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  • 1.Organic ChemistrySelected sections Ch 26 + Ch 11 The chemistry of life and living thingsThe chemistry of carbon compoundsChem 1AA32Chem 1AA33Evolution of the field1

2. Why is organic chemistry important? To understand how we interact with other organisms (food & nutrients, infections), our environment (aromas, pollutants), drugs, and ourselves (metabolism, growth, immunity, cancer) To understand how things are made, what they're made of, and how they react with each other Chem 1AA34Why is organic chemistry important? Because it is central to: Chemistry Chemical Biology Biochemistry Biology Engineering Material sciences Forensic Sciences Medicine To get into graduate/medical/dental school! Chem 1AA35Medical Application: Molecular Imaging18F-fluorodeoxyglucoseChem 1AA362 3. Organic Chemistry Components 1) Structure: The connectivity and 3-D nature of compounds2) Theory: Structure and reactivity in terms of atoms and the electrons that bind them togetherChem 1AA37Components (continued) 3) Synthesis: How to design new molecules and then make themChem 1AA38Organic Compounds Why is one element in the periodic table given its own field? 98% of all known chemical substances are organic Inorganic chemistry = the chemistry of everything else Nearly all pharmaceuticals are organic in nature Chem 1AA393 4. Organic Compounds: Biological11-cis-retinal HONH2Serotonin (neurotransmitter)HO N HChem 1AA310Diagnostic iClicker Question Which is the cis double bond in 11-cis-retinal?(b)(d)(c)(a)(e) HO Chem 1AA311Organic Compounds: Medicines NEtOOMe2NNN NS NHNOOOTamoxifen H N OOH NLipitorViagra OHO OHF Chem 1AA3124 5. Organic Compounds: DrugsCH3 OH CH3 CH3 HN NHStanozololChem 1AA313Organic Compounds: Industrial ChemicalsHNIndigo dye (blue jeans)OONHCO2H H NH 2NOAspartame OMeO Chem 1AA314Organic Compounds: Natural Products OO NCocaineO ONHOQuinineMeO NChem 1AA3155 6. AlkanesSection 26-1, 26-2Alkanes Hydrocarbons the simplest organic compounds (CnH2n+2) Saturated (use all bonding e to make single bonds) Methane (various representations):Chem 1AA317Chem 1AA318Ethane (C2H6)6 7. Propane (C3H8)Chem 1AA319Drawing Organic Molecules Guideline 1: Draw molecules in a Zig-Zag shape versus linear structures vsCH3CH2CH2CH2CH2CH3 Guideline 2: You can assume there are Hatoms attached to carbon atoms in a ZigZag structure giving a valence of 4 OHH HH H HHOH H Chem 1AA320Drawing molecules (continued) Guideline 3: For reactions, draw out the functional groups in detail and include lone pairs (electrons)OHOChem 1AA3217 8. Advice and hints Be neat messy structures lead to mistakes Count your carbon atoms! Count the substituents on carbon atoms (including implied H atoms) In this course, there are never more than four bonds to carbon 22Chem 1AA3PHDiagnostic iClicker Question Which of the following wedge-and-dash drawings of propane is incorrect?(a)HHH HHHH H HH H(d)H H HH HH HH HHHHHH H HH HH(c)(b)(e) don't knowH H23Chem 1AA3PBDiagnostic iClicker Question Which of the following wedge-and-dash drawings of propane is incorrect? H HH H HH(a) H(c)HHH HH H H(b)HH HH H H(d)H HH H HH HH HH(e) don't knowH HChem 1AA3248 9. JVDiagnostic iClicker Question Which of the following wedge-and-dash drawings of propane is incorrect?(a)(c)HHH HHH H HH(d)HHH HH HHHHHH H HH HHHH H H(b)H(e) don't knowH HChem 1AA325HSDiagnostic iClicker Question Which of the following wedge-and-dash drawings of propane is incorrect? H(a)H HH HH H H H(b)HH(c)H H HHH(d)H H HHH H HHHHHHH H H(e) don't knowH Chem 1AA326Chem 1AA327Fuels: Octane NumberOctane Number: used to indicate the resistance of a motor fuel to knockp. 10849 10. Fuels: Alcohols Alcohols can also be used as fuels: CH3OH(l) +1.5O2(g)CH3CH2OH(l) + 3O2(g)CO2(g) +2H2O(l) Ho = -726 kJ mol-12CO2(g) +3H2O(l) Ho = -1367 kJ mol-1H(combustion) for CH4, methane -891 kJ/mol C2H6, ethane -1560 kJ/mol http://pubs.acs.org/cen/coverstory/85/8551cover.html Chem 1AA328Structural Diversity Isomers, cycloalkanesConcept Check: Skeletal/Structural Isomerism Skeletal or structural isomers have: - The same molecular formula but different connectivity. - Different physical properties.Concept check: Draw structural isomers of C5H12 Chem 1AA33010 11. Concept Check: Solution H H H H H H C C C C C H H H H H HpentaneH H C H H H H H C C C C H H H H H H H C H H H H C C C H H H H C H H2-methylbutane2,2-dimethylpropane Chem 1AA331Conformations of alkanes Newman ProjectionsLower EChem 1AA332Conformation versus configuration Conformation: arrangement of atoms in a molecule that can be changed by simple rotation of single bonds, without breaking any bonds. Configuration: the permanent geometry of a molecule resulting from the spatial arrangement of its bonds. Must break bonds to change configuration.versus Chem 1AA33311 12. Conformations of disubstituted ethane H H R'RHHStaggered RR HHHHHHRR'R'HHHR'H H HLowest E 34Chem 1AA3Eclipsed Conformations EclipsedHR H HH R'HRR' R HHH HHR' HHHighest E All eclipsed conformations have higher energy than all staggered conformations. 35Chem 1AA3PHFormative iClicker Question #1 Which conformation has the lowest (most favourable) energy? R(a)H HR R'RHH H(b)R'H H(c)R(d)HR'HH HH HH R'R(e) HHHH HR'H Chem 1AA33612 13. PBFormative iClicker Question #1 Which conformation has the highest (least favourable) energy? RR R'RHHH(a)HH(b)(c)H HR' R(d)HHRR'HH HH R'R'(e)HHHHH HH 37Chem 1AA3JVFormative iClicker Question #1 Which conformation has the highest (least favourable) energy? R R'H(a)RHRHHHH(b)HHH(c) HHH R'R' R R'(d) HHRHR'(e) H HHHH 38Chem 1AA3HSFormative iClicker Question #1 Which conformation has the lowest (most favourable) energy? R(a)RHRHR'HH HHH(b)HH(c) HHH R'R' R R'(d) HHRHR'(e) H HHHH Chem 1AA33913 14. Ring Structures: Cycloalkanes CnH2nChem 1AA340Molecules are not always flat: CyclohexaneBoatChair Chem 1AA341Chem 1AA342Boat conformation movie14 15. Boat conformation movieChem 1AA343Chem 1AA344Chem 1AA345Chair conformation movieChair conformation movie15 16. Axial vs. equatorial substituents. Cyclohexane ConformationsBoatChairEquatorial H atoms are pink, axial H atoms are blueChem 1AA346Ring Strain in Cycloalkanespropane Bond angles (at C atoms) 109.5ocyclopropane Bond angles (at C atoms) 60o H-atoms are eclipsedChem 1AA347NamingSection 26-116 17. Naming Chemistry is a visual science: Structures are key to understanding reactivity and physical properties Systematic nomenclature: IUPAC rules (assumed knowledge) IUPAC: International Union of Pure and Applied ChemistrySee the supplementary information about naming in ELM for more informationChem 1AA349Names of common compounds OOAcetoneAcetaldehydeAcetic acidOO H OFormic acidHOHOHEthyl acetateEtherOCH2CH3CH3CH2OCH2CH3OAcetyl groupH3C Chem 1AA350Common compounds (continued) BenzeneToluene OHPhenolPyridineNChem 1AA35117 18. Some Common Alkyl Substituents(Table 26.1)Chem 1AA352Chem 1AA353Chem 1AA354More alkyl names n-butylRsec-butylRisobutylR Rtert-butylSubstituents Vinyl groups Allyl groupsRR RPhenyl groups Example: Allyl acetateO O18 19. PHDiagnostic iClicker Question What is the name of this compound?O O (a) sec-butyl acetate (b) butyl methyl carboxylic acid (c) ethyl butanoate (d) isobutyl acetate (e) n-butyl acetate Chem 1AA355PBDiagnostic iClicker Question What is the name of this compound?O O (a) sec-butyl acetate (b) propyl butanoate (c) ethyl butanoate (d) isobutyl acetate (e) n-butyl propanoate Chem 1AA356JVDiagnostic iClicker Question What is the name of this compound?O O (a) sec-butyl acetate (b) butyl methyl carboxylic acid (c) ethyl butanoate (d) isobutyl acetate (e) n-butyl acetate Chem 1AA35719 20. HSDiagnostic iClicker Question What is the name of this compound?OO (a) sec-butyl acetate (b) butyl methyl carboxylic acid (c) ethyl butanoate (d) isobutyl acetate (e) n-butyl acetate Chem 1AA358Reactions of AlkanesSection 26-2Concept Check C8H18(l) + O 2(g)?1) What are the products of the reaction at 298K? 2) Write a balanced chemical equation 3) Predict the signs of H, S and G 4) What type of reaction is shown?Chem 1AA36020 21. Concept Check: SolutionC8H18(l) +25 2O2(g) 8 CO2(g) + 9 H2O(l)H = -5.48 103 kJ mol1 (exothermic!) So is negative Go = H-TSo, Go should be negative (H is large) Reaction type: Combustion, redox Chem 1AA361Chem 1AA362Halogenation CH4X2CH3X + HX + CH3-CH3Light or heatHalogenation Initiation: Propagation:Cl-Cl or h2 ClH3C-H + Cl H3C + HCl H3C + Cl2 H3C-Cl + ClTermination:Cl + Cl Cl-Cl H3C + Cl H3C-Cl H3C + H3C H3C-CH3Applicable also for F2 (often explosive), Br2, I2 (slow) Chem 1AA36321 22. Grignard Reagent Mg R XEt2OR MgXX = Cl, Br or I Mg ClEt2OMgClLook at the change in oxidation state of the Mg: Mg(0) Question: What gets reduced?ClMg(II)Mg2+ClChem 1AA364Bonding in alkanes HybridizationSection 11-3Review: Electronic Structure and Bonding The following section, up to "Review: p-orbitals", is assumed knowledge and will not be discussed in class.The Atom: A dense nucleus surrounded by a much larger extranuclear spaceChem 1AA36622 23. Review: Principal Energy Levels Electrons are confined to shells defined by the principal quantum number (n) n = 1, 2, 3 Each shell can contain 2n2 electrons The lower the value of n-the lower the energy of the shell (nearest to the nucleus) Chem 1AA367Review: Orbitals Shells are divided into sub-shells labelled s, p, d, f p, d, and f orbitals are further divided up based on their spatial orientationChem 1AA368Review: Orbitals in Shells Shell n=1 n=2Orbitals in that shell 1s 2s, 2px, 2py, 2pzn=33s, 3px, 3py, 3pz, + 5 3dChem 1AA36923 24. Review: Electron Configuration Three principles/rules are used to determine the electron configuration: Aufbau Principle Pauli Exclusion Principle Hunds ruleChem 1AA370Review: Orbitals (subshells) Each type of orbital (s, p, d, f) has a distinct shape The shape represents the probability of finding an electron (quantum mechanics) Organic chemists are interested in shells 1, 2, and sometimes 3 Chem 1AA371Chem 1AA372Review: