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| From: |
pitsel()at()chemul.uni.lodz.pl (Piotr Seliger) |
| Date: |
Thu, 2 Nov 95 8:19:11 MEZ |
| Subject: |
summary AM1 vs PM3 |
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 | aholder;at;cctr.umkc.edu
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 burke -AatT- camden.rutgers.edu
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: mako %-% at %-% pdi.lodz.pl, sopekmir %-% at %-% mitr.p.lodz.pl
---------------------------------------------------------------
*******************************************************************************
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 kgu-: at :-lundbeck.dk
***************************************************************************
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: pitsel - at - chemul.uni.lodz.pl the right to life" (G.B.Shaw)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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