Subject: Re: CCL:Is Computational Chemistry a real science ?

From: Valentin Ananikov <[email-masked]>
Date: Thu, 14 Nov 2002 08:06:32 +0000

>Thus,  Computational Chemistry is not a real science?

It is a "complex" science, therefore including real and 
imaginary parts.  :))

best regards,
Valentin.

====================================================================
                                             ,         ,      ,   ,
Valentin  P. Ananikov                        |\\\\ ////|     /////|
NMR Group                                    | \\\|/// |    ///// |
ND Zelinsky Institute of Organic Chemistry   |  |~~~|  |   |~~~|  |
Leninsky Prospect 47                         |  |===|  |   |===|  |
Moscow,  119991                              |  |   |  |   |   |  |
Russia                                       |  | A |  |   | Z |  |
                                              \ |   | /    |   | /
e-mail: [email-masked]                     \|===|/     |===|/
http://nmr.ioc.ac.ru/Staff/AnanikovVP/          '---'      '---'
  Fax +7 (095)1355328   Phone +7 (095)9383536
====================================================================

---

From: "Curt M. Breneman" <[email-masked]>
Date: Wed, 13 Nov 2002 18:20:28 -0500

Folks,

I think it's time to take a step back, consider the origins of modern
Computational Chemistry, and recognize that there are some very
different subtypes of this activity.  In my view, one flavor of Comp
Chem grew from the need for theorists (read: Physical Chemists) to
automate algorithms otherwise impractical to apply analytically (quantum
chemistry, stat mech...etc come to mind here).  Another type arose from
the Physical Organic Chemistry community, where computational methods
became another tool for probing reaction mechanisms, transition states,
thermochemistry and related phenomena.  Molecular mechanics represents a
sort of a middle ground, where the development of potentials and
minimizers is a P-Chem exercise, but some of  these methods have nearly
become a commodity item.   A lot of Computational Chemistry is done to
probe the scope and applicability of various implementations of
force-field methods to address specific problems.

We actually have a problem in semantics - who is the Computational
Chemist?  The one who develops the methods, or the one who is familiar
with the field and applies the appropriate methods to solve specific
problems?  It would seem that a lot of product-oriented work is
accomplished by the latter type of Computational Chemist, but not
without the contributions of the former.

Curt Breneman
RPI Chemistry

"Dr. Daniel Glossman-Mitnik" wrote:

>
>
>      On Tuesday, November 12, 2002, James Robinson wrote:
>
>      ... So there is an added advantage. They have experience of
>      real science before attempting the computation
>
>   Thus,  Computational Chemistry is not a real science?   Everyone in
> this list agrees with this assert ? Best
> regards                                 Dr. Daniel
> Glossman-Mitnik  ****************************************************************************
>
> Dr. Daniel Glossman-Mitnik
> Centro de Investigacion en Materiales Avanzados (CIMAV)
> LAQUICOM - Laboratorio de Quimica Computacional
> Miguel de Cervantes 120 - Complejo Industrial Chihuahua
> Chihuahua, Chih. 31109 - Mexico
> Phone: (52) 614 4391151      FAX: (52) 614 4391112
> E-mail: [email-masked]
>             [email-masked]
>             [email-masked]
>
> ***************************************************************************

---

From: <[email-masked]>
Date: Thu, 14 Nov 2002 17:04:28 +0100 (CET)

> It is a "complex" science, therefore including real and 

Im agree this definition. :))
Best,
Csaba

------
Csaba Hetenyi, MSc, PhD
Dept. of Medical Chemistry, University of Szeged,
8 Dom ter, Szeged 6720, Hungary

---

From: Gustavo Mercier <[email-masked]>
Date: Thu, 14 Nov 2002 09:34:08 -0800 (PST)

Hi!
As "former" comp. chemist who did most of his work when the term was not fashionable, I'll throw my 0.02 of opinion.
I think Curt is on the right track...
Computational Chemistry may have had its origin in the theoretical work from Physical Chemistry, but today this field is very broad and embraces many areas. Curt writes about Physical Organic Chemistry. I would add other fields such as Biology/Biochemistry, Pharmacology, Statistics, Numerical Analysis, and Computer Science. For example, consider data mining applications that emphasize algorithms developed in Computer Science with a scoring function (that may or may not have a foundation on Physical Chemistry or Physical Organic Chemistry) to search for new lead compounds in drug development. Those individuals that code and make developments in theoretical physical chemistry with a more "classical" view of chemistry in their minds may feel that their work is very different from the example I described. Some may even feel that it is not CC! I would disagree and I think that the breath of topics covered by the many journals in CC are consistent with my view.
It is unfortunate that some feel that CC is not a "real" science. It is sad to see this "prejudice" perpetuated over 20 years! The contributions of CC are real. CC has grown and Pople's Noble prize is a reaffirmation of the significance of CC. I probably do not have to remind members of this list that Pople and his group have worked in both theoretical physical chemistry and computer science (not to mention numerical methods, etc.) to bring Gaussian to life.
The publication of the Reviews of Computational Chemistry and the longevity and popularity of this list are other landmarks that speak of the significance and reality of CC as a science. More important it shows that the field is mature. Slowly the field gets defined. The journals, meetings, Reviews, and this list help to do that. It is now creeping into the chemistry curriculum. With time I have no doubt that it will be another specialty in Chemistry. Depending on the strengths of the departments it may have different flavors - more theory oriented or more physical chemistry or more computer science, etc.
Finally, let me end with a comment on the issue of "computer work" as science. There is a line of thinking that takes computer simulations as just another "experimental tool". The experiment is not in a beaker, but in a machine - not different from a NMR machine. The exception is that an artificial (virtual) world that is normally very simple is created within the computer. It is this "world" that is being observed and measured. This is the kind of thinking that S. Wolfram discusses in his book a "New Kind of Science". (I know that his approach may be a bit pompous and has generated significant criticism, but there is still a valid point to his argument.) Experimentation (eg. simulation) within the virtual world created within a computer is an extension of our traditional experimental science. The success of the traditional science together with computer and other technologies allow us to evolve the concept of science without taking away from the foundation we have from experimenting with the natural world.
Enjoy!
Bye!
Gustavo Mercier, Jr.
 
  "Curt M. Breneman" &lt;[email-masked]&gt; wrote: Folks,

Curt Breneman
RPI Chemistry

--
Gustavo A. Mercier, Jr., MD,PhD
Seattle Nuclear Medicine & U/S Associates
1229 Madison, Suite 1150
Seattle, WA 98104-1377
voice: 206-386-6300; fax: 206-386-6312
[email-masked] 

---------------------------------
Do you Yahoo!?
New DSL Internet Access from SBC & Yahoo!

---

From: "Alexandre Hocquet" <[email-masked]>
Date: Thu, 14 Nov 2002 15:02:16 +0100

> without the contributions of the former.

But if you name "computational chemist" the one who develops the method,
then who is the "theoretical chemist", in your view ?

------------------------------------------------------------
Alexandre HOCQUET
Laboratoire de Physicochimie Biomoléculaire et Cellulaire
UMR CNRS 7033
[email-masked]
Fax: 33 1 44277560
LPBC, case courrier 138
4 Place Jussieu, 75252 PARIS Cedex 05 France
------------------------------------------------------------

---

From: <[email-masked]>
Date: Thu, 14 Nov 2002 15:12:54 -0500

A theoretical chemist is a type of chemist whose existence is proposed but
not experimentally verified.

Jim

----- Original Message -----
From: "Alexandre Hocquet" <[email-masked]>
To: <[email-masked]>
Sent: Thursday, November 14, 2002 9:02 AM
Subject: CCL:Who is the Computational Chemist ?

> -= This is automatically added to each message by mailing script =-
> [email-masked] -- To Everybody  | [email-masked] -- To
Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan:
[email-masked]

---

From: Maurice Cafiero <[email-masked]>
Date: Thu, 14 Nov 2002 20:10:02 +0000

hello:
    It is accepted in several places I have seen that the theoretical
chemist is the "method developer"
or the "programmer," while the computational chemist is the "user" who
is comfortable with not only black boxes like
Gaussian but also the less black box like Gamess and Dalton (and knows
what all the output means!). The "experimentalist cum computational
chemist" is the strictly Gaussian type user.
    It is ridiculous to say that computational chemistry (CC) is a
separate science. The problem is that from the chemistry point of view
it seems very alien. Even, in many cases, to the experimental physical
chemist.  From the Physics point of view it is plainly obvious that CC
or TC (theoretical) are small subsets of QM or even CM. Perhaps rather
than teach CC or TC in chemistry departments it be taught in physics
departments or in inter-disciplinary departments like the quantum theory
project.

--
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona