Introduction to Organic Chemistry

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Introduction to rganic hemistry 59 Introduction to rganic hemistry andout 3 - chanism u u http://burton.chem.ox.ac.uk/teaching.html rganic hemistry J. layden,. Greeves, S.

1 Introduction to rganic hemistry 59 Introduction to rganic hemistry andout 3 - chanism u u rganic hemistry J. layden,. Greeves, S. Warren Stereochemistry at a Glance J. Eames & J. M. Peach The majority of organic chemistry text books have good chapters on the topics covered by these lectures Eliel Stereochemistry of rganic ompounds (advanced reference text)

Introduction to rganic hemistry 60 acid base reactions a Lewis base is an electron pair donor (can be charged or neutral) when atom is negatively charged, the negative charge implies a lone pair

2 Introduction to rganic hemistry 60 acid base reactions a Lewis base is an electron pair donor (can be charged or neutral) when atom is negatively charged, the negative charge implies a lone pair (this is shorthand notation used by organic chemists) + electron a Lewis acid is an electron pair acceptor (can be charged or neutral) acid base reactions is sharing an electron pair and therefore becomes positively charged A A A A Lewis acid conservation of charge Lewis base A is accepting an electron pair and therefore becomes negatively charged

3 Introduction to rganic hemistry 61 ULY AWS indicate the movement of a pair of electrons the arrow starts at the origin of the pair of electrons (lone pair or bonding pair) and the head of the arrow indicates where the electrons end up (lone pair or bonding pair) bond (electron pair) formed between and atoms 1 st curly arrow starts from the negative charge which we treat as a lone pair 2 nd curly arrow starts from the bond pair + negative oxygen has donated electrons so becomes neutral positive nitrogen has accepted electrons and becomes neutral strictly speaking the arrow starts from an actual lone pair but it is normal practice to draw it from the negative charge + drawing the curly arrow to point at the atom to which it is forming a bond is also common practice + the lone pair is generally not drawn explicitly

Introduction to rganic hemistry 62 acid base reactions planar, fluoride, 8e tetrahedral 6e, sp 2 8e, sp 3 planar, 6e, sp 2 hydride, 2e (1s 2 ) tetrahedral 8e, sp 3 here the negative (formal)

4 Introduction to rganic hemistry 62 acid base reactions planar, fluoride, 8e tetrahedral 6e, sp 2 8e, sp 3 planar, 6e, sp 2 hydride, 2e (1s 2 ) tetrahedral 8e, sp 3 here the negative (formal) charge (although drawn on boron) does not represent a lone pair has 8 electrons from the bonding pairs l l l l a generic base + a common error X a curly arrow cannot begin from a proton has no electrons

5 Introduction to rganic hemistry 63 further examples some typical reactions of aldehydes and ketones orbitals cyanohydrin sp lone pair overlaps with p-orbitals Li Al 4 or a 4 arrow comes from a bond pair of electrons and transfers hydrogen with its pair of electrons i.e. as hydride (remember the negative charge on does not represent a lone pair) addition of a Grignard reagent 3 Mgr addition of a neutral nucleophile

6 Introduction to rganic hemistry 64 delocalisation a.k.a resonance = general alkyl group amines are basic the nitrogen lone pair is readily protonated amides, however, are essentially neutral the lone pair is delocalised into the carbonyl group lone pair in A is bonding pair in neither A nor actually exist the real structure is a weighted average of structures A and called a resonance hybrid A structures A and, are referred to as resonance structures note there is not an equilibrium between A and individual Lewis structures do not accommodate the electron distribution in certain functional groups, and delocalisation (a.k.a. resonance) is a simple method to account for the actual electron distribution effect on structure the curly arrows above represent the overlap of the nitrogen lone pair with the - π-orbitals the best overlap occurs if the -lone pair is in a p-orbital, i.e. is sp 2 hybridised

Introduction to rganic hemistry 65 A -sp 2 hybridised -lone pair in p-orbital -sp 3 hybridised -lone pair in sp 3 -orbital the curly arrows above represent the overlap of the nitrogen lone pair with

7 Introduction to rganic hemistry 65 A -sp 2 hybridised -lone pair in p-orbital -sp 3 hybridised -lone pair in sp 3 -orbital the curly arrows above represent the overlap of the nitrogen lone pair with the - π-orbitals (the antibonding π* orbital) the best overlap therefore is if the -atom is sp 2 hybridised resulting in the -lone pair being in a p-orbital with excellent overlap with the p-orbitals of the π-system if the -atom were sp 3 hybridised then the -lone pair would be in an sp 3 orbital which would result in poorer overlap with the adjacent - π-system generally better overlap (of full and empty orbitals) = greater stabilisation actual structure is composite of A and the geometry of amides is planar restricted rotation around bond A 2 X-ray crystal structure of dimethyl acetamide bond length: amines 1.47 Å, amides 1.33 Å

8 Introduction to rganic hemistry 66 some guidelines for drawing delocalised structures (resonance structures, canonical forms) all resonance structure must be proper Lewis structures the positions of the nuclei must be the same in all structures all structures must have the same number of paired/unpaired electrons 3 3 not a proper Lewis structure 10 electrons all atoms involved in delocalistion should be co-planar or nearly co-planar the overall structure of the molecule is a weighted average of the various resonance structures the more stable resonance structures contribute more to the overall structure of the molecule (and generally only the most stable resonance structures need to be considered) charge separation is destabilising the energy of the actual molecule is lower than any of the resonance structures

9 Introduction to rganic hemistry 67 some of the arrows of organic chemistry a a + reaction arrow A goes to + 2 l + equilibrium arrow - indicates a reversible reaction equilibrium arrow strongly favouring products equilibrium arrow strongly favouring reactants resonance arrow indicates actual structure of the molecule is a hybrid of the structures shown Ph Et r Ph Et curly arrows (double headed) indicates movement of a pair of electrons r r r + r curved single-headed arrow indicates movement of single electrons (homolysis of the bond in this example)

Introduction to rganic hemistry 68 esters one

atom is sp 2 hybridised one oxygen lone pair in

amide sp 2 sp 2 sp 3 X the above amide is much

of lone pair with p-orbitals S delocalisation in

10 Introduction to rganic hemistry 68 esters one oxygen lone pair in sp 2 hybrid orbital oxygen atom is sp 2 hybridised one oxygen lone pair in p-orbital esters are generally planar an unusual amide sp 2 sp 2 sp 3 X the above amide is much more basic than a normal amide impossible overlap of lone pair with p-orbitals S delocalisation in common functional groups carboxylic acids similarly carboxylate azides

11 Introduction to rganic hemistry 69 nitro groups ketones carbonate diazo compounds 2 2 in general if a π-system has an adjacent atom which carries a lone pair delocalisation of the lone pair into the p-system is possible enol ether enol ether enolate anion enamine

Introduction to rganic hemistry 70 double bond resonance benzene heats of hydrogenation Δ o hydrog = -120 kjmol -1 2 /Pt catalyst 2 /Pt catalyst Δ o hydrog= -210 kjmol -1 2 /Pt catalyst Δ o hydrog= 3

12 Introduction to rganic hemistry 70 double bond resonance benzene heats of hydrogenation Δ o hydrog = -120 kjmol -1 2 /Pt catalyst 2 /Pt catalyst Δ o hydrog= -210 kjmol -1 2 /Pt catalyst Δ o hydrog= 3 x -120 = -360 kjmol -1 (hypothetical, 1,3,5-cyclohexatriene) benzene 150 kjmol -1 more stable than expected (represents stability over hypothetical 1,3,5- cyclohextriene) termed the empirical resonance energy (values vary enormously) - sp 3 -sp Å - sp 3 -sp Å - sp 3 -sp 1.47 Å - sp 2 -sp Å - benzene 1.39 Å = 1.34 Å 1.21 Å benzene best represented like this but cannot draw curly arrow mechanisms from this representation we will therefore use the alternating double/single bond representation

13 Introduction to rganic hemistry 71 molecular orbital description all carbon atoms are sp 2 hybridised all bond angles are 120 there are six p-orbitals which overlap to give six molecular orbitals rost-musulin Diagram rost ircle simple method to find the energies of the molecular orbitals for an aromatic compound inscribe the regular polygon, with one vertex pointing down centred at the energy of an isolated p-orbital each intersection of the polygon with the circumference of the circle corresponds to the energy of a molecular orbital antibonding molecular orbital (empty) Energy bonding molecular orbitals (full) benzene the six electron are delocalised over the entire ring benzene is described as aromatic with aromatic stabilisation

14 Introduction to rganic hemistry 72 for aromaticity require (4n +2) π-electrons cyclically conjugated other common aromatic systems negative charge spread over 5 carbon atoms cyclopentadienyl anion (4n +2), n = 1, 6π electrons base : antibonding molecular orbital (empty) Energy bonding molecular orbitals (full) 6 electrons, 5 from the p-orbitals one from the negative charge tropylium cation (4n +2), n = 1, 6π electrons aromatic antibonding molecular orbital (empty) r r Energy bonding molecular orbitals (full)

15 Introduction to rganic hemistry 73 delocalisation in conjugated alkenes (non-aromatic) dienes overlap of p-orbitals on central carbon leads to new extended molecular orbital increased bonding a,b-unsaturated carbonyl compounds b a nucleophlies therefore react at the carbonyl carbon or the b-position similary with a,b-unsaturated nitro compounds and a,b-unsaturated nitriles or with triple bonded species

16 Introduction to rganic hemistry 74 some more simple reactions a, 5-10 a, 80 drawing delocalised structures, shows us where nucleophiles and electrophiles may attack substrates cyanide will add to the carbonyl carbon, or the b-position of an a,b-unsaturated ketones depending on the reaction conditions a, 5-10 a, 80

17 Introduction to rganic hemistry 75 these reactions can be reversible a, 5-10 a, 80 base + base +

Chapter 2. Molecular Representations

Chapter 2. Molecular Representations hapter 2. Molecular Representations 3 () 3 ( 3 ) 2 3 3 3 8 Lewis (Kekule) structure ondensed and par6ally condensed structure Skeletal (bond- line) structure Molecular formula Amoxicillin a widely prescribed