Organic Chemistry Dr Kennedy Ngwira Dr Maya Makatini Prof Amanda Rousseau Self study: Background notes – green booklet Chemistry the Central Science - Brown (Chapter 24) Extra reading: Organic Chemistry – McMurry (any edition) 1 Revision of Semester 1 Functional groups • Identify the functional groups in lopinavir Revision of Semester 1 • Identify the functional groups in Candarel Revision of Semester 1 Organic compounds C and H Hydrocarbon C and H plus Heteroatoms Saturated Unsaturated Saturated Unsaturated • C & H ONLY • σ / single bonds only • C & H ONLY • Multiple (π & σ) bonds present C=C, CΞC • C, H & other atoms such as O, N, S, P etc • σ / single bonds only • C, H & other atoms such as O, N, S, P • Multiple (π & σ) bonds present – C=C, CΞC, C=O, C=N, CΞN etc O14: Unique Properties of Carbon Structural and bonding properties 1) BOND STRENGTHS Strong bonds form between like elements H-H C-C (436 kJ/mol) (348 kJ/mol) Therefore it is favourable for C atoms to link up into chains (catenation). Note: Homonuclear bonds are rare amongst other elements. Carbon has the unique ability to form long chains and rings. Another strong bond is between the unlike elements C-H (413 kJ/mol) This bond is very common in organic compounds O14: Unique Properties of Carbon 2) NATURE OF BONDS There are a variety of possible bonds involving carbon e.g. C-C C=C C≡C C-X C=O C≡N (X= halogen or OH) The electron configuration of C: 1s2 2s2 2px1 2py1 2pz0 Core valence electrons Therefore there are 4 valence electrons and 4 valence orbitals. This means carbon must always form 4 bonds. No unused electrons No unused orbitals No “reactive spots” O14: Unique Properties of Carbon The carbon atom is small, and it is screened by the other atoms attached to it and therefore it is difficult to attack at the carbon centre (in order to react with the carbon). O14: Unique Properties of Carbon Reactivity • For all these reasons ALKANES ARE VERY UNREACTIVE • At room temperature alkanes do not react with acids, bases, or strong oxidizing agents • Therefore alkanes make good non-polar solvents. O14: Unique Properties of Carbon Elemental Carbon Elemental carbon has many allotropes (structural forms), including diamond, graphite and fullerenes. Buckyballs [5]-fullerene-C20 [6,4]-fullerene-C24 [5,6]-fullerene-C60 O15: Organic Reactions Introduction to Organic Reactions The key idea is to look for “patterns” of reactivity. In order to do this you must recognize 3 key things: 1) Identify the structural features in the molecules 2) Identify the types of reactions they might undergo 3) Identify the types of reagents that will cause the reaction to go O15: Organic Reactions Reaction types: 3 basic types 1. Addition (increases saturation at C) 2. Elimination (increases unsaturation at C) 3. Substitution (degree of saturation at C is not changed) O15: Organic Reactions Example: Identify the type of reaction in each of the following: a) b) c) O15: Organic Reactions Link between structural features and reaction type only σ-bonds (+H2O) (-H2O) π-bond (-2H) Oxidation only σ-bonds plus heteroatom (+2H) Reduction π-bond O15: Organic Reactions Reaction Pathways Substrates [Intermediates] Products Reaction mechanism: a detailed description of the reaction path There can be several intermediates in a reaction pathway and usually they are too unstable to isolate. This year we will look at some basic mechanisms and will also look at the substrate/product relationships. O16: Types of reagents and substrates Reagents and substrates can be classified according to how their electrons are arranged: 1) Unpaired electrons -Radicals (homolytic reactions) 2) Paired electrons (electron poor or electron rich species) (heterolytic/polar reactions) O16: Types of reagents and substrates Electron poor Electron rich Character + or δ+ − or δ− Examples F H2C B F H F + CH2 : NH3 Cl - Attracted to Electron rich sites of molecules Electron poor sites of molecules Name Electrophiles Nucleophiles Criterion One or more empty orbital One or more lone pair or π bond O16: Types of reagents and substrates What are electrophiles and nucleophiles? Electrophile: literally means “electron loving” • it is a fully or partially positively charged site • it is looking for electrons • It is Electron-poor Nucleophile: literally means “nucleus loving” • it is a fully or partially negatively charged site • it has got electrons to give • It is Electron-rich O17: Main principle underlying reactions Predicting Organic Reactions Reactions occur between sites of opposite polarity (i.e.+ or δ+ will react with – or δ-) Example: O17: Main principle underlying reactions Curly arrows are used to show movement of electrons in the reaction Examples: Electrophilic carbon Nucleophile Substitution reaction: electrons move from the nucleophile to the electrophile Addition reaction: electrons move from the nucleophile to the electrophile O16 & O17: Nucleophiles and Electrophiles Examples: Identify electrophilic and nucleophilic sites in the following molecules O18 & O19: Typical Reactions of Alkanes Two types of reaction: Substitution Elimination O18: Halogenation of Methane Radical Reaction These reactions don’t use nucleophiles or electrophiles, but instead they use “free radicals” which have unpaired electrons. Both reactants donate one electron to form the new bond. E.g. H Cl Substitution e.g. CH4 + Cl2 CH3-Cl CH3-Cl + Cl2 CH2-Cl2 CHCl3 CCl4 These reactions are difficult to control and therefore there are mixtures of products. O18: Halogenation of Methane Radical Reaction (Small %) Initiation Homolytic cleavage Propagation Propagation Termination (two radicals collide and combine) Both propagation steps alternate until the reactants are completely consumed (termination). This is a chain reaction and the chlorine radical can undergo further reactions. O20:Unsaturated hydrocarbons Alkenes and Alkynes σ and π bonds H2C CH2 π, π, and σ bonds HC CH Alkenes and alkynes have bonds which: 1) Are non-polar 2) have no lone pairs 3) have no vacant orbitals, BUT have π electrons that are exposed and therefore accessible. The π component is weaker than the σ C-C (348 kJ/mol) vs C=C (619 kJ/mol) π bonds contribute 271 kJ/mol This makes unsaturated hydrocarbons far more reactive than saturated hydrocarbons. O20:Unsaturated hydrocarbons Alkenes and Alkynes The typical reaction for unsaturated hydrocarbons is an addition reaction, where the π electrons from the double bond act as the nucleophile. The obvious reagent to react with an alkene in an addition reaction? An electrophile. Substitution and elimination reactions are less important for unsaturated systems. O20:Unsaturated hydrocarbons Examples of addition reactions to alkenes 1. Hydrogenation H-H is very strong (436 kJ/mol), needs a catalyst, eg. 1% Pd/C 2. Halogenation Cl-Cl is much weaker (254 kJ/mol) (also Br2 and I2). O20:Unsaturated hydrocarbons Examples of addition reactions to alkenes 3. Addition of hydrogen halides Addition of HCl across the double bond a. In the first slow step, a carbocation is formed b. In the second fast step, Cl- reacts with the carbocation O20:Unsaturated hydrocarbons Examples of addition reactions to alkenes 4. Addition of water (hydration) Water is a poor electrophile hence the need for trace amounts of H+ (acid) catalyst and heat O20:Unsaturated hydrocarbons Addition reactions to unsymmetrical alkenes MINOR PRODUCT MAJOR PRODUCT Alkyl substituents on the alkene speed up the rate of reaction with electrophiles. O20:Unsaturated hydrocarbons Carbocation intermediates (relative stability) CH3 H 3C + C H CH3 H3C H + C CH3 H 3C H + C H H + C H Increasing Stability In the addition of HX to an alkene, the H attaches to the C where there are more H’s and the X attaches to the C with less H’s (more alkyl substituents). The reason for this is that the reaction proceeds via the more stable carbocation intermediate. O20:Unsaturated hydrocarbons Alkynes • Alkynes undergo many of the same reactions alkenes do. • As with alkenes, the impetus for the reaction is the replacement of -bonds with -bonds. MINOR MAJOR When there is a halogen already attached to the alkene, the 2nd halide ion will add to the same position (the side with fewer hydrogens). O21:Chemistry of benzene Benzene A special type of unsaturated compound: C6H6 Molecule as a whole is PLANAR. Neither structure actually exists, which is the real structure? Auguste Kekule first realized that benzene has a ring structure when he dreamed of snakes biting their own tails. O21:Chemistry of benzene Benzene: the real structure Represented as: Resonance forms Evidence: All the C-C bonds in benzene are the same length and strength! Normal C-C single bond: 1.54 Å, normal C=C double bond: 1.34 Å Benzene bond lengths are all 1.40 Å: bond order between single and double O21:Chemistry of benzene Let us learn to dream, gentlemen, then perhaps we shall find the truth...” O21:Chemistry of benzene Benzene • Unlike alkenes and alkynes, -electrons do not sit between two atoms. Not alternating single and double bonds. • Electrons are delocalised around the ring; this stabilizes aromatic compounds. O21:Chemistry of benzene The Benzene Family The benzene family includes all “aromatic compounds” or “arenes” e.g. naphthalene, benzene etc. Many aromatic hydrocarbons are known by their common names. TO BE AROMATIC: THEY MUST HAVE RINGS – RINGS MUST BE PLANAR O21:Chemistry of benzene Aromatic compounds: 1) Cyclic structures (Rings) 2) The structure must be planar (only contains sp2 hybridized carbon atoms) 3) The double bonds must be able to delocalize around the ring (e.g. Single double single etc.) If the molecule meets these requirements then it is a very stable molecule! And it will try to stay aromatic. O21:Chemistry of benzene Using an analogy to alkene chemistry you might expect the following addition reaction to occur. This never happens! Being aromatic offers such additional stability that benzene will rather undergo a substitution reaction Nucleophile X must be electron-poor (electrophile), eg. NO2+, Cl+, CH3+ O21:Chemistry of benzene When there is more than one substituent: ORTHO META PARA O21:Chemistry of benzene Electrophilic Substitution Reactions, eg. 1. Nitration TNT O21:Chemistry of benzene Electrophilic Substitution Reactions, eg. 2. Halogenation O21:Chemistry of benzene Electrophilic Substitution Reactions, eg. 3. Alkylation (Friedel-Crafts) 4. Acylation (Friedel-Crafts) O22:Comparison of reactions Alkanes: Substitution reaction, radical mechanism Alkenes: Addition reaction Nucleophile Also HCl, H2O Arenes (special class of alkenes): Substitution reaction Nucleophile O22:Comparison of reactions Example: Indicate the reagent and/or catalyst required for the following transformations: O23: Saturated Heteroatom Compounds Overview of Reactivity Types of saturated heteroatom compounds: 1) Haloalkanes (Substitution vs Elimination) 2) Alcohols (Substitution, Dehydration, Oxidation) 3) Ethers 4) Amines 5) Organometallics • Ease of reactions (effect of nucleophile, leaving group, electrophile, acid) • Comparison with inorganics (water and ammonia) • Acid-Base properties O23: Saturated Heteroatom Compounds Reactivity of C-X 1. The C-X bond is polar; δ+ and δ- sites 2. The heteroatom has one or more lone pairs (or vacant orbitals) which are reactive centres (“Hot Spots”). 3. C-X is weaker than C-H (413 kJ/mol) e.g. C-Cl (326 kJ/mol) C-O ( 335 kJ/mol) C-N (293 kJ/mol) Therefore it is easy to break a C-X bond O23: Saturated Heteroatom Compounds Can be Electrophilic or Nucleophilic! Electrophilic C Nucleophilic C Haloalkanes Organometallics Alcohols Ethers Amines O24: Comparison with inorganics Water Ammonia Alcohol Ether Primary Secondary Tertiary Amine Amine Amine Alcohols, ethers and amines have chemical similarities to water and ammonia, especially acid/base properties O24: Comparison with inorganics As Bases (H+ acceptors) Nu E O24: Comparison with inorganics As Bases (H+ acceptors) Nu E NB Reaction for drug absorption O24: Comparison with inorganics Acid/Base properties E.g. Codeine (R=CH3), or Morphine (R=H) N.B. Basic properties are especially important for drugs as their solubility in blood or their ability to cross cell membranes is influenced by whether or not they are protonated. O24: Comparison with inorganics As Acids (H+ donors: give up H+) O25 & O26: Substitution and elimination HALOALKANES: What type of reactions do we expect to see?! Substitution or Elimination C-Cl is the reactive bond (Remember: Addition reactions require an unsaturated system) O25: Substitution HALOALKANES: Br- is the leaving group OH- is the nucleophile The C of C-Br is the electrophile (C-Br is reactive bond) O26: Elimination HALOALKANES: N.B. The nucleophile (NaOH) is acting as a base. Substitution and Elimination reactions are always in competition with each other, both can occur!!! O27: What favours S vs E? 1)Temperature: High temp. (> 200°C) favours Elimination, e.g. cracking Hot, conc. NaOH favours Elimination Low temp. favours Substitution 2) Size effects: Substitution is favoured for small nucleophiles - attack the carbon (inside the molecule). Elimination is favoured by large nucleophiles – attack hydrogen (on the surface of the molecule). O27: What favours S vs E? 3) Steric Hindrance: Absence of steric hindrance (small hydrogen atoms around the carbon centre) favours Substitution A sterically hindered carbon or a crowded carbon centre (bigger groups around the carbon) favours Elimination. Any hindrance favours elimination, eg. bulky nucleophile or crowded carbon centre O25 & O26: Substitution vs Elimination ALCOHOLS: Elimination? Or Substitution? -OH is not as good a leaving group as the halogens - C-OH is a strong bond 335 kJ/mol C-Cl is a weaker bond 326 kJ/mol Under the right conditions both substitution and elimination can take place! O25: Substitution ALCOHOLS: Effect of H+ CH3CH2OH + NaCl CH3CH2OH + HCl No reaction CH3CH2Cl + H2O Why? We have modified a poor leaving group (OH-) into a better leaving group (H2O). O26: Elimination ALCOHOLS: Elimination (Loss of H2O is also called dehydration) In the presence of an acid such as H2SO4 (and heat) there isn’t a good nucleophile therefore dehydration is favoured. O26: Elimination ALCOHOLS: Where more than one elimination is possible, that giving the most highly substituted alkene is favoured MINOR MAJOR O26: Elimination ALCOHOLS: Alternative eliminations This is also an elimination reaction, with the loss of 2 hydrogens, therefore we call it a dehydrogenation or oxidation reaction. An Oxidant is required, for example: Cr(VI) - K2Cr2O7 (Potassium dichromate) Mn(VII) - KMnO4 (Potassium permanganate) CrO3 (Chromium trioxide) O25: Substitution ORGANOMETALLIC COMPOUNDS: Reactivity of C-X where C acts as a nucleophile With organometallic reactions we always see Substitution The carbon attached to the metal is always the nucleophile, and it is such a good nucleophile that it will attack even a poor electrophile. O28: Unsaturated Heteroatom compounds These include imines and nitriles And more importantly the ketones and aldehydes π-bond R’=H, R=C (aldehydes) R’,R=C (ketones) REACTIVITY: POLAR; LONE PAIRS ON HETEROATOMS; EXPOSED π ELECTRONS – HOT SPOTS O28: Unsaturated Heteroatom compounds Reactivity The bonds in these compounds are strong. Compare C-O 335 kJ/mol C=O 704 kJ/mol vs C-C 348 kJ/mol C=C 619 kJ/mol The carbon-oxygen double bond is more than twice as strong than the carbon-oxygen single bond, whereas the carbon-carbon double bond is less than twice as strong than carbon-carbon single bond. O28: Unsaturated Heteroatom compounds Classified as a nucleophilic addition reaction What attacks first, nucleophile or electrophile? A good nucleophile will attack first: it attacks the carbon atom - the electrophilic centre. A poor nucleophile needs catalysis with H+ (H+ is an electrophile) O28: Unsaturated Heteroatom compounds Reactions with good nucleophiles, eg: Overall addition of H2 : reduction LiAlH4 and NaBH4 are both sources of “H-” “work-up” O28: Unsaturated Heteroatom compounds Reactions with good nucleophiles, eg: OR O28: Unsaturated Heteroatom compounds Acid-catalysed additions O28: Unsaturated Heteroatom compounds Nucleophilic addition • Nucleophile can be neutral (H2O, R-OH, NH3), which usually requires acid catalysis. • Nucleophile can be negatively charged [OH-, NC-, H-, R3C- (carbanion)] -doesn’t require acid catalysis. Oxidation reactions • Aldehydes are easily oxidized to carboxylic acids • Ketones resist oxidation Reduction reactions • Both aldehydes and ketones are reduced to alcohols when hydrogen adds to the carbonyl group • Typical reducing agents include LiAlH4, NaBH4. O29: Comparing addition reactions Adding Hydrogen, H2 H-H is a very strong bond. We need to activate it with a metallic catalyst: Pt, Pd, Rh (eg. 1% Pt/C) H2 H H metal surface Forward reaction = reduction (addition) Reverse reaction = oxidation (elimination) O30: Composite functional groups What are Composite Functional Groups? A simple functional group has one “special feature” (heteroatom or π bond) on a carbon atom e.g. CH3-OH, H2C=CH2, H2C=O etc. A composite functional group has more than one “special feature” (heteroatom and a π bond) at a single carbon atom O30: Composite functional groups Examples: Carboxylic acid Ester Acid Chloride Amide O30: Composite functional groups Reactions of Composite Functional Groups The double bond leads us to predict an addition reaction. The heteroatom leads us to predict a substitution or elimination. Remember addition + elimination = substitution, so overall we see a substitution reaction. X= halogen X= OH X= OR X= NR2 Carboxylic halide Acid Ester Amide O30: Composite functional groups Reactions of Composite Functional Groups, eg. Substitution reaction Substitution reaction O30: Composite functional groups Reactions of Composite Functional Groups Mechanism: 1. First there is a nucleophilic addition 2. Then there is an elimination Overall there is a substitution reaction O30: Composite functional groups Reactions of Composite Functional Groups Mechanism: 1. First there is a nucleophilic addition 2. Then there is an elimination Overall there is a substitution reaction O30: Composite functional groups Reactions of Composite Functional Groups Ease of reaction: substitution Addition plus elimination = substitution Second reaction proceeds much faster O30: Composite functional groups Don’t forget acid-base properties! N.B. Esters don’t have acidic protons O31: Modern Materials POLYMERS Polymers (greek for “many parts”) are giant molecules that are made up of many, many identical, smaller molecules. They typically have molecular weights greater than 1000. The building blocks for polymers are called monomers. Synthetic Polymers: plastics, rubber, nylon etc. Natural Polymers: wool, silk, natural rubber etc. Biopolymers: proteins, polysaccharides, nucleic acids We will examine 2 kinds of polymers: 1)Condensation polymers 2)Addition polymers O32: Modern Materials Condensation Polymers Condensation Polymerisation: molecules are joined by the elimination of a small molecule (e.g. water): O H O N H + H O C N C H + H O H Example of condensation polymerisation: formation of nylon. O32: Modern Materials Condensation Polymers In order to form a polymer, we need bifunctional molecules, eg. amino acids, diamines, dicarboxylic acids X X Y Y (-XY) X Y O32: Modern Materials Condensation Polymers Eg. Nylon 6,6 is a polyamide O32: Modern Materials Condensation Polymers (eg. polyester) repeat unit O32: Modern Materials Addition Polymers Example: ethylene H2C=CH2, can polymerise by using electrons from the C–C bond to form C–C bonds with adjacent ethylene molecules (with the help of radicals). See earlier! The result: polyethylene. This is called addition polymerisation because ethylene molecules are added to each other. O32: Modern Materials Addition Polymers Initiator (small %) Monomer Polymer n > 106 O32: Modern Materials Addition Polymers Eg. Polystyrene repeating unit O32: Modern Materials Addition Polymers Eg. Polyvinyl chloride (PVC) repeat unit monomer O32: Modern Materials Addition Polymers n CH2=CH2 −(CH2-CH2)n− n can be greater than a million! n H2C=CHX −(CH2-CHX)n− X=H X=CH3 X=Cl X=benzene X= -OCOCH3 X= CN F2C=CF2 CH2=C(CH3)CO2CH3 polyethylene polypropylene polyvinylchloride (PVC) polystyrene polyvinylacetate (PVA) Orlon Teflon Perspex O33: The Molecules of Life We are going to look at five classes of biological molecules: Amino Acids and Proteins Sugars and Carbohydrates Nucleic Acids and DNA Lipids Steroids O34 & O35: Amino Acids • There are 20 naturally occurring amino acids that are used by the body to make proteins • Amino acids contain an amine, a carboxylic acid and an R group side chain • Have a stereogenic centre There are four distinct classes of amino acids 1. Acidic 2. Basic 3. Hydrophobic (non-polar) 4. Hydrophilic (polar) α-amino acid O34 & O35: Amino Acids 1) Acidic amino acid (e.g. aspartic acid) 2) Basic amino acid (e.g. lysine) O34 & O35: Amino Acids 3) Hydrophobic (non-polar) amino acid (e.g. phenylalanine) 4) Hydrophilic (polar) amino acid (e.g. serine) O34 & O35: Amino Acids Zwitterions Amino acids fall into a class of molecules known as zwitterions. Zwitterions have both an acidic group (e.g. CO2H) and a basic group (e.g. NH2) and can be described as amphoteric (proton donor and proton acceptor). O34 & O35: Amino Acids Zwitterions In aqueous solvents at a specific pH (for each amino acid) the amino acid exists mainly as a zwitterion. This means they have one positive charge and one negative charge and are neutral overall, but dipolar. This pH is called the isolectronic point. Low pH Neutral pH High pH O34 & O35: Amino Acids and Proteins • Amino acids link together in long chains to form proteins. • They link by means of amide bonds: the amine group on one amino acid links to the carboxylic acid of another. • Proteins are polymers made up of repeating amino acid units. • Short chains of amino acids are called peptides and longer chains are called polypeptides. O34 & O35: Amino Acids and Proteins Formation of an amide bond Enzyme catalysis O34 & O35: Amino Acids and Proteins Show the amino acids that would form on hydrolysis of the following tripeptide: O34 & O35: Amino Acids and Proteins Protein Structure The sequence of amino acids that make up the protein is known as the primary structure of the protein. Chains of amino acids making up the protein coil or stretch in different ways. How the segments of chain are arranged in regular patterns (coiling, alpha helices, beta sheets) is known as secondary structure. This is often determined by the Hydrogen Bonding O34 & O35: Amino Acids and Proteins Protein Structure The overall shape of the protein is called the tertiary structure and is determined by various intramolecular bonding interactions, e.g. disulphide linkages: S-S Cysteine (an amino acid), present in the polypeptide facilitates cross linking by forming disulphide bridges. O34 & O35: Amino Acids and Proteins Tertiary Protein Structure O33: Sugars and Carbohydrates Sucrose (a dimer of glucose and fructose) amylopectin amylose STARCH (a glucose polymer - polysaccharide) O33: Nucleic Acids and DNA Heterocyclic base, sugar and phosphate: these building blocks make up a nucleotide. DNA and RNA are made up of long chains of repeating nucleotide units. O33: Nucleic Acids and DNA Nucleic acids O33: Fatty acids and lipids O33: Fatty acids and lipids O33: Steroids Steroids all contain the characteristic four-ring system, A-D C A B cholesterol oestrone D testosterone oestradiol