Chem 125 Lecture 1810/15/08

This material is for the exclusive use of Chem 125 students at Yale and may not

be copied or distributed further.

It is not readily understood without reference to notes from the lecture.

Four Functional Groups:

CarbonylAmide

Carboxylic AcidAlkyl Lithium

(then we’ll have a complete change of perspective)

Resonance:Intramolecular

HOMO/LUMO Mixing

Why the Amide Functional Groupis not an Amine and a Ketone

CN O••

vs. Amide

Pyramidal N Planar N

Easy N-C Rotation Barrier to Rotation

AmineCarbonyl

Stable More StableNaïve Prediction Experimental Observation

C

O

N

C

O

N

C

O

N

by 16 kcal/mole (1/4 C-N)

16 kcal/mole

by 0.14Å

by 0.03Å

wrecks *C=O-nN overlap

HOMO

LUMO

Long N-C Shorter N-C…

Short C=O Longer C=O…

net

(mostly) Opposing Dipoles Strongly Dipolar(in direction)

~1/3 e- transfer N O

Crucial forStructuralBiology

OC

*C=O “LUMO”

nN “HOMO”N

NNmight as well rehybridize

Partial C=N Double Bond

Partial C-O Single Bondn

NH3

*C=O

Basic and Acidic Relatively Unreactive Skin works

Resonance as aMake & Break correction to

a naïve, localized initial drawing! (best overlap)

formamideHOMO : electron pair

“from” Nshared with C=O

creates

electric dipole

-+

Repeating Unit in Protein -Helix

Stabilized by electrostatic “Hydrogen Bonding”

(reducing backbone “floppiness” by 1/3)and by local planarity of C-N-C-C groups

O

=

Acidity of Carboxylic Acids

R-OH

1011 stronger!

R-CO

OH pKa ~5+ H+R-C

O

O

pKa ~16R-O + H+

HOMO/LUMO REALLY stabilizes carboxylate anion.

R-CO

OHOMO/LUMO stabilizes

neutral acid compared to ROH.Predicts more uphill?

R-CO

OH+

higher

(Less “Uphill”)

LUMO+1 ()

Aggregationof CH3Li

HOMO () LUMO ()

Aggregationof CH3Li

HOMO ()

LUMO+1 ()2HOMO ()

2LUMO+1 ()

Dimerization

Aggregationof CH3Li

3-Center2-Electron

Bondsuse 2 AOsof each Li

LUMO ()LUMO+1 ()

Dimerization

Rotate to superimpose the red lobes.

Two vacantLi+ AOsstabilize unsharedpair of C

Aggregationof CH3Li

HOMO ()

LUMO+1 ()

LUMO+1 ()rotated 90°

LUMO+1 ()

HOMO ()

Aggregationof (CH3Li)4

HOMO(1 of 4)

LUMO(1 of 4)

DistortedCubic

Tetramer 4-Center2-Electron

Bond

H3C CH3O:

Excess Ether Rips Aggregates Apart by bonding with

Li AOs.

• 4 CH3OCH3

NON-BONDED INTERACTIONS & SOLVENT EFFECTS ARE

A VITAL PART OF LORE.(e.g. facilitating ionization)

Last Valence AO of Li(vacant)

3 vacantLi+ AOsstabilize unsharedpair of C.

But organic chemists were not at all surprised

by what they showed!

We have seen amazing modern tools for revealing the Å / psec world of molecules:

SPMX-ray Diffraction

Spectroscopy: IR, ESR, (NMR, etc.)

Quantum Mechanics(computer "experiments")

How Did They Know?

17th Century

1800

LavoisierOxidation

1900

PlanckQuantization

NewtonGravitation

BaconInstauration

LutherReformation

ColumbusNavigation

2000

Us

17001600

Robt. Hooke(1635-1703)

1500

CopernicusRevolution

Hooke (1665)

Science & Force Laws Electron bonds: observation

&quantum

mechanics

Development ofthe Organic

Structural Model

Yale Chemistry 1901S

Greek symbols denote substituent positions.

Cf. Clairvoyant

Benzene

Sheffield Chemistry Lab (SSS)

(only quantitative tool)

Yale Chemistry 1901S

BalanceBurettes

Analytical Balances Were Not Portable

Quantitative Tools?

C. Mahlon Kline (1901S)

Kline Chemistry Laboratory

(1964)

Kline Biology Tower

(1965)

Quartz

Silliman Crystal

Silliman Crystal

Boyle Lavoisier

Berzelius etc.

Wöhler/Liebig

Genealogy

GenealogyBottom

Genealogy Top

End of Lecture 18Oct. 15, 2008