From cletner@remcure.bmb.wright.edu Tue Apr 19 12:39:36 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id MAA02656; Tue, 19 Apr 1994 12:06:43 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA22165; Tue, 19 Apr 94 11:55:16 -0700 Date: Tue, 19 Apr 1994 10:48:46 -0700 (PDT) From: Charles Letner Subject: Re: CCL:Semiempirical parameterization yet again... To: Computational Chemistry List In-Reply-To: <01HBBXIOSRFQ9S3U9X@VAX1.UMKC.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Apr 1994 AHOLDER@VAX1.UMKC.EDU wrote: > ("The snake oil salesman mounted the soapbox to confront the angry > crowd. He began to speak:") > ... > I can safely say that MM has nothing to do with chemistry, > but is more or less a fit to a convenient set of functions. It > does have chemical validity in that it gives us good answers to some > questions. > QM is an entirely different situation, in that the actual arbiters of > chemistry, the electrons, are treated directly by mathematical functions. > The chemistry come OUT of a model that describes the electrons. > ... > ("The snake oil salesman descends from the soapbox to thunderous applause.") ("Then the one lone dissenter humbly approaches the soapbox.") I'd like to address the issue that MM "has nothing to do with chemistry". How can this be? Is this to imply that molecular structure is not in the realm of chemistry? MM invokes the Born-Oppenhimer approximation (a QM idea if I'm not mistaken) to allow us to ignore electrons. Of course by doing this we have to leave bond making and bond breaking (electronic processes) behind. However, nuclear motions are still allowed. Because MM takes a more simplified approach to modeling structure than does QM does not mean it has nothing to do with chemistry. However MM force fields do have terms that model chemical phenomenon. Examples include bond angles, bond lengths, etc. Granted, these are parmeterized based on chemical data. However, they do attempt to model chemically meaningfull aspects of molecular structure. Further, is not any mathmatical fomalism a model? This is to include QM, a more detailed and complicated model of atomic events. Yes, QM may have a higher level of theory involed than does MM but that does not relegate MM to the pesudo-chemistry domain. Each has their place in solving chemical problems. There are questions that MM can answer that QM and semi-emperical methods can not yet answer because of practical conciderations (Size of molecules). This is not to imply that MM can answer any question that QM can. Remember, processes that involve electrons have been left behind with this model of molecular structure. It is fair to say that one aspect of computational chemistry is knowing which methods can answer the question possed in the most efficent way. ("And with this the lone dissenter prays to the god that be that his life will be spared by the restless crowd") Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435