Introduction to Organic Chemistry

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1 PART 1 Introduction to Organic Chemistry Chapter 1. Structure, bonding, acid-base 2. Nomenclature, physical properties, drawing structure

2 Chapter 1 Structure and Bonding Acids and Bases Electronic structure Chemical bonds Acid-base

3 Organic compounds Ch 1 #3 vital force theory by Berzelius, 1807 compounds from living organisms ~ organic comp ds from minerals ~ inorganic death of VFT synthesis of urea ( organic ) from inorganic Wöhler, 1828 the current definition of organic comp ds compounds that contain carbon

4 Ch 1 #4 VFT is dead!! VFT-1: Organic compounds from living organism (plant or animal) only VFT-2: An organic compound still contains some of the life force of the organism that makes them. vitamin C, saponin, etc natural vs synthetic (p3) Vitamin C is vitamin C! vitamin C L-ascorbic acid

5 Chemistry of carbon comp d Ch 1 #5 organic chemistry = chemistry of carbon comp d why carbon? forms stable covalent bond to other carbon sharing electrons Li +, F - vs C 4+ or C 4- forms chain variety (16M org comp ds) forms bonds to heteroatoms (O, N, S, P, X, etc.) exceptions: CO, CO 2, Na 2 CO 3, etc. ~ inorganic

6 Components of org chem Ch 1 #6 organic compounds structure molecule bonding atoms properties physical chemical Chapter 1, 2, 3, 5, 7 organic (chemical) reactions mechanism thermodynamics kinetics Chapter 4, 6, 8, 9, 10, 11

7 In org chem 1 Ch 1 #7 Chapter 1. electronic structure and bonding acid-base 2. nomenclature, physical properties structure drawing, alkanes 3,4. alkenes 5. stereochemistry 6. alkynes 7. resonance structure substitution and elimination reactions 11. organometallics

8 Structure of an atom Ch 1 #8 Define the followings atomic number mass number isotope allotrope atomic weight atomic mass molecular weight [molar mass] amu

Electronic structure of an atom Ch 1 #9 quantum mechanics (Schrödinger) wave equation wave function [orbital] quantum numbers shell sub-shell [orbital] electronic

9 Electronic structure of an atom Ch 1 #9 quantum mechanics (Schrödinger) wave equation wave function [orbital] quantum numbers shell sub-shell [orbital] electronic configuration ~ distribution of e in orbital aufbau principle ~ building-up Pauli exclusion principle ~ two e with opposite spin Hund s rule ~ degenerate orbitals

10 Bonding Ch 1 #10 core vs valence electron octet rule by Lewis ~ Lewis structure 8 e at valence shell ~ stable atom Atoms lose, gain, or share e to satisfy octet rule and form bonding. ~ Lewis theory

11 Ionic bond Ch 1 #11 atom ion bonding ionic compound ionic solid high mp strong bond + network ionic molecule?

12 Covalent bond Ch 1 #12 sharing e valency mono, di, tri, or tetravalent covalent comp d molecule weak intermol interaction

13 Polar (covalent) bond Ch 1 #13 primary bonds ~ ionic or covalent polar bond in electronegativity of atoms EN ~ ability to attract e EN value not absolute but relative

14 Ch 1 #14 polar bond, polar molecule, dipole dipole moment µ = e d e ~ (partial) charge on the atom d ~ distance betw charges Read p12 and solve Prob 8 and 9!

15 Atomic radius and electronegativity Ch 1 #15 Both determined by nuclear charge (# of protons) # of shells (position of e)

16 (electrostatic) potential map e distribution, (partial) charge distribution size and shape of molecule reactivity and reactive site (relative) size of H in LiH, H 2, HF Ch 1 #16

17 Covalent ions Ch 1 #17 covalent compounds containing charge ion no ionic bond, though neutral neutral covalent ion molecule molecule ion charge = # of protons - # electrons for NH 4, = 1

18 Formal charge Ch 1 #18 charge assigned to an atom in a molecule charge distribution among atoms in a covalent species (ionic or neutral) FC = [# of valence e] [# of e it owns] = [# val e] [# non-bonding e + ½ (# bonding e)] non-bonding electrons = lone-pair e s = unshared pair of e s

19 Octet rule, formal charge, and stability CH 4 vs CH 3 radical Ch 1 #19 H H C H H H C :CH 3 H H + CH 3 satisfying octet rule stable [not reactive] NOT satisfying octet rule unstable [(very) reactive] HCN vs HNC H:C:::N: :C:::N:H satisfying octet rule satisfying octet rule formal charge ~ formal charge ~ stable unstable (actually, not likely present)

for carbon carbocation ~ species containing C +

20 Valency Ch 1 #20 # of bonds with no formal charge if formal charge monovalent divalent trivalent tetravalent for carbon carbocation ~ species containing C + carbanion ~ species containing C - oxonium ion radical ~ species w/

21 Drawing Lewis structure Ch 1 #21 Arrange the atoms. from center to peripheral ~ C, N, O, then X and H Bond atoms (with e) satisfying octet rule. Assign (formal) charge if needed. CH 4 O C 2 H 4 Practice. Prob 14 p16

22 Representing [drawing] structures Ch 1 #22 Lewis structure ~ valence e s Kekule structure ~ bond as line, no : line(-bond) structure condensed structure ~ no bond, if not necessary skeletal structure ~ bonds only Section 2.6 p78 bond-line structure a line for a bond; not showing C and H bonded to C OH

23 Ch 1 #23 Table 1.5 p18 N CH 3 CH 2 C(O)CH 3 -C(=O)H, -C(O)H O OH O -C(=O)OH, -C(O)OH O COOH

24 Atomic orbitals (AO) Ch 1 #24 AO describe the location of e (probability) density in atom quantum mechanics (Schrodinger eqn) quantum numbers orbital s orbitals + - node where wave function is zero no electron density An e behaves like a standing wave.

25 Ch 1 #25 p orbitals lobe knob 3 p orbitals

26 Molecular orbitals (MO) Ch 1 #26 MO describes the location of e density in molecule combination of AO s bonding MO bond in particle sense H 2 energy released = bond strength = bond dissociation energy bond length

27 Ch 1 #27 bond in wave sense conservation of orbitals ~ 2 AO s 2 MO s AO s in-phase ~ reinforcing ~ overlap bonding MO AO s out-of-phase ~ cancelling ~ node antibonding MO same e configuration in AO and in MO aufbau, exclusion 2 e in σ BMO, no e in σ* AMO σ bond σ bond head-on overlap σ σ H 2

28 Ch 1 #28 bond order # of bonds betw atoms (# bonding e - # antibonding e)/2 for H 2, bond order = (2 0)/2 = 1 ~ single bond Prob 20 p23 He 2+ exist? H 2 σ σ

29 Ch 1 #29 π bond side-to-side overlap π BMO and π* AMO weaker than σ bond π* π Prob 21 p25 σ, σ*, π, or π*?

30 Single bond and sp 3 hybridization Ch 1 #30 Experimental data for methane [CH 4 ] shows 4 identical bonds with tetrahedral geometry. tetrahedral VSEPR theory VSEPR theory determines molecular shape. sawhorse drawing

31 Ch 1 #31 valence-shell e pair repulsion (VSEPR) theory Rule 1: VSEPs (bonding or non-bonding) repel each other Rule 2: Lone pair repels more. Rule 3: Double and triple bonds as one EP

32 Ch 1 #32 hybridization [ 混成化 ] ~ to bond well (or to explain well) energy required bonding 4 sp 3-1s bonds repulsion tetrahedral club VSEPR-1 energy released energy out > in bond thru hybridization

33 Ch 1 #33 ethane [CH 3 CH 3 ] bond angles all 109.5º? not exactly (111.5º and 107.5º)

34 Double bond and sp 2 hybridization Ch 1 #34 Ethene [ethylene, CH 2 =CH 2 ] is planar. VSEPR-3 hybridization bonding

Ch 1 #35 double bond 1 σ + 1 π shorter and stronger than single bond C=C ~ 1.33 Å, 174 kcal/mol C-C ~ 1.54 Å, 90 kcal/mol 174 < 90 x 2 174 = 90 + 84?

35 Ch 1 #35 double bond 1 σ + 1 π shorter and stronger than single bond C=C ~ 1.33 Å, 174 kcal/mol C-C ~ 1.54 Å, 90 kcal/mol 174 < 90 x = ? π ~ side-to-side overlap ~ less overlap than σ π bond still strong enough to prevent = from rotating box p31 allotropes of carbon diamond, graphite, CNT, fullerene, graphene sp 3 vs sp 2

36 Triple bond and sp hybridization Ch 1 #36 Ethyne [acetylene, CH CH] is linear. hybridization bonding triple bond 1.20 Å, 231 kcal/mol

37 Carbon with 3 bonds Ch 1 #37 methyl cation [ + CH 3 ] 3 sp 2 -s σ bonds + 1 empty p orbital ~ VESPR-1 methyl radical [ CH 3 ] 3 sp 2 -s σ bonds + 1 p orbital w/ 1 e ~ VESPR-1

38 Ch 1 #38 methyl anion [ :CH 3 ] 3 sp 3 -s σ bonds + 1 lone pair ~ VESPR-1

39 H 2 O Ch 1 #39 bond angle close to tetrahedral angle, not 180º hybridization 104.5º < 109.5º VSEPR-2: non-bonding EP repels more. more diffuse [larger] e distribution than bonding EP

40 NH 3 and NH 4 + Ch 1 #40 NH 3 similar to H 2 O < < lone pair EP ~ VSEPR-2 NH identical bonds ~ 4 sp 3

41 Hydrogen halides [HX] Ch 1 #41 X ~ halogen [F, Cl, Br, I] sp 3 -s bond bond length and strength the shorter, the stronger H-F more overlap H-Cl less overlap

42 Dipole moment of molecule Ch 1 #42 is vector sum of bond (and lone-pair) dipoles nonpolar polar NF 3 µ = 0.24 D Lone-pair dipole contributes.

43 Ch 1 #43 halomethanes Cl Cl Cl H H H H H Cl H 110 Cl Cl µ = 1.54 D µ = 1.02 D bond angles ~ explainable dipole moments ~ rather complex

44 Summary: structure and bonding Ch 1 #44 the shorter, the stronger the greater the e density in overlap the more s character (25% s) (33% s) (112+62) (50% s)

45 ACIDS and BASES Ch 1 #45 Brφnsted-Lowry definition of acid and base acid ~ proton (H + ) donor ~ HA HX, H 2 O, ROH, RNH 2, RCH 3 base ~ proton acceptor ~ B: RNH 2, ROH, H 2 O (amphoteric), X - acid-base rxn = proton transfer rxn ~ an equilibrium rxn acid base base acid Equili moves to weaker acid (and base).

46 Acid strength ~ pk a Ch 1 #46 for acid HA in water K a = K eq [H 2 O] = [H 3 O + ][A - ]/[HA] or [H + ][A - ]/[HA] in dilute solution, [H 2 O] is constant at 55.5 M K a ~ acid dissociation constant, acidity constant, degree of ionization of acid in water pk a = log K a pk a of water? Prob 102 p67 pk a ~ acidity strong acid ~ K a > 1, pk a < 0 ph (of solution) vs pk a (of acid) strong and weak acid p43 ~ arbitrary

47 Ch 1 #47 conjugate base, acidity, and equilibrium Strong reacts to form weak. The stronger the acid, the weaker the conjugate base. The more stable the conjugate base, the more reactive the acid. stability vs reactivity

48 Organic acids and bases Ch 1 #48 common organic acid ~ carboxylic acid [RCOOH] compared with ROH why? inductive + resonance effect common organic base ~ amine [RNH 2 ] pk b = 4.75 pk b = 3.3 CH 3 CH 2 NH 2 pk a > 40 NH 4 + pk a = 9.25 why? inductive effect

Strong and weak acids Ch 1 #49 R ~ alkyl CH 3, CH 3 CH 2, -- HX inorg acids 10 strong acid ( 100%) 2 6 1.74 5 10 OH weak acid (partially ionized in water) 15.

49 Strong and weak acids Ch 1 #49 R ~ alkyl CH 3, CH 3 CH 2, -- HX inorg acids 10 strong acid ( 100%) OH weak acid (partially ionized in water) RNH 2 amines RH hydrocarbons very weak acid ( 0%) weak base medium base strong base X ϴ halide ion RCOO ϴ carboxy anion RO ϴ, HO ϴ alkoxide ion hydroxide ion R ϴ RNH ϴ

50 *Curved arrow ~ electron movement Ch 1 #50 Curved arrows show e movement reaction mechanism thermodynamics kinetics mechanism

51 Acidity: effect of atom bonded to H Ch 1 #51 The weaker [more stable] the conjugate base, the stronger the acid. effect of EN More EN atom accommodates (-) charge better. CH 3 OH vs CH 3 NH 2?

52 Ch 1 #52 effect of size H loosely bound to larger atom. Larger atom accommodates (-) charge better. Size effect overweighs EN effect. CH 3 OH vs CH 3 SH?

53 effect of hybridization Ch 1 #53

Acidity: inductive effect (of substituent) Ch 1 #54 substitution reaction ~ 置換反應 substituent ~ 치환기 EN X pulls e through σ bond better than H does inductive

54 Acidity: inductive effect (of substituent) Ch 1 #54 substitution reaction ~ 置換反應 substituent ~ 치환기 EN X pulls e through σ bond better than H does inductive e-withdrawing makes conj base stable acid strong weaken O-H bond better leaving H acid strong H < Br < Cl < F e-withdrawing groups ~ most ~ -CN, -X, -OR, -C=O, etc

55 Ch 1 #55 R [alkyl] pushes e better than H does inductive e-donating makes conj base strong acid weak e-donating groups ~ -R, -O -, -COO -, etc pk a ~ 13.1 pk a ~ 4.9 inductive effect (only)?

56 Acidity: resonance effect (of subs) Ch 1 #56 carboxylic acid vs alcohol RCOOH is much stronger acid than ROH inductive effect of C=O resonance effect ~ stabilize conj base by e delocalization

57 ph and pk a Ch 1 #57 Henderson-Hasselbalch eqn from definition of ph and pk a tells [acidic form, HA]/[basic form, A-] in solution of certain ph acidic form when ph < pk a basic form when ph > pk a

58 Ch 1 #58 useful for separation pk a = 5 pk a = 10 at ph = 2, both in acidic form RCOOH to ether, RNH 3+ to water charged (ionic) to water (polar); neutral (organic) to ether (organic). ph pk a > 2 for better separation (< 1/100) Q. What ph for amine in ether and acid in water? Do Prob 103 and 104 p67

59 Buffer solution Ch 1 #59 buffer solution with weak acid and its conj base RCOOH RCOO ϴ + H + RCOONa RCOO ϴ + Na + when ϴ OH or H + added no change in ph preparation using H-H eqn for ph, pk a, and buffer, Study guide pp36-55

60 Lewis acids and bases Ch 1 #60 Lewis acid ~ accepts (a share in) an electron pair Lewis base ~ donates (a share in) an electron pair Lewis bases are BL bases. Lewis acids are not limited to BL acids. Protonic acids are Lewis acids. ~ H + accept e pair. AlBr 3, BF 3, FeCl 3, BH 3, etc ~ usually-called Lewis acid do not give out H + ; accepts e pair with empty orbital

61 Exercise Ch 1 #61 Do (all the) problems! Prob 95. Which N more basic? N sp 3 N sp 2 H N H N H N N pyrrolidine basic pyrrole much less basic imidazole basic pyridine basic

Organic Chemistry 6 th Edition Paula Yurkanis Bruice. Chapter 1. Electronic Structure and Bonding. Acids and Bases Pearson Education, Inc.

Organic Chemistry 6 th Edition Paula Yurkanis Bruice Chapter 1 Electronic Structure and Bonding Acids and Bases 2011 Pearson Education, Inc. 1 Organic Chemistry Carbon-containing compounds were once considered