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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
Copyright © J. M. McBride 2009. Some rights reserved. Except for cited third-party materials, and those used by visiting speakers, all content is licensed under a Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0).
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The following attribution may be used when reusing material that is not identified as third-party content: J. M. McBride, Chem 125. License: Creative Commons BY-NC-SA 3.0