From AHOLDER@VAX1.UMKC.EDU  Fri Jun 25 10:05:50 1993
Date: Fri, 25 Jun 1993 15:05:50 -0500 (CDT)
From: AHOLDER@VAX1.UMKC.EDU
Subject: SAM1 reference and assorted comments following
To: CHEMISTRY@ccl.net
Message-Id: <01GZSSNQIWX2AOKE3K@VAX1.UMKC.EDU>


Netters,

  In a recent posting, Graham Hurst at Hypercube is "disturbed" at
the publication of results without a thorough description of the model
being present.  I have spoken with Graham on the phone since I received
his note and I had a few points I wanted to make:

1.  He did not obtain the paper and examine it before making his
    statement.

2.  The paper DOES contain a limited discussion of the method.  A more
    detailed explanation may be found in James Ruiz's dissertation
    as published at the University of Texas at Austin in 1990, which 
    is clearly referenced in the paper.

3.  This paper was submitted, refereed, and accepted by knowledgeable
    scientists as a preliminary description of work of high interest
    to the chemical community in a journal that somewhat specializes
    in that activity.  It will be followed up by a more complete
    paper.  The purpose of this paper was to allow users to make
    independent conclusions about the performance of the new method
    on classes of compounds of interest to them.  This is in keeping
    with the formats of the MNDO and AM1 papers.

4.  It should be noted that, whatever is stated to the contrary, suff-
    icient detail will be published on SAM1 so that other establishments
    and individuals will be able to generate reproducible code.  Note
    that none of MJS Dewar's previous methods could have been coded 
    from scratch as many have claimed, (see above) without reference 
    to the code itself, either MOPAC or AMPAC.  it is impossible to 
    obtain completely correct results for AM1
    and MNDO from the papers alone.  Certain special corrections were
    omitted from publication due to an oversight.  (These corrections
    form the subject of another paper to be released shortly.)

So, while Dr. Hurst's point is well-taken and fully subscribed to by me
both in my capacity as a university researcher and president of
Semichem, there is no intention to "hide" anything.  
I understand the sensitivity of this issue and I am committed to the pur-
suit of science in an open atmosphere.  I also realize that other scientists 
must be able to reproduce our results for them to be considered valid.

The development of SAM1 is my primary research activity
at UMKC, but Semichem is also spending money to develop this method and
will be giving it to the scientific community freely.  We withold only our 
code. We have completed a number of non-d-orbital parameter-
izations and these are what is presented in the referenced paper.  The
d-orbital work is under way, but not to a sufficient stage to be desc-
ribed in any detail, as we are not yet sure how it will turn out when
the model is finalized.

It should be noted, however, that some interests are not scientific, but
competitive.  This aspect of the situation seems to be of the most 
concern to Dr. Hurst and Hypercube.  This company includes a number
of Michael Dewar's previously released methods in their software.

Iam committed to keeping AMPAC development and my scientific activities
as divided as possible.  This is not always as clear as I would like,
but I do my best.  Please give me the benefit of the doubt whenever
possible.  I will be more than happy to discuss the details of this with
anyone who wishes to pursue the matter further.

   Andy Holder