Summary: Which method is better for a rather big molecule.
- From: "Yubo Fan" <yubofan { *at * }
guomai.sh.cn>
- Subject: Summary: Which method is better for a rather big
molecule.
- Date: Tue, 8 Jul 1997 23:59:08 -0000
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
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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
>
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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 { *at * } 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,
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You may use RHF with small basis sets. However, it still
depends how many memory your computer has.
=================================================================
Dr. Buyong Ma buyong { *at * } 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 { *at * } guomai.sh.cn
> -- Original Sender From: Address: yubofan { *at * } guomai.sh.cn
> CHEMISTRY { *at * } www.ccl.net: Everybody | CHEMISTRY-REQUEST { *at * }
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> MAILSERV { *at * } www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher:
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73
> Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH { *at * } 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.