University of Sydney Chemistry 1B (CHEM1102) Organic Chemistry Lecture Notes

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1 University of Sydney hemistry 1B (EM1102) rganic hemistry Lecture Notes Topic 1 Introduction & isomers 2 Topic 2 Alkenes, alkynes, arenes 23 Topic 3 Structure determination 32 Topic 4 Alcohols and amines 43 Topic 5 Stereochemistry 49 Topic 6 Alkyl halides, carbonyls 55 Topic 7 arboxylic acids & derivatives 69 Summary of Reactions 79 Inorganic & General hemistry Lecture Notes Topic 8 Acids and Bases 85 Topic 9 Topic 10 Topic 11 Solubility oordination hemistry Kinetics Unless otherwise stated, all images in this file have been reproduced from: Blackman, Bottle, Schmid, Mocerino and Wille, hemistry, 2012 (John Wiley) ISBN:

2 Topic 1 Introduction, representation of structures, functional groups, nomenclature, isomers Introduction - Definition of rganic hemistry rganic chemistry deals with compounds in which carbon is the principal element rganic substances arise in all sorts of places - plants, animals, food, medicines, industry, research laboratories Every living organism is made of organic chemicals 15 million organic substances - number increases by 10,000 per week! The Unique Nature of arbon Bonding in rganic arbon atenation - arbon atoms can bond together to form Stable extended chains of atoms Rings Multiple bonds arbon has atomic number = 6 Electronic configuration: 1s 2 2s 2 2p 2 Valency of 4 four bonds to completely fill outer electron shell of carbon arbon forms bonds to Itself single, double, triple Metals Na, K, Fe, u, Mg eteroatoms N, P,, S, X - and - bonds are strong - and - bonds are non- polar kj mol Si- Si 176 N- N I- I 152 A combination of the strength and non- polar nature make - and - bonds unreactive 1. Propane is (a chain of 3 carbons, with the number of hydrogens indicated attached to each carbon). Draw a picture to show the structure of this molecule. ould you draw your picture quickly and efficiently? ow well would this drawing method work for a bigger molecule (e.g. octane ( 8 18 ), octadecane ( ) or taxol ( N 14 ))? ow well does the picture above represent the actual structure of propane? 2

3 Representation of rganic Molecules rganic compounds may be represented in several ways as illustrated in the examples below oncept atenation chains and rings of carbon atoms Bonding single, double, triple bonds possible Geometry depends on hybridisation of carbon atom Valence 4 for carbon (3 N, 2, 1, l,, I) Reactivity often associated with heteroatoms (atoms other than or ) In the stick representation: Ø is basis of structure Ø arbon atoms are not usually shown but assumed to be at the intersection of 2 or more bonds and at the end of each line Ø 1, 2 or 3 lines to represent single, double and triple bonds Ø Indicate bond angles (~ or ) Ø mit all - bonds, hydrogen count assumed Ø Specify all heteroatoms (, N, F, l, B, I, S etc) and heteroatom bond Ø When drawing neutral organic molecules: Ø always has a valence of 4 Ø N always has a valence of 3 Ø always has a valence of 2 Ø X (halogen) always has a valence of 1 3

4 Example: From a condensed structural formula, first draw the structure out in full then remove all atoms with the attached to them and replace them with a kinked chain showing all - bonds. Show all heteroatoms and attached to heteroatoms. With practice you will be able to convert condensed structural formula to stick structures directly. ondensed Structural Formula Structural Formula Stick representation or l= 2 or 3 l 2 l l Now draw a line structure for octane, 8 18 (remember lines represent bonds, atoms aren t shown (they re assumed to be at the intersections and ends of lines) atoms aren t shown, and angles are drawn close to the actual bond angles. ow quickly/ efficiently could you draw that picture? ow well does it represent the actual structure of the molecule? 4

5 3. Next try drawing line structures for 1- pentanol, 2- bromopropane and 2- aminobutane. 1- pentanol ( ) 2- bromopropane ( 3 3 ) 2- aminobutane ( 3 (N 2 ) 2 3 ) 4. And now work backwards and draw condensed formulae (e.g ) for these structures. an you name any of these three compounds? Where it is important to represent the three- dimensional shape of a molecule, the following convention is adopted: Bonds in the plane of the paper Bonds coming towards the observer A A B B Bonds going away from the observer A B or A B For example, 4 5

6 5. Try drawing 3D structures for these compounds, using wedges and dashes to show bonds coming out of/ going into the page. dichloromethane ( 2 l 2 ) methanol ( 3 ) dimethylpropane ( 3 ( 3 ) 3 ) For more practice, try these extra questions 6. Try converting the following to stick structures. 6

7 Reverse the process to go from a stick structure to a condensed molecular formula by first drawing in the atoms then add atoms to ensure the valence of each is four. Example: 7. Try converting the following stick structures to condenser structural formula. 7

8 ybridisation 8. Methane ( 4 ) has a tetrahedral shape. A tetrahedron is symmetrical: What does this tell you about the four bonds in methane? What does this tell you about the four atomic orbitals at carbon that are involved in forming these four bonds? There are four experimentally observed bonding arrangements for carbon: Type of bonds ybridisation Geometry Examples 4 single bonds sp 3 Tetrahedral 4, single, 1 double bond sp 2 Trigonal planar 2 = 2, 2 = 1 single, 1 triple bond 2 double bonds sp Linear == 9. Let s look at this another way. What is the electronic configuration of carbon? So which of carbon s atomic orbitals are involved in making these bonds to the hydrogens? What shape would methane have if these orbitals behaved as separate, independent orbitals (i.e. one 2s orbital + three 2p orbitals)? 10. Now imagine you run a juice bar. You have one apple and three carrots, a blender but no knife. (It s a poorly equipped juice bar.) ow many different juice blends can you make? What is the apple : carrot ratio in each of them? ow many carrots are left out in each case? Juice Blend Apple : arrot Ratio Left ver arrots 8

9 11. Now it s orbitals you are mixing. You have one s orbital and three p orbitals, and again a blender (hybridizer) but no knife. ow many different orbital blends can you make? What is the s : p ratio in each of them? ow many p orbitals are left out in each case? rbital Blend s : p Ratio Left ver p orbitals ybridisation is a convenient way of describing the sigma- bonding orbitals and lone pair orbitals (if present) of an atom. In alkanes, hybridisation gives four identical sp 3 orbitals, which form a tetrahedral shape to minimise repulsion between the orbitals. Energy ybridisation arbon - ground state arbon - bonding state arbon - four sp 3 orbitals Note: A quick way of determining the hybridisation of an atom is to count the σ bonds and lone pairs around that atom and assign one hybrid orbital to each. 2 electron pairs sp, 3 electron pairs sp 2, 4 electron pairs sp 3 Example: Work out the hybridization of nitrogen in the following molecules: 9

10 12. So what is the hybridization at each carbon in propane, propene and propyne shown below? nce you ve answered that, match the correct name to each compound. What is the bond angle around the central carbon in each of these compounds? Now draw structures for 1- pentyne ( ) and 2- pentyne ( ), taking care that your bond angles reflect the hybridization. 1- pentyne ( ) 2- pentyne ( ) Functional Groups rganic compounds are classified by Functional Groups, which are responsible for chemical behaviour. Functional groups are involved in naming organic compounds. =, and the polar bonds from carbon to heteroatoms are more reactive than - or - bonds and hence where the chemistry takes place. This part of the molecule is called the Functional Group. An organic compound can be viewed as a backbone (skeleton) of carbon- carbon single bonds with other groups of atoms, functional groups, attached at various points. 10

11 Functional group The combination of the ability to form a vast range of unreactive carbon frameworks to which can be added special reactive sites gives the diversity of organic chemistry. Functional groups confer the characteristic chemical and physical properties of the compounds that contain them. Functional groups undergo the same chemical reactions irrespective of the type of molecule that contains them. A molecule containing several functional groups displays reactions that represents the sum of the reactions of each functional group. 3 Acetyl salicylic acid (aspirin) shows the properties of - a carboxylic acid - an ester - an aromatic compound 14. ircle or highlight all the functional groups in the structure of taxol below. ow many are there? Taxol (paclitaxel) 11

12 Summary Table of Functional Groups Note: R is the general abbreviation for the rest of the molecule. lass General formula Examples & alkane R alkene R 2 =R 2 alkyne aromatic compound R R ,, - - alcohol R- 3 2 ether,, = aldehyde ketone carboxylic acid R--R ester R R,, N amine R 3 N,, N,,, l, amide acid chloride R R R R R R NR 2 l ( 3 ) 3 N N 2 3 N 3 3 l l N 2,, X Alkyl halide R-X (X = l,, I) 3 2 l 12

13 15. Name the functional groups in the following molecules: Vitamin A Acetyl salicylic acid 3 Morphine N 3 ( 3 2 ) 2 N N 3 Lysergic acid diethyl amide N 13

14 Nomenclature The name of an organic molecule consists of several parts: Number(s) Substituent Stem Ending The stem indicates the number of carbon atoms in the longest chain containing the functional group. The ending indicates the nature of the functional group present. Substituents are indicated by prefixes and a number is used to locate any substituent or functional group unambiguously in a molecule. Rules: Find and name the longest carbon chain stem Identify substituents stemane Number longest carbon chain to give lowest numbering for substituents Allocate a number to every substituent List substituents in alphabetical order Identical side chains are indicated by using prefixes: di (2), tri (3), tetra (4) etc alkane number of carbons Methane 4 Ethane 3 3 Propane Butane Pentane exane eptane ctane Nonane Decane Alkane Alkyl group substituent propane propyl butane butyl

15 16. Give the name of the following molecules: l l Isomerism The problem of isomers ow many different compounds are there with the formula 2 2 l? (Excluding those with charged atoms and l or bonds) ow do we tell them apart? ow do we name them? ow are they different? Do they have different properties? There are 16 different possible compounds l 2 l l l 2 l l l l l l l l l l l l Isomers are ompounds that have the same molecular formula but different structures. Very important in chemistry but especially important in the chemical reactions that take place in living organisms - the shape is as important as the functional groups present! lassified according to type. 15

16 17. In the ancient Greek, isos = equal and meros = part, so what are isomers? ere are three to help you: (While we re looking at them, can you name these three compounds?) lassification of isomers Isomers same molecular formula onstitutional Isomers Different nature/sequence of bonds Stereoisomers Different arrangement of groups in space onformational Isomers Differ by rotation about a single bond onfigurational Isomers Interconversion requires breaking bonds Enantiomers Non-superposable mirror images Diastereoisomers Not mirror images 18. Match these three words beginning with with their dictionary.com definitions. constitution configuration conformation the way in which a thing is composed or made up the relative disposition or arrangement of the parts or elements of a thing manner of a formation, structure or form as a physical entity 16

17 onstitutional isomers Isomers differ in the nature and/or sequence of bonding Within a homologous sequence of alkanes, the number of constitutional isomers increases rapidly n : n 2n : No. of onstitutional iosmers : onstitutional formula AND ow many constitutional isomers are there of molecular formula 6 14? Draw them. The physical and chemical properties of constitutional isomers may be very different, particularly when different functional groups are present. For example the molecule with formula 4 8 may be a ketone, aldehyde, alkene/ether or alkene/alcohol. 17

18 Stereoisomers Stereoisomers have the same nature and/or sequence of bonding but differ in the arrangement of groups in space. There are two groups of stereoisomers onformational isomers or conformers differ by rotation about a single bond and can not normally be separated from each other at room temperature. onfigurational isomers may be interconverted only by breaking and remaking bonds. This process normally requires considerable energy and does not happen at room temperature. onformational isomers Straight chain alkanes Rotation around each - bond readily occurs. onformational isomers result. Use ethane as an example ( 3 3 ) Sawhorse representation rotate back carbon 60 eclipsed Newman projection staggered onformers differ in energy In straight chain alkanes rotation about a - single bond occurs rapidly at room temperature The difference in energy between conformers arises from steric interaction 20. Two conformational isomers of ethane are shown below. ne of these is called the staggered conformation, the other is an eclipsed conformation. Which do you think is which? 18

19 onfigurational isomers Diastereoisomers Inn cyclic alkanes Rotation is restricted within a ring of carbon atoms. This is because rotation would require the atoms attached to carbon to pass through the centre of the ring this has a high energy barrier. Disubstituted cycloalkanes A number of types of isomers are possible. onstitutional: eg 1,1- dichlorocyclopentane, 1,2- dichlorocyclopentane and 1,3- dichlorocyclopentane. onfigurational: eg two forms of 1,2- dichlorocyclopentane: Nomenclature: cis and trans These structures are diastereoisomers. They have different physical and chemical properties. The terms cis and trans are used to distinguish them. 21. Three pairs of cyclobutanes are shown below. What type of isomerism is shown in each? 19

20 Alkene diastereoisomers 22. Are these the same compound? Why so/ why not? What about these two? Why so/ why not? What type of isomers are these? And what is required for this type of isomerism to occur? A double bond is constructed of a σ- and π- bond. Pi- bonds result from p- orbital overlap and are directional with a fixed geometry. Electron density concentrated above and below plane. Rotation around the - axis would require breaking the pi- bond (~128 kj mol 1 ) and does not occur at room temperature. 3 3 melting point = -139 º boiling point = 4 º Different compounds! 3 3 melting point = -106 º boiling point = 1 º (Z)- 2-butene (E)- 2-butene π - bond σ - bond Both ends of the = bond must have two different groups. If these conditions are met, TW diastereoisomers result: A X A B X Y B Y But A and B can be the same as X and Y l The same compound! Different compounds! l 20

21 21

22 Nomenclature: Z and E The rules Z/E determined by assigning a priority to each of the pairs of groups on each carbon of the double bond. The higher the atomic number of the atom attached, the higher the priority. If identical atoms are attached to each carbon of =, work outwards along the chain until the first point of difference is reached. If groups of high priority are on the same side of the double bond the alkene is denoted (Z). If groups of high priority are on the opposite side of the double bond the alkene is denoted (E). igher priority groups on the same side of double bond alkene is denoted (Z) igher priority groups on opposite sides of double bond alkene is denoted (E) Example: l (Z)- 2-butene higher priority groups on same side (E)- 2-butene higher priority groups on opposite sides (E)-1-bromo-2-chloropropene higher priority groups on opposite sides 23. Question: name these molecules, including stereochemical descriptor where appropriate (cis/trans, Z/E) A... B What is the isomeric relationship between the pairs: D... A and B.. and D.. 22

23 Note: No diastereoisomers of alkynes Two pi bonds and two sigma bonds associated with each carbon of the triple bond. Geometry of both carbon atoms is linear. There is only one way to attach two substituents in a straight line. 3 π - bonds 23