PART 1

Introduction to
Organic Chemistry

Chapter
1. Structure, bonding, acid-base
2. Nomenclature, physical properties,
drawing structure
Chapter 1

Structure and Bonding

Acids and Bases

Electronic structure
Chemical bonds
Acid-base
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”
 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

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 C4+ or C4-
 forms chain  variety (16M org comp’ds)
 forms bonds to heteroatoms (O, N, S, P, X, etc.)
 exceptions: CO, CO2, Na2CO3, etc. ~ inorganic
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
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
8-10. substitution and elimination reactions
11. organometallics
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 configuration ~ distribution of e in orbital
 aufbau principle ~ ‘building-up’
 Pauli exclusion principle ~ two e with opposite spin
 Hund’s rule ~ degenerate orbitals
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’
Ionic bond Ch 1 #11

 atom  ion  bonding

 ionic compound
 ionic solid
 high mp
 strong bond + network
 ionic molecule?
Covalent bond Ch 1 #12

 sharing e

 valency
 mono, di, tri, or tetravalent

 covalent comp’d
 ‘molecule’
 weak intermol interaction
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
 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!

Atomic radius and electronegativity Ch 1 #15

 Both determined by
 nuclear charge (# of protons)
 # of shells (position of e)
 Ch 1 #16

 (electrostatic) potential map

 e distribution, (partial) charge distribution
 size and shape of molecule
 reactivity and reactive site (relative) size of H
in LiH, H2, HF
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 NH4, 7 + 4 – 10 = 1
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

Octet rule, formal charge, and stabilityCh 1 #19
 CH4 vs CH3 radical
H H −:CH
3
H C H H C
+CH
H H 3

satisfying octet rule NOT satisfying octet rule

stable [not reactive] unstable [(very) reactive]

 HCN vs HNC
H:C:::N: :C:::N:H
satisfying octet rule satisfying octet rule
formal charge ~ 0 0 0 formal charge ~ -1 +1 0
stable unstable (actually, not likely present)
Valency Ch 1 #20

 # of bonds with no formal charge

monovalent divalent trivalent tetravalent

 if formal charge

oxonium ion
 for carbon
 carbocation ~ species containing C+
 carbanion ~ species containing C-

 radical ~ species w/ •
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.

CH4O

C2H4

 Practice. Prob 14 p16

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
 Ch 1 #23

Table 1.5 p18

CH3CH2C(O)CH3

O
-C(=O)H, -C(O)H OH

COOH
-C(=O)OH, -C(O)OH O
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

+
-

 An e behaves like a standing wave.

 node
 where wave function is zero
 no electron density
 Ch 1 #25

 p orbitals

lobe knob

 3 p orbitals
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

H2

 energy released
= bond strength
= bond dissociation energy
 bond length
 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
H2
 Ch 1 #28

 bond order
 # of bonds betw atoms
 (# bonding e - # antibonding e)/2
 for H2, bond order = (2 – 0)/2 = 1 ~ single bond
H2
 Prob 20 p23 He2+ exist? σ∗

σ
 Ch 1 #29

 π bond
 side-to-side overlap
 π BMO and π* AMO π*
 weaker than σ bond
π

 Prob 21 p25 σ, σ*, π, or π*?

Single bond and sp3 hybridization Ch 1 #30

 Experimental data for methane [CH4] shows

 4 identical bonds
 with tetrahedral geometry.
 tetrahedral  VSEPR theory
 VSEPR theory determines molecular shape.

≈ sawhorse drawing
 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
 Ch 1 #32

 hybridization [混成化] ~ to bond well (or to explain well)

energy
required

 bonding club

 4 sp3-1s bonds  repulsion  tetrahedral

energy out > in

VSEPR-1  bond thru hybridization
energy released
 Ch 1 #33

 ethane [CH3CH3]

bond angles all 109.5º?

not exactly
(111.5º and 107.5º)
Double bond and sp2 hybridization Ch 1 #34

 Ethene [ethylene, CH2=CH2] is planar.

VSEPR-3

 hybridization

 bonding
 Ch 1 #35

 double bond
 1σ+1π
 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?
 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
 sp3 vs sp2
Triple bond and sp hybridization Ch 1 #36

 Ethyne [acetylene, CH≡CH] is linear.

 hybridization

 bonding
 triple bond
1.20 Å, 231 kcal/mol
Carbon with 3 bonds Ch 1 #37

 methyl cation [+CH3]

 3 sp2-s σ bonds + 1 empty p orbital ~ VESPR-1

 methyl radical [•CH3]

 3 sp2-s σ bonds + 1 p orbital w/ 1 e ~ VESPR-1
 Ch 1 #38

 methyl anion [−:CH3]

 3 sp3-s σ bonds + 1 lone pair ~ VESPR-1
H2O 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
NH3 and NH4+ Ch 1 #40

 NH3
 similar to H2O

 104.5 < 107.3 < 109.5  1 lone pair EP ~ VSEPR-2

 NH4+
 4 identical bonds ~ 4 sp3
Hydrogen halides [HX] Ch 1 #41

 X ~ halogen [F, Cl, Br, I]

 sp3-s bond

 bond length and strength

 the shorter, the stronger

H-F H-Cl
more overlap less overlap
Dipole moment of molecule Ch 1 #42

 is vector sum of bond (and lone-pair) dipoles

 nonpolar

 polar

NF3 µ = 0.24 D

 ‘Lone-pair dipole’ contributes.

 Ch 1 #43

 halomethanes

Cl Cl Cl
108 112 110
H Cl Cl
H 111 H 112 H
H H Cl

µ = 1.54 D µ = 1.02 D

 bond angles ~ explainable

 dipole moments ~ rather complex
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)
ACIDS and BASES Ch 1 #45

 Brφnsted-Lowry definition of acid and base

 acid ~ proton (H+) donor ~ HA
 HX, H2O, ROH, RNH2, RCH3
 base ~ proton acceptor ~ B:
 RNH2, ROH, H2O (amphoteric), X-
 acid-base rxn = proton transfer rxn ~ an equilibrium rxn

acid base base acid

 Equili moves to weaker acid (and base).

Acid strength ~ pKa Ch 1 #46

 for acid HA in water

Ka = Keq [H2O] = [H3O+][A-]/[HA] or [H+][A-]/[HA]

 in dilute solution, [H2O] is constant at 55.5 M
 Ka ~ acid dissociation constant, acidity constant,
degree of ionization of acid in water
pKa of water?
Prob 102 p67
pKa = – log Ka
 pKa  ~ acidity  strong and weak acid
 strong acid ~ Ka > 1, pKa < 0 p43 ~ arbitrary
 pH (of solution) vs pKa (of acid)
 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
Organic acids and bases Ch 1 #48

 common organic acid ~ carboxylic acid [RCOOH]

compared
with ROH

 why? inductive + resonance effect

 common organic base ~ amine [RNH2]
CH3CH2NH2
pKa > 40
pKb = 4.75 pKb = 3.3

NH4+
pKa = 9.25

 why? inductive effect

Strong and weak acids Ch 1 #49

R ~ alkyl
CH3, CH3CH2, --

HX –2 RNH2
inorg amines
acids 35-40
–10 –6 5 OH
15.74
10 RH
hydrocarbons
–1.74 weak acid 25-50
(partially ionized in water)
strong acid very weak acid
(≈100%) (≈0%)

weak base medium base strong base

ROϴ, HOϴ Rϴ
Xϴ RCOOϴ
halide ion carboxy anion
alkoxide ion RNHϴ
hydroxide ion
*Curved arrow ~ electron movement Ch 1 #50
 Curved arrows show  thermodynamics
 e movement  kinetics
 mechanism
 reaction mechanism
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.

 CH3OH vs CH3NH2?
 Ch 1 #52

 effect of size

 H loosely bound to larger atom.

 Larger atom accommodates (-) charge better.
 Size effect overweighs EN effect.

 CH3OH vs CH3SH?
 Ch 1 #53

 effect of hybridization
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
 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

pKa ~ 13.1 pKa ~ 4.9 inductive effect (only)?

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
pH and pKa Ch 1 #57

 Henderson-Hasselbalch eqn

 from definition of pH and pKa

 tells [acidic form, HA]/[basic form, A-]

in solution of certain pH
 acidic form when pH < pKa
 basic form when pH > pKa
 Ch 1 #58

 useful for separation

pKa = 5

pKa = 10

 at pH = 2, both in acidic form

 RCOOH to ether, RNH3+ to water
 charged (ionic) to water (polar);
neutral (organic) to ether (organic).
 |pH – pKa| > 2 for better separation (< 1/100)

Q. What pH for amine in ether and acid in water?

 Do Prob 103 and 104 p67
Buffer solution Ch 1 #59

 buffer solution with weak acid and its conj base

RCOOH RCOOϴ + H+
RCOONa RCOOϴ + Na+

 when ϴOH or H+ added

 no change in pH

 preparation
 using H-H eqn

 for pH, pKa, and buffer, Study guide pp36-55

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.
 AlBr3, BF3, FeCl3, BH3, etc ~ usually-called Lewis acid
 do not give out H+; accepts e pair with empty orbital
Exercise Ch 1 #61

 Do (all the) problems!

Prob 95. Which N more basic?

N

sp3 sp2
N H N H N H N
N

pyrrolidine pyrrole imidazole pyridine

basic much less basic basic basic