Unit One Part 2: Naming and Functional Groups

gjr-–- 1 Unit One Part 2: naming and functional groups

• To write and interpret IUPAC names for small, simple molecules • Identify some common functional groups found in organic molecules

O CH3 H3C N H N O N N

O H3C S N O N H3C

viagra™ (trade name) sildenaﬁl (trivial name) 5-(2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl)-1-methyl-3-propyl-1H- pyrazolo[4,3-d] pyrimidin-7(6H)-one dr gareth rowlands; [email protected]; science tower a4.12 http://www.massey.ac.nz/~gjrowlan gjr-–- 2 Systematic (IUPAC) naming

PREFIX PARENT SUFFIX

substituents / minor number of C principal functional functional groups AND multiple bond group index

• Comprises of three main parts • Note: multiple bond index is always incorporated in parent section

No. Carbons Root No. Carbons Root Multiple-bond 1 meth 6 hex Bond index 2 eth 7 hept C–C an(e) 3 prop 8 oct C=C en(e) 4 but 9 non C≡C yn(e) 5 pent 10 dec gjr-–- 3 Systematic (IUPAC) naming: functional groups

Functional group Structure Sufﬁx Preﬁx General form O –oic acid acid –carboxylic acid carboxy R-COOH R OH O O –oic anhydride anhydride –carboxylic anhydride R-C(O)OC(O)-R R O R O –oyl chloride acyl chloride -carbonyl chloride chlorocarbonyl R-COCl R Cl O –oate ester –carboxylate alkoxycarbonyl R-COOR R OR O –amide amide –carboxamide carbamoyl R-CONH2 R NH2 nitrile R N –nitrile cyano R-C≡N O –al aldehyde –carbaldehyde oxo R-CHO R H O ketone –one oxo R-CO-R R R alcohol R OH –ol hydroxy R-OH

amine R NH2 –amine amino R-NH2 O ether R R –ether alkoxy R-O-R alkyl bromide bromo R-Br (alkyl halide) R Br (halo) (R-X) gjr-–- 4 Nomenclature rules 1. Parent - root derived from number of carbon in longest unbranched chain .containing functional group

CH CH3 3 OH 4 2 H C CH H3C 3 3 5 3 1 4-methylheptane 2-propyl-1-pentanol

2. Sufﬁx - basic name derived by adding ending of major functional group (FG)

O CH3 O

H3C OH H3C NH2 butanoic acid 3-methylbutanamide 3. Position - position of FG denoted by Arabic numeral placed before whole ....name or just before ending. Numbering achieves lowest number for FG O

H3C CH3

2-pentanone pentan-2-one NOT 4-pentanone gjr-–- 5 Nomenclature rules II 4. Preﬁx - substituents are designated by preﬁx & Arabic number indicating ....position (lowest possible numbering)

CH3 Cl CH3

H3C CH3 H3C CH3

H3C CH3 CH3 2,2,5-trimethylheptane 8-chloro-2,3-dimethylnonane NOT 3,6,6-trimethylheptane NOT 2-chloro-7,8-dimethylnonane 5. FG - if more than one FG name & number based on principle FG. List of ....priorities given in course notes. Multiple bonds are added to parent (end), ....all others are preﬁxes

O O CH3

H3C OH HO OH

H3C CH3 O 5-hydroxy-2,2-dimethylpentanoic acid 2-methyl-4-oxohex-2-enoic acid

6. Minor FG - halo-, nitro- (-NO2), nitroso- (-NO) & azo- (-N2-) are considered ....substituents & not FG for nomenclature only

7. Order - substituents are written in alphabetical order gjr-–- 6 Examples: structure to name

OH O OH O

H3C N CH3 H3C N CH3 H H N-ethyl-3-hydroxy-5-methylhept-6-enamide

Step 1: root Step 7: complete

OH O OH O

5 3 1 H3C N CH3 H3C N CH3 H 4 2 H hept 3-hydroxy-5-methylhept-6-enamide

Step 2: sufﬁx Step 5: substituents (preﬁx)

OH O OH O

3 1 H3C N CH3 H3C N CH3 H 2 H hept amide 3-hydroxyhept-6-enamide

6 OH O Step 3: multiple- Step 4: functional bond index H3C 5 3 1 N CH3 groups (preﬁx) 4 2 H hept-6-enamide gjr-–- 7 Examples: name to structure • Draw the structure for 4-ethyl-3-hydroxycyclohexanone (please)

draw the root add major functional group 4-ethyl-3-hydroxycyclohexanone 4-ethyl-3-hydroxycyclohexanone

O O

H3C H3C

add substituent add minor functional group 4-ethyl-3-hydroxycyclohexanone 4-ethyl-3-hydroxycyclohexanone gjr-–- 8 Functional groups: alkanes • Saturated hydrocarbons - contain only C & H and no multiple bonds • Non-cyclic alkanes have the formula CnH2n+2

H C H H H methane propane pentane cyclopentane CH4 C3H8 C5H12 C5H10

CH4

• Alkanes are a little dull - used as solvents or burnt as fuel • Methane is a fuel, a chemical feedstock & a green house gas propane gjr-–- 9 Functional groups: alkanes II

isooctane 2,2,4-trimethylpentane C8H18

• Isooctane is used in petrol - branched structure means it burns smoothly • Octane is a long change and burns explosively • Octane number of petrol is based on isooctane = 100 & heptane = 1 Unleaded 91 petrol = 91% isooctane & 9% heptane

• Structural isomers have same formula but different atoms joined differently • Isomers can have very different properties

pentane 2-methylbutane 2,2-dimethylpropane bp 36.2˚C bp 28˚C bp 9.6˚C gjr-–- 10 Functional groups: alkenes

H H

H H ethene

• Ethene - simplest alkene. Very important industrially • Carbon is trigonal planar - ﬂat and triangular! • New form of isomerism - conﬁgurational isomers • All atoms bonded in the same manner but different orientation in space

CH3

H3C CH3 H3C 1-butene trans-2-buten2e-butenecis-2-butene 2-methylpropene cyclobutane C4H8 C4H8 C4H8 C4H8

CH3 H3C CH3 H3C CH3 H3C (1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-ene α-pinene gjr-–- 11 Functional groups: alkynes & cyclic structures

O H H OH O H C OME O ethyne 3 pent-3-yn-1-ol O O C2H2 NOT pent-2-yn-5-ol

H3C O

OH O MeHN HO • Ethyne is an explosive gas O CH3 • Triple bond makes molecular linear (cylinder) OH • Examples found in nature (example cleaves DNA) neocarzinostatin chromophore A Cycloalkanes and cycloalkenes

H3C CH3 cyclopropane 1,3-dimethylcyclohexane cyclohexene benzene • Cyclic hydrocarbons are common - note that most are not ﬂat gjr-–- 12 Cyclic structures in nature

H3C

CH3

CH3 H CH3

H H H3C

(8R,9S,10S,13R,14S,17R)-10,13-dimethyl-17-(6- methylheptan-2-yl)-hexadecahydro-1H- cyclopenta[a]phenanthrene cholestane - steroid

• Ring systems are common in natural products & pharmaceuticals • Example below shows the importance of another form of isomerism - stereoisomers

CH3 CH3 H3C H3C

H H (R)-1-methyl-4-(prop-1-en-2- (S)-1-methyl-4-(prop-1-en-2- yl)cyclohex-1-ene yl)cyclohex-1-ene (R)-limonene (S)-limonene smells of oranges smells of lemons gjr-–- 13 Functional groups: alcohols

H3C CH primary 3 tertiary (1°) CH3 (3°) CH3 CH3 CH3 H CH3 H3C OH H3C H H H3C OH HO CH3 (R)-3,7-dimethyloct-6-en-1-ol cholesterol (R)-1-isopropyl-4- citronellol all animals methylcyclohex-3-enol citronella oil secondary terpinen-4-ol (2°) tea tree oil • Alcohols contain OH (hydroxy) group • Found in many natural systems (especially on Friday night) • Three classes depending on how many C attached to C–OH • Compounds can have more than one OH (improves water solubility)

HO OH HO O HO OH HO 1,2-ethandiol 6-(hydroxymethyl)-tetrahydro- ethylene glycol 2H-pyran-2,3,4,5-tetraol antifreeze glucose sugar I guess! gjr-–- 14 Functional groups: phenols and ethers Phenols Cl OH OH

Cl Cl phenol 2,4,6-trichlorophenol carbolic acid TCP antiseptic • Phenols are distinct from alcohols as attached to phenyl ring - acidic O–H Ethers

O O O O

H3C O CH3 O O ethoxyethane O diethyl ether tetrahydrofuran ether THF 18-crown-6 • Most commonly used as solvents • 18-Crown-6 enables metal cations (M+) to dissolve in organic solvents gjr-–- 15 Functional groups: alkyl halides and thiols

Cl Cl H F Cl Cl O Cl H Cl F Cl Cl Cl H Cl dichloromethane dichlorodifluoromethane dieldrin H DCM Freon (refrigerant) a CFC • Alkyl halides are incredibly useful compounds - used extensively • Down side is they appear to be bad for us and the environment Thiols

CH3 SH HS HS SH CH3 O HS H3C H H2N H3C CH3 H3C CH3 CO2H CH3 (R)-2-amino-3- 2-(4-methylcyclohex-3- propane-2,2-dithiol 4-methyl-4- sulfanylpropanoic acid enyl)propane-2-thiol sulfanylpentan-2-one cysteine taste of grapefruit • Thiols are the sulfur analogue of alcohols - and they smell, bad... • Humans can detect 2x10–5 ppb of the second compound (1 drop in a lake) • One of the last two compounds is the smelliest known - but no one is ...prepared to make them again to ﬁnd out which! gjr-–- 16 Functional groups: amines

CH3 O

NH2 H3C N H2N OH H2N H CH3 triethylamine butane-1,4-diamine (S)-2-amino-3-phenylpropanoic acid smells of fish putrescine phenylalanine smells of decay amino acid

• Vital in biological systems • Many smell (bad but not as bad as thiols) • Found in many compounds that are physiologically active...

CH N 3 O CH3 O N H O CH N 3 O (S)-3-(1- methyl 3-(benzoyloxy)-8-methyl- methylpyrrolidin-2-yl) 8-aza-bicyclo[3.2.1]octane-2- pyridine carboxylate nicotine cocaine gjr-–- 17 Functional groups: amines II

N H N H H3C H H3C NH2 N CH3 H H3C CH3 H3C ammonia methylamine dimethylamine trimethylamine 1° amine 2° amine 3° amine • Just to confuse, amines are labeled by the number of C attached • This is different to alcohols (labeled by C attached to C–OH)

secondary position H (2°) N H3C CH CH3 O 3 H3C trimethylammonium ion H3C OH 4° ammonium (salt) NH2 valine primary If add four groups amine everything changes! (1°) gjr-–- 18 Functional groups: the carbonyl group • Carbonyl group C=O – analogous to alkene • Two groups, aldehydes RCHO and ketones R2C=O Aldehyde

O OH OH O O O H HO H H H3C H OH OH H methanal ethanal benzaldehyde (2R,3S,4R,5R)-2,3,4,5,6- formaldehyde acetaldehyde pentahydroxyhexanal glucose Ketones

CH3 CH3 O O O

H C CH 3 3 HO H3C O H3C H H CH3

propanone (R)-2-methyl-5-(prop-1-en- (S)-2-methyl-5-(prop-1-en- 4-(4-hydroxyphenyl) acetone 2-yl)cyclohex-2-enone 2-yl)cyclohex-2-enone butan-2-one (R)-carvone (S)-carvone raspberry ketone spearmint caraway gjr-–- 19 Functional groups: carboxylic acids & derivatives

H oxidation H oxidation H oxidation OH R C H R C H R C R C reduction reduction reduction H OH O O hydrocarbon alcohol aldehyde carboxylic acid

• Many of the functional groups are 'linked' • If we replace one C–H at a time by a C–O we see how these groups relate

CH O H3C CH3 3 O HO2C CO2H H3C OH H3C OH CO H OH 2 O CH3 ethanoic acid maleic acid (S)-2-hydroxypropanoic acid (2Z,4E)-3-methyl-5-(2,6,6- acetic acid L-(+)-lactic acid trimethyl-4-oxocyclohex-2- vinegar enyl)penta-2,4-dienoic acid abscisic acid leaf fall gjr-–- 20 Functional groups: derivatives O O + NaOH Na + HOH H3C OH H3C O ethanoic sodium sodium ethanoate water acid hydroxide carboxylate ion

• Reaction of a carboxylic acid with a base (eg. NaOH) gives carboxylate ion Derivatives

O O O H3C CH3 O Cl H3C O CH3 CH3 ethyl ethanoate 2-methylpropyl propanoate benzoyl chloride ethyl acetate isobutyl propionate acid chloride solvent smell of rum ester ester NH2 O H HO2C N OMe O O O H3C O CH3 aspartame ethanoic anhydride sweetener acetic anhydride amide acid anhydride gjr-–- 21 Classiﬁcation of functional groups • Functional groups can be classed by the degree of oxidation (removal of H)

alkanes

ogen) alkyl alcohols ethers amines halides thiols ee of oxidation

aldehydes ketones emoval of hydr (r easing degr carboxylic esters amides acyl acid nitriles incr acids chlorides anhydrides

H oxidation H oxidation H oxidation OH R C H R C H R C R C reduction reduction reduction H OH O O hydrocarbon alcohol aldehyde carboxylic acid gjr-–- 22 Overview

What have we learnt? • How to name simple organic molecules • To recognise common functional groups • Common examples of these functional groups

What's next? • To looking at the bonding in molecules in detail • To understand how bonding effects the shape of molecules

dr gareth rowlands; [email protected]; science tower a4.12 http://www.massey.ac.nz/~gjrowlan