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Organisation Chemistry for Health Sciences Michaelmas term ¾ Organic Chemistry • Me! Dr. Thorfinnur Gunnlaugsson – 5 weeks (almost!) 2003 ¾ Physical Chemistry • Prof. John Corish • Dr. Dónall Macdónaill – 4 weeks Organisation Organic Chemistry Introduction Bonding Simple Hydrocarbons Stereochemistry Lecturer: • Dr. Thorfinnur Gunnlaugsson. – Room: 2.4 – E-mail: [email protected] – Phone: 608 3459 Textbooks: • Organic Chemistry: A Short Course – by H. Hart (Houghton Mifflin, Boston) • Organic Chemistry. 7th Ed – by T. W. Solomons • Organic Chemistry – by Clayden, Greeves, Warren and Wothers Organisation Department of Chemistry Overview ¾ Introduction • Simple functional groups • Drawing organic structures • Nomenclature of Organic chemistry ¾ Bonding • Intramolecular – ionic bonds, covalent bonds (hybridisation) • Intermolecular – Hydrogen bonding, Dipole-dipole interactions 1 Organisation Introduction Overview ¾ Alkanes, Alkenes, Alkynes and Benzene ¾ What is Organic Chemistry? • Chemistry: – Small or large assembly of covalently liked atoms where carbon and hydrogen dominate! Eg. Alcohols, small drugs etc. Halogen Compounds, Alcohols, • Stereochemistry • Isomers, chirality ¾ • Biology: – living organisms Eg. Cells, plants and animals Phenols, Ethers, Amines • Biochemistry: Duration ¾ – The chemistry of life Eg. Enzymes and their role, DNA , Carbohyhdrates etc. 5 weeks; 20 lectures (more like 18!!) Introduction Introduction Deals with compounds in which carbon (C) is the principle element ¾ Not whole periodic table ¾ Organic Chemistry ¾ May/may not involve natural process A H Li B Na Mg Cr Mn Cu Zn Pd • Organic chemists use REAGENTS / CATALYSTS in SYNTHESIS, employing solvents, heat, pressure, etc. • Nature uses ENZYME, cofactors etc. Se Br Sn I Hg Os Introduction OH HH Ethanol H Introduction ¾ H H H H C HH B F Al Si P S Cl Ti K C N O O Even enzymes are organic! Ethanal (acetaldehyde) Nature uses ADH ¾ Organic chemist uses: O ¾ C C N H H H C C O H N O C H H C N H C • Oxidising agent - H2O2, HNO3, etc. 2 Introduction Introduction Organic Chemistry ¾ Many branches Organic substances are everywhere plants animals industry • • • • • • • research labs Medicinal and pharmaceutical chemistry Perfume and Food chemistry Synthesis Mechanistic natural product chemistry Polymers Supramolecular! Introduction Introduction Pharmaceuticals Eg. Ranitidine: sales > £1,000,000,000 per annum for Glaxo-Wellcome ~ 12 million organic substances • increases by 10,000 per week! ¾ NO2 N S Number O ¾ N H Eg. Viagra: Rapidly expanding market! EtO N N N NH N 1900 1920 1940 1960 1980 N H 2000 O S N O O Aims of Course O Cl Me O H O O N MeO Me N Me Me OH OMe To understand …. ¾ Structures and shapes Me Me O Me O O OH OH OH N MAYTANSINE A very potent anti-tumour agent E. J. Corey et. al. 1978-1980 O • BONDING O O ? ? ¾ Basic reaction mechanisms • HOW SHAPES ARE CREATED 3 The Basics Drawing Chemicals Molecular Formula Drawing Chemicals • • • • • • Actual number and type of atoms eg. Ethanol = C2H6O eg. Dimethyl Ether = C2H6O Molecular Formula Condensed Structural Formula Lewis Forms Kekule Structure Skeletal Structure Condensed Structural Formula • Shows which way atoms are bonded/connected, but doesn’t require all bonds to be drawn eg. Ethanol = CH3CH2OH eg. Dimethyl Ether = CH3OCH3 Nomenclature • Functional Groups • Examples Drawing Chemicals Drawing Chemicals Valence shell! • We know that eight electrons in –an electron octet- in the outermost shell, or valence shell, impart special stability to the noble-gas elements: Neon 2+8, Argon (2+8+8) etc. • These valence electrons are the one that participate in bonding. • Methane is one of these molecules that forms an octet. Carbon has 1s2 2s2 2p3 electrons and needs 4 more to form the octate. Hydrogen has 1s1, i.e. we need four of these: CH4 is methane! Drawing Structures ¾ • Dots are used to represent all valence electrons Kekule Structure • Dots represent nonbonding valence electrons (not used e-), or lone-pair electrons! e.g. NH3!! • Lines represent bonding valence electrons Example: CH3Cl (Chloromethane) H H C H H H C H H C O H H H O C H H H H H C C O H H H H H H C O C H H H Drawing Chemicals Skeletal Structure Structures in Reality! HH HH HH C H Structural Formula Lewis Structure 8 max!! C C HH C C HH H • The carbon backbone is represented by a zigzag line (reflects reality) • All hydrogens attached to the carbon backbone are neglected (convenient and fast) • Carbon atoms are the corners and ends • Important for drawing larger chemicals and highlighting functional groups OH O 4 Drawing Chemicals Functional Groups Guidelines • Realistic • Economical! • Clear Introduced bond angles HH H H C C O H Definition ¾ An atom or group of atoms that is part of a larger molecule and that has a characteristic reactivity eg. alcohol = HH C H OH H Ethanol, Ethan-2-ol C H C H C H Alkanes C C C H H Alkenes H C C C C HH Ethanol • R is chemists shorthand for ‘alkyl’ H HH C H eg. R = ethyl = Alkynes R H H C C C HH Cl Alkyl Halides H H eg. H C H Aromatic Hydrocarbons H H Cl C HH Functional Groups Functional Groups Hydrocarbon Derivatives cont. Hydrocarbon Derivatives cont. cont. ¾ ¾ Alcohols R—OH Ethers ¾ Amines ¾ Phenols H Hydrocarbon Derivatives H HH HH O C Functional Groups Hydrocarbons H C Ethane Functional Groups HH HH C H H O R—O —R Carbonyl group R C O H R Aldehyde R—NH2 O OH R C C R Ketone O OH Carboxylic acids R C O OR Esters R C NH2 Amides 5 Functional Groups Naming Chemicals Importance ¾ Determine chemical behaviour Overview (IUPAC system) ¾ Names of chemicals have 4 main parts: OH CH2OH O O2N C H C H N H C CHCl2 chlorampenicol: an antibiotic O F C OH C C C N H2 H2 H2 haloperidol: an anaesthetic and antipsychotic Cl • Parent name: describes the main carbon section of the molecule. • Suffix: identifies the principle functional group • Prefix: identifies the substituents on the main chain or ring • Locants: shows where the substituents are located Naming Chemicals Naming Chemicals Common Parent and Substituent Names Overview ¾ Names of chemicals have 4 main parts: Number of Carbons 1 2 3 4 5 6 7 8 9 10 Parent Name methane ethane propane butane pentane hexane heptane octane nonane decane Substituent Name methyl ethyl propyl butyl pentyl hexyl heptyl octyl nonyl decyl Naming Chemicals Rules 1. Name the Parent • Identify the longest carbon chain containing the most important functional group 2. Add the Suffix • Identify the most important functional group and add the appropriate suffix Locant Prefix 2 Methyl Parent Suffix hex ane eg. 2-Methylhexane locant: prefix: parent: suffix: 2methyl hex ane 2 1 4 3 6 5 Naming Chemicals 3. Add the Prefix ¾ Name any substituents • Substituents are arranged in alphabetical order • If more than one group is present use ‘di’, ‘tri’, ‘tetra’, ‘penta’, ‘hexa’, ‘hepta’, ‘octa’, ‘nona’ or ‘deca’ before the group Note: these additional prefixes do not count when alphabetising the substituents eg. Alkanes = ‘ane’ 6 Naming Chemicals 4. Include the Locants ¾ Specify substituent location • Number the parent chain from the end closest to the functional group • Different substituents can have the same number if they are attached to the same carbon • Use hyphens to separate no. and letters • Use commas to separate no. form no. Naming Chemicals Alkanes ¾ name the following alkane: CH 2CH3 CH3 C CH 3 Naming Chemicals Alkanes Step 1: Name the Parent Chain ¾ find the longest continuous chain CH2CH3 CH3 C Naming Chemicals Alkanes Step 2: Add the Suffix ¾ The chemical is an alkane ➠ heptane CH 2CH2CH 2CH3 CH3 ¾ assign appropriate parent name ➠ hept Step 3: Add the Prefix ¾ Describe any substituents attached to the parent chain ➠ Dimethylheptane Naming Chemicals Alkanes Step 4: Include the Locants ¾ Include the position of attachment • use the lowest possible option ¾ CH 2CH 2CH 2CH 3 3,3-Dimethylheptane • Not 5,5-Dimethylheptane Naming Chemicals Alkanes 1. Name the Parent Chain • oct Example 2: 2. Add the Suffix • octane 3. Add the Prefix • Ethylmethyloctane 4. Include the Locant • 4-Ethyl-3-methyloctane 7 Naming Cyclic Chemicals Alkenes and Alkynes Cycloalkanes 1. Name the Parent Chain (must include functional group) 1. Name the Parent • cyclohex • hept 2. Add the Suffix • cyclohexane 6 5 4 5 1 3 3 2 1 4 3. Add the Prefixes propylcyclohexane • methylpropylheptene 4. Include the Locants • 6-methyl-3-propylhept-2-ene 1-propylcyclohexane Naming Chemicals Naming Chemicals Aromatic Hydrocarbons ¾ ‘Substituent name’ followed by ‘Benzene’ eg. 7 2 • heptene 4. Include the Locant • 6 2. Add the Suffix 3. Add the Prefix • Naming Chemicals NO2 Cl CH3 Aromatic Hydrocarbons ¾ A large number of aromatic hydrocarbons have non-systematic (common) names OH NH2 eg. Benzene Chlorobenzene Methylbenzene Nitrobenzene Naming Chemicals Naming Chemicals Aromatic Hydrocarbons • When there is >1 substituent, locants are used to specify their relative position • ortho-, meta- and para- maybe used in place of numerical locants Halogen Compounds ¾ As for alkanes ¾ The halogen is named as a substituent with an ‘o’ (eg. bromine becomes bromo) Cl Cl Cl Aniline Toluene Phenol (Methylbenzene) (Hydroxybenzene) (Aminobenzene) Cl Br Cl 1,2-dichlorobenzene (ortho-dichlorobenzene) 1,3-dichlorobenzene (meta-dichlorobenzene) Cl 1,4-dichlorobenzene (para-dichlorobenzene) ➠ 3-Bromo-3-methylheptane 8 Naming Chemicals Naming Chemicals Alcohols Ethers ¾ substituents are listed alphabetically followed by the word ‘ether’ eg. 1. Name the Parent Chain • octane HO 2. Remove ‘e’ and add the Suffix ‘ol’ to alkane name OH • octanol O 3. Add the Prefix • Dimethyloctanol 4. Include the Locants • 3,5-Dimethyloctan-4-ol OH You try these! Naming Chemicals ➠ Ethyl methyl ether Naming Chemicals Amines Aldehydes 1. Name the Parent Chain as 1. Name the Parent Chain substituent • heptane • propyl 2. Remove ‘e’ and add Suffix ‘al’ to alkane 2. Add the Suffix • propylamine N 3. Add the Prefix H • heptanal • Ethylheptanal 4. Include the Locant 4. Include the Locant • N-Methylpropylamine • 4-Ethylheptanal Naming Chemicals Naming Chemicals Ketones Carboxylic Acids 1. Name the Parent Chain 1. Name the Parent Chain • heptane • heptane 2. Remove ‘e’ and add Suffix ‘one’ to alkane 3. Add the Prefix • Ethylheptanone 4. Include the Locants • 4-Ethylheptan-2-one H 3. Add the Prefix • Methylpropylamine • heptanone O 2. Remove ‘e’ and add Suffix ‘oic acid’ to alkane O • heptanoic acid 3. Add the Prefix O OH • Ethylheptanoic acid 4. Include the Locant • 4-Ethylheptanoic acid 9 Naming Chemicals Naming Chemicals Esters 1. Parent: • Hexane 2. Remove ‘e’ and add ‘ate’: • Hexanate 3. Prefix: the other alkyl segment with a space: • propyl Hexanoate 4. Locants: Not required for this example Acid Chlorides O • replace ‘ic acid’ with ‘yl chloride’ Anhydrides R C • replace ‘acid’ with ‘anhydride’ Amides R C O O C R O • replace ‘ic acid’ with ‘amide’ R C Nitriles O Cl O • replace ‘ic acid’ with ‘nitrile’ R C NH2 N O Naming Chemicals >1 Functional Group Priority List 1. Carboxylic acids 5. 2. Aldehydes 6. 3. Ketones 7. 4. Alcohols 8. Naming Chemicals >1 Functional Group 1. Amines Alkenes Alkynes Alkanes Identify Priority gp. Carboxylic acid, alcohol 2. Name parent and suffix as usual 3. prefix for alcohol substituent OH octanoic acid CO2H hydroxyoctanoic acid 4. Locants 6-hydroxyoctanoic acid Naming Chemicals Suffix and Prefix Naming Chemicals Suffix and Prefix ¾ Alkenes and alkynes Group suffix prefix aldehyde -al formyl- ketone -one oxo- alcohol -ol hydroxy- amine -amine amino- • Specify location ‘within’ parent • Essentially as before! CO2H But-2-yne But-2-ynoic acid 10 Naming Chemicals Further Example 1. Priority alcohol aldehyde and alkene 2. Parent + suffix oct, ene and al = octenal 3. Substituents hydroxy 4. Locants 5-hydroxyoct-3-enal Bonding ¾ Intramolecular (within molecules) • Ionic • Covalent • Polar covalent ¾ Intermolecular (between molecules) • • • • OH O H Atomic Structure Ionic Hydrogen bonding Dipole-dipole Van der Waals interactions Atomic Structure Shells Electron Configuration 2e- + 8e- 18e- + 3d E Orbitals ¾ ¾ 3rd SHELL 3p 3s Each shell contains orbitals most probable location of an electron s p 2nd SHELL d 1st SHELL 2p x y z 2s 1s Blame Schrödinger and Einstein Atomic Structure Atomic Structure Ground State Configuration Lowest energy orbitals fill first Electron Configuration z z z x x y y ¾ (Aufbau principle) x y 2py 2px ¾ 2pz z 2nd SHELL 2p x y Each orbital can contain up to two electrons • electrons have opposite spins z (Pauli exclusion principle) 2s x y ¾ 2s Orbitals of equal energy fill evenly (Hunds rule) 11 Atomic Structure Intramolecular Bonding Ground State Configuration ¾ Eg. Sodium. 11 electrons 3s E atoms join together to obtain a more stable configuration most stable configuration = octet in the valence shell 2px,y,z 2s ¾ 1s This desire determines an atoms type of bonding (ionic or covalent) Na: 1s2 2s2 2p6 3s1 Ionic Bonding ¾ donation of electrons Example Na (1s2 2s2 2p6 3s1) + Cl (1s2 2s2 2p6 3s23p5) ↓ Na+ (1s2 2s2 2p6 ) Cl- (1s2 2s2 2p6 3s2 3s6) Na Cl + – Na Cl 12