Subject: Which Company Would Consider A Novel Proposal?

From: [email-masked] (Yu-Ran Luo)
Date: Thu, 18 Jul 1996 00:41:08 -0500 (CDT)

Which Company Would Consider A Novel Proposal?

>Hi, Neters,
>
>     Are you interested to predict BOND DISSOCIATION ENERGIES (BDEs)
>in large organic species ?
>
>     You know, the BDEs are considered to be fundamental to chemistry and
>biochemistry. However, about thousands of the experimental BDEs values in
>organic species are available today although several hundreds of research
>groups measured for sixty years.
>
>     We thus need theory to help enlarge our knowledge. Here I would share a
>good news with you. 
>
>     I found a reliable and simple method for predicting BDEs during the past
>nine years. It is most powerful to large organic, organometallic and
>biologically active species. Now the values of trillions of BDEs can be
>estimated easily by my approach and a calculator (not computer so far!). The
>large-size species include biologically active species (eg., Vitamins A, C, D,
>E, K), drugs (nicotine, hormones), toxicant, explosives/energetic materials
>(eg., TNT, RDX, NTO), fuels/coals and so on. Once an organic molecular
>structure is drawn, I can quickly point out where the weakest bond is, how
>large this BDE is, what the stability and reactivity of this molecule are, and
>which position in this molecule will react first (active site or reaction
>center). These predictions will save a lot of money and time for scientists
>and engineers, and very useful for the computer-aided molecular design. 
>
>     You may give me a test. Which molecules you are interested? Please show
>me and draw the structures. I would give you the answers ASAP.  
>
>     I hope my research will be a new and powerful tool for chemistry,
>chemical engineering, energy science, molecular biology, medicinal chemistry,
>protein/enzyme chemistry. Why is the human visual system sensitive only to
>light of wavelengths from about 760 to 380 nm? Why is "super-vitamin E"
>possible? Which structure is a super-vitamin E? I can give quantitative
>answers now. The main reason is that I can describe the species energetics and
>its change/transfer. 
>
>     My method is different from MO theory, FDT, MM and the group additivity.
>But my results can compare with the FDT calculations based new Gaussian
>package and supercomputer. 
>
>     My method is a key to open the unknown door of molecular energetics.
>Some scientists thus advised me to make an electronic version of my method and
>link it with a good software available so that you only play a mouse and
>keyboard when predicting the BDEs. This is a good suggestion. You know, there
>are so many chemical/biochemical software companies. Unfortunately, they have
>not known my method. 
>
>     Which company would consider this project and make this link? Please
>tell me. My proposal is 
>     
>     My Method For BDEs + A Best Structure Software  ---> A New Program
>
>          Thank you for your attention.
>
>          Yu-Ran Luo, Ph. D.
>   (3100 Verbena Drive, Plano, TX 75075, Phone and Fax 214-509-2075, 
>   E-Mail:  [email-masked])

From [email-masked] Jul 27 10:55:40 1996
Date: Fri, 5 Jul 1996 12:06:02 -0500 (CDT)
From: YONG HUANG <[email-masked]>
To: [email-masked]
Subject: From CCL archive ---------Yong (Texas A&M)
Status: RO
Content-Length: 17524

From:	SMTP%"[email-masked]"  2-NOV-1995 06:52:30.77
To:	Y0H8797
CC:	
Subj:	CCL:G:summary AM1 vs PM3

From: [email-masked] (Piotr Seliger)
To: [email-masked], [email-masked], [email-masked],
        moralega%a1@lldmpc
Subject: CCL:G:summary AM1 vs PM3
Date: Thu, 2 Nov 95 8:19:11 MEZ
Sender: Computational Chemistry List <[email-masked]>

This is the summary of the responses I got to my request about 
AM1 vs PM3 references.

Thanks for help.
----------------

*****************************************************************************

Dear Dr. Seliger,

Following is a note that I sent to the next over a year ago.  Perhaps it will 
be informative.  Our SAM1 papers also extensively documented PMs vs AM1 as 
well as SAM1.  The references for these are:

1. Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003.
2. Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627.
3. Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; 
Smith, D. A.;  American Chemical Society, Washington, DC, 
1994; pp 113.

Please let me know if I can be of further assistance

Regards, Andy Holder

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 
UUUU  UUU MMM   MMKK KKKK   CCCC   |           ANDREW J. HOLDER
 UU    U   MM   MMK   K    CC  CC  | Assoc. Prof. of Comp./Org. Chemistry
 UU    U   MMM M MK KK    CCC      |          Dept. of Chemistry
 UU    U   M MM  MK   KK   CC  CC  |  University of Missouri-Kansas City
  UUUUU   MMM M MMKK   KK   CCCC   |         Kansas City, MO  64110
                        KK         |          [email-masked]
                          K        |  (816) 235-2293, FAX (816) 235-5502
 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

Netters,

   A few weeks ago, Jeffrey Nauss asked about a comparison between the AM1 and
PM3 semiempirical methods.  Both of these semiempirical methods are
included in most programs that support semiempirical calculations (AMPAC,
MOPAC, etc.).  Please note that the following discussion is MY OPINION and 
a compendium of MY EXPERIENCES.  I hope you find it somewhat useful.   

   The lead references to each method follows:

AM1: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J.
        P. J. Am. Chem. Soc. 1985, 107, 3902.

PM3: Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209.

   AM1 stands for "Austin Model 1" and PM3 stands for "Parameterization 
Method 3".  Both methods implement the same basic NDDO theory pioneered 
by Michael Dewar while at the University of Texas at Austin.  The differ-
erence is in how the parameters that the semiempirical methods utilize to 
replace portions of the full ab initio implementation of Hartree-Fock theory.
   Perhaps the most important difference between AM1 and PM3 is the
involvement of the researcher in the parameterization process.  PM3 was
developed using a largely undirected mathematical optimization process
with greatly reduced guidance from chemical knowledge or intuition,  an 
addition that the Dewar methods consider essential.  The human
researcher knows for which molecules it is necessary to obtain the best fit.
For instance, it is useless to obtain parameters for carbon and hydrogen that
describe the properties of cubane correctly if the results for benzene are
significantly different from experiment.  An attentive and knowledgeable
chemist can also guide the search into areas of the parameter hypersurface 
that make sense as far as the absolute magnitude of the parameters themselves 
are concerned.  As with many chemical properties, the parameter values should 
vary periodically.  While this should not unduly constrain the final values,
parameters should follow well-defined general trends for proper interaction
with other elements.
    In terms of the actual NDDO model, the actual parameters allowed to vary 
in the two methods are quite different.  In AM1, a large number of values we
used from spectroscopy for some of the one-center terms and the other
parameters derived with these values fixed.  (This is possible only for the
lighter elements in the Main Group.)  PM3 allowed ALL of these values to 
float, resulting in substantially more parameters.
    AM1 also had a quite different concept as to the application of the
Guassian functions introduced with AM1 to adjust the core-electron/core-
electron repulsion function.  Workers in the Dewar group and subsequently 
in my group see Gaussian functions as PATCHES to the theory, not integral 
parts.  All models fail at some point and the Gaussians were introduced 
to help with some of the systematic errors in MNDO.  Traditionally, these 
patches were applied to adjust for difficult molecular systems AFTER 
semiempirical parameters were stabilized.  PM3 includes these Gaussian 
functions (two for each element) FROM THE BEGINNING.  Our experience 
indicates that in such a situtaion, the chemistry os the element will 
very likely be very strongly effected by the presence of these functions 
and the importance of the "real", "chemical" parameters will be reduced 
and swallowed up bu the Gaussians.   In short, Gaussians should only be 
used where absolutely needed, and then viewed with askance.  
    The essence of the difference between the two philosophies is evident:
the theoretical basis for the method is either accepted or denied.  
Significant approximations are made to gain the speed advantage that 
semiempirical methods enjoy over their ab initio quantum mechanical 
brethren.  But both the ab initio and semiempirical models are based on 
the Hartree-Fock set of ideas.  These ideas possess theoretical rigor as 
regards solution of the Schrodinger Equation.  If one simply views the 
semiempirical parameters as adjustables within a curve-fit scheme rather 
than as components of a theoretical model, little faith or importance 
resides in the meaning of their final values.  Simply put, the method of 
parameterization described above and used so successfully with AM1 and 
MNDO (and now SAM1) expresses confidence in the theory.  With a firmer 
footing in chemical reality, AM1 parameters are more likely to yield 
useful results for situations not specifically included in the molecular 
basis set for parameterization (MBSP).

                      Some Practical Considerations
                      -----------------------------
   The differences in errors between the two methods as published are 
minimal, but that does not relate the real story of how the methods perform
differently.  Some key points:

  -  PM3 is clearly better for NO2 compounds as a larger number of these
      were included in the MBSP.

  -  PM3 is usually a little better for geometries, as these were also 
      heavily weighted.

  -  The molecular orbital picture with PM3 is usually different from that
      expected or that predicted by other methods.  This is a direct 
      consequence of the lack of attention paid to the absolute values of 
      Uss and Upp.  It can be seen in the lack of performance in ionization 
      potentials.

  -  PM3 charges are usually unreliable, again a result of the rather strange
      values that some of the parameters take on, even when other experimental
      data such as heats of formation and geometries are acceptable.  This
      makes PM3 essentially useless for the derivation of molecular m echanics
      force fields.  Perhaps the best known example of this is the case of 
      formamide.  The partial charges for the atoms in the molecules are 
      listed below.  The lack of any appreciable charge on N has led to a 
      reversal of the actual bond dipole between C and N in this molecule!

         Atom        AM1       PM3           HF/6-31G*
         ---------------------------------------------
          O       -0.3706    -0.3692         -0.5541
          C        0.2575     0.2141          0.5079
          N       -0.4483    -0.0311         -0.8835

                  O
                 //
               H-C
                 \
                  NH2

  -  Several papers have been published describing the performance of
      AM1 vs. PM3:

Dewar, M. J. S.; Healy, E. F.; Yuan, Y.-C.; Holder, A. J. J. Comput. Chem.
      1990, 11, 541.
Smith, D.A.  J. Fluor. Chem. 1990, 50, 427
Smith, D.A.; Ulmer, C.W.; Gilbert, M.J.  J. Comput. Chem. 1992, 13, 640.

  -  Most reserachers in my experience have stopped using PM3 and have
      returned to AM1. 

             An Example of Parameterization Values for Aluminum
             --------------------------------------------------
        Parameter              AM1            MNDO             PM3     

        Uss, eV            -24.353585      -23.807097      -24.845404
        Upp, eV            -18.363645      -17.519878      -22.264159
        zetas, au            1.516593                        1.70288
                                          }  1.444161
        zetap, au            1.306347                        1.073269
        betas, eV           -3.866822                       -0.594301
                                          } -2.670284
        betap, eV           -2.317146                       -0.956550
        alpha                1.976586        1.868839        1.521073

        Gaussians:
        Intensity #1, eV     0.090000          -            -0.473090
        Width #1            12.392443          -             1.915825
        Position #1          2.050394          -             1.451728
        Intensity #2, eV        -              -            -0.154051
        Width #2                -              -             6.005086
        Position #2             -              -             2.51997

    The point on the potential surface located by PM3 is significantly
different than that located by AM1.  This is immediately apparent from the 
large discrepancy between the Upp values.  These are the important one-
electron energy values and they have strong influence on the parameter 
hypersurface.  Also, the difference between Uss and Upp for both MNDO and AM1 
is about 6 eV.  This has been reduced to 2.5 eV in PM3.  The real difficulty,
however, is in the Beta values.  These parameters are the two-center/one-
electron resonance terms and are responsible for bonding interactions between 
atoms.  The PM3 values are almost zero, resulting in the conclusion that 
there is very little bonding between atoms involving aluminum!  (Note that 
the AM1 values for betas and betap spread out around the single MNDO value 
for beta.  This suggests that the MNDO values were reasonable and AM1 adds 
greater flexibility.)  PM3 regains the bonding interactions lost in the low 
beta values with two strongly attractive Gaussians spanning the bonding 
region.

*******************************************************************************

We did a short note on rotational barriers in branched alkenes: L. A. Burke et
al. J. Physical Organic Chem vol 5,614-616(1992). We were surprised at the time
that no one else seemed to have published such results.

Luke Anthony Burke              tel:609-225-6158
Department of Chemistry	        fax:609-225-6506
Rutgers University              e-mail:
Camden, NJ 08102                [email-masked]
USA

******************************************************************************

The comparison of AM1 against PM3 has been quite recently
discussed on this list. You may try to search trough
archives.
My three pens to that discuss may be that AM1 absolutely
incorrectly describes interaction in small water clusters;
while it was known that it gives not correct hydrogen
bond geometry for dimers - I found that it also fails
for geometry of larger systems: tetramers, octamers etc.
The geometry is absolutely different from what we expect
for such clusters (as known from ab-initio and MD studies).
In the same time PM3 reproduces these geometries acceptably
good - difference in oxygen position between PM3 and HF/6-31G*
is ~ 0.1 A for octamers.
This is a reason that I am now using PM3 in my Molecular Dynamics
studies that use semi-empirical energy surface to derive forces
(kind of "quantum" dynamics).

Mirek
---------------------------------------------------------------
dr Miroslaw Sopek
MAKO-LAB Computer Graphics Laboratory
ul. Piotrkowska 102a
90-026 LODZ, POLAND
tel. (48)(42)332946,322346
fax. (48)(42)332937
e-mail: [email-masked], [email-masked]
---------------------------------------------------------------

*******************************************************************************

1995  Oct 28

Recently the NET was asked for refs to (1) AM1 compared to PM3, and
(2) Sigma-aromaticity.  Here are some refs:

AM1 cf. PM3

1)  Extensive comparison: J Computer-Aided Molecular Design, 4 (1990) Issue 1
    (Special issue) ; discusses PM3, AM1 and MNDO
2)  W. Thiel, Tetrahedron, 44 (1988) 7393
3)  J. J. P. Stewart, J Comp Chem 11 (1990) 543
                                  10 (1989) 209
                                  10 (1989) 221
                                  12 (1991) 320
4)  Dewar et al J Comp Chem 11 (1990) 541
5)  Smith et al J Comp Chem 13 (1992) 640
6)  In a letter to the Net (1995), Andy Holder (SemiChem) said:
        PM3 is better than AM1 for NO2 compounds and usually a little better
        for geom's.  It is not as good for MO's and is unreliable for charges.

Sigma-aromaticity

1)  M. J. S. Dewar "Chemical Implications of Sigma Conjugation"
        J Am Chem Soc 106 (1984) 669
2)  Inagaki et al  JACS 116 (1994) 5954
3)  Ichikawa et al  J Phys Chem 99 (1995) 2307
4)  Hiberty et al  JACS 117 (1995) 7760
===========
Errol Lewars  Chem Dept Trent U, Peterborough  Ontario  Canada
=====

*****************************************************************************8

Piotr-

    We have a  paper in press with Spectrochimica Acta comparing AM1 and PM3
for the prediction of carboxylate stretches.  Briefly, PM3 is much closer in
absolute terms, but AM1 represents differences between compounds more reliably.
  This is a very limited specific application, of course, and probably only
useful to spectroscopists.  I would be interested in hearing what others have
to say about more general comparisons.

Regards,  Steve Cabaniss

******************************************************************************

If you mean comparison of conformational energies you might want to have a 
look at our paper in J.Comp:Chem. 12, 200 (1991).

Kind Regards

*       Klaus Gundertofte
*       Head,  Department of Computational Chemistry
*       H.Lundbeck A/S
*       Ottiliavej 9
*       DK-2500 Valby - Denmark              Fax   +45  3630 1385
*                                            Phone +45  3644 2425-3206
*       E-mail [email-masked]

***************************************************************************

Hi Piotr,

The performance of this methods in relation to which property ?
If you are interested in heats of formation both are OK
with about the same results.
For minimum energy conformations PM3 has lots of problems.
I performed many calculations with PM3, AM1 and ab initio
and PM3 is qualitatively wrong in most cases.
For electronic properties I didn't tried PM3.

Best regards,

Edgardo Garcia
Cristol Chem & Biochem
University of Colorado
BOULDER CO   USA

****************************************************************************

Note:

%0 Journal Article
%A Gano, J.E.
%A Jacob, E.J.
%A Roesner, R.
%D 1991
%T Evaluation of PM3, AM1, and MNDO  for Calculation of Higher Energy
Ionization Potentials
%B J. Computat. Chem.
%V 12
%P 127-134

James E. Gano, Director
Instrumentation Center in Arts and Sciences
University of Toledo
Toledo, Ohio 43606

Instrumentation Center :  http://www.icenter.utoledo.edu
Department of Chemistry:  http://www.chem.utoledo.edu

419-530-7847
419-530-4033 (FAX)

******************************   THE END   *********************************
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Piotr Seliger                                  PPP  I  TTT  SSS  EEE  L 
  Department of General                          P P  I   T   S    E    L
  and Inorganic Chemistry,                       PPP  I   T   SSS  EE   L
  University of Lodz,                            P    I   T     S  E    L
  Narutowicza 68,                                P    I   T   SSS  EEE  LLL
  90-136 Lodz, POLAND
                                            "The right to knowledge is like
  E-mail: [email-masked]          the right to life" (G.B.Shaw)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~