INTRODUCTORY TOPICS Content Molecular, structural and empirical formulae Functional groups and the naming of organic compounds Characteristic organic reactions Shapes of organic molecules; o and n bonds Isomerism: structural; geometrical; optical Structural formulae &.8. CHsCH2CH2OH for propan-1-ol, not C;H;OH. Displayed formulae should show both the relative placing of atoms and the number of bonds between them, e.g. i fe} | 4 #—-¢— e | O—H H for ethanoic acid Skeletal formulae A skeletal formula is a simplified representation of an organic formula. It is derived from the structural formula by removing hydrogen atoms (and their associated bonds) and carbon atoms from alkyl chains, leaving just the carbon-carbon bonds in the carbon skeleton and the associated functional groups.The skeletal formula for butan-2-ol and a partial-skeletal formula for cholestero! are shown below. HC CH3 The O convention for representing the aromatic ring is preferred. Optical Isomers indicate the three-dimensional structures according to the convention used in the example below. CH; ' CH c : c /YoH : 7 HO conH : co,H OH mirror plane Molecular, structural and empirical formulaeOrganic compounds < The carbon atoms are also commonly bonded covalently to non-metal atoms such as oxygen and halogens. = \t excludes simple compounds such as carbon monoxide, carbon dioxide and the carbonate ion. & Sources of organic compounds include crude oil and fossil fuels. & Organic compounds can also be found in carbohydrates, proteins and fats in human beings. Nature of the carbon atom <& Carbon is a small atom with 4 electrons in its outermost shell. Carbon ions are not formed, as high energy changes would be involved in the gain or loss of 4 electrons. Therefore, carbon forms covalent bonds in its compounds. a Carbon can also form multiple bonds with other carbon atoms or atoms such as oxygen and nitrogen. In addition, carbon can form stable chain or ring structures of different sizes. Catenation is the occurrence of carbon chains, leading to the production of many carbon compoundsNatural sources of carbon % Crude oil and coal are rich sources of hydrocarbons. < Crude oil is produced from the gradual breakdown of fossil fuels, and can be separated into different fractions by fractional distillation. The fractions have different composition and boiling points. Fractional distillation is a physical process of separation which does not alter the composition of the fractions. Coal can be converted into liquid fuel by increasing the hydrogen : carbon rati io. The various methods of achieving this include salvation, hydrogenation, destructive distillation and the Fischer-Tropsch process. The products of decomposition of coal and the fractions obtained from the fractional distillation of crude oil are used as fuels. Cracking is a chemical process used to convert longer chain alkanes into shorter chain alkanes and alkenes. The products are more useful as fuels. Thermal or catalytic cracking is employed for this purpose. Catalysts such as aluminium oxide or silicon dioxide are used at a lower temperature of 450°C. Cracking provides extra gasoline and is a source of alkenes. Gasoline of a high octane rating is obtained as cracking produces branched-chain alkanes. + Catalytic reforming is carried out in oil refineries to convert straight chain hydrocarbons to aromatic molecules. A temperature of 400°C, a pressure of 10 atm and a platinum catalyst are needed.© Anexample illustrating cracking is as follows: CiyHae —> CoHie + CH3CH=CH, + 3CH,=CH) © Anexample of catalytic reforming is: CH;(CH2)4,CH; —2> C) 1, © There are basically three different types of organic compounds which are grouped according to the structure of their carbon skeleton. © Aliphatic compounds © Alicyclic compounds © Aromatic compounds Aliphatic compounds J The carbon atoms in these compounds may form single, double or triple bonds. @ CH.CH,CH, is an unbranched aliphatic compound. cH. | @ —CHjCHCHCH.CH; isa branched aliphatic compound. | crAlicyclic compounds An alicyclic compound contains rings of -CHz- units joined by single bonds. % Their general formula is C,H2», the simplest member being cyclopropane (CsHe). © (J {cyclopentane) is an alicyclic compound. Aromatic compounds ° (benzene) is an aromatic compound. Carbon nits pure form carbon exists as diamond or graphite. Carbon has 3 unique nature in that itis able to catenate and form millions of organic compounds. ‘© Catenate refers to the ability to form bonds with its own atoms to produce long chain molecules.Displayed formula (© Thestructurl formule ofbenzen is General formula Alkane CoHans2 Cycloalkane CoHan Alkene. Catan Halogenoalkane CyHan aX where X is the halogen atom Halogenoarene x where X is the halogen atom Alcohol CyHanetOH Phenol OHAldehyde Ketone where = alkyl or aryl group. Carboxylic acid o I —OH where R=H, alkyl or phenyl Acid chloride oO ] R-C-—cl where R, R’ = alkyl or phenyl Ester. oO I —C—oR’ where R, R’=alkyl or phenyl Amine CoHonei ~ NH Amide ° I R—C—NH, where R, R’ = alkyl or phenyl Amino acid 4 | R—C—NH, | COOH where R= or a variety of groups Nitrile CrHansa CNWorked Examples Draw the displayed formula of the following organic compounds. (a) (b) (c) (d) (e) (f) (g) (h) (i) butane ethene chlorobutane benzene chlorobenzene butanol phenol methanal methanoic acid methanoyl chlorideSolution: (a) (ans) (ans) Functional groups and naming of organic compounds Define Functional groupAlkane lod —~c—c— | Alkene \ 7 c=C 7 N\ Alkyne -c=C- Alcohol -OH Aldehyde —CHO Carboxylic acid —COH Ester COR Acid halide —cox where Xis the halide atom Nitrile -CN Ether -O- <> The functional group will affect the physical properties of the organic compound Organic compounds with functional groups that can form hydrogen bonds will have a higher melting and boiling point than those which do not. These organic compounds will also be soluble in water as they can form hydrogen bonds with the water molecules. The carbon chain can also affect the physical properties of organic compounds such as melting point and solubility.Carboxylic acid -oic acid Carboxy- Ester -alky! halide Alkoxycarbonyl- Acid halide -oyl halide Halogenocarbonyl- Amide -amide Carbamoyl- Nitrile -nitrile Cyano- Aldehyde -al Oxo- Ketone -one Oxo- Alcohol -ol Hydroxyl- Alkyne -yne - Alkene -ene - Alkane -ane -The prefix is used to indicate other substituent groups such as those shown below. OH- Hydroxyl- NH,- Amino- NO,- Nitro- CeHs— Phenyl- CcN- Cyano- =: Fluoro- cl- Chloro- Br- Bromo- I- lodo- © Prefixes can also be alkyl groups, such as methyl (CH3-) group and ethyl (CH3CH.-) group. <} Steps to naming organic compounds: @ Select a root according to the number of carbons in the longest continuous chain. Select the suffix, The carbon atoms in the main carbon chain are then numbered from one end so that the smallest possible number will be given to the carbon atom attached to the suffix.@ Determine the prefixes present. © [fit occurs more than once, add the terms, di-, tri-, etc. The number of position numbers should correspond to the number of times the prefix is present. If there are more than one type of prefix, arrange them in alphabetical order. The di- and tri- terms do not affect this order. ° © Add the prefix(es), root and suffix together. © Commas are used to separate numbers while hyphens are used to separate numbers and words. Worked Examples (a) Define functional group. (b) Name the following functional groups. (i) ° I —C—OH (ii) oO I —c—o-Solution: (a) Functional group refers to an atom or group of atoms in the formula of an organic compound that gives it its characteristic chemical properties. (ans) (b) (i) Carboxylic acid. (ans) (ii) Ester. (ans) (iii) Aldehyde. (ans) Give the systematic name for each of the following organic compounds. (a) CH; | CH3CHCHCH,CH3 Br (b) on{_)-a (c) NH, CH3CHCH,COOHSoluti (a) 3-bromo-2-methylpentane. (ans) (b) 4-chlorocyclohexanol. (ans) (c) 4-aminobutanoic acid. (ans) Give the systematic name for each of the following organic compounds. (a) CH3CH,CH=CHCH, (b) SEES cl (c) Br | CH senenChs Br Solution: (a) Pent-2-ene. (ans) (b) 2-chlorobutane. (ans) (c) 2,3-dibromobutane. (ans)Characteristic organic reactions Organic reactions } Organic reactions can be classified according to the type of reagent being used. © Nucleophilic reactions in which nucleophiles are involved © Electrophilic reactions in which electrophiles are involved. Organic reactions can also be classified according to what happens when the reaction is over. * Addition reactions in which atom(s) or group have been added. * Substitution reactions in which atom(s) or group have been replaced. * Elimination reactions in which atoms from two neighbouring carbon atoms have been lost. Q Organic reactions take place in three stages — the initiation stage, the propagation stage and the termination stage. Homolytic fission Free radicals are atoms or groups of atoms with an unpaired electron and are very reactive. A-B —““5 Ae+Be (free radicals) © The eOH free radical is formed by the decomposition of hydrogen peroxide, HO,Heterolytic fission + Carbocations (carbonium ions) are carbon species that carry a positive charge. < Carbanions are carbon species that carry a negative charge. A-B > A+B Nucleophile Examples of nucleophiles include NH3, H30, CN” and Ci. Electrophile < Examples of electrophiles include H', C/' and NO; .Hydrolysis Oxidation Reduction In equations for organic reactions, the symbols [0] and [H] are acceptable. Inductive effect Polarisation of a covalent bond occurs when a carbon atom is bonded to another more electronegative atom. The more electronegative atom will draw the electrons in the bond towards itself. Electron-withdrawing groups such as C/, CN and COOH exhibit a negative inductive effect & Electron-donating groups such as alkyl groups exhibit a positive inductive effect.Conventions for writing reaction mechanisms Drawing organic molecules & The molecular formula counts the numbers of each sort of atom present in the molecule, but tells you nothing about the way they are joined together. <> The structural formula shows how the constituent atoms of a molecule are ijoined together. e@ To show the three-dimensional arrangement of molecules, some conventional symbols are used. — bond in plane of paper - bond going back into paper away from you —=™ bond coming out of paper towards you & The displayed formula shows the relative placing of atoms and the number of bonds between them. The skeletal formula shows a carbon skeleton with functional groups attached to it. All the hydrogen atoms are removed from carbon chains. @ The molecular formula of butane is C4Hyo. @ The structural formula of butane is CH3CH2CH2CH3. H H H H bot tod © The displayed formula of butane is H— C—C—C—C—H I tot | H H H H ® The skeletal formula of butane is \//7\_Use of curly arrows % Curly arrows are used in mechanisms to show the various electron pairs moving around. The arrow tail is where the electron pair starts from. . Shapes of organic molecules; o and 1 bonds Structure of hydrocarbons 4 Hydrocarbons can be saturated, unsaturated or aromatic. The structures and shapes of saturated, unsaturated or aromatic hydrocarbons can be illustrated by methane and ethane, ethene and ethyne, and benzene respectively. Promotion of an electron Below is the ‘electrons-in-boxes’ diagram of carbon. The only electrons ao directly available for sharing are the 2p electrons. 1s 2s 2p t | t & & N S é NWhen bonds are formed, energy is released and the molecule becomes more stable, If carbon forms 4 bonds rather than 2, twice as much energy is released and so the resulting molecule becomes even more stable. } There is only a small energy gap between the 2s and 2p orbitals, hence the carbon atom requires only a small amount of energy to promote an electron from the 2s to the empty 2p orbital to give 4 unpaired electrons. This energy requirement is negligible compared to the extra energy released when the bonds are formed 1s 2s 2p tit) t Energy > [*] < The carbon atom is now in an excited state. sp° hybridisation The electrons rearrange themselves again in a process called hybridisation. This reorganises the electrons into four identical hybrid orbitals called sp” hybrids (formed from one s orbital and three p orbitals) tT\T)T sp" hybrids The electrons of the sp’ hybrid orbitals repel each other, directing the orbitals at 109.5° to each other ina tetrahedral arrangement.Methane x & a In methane, each carbon atom uses one 2s and three 2p atomic orbitals to form four identical sp® hybrid orbitals, thus it is sp” hybridised. The hybrid orbitals are directed at 109.5° to each other ina tetrahedral arrangement. 109.5" Aa H | Cc n7/ The C-C and C-H bonds are sigma bonds. q Ethane > 8 & In ethane, each carbon atom uses one 2s and three 2p atomic orbitals to form four identical sp* hybrid orbitals, thus it is sp’ hybridised The hybrid orbitals are directed at 109.5° to each other in a tetrahedral arrangement. The C-C and C-H bonds are sigma (c) bonds. Ethane is non-planar, and is relatively unreactive. 109.5" For larger alkanes, the carbon chain has a ‘zig-zag’ structure. 4 H sp” hybridisation This reorganises the electrons into three identical hybrid orbitals called sp” hybrids (formed from one s orbital and two p orbitals) [1] ale [*]* =e sp" hybrid 2p, O< The electrons of the sp’ hybrid orbitals repel each other, directing the orbitals at 120° to each other ina trigonal planar arrangement, with the unhybridised 2p orbital perpendicular to this plane. four single bonds * sp” hybridisation = one double bond and two single bonds * sp hybridisation = one triple bond and one single bond © The bonds present in HC=CCH2CH=CH; are: bond bond 1s-2sp hybrid bond —2sp’-2sp’ hybrid ¢ bond \ 4s-2sp" hybrid e ly HL 1s-2sp” hybrid ay Lie c=c a C—H 1 and 2x bonds 8 \ 2sp-2sp hybrid bond 16 and 1n bonds 2sp-2sp” hybrid 2sp’-2sp” hybridStructural elucidation @ In order to elucidate (to shed light on) the structures of organic compounds, analyses of physical and chemical properties and spectroscopic data are carried out The empirical and molecular formulae of hydrocarbons can be determined by combustion in excess oxygen and from its composition by mass. Structural formulae are deduced from the reactions of the functional groups and physical properties of the organic compounds. Spectroscopic methods which can be used include: Mass spectroscopy where the compounds undergo fragmentation when bombarded by high energy electrons. The relative molecular mass and structure of the organic compound can be deduced from the characteristic fragmentation pattern of fragment ions. Spectra of isomers can be distinguished through the structures of their major fragments. Infra-red spectroscopy which can help give information on the type of bonds and functional groups in a particular organic molecule. Different bonds will absorb infra-red light at different frequencies. X-ray crystallography where the relative positions of atoms can be deduced from the diffraction patter. A diffraction pattern is formed when the x-rays scattered by the electrons in atoms are diffracted by the regular arrangement of the atoms in a crystal Nuclear magnetic resonance (NMR) spectroscopy where the number of protons and their chemical environment can be deduced. An NMR absorption spectrum is produced as protons absorb energy when placed in a magnetic field.The following fragment ions are present in the mass spectrum of ethanol. 1s 28 CHa" Fragment ions 31 CH,0H" 45 C,H;0" 46 CjHs0H* Molecular ion NMR spectroscopy a NMR detects the energy absorbed in the transition from a low energy state toa slightly higher energy state In the low energy state, the nuclear spin is aligned with an external magnetic field. In a higher energy state, the nuclear spin is aligned against the external magnetic field. The direction of the nuclear spin changes with energy absorption. The frequency of absorption depends on the chemical environment of the proton. The NMR spectrum is a plot of absorbance versus chemical shifts (5 units).Aliphatic ketones 1702 - 1725 (C=O) Alcohol 3600 (O—H) 1051 (C—O) Alkyne 2100 (C=C) 3300 (C—H) Alkene 1620 - 1680 (C—C) Alkane 1400 — 1470 or 2850 — 3000 (CH) Worked Examples Ethene and ethyne are both unsaturated hydrocarbons. Compare the type of hybridisation present in both molecules. Solution: In ethene, each carbon atom uses one 2s and two 2p atomic orbitals to form three identical sp” hybrid orbitals, which are directed at 120° to each other ina trigonal planar arrangement. In ethyne, each carbon atom uses one 2s and one 2p orbital to form two identical sp hybrid orbitals, which are 180° to each other ina linear arrangemen The two unhybridised 2p orbitals are in planes at mutually right angles. (ans) Ethene has a carbon-carbon double bond while ethyne has a triple bond. (ans)The NMR spectrum of compound B, C;H:0, shows three peaks apart from that of TMS. 1 isolated proton, 3 equivalent protons and 4 equivalents protons are shown at 5.06, 2.26 and 6.96 respectively. Deduce the structure of B. Solution: Absorption of 3 equivalent protons at 2.26 indicates a CH; group while the absorption of 4 equivalent protons at 6.96 suggests a di-substituted benzene ring. The isolated proton at 5.08 indicates a phenolic -OH The structure of B is: OH CH3 (ans) The carbon-carbon bonds of and organic compound is given below. w Oxout Which bonds are made up of an sp’-sp’ overlap? z ~cH=cH, Solution: w: sp*—sp* overlap 22 x: sp*-sp* overlap y: sp*-sp” overlap and x bond H z: sp’—sp’ overlap Hence w, x, y, and z have sp*-sp* overlap bonds.Isomerism Define Isomerism There are two main types of isomerism: @ Structural isomerism © Stereoisomerism Structural isomers % There are three types of structural isomers. @ Chain isomers, where the isomers differ in the arrangement of their carbon chains. The carbon chain may be straight or branched. ® Positional isomers, where the isomers differ in the positions of a functional group, but posses the same carbon skeleton. © Functional group isomers, where the isomers differ in the functional group.© Chainisomers for CgHio: 7 0-5 H | —cH | H =—o—= 2 d= | x ® Positional isomers: H oH zon | = C= | H x= = © Functional isomers: HoH OH I | oi H—C—C—C—C—OH CH3CH,—O—CH,CH3 roto H HH The different types of structural isomers have varying physical and chemical properties.Stereoisomers There are two types of stereoisomers. Geometric (cis-trans) isomers, where the isomers have restricted rotation about a double bond, thus giving rise to two ways of arranging the four groups across the double bond. ° Geometric isomers exist in pairs but they have different physical properties Geometric isomers have similar chemical properties (react with the same reagents but at different rates). The cis isomer has the two groups on the same side of the double bond but the trans isomer has the two groups on different sides of the double bond. Geometric isomerism cannot occur if either carbon has two identical groups. The cis isomer generally has a higher boiling point due to its higher polarity. It also has a lower melting point as it is not as symmetrical, forming less regular crystal lattices.@ Optical isomers, where the isomers differ in their symmetry and are able to rotate the plane of polarization of plane-polarised light. © This occurs when the four covalent bonds formed by a central carbon atom (chiral carbon) are tetrahedrally arranged around it. There is no plane of symmetry in the compounds. © This results in two optical isomers that are mirror images of each other and are non-superimposable upon each other © If the central carbon atom has more than 1 identical group, it is superimposable on its mirror image and thus does not exhibit optical isomerism. Thus the compound is optically inactive. Optical isomers can be grouped in 2 ways: © Optical isomers which are mirror images of each other and are non- superimposable are termed enantiomers. © They have identical physical and chemical properties but they differ in their effect on plane polarized light. They will rotate the plane of polarized light by equal amounts in opposite directions. o The enantiomers rotate plane polarized light by equal angles but in two different directions — dextrorotatory enantiomer (d or +) rotates plane polarized light to the right while the /aevorotatory enantiomer (/ or -) rotates plane polarized light to the left.® |famixture contains equal amounts of d and / enantiomers (racemic mixture), they are optically inactive as the effects cancel out one another and the mixture is unable to rotate plan polarized light. & Inliving organisms, compounds are usually chiral and only one enantiomer is found in the same biological system. Generally, only one enantiomer can be used by an organism. + Different stereoisomers have different biological actions. One enantiomer could be a useful drug while the other enantiomer may be ineffective or cause serious side effects. B Chiral drugs are developed for efficiency and protection against the side effects of its mirror image form. @ Geometric isomers: Br Br Br H N 7% N 7 OX LS \ H H H Br Cis isomer Trans isomer @® Optical isomers H o— ° = x 3 Note that the three-dimensional structure of optical isomers should be indicated according to the convention used in this example.Worked Examples Isomerism refers to molecules having the same molecular formula but different arrangements of their atoms. (a) Distinguish between structural isomers and stereoisomers. {b) Draw the structural isomers of the organic compound with the formula and name them. (c) By changing the position of the functional group in CsH1:C/, deduce the number of structural isomers that are possible. Draw their structures and name them. Solution: (a) Structural isomers are organic compounds with the same molecular formula but different structural formulae, while stereoisomers are organic compounds with the same molecular and structural formulae but differ in the orientation of the atoms or groups of atoms in space. Structural isomers consist of chain, positional and functional group isomers, while stereoisomers consist of geometrical and optical isomers. (ans) ({b) These are known as chain isomers. (ans) 2-methylbutane 2,2-dimethylpropane(c) rida if TTT TT H H H H H H H chloropentane 2-chloropentane HoH cl oH H I to to tol H—C—C—C—C—C—H riot tod H H H H H 3-chloropentane (a) Define functional group isomers. (b) Draw the possible functional group isomers for organic compounds with the following molecular formula and name them (i) CsH¢O (ii) CHO Solution: (a) Functional group isomers are molecules with the same molecular formula but with different functional groups. (ans)(b) (i) HOH 8 6 L o \ HoH H Propanal (ii) HOH a ———G—-0—A H oH Ethanol H H FGF, 1 il H ° H Propanone H 4 Methoxymethane Compare the physical and chemical properties between chain, positional and functional group isomers. Solution: Chain isomers generally have the same chemical properties as their functional groups are the same. However, their physical properties may differ. For example, long chain molecules will have a higher boiling point than branched molecules. Positional isomers also generally have similar chemical and physical properties as their functional groups and carbon chain length are the same. The positions of the functional groups may influence the rates and the types of mechanism in their reactions. Functional group isomers differ in both chemical and physical properties as they have different functional groups. (ans)(a) Describe what gives rise to geometrical isomers (b) State the names given to the two types of geometrical isomers. (c)_ Draw the geometrical isomers for 1,2-difluoroethene. (d)_ Explain why cis-1,2-difluoroethene has a higher boiling point than trans-1,2- difluoroethene. © Optical isomers have identical chemical properties except in their interactions with another chiral molecule. (b) Chiral centre. (ans) (c)_Itis said to be laevorotatory and is called the / or— enantiomer. (ans) (d) Aracemic mixture does not show optical activity as it contains equal amounts of d and / enantiomers. The rotation of one form is cancelled out by the other. (ans) For the following compounds, mark with an * the presence of chiral carbons. (a) (b) cH, ch SOx HAC! HAN’ (OHSolution: (a) CH H H3c (ans) (b) H H HON u OH (ans) Octane, CeHis, is passed over a heated catalyze to produce 1,4-dimethylbenzene - CHCH,CH,CH,CHCH,CH, = = =e= + 4H, Deducing the CsH11s isomers that could give 1,4-dimethylbenzene, Isomer 1: H,CH,C, \CHCH,CH,CHy \ + aH, Isomer 2: s Ms \CHCH,CH,CH © ——» Non HAC’ asTartaric acid, HO,CCH(OH)CH(OH)CO;H has the following structural formula: CO,H HC OH H—C—OH CO,H There are 3 different types of tartaric acid molecules: ¢ Molecule @ rotated plane polarised light to the right ¢ Molecule @ rotated plane polarised light to the left * Molecule @ had no effect on plane polarised light Deducing an explanation for these observations, co CO,H CO,H H—c*-oH HO—C*-H H—c*-oH I, i cece eee clge nen nite Ho— CH H—C-OH H—C™-OH cO,H CO,H cO,H molecules @ and @ molecule © chiral achiral Molecule @ The molecule is chiral, hence it is not superimposable on its mirror image. It is an enantiomer and is optically active. It rotates plane polarised light to the right. Molecule @ The molecule is chiral, hence it is not superimposable on its mirror image. It is an enantiomer and is optically active, It rotates plane polarised light to the left. Molecule © The two chiral carbon atoms have the same four substituents and are symmetrical. They rotate plane polarised light to the same degree but in opposite directions. This phenomenon results in an internal cancellation of optical activity. It has no effect on plane polarised light.