Subject: semantics : a summary

From: Alexandre Hocquet <[email-masked]>
Date: Thu, 26 Jun 1997 20:47:46 +0400

Dear CCLers,
I have recently posted a message regarding the different possible
interpretations of the expression "molecular modelling" in the CCL
community. Thanks to all who replied.
The answers seemed to converge on the fact that two different
common interpretations may be understood (as defined in my original
 posting) and that the "classical methods"  definition originates in that
part of the "community" involved with drug design, biomolecular
modelling, etc...
Quite surprinsingly, the debate that followed focused on definitions
of "computational chemistry", a theme that has been already discussed
 (again see original message).
Anyway, be it computational chemistry or molecular modelling, it appears
that everyone has his definition, depending on what computational
chemistry (or what molecular modelling) he is involved in.
Should this situation linger on, as a proof that computational chemistry is
interdisciplinary , or do we need something like a iupac definition (as
apparently such a thing does not exist) ? Well, i guess this is another
discussion...
By the way, thanks to Georg Schrekenbach for his spelling enlightment.
Both spellings seem acceptable...

The original message  :

Dear CCLers,
While Boyd and Lipkowitz once intended to review definitions of 
"computational chemistry" (Reviews in Computational Chemistry, Vol 1, page vii),
the words "molecular modelling" still appear confusing to me :
While it seems logical to think that "molecular modelling" is that part
of "computational chemistry" that describes behaviour of molecules by
 the formalism of some theoretical model, there seems to exist in the 
community a much more restrictive use of "molecular modelling".
This second definition could be "Use of any non quantum mechanics model
 to describe the behaviour of molecules".
If one looks at the scope of the Journal of Molecular Modeling, no 
semi empirical, ab initio, dft methods are quoted, while the general 
guidelines state that "The Journal of Molecular Modeling will cover
all aspects of computational chemistry".
Another example, the ICCCRE XII congress divides the scientific program
in different topics. Amongst them :
- Semi empirical and Ab initio quantum chemistry, dft methods
- Molecular Modeling, QSAR

Any hints on a proper definition ?
Any historical reason for different uses of "molecular modelling" ?
And, above all, one or two l ?

The replies that did not appear directly in the CCL :

Alexandre ,
	In my humble opinion the term "molecular modelling" is indeed
confusing at best, i think that in most circumstances the term is used
where "molecular mechanics" would be better - i.e. solving classical
equations of motion. (and both can be abrieviated to "MM")

	noj

-- 
Dr. Noj Malcolm			
Theory Group,			
Dept. of Chemistry,		
University of Manchester,	
Oxford Road,			
Manchester.			
M13 9PL			

	Yo estoy de acuerdo con la definicion que das antes, son tecnicas 
de quimica computacional que permiten simular o medelar sistemas 
moleculares a travez de formulismo de modelos teoricos, yo pienso que no 
se restringen exclusivamente a metodos no-QM, lo que pasa es que en 
general se atribuye el termino de modelado molecular a tecnicas usadas en 
biomoleculas o en macromoleculas en general, y con tal cantidad de atomos 
quedan descartado los metodos de QM, si se quieres analizar todo esa 
macromolecula... en todo caso hay varios trabajos que mezclan tenicas de 
dinamica molecular y de QM, primero estudiando las conformaciones de la 
macromolecula con DM y luego en un entorno mas especifico, el sitio 
activo (con mucho menos atomos), con QM. La otra tecnica que creo que ha 
cobrado gran interes son los metodos hibridos QM/MM, en dosnde se definen 
zonas QM y zonas MM, se mezclan los Hamiltonianos de las zonas QM con los 
Potenciales de MM, y "ojo" que no se tienen malos resultados en cuanto a 
calculos de delta G, y otras energias. 
En resumen, el molecular modelling, a mi juicio, no esta restringido 
estrictamente a metodos no-QM, sino que a todos los metodos para 
simulacion de sistemas macromoleculares, especilemente de interes 
biologico, tal vez por la estrecha relacion que existe entre molecular 
modelling y "molecular desing", de gran interes en la industrias 
Farmaceuticas

Espero que te ayuda en algo esto, nos vemos en algun congreso!

Danilo Gonzalez.
Universidad de Santiago de Chile
Facultad de Quimica y Biologia
http://quimbio.usach.cl/~danilo/

Hi Alexandre,

this sounds like an interesting question so a summary in the CCL
would be appreciated. I have seen both of your definitions with the second
one being more often used (to increase confusion, you can also add
"simulation" vs. "modelling" ...).

One more little comment

>And, above all, one or two l ?

My dictionary (Langenscheidt English - German) doesn't contain
 "model(l)ing", however, for "model(l)er" both one and two l are offered
without any preference.

Regards, Georg

You raise an interesting point.

> Any hints on a proper definition ?

For some reason, "molecular modeling" is usually used to encompass
non-quantum-mechanical treatments of chemical structures.  In common
usage, it tends to refer to molecular mechanics as well as pure
visualization, and to things "in between", such as rule-based methods
for docking and hand-manipulation of structures, generally on a
computer.

I really don't have any good idea why or how the term got to
include these things and to exclude others, nor am I aware of
any formal definition.

Like your original comments, my sense of how the word is used
is based on how I've seen the term used -- not on any formal
definition I've seen.

	-P.

-- 
**** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) ***
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

Alexandre Hocquet

Facultad de Ciencias Fisicas
Universidad de Chile
Blanco Encalada, 2008
Santiago Centro
CHILE
fono : 56 2 678 45 19
fax : 56 2 696 73 59