From yubofan@guomai.sh.cn Tue Jul 8 12:50:41 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id MAA16003; Tue, 8 Jul 1997 12:00:45 -0400 (EDT) Received: from aopen-k6-166 ([210.0.0.27]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id AAA23661 for ; Wed, 9 Jul 1997 00:56:54 +0800 Message-Id: <199707081656.AAA23661@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Which method is better for a rather big molecule. Date: Tue, 8 Jul 1997 23:59:08 -0000 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 8bit Hi, Thanks for the advice. Here's the summary. Hi, All, I want to optimize the conformations of some big molecules, for example, N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable for this kind big system. Also, some semi-empirical methods are not accurate enough for such calculations. Which method can do this kind work? Thank you very much! Y. FAN -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: yubofan@guomai.sh.cn -- Original Sender From: Address: yubofan@guomai.sh.cn CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== Hello, Your molecule is not as big as you think. Have you tried the RIS method to find the minimum potential energy conformation ? My friends once studied the polybenzozaxine dimer using this method, and it worked very well. But you have to write the code or find a package containing RIS module. Good luck. On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: yubofan@guomai.sh.cn > -- Original Sender From: Address: yubofan@guomai.sh.cn > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > A classic way of handling a molecule of this size is to break it down to logical pieces. Perhaps do at least two optimizations 1) N-ethyl-N-methylanaline, 2) N-dimethyl-N-alkylamine. Personally, I don't know of any other way. -- Luke Anthony Burke tel:609-225-6158 (-6142) Professor and Chair, fax:609-225-6506 Department of Chemistry e-mail: Rutgers University burke@camden.rutgers.edu Camden, NJ 08102, USA http://camchem.rutgers.edu/~burke > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN I think the best way is to do a DFT calculation, starting with B3LYP/4-31G DFT is a good method for large molecules. bye, *-----*-----*-----*-----*-----*-----*-----* / / / Anselmo Elcana de Oliveira / * Cidade Universitaria Zeferino Vaz * / IQ - UNICAMP CEP 13083-970 \ / Campinas, SP - Brasil \ * elcana@iqm.unicamp.br * / http://chope.iqm.unicamp.br \ / \ * To err is human, * / To really foul up requires the root password \ / \ *-----*-----*-----*-----*-----*-----*-----*-----*-----*-----* You may use RHF with small basis sets. However, it still depends how many memory your computer has. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: yubofan@guomai.sh.cn > -- Original Sender From: Address: yubofan@guomai.sh.cn > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Optimize? You did not indicate what you wish to optimize but I shall assume that you are looking for the global minimum, i.e. the conformation with the minimum energy. This is a non-trivial task and you want to use classical methods to search conformational space for candidates. I use molecular dynamics at 1000 K or 2000 K. I have also used Crippen's distance geometry algorithm. Jeff Blaney has written a nice implementation of distance geometry which is available through QCPE. Once you have sampled conformational space, you need to minimize each structure using molecular mechanics and then sort the structures as to energy. If you want a good ab initio energy, you then want to apply quantum-mechanical methods to the best structures identified by the classical approach. You won't be able to do the entire problem quantum mechanically. Millions of structures are involved.