|
|
| From: |
"Park, Tae-Yun" <tp &$at$& elptrs7.rug.ac.be> |
| Date: |
Thu, 1 Aug 1996 12:59:34 +0200 (DFT) |
| Subject: |
Summary of my earlier questions, answers & thanks(part 1 of 3) |
Dear all,
During last a few weeks, I posted several questions
on my Ph.D. work to CCL, which is related to comput-
ataional chemistry field.
Hereby, I summerized my questions and answers from
many CCLers, which gave me a great help. I have
decided to post this summary since there are other
CCLers who want to know what I have got from this
e-mail communication.
Let me express my deep thanks to all the CCL members
who are interested in my questions and sending me
impressive and helpful answers. Especially, I'd like
to express my sincere thanks to Mr. Ernest Chamot
who sent me a detailed and valuable message which
give me a great help and encoregement.
What I'm afraid now is that this summary would be
too long to send by e-mail so that it occupies too
much disk space. Please execuse me if this message
creates any disk space problem on your mail box.
Sincerely,
Park, TAE-YUN
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
State University of Ghent
Laboratorium voor Petrochemische Techniek
Krijgslaan 281, Blok S5
9000 Gent, Belgium
TEL:+(32)-0(9)-264-4527
FAX:+(32)-0(9)-264-4999
e-mail: tp "-at-" elptrs7.rug.ac.be
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
-------------------------------------------------------
PART I
subject: HELP!(urgent):theoretical discrimication
& software
-------------------------------------------------------
####################(questions)########################
*** About the structure of surface carbenium ions and
symmetry number ***
First thing I have to calculate is the symmetry number
of surface carbenium ions on the zeolite surface, which
is formed by protonation of various olefins.
1. How can we describe the bonding of carbenuim
ions to the surface? Is the bonding more
ionic or covalent? I know the proton is surely
covalently bound, but it is less clear for the
case of hydrocarbons(more exactly olefins) adsorbed
on zeolite.
2. What is the symmetry number for such surface carbenium
ions comparing with corresponding gas phase carbenium
ions? In most cases, I believe, the symmetry number
of surface ions are identical with those in gas phase,
if there is no 2-fold axes.
Consider the following examples.
C
\
C-C+-C (secondary ion in gas phase)
/
C
symmetry number=3*3*3=27
C
\
C-C-C (secondary ion on the surface)
/ |
C |
--(+)--
symmetry number=3*3*3=27
If there is two-fold axes, however,
C
\
2-fold axes.....C+-C-C (tertiary ion in gas phase)
/
C
symmetry number=(3*3*3)*2=54
C
\
Not a 2-fold axes(?)...C+-C-C (tertiary on the surface)
/|
C |
--(+)--
symmetry number=3*3*3=27
I think the surface ion loose its 2-fold axes due to
the bonding to the catalyst surface.
I just want to know whether those approach to calculate the
symmetry number of surface carbenium ions is theoretically
correct. To check this point, I think, the bonding of carbenium
ions to the surface should be defined first, in a certain way
of theoretical approach.
**** About the structure of activated complex ******
Next problem that I have to solve is concerning the structure
of activated complex in transition state for beta-scission.
That is, an elementary step representing beta-scission,
R1 ---> (Transition State) ----> R2 + O
where R1 and R2 are the reactant and product carbenium ion,
respectively, and O is the product olefin.
What I want to know is the structure of the activated complex
in the transition state, as detailed as possible in a certain
theoretical way; how many bonds are related, which bonds are to
be broken, which bond will be formed, and what does the activated
complex look like(is it more like carbenium ion or more like
olefin?), etc.
**** About heat of formation for gas phase carbenium ions ***
My final question is about the calculation of thermodynamic data,
more exactly, the heat of formation of gas-phase carbenium ions.
Recently, a solution to solve the problem associated with
the large number of the parameters has been considered, i.e,
by applying the "Polanyi relation". This relation needs
only relative differences in heat of reactions in each elementary
steps. This means that the heat of formation for the surface
carbenium ions are not necessary, but, at least, heat of formation
of gas-phase carbenium ions appearing in the reaction network
should be given. Unfortunately, only limited amount of data
can be found in the literature, so that some analytical method
to calculate the heat of formation is necessary.
Benson's group contribution method has been known as one of
the most approprate way to calculate the thermodydamic properties.
The group contribution value of positively-charged carbon atom
involved in the carbenium ions is, however, not available at
the moment.
The only solution I found recently is using a certain quantum
chemistry package such as "MOPAC". My question is that is this
a suitable package (accurate enough) to calculate the heat of
formation data I need? If so, how can I obtain a copy of this
package? If not, is there any other software in the field of
computational chemistry to calculate these data?
*************** End of my questions *************************
#####################(answers)##########################
From echamot(-(at)-)xnet.comSat Jul 27 10:23:18 1996
Date: Thu, 27 Jun 96 14:25:24 EDT
From: Ernest Chamot
To: "Park, Tae-Yun"
Subject: Re: CCL:M:HELP!(urgent):theoretical discrimication & software
Hi TAE-YUN,
I'm sure you realize you are taking on quite a task for your research:
>I'm a ph.D. student of State University of Ghent, Belgium.
>I'm working with zeolite HZSM-5. The goal of my work is
>to develop a detailed kinetic model for hydrocarbon
>transformation process over HZSM-5 catalyst.
A tremendous amount of research has gone into working out the kinetics for
the strictly thermal processes of cracking hydrocarbons to olefins. The
catalytic process is, of course, more complicated. And zeolites in
particular have been subject to a great deal of study, both theoretically
and experimentally, just to understand the nature of their catalysis, not to
mention working out the detailed kinetics that result as a consequence. I
have done some work in both areas, so I offer the following observations in
addition to some specific responses to your query.
1) The mechanism that leads to the formation of olefins (among other
products) from hydrocarbons is very complicated. The beta scission reaction
to eliminate an olefin from a free radical is the dominant process in the
thermal reaction of light hydrocarbons. This cascade takes place in
competition with an array of rearangement reactions and cyclizations (which
lead to aromatics and ultimately to coke). I am attaching a .gif file of
part of the mechanism showing this cascade and a few of the rearrangement
reactions. (I had a more complete mechanism, showing the steps leading to
various cyclics and aromatics and coke precursors, but I can't lay my hand
on it at the moment.)
2) The same mechanism applies to the carbenium ion process (initiated by
"acid" catalysis), except the relative rates will be different. The
rearrangement and cyclization reactions are known to be much faster,
relative to the beta-scission. (The major reason a cracking catalyst for
hydrocarbons to light olefins has never been commercialized is due to the
fact that zeolites and other acid catalysts all coke virtually
instantaneously at temperatures at which olefins are favored
thermodynamically over paraffins.)
3) One way zeolite catalysts exhibit selectivity is by imposing geometrical
constraints upon the "activated complex" of the reactant and the catalytic
site, as you propose studying. More commonly, observed selectivities are
due to geometric constraints on either the ingress of reactants or the
egress of products: all possible products can form within the pores, but
only the ones that can fit through the pores to get out are observed. Other
products stay inside and continue to reversibly interconvert back to
reactants and forward to the mix of potential products. Hence, the
energetics of the "activated complex" as affected by the geometric
constraints about the acidic site inside a zeolite pore will only be
relavent for reactions with both reactants and products small enough to pass
completely unhindered into and out of the zeolite pores.
So far as your specific questions:
>I have some urgent questions for my ph.D. work, which have
>been discussed with many people who were in the field of
>chemical engineering/organic chemistry/electrical chemistry
>in my university or in the internet.
>
>So far, I could not get reliable solutions, which have stuck
>me for relatively long time. During searching for the solutions,
>I realized that the best people who can give me an advice are
>in the field of computational chemistry.
>
>Please take some time to read the following questions
>and give me some informaion/advice if it doesn't bother
>you too much.
>
>
>*** About the structure of surface carbenium ions and symmetry number ***
>
>First thing I have to calculate is the symmetry number
>of surface carbenium ions on the zeolite surface, which
>is formed by protonation of various olefins.
>
>1. How can we describe the bonding of carbenuim
> ions to the surface? Is the bonding more
> ionic or covalent? I know the proton is surely
> covalently bound, but it is less clear for the
> case of hydrocarbons(more exactly olefins) adsorbed
> on zeolite.
If you really mean to model the "surface" of the zeolite, you will have to
consider a combination of sites, all contributing to an overall reaction.
There are several sites within a zeolite that can be acidic, depending on
where the trivalent atom (Al, B, etc.) substitutes for the tetravalent atom
(Si), forcing the adjacent oxygen to be capped with an acidic hydrogen:
O O O O O O
| H+ | | | | |
- Si - O - Al(-) - O - Si - vs. - Si - O - Si - O - Si -
| | | | | |
O O O O O O
These are referred to as "T sites" based on the labeling of the definitive
XRD data: T1, T2, T3, ... T8 for the MFI class of zeolites (ZSM-5) for
instance. A great deal of computational studies have gone into trying to
determine which sites are the catalytically active ones, but although
several claim to have determined the preferred sites or the active sites,
none are without serious questions. The only calculations (in my opinion)
that aren't seriously flawed by either unrealistic assumptions about the
geometry or by electronically unrealistic choice of model compounds (to make
the calculations tractable) are those by Tony Hess's group, and the most
recent work of van Santen's group:
Teunissen, Jansen, and R. A. van Santen, J. Phys. Chem., 99, 1873-9 (1995)
(and references therein to A. Hess).
"Surface" sites will be constructed from each of these T-sites with one or
more connections missing. Here again, there is a continuing argument as to
what you end up with. Some have assumed everything ends up with hydroxyl
caps. Others are convinced that there are extra bridging oxygens, etc.
H H+ H
/ / /
O O O O O
| | | / \ / \
- Si - O - Al(-) - O - Si - vs. -Si- O -Si- O -Si- O -Si-
| | | | | | |
O O O O O O O
There is also continuing discussion of whether the "acidic" site is a
Bronsted acid (H+) or a Lewis acid (RO3Al), usually depending on whether the
reaction conditions are such that elimination of water would be expected.
Basically, although there is plenty of opinion, there is no consensus on
either where "the" active acid site is in a zeolite, or what that site looks
like. You will need to pick what you believe is most reasonable and either
prove it, or at least be consistent with it when you associate an olefin
with the site, or create an ion pair by protonation of the olefin next to
the site.
>2. What is the symmetry number for such surface carbenium
> ions comparing with corresponding gas phase carbenium
> ions? In most cases, I believe, the symmetry number
> of surface ions are identical with those in gas phase,
> if there is no 2-fold axes.
As there is not a consensus on the structure of the acidic site, the
structure of the activated complexes which incorporate the site is not
known. Much modeling has assumed there is symmetry (at least a plane of
symmetry, and sometimes 2 planes of symmetry), but this is definitely not
correct. In a zeolite the different T sites each occupy unique assymetric
centers. The only way there could be any element of symmetry in an absolute
sense would be for every unit cell of the zeolite to also have a similarly
bonded activated complex at the same time. This is not a reasonable
expectation.
Local symmetry may be more important than absolute symmetry, however. For
this, you would have to consider each of the T sites in the zeolite you are
interested in, and decide how locally you want to define the system. Then
there may be a few sites with a local plane of symmetry, but for the most
part these won't be symmetric either. Calculations I had done on the T2
site in MFI zeolites showed that you will have to include at least 2 layers
of silicon-oxygen bonds away from the acidic site to even directionally
calculate the relative acidities of aluminosilicates and borosilicates.
E. Chamot, Modeling Acid Sites in MFI Zeolites with Realistic Geometric
Constraints," Preprints Division of Petroleum Chemistry, Inc. Vol 37, No. 2,
ACS San Francisco Meeting, March, 1992.
I assume the symmetry "number" you are asking about is defined by the
engineering software or method you are planning on using to predict energies
(CHETAH? Benson?) Chemically, the symmetry group would be C1: no elements
of symmetry, unless by coincidence one of the sites nearly has 2-fold
symmetry when considered locally. (Orienting the carbenium ion next to the
active site will not increase the symmetry, obviously, only decrease the
symmetry.)
>
>**** About the structure of activated complex ******
>
>Next problem that I have to solve is concerning the structure
>of activated complex in transition state for beta-scission.
>
>That is, an elementary step representing beta-scission,
>
> R1 ---> (Transition State) ----> R2 + O
>
>where R1 and R2 are the reactant and product carbenium ion,
>respectively, and O is the product olefin.
>
>What I want to know is the structure of the activated complex
>in the transition state, as detailed as possible in a certain
>theoretical way; how many bonds are related, which bonds are to
>be broken, which bond will be formed, and what does the activated
>complex look like(is it more like carbenium ion or more like
>olefin?), etc.
>
>Is there any reference/software to describe the structure
>of activated complex for this reaction in a theoretical way?
This is something that would be quite amenable to computation, once one
determined the appropriate structure of the catalytic site to use when
building the activated complex. A Quantum Mechanical method would have no
problem determining where bonds actually existed, what the atom-atom
distances and angles were, or how the electronics would reorganize to
distribute partial charges and bonds. The software is certainly there, but
again, I am not aware of any consensus on the correct system to model, however.
>**** About heat of formation for gas phase carbenium ions ***
>
>My final question is about the calculation of thermodynamic data,
>more exactly, the heat of formation of gas-phase carbenium ions.
.
.
.
>The only solution I found recently is using a certain quantum
>chemistry package such as "MOPAC". My question is that is this
>a suitable package (accurate enough) to calculate the heat of
>formation data I need?
Yes, this would be an entirely appropriate use of computational chemistry:
calculating a thermodynamic value or series of thermodynamic values that are
difficult to come by experimentally. MOPAC will do this quite easily, and
should be able to handle molecules and ions large enough for your purposes
(up to 70-100 atoms with reasonable compute power.) Moreover, although one
normally thinks of zeolites as inorganic, the zeolite structure turns out to
be very covalent in nature and MOPAC (which contains parameters for Si and
Al) works very well for modeling the system when compared to high level ab
initio calculations (see Hess's work).
As you point out, you need to consider the accuracy of the calculation. Ab
initio methods can always be made more accurate, but you rapidly become
limited by how large a molecule you can handle: you may be limited to C6 and
less (especially if you are to consider all isomers.) Heats of formation
have been calculated with MOPAC using the AM1 parameterization and in the
case of a series of cations the calculations reproduced the experimentally
available data to within 4.7 kcal on the average:
Dewar, Zoebisch, Healy, and Stewart, J. Amer. Chem. Soc., 13, 3901 (1985).
Not too exciting, but if you can use RELATIVE energies (especially between
"isodesmic" reactions) you can probably do a lot better.
> If so, how can I obtain a copy of this
>package? If not, is there any other software in the field of
>computational chemistry to calculate these data?
MOPAC is available in several forms. I believe some version of it is still
available from the QCPE for a nominal charge. It is sold as part of the
CAChe worksystem (which includes a very easy to use interface, and standard
procedures already built for using MOPAC), and by MSI/Biosym. The
parameters themselves (AM1 and PM3) are part of both Spartan and HyperChem.
The URL's I have for these organizations are:
CAChe
http://www.oxmol.com/
MSI/Biosym
http://www.msi.com/
Spartan
http://wavefun.com/
HyperChem
http://www.hyper.com/
Good luck. And as a final piece of advice, make sure you carve out a piece
of this problem that is doable.
EC
---
Ernest Chamot
Consultant in Computational Chemistry Applications
Chamot Laboratories, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
(708) 637-1559 (Voice & Fax)
echamot.,at,.xnet.com
http://www.xnet.com/~chamotlb
Enclosure: RxnScheme.GIF [14,877 bytes]
(I cut off this scheme due to its large size. If someone needs this
image, please contact me or Mr. Ernest Chamot)
From branch &$at$& acetsw.amat.comSat Jul 27 10:26:32 1996
Date: Mon, 24 Jun 1996 08:47:48 -0700 (PDT)
From: "Michael A. Branch"
To: "Park, Tae-Yun"
Subject: Re: CCL:M:HELP!(urgent):theoretical discrimication & software
contact Mike Schmidt (mike ( ( at ) ) si.fi.ameslab.gov) and ask him
if you can get a copy of GAMESS. It can do the transition
state searchs, IRC, etc.
good luck. Let me know if I can be of assistance.
Mike
---------------------------------------------------------
Michael A. Branch "I turn big problems into
Process Engineer, HDP-CVD little problems."
Applied Materials, Inc. (408) 563-0689
Santa Clara, CA 95051
mbranch %! at !% hammerhead.eecs.berkeley.edu
---------------------------------------------------------
From guojx -x- at -x- infoc3.icas.ac.cnSat Jul 27 10:41:06 1996
Date: Tue, 25 Jun 1996 08:16:02 +0900
From: Guo Jian-xin
To: "Park, Tae-Yun"
Subject: Re: CCL:M:HELP!(urgent):theoretical discrimication & software
Dear Park,
You can got the MOPAC software from the fellowing address at
anonymous FTP FTP.www.ccl.net
I am wondering what it mean " The Symmetry Number" in your mail, It
seems be connected with your questions.
Guo, Jian-xin
From JDA03546 (+ at +) niftyserve.or.jpSat Jul 27 10:42:37 1996
Date: Tue, 25 Jun 1996 13:24:00 +0900
From: "JDA03546 "at@at" niftyse"
To: "Park, Tae-Yun"
Subject: RE:CCL:M:HELP!(urgent):theoretical discr
Hi Park,
I'm studying zeolite by means of coputational techniques.
Regarding to your post, there are millions of literatures about
the computational simulations on zeolites, both by MD and MO.
So why don't you search the literature first?
Anyway, for the mechanism of the hydrocarbon cracking over zeolite,
you may start from the report by R. A. Santen, et. al. appeared on
Cat. Lett., 27, p345, 1994, and ibid. 28, p211, 1994.
Good luck.
---
Teraish Kazuo
TEL:0492-66-8375
FAX:0492-66-8359
E-MAIL:JDA03546 "-at-" niftyserve.or.jp
-------------------------------------------------------
PART II
Subject: Heat of formation calculation using MOPAC.
-------------------------------------------------------
####################(questions)########################
Hi!
I have a question on the parameters in MOPAC.
I'm tring to calculate the heat of formation
for more or less 100 different gas-phase
carbenium ions.
Which parameter would be suitable for this
calculation? PM3? AM1?
I tried to compare the results obtained
from MOPAC with a few experimental data
available in the literature, and found
that AM1 is much closer to those experimental
data than the case of PM3 when the molecule
contains the cabon atoms up to 5.
According to the manual of MOAPC, however,
PM3 is more improved parameter than AM1!
My question is that the AM1 would also produce
better result if the molecule becomes larger
(upto C8)?
Any suggestion would be greatly appreciated.
#####################(answers)##########################
From Y0H8797 : at : ACS.TAMU.EDUSat Jul 27 10:55:40 1996
Date: Fri, 5 Jul 1996 12:06:02 -0500 (CDT)
From: YONG HUANG
To: TP # - at - # elptrs7.rug.ac.be
Subject: From CCL archive ---------Yong (Texas A&M)
From: SMTP%"pitsel.,at,.chemul.uni.lodz.pl" 2-NOV-1995 06:52:30.77
To: Y0H8797
CC:
Subj: CCL:G:summary AM1 vs PM3
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From: pitsel \\at// chemul.uni.lodz.pl (Piotr Seliger)
X-Mailer: SCO System V Mail (version 3.2)
To: chemistry at.at ccl.net, jlye at.at tx.ncsu.edu, m.t.cronin at.at
livjm.ac.uk,
moralega%a1 : at : lldmpc
Subject: CCL:G:summary AM1 vs PM3
Date: Thu, 2 Nov 95 8:19:11 MEZ
Sender: Computational Chemistry List
Errors-To: ccl "-at-" www.ccl.net
Precedence: bulk
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 #*at*# 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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From ZUILHOF(-(at)-)rulgca.LeidenUniv.nlSat Jul 27 10:59:16 1996
Date: Sat, 06 Jul 1996 00:55:02 +0100 (MET)
From: Han Zuilhof
To: tp.,at,.elptrs7.rug.ac.be
Subject: carbenium ions
Dear Park,
Several years ago I've computed the stability of a variety of alkyl and
vinyl cations using AM1, PM3, and several ab initio methods. A preliminary
report on this was published: Tetrahedron Lett. 1994, 35, 265. In my
experinece AM1 is somewhat better than PM3. It makes no sense to go to
ab initio methods when one does not include correlation energy corrections.
MP2/6-31G*//6-31G* did best (even better than the MP3 equivalent) of the
methods we looked at (AM1, PM3, HF/6-31G*, MP2/6-31G*//6-31G* and
MP3/6-31G*//6-31G*). A full report on this issue should be published
soon. A copy of the chapter of my Ph. D. thesis -which deals in part with
this issue- can be obtained from: dr. Gerrit Lodder; Dept. of Chemistry,
Gorlaeus Laboratoria; Rijksuniversiteit Leiden; Postbus 9500; 2300 RA Leiden;
Nederland.
I hope this will help you. If I can assist you in any other way, please let me
know.
With best regards,
Han Zuilhof
******************************************************************************
** Dr. Han Zuilhof ** e-mail: ZUILHOF "-at-" chem.chem.rochester.edu
**
** Department of Chemistry ** (optional: ZUILHOF-0at0-rulgca.leidenuniv.nl)
**
** University of Rochester ** **
** Rochester, NY, 14627 ** Fax: (716) 473-6889 **
** USA ** Voice: (716) 275-2219 **
******************************************************************************
** **
** "Excite a photochemist!" **
** **
******************************************************************************
From echamot[ AT ]xnet.comSat Jul 27 11:01:35 1996
Date: Sun, 7 Jul 96 20:18:00 EDT
From: Ernest Chamot
To: "Park, Tae-Yun" elptrs7.rug.ac.be>
Subject: Re: CCL:M:Heat of formation calculation using MOPAC.
Hi TAE-YUN,
I haven't seen a head-to-head comparison of AM1 to PM3 specifically for
carbenium ion heats of formation, though there have been several published
comparisons of the two methods. I am not surprised, however, that you are
finding:
>AM1 is much closer to those experimental
>data than the case of PM3 when the molecule
>contains the cabon atoms up to 5.
Even though:
>According to the manual of MOAPC, however,
>PM3 is more improved parameter than AM1!
The main difference, relevant to your use, is that the AM1 parameterization
was developed to be theoretically consistent, whereas the PM3
parameterization was developed to most closely reproduce known experimental
data. That means that more molecules were used to develop the PM3
parameters than the AM1 parameters (something like 657 vs. 100), but most
experimental data is on stable, ground state molecules, so it isn't
necessarily as good for species not readily observed: transition states,
intermediates, etc. I would expect carbenium ions to be among those
difficult to observe species that are not well represented in the
parameterizations.
An old reference I have shows AM1 coming within 4.7 kcal rms error for a
series of cations. Is this comparable to the numbers you are getting? If
so, then yes, I would expect that:
>the AM1 would also produce
>better result if the molecule becomes larger
>(upto C8)?
EC
---
Ernest Chamot
Consultant in Computational Chemistry Applications
Chamot Laboratories, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
(708) 637-1559 (Voice & Fax)
echamot # - at - # xnet.com
http://www.xnet.com/~chamotlb
(Concluding Remarks for part II)
I concluded that AM1 is slightly better than PM3 for the
calculation of heat of formation for various carbenium ions.
Similar Messages
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06/24/1996: HELP!(urgent):theoretical discrimication & software
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03/02/1992: Oh, boy, oh, boy! Real scientific controversy!
08/01/1995: Spin contamination, effect on energy and structure.
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