Re: A gadfly forever..... (How far can you push semi-empirical

[radomski (- at -) mond1.ccrc.uga.EDU]

David Case wrote:
 >I too would enjoy hearing from people that know about this.  When I
 >wrote a review a few year ago [in "Conformational Analysis of
 >Medium-Sized Heterocycles", edited by Richard Glass] semiempirical
 >methods seemed to have very poor performance for non-bonded
 >interactions and hydrogen bonds -- things that are crucial to most
 >peptide and protein simulations.  Errors in barriers to rotation about
 >bonds, or in ring conformations (e.g. planar cylcopentane) were also
 >common.  But at that time, not much had been published with AM1,
 >although that appeared to give improved results in these areas.
 Both AM1 and PM3 yielded almost flat cyclopentane ring when run in full
 geometry optimization mode. The same goes for proline and both ribose
 and 2-deoxyribose. Which makes one to ask of what use is 'chemical
 meaningfulness' od semi-empirical parameters (as stated recently
 by Andy Holder) if the method cannot predict pentose pseudorotation?
 To put it differently - how far away is semiempirical parametrization
 good enough for flexible ring molecules?
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 Jan P. Radomski
 Department of Biochemistry,
 Complex Carbohydrate Research Center,
 University of Georgia,
 220 Riverbend Rd, Athens GA 30602 USA
 e-mail: radomski (- at -) mond1.ccrc.uga.edu
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