1. Carbon Compounds John Leaver

2. Organic Chemistry The vast majority of the compounds of the element carbon are called ‘ Organic Compounds ’ and their study is known as ‘ Organic Chemistry ’. Their large number is a consequence of the ability of carbon atoms to link together to form ‘ chains ’ and ‘ rings ’

3. Why ‘ organic ’ compounds? These substances are frequently found in living, or once living, matter – hence the name organic. It was once thought that they could only be created by ‘ organic ’ processes (i.e. from living material).

4. Note on Nomenclature The naming of organic compounds is an extensive subject with its own literature. This presentation is concerned more with giving an impression of the variety of organic compounds No attempt will be made in this session to teach the rules for naming organic compounds in a systematic way Although you are likely to ‘ pick up ’ some aspects of the topic

5. Hydrocarbons The least complicated organic compounds, with respect to their chemical behaviour, are those that contain only carbon and hydrogen atoms. These are called ‘ hydrocarbons ’. There are several classes of hydrocarbon – they differ with respect to the bonding present between carbon atoms.

6. Alkanes (old name ‘ paraffins ’ ) In alkanes there are only single bonds between carbon atoms. Each carbon atom is able to form four bonds in total In alkanes all ‘ spare ’ bonds are to hydrogen atoms

7. Alkanes – Example: Butane Butane C 4 H 10 or CH 3 CH 2 CH 2 CH 3 is a gas used as a fuel A chain of Four carbon atoms joined by single bonds All remaining bonds have hydrogen atoms attached, each carbon atom having four bonds in total

8. Note on the Representation of Organic Molecules It is important to be aware that in all but the most introductory of text books it is usual to assume the presence of most of the carbon and hydrogen atoms when depicting organic molecules Hence butane is more commonly shown as:

9. Representation of molecules - 2 You may also see 3D representations of molecules in ‘ ball and stick ’ form:

10. Representation of molecules - 3 You may also encounter ‘ space filling ’ views that give an indication of the ‘ surface ’ of the molecule

11. General formula for Alkanes The molecular formulae of the series of straight chain alkanes may be represented by the following formula: C n H 2n+2 The first fifteen are named on the next slide (notice that after the first four the name tells you how many carbon atoms are present).

12. Names of Alkanes Methane (n=1) Ethane (n=2) Propane (n=3) Butane (n=4) Pentane (n=5) Hexane (n=6) Heptane (n=7) Octane (n=8) Nonane (n=9) Decane (n=10) Undecane (n=11) Dodecane (n=12) Tridecane (n=13) Tetradecane (n=14) Pentadecane (n=15) As chain length increases physical properties change: e.g. at room temp n=(1-4) gases, n=(5-16) liquids, n>16 solids

13. More complex alkane chains It is also possible to have branched alkane chains such as: 8-butyl-5,11-diethyl- pentadecane This should help to indicate the enormous possibilities with respect to both size and complexity for alkane molecules

14. Alkenes (old name ‘ olefins ’ ) Alkenes contain at least one example of a double bond between carbon atoms. As with alkanes, the remaining (non Carbon to Carbon) bonds are to hydrogen atoms. Alkenes are said to be ‘ unsaturated ’ i.e. there is scope for the addition of other atoms or radicals. They are therefore more chemically reactive than the ‘ saturated ’ alkanes.

15. Alkenes – Example: But-2-ene Double bond The ‘ 2 ’ indicates the position of the bond NB Alkenes have a higher percentage of carbon than do alkanes – they therefore burn with a smokier flame

16. But-2-ene: other representations The double bond on the ball and stick structure is represented by being shorter than the single bonds (more electrons are involved in forming the bond so the carbon atoms are pulled closer together)

17. More complex alkenes Obviously hydrocarbon molecules may contain more than one double bond They are then ‘ poly-unsaturated ’ :

18. Alkynes (old name ‘ acetylenes ’ ) Alkynes are hydrocarbons containing at least one ‘ triple bond ’ between carbon atoms. They are rather reactive compounds. The simplest example is ethyne:

19. Cyclic hydrocarbons As well as chains of carbon atoms it is also possible to have rings These are called cyclic compounds The three sorts of hydrocarbon we have seen so far can exist in rings and these are called cycloalkanes, cycloalkenes and cycloalkynes respectively (the latter are not commonly encountered)

20. Cycloalkanes and Cycloalkenes Some examples: Cyclohexane Cyclopenta-1,3-diene Methylcyclopropane

21. Aromatic compounds It might be supposed that a compound with this structure would be named cyclohexa- 1,3,5-triene and would behave as though it had alternate single and double bonds However, when a ring of six carbon atoms, each attached to one hydrogen atom is made, it behaves as though all the carbon-carbon bonds are equivalent

22. Benzene In such a ring structure as on the previous slide the bonding electrons are able to spread around the ring (or ‘ delocalise ’ ) and the C 6 H 6 ring is actually called benzene Compounds containing this structure are called ‘ aromatic ’ compounds

23. Representing benzene Sometimes it is convenient to represent benzene rings with alternate single and double bonds, like this: Alternatively they may also be represented by a hexagon containing a circle to indicate the delocalised electrons:

24. Other aromatic hydrocarbons It is possible for several benzene rings to join together to make larger molecules, such as: anthracene phenanthrene

25. Heterocyclic Compounds It is also possible for one or more of the carbon atoms in a ring system to be replaced by another sort of atom (for example oxygen or nitrogen) Such compounds are called ‘ heterocyclic ’ Many important biological molecules are heterocyclic (e.g. see sugars later)

26. Example of a Heterocyclic Compound Deoxy-ribose

27. Functional Groups Organic chemicals often display characteristic properties as a consequence of the functional groups that they contain Functional groups are small groups of atoms that allow the molecule to react with other molecules in specific ways. Some examples will be found on the following few slides

28. Some Important Functional Groups ClassFormulaExampleName Alcohol-OHCH 3 OH Methanol Aldehyde-CHOCH 3 CHO Ethanal Amine-NH 2 CH 3 NH 2 Methylamine Carboxylic acid-COOHCH 3 COOH Ethanoic acid Ester-COORCH 3 COOCH 3 Methyl methanoate Ether-O-CH 3 OCH 3 Methoxymethane Halogens-XCH 3 Br Methyl bromide Ketone=COCH 3 (CO)CH 3 Propanone

29. Functional Groups in more detail In the next few slides we will look at each of the functional groups from the table In particular we will consider: Alternative names Properties Biological examples

30. Alcohols – the hydroxy group, -OH Alcohols contain the hydroxy group, OH. E.g. CH 3 CH 2 OH ethanol or ethyl alcohol (a familiar compound to many) cyclohexanol Phenol The aromatic alcohols are known as phenols

31. Alcohols - 2 Alcohols sometimes have a pleasant odour although the longer chain alcohols can have a rather ‘ sickly ’ smell. Aromatic alcohols have a sharper smell. Many alcohols are flammable. Some liquid alcohols (those with shorter chains and smaller rings) are also used as solvents and are miscible to some extent with water.

32. Alcohols - 3 The hydroxy group is common in biological molecules and pharmaceutical compounds:  -D–glucose (a sugar) Dopamine (a neural transmitter and sympathomimetic drug)

33. Aldehydes -CHO The simplest aldehyde is ‘ formaldehyde ’ HCHO (proper name, methanal,) used to preserve biological specimens. The aldehyde structure contains a ‘ carbonyl ’ group (C=O) Ethanal (old name, Acetaldehyde)

34. Aldehydes - 2 Aldehydes are often rather pungent. Benzaldehyde – is the constituent of almonds that gives them their characteristic ‘ marzipan ’ smell

35. Aldehydes - 3 The carbonyl group in aldehydes makes them somewhat reactive Under the right conditions aldehydes may be ‘ reduced ’ to alcohols or ‘ oxidized ’ to carboxylic acids

36. Aldehydes - 4 Examples of the aldehyde group in biological/medicinal compounds Vanillin Cinnamaldehyde

37. Amines – the amino group NH 2 Simple examples are: CH 3 NH 2 methylamine or aminomethane cyclohexylamine or aminocyclohexane aminobenzene or aniline

38. Amines - 2 Amines often have a ‘ fishy ’ odour and are associated with decomposition: “ Putrescine ” (butane-1,4-diamine) “ Cadaverine ” (pentane-1,5-diamine) Both compounds are found in decomposing corpses!

39. Amines - 3 Examples of the amino group in biological/medicinal compounds Adenine – one of the five nucleic acid bases Amphetamine – a CNS stimulant etc

40. Carboxylic acids -COOH Common example: Ethanoic acid (CH 3 COOH) – commonly known as ‘ acetic acid ’. The active ingredient of vinegar. It forms when ethanol is oxidised, causing the vinegary taste of stale wine.

41. Carboxylic acids - 2 The smaller carboxylic acids tend to be pungent, corrosive liquids: ‘ Formic acid ’ or methanoic acid (HCOOH) – a corrosive substance sprayed by ants ‘ Butyric acid ’ or butanoic acid occurs in rancid butter and stale sweat

42. Carboxylic acids - 3 Biological/medicinal examples of compounds containing -COOH Citric acid – gives citrus fruits their sharp flavour Kainic acid – an anthelmintic

43. Esters –COOC- Esters form when carboxylic acids react with alcohols. They often have fruity odours: For example: Pineapples smell of ethyl propanoate CH 3 CH 2 COOCH 2 CH 3 and other esters ‘ Ester linkage ’

44. Esters - 2 Biological/medicinal examples Dimethy phthalate ( ‘ DIMP ’ ) an insect repellent benzocaine – a local anaesthetic

45. Ethers: -O- Ethers contain carbon atoms linked by an oxygen atom The oxygen atom may link chains or rings, or be within a ring (cyclic ethers). diethyl ether or ethoxyethane commonly just called ‘ ether ’ A ‘ crown ’ ether – this one is 18-crown-6

46. Ethers - 2 The smaller ethers are liquids with low boiling points, flammable and immiscible with water They are used as solvents Ethers are generally rather un-reactive Diethyl ether has been used as an anaesthetic Larger ethers with many ether links may be water miscible

47. Ethers - 3 Biological/medicinal examples Cineole (1,3,3-trimethyl-2- oxabicyclo[2.2.2]octane) a constituent of eucalyptus oil Myristicin – a psychotropic constituent of Nutmeg

48. Halogen compounds: -X The halogens fluorine (F), chlorine (Cl), bromine (Br) and iodine (I) may bind to carbon atoms in organic compounds The properties of these compounds are rather diverse as a consequence of the differences between the chemical properties of the halogens Some examples will be found on the next slide

49. Halogen compounds - 2 trichloromethane or ‘ chloroform ’ a solvent and anaesthetic ‘ Circladin ’ an anticoagulant ‘ Capacin, a thyroid inhibitor Myelotrast a radio-opaque agent

50. Ketones: C=O Ketones contain a carbonyl group, C=O Smaller ketone molecules are liquids and are often good solvents for other organic compounds Acetone (propan-2-one) is a commonly used solvent:

51. Ketones - 2 Biological/medicinal examples Carvone – a constituent of Caraway oil with carminative properties ‘ Entobex ’ an anti-amoebic

52. Bio-molecules The following few slides briefly outline some of the classes of bio- molecules that you may encounter: –Amino acids –Carbohydrates –Fatty acids –Peptides –Sugars –Vitamins

53. Amino acids The molecules which combine to make protein chains and polypeptides They contain an amino group and a carboxylic acid group: Alanine Aspartic acid

54. Carbohydrates A group of compounds such as sugars, starches and celluloses that are found in plants and animals They have the general formula C x (H 2 O) y Fructose

55. Fatty acids A general term for saturated and unsaturated aliphatic carboxylic acids. The longer chain fatty acids are obtained from animal and vegetable fats. Stearic or octadecanoic acid – obtained from animal fat

56. Peptides Molecules composed of sequences of amino acids joined by ‘ peptide linkages ’. They may be just two amino acids (dipeptides) or a few (oligopeptides) or many (polypeptides) Phenylalanine Aspartic acid A dipeptide Peptide link

57. Sugars Water soluble carbohydrate molecules occurring in plants and animals Three different representations of the same sugar molecule

58. Vitamins The vitamins are a structurally heterogeneous group of compounds which are needed, usually in small amounts, for an organism to function Two examples follow, showing the lack of chemical similarity

59. Vitamin B 12

60. Vitamin C

61. Some more examples Organic compounds are used for a great variety of different purposes. Often a molecule will contain more than one of the functional groups (and others that have not been mentioned). The following few slides give some indication of the variety of organic compounds.

62. Aspirin Aspirin is: 2-ethanoyloxybenzoic acid It has been in use as an analgesic and anti- inflammatory drug for many years, having been introduced in 1899 by Baeyer.

63. Caffeine The stimulant that occurs in tea, coffee and some carbonated drinks 1,3,7-trimethyl-3,7-dihydropurine-2,6,-dione

64. Camphor A compound used in some medicinal preparations such as liniments. It is obtained from the wood of a tropical tree. 1,7,7-trimethylbicyclo[2.2.1]heptan-2-one

65. Nicotine An addictive component of tobacco. It is addictive in small doses but highly toxic in larger doses and causes nausea, convulsions and death. Nicotine or 3-(1-methylpyrrolidin-2-yl)pyridine

66. Quinine Anti-malarial extracted from bark of S. American tree (6-methoxyquinoline-4-yl)- (5-vinyl-1-azabicyclo[2.2.2]oct-2-yl)-methanol

67. Saccharin Artificial sweetener 1,1-dioxo-1,2-dihydro-1lambda*6*-benzo[d]isothiazol-3-one

68. Xylocaine Local anaesthetic used in dentistry [(2,6-dimethyl-phenylcarbonyl)- methyl]diphenylammonium chloride

69. Conclusion The aims of this session were to: – indicate the diversity of carbon compounds, especially in the context of biology and medicine –allow you to gain some knowledge of the different functional groups –indicate the complexity and vast number of carbon compounds you may encounter –allow you to identify some of the broad classes of carbon compounds –become more familiar with ways of representing organic molecules