Subject: New ideas for chemistry software

From: Ferenc Csizmadia <[email-masked]>
Date: Sat, 09 Jan 1999 20:50:41 +0100

A few weeks ago I posted the following letter to CCL:

=====

I would like to know your opinion about future trends in chemical
software development. What will be the hottest topics in the near
future? What are the areas that need new approaches from program
developers?

=====

Thank you for the contributions. Here are the answers I received so far.

1. =====

I would like to submit an idea which is based on the article of 

Mok, Neumann and Handy, J. Phys. Chem. 1996, 100, 6225-6230.

Precise calculations (approaching FCI-quality) should be quite
possible,  at a cost scaling as CASSCF, if one were to include only
excitations corresponding to nondynamical correlation in a CASSCF
calculation, and afterwards using a correlation functional fittet to
only dynamical correlation (He or Ne) in a DFT calculation based on
densities from the CASSCF calculation.

Thomas Bligaard Pedersen
University of Strasbourg and Technical University of Denmark
 <[email-masked]>

2. =====

It seems nearest future trends in chemistry are more or less visible.

To make it short: Biology, Biochemistry and related topics.

>From the clear domination of physics up to the middle of our century
scientific world is moving into "the living cell". You can proof it by
analyzing the number of publications, impact-factors of various
journals, the number of grants in difference fields of chemistry, and
activity of funding organizations in general. Even in this List,
proteins and DNA modeling and visualization, docking, MD, structure
determination, ..., are the topics discussed quite often. Significant
contribution and support are coming from the medicine related
applications, i.e., QSAR, screening, drug design, etc.

I am not to say that I like the situation, but one has to accept obvious
things.

Concerning the possible arias of software development, very likely it
could be a structure calculation, refinement, prediction and analyzing
programs for the most important biological molecules like proteins, DNA,
etc. Of course all of the above with up to date Graphics User Interface.

So, if you are going to start new software project, try to collect more
info about structural biochemistry stuff.

Valentin P. Ananikov
NMR Group
ND Zelinsky Institute of Organic Chemistry 
<[email-masked]>

3. =====

It would be nice to have a Windows program that would calculate the
enthalpy of formation at 0K and at 298.15 K, and a program that would
calculate rate constants.  You would take the output file from a
Gaussian 94 or Gaussian 98 calc and drag it into the Chemaxon window,
click Start, and the program would calculate heats of formation or rate.
For heat of formation the Gaussian output might be a G2, G2(MP2) or CBS
job. The algorithm could be bases onA. Nicolaides, A. Rauk, M. N.
Glukhovtsev, L. Radom, JPC, 1996, 100, 17460.  for rate constants,
methods might come from standard books on statistical thermodynamics
(e.g. Steinfeld, Francisco and Hase).

E. Lewars
<[email-masked]>

4. =====

How to determine crystal structures from powder diffraction data is
still hot topic. The 5 last years have seen the emergence of many ways
of locating optimally a molecular model inside a cell (Monte Carlo,
simulated annealing, genetic algorithm, packing considerations,
optimized grid search,...). It seems that developers believe that
pharmaceutical companies are, or will be interested. You cannot find any
of these new softwares in the public domain, nor in the commercial one!
See http://www.cristal.org/iniref.html for more details

Structure/properties prediction is the way to continue to explore, not
really new, but not really successful till now.

Armel Le Bail - Université du Maine, Laboratoire des Fluorures
<[email-masked]>

5. =====

In my humble opinion, linear scaling SCF theory will continue to get
hotter, as applications become more wide spread and algorithms get more
robust.

Matt Challacombe
Los Alamos National Laboratory
Theoretical Division
email: [email-masked]

6. =====

I think that some of the types of calculations that exist, but are
seldom done, will become more widely used.  Here are some of my picks.

relativistic calculations
solvent effects
band structure calculations
mesoscale calculations
synthesis route prediction
ab initio molecular dynamics

Dave Young
<[email-masked]>

7. =====

I am just reading -- again -- a very nice and very general article by
Martin Head-Gordon that appeared in the centennial issue of J. Phys.
Chem. He lists a lot of trends and challenges for electronic structure
theory, and almost all of them are longer term, and still valid today.
The reference is J. Phys. Chem. 1996, 100, 13213. In fact, the entire
issue is worth a look as it contains various general reviews.

Georg Schreckenbach
<[email-masked]>

8. =====

I think the new ideas for chemistry software is:
       1. Better organized interface. It is easy to learn.
       2. Moved to cheaper but hign performance PC.

FengLou Mao
Peking University
<[email-masked]>

9. =====

I think that simulation using virtual reality in all branches of
chemistry.

Jorge Arce Molina
Instituto Superior Minero Metalurgico
Las Coloradas s/n.
<[email-masked]>

10. =====

I think we don t really need a lot of _new_ programmes; rather, we need
a lot of extant programmes/source codes to be ported into Win95/WinNT
executables.  Now that the price of RAM is so low and we will soon have
PCs with clock speeds exceeding 500 MHz, we should be able to run a lot
of programmes on the PC that heretofore have been restricted to Unix
workstations.

For example, so far as I know, there is no simple, stand-alone programme
for the PC that will calculate the molecular volume or
solvent-accessible surface of a macromolecule (or even of a small
molecule) from its .ent or .mol2 file.  This would be a very useful tool
for the community of PC computational chemists.

Whilst MOPAC and AMPAC have been ported to DOS/Win, I know of no DOS/Win
programme that can perform a conformational search in order to identify
the (most likely) global energy minimum of a molecule _in an aqueous
environment_.  I believe that MacroModel contains a module which does
this, so in principle it is possible to obtain a DOS/Win executable that
can also do this.

So far as I am aware, there are no publically-available DOS/Win
programmes that use genetic algorithms for optimal selection of
variables for linear regression analysis.  Neither, so far as I know,
does there exist a recent version of GOLPE that runs under DOS/Win.
These would be very valuable chemometric tools for the PC compurtational
chemist.

Around April 1999 the C source code for the programme LigBuilder should
be released.  When it is, it will be a very useful addition to the PC
computational chemistry armamentarium, if only someone would port it
to a DOS/Win executable.

The JPC solvent version was recently described [J. Chem. Phys. 109(1):
260 ( 98)].  However, there is no DOS/Win-compatible release of this
method; such a release would be a valuable addition to the PC
computational chemist s methodological arsenal.

And there are other programmes so far available only for Unix which
ought to be made available to PC users: PARM and GRID are two which
spring to mind at the moment.  And, of course, there remains a need
for new and better ways of quickly calculating log P, log D, pKa,
aqueous solubility, &., &c.

S. Shapiro
<[email-masked]>

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The discussion is still open. If anyone would like to contribute please
send a letter to CCL or me.

Ferenc

~~~~~~
Ferenc Csizmadia, Ph.D.
ChemAxon Ltd.
Valyog u. 7, H-1032 Budapest, Hungary
http://www.chemaxon.com
T:+3620 9570988
mailto:[email-masked]