Subject: CCL: Branched vs straight chain alkanes

From: [email-masked] (Alan Shusterman)
Date: 07 Aug 96 11:10:52 PDT

--- Matthew Harbowy wrote:
So, yes, it would seem that both semi-empirical systems *and* molecular
mechanics (which should work great) fail to reproduce the experimental figures.
     
Or, I've made a mistake.
--- end of quote ---

A number of comments (such as the one above) regarding AM1 and MM+, and their
apparent inability to reproduce the effect of branching on experimental heats
of formation are misplaced.

First, molecular mechanics strain energies (MM+) should never, by themselves,
be used to compare heats of formation of geometric isomers, such as octane and
2,2,3,3-tetramethylbutane.  Different parameters are used to calculate the
strain energies of geometric isomers.  Therefore, even if both isomers were
calculated to have identical energies they might still have different heats of
formation.  Strain energy comparisons are only useful for stereoisomers,
conformational isomers, and other molecules whose energies are calculated using
identical parameters.

Second, as has already been remarked by others, AM1 (and PM3) heats of
formation do not reproduce experimental heats of formation with arbitrary
precision.  This was never claimed by the inventors of these methods, and
thousands of calculations have borne this out.  "Typical" errors for these
methods are in the range of 5-10 kcal/mol, but much larger errors are
frequently encountered.

Third, it is important before complaining about poor computational results to
analyze the results correctly.  This means taking a good look at the structure
of the calculated molecule.  Many of the molecular formulas that have recently
been attributed to various hydrocarbons and carbocations have been incorrect
(note: it is much easier to identify the correct formula when a graphical model
is used than when a Z matrix is used, but one must still be careful).

Fourth, 2,2,3,3-tetramethylbutane is hardly a typical "branched" hydrocarbon. 
Although it is highly branched and should, therefore, have a "low" heat of
formation, it is also very crowded, and this should raise its heat of
formation, i.e., its heat of formation results from compensating factors.  This
is borne out by the following series of C8 experimental heats of formation:
octane (-49.8), 4-methylheptane (-50.7), 2,2-dimethylhexane (-53.7),
2,5-dimethylhexane (-53.2), 2,2,3,3-tetramethylbutane (-54.0).

By the way, AM1 provides reasonable estimates of these heats of formation for
all but two molecules: octane (-58.5), 4-methylheptane (-54.9),
2,2-dimethylhexane (-51.2), 2,5-dimethylhexane (-53.3),
2,2,3,3-tetramethylbutane (-40.0).  Three of the errors are less than 5
kcal/mol, and only one is greater than 10 kcal/mol.  Not bad, but not useful
for comparing the effects of branching.  Unfortunately, while one might have
guessed that the most crowded molecule, 2,2,3,3-tetramethylbutane, would be the
most difficult to model correctly, one would not have guessed that the most
"normal" molecule, octane, would be the next worse in this series.

Modeling is not for the careless.

Alan Shusterman
Department of Chemistry
Reed College
Portland, OR  97202