From chemistry-request /at\www.ccl.net Wed Jan 6 10:46:08 1999 Received: from mail.matav.hu (mail.matav.hu [145.236.224.244]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA17905 Wed, 6 Jan 1999 10:46:00 -0500 (EST) Received: (qmail 14138 invoked from network); 6 Jan 1999 16:45:30 +0100 Received: from unknown (HELO inhale) (195.70.54.253) by mail.matav.hu with SMTP; 6 Jan 1999 16:45:30 +0100 Message-ID: <369384E9.24EE747D ":at:" chemaxon.com> Date: Wed, 06 Jan 1999 16:44:41 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.01 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry&$at$&www.ccl.net Subject: New year -> new ideas for chemistry software X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 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 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 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 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 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: mchalla "-at-" t12.lanl.gov 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 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 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 9. ===== I think that simulation using virtual reality in all branches of chemistry. Jorge Arce Molina Instituto Superior Minero Metalurgico Las Coloradas s/n. 10. ===== I think we dont 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 chemists 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 ===== The discussion is still open. If anyone would like to contribute please send a letter in the subject to me or CCL. Ferenc ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz %-% at %-% chemaxon.com