From qsar!qsar.chem.msu.su!baskin@gamma.srcc.msu.su Fri Sep 1 04:42:00 1995 Received: from gw.srcc.msu.su for qsar!qsar.chem.msu.su!baskin@gamma.srcc.msu.su by www.ccl.net (8.6.10/950822.1) id EAA22877; Fri, 1 Sep 1995 04:33:14 -0400 Received: from srcc.UUCP (uusrcc@localhost) by gw.srcc.msu.su (8.6.12/8.6.12) with UUCP id MAA29733 for CHEMISTRY@www.ccl.net; Fri, 1 Sep 1995 12:33:05 +0400 Received: by gamma.srcc.msu.su; Fri, 1 Sep 1995 12:32:59 +0400 Received: by qsar.chem.msu.su (dMail for DOS v1.23, 15Jun94); Fri, 1 Sep 1995 11:57:20 +0400 To: CHEMISTRY@www.ccl.net Message-Id: Organization: Lab. of Org.Synth., MSU Date: Fri, 1 Sep 1995 11:57:20 +0400 (MSD) From: "Igor Baskin" X-Mailer: dMail [Demos Mail for DOS v1.23] Subject: Finding conformations analytically Lines: 25 Dear CCL'ers, Although some sort of systematic or random search for a complete set of all conformations corresponding to local minima is usually applied, an analytical solution (i.e., by algebraic means, without numerical optimization) of this problem (at least for some general- purpose force fields) seems to exist [see, for example, A.D. Kuntsevich, P.E. Kuznetsov, Iu.N. Liulin, A.A. Scherbakov, "Analytical solution for the problem of stable conformations", Dokl. Akad. Nauk. SSSR, 1990, v.309, N 5, pp. 1131-1136 (in Russian)]. Has anybody used analytical methods for exhaustively searching conformational space in practice? Are there other theoretical works in this direction? Thanks, Igor Baskin -- ------------------------------------------------------------------ Igor I. Baskin, Ph.D. | Tel: 7-095-939-3557 Department of Chemistry | 7-095-451-6997 (home) Moscow State University | Fax: 7-095-939-0290 Moscow 119899, Russia | E-mail: baskin@qsar.chem.msu.su From toukie@zui.unizh.ch Fri Sep 1 07:12:00 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id HAA24239; Fri, 1 Sep 1995 07:11:50 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA04479; Fri, 1 Sep 95 13:11:32 +0200 X-Nupop-Charset: Swiss Date: Fri, 1 Sep 1995 13:11:33 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <47493.toukie@zui.unizh.ch> To: chemistry@www.ccl.net, toukie@zui.unizh.ch Subject: Questions re dielec. const. & conformers Dear Colleagues; I would like to be able to locate global minimum energy conformations for molecules not only in the gas phase but also in solvents with different dielectric constants, e.g., n-octanol or water. I have examined several molecular mechanics programmes, which have an adjustable dielectric constant parameter as well as an option for using a distance-dependent dielectric. However, the literature accompanying the programmes do not discuss at length the matter of adjusting the dielectric. For example, one programe has a de- fault setting of 1.5 for the dielectric constant, and remarks that "It is rare for increases in [the value of the dielectric constant] to reproduce the properties of molecules in higher dielectric solvents, so this should be used with great care. ... [The] distance-dependent dielectric constant ... option .... [has been] used successfully in the AMBER program when attempting to model the effects of a polar solvent ...." My questions are as follows: (i) For molecular mechanics calculations, what is the _cut-off_ value for the dielectric constant above which the results can no longer be regarded as reliable? 5? 10? 25? Does this upper limit for the value of the di- electric constant depend on the force field implemented, or is it applicable to molecular mechanics calculations employing _any_ force field? (ii) Solvents of prospective interest can have a wide range of dielectric constants, from ca. 2 for n-alkanes and cycloalkanes to ca. 80 for water. However, if I understand this correctly, a distance-dependent dielectric will treat _all_ "higher" dielectric solvents equally, despite the fact that values for "higher" dielectric constants can range over at least an order of magnitude. Can anyone offer any practical advice regarding the use of the distance-dependent dielectric option in molecular mechanics calculations of molecules in organic solvents? Of course, references to any publications directly addressing this matter are most welcome. (iii) In relation to the preceding two questions, I have a molecular mechanics programme with a "dihedral driver" that will systematically rotate a maximum of two bonds in a molecule per run, to generate an m x n matrix in which each element corresponds to a particular conformation (and steric energy) generated during that run. Since the molecule in which I am inter- ested has more than two conformationally-interesting bonds, I thought to ap- ply the dihedral driver stepwise to pairs of bonds in order to locate a glo- bal minimum energy conformation (lowest steric energy conformation of the en- tire conformational space sampled) _in vacuo_, then feed that minimal energy conformation to MOPAC with the COSMO subroutine engaged, assigning the value of the dielectric constant of the solvent in which I am interested to "EPS". (In other words, if I am interested in a molecule in the solvent n-octanol, which has a dielectric constant of ca. 10, I would use "EPS=10" as one of my keywords in MOPAC.) However, I am not confident that the COSMO run will lead to a global minimum energy conformation for the molecule in the solvent rather than simply a local minimum closest to the input geometry. Does any- one have any suggestions, comments, or criticisms of the above strategy, ei- ther with respect to the stepwise application of the dihedral driver or the combination of molecular mechanical plus semi-empirical quantum mechanical methods to try to find a global minimum energy conformation in a given sol- vent? Thanks in advance to all responders. Yours sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 Zuerich 7 Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From murakami@lab.takeda.co.jp Fri Sep 1 07:57:01 1995 Received: from mail0.iij.ad.jp for murakami@lab.takeda.co.jp by www.ccl.net (8.6.10/950822.1) id HAA24550; Fri, 1 Sep 1995 07:53:52 -0400 Received: from uucp0.iij.ad.jp (uucp0.iij.ad.jp [192.244.176.51]) by mail0.iij.ad.jp (8.6.12+2.4W/3.3W9-MAIL) with ESMTP id UAA22698 for ; Fri, 1 Sep 1995 20:53:50 +0900 Received: (from uucp@localhost) by uucp0.iij.ad.jp (8.6.12+2.4W/3.3W9-UUCP) with UUCP id UAA20684 for chemistry@www.ccl.net; Fri, 1 Sep 1995 20:53:53 +0900 Received: from C83009 by lab.takeda.co.jp (AIX 4.1/UCB 5.64/IIJ-U1.1) id AA23612; Fri, 1 Sep 1995 20:11:41 +0900 Date: Fri, 1 Sep 1995 20:11:41 +0900 Message-Id: <9509011111.AA23612@lab.takeda.co.jp> To: chemistry@www.ccl.net From: murakami@lab.takeda.co.jp (Morio Murakami) Subject: Inquiry about Computer Assisted Organic Synthesis Cc: murakami@lab.takeda.co.jp (Morio Murakami) Return-Receipt-To: murakami@lab.takeda.co.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8-J13) Inquiry about Computer Assisted Organic Synthesis Dear CCLers: I am looking for the information about the computer assisted organic synthesis design using the database and artifical intelligence. Now I am attempting to track down research on computer-assisted organic synthesis and reaction prediction system. The examples I know on are as follows. a) Computer-assisted organic synthesis design system 1) LHASA E.J.Corey and W.T.Wipke, Science, 166, 178 (1969) A.P.Jonson, C.Marshall and P.N.Judson, J.Chem.Inf.Comput.Sci, 32, 411 (1992) A.P.Jonson and C.Marshall, J.Chem.Inf.Comput.Sci, 32, 418 (1992) A.P.Jonson and C.Marshall, J.Chem.Inf.Comput.Sci, 32, 426 (1992) A.K.Long and J.C.Kappos, J.Chem.Inf.Comput.Sci, 34, 915(1994) A.K.Long, J.C.Kappos, S.D.Rubenstein and G.E.Walker, J.Chem.Inf.Comput.Sci, 34, 922(1994) 2) SECS W.T.Wipke, H.Braun,G.Smith,F.Choplin and W.Sieder, "SECS-Simulation and Evaluation of Chemical Synthesis", In Computer-Assisted Organic Synthesis, W.T.Wipke and W.J.Howe, Eds., ACS Symposium Series 61 (1977) 97. 3) WODCA J.Gasteiger, W.D.Ihlenfeldt and P.Rose, Recl. Trav. Chim. Pays-Bas, 111, 270 (1992). 4) AIPHOS (Artificial Intelligence for Planning and Handling Organic Synthesis) K.Funatsu and S.Sasaki, Japan b) Reaction prediction system 1) EROS 6.0 (Elaboration of Reaction for Organic Synthesis) J.Gasteiger, Erlangen-Nurnberg University P.Rose and J.Gasteiger, Anal.Chim.Acta, 235, 163 (1990). 2) CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) W.L.Jorgensen, Yale University G.D.Paderes and W.L.Jorgensen, J.Org.Chem., 54, 2058 (1989). c) Organic reaction database 1) SYNLIB (Synthesis Library) Distributed Chemical Graphics 2) REACCS (Reaction Access System) MDL 3) ORAC (Organic Reaction Accessed by Computer) Pergamon 4) CrossFire, CrossFirePlusReaction Beilstein Information Systems Please inform me about the same kind of the latest papers and computer systems including academic and commercial softwares, related to computer assisted organic synthesis. If possible, please tell me the limitation of these systems in the case of applying to actual organic synthesis and reaction. Thank you for your courtesy. Sincerely, Morio Murakai (E-mail; murakami@lab.takeda.co.jp) ************************************************* Morio Murakami Molecular Chemistry Laboratory Pharmaceutical Research Division Takeda Chemical Industries, LTD. 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532, JAPAN E-mail. murakami@lab.takeda.co.jp FAX 81-6-300-6306 TEL 81-6-300-6618 ************************************************* From murakami@lab.takeda.co.jp Fri Sep 1 08:42:01 1995 Received: from mail0.iij.ad.jp for murakami@lab.takeda.co.jp by www.ccl.net (8.6.10/950822.1) id IAA24988; Fri, 1 Sep 1995 08:27:52 -0400 Received: from uucp0.iij.ad.jp (uucp0.iij.ad.jp [192.244.176.51]) by mail0.iij.ad.jp (8.6.12+2.4W/3.3W9-MAIL) with ESMTP id VAA24520 for ; Fri, 1 Sep 1995 21:27:50 +0900 Received: (from uucp@localhost) by uucp0.iij.ad.jp (8.6.12+2.4W/3.3W9-UUCP) with UUCP id VAA24159 for chemistry@www.ccl.net; Fri, 1 Sep 1995 21:27:53 +0900 Received: from C83009 by lab.takeda.co.jp (AIX 4.1/UCB 5.64/IIJ-U1.1) id AA23996; Fri, 1 Sep 1995 20:38:16 +0900 Date: Fri, 1 Sep 1995 20:38:16 +0900 Message-Id: <9509011138.AA23996@lab.takeda.co.jp> To: chemistry@www.ccl.net From: murakami@lab.takeda.co.jp (Morio Murakami) Subject: CCL:Inquiry about Computer Assisted Organic Synthesis Cc: murakami@lab.takeda.co.jp (Morio Murakami) Return-Receipt-To: murakami@lab.takeda.co.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8-J13) Inquiry about Computer Assisted Organic Synthesis Dear CCLers: I am looking for the information about the computer assisted organic synthesis design using the database and artifical intelligence. Now I am attempting to track down research on computer-assisted organic synthesis and reaction prediction system. The examples I know on are as follows. a) Computer-assisted organic synthesis design system 1) LHASA E.J.Corey and W.T.Wipke, Science, 166, 178 (1969) A.P.Jonson, C.Marshall and P.N.Judson, J.Chem.Inf.Comput.Sci, 32, 411 (1992) A.P.Jonson and C.Marshall, J.Chem.Inf.Comput.Sci, 32, 418 (1992) A.P.Jonson and C.Marshall, J.Chem.Inf.Comput.Sci, 32, 426 (1992) A.K.Long and J.C.Kappos, J.Chem.Inf.Comput.Sci, 34, 915(1994) A.K.Long, J.C.Kappos, S.D.Rubenstein and G.E.Walker, J.Chem.Inf.Comput.Sci, 34, 922(1994) 2) SECS W.T.Wipke, H.Braun,G.Smith,F.Choplin and W.Sieder, "SECS-Simulation and Evaluation of Chemical Synthesis", In Computer-Assisted Organic Synthesis, W.T.Wipke and W.J.Howe, Eds., ACS Symposium Series 61 (1977) 97. 3) WODCA J.Gasteiger, W.D.Ihlenfeldt and P.Rose, Recl. Trav. Chim. Pays-Bas, 111, 270 (1992). 4) AIPHOS (Artificial Intelligence for Planning and Handling Organic Synthesis) K.Funatsu and S.Sasaki, Japan "Computer-Assisted Organic Synthesis Design and Reaction Prediction System, AIPHOS", Tetrahedron Computer Methodology, 1, 27 (1988) b) Reaction prediction system 1) EROS 6.0 (Elaboration of Reaction for Organic Synthesis) J.Gasteiger, Erlangen-Nurnberg University P.Rose and J.Gasteiger, Anal.Chim.Acta, 235, 163 (1990). 2) CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) W.L.Jorgensen, Yale University G.D.Paderes and W.L.Jorgensen, J.Org.Chem., 54, 2058 (1989). c) Organic reaction database 1) SYNLIB (Synthesis Library) Distributed Chemical Graphics 2) REACCS (Reaction Access System) MDL 3) ORAC (Organic Reaction Accessed by Computer) Pergamon 4) CrossFire, CrossFirePlusReactions Beilstein Information Systems Please inform me about the same kind of the latest papers and computer systems including academic and commercial softwares, related to computer assisted organic synthesis. If possible, please tell me the limitation of these systems in the case of applying to actual organic synthesis and reaction. I will summarize the responses accordingly. Thank you for your courtesy. Sincerely, Morio Murakai (E-mail; murakami@lab.takeda.co.jp) ************************************************* Morio Murakami Molecular Chemistry Laboratory Pharmaceutical Research Division Takeda Chemical Industries, LTD. 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532, JAPAN E-mail. murakami@lab.takeda.co.jp FAX 81-6-300-6306 TEL 81-6-300-6618 ************************************************* From moshe_o@VNET.IBM.COM Fri Sep 1 09:57:03 1995 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.10/950822.1) id JAA26695; Fri, 1 Sep 1995 09:47:25 -0400 Message-Id: <199509011347.JAA26695@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R3) with BSMTP id 8565; Fri, 01 Sep 95 09:47:13 EDT Date: Fri, 1 Sep 95 16:47:33 IST From: "Moshe Olshansky" To: chemistry@www.ccl.net Subject: Direct versus conventional SCF Dear netters! About a week ago I asked a question related to the comparison of speeds of direct versus conventional SCF. I want to thank all those who responded. Some of the responses were quite interesting. Now I suggest that everyone interested in the summary contacts me. If there is enough interest, I will send the summary to the list; otherwise I will send it individually to the interested people. Moshe Olshansky e-mail: moshe_o@vnet.ibm.com From moshe_o@VNET.IBM.COM Fri Sep 1 11:27:04 1995 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.10/950822.1) id LAA28480; Fri, 1 Sep 1995 11:13:46 -0400 Message-Id: <199509011513.LAA28480@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R3) with BSMTP id 1208; Fri, 01 Sep 95 11:13:22 EDT Date: Fri, 1 Sep 95 18:13:29 IST From: "Moshe Olshansky" To: chemistry@www.ccl.net Subject: Direct versus conventional SCF - summary of responses Dear netters! I am getting many requests to send a summary of responses to my question about direct versus conventional SCF, so here it is: The original question was: > Dear netters! About a month ago someone mentioned that conventional SCF is faster (the total wallclock time) than the direct one only for systems with 100 - 150 basis functions. This looks strange to me - isn't it true that for a large number of ERIs both the time needed to compute them or to read them from the disk is almost a linear function of their number, so one method should be always faster than the other (as soon as the number of basis functions is large enough)? Could that person please explain his/her claim (either to CCL or directly to me)? > Below are the responses (stripped off headers and signatures): ========================================================================= From: Jiri Czernek Date: Thu, 24 Aug 1995 18:56:46 +0200 (MET DST) A thorough discussion of the topic is in "Exploring Chemistry with Electronic Structure Methods", mainly Exercise 2.5: Resource Usage. If you use GAUSSIAN you most probably have this book. I think the topic is the graphs of functions you mentioned can INTERSECT - there is a crossover point (it depends on the computer system; e.g., in the exercise from "Exploring ..." it was around 60 basis functions) and "those" total CPU time diferences result (depending on whether you have lower - conventional SCF faster - resp. higher - direct faster - number of basis functions than is the value in a crossover point). The another topic is neither function you mentioned does not have the same slope on all its domain. ========================================================================= From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp) Date: Thu, 24 Aug 1995 19:01:15 +0200 (MES) I guess the idea was (I'm not the original ''claimer'') that below 100 functions you can keep the integrals in core memory on typical machines (which is of course the fastest of all possibilities), whereas above 150 functions the direct algorithm is faster than the conventional. ========================================================================= Date: Thu, 24 Aug 95 12:10:08 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) I wasn't the original poster, but I can give you the standard argument. In Direct SCF, the small ERIs can be screened at three levels: atom quartet, shell quartet, and density. Early in the SCF procedure, loose thresholds may be used in the first two levels to eliminate the effort associated with unimportant integrals; near convergence the thresholds may be tightened to ensure sufficient accuracy. But near convergence, the density doesn't change very much, so the last level of screening becomes effective (F is computed in this case as F=Fold+F(DeltaD)). With conventional SCF (I/O based), it is usually not possible to avoid the I/O on small integrals, so this kind of screening is not beneficial. There is some controversy in the literature about how effective such screening can be. For the DeltaD screening, some claim an order of magnitude saving of effort, while others claim that it is only marginally better than simply computing a new F straight from D. BTW, no one claims to be able to compute integerals faster than doing I/O on them. That would be nice, but so far it is not possible. The Direct SCF argument always involves these screening/tolerance/threshold type arguments that benefit more Direct SCF than I/O-based SCF. The screening affects more large molecule cases than small molecule cases, and it works best for large linear molecules, then for large planer systems, and finally for large space-filling molecules. ========================================================================= Date: Thu, 24 Aug 1995 14:52:04 -0230 (NDT) From: Uli Salzner Dear Moshe, that direct SCF is faster than conventional SCF for 100-150 basis functions is a rule of thumb. Which method performs better depends first of all on your computer. For direct SCF the time to evaluate integrals is crucial, for conventiuonal SCF it is crucial how fast input output operations can be done. Conventional SCF also needs to find the right integrals, that is it has to sort through huge numbers of intergrals. Timings for input/output operations, searching for integrals and calculation of integrals do not necessarily increase parallel. The direct procedure is especially competitive since after calculating the integrals once, efficient cutoffs can be used. That is small integrals will not be recalculated but neglected. ========================================================================= Date: Thu, 24 Aug 1995 20:12:23 +0100 (BST) From: A J Turner This ties in with what I am doing right now. What you say is resonably correct except that disk access does decrees in speed with file size because of the number of separate times the unix (if your using unix - I cannot comment on VMS etc) subsystem has to read the disk to locate the end bits of large files. If the disk is badly fragmented - this gets even worse. Thus, I would expect that in some situations, especially on heavily loaded disks, with multiple users (therefore trashing the cash) there could be a point where direct gets faster than disk scf. ========================================================================= Date: Thu, 24 Aug 1995 16:10:23 -0700 (MST) From: XIANZ@ASUCHM.LA.ASU.EDU (Xianzhang Gu) I read your post about conventional vs direct SCF. Although I am not the person who made that claim, several years ago I implemented direct SCF method with Gaussian86 which I ported completely on PC-DOS. Here I try to give my comments about speed comparison. >From point of view of CPU time, conventional SCF is always faster than direct one. But for clock time, it is quite different. When using PC or single user machine, waiting or seeking time (harddrive) can be very long especially when the harddisk is near full or the file consists of small separate peices on harddisk ( which means you spend more time to try to find those peices). If machine got multiple users or many jobs running concurrently, you have to wait to get your turn for using disk resources. Generally there are some limit on how big the disk space each user can use or say each job can use to avoid that one job may eat up all the time of disk resources. If you have big enough diskspace, I think, conventional SCF would be faster. The problem is diskspace running out quite quickly. Secondly, CPU time needed to compute 2-e integrals is proportional to ns**n (n is around 3 something) and n decreases while ns ( number of basis ) increases(of course, very slowly). The time needed for SCF part is also proportional to ns**m ( m is around 2.6, it depends on the method how you form Fork matrix). m does not change much while ns increases compared to n ( m may increase a little bit). This is because certain method is used to screen 2-e integrals before they are actually calculated. So computation of SCF part is getting equally or more critical when ns gets bigger. Hope this may give you some hints about speed comparison. ========================================================================= Date: Fri, 25 Aug 1995 09:57:43 +0200 (MET DST) From: Patrick Bultinck Well, I once posted a similar question to CCL. From the discussion that followed and own experience (ab initio with upto 400 BF's) I can tell the following : Direct SCF is in my experience always slower, i.e. needs more CPU time; and more wall clock time. That is if you have some more or less modern storage, I can imagine that if you were to put everything on tape (...) you would be faster with Direct, but otherwise, no. Modern disks (SCSI II f/w) are so fast that you have to lose whan you have to recalculate your integrals every time. When you do have an advantage (and even shorter wall clock times) is when you're working on an I/O slow machine, let's say your average university central computer with 250 people reading their mail and 200 more doing LaTex...). So if you have such a machine, it is *sometimes* better to do direct. Other reasons include : - program cannot pack the number of integrals (e.g. GAMESS : max 360 BF's can be packed into an integral file) - You don't have 6 Gigabytes Scratch... - From my experience I hace found that *sometimes* when you're using a pvm or tcgmsg job over several UNIX boxes you're faster off with direct, but that's up to you to find out at your site. Maybe the most remarkable thing about a direct SCF is the following : when you do a GAMESS run; you will find that CPU time is about 75 % of real time for conventional SCF CPU time is about 99 % of real time for direct SCF. Maybe you can extrapolate what CPU you need to make direct become faster than conventional... (you have ibm.com, so...) Anyway, you are not restricted to conventional or direct SCF, you may also use what is called the Multiplicative Integral Approximation (MIA) developped at the University of Antwerp... ******************************************************************************** THE END ******************************************************************************** Once again, I wish to thank all those who responded. Moshe Olshansky moshe_o@vnet.ibm.com From shenkin@still3.chem.columbia.edu Fri Sep 1 12:27:06 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/950822.1) id MAA29705; Fri, 1 Sep 1995 12:26:08 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA28263 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@www.ccl.net>); Fri, 1 Sep 1995 12:26:01 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@www.ccl.net id AA24091; Fri, 1 Sep 95 12:29:17 -0400 Date: Fri, 1 Sep 95 12:29:17 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9509011629.AA24091@still3.chem.columbia.edu> To: toukie@zui.unizh.ch, chemistry@www.ccl.net, toukie@zui.unizh.ch Subject: Re: CCL:M:Questions re dielec. const. & conformers > From chemistry-request@www.ccl.net Fri Sep 1 08:56:02 1995 > > I would like to be able to locate global minimum energy conformations > for molecules not only in the gas phase but also in solvents with different > dielectric constants, e.g., n-octanol or water. I have examined several > molecular mechanics programmes, which have an adjustable dielectric constant > parameter as well as an option for using a distance-dependent dielectric. > However, the literature accompanying the programmes do not discuss at length > the matter of adjusting the dielectric.... BatchMin, which is the part of the MacroModel package that performs energy calculations, employs an implicit solvation model that would appear, in principle, to do what you want. We utilize the GB/SA model, which uses an approach based on the generalized Born equation for electrostatics (see JACS, 1990, 112, 6127-6129) and a conventional area-based method of accounting for the "solvophobic" effect (generalization of "hydrophobic"). For an example of its application, see: McDonald, D. Q.; Still, W. C., "Conformational Free Energies from Simulation: Stochastic Dynamics/Monte Carlo Simulations of a Homologous Series of Gellman's Diamides", J. Am. Chem. Soc. , 1994, 116,11550. The problem with using just a dielectric constant for electrostatics is that this doesn't account for the displacement of some volume of the solvent by the molecule itself. For example, if one is calculating the interaction of, say, a charged pair of atoms from the ends of glycine zwitterion, one has to account for the fact that part of the solvent between them is displaced by the intervening atoms of the GLY (for example, the carbon-alpha). These displaced regions can be viewed as regions of low dielectric embedded in a possibly high-dielectric solvent. Clearly, the precise geometry of the situation should ideally be taken into account; electrostatic theory demonstrates that regions of displaced solvent not "between" but "outside of" the interacting atoms have to be taken into account as well. The effects of the shape of the molecule can be taken into account reasonably rigorously, given a full charge distribution, by a solution of the Poisson-Boltzmann equation. This is carried out by the well-known program DELPHI and the somewhat less well-known GB-SOLV. However, this rigorous computation is too slow to be used on the fly during molecular mechanics simulations. The GB/SA model is an attempt to approximate these effects, and is fast enough to be used in such simulations. We supply parameterizations for water and chloroform right now. Other methods are used as well. Purely area-based models have been proposed by Eisenberg and by Scheraga; they take only the local environment into account. A still simpler attempt to incorporate these effects involves the use of a distance-dependent dielectric; this doesn't even take local environment into account. > (i) For molecular mechanics calculations, what is the _cut-off_ value > for the dielectric constant above which the results can no longer be regarded > as reliable? 5? 10? 25? Does this upper limit for the value of the di- > electric constant depend on the force field implemented, or is it applicable > to molecular mechanics calculations employing _any_ force field? Perhaps I misunderstand you, but if not, I think you misunderstand the meaning of the term "cutoff". These values (5, 10, 20) are in *Angstroms*, not in the units of dielectric constant. Atom pairs further apart than this cutoff are considered not to interact. Conventionally used values for this cutoff are in the range, say, 12 to 20 Angstroms, for electrostatics. > (ii).... > ...Can anyone offer any practical advice regarding the use of the > distance-dependent dielectric option in molecular mechanics calculations of > molecules in organic solvents? Of course, references to any publications > directly addressing this matter are most welcome. Assuming that you really are talking about cutoffs in Angstroms, we can address this algebraically. Suppose Rw is the cutoff used for water; call it 12 for now. We want to calculate Ro, the cutoff to be used for some organic solvent. Let's assume the organic solvent has a dielectric constant (Do) of 5 for illustration, and that water has a dielectric constant (Dw) of 80. If the energy of a charged pair at the cutoff is considered too small to be considerable, then this energy for some charged pair in water is: E_cutoff,w = q1*q2/(Dw*Rw**2) Now, for the same charged pair in the organic solvent, we want to pick the cutoff so that E_cutoff has the same (inconsiderable) value: E_cutoff,o = Ecutoff,w = q1*q2/(Do*Ro**2) This gives: (Ro/Rw)**2 = Dw/Do, or (Ro/Rw) = SQRT( Dw/Do ) Using the above values for Dw and Do, we get (Ro/Rw) = 4. So if Rw = 12 in water, you have to use Ro = 36 in an organic solvent with a dielectric constant of 5. A 36-Angstrom cutoff sounds like a huge number, but most molecules studied in organic solvents are small anyway, so you might as well run with the complete pair-list. Incidentally, for small to medium-sized systems, this is what we recommend for the GB/SA model. For GB/SA, long cutoffs are especially helpful, since the model takes into account the entire environment, not just the interacting pair, and not even just this pair plus its neighboring atoms. > (iii) In relation to the preceding two questions, I have a molecular > mechanics programme with a "dihedral driver" that will systematically rotate > a maximum of two bonds in a molecule per run, to generate an m x n matrix > in which each element corresponds to a particular conformation (and steric > energy) generated during that run. Since the molecule in which I am inter- > ested has more than two conformationally-interesting bonds, I thought to ap- > ply the dihedral driver stepwise to pairs of bonds in order to locate a glo- > bal minimum energy conformation (lowest steric energy conformation of the en- > tire conformational space sampled) _in vacuo_.... > ...However, I am not confident that the COSMO run will lead > to a global minimum energy conformation for the molecule in the solvent... If I understand you right, you're trying to minimize with molecular mechanics in vaccuo, holding certain dihedral angles constant, at a number of values of dihedral constant, then feed the input conformations to MOPAC. It would seem that if any of the above solvent models have any validity at all, you'd be better off preparing your input conformations with the molecular-mechanics solvation model turned on. Then, if you try to run MOPAC with solvation turned on (which I understand you to be saying -- I've never used MOPAC), hopefully your input conformations would be closer to the true quantum mechanical solvated minimum. I'd think this procedure would speed the quantum calculation, as well as diminish somewhat the chance of getting stuck in a local minimum. Incidentally, you have to be careful if the results of the quantum calculation are to be used later in further molecular mechanics runs. The solvation models that are associated with various force-fields are parameterized for use with various sorts of charge sets. For example, our GB/SA model works best when the charges are closest to the in-vaccuo (not the solvated) fitted charges from quantum calculations. This is at least in part because of the way GB/SA has been parameterized. This has been wordy, but I hope it helps. -P. ************ "There Won't Be Any More." Charlie Rich, RIP *********** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* *NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039* ********* John Gilmore, RIP. Not to mention S. Chandrasekhar. ********* From sschulz@chemie.fu-berlin.de Fri Sep 1 12:42:05 1995 Received: from weasel.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/950822.1) id MAA29762; Fri, 1 Sep 1995 12:31:00 -0400 Message-Id: <199509011631.MAA29762@www.ccl.net> Received: by weasel.chemie.fu-berlin.de (1.37.109.16/16.2) id AA073873033; Fri, 1 Sep 1995 18:30:33 +0200 From: Stefan Schulz Subject: SPARTAN MANUALS To: chemistry@www.ccl.net Date: Fri, 1 Sep 95 18:30:32 MESZ X-Hpvue$Revision: 1.8 $ Mime-Version: 1.0 Content-Type: Message/rfc822 X-Vue-Mime-Level: 4 Mailer: Elm [revision: 70.85] Hi CCLers, our local computer center has SPARTAN SGI Version 4.0.3 installed. Since I would like to start working with this program I need some documentation. If you know of some place on the web where I can find documentation for this program please let me know. Regards, Stefan Schulz =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | Stefan Schulz | | sschulz@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5384 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From underhil@hp.rmc.ca Fri Sep 1 13:42:05 1995 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.6.10/950822.1) id NAA00926; Fri, 1 Sep 1995 13:33:10 -0400 Message-Id: <199509011733.NAA00926@www.ccl.net> Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP (1.37.109.15/16.2) id AA242496847; Fri, 1 Sep 1995 13:34:07 -0400 Date: Fri, 1 Sep 1995 13:34:07 -0400 X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: GEAR integration of chemical reactions I'm having a few problems with the integration of some chemical reactions using the GEAR method. The code is part of a Finite Element code. Basicly as the material heats up the reaction starts to run away so the GEAR integrator starts decreasing the time step in an effort to keep changes small. As the reaction goes to completion, however, rounding error can make the concentrations go negative. Once this happens the problem can very quickly diverge. Obviously one would like to insert constraints that prevent the concentrations from going negative (or greater than 1). Does anybody know of an implementation of the GEAR method which allows for such constraints to be put in? Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 From jim@wavefun.com Fri Sep 1 13:57:06 1995 Received: from volvo.wavefun.com for jim@wavefun.com by www.ccl.net (8.6.10/950822.1) id NAA01087; Fri, 1 Sep 1995 13:47:01 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA02094; Fri, 1 Sep 95 10:47:13 -0700 Message-Id: <9509011747.AA02094@volvo.wavefun.com> Received: from isuzu.wavefun.com(198.147.95.111) by volvo.wavefun.com via smap (V1.3) id sma002092; Fri Sep 1 10:46:49 1995 X-Sender: jim@acura.wavefun.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Sep 1995 10:49:30 -0800 To: chemistry@www.ccl.net From: jim@wavefun.com (jim Parisi) Subject: Wavefunction/Spartan Manuals In case anyone is interested, you can acquire information about Wavefunction's manuals and publications by visiting our WEB page at http://wavefun.com, or contacting Wavefunction at sales@wavefun.com. Here is a current list or the publications: -------------------------------------------------------------------------------- Experiments in Computational Organic Chemistry. (Hehre, Burke, Shusterman, Pietro) Practical Strategies for Electronic Structure Calculations. (Hehre) Chemistry With Computation: An Introduction to Spartan. (Hehre, Huang) Spartan LIVE! "Visualization of Chemical Structures & Reactions". (CD-ROM by Hehre, Burke, Huang, Hehre) Spartan Version 4.0 User's Guide. Spartan Version 3.1 Users Guide, Spiral Bound. (limited) Spartan Version 3.1 Tutorial Spiral Bound. (limited) -------------------------------------------------------------------------------- Thanks! Jim Parisi Marketing/Sales Coordinator _________________________________________________________________ WAVEFUNCTION, INC. Phone: 714-955-2120 18401 Von Karman, Suite 370 FAX: 714-955-2118 Irvine, CA e-mail: jim@wavefun.com 92715 USA WEB: http://wavefun.com ----------------------------------------------------------------- C A R P E D I E M _________________________________________________________________ From sgustaf@appsdiv.cray.com Fri Sep 1 14:12:09 1995 Received: from timbuk.cray.com for sgustaf@appsdiv.cray.com by www.ccl.net (8.6.10/950822.1) id NAA01242; Fri, 1 Sep 1995 13:59:29 -0400 Received: from giraf.cray.com (giraf.cray.com [128.162.171.5]) by timbuk.cray.com (8.6.12/CRI-8-1.16) with SMTP id MAA08510 for ; Fri, 1 Sep 1995 12:59:26 -0500 Received: by giraf.cray.com (931110.SGI/CRI-5.14) id AA15502; Fri, 1 Sep 95 12:59:00 -0500 From: sgustaf@appsdiv.cray.com (Susan M. Gustafson) Message-Id: <9509011759.AA15502@giraf.cray.com> Subject: Announcing UniChem 3.0 To: chemistry@www.ccl.net Date: Fri, 1 Sep 1995 12:58:59 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1001 Cray Research, Inc. announces the release of UniChem 3.0. UniChem incorporates three chemistry simulation codes with a graphical user interface (GUI). Users may run DGauss 3.0, MNDO94, or CADPAC 5.2. UniChem 3.0 also provides an optional interface to GAUSSIAN and a code attachment facility. Major new features include: - analytic second derivatives for DFT - reaction field model for both DGauss 3.0 and MNDO94 - MNDO/d parameters for 4 additional elements in MNDO94: Ti, Fe, Cu, Zr - semiempirical molecular dyanmics - a quick cleanup option in the molecular builder - the ability to perform computation and analysis on a series of structures. UniChem 3.0 runs in client/server mode, with the GUI operating on a Sun or SGI workstation and the chemistry codes on either SGI or Cray platforms. A version for the IBM RS6000 version is forthcoming. More details on UniChem 3.0 can be found in the UniChem WWW page (http://www.cray.com/apps/UNICHEM/), or by contacting unichem@cray.com. From smb@smb.chem.niu.edu Fri Sep 1 15:12:11 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id PAA03556; Fri, 1 Sep 1995 15:06:29 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA04749 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Fri, 1 Sep 1995 14:06:29 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA07898; Fri, 1 Sep 95 13:42:53 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA08513; Fri, 1 Sep 95 13:42:52 -0500 Date: Fri, 1 Sep 95 13:42:52 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9509011842.AA08513@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: ECCC-2 Abstracts Due Date Just a reminder to those of you thinking about participating in the Second Electronic Computational Chemistry Conference (ECCC-2) that the deadline for submission of abstracts is SEPTEMBER 29, 1995. Complete information on the conference and how to submit an abstract can be obtained at URL http://hackberry.chem.niu.edu/ECCC2 One other note: we are close to finalizing the manner in which the proceedings of ECCC-2 will be publsihed. Stay tuned for more info. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From jkl@ccl.net Fri Sep 1 16:57:13 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id QAA06395; Fri, 1 Sep 1995 16:48:01 -0400 Received: from SLVAXA.umsl.edu for C1790@SLVAXA.UMSL.EDU by bedrock.ccl.net (8.6.10/950822.1) id QAA00148; Fri, 1 Sep 1995 16:47:59 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HURMS50PU49OCWJ3@SLVAXA.UMSL.EDU>; Fri, 1 Sep 1995 15:50:48 CDT Date: Fri, 01 Sep 1995 15:50:48 -0500 (CDT) From: BILL WELSH Subject: Postdoctoral Position(s) To: chemistry@ccl.net Message-id: <01HURMS50ZHA9OCWJ3@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Applications are invited for one and possibly two postdoctoral positions in several specific areas of computational chemistry: (1) computer-aided polymer design with emphasis on mechanical and NLO properties and on permeability of gases and/or water in polymers. (2) chemometrics including neural networks, QSAR, and multivariate regression; (3) applications of protein biomimetics as surface-active and/or interface-active agents (e.g., corrosion inhibitors); (4) applications 3-D QSAR techniques (e.g., CoMFA) and related methods. Topics 1 and 3 are of highest priority. For Topic #1, facility with the Cerius_2 Polymer and Mechanical Properties modules is a big plus. For all Topics, facility with Sybyl (e.g., CoMFA), Insight/Discover, and Cerius_2 is a plus. Good oral and written communication skills in English are mandatory. These positions offer excellent opportunities to interact and publish within a dynamic and multi-project research team, so good "people skills" is a must. Excellent hardware/software facilities are available. Send cover letter, complete vita, list of publications, and the names of 3 references to: Prof. William J. Welsh, Department of Chemistry & Center for Molecular Electronics, University of Missouri-St. Louis, St. Louis, MO 63121. Applications will be accepted until the positions are filled. The position(s) will open on or around November 1, 1995. Funding for these positions is available for one year with good prospects for multiple years. From post1@lascar.puc.cl Fri Sep 1 18:27:09 1995 Received: from lascar for post1@lascar.puc.cl by www.ccl.net (8.6.10/950822.1) id SAA07565; Fri, 1 Sep 1995 18:19:15 -0400 Received: from [146.155.24.91] by lascar with SMTP id AA08708; Fri, 1 Sep 1995 18:18:29 -0500 Date: Fri, 1 Sep 1995 18:18:29 -0500 Message-Id: <9509012318.AA08708@lascar> X-Sender: post1@lascar.puc.cl (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: post1@lascar.puc.cl (postgrado quimica1) Subject: Photochemical amine , Nuclear Magnetic Resonance and Organic synthesis Please, we need to subscript at yours information service. Our names are Juan Luis Arroyo and Cesar Centella Velasquez, we are Phd Students of Catholic University in Chile. Thanks you