I, too, started small……..

Peter VollhardtUniversity of California at Berkeley

Organic Chemistry:Organic Chemistry:The Chemistry of CarbonThe Chemistry of Carbon

Organic Organic ChemicalChemical

s in s in ActionAction

ChemicalsChemicals

Saccharin (1879): 300 Saccharin (1879): 300 Times as Sweet as Times as Sweet as

SugarSugar

MmmmmmmmmmmmmhhhMmmmmmmmmmmmmhhhh!!!!h!!!!

Chemical Warfare in Chemical Warfare in Nature:Nature:

BenzoquinonBenzoquinone,e,

Hydrogen Hydrogen peroxide, peroxide,

100ºC100ºC

The Bombardier BeetleThe Bombardier Beetle

SeahareSeaharePinkFloydPinkFloyd

Chemical Protection in Chemical Protection in NatureNature

Nature is not always Nature is not always green….green….

Polyacetylene: Polyacetylene: Organic ConductorsOrganic Conductors

The Polyamide The Polyamide KevlarKevlar Bulletproof!Bulletproof!

Organics Harder Than Organics Harder Than MetalMetal

Polystyrene Polystyrene from styrenefrom styrene Suntan lotionSuntan lotion

The Sands Hotel, Las Vegas,

11.26.1996

Nature is the Biggest Nature is the Biggest PolluterPolluter

Top Four US Prescription Top Four US Prescription DrugsDrugs

Total U.S. sales of pharmaceuticals reached $224 billion in 2003, with lipitor leading at $6.3 billion.

Male Male ChromosomesChromosomes

ClonesClones

DNA: the Double HelixDNA: the Double Helix

Ban Dihydrogen Ban Dihydrogen MonoxideMonoxide

Matthew  James Tvedten (Poison:

Chlordane) Michigan (1/27/81)

6,000+and continuing at a rate of 10 to 15 per month

(Poison:  methyl

isocyanate and others)

Bophal, India (Deaths since

12/2/84)

Death/Injury ongoing (Poison: Dow's Agent Orange) New Plymouth,

NZ (1965-present)

Jesse (Poisons: 

NIX ® and

Lindane) U.S.

(9/11/93)

Dedicated to the Martyrs of Pesticide Poisoning Dedicated to the Martyrs of Pesticide Poisoning May they (and we) find justiceMay they (and we) find justice

Baby Evans (Poison:

Termiticide) St. Petersburg,

FL (5/2000)

Colette Chuda

(Poison: various

pesticides)  New Jersey

(4/21/91)

Cindy Duehring (Poison: various

pesticides) Bismark, ND

(6/30/99)

24 Children (Poison:  methyl

parathion by Bayer)

Tauccamarca,

Peru (10/24/99) Julia

Kendall (Poison:

Malathion)

California (7/12/97)

Marianna Cates and Family

(Poison:  various agricultural)

Ulster County, New York (6/1995)

Memorial Memorial 547 Men, Women and Children will Die today 547 Men, Women and Children will Die today

from Pesticide Poisoning from Pesticide Poisoning (Statistically known as "acceptable risks" for pesticide poison registration)(Statistically known as "acceptable risks" for pesticide poison registration)

No Chemicals in KailuaNo Chemicals in Kailua

Water: The Solvent of Water: The Solvent of LifeLife

The Hydronium IonThe Hydronium IonOrbitalOrbital

H

H

HO

ChargeCharge

Cornflowers:Cornflowers: Blue Blue (Unprotonated)(Unprotonated)

Poppies:Poppies: RedRed (Protona(Protonatedted))

What to Expect: an What to Expect: an OutlineOutline

CC CCHH

HHHH

HHHH

HHStructure and BondingStructure and Bonding

AlkanesAlkanes

HaloalkanHaloalkaneses

CycloalkanCycloalkaneses

StereoisomerisStereoisomerismm

CCHH33 ClCl--++

CCHH22

CCHH22

CCHH22

HH22CC

HH22

CC

CCHH22

Basic ReactionsBasic Reactions

CCHH33 HH ++ClCl22 CCHH33 ClCl ++HHClClhvhv,, Δ

SubstitutionSubstitution

CCHH33 ClCl++K K II++ -- CCHH33 II K K ClCl++ --++

Radical HalogenationRadical Halogenation

Reaction versus MechanismReaction versus Mechanism

CHCH22 CHCH22 ++ HH22C CHC CH22

HH IIbasbasee

EliminationElimination

Reaction:Reaction: The recipe and molecular alteration. The recipe and molecular alteration.Mechanism:Mechanism: What is the exact pathway by which What is the exact pathway by which alteration occurs? alteration occurs?

Functional GroupsFunctional Groups

OHOHCC C CC C C CC C

RRCOCOHH

OO

RR RR’’

OOCC NHNH22RR

Spectroscopy: Spectroscopy: NMR, IRNMR, IR

SynthesisSynthesis: : Wöhler (1828): Wöhler (1828): Made anMade an “organic” “organic” compound from an compound from an “inorganic” “inorganic” salt.salt.

Pb(OCN)Pb(OCN)22 + 2 H + 2 H22O + 2 NHO + 2 NH33 2 H 2 H22NCNHNCNH22 + + Pb(OH)Pb(OH)22

OO

UreaUrea

How do we make How do we make penicillin?penicillin?

OO OO

NN

NN

SS

CCOOOOHH

Or Or cubane ?cubane ?

HH HH

HH

HH

HH

HH

HHHH

Before we get into this, we need to review the basics.Before we get into this, we need to review the basics.

HH

BondingBondingAtom 1Atom 1 + + Atom 2Atom 2 A:A:AA or or A A A A ““favorable”favorable”““Rules”Rules”

::1.1. Opposite charges attract each Opposite charges attract each

other (other (Coulomb’s LawCoulomb’s Law).).

2. Electrons spread out in space 2. Electrons spread out in space (delocalization).(delocalization).

3. Noble gas configuration is 3. Noble gas configuration is desirable.desirable.

1736-18061736-1806

Covalent Bonding: Covalent Bonding: Sharing ElectronsSharing Electrons

DimensionDimensions:s:

Nuclear diameter ~ 10Nuclear diameter ~ 10-15-15 m mElectronic orbit ~ 10Electronic orbit ~ 10-10-10 m m

five five orders of orders of magnitudmagnitudeeMass ratio proton : electron = ~ Mass ratio proton : electron = ~

18001800

Internuclear PotentialInternuclear Potential

Ionic Bonding:Ionic Bonding: “No” Sharing of “No” Sharing of

Electrons Electrons

Who donates and who accepts?Who donates and who accepts?

Valence electrons

Duet

Octets

Partial Periodic TablePartial Periodic Table

Why Do Elements Why Do Elements React?React?

AiAimm1.1. ““Ionic” Ionic”

BondsBondsLiLi2,12,1

NaNa2,8,12,8,1

FF2,72,7

[Li[Li22]]++

[Na[Na2,82,8]]++

[F[F2,82,8]]--+1+1ee

--1e1e--

1e1e

Therefore:Therefore:++ --

Noble Gas ConfigurationNoble Gas Configuration

2 Na F2 Na FFF222 Na2 Na ++

Transfer Transfer of of

Valence Valence ElectronsElectrons

Covalent Bonds

-4e-4e

Shows onlyShows onlyvalencevalence ee

(He)(He) (Ne)(Ne)

Compromise: electron-sharingCompromise: electron-sharing

CC..

HHHH

HHHH...

. . .

HH O O HH. ... ....

2. “Covalent” Bonds2. “Covalent” Bonds

CC44++

+4e+4e

4 4 HH

CC

CC

2 2 HH22 OO22++

++

CC4-4-

Elements in the “middle” of the periodic Elements in the “middle” of the periodic table have a problem with table have a problem with electron affinity electron affinity (EA)(EA) and and ionization potential (IP)ionization potential (IP)::

Lakehurst, NJ,Lakehurst, NJ,May 3, 1937May 3, 1937

The Hindenburg:The Hindenburg:

3. Most Bonds Are “Between” Covalent 3. Most Bonds Are “Between” Covalent and Ionic:and Ionic:

Polar CovalentPolar Covalent

PaulingPauling electronegativity electronegativity scalescale

HH II ClCl HH33CCFF

:::::: ::--++ :::::: ::--++ --++ FF

:::::: ::

AA ::BB--++

1901-1994 Nobel prizes for chemistry and 1901-1994 Nobel prizes for chemistry and peacepeace

push pull

:: 0.3 < 0.3 – 2.0 < 0.3 < 0.3 – 2.0 < 2.02.0CovalenCovalen

ttPolar Polar

CovalenCovalentt

IonicIonic

Increase

Decrease

The Shape of MoleculesThe Shape of MoleculesControlled by Controlled by valence electron valence electron

repulsionrepulsionDiatomics:Diatomics: linear (of course), linear (of course), e.g.e.g. Triatomics:Triatomics: either linear (i.e. not bent), either linear (i.e. not bent), e.ge.g.

HH :: HH LiLi :: HH

FF

:::::: :: FF

:::::: ::BB

eeFF

:::::: :: ::

FF

:::: ::

BBee

or bent, when there are lone e-pairs, or bent, when there are lone e-pairs, e.g. e.g.

Tetraatomics:Tetraatomics: either trigonal, e.g.either trigonal, e.g.

OO

:::::: ::HH HH

ClCl

:::::: ::

ClCl::::::

::

ClCl::::::

::BB

nonott

FF

:::::: :: FF

:::: ::

Or pyramidal, when there are lone e-pairs, e.g.Or pyramidal, when there are lone e-pairs, e.g.

Pentaatomics:Pentaatomics: tetrahedral, e.g. tetrahedral, e.g.

But other shapes are possible, when there are But other shapes are possible, when there are more electrons,more electrons,e.g. in transition metals (octahedral etc.).e.g. in transition metals (octahedral etc.).

HHHHHH

HH

NN

:

HHHH

HH

CC

Lewis StructuresLewis Structures Draw molecular skeleton (given)Rule 1:Rule 1:

Count total number of valence electronsCount total number of valence electronsRule 2:Rule 2:

Octet (Duet) RuleOctet (Duet) RuleProvide octets (duets for H) around all atomsProvide octets (duets for H) around all atoms

Rule 3:Rule 3:

How to distribute valence electrons:How to distribute valence electrons:

COCO22 O C OO C O CHCH44 CCHH

HH HHHH

CC.. ....

.. .. ..OO ::....HH BrBr

:::::: ....

HH :: HH FF

:::::: :: FF

:::: :: OO

::::::::

HH HH

Take care of charges, if any. Charges occur Take care of charges, if any. Charges occur when the formal when the formal “effective” electron count“effective” electron count around the nucleus differs from around the nucleus differs from valence valence electron countelectron count..

““Effective” electron count:Effective” electron count: Each bond with twoEach bond with twoshared electrons counts as 1e; lone pairs count as 2e.shared electrons counts as 1e; lone pairs count as 2e.

HH33OO NONO COCO

Rule 4:Rule 4:

:NN:::OO: ++:CC:::OO:

++--HH:OO:HH

HH....

++

Valence electron count:Valence electron count: Rule 2 Rule 2 (# of valence (# of valence electrons).electrons).

++++

ExamplExample:e:1. Atom 1. Atom

arrangement:arrangement:2. Valence 2. Valence electrons:electrons:3. Octet rule3. Octet rule

Shortcut:Shortcut:1. Connect all bonded atoms with “2e 1. Connect all bonded atoms with “2e line”. line”. 2. If there are e left, add them as lone pairs to any 2. If there are e left, add them as lone pairs to any atom to give it an octet until no e left. atom to give it an octet until no e left. 3. If some atoms lack octet, move lone pairs into 3. If some atoms lack octet, move lone pairs into shared positions.shared positions.

COCO22

:....

..:..OO CC OO

OO CC OO

..

......OO CC OO:

..

....

:..OO CC OO

O C OO C OOO 66ee,, CC 44ee 1616ee totaltotal

Gilbert LewisGilbert Lewis(arrived in Berkeley in 1912)(arrived in Berkeley in 1912)

ResonanceResonanceOften several octet structures are Often several octet structures are possible for a molecule: possible for a molecule: Resonance Resonance formsforms

Form A Form A form Bform B move move

electronselectrons(pairs)(pairs)

Molecule is a Molecule is a superposition superposition of these formsof these forms

Carbonate, COCarbonate, CO332-2-. All forms are equivalent. All forms are equivalent

..

OO

OOCC

OO----

..

....

.... OOCC

OO--

.... ........OO

CCOO-- ....

. . . . . . ..

--:OO:..--:OO:

..

The carbonate ion is delocalized:The carbonate ion is delocalized:symmetrical!symmetrical!

Electrostatic Potential Map: Electrostatic Potential Map: RedRed = relatively = relatively electron electron richrich BlueBlue = relatively = relatively electron electron poorpoor

Resonance FormsResonance Forms

OOCC

OO--

.... .... ..

--:OO:..

RulesRules1. 1. Octet ruleOctet rule (wins over all other) (wins over all other)

Nonequivalent Resonance Nonequivalent Resonance FormsForms

66ee--

majormajor

OO OO

HHCC CC

HH HH HH++

66eemajormajorNN NN OO++ ++

which ones are better?which ones are better?

OO

2. When there are two or more forms with 2. When there are two or more forms with complete octets: complete octets: electronegativity electronegativity rules.rules.

Example: enolate Example: enolate ionion

charge on charge on more e-negative more e-negative elementelement majormajor

HH----

HH

HHHHHH

HHCC CC CC CC

OOOO

But:But: 66eemajormajor

NN NN OO++ ++OO When in doubt, rule 1 wins !When in doubt, rule 1 wins !

3. 3. Minimum charge separationMinimum charge separation

Formic acidFormic acidmajormajor

--

HHCC CC

HH HH HH

OO OO

++OO OO

Note: Rule 1 wins !Note: Rule 1 wins !:CC:::OO:++--

19001900 Planck, EinsteinPlanck, Einstein: Light = : Light = photonsphotons E = h E = hνν

νν = c/ = c/λλ c = 300,000 km sec c = 300,000 km sec-1-1

Atoms absorb/emit energy in discrete Atoms absorb/emit energy in discrete packages: packages: quantaquanta (to avoid “ultraviolet (to avoid “ultraviolet catastrophe”)catastrophe”)19231923 DeBroglieDeBroglie: All mass (m) moving with velocity v : All mass (m) moving with velocity v has a has a wavelengthwavelength λλ . .

Quantum MechanicsQuantum MechanicsLight and objects as waves or particlesLight and objects as waves or particles

hh

mv mv λλ = =

19271927 HeisenbergHeisenberg: : Uncertainty Uncertainty (∆)(∆) principle principle ∆ ∆ (position) x ∆ (momentum) > h(position) x ∆ (momentum) > h

h = Planck’s constant = 1.34 x 10h = Planck’s constant = 1.34 x 10-34-34 cal seccal sec

OrbitalsOrbitals: : SolutionsSolutions to wave to wave equations equations (wavefunctions)(wavefunctions)

BornBorn: Square of a value of the : Square of a value of the wavefunction = wavefunction = probability of finding probability of finding the electron therethe electron there

19271927 SchrödingerSchrödinger: : Wave equationsWave equations for an electron moving around the for an electron moving around the nucleusnucleus

Spherical (three-dimensional) Spherical (three-dimensional) shape.shape.Contrast to mechanical waves Contrast to mechanical waves (guitar string, rubber band)(guitar string, rubber band)Two-Two-dimensional dimensional wavewave

+/-+/- = signs, not charges = signs, not charges

OrbitalsOrbitals

nodenode

amplitudeamplitude ++--00

“ “ball”ball” spherical spherical “eight”“eight”

Actual solutions: 1Actual solutions: 1ss, 2, 2ss, 2, 2ppxx, 2, 2ppyy, 2, 2ppzz, , 33ss, 3, 3ppxx, 3, 3ppyy, 3, 3ppzz, etc. , etc.

((increasing energyincreasing energy))

++

--

nodenode

Most important orbitals Most important orbitals (for us):(for us):

#s are related to#s are related toclassical shellsclassical shells

s Orbitals Orbital p Orbitalp Orbital

The 1s OrbitalThe 1s Orbital

s-Orbital

The 2s OrbitalThe 2s Orbital

The Three 3p OrbitalsThe Three 3p Orbitals

p-Orbitalp-Orbital

Energy diagram depicting solutions as energy Energy diagram depicting solutions as energy “levels”:“levels”:

There are rules There are rules for “filling up” for “filling up” levels withlevels with ee

1.1. Lower energy orbitals filled first (Lower energy orbitals filled first (closed shellclosed shell))2.2. PauliPauli: : Exclusion principleExclusion principle: 2: 2ee max max3.3. Hunds Hunds rulerule: Equal energy orbital (i.e. : Equal energy orbital (i.e. ppx,y,zx,y,z) filled ) filled

with one with one ee each first each first

electrons (He)electrons (He)11ss

22ss ppxx ppyy ppzz

Aufbau PrincipleAufbau Principleor: where the electrons goor: where the electrons go

Energies of Orbitals Calculated for H Energies of Orbitals Calculated for H AtomAtom

Therefore, Therefore, electronic electronic configurations:configurations:H(1H(1ss))11; ; He(1He(1ss))22; ; Li(1Li(1ss))22(2(2ss))11; ; Be(1Be(1ss))22(2(2ss))22; ; B(1B(1ss))22(2(2ss))22(2(2pp))11; ; C(1C(1ss))22(2(2ss))22(2(2pp))22..

BondingBonding occurs by occurs by overlapoverlap of of atomic orbitals to give atomic orbitals to give molecular molecular orbitalsorbitalsIn phaseIn phase overlap overlap bondingbonding molecular molecular orbitalorbitalOut of phaseOut of phase overlap overlap antibondingantibonding molecular molecular orb.orb.

antibondingantibonding(node)(node)

bondingbonding

Energy Energy diagramsdiagrams 11ss 11ss 11

ss

22pp

BondingBonding

EE

-Orbitals “split” energy levels when entering into overlap.-The better the overlap [e.g. same type of orbital, same energy (shell)], the larger the splitting. -For orbitals of unequal energy, the higher orbital “goes up”, the lower “down”.

e go downe go down

no eno e

goodgood

badbad

11ss

22pp

The Types of Orbital The Types of Orbital OverlapOverlap

This is Real!This is Real! Direct Observation of d-Orbitals in CuDirect Observation of d-Orbitals in Cu22OO

Zuo et al.Zuo et al. Nature Nature 19991999,, 401 401, 49., 49.

Li : H 2Li : H 2ss + 1 + 1ss no shape “issues” no shape “issues”

H : Be : H is linear; but Be H : Be : H is linear; but Be atom has filled shells atom has filled shells (1(1ss))22(2(2ss))22!!How does it bond?How does it bond? Use an empty Use an empty pp

orbital:orbital:

Hybridization and Hybridization and ShapeShape

--++++--

This allows for bonds, but gives This allows for bonds, but gives wrong structure:wrong structure:

Intraatomic overlapIntraatomic overlap of 2s and one 2p of 2s and one 2p orbitals generates two new hybrid orbitals generates two new hybrid molecular orbitals: molecular orbitals: s + p s + p two two spsp hybrids, hybrids, with with linearlinear arrangement: arrangement:

Better: “Hybridization” of OrbitalsBetter: “Hybridization” of Orbitals

sp-Hybridsp-Hybrid

Note: Note: nn atomic orbitals atomic orbitals nn new new orbitalsorbitals

We shall see next that other We shall see next that other combinations of intraatomic overlap combinations of intraatomic overlap (hybridization) are possible: (hybridization) are possible: s + p + p s + p + p 3 3 spsp22 with with trigonaltrigonal shapeshapes + p + p + p s + p + p + p 4 4 spsp33 with with tetrahedraltetrahedral shape shape

Example: Bonding in BHExample: Bonding in BH33. . Hybridization to TrigonalHybridization to Trigonal

spsp22-Hybrid-Hybrid

Bonding in Methane: Bonding in Methane: Hybridization to Hybridization to

TetrahedralTetrahedral

spsp33-Hybrid-Hybrid MethaneMethane

Bonding in Ethane: Bonding in Ethane: Overlap of Two Overlap of Two spsp33 Hybrid Hybrid

OrbitalsOrbitals

EthaneEthane

More More spsp33 Hybrids: NH Hybrids: NH33 and and HH22OO

Double and Triple Double and Triple Bonds: A PreviewBonds: A Preview

EtheneEthene EthyneEthyne

Delocalized Electrons: Delocalized Electrons: Fe Atoms on a Cu Fe Atoms on a Cu

SurfaceSurface

Molecular Models: Molecular Models: Use Them!!!Use Them!!!

The Dashed-Wedged The Dashed-Wedged Line NotationLine Notation

RhondaRhonda WalbaWalba