RE: Discussion #2

["Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>]

How about this approach -- instead of trying to agree on
a definition of a molecule, should we not be trying to clearly
state a reasonable set of chemical views of matter and, where
possible the relationships snd/or transormations among those
views, as has already been started for macromolecules.
The graph-based approaches, chemical formulae, 3-D structures,
charge density maps, residue-based polymeric descriptions,
all have something to say about have various chemical entities
can interact with other chemical entities, which is, after all,
what Chemistry is all about.
     -- Herbert




At 5:47 PM -0500 12/1/03, Bollinger, John Clayton wrote:
>David Brown wrote:
>
>[...]
>
>>      HDF, coming at this problem from a different direction,
>>  expressed shock at the thought that the chemists have no
>>  unique way of defining a molecule.
>>
>>      From what I learned at the workshop, chemists not only
>>  have no unique way of defining a molecule, they don't even
>>  care!  Most of the ontologies
>>  (dictionaries) being developed in chemistry are, like CIF, closely
>>  related to
>>  an experimental technique where the question of defining a
>>  molecule is not important.  Peter Murray-Rust's CML defines a
>>  molecule as a composed of
>>  atoms,
>>  but leaves it to the author to state which atoms.  Miloslav
>>  Nic in Prague is developing GTML (Graph Theory Mark-up
>>  Language) which can be used for molecular descriptions, but
>>  this also assumes that the molecular graph is already known.
>
>[...]
>
>>  properties.  The use of graph theory separates out the
>>  intrinsically chemical concepts from the graph theoretical
>>  description that can be manipulated mathematically.
>>
>>      The bond graph represents a chemical interpretation of
>>  the 3D geometry, i.e., the geometry tells us which atoms are
>>  neighbours but not where the
>>  bonds
>>  are to be found.  The bonds are assigned by applying various rules
>>  relating to
>>  the chemical properties of the atoms.  However, not all bonds
>>  are of equal value; some are clearly stronger than others,
>>  i.e., they survive many of the physical and chemical
>>  treatments we can subject them to such as melting or
>>  dissolution in a solvent.  Weaker bonds do not survive this
>>  treatment.
>  > We can
>  > thus imagine that each of the possible edges in the graph is
>  > associated
>  > with a
>  > number representing its 'strength'.  (The 'strength' would be
>  > zero for the edges that could not possibly represent a
>>  chemical bond).  I will
>>  deliberately
>>  avoid defining in detail what I mean by 'strength', but
>>  qualitatively it represents the number of electron pairs
>>  associated with the bond and it
>>  obeys
>>  (by definition in some treatments) the rule that the sum of
>>  the bond 'strengths' received by any atom is equal to the
>>  number of valence electrons the atom uses for bonding. 
>>  (Implicit in this description is the notion
>>  that a
>>  bond 'strength' is not restricted to integer values).  For
>>  over a century chemists have struggled to find a tight
>>  quantitative definition for bond 'strength' under such names
>>  as bond order, bond number, bond valence, electrostatic bond
>>  strength, etc., each definition trying to capture the concept
>>  in numeric form.  All of these definitions are incomplete in
>>  one way or another, but in principle they allow us to order
>>  the bonds from strongest to weakest.  Assuming that we can at
>>  least determine this order even if we cannot assign actual
>>  numbers to the bond 'strength', our problem then
>>  reduces
>>  to the question of where to place the cut-off between the
>>  bonds that are
>>  shown
>>  on the graph and those that are omitted.
>
>[...]
>
>>      Before we try to define CIF items for particular chemical
>>  concepts, we need to have a consensus about the definition of
>>  a molecule.  I have
>>  made some
>>  suggestions above, and I would be interested in people's
>>  comments.  Is graph theory a fruitful way to go or should we
>>  take a different approach? 
>  > What are
>>  the problems we might encounter using the approach described above?
>
>I find the idea of relating chemical properties to a bond graph to be
>rather attractive, although I confess to the influence of a bit of
>background in formal mathematics.
>
>One aspect that David left unexplored is the possibility of applying
>multiple properties to bond graph edges.  One need not choose a single
>measure of bond strength, nor make measures of bond strength the only
>properties a bond graph edge may have.  For instance, one could apply an
>explicit bond categorization (e.g. "covalent", "dative", "hydrogen
>bond", "non-bond").  One could also express purely chemical information,
>such as the fact that "this is the bond that is broken in the course of
>the von Foo reaction".  CIF is conveniently flexible in this regard, as
>authors may include exactly the properties they wish to describe while
>ignoring all others.
>
>One oddity I see with that approach is that the interatomic distances
>currently described by _geom_bond_distance fit nicely into the
>collection of properties that could be associated with bond graph edges,
>but many other _geom_* items do not.  Graph theorists do have concepts
>that could be applied there, but we must take care to avoid making CIF
>(more) incomprehensible to mere mortals.  Perhaps, though, it does make
>sense to consider whether all the various geom_* categories should be
>subsumed into a scheme such as this -- they are all examples of data
>that have both crystallographic significance and chemical significance.
>
>As chemists in general have no single consistent definition of a
>molecule, it would be fruitless for us to attempt to impose a universal
>one of our own in hopes of satisfying everyone.  The alternatives I see
>are
>
>(1) to choose our own definition for CIF purposes and use it
>consistently;
>(2) to support diverse CIF items with which to describe multiple
>different molecule concepts;
>(3) to provide sufficient data for a chemist to apply his or her own
>definition of "molecule"; or
>(4) to attempt to ignore molecules altogether.
>
>Although (4) is perhaps most true to pure crystallography, I think it is
>least suitable for our purpose.  Option (2) strikes me as inelegant and
>short-sighted.  Option (1) might be feasible if we could actually come
>up with a suitable definition, but I question whether that is possible.
>That leaves option (3), to which category I would assign most
>applications of the bond graph approach that I have imagined so far.
>
>
>John Bollinger
>
>--
>
>John C. Bollinger, Ph.D.
>Indiana University
>Molecular Structure Center
>
>jobollin@indiana.edu
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-- 
=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
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