Chemistry 125: Lecture 35 Understanding Molecular Structure and Energy through Standard Bonds Although molecular mechanics is imperfect, it is useful for.

Chemistry 125: Lecture 35

Understanding Molecular Structure and Energy

through Standard Bonds Although molecular mechanics is imperfect, it is useful for discussing molecular structure and energy in

terms of standard covalent bonds. Analysis of the Cambridge Structural Database shows that predicting

bond distances to within 1% required detailed categorization of bond types. Early attempts to predict

heats of combustion in terms of composition proved adequate for physiology, but not for chemistry.

Group- or bond-additivity schemes are useful for understanding heats of formation, especially when

corrected for strain. Heat of atomization is the natural target for bond-energy schemes, but experimental

measurement requires spectroscopic determination of the heat of atomization of elements in their standard

states.Synchronize when the speaker finishes saying

“…and the answer is yes.” Synchrony can be adjusted by using the pause(||) and run(>) controls.

For copyright notice see final page of this file

Are They “True”?

YESThey are indispensable.

Are Molecular MechanicsPrograms Useful?

NO

C

Br

•

••

••

van der WaalsRadius

Br•••BrContact

Br neighborpositions

from manycrystals(CSD)

Nyburg & Faerman, Acta Crystallographica B41, 274-279 (1985)

C

Br

•

•To balance attractive and repulsive

forces between neighboring molecules, the closest atoms must be "too" close.

Bromineatoms

seem notto be

spherical!

MolecularMechanicsProgramsAssume

They Are!

?

Br•••BrContact

Angiostatinanti-cancer drug

“We optimized kringle 1 with the AM1 method using Gaussian 03.Plasminogen kringle 1 contains 1200 atoms, which are made up of

642 heavy atoms and 578 hydrogen atoms. The job takes about650 optimization steps starting from the MM+ geometry.”

M. J. Frisch, Gaussian, Inc., 2003

largest molecule

calculated byquantum

mechanics

Despite its problemsMM is necessaryfor complex structures

Is the standard Structural Model

realistic in geometric detail?

X-Ray Diffraction

Cambridge Structural DatabaseT

otal

X-R

ay S

truc

ture

s

YearAtomsper

Structure 27 44 54 73

>500,000predictedby 2010

30,572,792atomic

positionsJan 2008

http://www.ccdc.cam.ac.uk

>40,000,000BONDS

CSD1

CSD1

Number ofMean BondLengths Tabulated.(specialized because ofinfluence of neighborson precise bond distance)

175CC

97CN

119CO

119 different types of CO bonds27 different typesof Csp3-Csp3 bonds

CSD1

mean high1/4

median low1/4

#obs

stddev

3

C* meansC bearingC,H only

C# meansany Csp3

crowdingstretches bond

evenmoreso

shortlong

R2CH CR3

R2CH CHR2

R3C CR3

RCH2 CH3

R2CH CH3

R3CH CH3

~1%

C-C bond lengths

single 1.53 Ådouble 1.32triple 1.18

aromatic 1.38(one-and-a-half bonds)

single: sp3-sp2 1.50 sp2-sp2 1.46

N to

Caromatic

BondLengths

N Planar N Pyramidal

N

N+

_

poor overlap

Twist

Bimodal?

N

:

••

How Complex Must a Model beto Predict Useful Structures?

To get standard deviations in bond distance of 0.015Å(~1%) the Cambridge crew defined:

682 kinds of bonds altogether

175 different kinds of CC bonds(differing in multiplicity, hybridization,

attached groups, rings, etc.)

97 different types of CN bonds

119 different types of CO bonds

We want to understand all “Stuff”

Its Properties & Transformations

Key:Structure & Energy

Bonds?

How Standard are Bond Energies?

Obviously there will be correction for conformation and strain,

but is there an underlying energy for composition or constitution?

Adolph Oppenheim: On the Relationship of Heat of Combustion with the Constitution of Substances.

1868

Ludimar Hermann: On the Regularity and Calculation of Heat of Combustion of Organic Compounds. By a frequently expressed need of physiology to be able to calculate heats of combustion, I have been led to study the current situation…

HCombustion by C / H Content?

SubstanceCarbons

atoms/moleHydrogensatoms/mole

Theory Hcombust

kcal/moleError

kcal/moleError

%

Graphite [1] 0 -94.05 - -

Hydrogen 0 2 -57.8 - -

c-Hexane 6 12 -911.1 -881.6 -29.5 -3

c-Hexanol 6 12 -911.1 -842.7 -68.4 -8

Ethene 2 4 -303.7

Glucose 6 12 -911.1 -670.4 -240.7 -36

Not too bad for fuel purposes, especially if one were to include some kind of correction for partial oxidation.

[-57.8] per H2

[-94.05] per C

= 2 94.05 + 2 57.8

H2C=CH2 has extra energy to give off. One of its bonds () is not very stabilizing,

so it starts unusually high in energy.

O1

O6

partially"pre-oxidized"

-316.2 +12.5 +4

Composition:Atom Additivity

How Complex Must a Model be to Predict Chemically Useful Energies?

For physiology purposes you might be content with ± 5% in heat of combustion.

But for predicting the equilibrium constant between c-hexane and c-hexanol, being off

by 1% (9 kcal/mole) means being off

in Keq by a factor ofA useful model must go beyond composition.

How about constitution?

107!

C6H12

Energy

-911.1

= -29.5

CO2 / H2O

graphite / hydrogen

-881.6Hcombustion

Hformation

Ene

rgy

(kca

l/m

ole)

Comparedto What?

easilymeasured

How to measure?

( elements in their “standard states”)

Hf

APPENDIX I

HEATS OF FORMATION

From Streitwieser, Heathcock, & Kosower

Hf

APPENDIX I

HEATS OF FORMATION

From Streitwieser, Heathcock, & Kosower

Hf

APPENDIX I

HEATS OF FORMATION

From Streitwieser, Heathcock, & Kosower

formationcyclo

minimum

Expt. - Theory

Hf + n 4.9

Group Additivity

“unstrained”

2 -4.9 = -9.8

StrainlessTheory

(n -4.9)

?

From Streitwieser, Heathcock, & Kosower

“Transannular” Strain

similar

c-hexane

c-octane

Small-Ring Strain

ve Bond Energies

Can one sum bond energies to getuseful "Heats of Atomization"?

Bond Additivity (between atoms and groups)

From Streitwieser, Heathcock, & Kosower

How well can “Bond Energies”

predict Hatomization?

Where does Hatomization come from?

C6H12

Energy1680.1

atoms

Hatomization 1650.6

-911.1 -29.5

CO2 / H2O

graphite / hydrogen

-881.6Hcombustion

Hformation

Ene

rgy

(kca

l/m

ole)

Comparedto What?

How CanYou KnowHformation

for an atom?

= - 881.6

+ 911.1

+ 1650.6

How to measure?

Atom Energy from Spectroscopy

lightenergy

X-Y

X + Y

H-H 104.2 kcal/mole (Hf H = 52.1)

O=O 119.2 kcal/mole (Hf O = 59.6)

CO 257.3 kcal/mole

X* + YMaybe this is the observed transition at 257.3?

141? 257.3

Hf C=O = -26.4

Hf H 02___

Hf O 02___

X*’+ YOr maybe this is the observed transition at 257.3?

125? 257.3

spectroscopic value precise, but uncertain

Which to choose?

CO

Hf C

Hf O

graphite O2

C + O

graphite O

(Hf C = 171.3)

But Nobel Laureates Worried.

End of Lecture 35Dec. 5, 2008

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