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) O draw the root add major functional group 4-ethyl-3-hydroxycyclohexanone 4-ethyl-3-hydroxycyclohexanone O O OH 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 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.