Subject: Summary Interaction

From: [email-masked] (Palavo Subramanian)
Date: Mon, 10 Oct 94 12:53:41 CDT

Hi,
  Sometime back I had posted a query regarding using MOPAC to calculate
interaction energy of octane, I have summarised all the responses that 
I recd.  Thank you all for the responses The general consensus seems
to be to use MM rather than semi-empirical procedures.

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        A quick tip:  One of the main (long-range) interactions between
alkanes is London dispersion forces.  As these are an effect of electron
correlation, you will not be able to account for these using a semi-empiric
calculation (eg, MOPAC).
        If you want a result, use a molecular mechanics method.  MM2 and
MM3 are parameterized to reproduce alkane heats of sublimation, so
interactions between octanes should be OK (at least in MM3).
        If you want to get a non-MM, non-experimental result (why would
you?), you have to go to fairly large ab initio methods with electron
correlation.

        Per-Ola Norrby

 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
 *  Internet: [email-masked]

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I've found that you can only get quasi-decent interaction energies using MOPAC
for materials that have strong H-bonding interactions, like base pairs in DNA.
For weaker interactions, you won't get much of anywhere, which is the case
for octane.  

There's a program called AMYR that lets you calculate the interactions between
2 *rigid* molecules that WILL give you results for weaker interactions, but
won't compute any structural changes.

For the full treatment, you'd be better off using a properly parametrised 
force field & molecular dynamics.  I assume texaco has some sort of library
service?  A search ought to reveal some references.

I had a file with references to AMYR somewhere, but can't seem to locate it
right now, sorry...

Good luck,
Irene Newhouse
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I would have thought that you would want to calculate the interaction of the 
octane molecules using a MD package as opposed to Mopac.  Simply duplicate 
the basic molecule and turn it loose in a periodic box.  Knowing the energy 
of an individual molecule and determining the energy of the liquid you would 
come up with an interaction energy.  Because the geometry of two interacting 
molecules is highly variable, it seems it would be extremely tedious to do 
using a semi-empirical technique.  You can do MD using semi-empirical 
techniques in Hyperchem but to handle more than a couple of molecules would 
be very time consuming.      

Ross Underhill
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With regard to using MNDO for calculating the intereaction energy
of octane or any weakly intereaction system, it is possible in 
a computational sense, i.e. one will get a number, but the results
are of no particularly value (not publishable in a well reviewed 
journal).

Why?  Semiempirical methods present in MOPAC were not developed for 
weak interaction calcutions. The interaction energies would be
weak in such a case (less than 1-2 kcal),which is far smaller than
the standard deviation errors of the method. Even in ab initio theory,
where basis set composition, basis set superposition error, and
correlation can be taken into account the interaction energy between
two alkanes would be a formidable calculation. 

One method which has been used in computing crystallization enthalpies
is Allinger's molecular mechanics programs, espcially those which 
take into account dispersion terms. Since there are no strong dipole
dipole intereactions, the interaction energy in alkcanes is dominated
by dispersion forces, and the van der Waals type interaction potentials
used in some modeling schemes will take into account this. 

Good luck

Earl Evleth 
*********************************************************************** 
There's no big problem DOING the type of calculation you are attempting:

>    I am interested in calculating interaction energies between 2 
> octane molecules. I would like to use MOPAC.  Could someone let me know 
> as to how I should go about setting the calculation etc. ( I am 
> assuming that this can be done using MOPAC!). 

It would be another matter, however, to get MEANINGFUL results.  If an 
interaction energy for a specific geometry is adequate (a geometry from an X-
ray Crystal Structure, for instance) then you could just input the geometry 
with two octanes and calculate the enthalpy and subtract the enthalpy of a 
single octane.  (If you need free energies, you will need to do a FORCE 
calculation to include the entropy, but an XRD geometry will not be suitable: 
you will have to optimize the geometry within the semi-empirical method.  
Otherwise, you will end up with negative eigenvalues and the frequency 
calculations will be meaningless.)

If you are trying to study the interaction energy in the bulk liquid, there 
are two problems.
 1) You will need to consider the many possible conformations and 
orientations of the two octanes relative to each other.  You could generate a 
set of representative starting geometries to sample the real distribution, 
then optimize each, calculate the energies, and calculate a weighted average 
(assuming a Boltzman distribution).  This would not be a pleasant task to do 
manually with Mopac, although I have done this sort of thing.  Even then, you 
will not be sure how accurately your sample represents the true distribution 
(especially if you missed the most stable configuration which would be the 
major contributor to the energy).  A Monte Carlo, or Molecular Dynamics type 
code which uses AM1 or PM3 energy calculations would do a more proper job of 
sampling, but I don't know of a commercial product to recommend.
 2) In my experience, I have not found Mopac (or any of the semi-empirical 
Hamiltonians) to represent long range interactions (ie. intermolecular) very 
accurately:  it is difficult to even find stable geometries for molecule 
pairs.  For your type problem, I would expect Molecular Mechanics to provide 
better answers.  MM is what is typically used in the commercial Molecular 
Dynamics and Monte Carlo codes, anyway, and hydrocarbons should be handled 
particularly well.

I hope this helps.

                                        EC

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Unfortunately I stripped off the header info. while saving and some
of the respondents email info. is missing.  My apologies for that.
Once again thank you all for taking the time.

P.S.Subramanian
[email-masked]