mechanism: A detailed step by step representation of how a reaction actually takes place and is far more complicated than the 'usual' stoichiometric equation because, in most cases, intermediate unstable species are shown for each step of the reaction mechanism. - it is what most of this page is about, at the end is a list of mechanism pages.

• molecularity : This can mean several things unfortunately and is frankly confusing for students at times.

  1. The number of species involved in a chemical change or reaction step. Since most reactions occur via one or more steps involving bimolecular collisions, so their molecularity is often 2.

  2. Some reactions, whose rate depends on just one reactant are described as 'unimolecular' or if the reaction depends on two reactant concentrations it may be described as 'bimolecular'. The use of the 'molecularity' here has more to do with kinetic studies of reactions (e.g. the nucleophilic substitutions of halogenoalkanes, see S_N1 and S_N2).

• non-polar bond: A 'relative term' for a bond where the to atoms have similar electronegativities and the bonding pair of electrons is more or less 'equally shared'.

  • e.g. C-H, C-C, C-P etc. (see Pauling electronegativity scale above)

• non-symmetrical/unsymmetrical alkene: An alkene in which the groups attached to each carbon of the double bond are NOT identical. (see alkene mechanisms) e.g.

  • propene CH₃-CH=CH₂, methylpropene (CH₃)₂C=CH₂ or but-1-ene CH₂=CH-CH₂-CH₃ 

  • If an unsymmetrical reagent e.g. HX is added to these, two isomeric products can be formed.

  • e.g. CH₃-CH₂-CH₂X or CH₃-CHX-CH₃ from electrophilic addition of HX to propene.

• nucleophile: An 'reagent' electron pair donor (Lewis base) that will 'attack' an electron deficient part of a molecule (δ+).

  • e.g. the 'positive' of polarised bonds W^δ+X^δ-, in halogenoalkanes C-X, or aldehydes/ketones >C=O or acyl (acid) chlorides RCOCl (or O=C-Cl) are attacked by nucleophiles. Electronegativity of O > X > C creating the polar bond.

  • In the mechanism the nucleophile donates an electron pair to an electron deficient carbon atom to form a covalent bond.

  • A nucleophile is effectively an electron pair donor (a Lewis Base and often Bronsted-Lowry base too).

  • The electron pair is usually from an oxygen or nitrogen on the nucleophile.

  • e.g. hydroxide ion :OH^-, ammonia :NH₃, ethanol CH₃CH₂OH, water H₂O:, cyanide ion :CN^-, halide ion :X^-, amine RNH₂

• nucleophilic addition: An nucleophilic reagent adds to a molecule (without any elimination). (see aldehyde/ketone mechanisms) e.g.

  • e.g. ethanal reacts with cyanide ions (the nucleophile) to form a hydroxynitrile

    • CH₃CHO + HCN ===> CH₃C(OH)CN 

    • Its the equivalent of adding H-CN across the C=O double bond.

• nucleophilic addition-elimination: A nucleophilic reagent adds to another molecule and then a small molecule is eliminated to give the final product.

  • e.g. ethanoyl chloride reacts with methanol to make methyl ethanoate and hydrogen chloride is eliminated in the process. The electron pair (on the oxygen) donating nucleophile is methanol. (see mechanisms Part 10.7)

  • CH₃COCl + CH₃OH ===> CH₃COOCH₃ + HCl 

• nucleophilic attack: The interaction of a nucleophile reagent (electron pair donor) interacting with an electron pair acceptor molecule prior to forming the initial products of that mechanism step e.g. 'attacks' on ...

  •  or or Halogenoalkanes - 3 examples

     

  • or Aldehydes and ketones - 2 examples

     

  • or Acyl chlorides - 2 examples

  • The nucleophiles illustrated here are the hydroxide ion, cyanide ion, ammonia, hydride ion and water.

• nucleophilic substitution: A nucleophilic reagent displaces/replaces an atom or group of atoms in another molecule.

  • e.g. halogenoalkanes react with electron pair donating reagents (see nucleophilic attack above).

• oxidation: A process of electron loss, increase in oxidation state of an atom or ion or oxygen gain.

  • e.g. the oxidation sequence of an alcohol  ===>  aldehyde  ===>   carboxylic acid

    • CH₃CH₂OH  + [O]  ===>   CH₃CHO  +  H₂O  then  CH₃CHO  + [O]  ===> CH₃COOH

• photochemical reaction, photodissociation and photolysis:

  • A reaction that is promoted by photons (e.g. uv radiation) is described as a photochemical reaction.

  • e.g. the reaction between hydrogen and chlorine is facilitated by uv radiation: H₂  +  Cl₂  ===>  2HCl

  • The initiation step is the homolytic bond fission of a chlorine molecule: Cl₂ == uv ==> 2Cl•

  • This is an example of photodissociation, the chlorine molecule is split by a photon of EM radiation.

  • The general term photolysis refers to any chemical reaction step in which a bond is broken by the absorption of a photon of light (visible or uv).

• polar bond: A covalent bond in which the two atoms have different electronegativities leading to an unequal sharing of the bonding pair(s) of electrons.

  • e.g. a carbon-chlorine bond C^δ+-Cl^δ- or the carbon-oxygen double bond (carbonyl) >C^δ+=O^δ- 

    • See Pauling electronegativity scale above.

    • In organic chemistry, the delta positive carbon atom of a polar bond is susceptible to attack from an electron pair donating nucleophile.

• polymerisation: The process by which thousands of monomer molecules bond together to form long chain polymer molecules.

  • Addition polymerisation only produces one product.

    • e.g. ethene ===> poly(ethene): n CH₂=CH₂  ====>  -(-CH₂=CH₂-)_n-   where n is a very large number

  • Condensation polymerisation involves the elimination of a small molecule between two monomer molecules to build up the polymer chain. Quite often two different monomer molecules are condensed together.

    • e.g. nylon-66:

• primary (prim or 1^o): A structural term in organic chemistry to indicate no or just one alkyl/aryl group are attached to the carbon or nitrogen atom of the functional group e.g.

  • bromomethane CH₃Br and 1-chloropropane CH₃CH₂CH₂Cl are primary halogenoalkanes

  • methylamine CH₃NH₂ and propylamine CH₃CH₂CH₂NH₂ are primary aliphatic amines

  • methanol CH₃OH and butan-1-ol CH₃CH₂CH₂CH₂OH are primary alcohols

  • CH₃⁺ and CH₃CH₂CH₂⁺ are primary carbocations

  • see also secondary and tertiary for comparison.

  • You can get reactivity trends e.g. in RX hydrolysis it is usually tertiary > secondary > primary for isomeric halogenoalkanes.

• propagation step: Type of mechanism step in free radical chain reactions, where a radical reacts with a substrate molecule, but also produces another reactive free radical which continues the reaction .e.g.

  • CH₃^.  +  Cl₂  ===>  CH₃Cl  +  ^.Cl

    • (which produces the product in the chlorination of methane AND a reactive chlorine radical)

    • Strictly speaking the methyl radical CH₃^. should be written as ^.CH₃ or H₃C^. because the unpaired electron is on the carbon atom.

  • RO-CH₂-CH₂^.  +  CH₂=CH₂  ===>  RO-CH₂-CH₂-CH₂-CH₂^.

    • (in the free radical polymerization of alkenes, a peroxide radical adds to an alkene (1st reactant on left) and this radical adds to another alkene molecule (right product) which is itself a radical and continue reaction building up the polymer chain until terminated!)

• protonation: Adding a proton, H⁺, to a species e.g. protonation of some organic molecules e.g.

  • CH₂=CH₂ + H₂SO₄ ===> CH₃-CH₂⁺ + HSO₄^- (in the electrophilic addition of sulfuric acid to alkenes)

  • CH₃CH₂OH + H₃O⁺ ===> CH₃CH₂OH₂⁺ + H₂O (in the OH substituted reactions of alcohols)

• quaternary (quat or 4^o): The term used to describe the alkylammonium salts formed when nitrogen is bonded to four alkyl groups i.e. all four hydrogens on the ammonium ion are replaced by alkyl groups.

  • [(CH₃)₄N]⁺Cl^- is tetramethylammonium chloride, and can be formed by multiple nucleophilic substitutions happen when e.g. bromoethane is reacted with ammonia.

• radicals: See free radicals

• rate determining step: A step in a mechanism which solely determines the rate of a reaction e.g. it might be an initiation or intermediate step with a high activation energy - but in a multi-step mechanism, other steps are also important to understand how the reaction takes place.

• reaction mechanism - see mechanism

• reduction:  A process of electron gain, decrease in oxidation state of an atom or ion or hydrogen gain or oxygen loss.

  • e.g. an alkene reduced by hydrogen gain: CH₂=CH₂  +  H₂  == Ni ==>  CH₃CH₃

• saturated molecule: A molecule in which the carbon atoms are combined with the maximum number of atoms i.e. there are no double or triple bonds such as an >C=C< or >C=O in the molecule. The term is often applied to hydrocarbons.

  • Saturated molecules tend to react mainly by substitution reactions, or less common, by elimination reactions.

  • e.g. free radical substitution reaction between alkanes and chlorine to give chloroalkanes.

  • CH₃CH₂CH₃  +  Cl₂  ===>  {CH₃CH₂CH₂Cl  or  CH₃CHClCH₃}  +  HCl

• secondary (sec or 2^o): A structural term in organic chemistry to indicate two alkyl/aryl groups are attached to the carbon or nitrogen atom of the functional group e.g.

  • 2-chloropropane CH₃CHClCH₃ is a secondary halogenoalkane

  • diethylamine (CH₃CH₂)₂NH is a secondary aliphatic amine

  • CH₃CH⁺CH₃ is a secondary carbocation

  • butan-2-ol CH₃CH₂CHOHCH₃ is a secondary alcohol

  • see also primary and tertiary for comparison

  • You can get reactivity trends e.g. in RX hydrolysis it is usually tertiary > secondary > primary for isomeric halogenoalkanes.

• shift of electrons: see use of arrows in mechanisms

• S_N1: Shorthand for a nucleophilic substitution reaction in which the rate determining step is the formation of carbocation involving just one of the reactant molecules or intermediates (X) and the rate is independent any other reactant or intermediate.

  • This results in overall 1st order reaction kinetics: e.g. rate = k₁[X]

    • and sometimes referred to as a 'unimolecular' reaction. (see mechanisms Part 10.4)

• S_N2: Shorthand for a nucleophilic substitution reaction in which the rate determining step is a bimolecular collision of two reactant molecules (X and Y) and the rate is independent of any other reactant or intermediate.

  • This results in overall 2nd order reaction kinetics: e.g. rate = k₂[X][Y]

    • and sometimes referred to as a 'bimolecular' reaction. (see mechanisms Part 10.4)

• stereospecific/stereospecificity: means the change reactants ===> products is dependent in some way on the spatial orientation of at least one of the reactants or intermediates.

  • e.g. in the key-lock mechanism of enzymes, the 'key into lock' interaction, i.e. the stereospecificity of enzymes, partly depends on the spatial orientation of the enzyme's protein structure and the shape of the substrate molecule, particularly from the point of view of bond formation or the inter-molecular force of hydrogen bonding.

• steric hindrance: This means a reaction is inhibited because of some spatial/orientation limitation, e.g. bulky groups attached to an atom/bond that theoretically is susceptible to attack by a particular reagent.

• substitution: When one atom or group of atoms is replaced by another atom or group of atoms. (see mechanism index for lots of examples).

  • e.g.   R-X  +  OH^-  ==>  R-OH  +  X^-  (where OH replaces/displaces X, hydrolysis of halogenoalkanes)

  • C₆H₆  +  HNO₃  ===> C₆H₅NO₂  +  H₂O  (NO₂ replaces H in a benzene ring, electrophilic substitution)

• symmetrical alkene: An alkene in which all the groups attached to each carbon of the double bond are identical. (see alkene mechanisms) e.g.

  • ethene H₂C=CH₂ or but-2-ene CH₃-CH=CH-CH₃ 

  • If an unsymmetrical reagent e.g. HX is added, only one product is formed.

  • e.g. CH₃-CH₂X or CH₃-CH₂-CHX-CH₃ from ethene or but-2-ene.

  • Asymmetric alkenes have different groupings attached to the two carbon atoms of the alkene double bond.

    • e.g. but-1-ene H₂C=CH-CH₂-CH₃ and two addition products are possible with a HX reagent.

• termination step : A step in a free radical chain reaction in which two radicals combine to bring that particular 'chain' to a halt.

  • e.g. in the chlorination of methane two methyl radicals can combine to form ethane. (see mechanisms Part 10.2)

    • 2H₃C^. ==> H₃C-CH₃ 

• tertiary (tert or 3^o): A structural term in organic chemistry to indicate three alkyl or aryl groups are attached to the carbon or nitrogen atom of the functional group e.g.

  • 2-chloro-2-methylpropane (CH₃)₃CCl is a tertiary halogenoalkane

  • trimethylamine (CH₃)₃N: is a tertiary aliphatic amine

  • 2-methylpropan-2-ol (CH₃)₃COH is a tertiary alcohol

  • (CH₃)₂C⁺CH₂CH₃ is a tertiary carbocation

  • see also primary and secondary for comparison

  • You can get reactivity trends e.g. in RX hydrolysis it is usually tertiary > secondary > primary for isomeric halogenoalkanes.

• transition state: see activated complex

• 'unimolecular' mechanism/kinetics : see S_N1

• unsaturated molecule: A term usually applied to an organic hydrocarbon molecule with a double or triple carbon-carbon bond to which atoms can add across. The term is often applied to hydrocarbons like propene and ethyne, but technically, compounds like aldehydes and ketones can also be considered unsaturated with the >C=O group.

  • Unsaturated molecules often react by addition reactions.

  • e.g. addition of hydrogen bromide to propene (electrophilic addition mechanism)

  • CH₃CH=CH₂  +  HBr  ===>  {CH₃CH₂CH₂Br  or  CH₃CHBrCH₃}

• unsymmetrical alkene: structure and addition to, see non-symmetrical alkene

TOP OF PAGE

APPENDIX

 COMPLETE MECHANISM and Organic Synthesis INDEX (so far!)

• PART 10 An Introduction to organic chemical reaction mechanisms and technical terms explained

• Organic Synthesis - MECHANISMS INDEX

• Part 10.2 ALKANES - an introduction to their chemistry

  • Free radical chlorination/bromination to give halogenoalkanes (haloalkanes, alkyl halides)

  • Free radical mechanism for cracking hydrocarbons to give shorter alkanes and alkenes

  • Ionic mechanism for cracking hydrocarbons

• Part 10.3 ALKENES - introduction to their chemistry

  • Electrophilic addition of hydrogen bromide [HBr_{(conc. aq)} and HBr_{(g/non-polar solvent)}] to form halogenoalkanes

  • Electrophilic addition of bromine with pure bromine or in non-polar solvent (non-aqueous Br_2(l/solvent)) to give dibromoalkanes AND addition using bromine water [aqueous Br_2(aq)] to give bromo-alcohols

  • Electrophilic addition of sulfuric acid AND electrophilic addition of water [acid catalyst] to form alcohols

  • Free radical polymerisation to give poly(alkene) polymers e.g. ethene ==> poly(ethene)

  • Hydrogenation to give saturated alkanes

• Part 10.4 HALOGENOALKANES - introduction to the chemistry of haloalkanes/alkyl halides

  • Nucleophilic substitution by water/hydroxide ion [S_N1 or S_N2, hydrolysis to give alcohols]

    • with extra notes on kinetics, rds, molecularity, rate expression, activated complex etc.

  • Nucleophilic substitution by cyanide ion to give a nitrile [S_N1 or S_N2]

  • Nucleophilic substitution by ammonia/primary amine to give primary/secondary amines etc. [S_N1 or S_N2]

  • Elimination of hydrogen bromide to form alkenes [E1 and E2]

• Part 10.5 ALCOHOLS - introduction to their chemistry

  • Conversion of an alcohol to a halogenoalkane

  • Elimination of water from an alcohol to give an alkene [acid catalysed, E1 and E2]

• Part 10.6 Carbonyl compounds - ALDEHYDES and KETONES - introduction to their chemistry

  • Nucleophilic addition of hydrogen cyanide to form a hydroxy-nitrile

  • Addition of hydrogen - reduction with LiAlH₄ or NaBH₄ to give alcohols

  • The iodination of ketones e.g. a 2-one like propanone (a methyl ketone) to give iodo-ketones

• Part 10.7 Carboxylic Acids and ACID CHLORIDES - introduction - all nucleophilic addition-elimination reactions

  • Hydrolysis of acid chlorides with water to give a carboxylic acid

  • Esterification of acid chlorides with alcohols to give an ester

  • Amide formation from reaction of acid chlorides with ammonia or primary amines

• Part 10.8 AROMATIC HYDROCARBONS - introduction to arene electrophilic substitutions

  • Nitration to give nitro-aromatics like nitrobenzene

  • Chlorination to chloro-aromatics like chlorobenzene

  • Alkylation to give alkyl-aromatics like methylbenzene [Friedel-Crafts reaction]

  • Acylation to give aromatic ketones [Friedel-Crafts reaction]

  • Sulfonation to give a sulfonic acid like benzenesulfonic acid

  • The orientation of products in aromatic substitution (2,4,6 or 3,5 positions, ortho, para & meta substitution products)

• Other important associated links

  • Isomerism - chain isomerism, positional isomerism, functional group isomerism & Tautomerism
  • Stereoisomerism introduction, E/Z isomerism ('ex' Geometric/Geometrical cis/trans Isomerism)
  • R/S (Optical) Isomerism and chiral auxiliary synthesis
  • All Advanced Organic Chemistry Notes
  • Summary of Organic Functional Groups
  • Quiz on Organic Structure Recognition
  • Summary of organic chemistry functional group tests
  • The shapes and bond angles of simple organic molecules
  • Aliphatic compound structure and nomenclature m/c BUMPER QUIZ
  • Type in name of aliphatic compound nomenclature BUMPER QUIZ

1. INDEX of ALKANES and the petrochemical industry revision notes INDEX

2. INDEX of ALL advanced revision notes on ALKENES

3. INDEX of ALL revision notes on HALOGENOALKANES (haloalkanes)

4. INDEX of all revision notes on ALCOHOLS (and mention of ethers)

5. INDEX of ALL revision notes on ALDEHYDES and KETONES

6. INDEX of all revision notes on CARBOXYLIC ACIDS and DERIVATIVES

7. INDEX of all AROMATIC COMPOUND chemistry revision notes

8. INDEX of all ORGANIC NITROGEN COMPOUND chemistry pages

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