[Molecularmechanics] molecule

[Pengyu Ren]

>At 10:25 07/11/2003 -0600, Pengyu Ren wrote:
>>Hi Konrad
>>
>>I just took a quick look at the two proposals by you and David. David's 
>>certainly more specific to protein. In your proposal two however each 
>>residue/fragment is a "molecule" (why can't we just call it fragment?). 
>>It's then easy to make a new molecule by resuing fragment libraries.
>
>"molecule" is re-used from CML, I assume. The downside is that it may refer 
>to things that people feel are not "molecule"s. [Computers don't care.] 
>That might bias people against its use. The upside is that there is already 
>a lot of usage in CML, including software, that will support <molecule> 
>elements.

>The golden rule is that for each element you create you will probably have 
>to write a class and document the semantics. If someone has already written 
>that class you can probably re-use it. So whereas CML might use <fragment>, 
><group> or similar term it complicates the software.
>
I couldn't careless how it is called, as long as I see/understand the semantics.

>When fragments are assembled into a macromolecule do you wish to preserve 
>the fragment identity? If so, what for? The chemical properties? The 
>protein hierarchy? the forcefield? the structural unit? It will be useful 
>to define the semantics, regardless of what it is called.
>

For visualization, structural allignment etc. it's desire to know what are the fragments (backbone, side chain, alpha carbon,....). For forcefield calculations, we are using fragment libraries to preserve electrostatic and vdw parameters.  All bond, angle and torsion parameters are defined for specific combinations, so the neighbor "molecule" will obviously matter.


>FWIW here are IUPAC's definitions
>
>molecule
>An electrically neutral entity consisting of more than one atom (n > 1).
>Rigorously, a molecule, in which n > 1 must correspond to a depression
>on the potential energy surface that is deep enough to confine at least one
>vibrational state.

According to this we couldn't call an ion "molecule", even though they are "molecular entity" -;)

>
>molecular entity
>
>Any constitutionally or isotopically distinct atom, molecule, ion, ion pair,
>radical, radical ion, complex, conformer etc., identifiable as a separately
>distinguishable entity.
>Molecular entity is used in this Compendium as a general term for singular
>entities, irrespective of their nature, while chemical species stands for sets
>or ensembles of molecular entities. Note that the name of a compound may
>refer to the respective molecular entity or to the chemical species, e.g.
>methane, may mean a single molecule of CH4 (molecular entity) or a molar
>amount, specified or not (chemical species), participating in a reaction.
>The degree of precision necessary to describe a molecular entity depends
>on the context. For example 'hydrogen molecule' is an adequate definition
>of a certain molecular entity for some purposes, whereas for others it is
>necessary to distinguish the electronic state and/or vibrational state and/or
>nuclear spin, etc. of the hydrogen molecule.
>1994, 66, 1142
>IUPAC Compendium of Chemical Terminology 2nd Edition (1997)
>
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