Subject: Summary: Drawing Lewis structures

From: "Gurp, Ron van" <[email-masked]>
Date: Wed, 10 Feb 1999 08:32:57 +0100

Dear Netters,

Recently I posted the following question onto the list:
>
>We are looking for software (Linux/Windows95/98 or NT) that can draw Lewis
>structures of organic molecules, depicting all electron lone  pairs as well
>as bonding pairs. Is there any computer program  available that generates
>such structures semi-automatically? 
> 
As promised, here's my summary of your replies. 
Thanks to Douglas E. Stack, Dr. Dragan Lj. Vuckovic, Allan Adler, Kenward
Vaughan, Mark Forster and Dr. Wolf-D. Ihlenfeldt for your valuable remarks.
We are currently pursuing your tips and comments. 

1)	I recall seeing a program called "Beaker" do what you describe.
Unfortunately,
all I remember is the name, I don't know who markets this program.  It also
provided nomenclature, reaction predictions and other handy calculations on
organic structures.  Perhaps an internet search engine could locate a
seller.

Douglas E. Stack
[email-masked]

2)	EduChem HS has a Molecule Viewer that can generate 3D
Lewis structures automatically. Check our web page and our
downloadable demo (Molecule Viewer plus some  molecular
files) at http://www.etci.on.ca.

Dr. Dragan Lj. Vuckovic
[email-masked] ; [email-masked]
URL: http://www.etci.on.ca

3)	I asked about this several years ago. At the time, people referred
me to ChemTeX, which draws chemical formulas, but it doesn't seem
to handle Lewis structures. In Latex, one could probably use the
resident graphics capabilities to write macros or enhance the ones
that come with ChemTeX. If I were to do it, I would probably write
some programs directly in PostScript, but that is a matter of taste
and endurance.

Does "semi-automatically" imply that the program will figure out the
Lewis structure as well as draw it? The problem with that, in
my perception, is that, at least as it is described in textbooks,
the procedures for determining Lewis structures are not consistent.
There is an exception in the case of books which dumb down the rules
to apply only to a small class of examples (the "This is a course on
how to pass this course" approach), but let's not even mention that.

People have been complaining about this all the way back to Lewis, who
never intended that his innovation should be used to prop up the same
kind of arbitrary rule-based pedagogy about bonding that he himself had
to go through and which he had hoped to dispel by inventing Lewis
structures.
I have a list somewhere, guaranteed not to be complete, which I compiled
when I was thinking of writing an article about how screwed up pedagogy
seems to be on this point. I abandoned the project when I realized that
people have long complained about this in print and it has had no effect
whatsoever on pedagogical practice.

Apart from such inconsistencies, different authors try to do different
things with Lewis structures. For example, Wheland's book on resonance
has much fancier versions of Lewis structures with different kinds of
electrons, and if I remember correctly he refers to other literature
that I was unable to obtain that takes it even further. At any rate,
there seem to be a lot of versions of "Lewis structures" in the literature.

Allan Adler
[email-masked]

4)	You might look at Chem 4D Draw, by Cheminnovation.  It does not
automatically add lone pairs, but will generate Lewis structures from a
IUPAC-correct name.  Lone pairs can then be added where desired.  Like other
software, you can draw structures as well
from scratch, and add elemental symbols directly and fairly simply.

Examples of drawings can be found at
http://www.bc.cc.ca.us/programs/sea/chemist/kvaughan/structure.html
(my Chime link in that page is broken for unknown reasons, but some of the
early images are from Chem 4D).  You can see if this is what you are looking
for, and follow up on it.  (The ball and stick models are from another
package, which will also show lone pairs.)

Kenward Vaughan
[email-masked]

5)	(See Also #6 below!)

For a very inexpensive windows based package look at Molecules 3D from
molecular arts corporation. Some contact information on them follows.
Unfortunately their WWW page (http://www.molecules.com) does not seem
to be functioning.

Mark Forster 
[email-masked]

6)	(In reply to Mark Forster's message)

Yes , this package does have a Lewis structure drawing module.

However, this company has a very dubious track record:

a) They are the first chemistry software company I am aware of which was
found guilty of email spamming by their ex-provider host4u.net
(Host4u Abuse Team message dated 8 Sep 1998) after mass-mailing a typical
spam mail (complete with their own private uncontrolled
and unverifyable opt-out list and a reference to alleged compliance with
federal bill 1619) advertising their 3D structure builder.

b) They are selling for $199 apiece a 'Giant Library of 3D Molecular
Models' and a 'Pharma CD'. These CDs are essentially unapproved copies of
an old release of the NCI/NIH DTP structure database.
The same structure data is freely available from various Internet sites
(see for example http://www2.ccc.uni-erlangen.de/ncidb/, and the
NCI DTP homepage http://dtp.nci.nih.gov/). They
do not give (at least not on their Website) any credit for the
origin of the data, or the coordinates of the structures
(computed by the CORINA program, not their model builder)

c) Compare that to their usage conditions of their WebMolecules(TM)
online 3D structure display service usage conditions:

This WebMolecules site contains copyrighted material, which is protected by
US Federal Law and International Treaties.
Unless you have our prior written agreement, all other uses, including
     but not limited to reverse engineering, repackaging, or any other reuse
     of the graphics, underlying data, or data manipulation source code is
     strictly prohibited.

(The content of this service is not identical to the aforementioned
data CDs, it contains only a few hundred structures)

My personal opinion is that these business practices are deplorable
and unethical. I would never consider to buy anything
from a proven spammer.

Dr. Wolf-D. Ihlenfeldt
[email-masked]

Ron A. Rumley- Van Gurp, M.Sc. 
TNO Prins Maurits Laboratory
Chemical Toxicology
E-mail: [email-masked]
Tel: + 31 15 284 3532
Fax: + 31 15 284 3963
URL: http://www.tno.nl/instit/pml/