AGJ Organic Chemistry 1 (OC1) Lecture Notes 2024 PDF

ORGANIC CHEMISTRY 1 (OC1) lecture 1 Prof Andrew Jamieson  Course overview Who: Prof Andrew Jamieson What: Core 1st year organic chemistry module Aims: To introduce the principles of organic chemistry, to relate atomic and m...

ORGANIC CHEMISTRY 1 (OC1) lecture 1 Prof Andrew Jamieson  Course overview Who: Prof Andrew Jamieson What: Core 1st year organic chemistry module Aims: To introduce the principles of organic chemistry, to relate atomic and molecular structures to properties and reactions. When: 6 Lectures + 1 problem session Chemistry 1 Timetable 2024/25 Week 1 2 3 4 5 6 7 8 9 10 11 12 13 17 18 19 20 21 22 23 24 25 26 27 Begins 23 Sep 30 Sep 07 Oct 14 Oct 21 Oct 28 Oct 04 Nov 11 Nov 18 Nov 25 Nov 02 Dec 09 Dec 16 Dec 13 Jan 20 Jan 27 Jan 03 Feb 10 Feb 17 Feb 24 Feb 03 Mar 10 Mar 17 Mar 24 Mar 21 Apr 28 Apr Where: 10 E&A E&A C&M C&M OC1 OC1 OC2 PS-OC2 OC3 A&R A&R DA CE PS-CE CK EQU EQU PS-EQU TM INF Mon 3 E&A E&A C&M C&M OC1 OC1 OC2 PS-OC2 OC3 A&R A&R Revision DA CE PS-CE CK EQU EQU PS-EQU TM INF 10 E&A E&A C&M PS-C&M OC1 PS-OC1 OC2 OC3 OC3 A&R A&R DA CE CK CK EQU EQU TM TM MM MM MM Tue 3 E&A E&A C&M PS-C&M OC1 PS-OC1 OC2 OC3 OC3 A&R A&R DA CE CK CK EQU EQU TM TM MM MM MM Start of Exam Period Revision Exams 10 E&A LAB C&M OC1 OC1 OC2 OC2 OC3 PS-OC3 A&R A&R LAB CE CK CK EQU EQU TM TM MM MM MM Wed 3 E&A LAB C&M OC1 OC1 OC2 OC2 OC3 PS-OC3 A&R A&R LAB CE CK CK EQU EQU TM TM MM MM MM PS-E&A RT RT OC3 RT CE CE CK PS-CK RT RT TM PS-TM RT MM PS-MM Exams 10 Thu 3 PS-E&A RT RT OC3 RT CE CE CK PS-CK RT RT TM PS-TM RT MM PS-MM 10 E&A C&M C&M OC1 T OC2 OC2 OC3 T RT PS-A&R CE CE T T RT Fri 3 E&A C&M C&M OC1 T OC2 OC2 OC3 T RT PS-A&R CE CE T T RT Labs S S S S S S S S Q Q Q Q Q Q Q Q OC2 = Dr Thompson, OC3 Dr Soler  Course overview Title: Organic Chemistry 1 Duration: 6 lectures + 1 problem session Lecturer: Prof Andrew Jamieson Aims: To introduce the principles of organic chemistry, to relate atomic and molecular structures to properties and reactions. Outline: Atomic and molecular structure derived from VSEPR theory and sand pbonds; electron counting; structural isomers with tetrahedral, trigonal and digonal carbons; lone pairs, drawing organic structures; the foregoing principles developed alongside the chemistry of alkanes, alkenes, alkynes, alkyl halides, alcohols, ethers, aldehydes, ketones, carboxylic acids and their derivatives, amines and amides; functional groups and nomenclature; rotation about single bonds and equivalent hydrogens; chirality and geometrical isomerism; polar and non-polar bonds; nucleophiles and electrophiles; reaction mechanisms understood in terms of electron pair movement indicated by curly arrows; Markovnikov’s rule for addition reactions; nucleophilic substitution and elimination reactions; hydrogen bonding and polarity; physical properties related to structure, combustion analysis and molecular weights.  C3(458) Chemistry3 Introducing Inorganic, Organic, and Physical chemistry by Burrows, Holman, Parsons, Pilling, Price 3rd edition Available from John Smith’s Bookshop Other text books are available…don’t buy them, they are in the library. J Clayden, N. Greeves, S. Warren and P. Wothers, Organic Chemistry, 2nd Edition, OUP Oxford P. Bruice, Organic Chemistry, 6th Edition, Pearson (7th Edition new available)  Study Tips 1. Read the suggested textbook chapters before coming to lectures and record the main ideas. 2. After each lecture, summarise the major ideas and concepts in your notes. 3. Annotate these summaries from your study of the textbook. 4. Attempt the tutorial questions independently. 5. Try to understand the material from each lecture before going to the next one. 6. Spend a few minutes each day on review to prevent becoming overwhelmed on the night before an exam.  C3(223) Structure of Molecules The 3D shape of molecules is important! Nature Communications, 2016, 7, 11262. Valence Shell Electron Pair Repulsion (VSEPR) The repulsion of electrons to get as far as possible from each other  Bonding in Organic Chemistry Carbon electron configuration Co [He] 2s2 2p2 C4 - [He] 2s2 2p6 or [Ne] Carbon makes 4 bonds - tetracovalent  C3(224) VSEPR Theory applied to Methane CH4 valance electrons at back Central C atom 4 H 4 bonds to H 4 C H H total 8 H in front = 4 pairs Methane is tetrahedral  C3(237) Hybrid Orbitals Carbon has 4 valence orbitals 2s, 2px, 2py, 2pz Valence orbitals Hybrid orbital but in methane there are 4 identical hybrid orbitals (sp3)  C3(237) sp3 Hybrid Orbitals The number of hybrid orbitals must be the same as the valence orbitals. Rear of sp3 x4 orbitals left out for clarity ORGANIC CHEMISTRY 1 (OC1) lecture 2 Prof Andrew Jamieson  Revision (Wednesday) The 3D shape of molecules is important! VSEPR Theory sp3 hybridised carbon atom tetrahedral  H Sp3 hybridized carbon C H Tetrahedral H H 109.5º bond angle H H Sp2 hybridized carbon C C Trigonal planar H H 120º bond angle Sp hybridized carbon H C C H Linear 180º bond angle  C3(239) sp2 Hybrid Orbitals Made by mixing 1 x s and 2 x p orbitals This makes 3 x sp2 and 1 x p orbitals  Double bonds ethene H H C C H H  C3(241) sp Hybrid Orbitals Made by mixing 1 x s and 1 x p orbitals This makes 2 x sp and 2 x p orbitals acetylene H C C H  Electron counting Hydroxide HO- (not OH-) circle charges Total valence electrons Oxygen 6 H O lone pair Hydrogen 1 Negative charge 1 bond pair 8 8 electrons around O = 4 pairs 2 electrons around H Represent each pair by a line  C3(220) Formal Charge H O Why is the negative charge on O? O “owns” both electrons in a lone pair Bond pair is shared O “owns” one from the bond pair Remove valence electrons charge from O (6) 6+ Add 3 lone pairs (3 x 2) 6- Add share of one bond pair 1- __ formal charge 1-  Cyanide useful one carbon unit CN for increasing chain lengths Total valence electrons Nitrogen 5 Carbon 4 C N Negative charge 1 10 = 5 pairs Homework - verify that the charge is in the right place  Charged carbons carbanion carbocation (carbonium ion) C H H H H C H H tetrahedral trigonal planar 8 electrons around C 6 electrons around C  Organic Compounds Millions of compounds known Only a few general ideas needed to understand organic chemistry Functional Groups Mechanisms help us understand how the groups react  compoundchem.com Facebook – Compound Interest Twitter - @compoundchem ORGANIC CHEMISTRY 1 (OC1) lecture 3 Prof Andrew Jamieson  Revision sp3 hybridised carbon eg H Tetrahedral Bond angles 109.5° C H H H sp2 hybridised carbon eg H H Trigonal planar C C Bond angles 120° H H sp hybridised carbon eg linear H C C H Bond angles 180° 180°  Cyanide charge Homework - verify that the charge is in the right place C N For Carbon Charge Remove valence electrons on C 4+ 1 lone pair 2- 3 bonds 3- formal charge on C 1-  C3(79) Alkanes CnH2n+2 Saturated – no multiple bonds branched or unbranched Alkane nomenclature - basis of naming complex structures Homologous series – differ by CH2  C3(80) Unbranched chains CH4 methane C6H14 hexane C2H6 ethane C7H16 heptane C3H8 propane C8H18 octane C4H10 butane C9H20 nonane C5H12 pentane C10H22 Decane systematic names [semi-systematic & trivial/common]  Homologous series mnemonic competition Please email 1) fun mnemonic 2) Your name 3) 10am or 3pm lecture cohort [email protected] 10 am lecture – deadline 5 pm Monday 21st 3 pm lecture – deadline 9 am Tuesday 22nd  C3(82) Stick Diagrams propane clear H H H C H CH2 C C H3C CH3 H HH H r CH2 e good but H3C CH3 d u confusing CH2 H3C CH3 c e accurate model Sticks are best  C3(82) Structural isomers same molecular formulae - different bond pattern CH3 C4H10 CH2 CH3 CH H3C CH2 H3C CH3 butane 2-methylpropane (isobutane)  C3(79) Rules for nomenclature 1.Identify the longest chain of C atoms 2.Other bits are substituents 3. Number chain - substituents have lowest number 4. List the substituents alphabetically (ignore di-, tri-, etc) 5. Hyphens between numbers and letters 6. Commas between numbers  C3(81) Rules for nomenclature Step 1) Find the parent hydrocarbon (e.g. hexane) 1 Step 2) Number the atoms in the main chain. 6 5 4 3 2 methyl Step 3) Identify and number the substituents. 3 3-methylhexane  C5H12 pentane 2-methylbutane 2 4 1 3 2,2-dimethylpropane 2 1 3  C3(83) Alkyl groups Names derived from corresponding alkanes CH3- = methyl CH3CH2- = ethyl etc. 7 5 3 1 6 4 2 4-ethyl-3,3-dimethylheptane  C3(84) Cycloalkanes Monocyclic CnH2n CH2 H2C CH2 cyclopropane cyclohexane 1,2-dimethylcyclopentane cycloalkanes occur in many important compounds e.g steroids  Stereoisomers Same formulae and bond pattern - different arrangement of atoms in space. Chirality or Optical Isomerism Must have a carbon with four different groups. Geometric or cis/trans isomers Must have double bond and each end must have two different groups.  C3(838) Chirality Greek , cheir, hand chiral molecule or object is not superimposable on its mirror image  Achiral Achiral molecule is superimposable on its mirror image. It has a plane of symmetry  C3(838) Chiral centres Must have four different groups H3C CH3 CH2 C Br * *C Br H CH3 H CH3 chiral centre achiral (has H, methyl, chiral two groups ethyl, propyl centre the same groups) ORGANIC CHEMISTRY 1 (OC1) lecture 4 Prof Andrew Jamieson  Stereoisomers Same formulae and bond pattern - different arrangement of atoms in space. Chirality or Optical Isomerism Must have a carbon with four different groups. Geometric or cis/trans isomers Must have double bond and each end must have two different groups.  C3(840) Optical Activity Chiral molecules rotate the plane of plane polarised light Polarimeter optical Clockwise or right = + rotation []D Anticlockwise or left = -  C3(840) Enantiomers are mirror images e.g. lactic acid mirror CO2H CO2H []D –3.33 OH HO []D +3.33 H3C H CH3 H equal mixture of the two enantiomers - optical rotation = 0 - called a racemate (C3 page 839) - interesting history)  Stereoisomers Same formulae and bond pattern - different arrangement of atoms in space. Chirality or Optical Isomerism Must have a carbon with four different groups. Geometric or cis/trans isomers Must have double bond and each end must have two different groups.  C3(833) Geometric isomers cis/trans or E/Z isomers H H H3C H flat C C C C cannot rotate H CH3 H3C CH3 have plane of cis trans symmetry H H No geometric isomer C C H CH3 both ends must have different groups  E/Z Convention C3(834) cis/trans system - problems with highly substituted double bonds 1. Assign priority to atom with F Br highest mass at each end of C C double bond Cl I 2. If highest priority atoms on Zame Zide call it Z (German Highest zusammen) priority on 3. If on opposite side call it E same side - (German entgegen) Z  C3(870) Electronegativities  C3(870) Polar Covalent Bonds C-C and C-H bonds are non-polar (C and H have similar electronegativity) Alkanes and cycloalkanes - not reactive Most other bonds are polar (electrons in the bond move towards the most electronegative atom) + - + - + - - + - + C N C O C Cl C Mg O H  C3(879) Nucleophiles (nucleus seeking) Electron-rich – willing to give away electrons Negative or partially negative e.g. H H H O C H N H H C C H H H H H C N  C3(882) Electrophiles (electron seeking) Electron-deficient – looking for electrons Positive or partially positive e.g. H H + - + - C H3C Cl C O H H H H  Reactions Nucleophiles react with electrophiles e.g. H+ reacting with HO - H O H O H H  Curly arrows C3(863) Show the movement of a pair of electrons to a positive centre H H N H N H H H H H  C3(79) Alkenes CnH2n Nomenclature Identify longest chain containing double bond Number to give double bond lowest number but-1-ene but-2-ene  C3(82) Larger alkenes 3 4 1 2 2-ethylbut-1-ene 1 buta-1,3-diene 3 ORGANIC CHEMISTRY 1 (OC1) lecture 5 Prof Andrew Jamieson  C3(974) Reactions of alkenes Alkenes are unsaturated, electron rich, nucleophiles Main reactions - addition reactions e.g. Bromination of ethene Br2 Br H2C CH2 H2C CH2 Br C3(978)  C3(975) Bromination Alkene reacts with bromine Br Br Br Br H2C CH2 H2C CH2  Bromonium ion Br Br H2C CH2 H2C CH2 carbocation Br Br H2C CH2 Br Curly arrows always move towards positive centres  C3(977) Hydrobromination H Br H H2C CH2 H2C CH2 Br + - HBr has a polar bond H Br Alkene is nucleophile  Mechanism of C3(977) Hydrobromination carbocation H Br H H2C CH2 H2C CH2 H H2C CH2 Br Br Curly arrows always start from a pair of electrons – centre of line Addition to unsymmetrical C3(978) alkenes H3C H3C Br H Br H3C H C CH2 C CH2 C CH2 or H H H propene Br H Two possible products – only one formed – why? Markovnikov’s rule (1870) H of H-X adds to carbon with the most H’s  C3(971) Stability of Carbocations R R R R R H H H C C C C R > H > H > H tertiary secondary primary methyl Alkyl groups, R, stabilise carbocations The most stable carbocation will be formed  C3(970) Markonikov’s rule explained H3C H primary H3C H C CH2 H C CH2 not formed H H H3C H C CH2 secondary H Br H3C Br more C CH2 stable H H  C3(980) Hydration of alkenes H3C H2O H3C OH obeys C CH2 C CH2 Markovnikov’s H+ catalyst H H H rule H H H O H H H3C H3C O H C CH2 C CH2 H H H H  C3(968) Hydrogenation of alkenes reduction H2 Catalyst e.g. cyclopentene Pd or Pt H H cyclopentane H’s delivered to H H the same side of the alkene catalyst surface  C3(986) Dihydroxylation of alkenes lab test – KMnO4 decolourisation of basic KMnO4 NaOH HO OH cyclopentane-1,2-diol 1,2-diols are called glycols OH e.g. ethylene glycol CH2 CH2 (ethane-1,2-diol) used HO as antifreeze  Oxidation of alkenes with acidic permanganate Further oxidation – cleavage of diol KMnO4 H3O+ carboxylic acids KMnO4 H3O+ ketone  C3(992) Ozonolysis of alkenes Lysis or cleavage using ozone Two stage process – overall reaction: 1. O3 O 2. Zn, H+ O propanone 2,3-dimethylbut-2-ene  Ozonolysis Addition of ozone (an electrophile) O O addition O O O O molozonide O rearrangement O ozonide O  Reduction of ozonides Ozonides are highly explosive usually decomposed chemically e.g. by reduction Zn, H+ O O O O O  Overall reaction Products of ozonolysis break C=C and add O to each end O O ORGANIC CHEMISTRY 1 (OC1) lecture 6 Prof Andrew Jamieson  Ozonolysis questions Two types of questions 1. What are the products of ozonolysis of alkene A? O O A H 2. What is the structure of alkene B that gives X and Y after ozonolysis? H H O O ? H H B X Y  Addition reactions to alkenes Br Br Br hydrobromination HBr H2/Pd bromination Br catalyst 2 hydrogenation O3 H2O, H+ catalyst KMnO4 ozonide NaOH OH HO OH hydration dihydroxylation  C3(87) Acetylenes (Alkynes) CnH2n-2 H C C H ethyne or acetylene Linear, one  bond and two  bonds H3C C C CH3 but-2-yne Acetylenes are unsaturated - two successive addition reactions Markovnikov’s rule is obeyed  C3(994) Addition reactions of acetylenes H3C C CH Markovnikov’s Br2 propyne rule HBr H3C Br C C H3C H Br H can stop C C here Br H Br2 HBr Br excess Br Br Br reagent Br Br 1,1,2,2-tetrabromopropane 2,2-dibromopropane Mechanism of HBr Addition H3C C CH H H3C C C H Br H more stable carbocation Br H3C H HBr C C Br Br as for Br H alkenes  Hydrogenation C3(967) H3C C C CH3 H2 but-2-yne Lindlar’s H2/Pd catalyst catalyst H3C CH3 C C H H cis-but-2-ene butane Useful for making cis double bonds  Terminal acetylenes C3(995) H3C C CH weakly acidic H can be removed with strong NH2 base e.g. sodium amide Na NH2 H3C C C an acetylide Useful carbanion H (good nucleophile) NH2