Subject: Re: CCL:Branched vs straight chain alkanes

From: [email-masked] (Per-Ola Norrby)
Date: Wed, 7 Aug 1996 19:21:02 +0200

Matthew Harbowy wrote:

>     My results for AM1 and MM+ show (Hyperchem 3.0 calculations)
>
>                         am1                mm+               exp
>
>     octane             -58.628            (6.448 s.e.)       -49.82
>
>     2,2,3,3,TMB        -40.155            (12.36 s.e.)       -53.99
>
>     -------------     ----------        --------------      ------------
>
>     oct - tmb          -18.473            -5.912              4.17
>
>
>     So, yes, it would seem that both semi-empirical systems *and*
>     molecular mechanics (which should work great) fail to reproduce the
>     experimental figures.

        The semi-empirical results are one thing, the molecular mechanics
something completely different.  You *CANNOT* use molecular mechanics
steric energies as heats of formation.  In fact, you can only compare
molecular mechanics steric energies when you have identical connectivities.
Naturally the steric energy of tmb is higher than oct, it is much more
congested.

        Of the molecular mechanics programs I'm aware of, only the true MM2
and MM3 from Allinger are able to estimate heats of formation.  (I don't
think any of the various MM2-copies out there includes this feature).  Even
in the Allinger programs, this feature is limited to a small number of
structural features for which corrections have been included.  However, the
alkanes are there.  The MM2(91) values for octane and tmb are given below
(in kcal/mol)

                            steric energy          heat of formation

    octane (all trans)          4.7433                  -53.59

          tmb                  11.7932                  -54.00

        As you can see, the trend is right.  I believe the value for octane
will get closer to the experimental value if you include the contributions
from other conformations.

        As for the AM1 values, energy errors average 1-2 kcal/mol even when
you compare conformations (Gundertofte et al, J.Comp.Chem. 12, 200, 1991),
so isomeric energies should have larger errors.  I'm a bit surprised by an
error of over 20 kcal/mol though, I had expected better.

        Per-Ola Norrby

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 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
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