Subject: A fire extinguisher/olive branch.

From: <[email-masked]>
Date: Wed, 20 Apr 1994 16:37:47 -0600 (CST)

Netters,

  Well, I stuck my foot in it again.  In trying to illustrate a point, it 
seems I used a bad illustration.  It also seems that some folks got upset
about that and took some of my comments a bit out of context and "went to
the weeds" as we say where I'm from.  I DID NOT say that molecular mech-
anics was not "REAL CHEMISTRY".  I DID NOT intend to convey any sense of
superiority about one model over another.  I WAS NOT being superior.  I
didn't even say I was doing "REAL CHEMISTRY" and other people
were not!  I DID NOT intend to offend anyone or to denigrate anyone else's 
work.  Let's take a quick look at what I DID say that apparently 
irritated some people:

>  The development of a semiempirical quantum mechanical model is indeed
>similar to the development of a molecular mechanics force field in that
>the objective is to reproduce experimental data.  That is about where
>the similarity ends.  The underlying guts of the models are totally
>different!  I can safely say that MM has nothing to do with chemistry,
>but is more or less a fit to a convenient set of functions.  It
>does have chemical validity in that it gives us good answers to some
>questions.
>  QM is an entirely different situation, in that the actual arbiters of
>chemistry, the electrons, are treated directly by mathematical functions.
>The chemistry come OUT of a model that describes the electrons.
>This may seem to be a matter of degree to some, but I think that it is an
>important distinction, especially as it finally applies to parameterization
>of quantum chemical models.

Let's also recall the context of my posting, which was semiempirical PARAM-
ETERIZATION.  I was using this section to set up the idea that parameter-
izing for specific properties is not the best choice.  My purpose was to
contrast and compare SE to MM because so many more people are familiar with
MM parameterization.  MM is a good chemical model.  In fact MM is a
WODERFUL model.  It does not do electronic properties, however, which is
why quite a number of us turn to quantum mechanics.  The derivation of
a general model such as AM1 requires an extraordinary care so that the
method reproduces many properties with acceptable accuracy.
This was my point, and my ONLY point.  I did not intend to attack MM.  It is 
a useful and valid tool (note how clearly I state this at the end of the 
first paragraph of the excerpt above).

I am not a scientific (or I hope any other type) of elitist.  (If you
knew where I came from in my early life, you'd know I couldn't afford to
be an elitist!) I simply expressed an opinion and was attacked.  Oh well, 
I can take that.  I enjoyed reading the comments of others that posted after 
me (and sent me private mail) with reasoned dis-agreements to my position.  
I am not married to my view, it is simply an opinion I hold and wanted to 
take an opportunity to express since some things had been said.  A number of 
people have expressed thanks for some of my previous postings in SE theory, 
where I have been working for a number of years.  It was my impression that
the list should primarily function as a forum for discussion and exchange of
information, which task I think it adequately performs.

In this regard, note that I am a SEMIEMPIRICAL researcher!  Some ab initio
workers call us "number-twiddlers"!  I readily admit that ab initio HF
theory will usually give a better and certainly more reliable answer than
semiempirical methods if they can be applied to the system.  Also, MM
usually does better for heats for formation and conformer energetics than
semiempirical.  See, I'm not an elitist, really, really

I fully agree with Dr. Burkhart's assertion about models and science.  Science
is indeed nothing but the construction of models in which to organize and
explain our data.  I get to teach General Chemistry I relatively frequently
as prt of my duties here at the University of Missouri-Kansas City.  I make
this point the first day bt telling the students that the "search for ultimate
truth begins down the hall in religion class.  This is science.  We are
in the business of building and expanding models to help our limited brains
understand a universe that is otherwise far too complex for comprehension."
When I was with Michael Dewar, he made a point of convincing all of us that
the "religion of models" was doomed to failure, because a better one will 
always come along.

Anyhow, I hope that this clears up that I am NOT an elitist and that I DO
think that molecular mechanics is worthwhile.  It is quite painful for me to
learn these lessons in public, but I will try to be more precise with my 
wording in the future if I can ever work up the nerve to post to the CC 
list again.  (That last part was a joke.)

Finally, I would like to say something about context that probably applies to
all forms of electronic communication, where it seems a lot of us spend a
substantial amount of time.  It is quite easy to MISS THE CONTEXT of someone's
statements when looking at an e-mail message because there are no verbal
or physical (body-language) clues.  It is also easy to READ IN meaning where
none was intended.  I constantly guard against this, and seemed to have let
myself slip by not being as clear as possible with my statements in the 
original posting.  I would like to call for all of us to give one another
the benefit of the doubt in future discussions.  If you say to yourself
"He/she/it COULDN'T mean that!", they probably didn't.  Why not check
privately with them?  Let's allow reason to re-assert itself.

   Andy Holder

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
                              DR. ANDREW HOLDER
             Assistant Professor of Computational/Organic Chemistry

Department of Chemistry              ||
University of Missouri - Kansas City ||  Internet Addr: [email-masked]
Spencer Chemistry, Room 315          ||  Phone Number:  (816) 235-2293
Kansas City, Missouri 64110          ||  FAX Number:    (816) 235-5502
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=