Subject: PM3 summary

From: [email-masked] (Leif P. Olson)
Date: Wed, 8 Nov 1995 15:57:02 -0600

Greetings CCLers,

Last week I asked the question:

>A referee for a paper I submitted states that "PM3 is well-known to
>overestimate proton barrier heights".  He/she may be right (although   
>this has no effect on the conclusions in the paper), but in any case
>I need to find a specific reference which addresses this "well-known"
>fact.  I would appreciate it if someone could point me to such a 
>reference.
>
>Thank you.

Of course I should have specified proton *transfer* barrier heights.
Opinion was unanimous: the referee was right.  Here are the replies 
that I received, which directed me to several very nice papers...

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Hmmmm...  I'm not sure of a specific reference, but that does seem correct.  I 
know that MNDO does this.  I can point you to a reference where this was 
documented and you can take it from there.

Bofill, J. M.; Castells, J.; Olivella, S.; Sole, A. J. Org. Chem. 1988, 53, 
5148.

Hope that this helps.

Best regards, Andy Holder

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                    DR. ANDREW HOLDER
                         President
 
Semichem, Inc.            ||  Internet Addr: [email-masked]
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 Yes. It's true that semiempirical molecular orbital methods such as
 AM1 and PM3 tend to overestimate barrier involving proton transfer. The
 most obvious reason is that the heat of formation for proton is off by
 very large amount, so it affects the transition state too. I do not
 have any specifc reference other than my own. 
  Zheng, Y.-J.; Merz, K. M., Jr.; Farber, G. K. Protein Engineering 1993, 6
  , 479-484. Hope this is useful.  Yajun

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I think that the referee is right.
Unfortunately I do not know references about that problem, but my own 
work shows (J. Comput. Chem. 13, 860-866, 1992) that PM3 barriers for 
proton transfer are up to 300 % higher than ab initio/experimental values.
All the standard semiempirical methods are practically useless to 
describe accurately the hydrogen bonds. Both geometry and barriers are 
bad described with MNDO, AM1 or PM3. PM3 is better for geometries, but is 
worse than AM1 for barriers.
Only the modified semiempirical methods seem to provide a way to solve 
the hydrogen bond topic.

Best regards

Jesus Rodriguez
Departamento de Quimica Fisica
Facultad de Quimica, Universidad de Santiago
15706 Santiago de Compostela, SPAIN
e-mail: [email-masked]  

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Thanks to the respondents for solving my problem.  These references will
definitely be added to the paper.

Leif Olson, Ph.D.                       [email-masked]
Department of Structural Biology
Abbott Laboratories
Abbott Park, IL