From owner-chemistry@ccl.net Sun Aug 8 13:55:01 2010 From: "Serdar Badoglu sbadoglu||gazi.edu.tr" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42475-100808135301-16778-2/seb8LrI7I1vdV4ipGQNQ..server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Sun, 8 Aug 2010 13:52:58 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu[a]gazi.edu.tr] Hi CCLers, I'm using Gaussian 03. I need to specify one or more charged atoms in a neutral molecule. How can I do that? Thanks. Serdar Badoglu From owner-chemistry@ccl.net Sun Aug 8 16:46:01 2010 From: "Radoslaw Kaminski rkaminski.rk===gmail.com" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42476-100808164418-10464-F/VE7DwBkAJoQ93iOifhDQ]![server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=001517503bc416a378048d55f63d Date: Sun, 8 Aug 2010 16:44:07 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk|-|gmail.com] --001517503bc416a378048d55f63d Content-Type: text/plain; charset=ISO-8859-1 Hi Serdar, I don't get it. Some of the atoms are always neutral, some of them are positive, some of them are negative. It depends on the electron density distribution in a given molecule. Charges of the atoms also depend on the used partitioning scheme (Bader, Hirshfeld etc.). What exactly you wanna do? Radek PS. Molecule is always neutral. If not it is an ion. 2010/8/8 Serdar Badoglu sbadoglu||gazi.edu.tr > > Sent to CCL by: "Serdar Badoglu" [sbadoglu[a]gazi.edu.tr] > Hi CCLers, > > I'm using Gaussian 03. I need to specify one or more charged atoms in a > neutral > molecule. How can I do that? > > Thanks. > > > > Serdar Badoglu> > > -- Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://acid.ch.pw.edu.pl/~rkaminski/ --001517503bc416a378048d55f63d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Serdar,

I don't get it. Some of the atoms are always neutral,= some of them are positive, some of them are negative. It depends on the el= ectron density distribution in a given molecule. Charges of the atoms also = depend on the used partitioning scheme (Bader, Hirshfeld etc.). What exactl= y you wanna do?

Radek

PS. Molecule is always neutral. If not it is an ion.

2010/8/8 Serdar Badoglu sbadoglu||gazi.edu.tr <owner-chemistry:-:ccl.net>

Sent to CCL by: "Serdar =A0Badoglu" [sbadoglu[a]gazi.edu.tr]
Hi CCLers,

I'm using Gaussian 03. I need to specify one or more charged atoms in a= neutral
molecule. How can I do that?

Thanks.



Serdar Badoglu



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--
Radoslaw Kaminski, M.Sc= . Eng.
Ph.D. Student
Crystallochemistry Laboratory
Department of C= hemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Poland
http://acid.ch.pw.edu.pl/~= rkaminski/
--001517503bc416a378048d55f63d-- From owner-chemistry@ccl.net Sun Aug 8 17:21:00 2010 From: "N. Sukumar nagams],[rpi.edu" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42477-100808164418-10473-8jw26Kxcgumhn/98xH6KSQ|,|server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sun, 08 Aug 2010 16:44:13 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams:-:rpi.edu] "Charged atoms" don't exist in a neutral molecule. If you refer to the polarization of the electron density, the electrostatic potential of which is approximated or FITTED by fractional atomic charges in a classical point charge MODEL, then Gaussian or any other quantum chemistry program will determine the electron density (and hence any atomic partial "charges") from the molecular wavefunction. You do not specify it. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "It is nice to know that the computer understands the problem. But I would like to understand it too." -- Eugene P. Wigner ==============Original message text=============== On Sun, 08 Aug 2010 13:52:58 EDT "Serdar Badoglu sbadoglu||gazi.edu.tr" wrote: Sent to CCL by: "Serdar Badoglu" [sbadoglu[a]gazi.edu.tr] Hi CCLers, I'm using Gaussian 03. I need to specify one or more charged atoms in a neutral molecule. How can I do that? Thanks. Serdar Badogluhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Sun Aug 8 19:00:00 2010 From: "Serge Gorelsky gorelsky###gmail.com" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42478-100808185925-20973-qHW0w21DN6Ce71lc+xnEkw^^^server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 8 Aug 2010 18:59:10 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky%gmail.com] Yes, you can specify the atomic or fragment charges: one can build a neutral molecule from ions for Gaussian calculations! Sometimes this is the ONLY(!) WAY to get the correct ground state wave function. " For details see the AOMix manual (www.sg-chem.net). On Sun, Aug 8, 2010 at 4:44 PM, N. Sukumar nagams],[rpi.edu wrote: > > Sent to CCL by: "N. Sukumar" [nagams:-:rpi.edu] > "Charged atoms" don't exist in a neutral molecule. If you refer to the > polarization of the electron density, the electrostatic potential of > which is approximated or FITTED by fractional atomic charges in a > classical point charge MODEL, then Gaussian or any other quantum > chemistry program will determine the electron density (and hence any > atomic partial "charges") from the molecular wavefunction. You do not > specify it. > > Dr. N. Sukumar > Rensselaer Exploratory Center for Cheminformatics Research > http://reccr.chem.rpi.edu/ -------------------------- > "It is nice to know that the computer understands the problem. But I > would like to understand it too." -- Eugene P. Wigner > > ==============Original message text=============== > On Sun, 08 Aug 2010 13:52:58 EDT "Serdar Badoglu sbadoglu||gazi.edu.tr" wrote: > > > Sent to CCL by: "Serdar  Badoglu" [sbadoglu[a]gazi.edu.tr] > Hi CCLers, > > I'm using Gaussian 03. I need to specify one or more charged atoms in a > neutral > molecule. How can I do that? > > Thanks. > > > > Serdar Badogluhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- Best regards,   Serge Gorelsky From owner-chemistry@ccl.net Sun Aug 8 20:32:00 2010 From: "Serge Gorelsky gorelsky!^!gmail.com" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42479-100808203027-10029-H5DZrthGd40N0uTeLP/Tng]![server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 8 Aug 2010 20:30:19 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky,gmail.com] also, If we are being the purist (with statements like "Charged atoms" don't exist in a neutral molecule), one can further say "ATOMS don't exist in any molecule or molecular ion" (an atom in a molecule is a model construct - we like to see atoms with "borders" but they do not have those "borders"!). Do these statements (correct statements!) help in terms of helping us to understand and explain chemistry? I think not. > On Sun, Aug 8, 2010 at 4:44 PM, N. Sukumar nagams],[rpi.edu > wrote: >> >> Sent to CCL by: "N. Sukumar" [nagams:-:rpi.edu] >> "Charged atoms" don't exist in a neutral molecule. If you refer to the >> polarization of the electron density, the electrostatic potential of >> which is approximated or FITTED by fractional atomic charges in a >> classical point charge MODEL, then Gaussian or any other quantum >> chemistry program will determine the electron density (and hence any >> atomic partial "charges") from the molecular wavefunction. You do not >> specify it. >> >> Dr. N. Sukumar >> Rensselaer Exploratory Center for Cheminformatics Research >> http://reccr.chem.rpi.edu/ -------------------------- >> "It is nice to know that the computer understands the problem. But I >> would like to understand it too." -- Eugene P. Wigner >> >> ==============Original message text=============== >> On Sun, 08 Aug 2010 13:52:58 EDT "Serdar Badoglu sbadoglu||gazi.edu.tr" wrote: >> >> >> Sent to CCL by: "Serdar  Badoglu" [sbadoglu[a]gazi.edu.tr] >> Hi CCLers, >> >> I'm using Gaussian 03. I need to specify one or more charged atoms in a >> neutral >> molecule. How can I do that? >> >> Thanks. >> >> >> >> Serdar Badogluhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> >> >> > > > > -- > Best regards, >   Serge Gorelsky>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- Best regards,   Serge Gorelsky From owner-chemistry@ccl.net Sun Aug 8 23:55:00 2010 From: "N. Sukumar nagams#%#rpi.edu" To: CCL Subject: CCL:G: charged atoms in neutral molecule Message-Id: <-42480-100808235207-29661-eDAy5arUVRUdMo0s1jdFiw-#-server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sun, 08 Aug 2010 23:52:03 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams:-:rpi.edu] I will concede that we should not talk of "atoms" in molecules without specifying what kinds of atoms we are referring to, but any talk of "charges" has no meaning except in a classical model or in terms of the integrated and/or partitioned electron density. If one is going to "understand and explain" chemistry exclusively in terms of classical models, one might as well avoid the expense of performing quantum calculations. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "It is nice to know that the computer understands the problem. But I would like to understand it too." -- Eugene P. Wigner ==============Original message text=============== On Sun, 08 Aug 2010 20:30:19 EDT "Serge Gorelsky gorelsky!^!gmail.com" wrote: Sent to CCL by: Serge Gorelsky [gorelsky,gmail.com] also, If we are being the purist (with statements like "Charged atoms" don't exist in a neutral molecule), one can further say "ATOMS don't exist in any molecule or molecular ion" (an atom in a molecule is a model construct - we like to see atoms with "borders" but they do not have those "borders"!). Do these statements (correct statements!) help in terms of helping us to understand and explain chemistry? I think not. > On Sun, Aug 8, 2010 at 4:44 PM, N. Sukumar nagams],[rpi.edu > wrote: >> >> Sent to CCL by: "N. Sukumar" [nagams:-:rpi.edu] >> "Charged atoms" don't exist in a neutral molecule. If you refer to the >> polarization of the electron density, the electrostatic potential of >> which is approximated or FITTED by fractional atomic charges in a >> classical point charge MODEL, then Gaussian or any other quantum >> chemistry program will determine the electron density (and hence any >> atomic partial "charges") from the molecular wavefunction. You do not >> specify it. >> >> Dr. N. Sukumar >> Rensselaer Exploratory Center for Cheminformatics Research >> http://reccr.chem.rpi.edu/ -------------------------->> "It is nice to know that the computer understands the problem. But I >> would like to understand it too." -- Eugene P. Wigner >> >> ==============Original message text=============== >> On Sun, 08 Aug 2010 13:52:58 EDT "Serdar Badoglu sbadoglu||gazi.edu.tr" wrote: >> >> >> Sent to CCL by: "Serdar  Badoglu" [sbadoglu[a]gazi.edu.tr] >> Hi CCLers, >> >> I'm using Gaussian 03. I need to specify one or more charged atoms in a >> neutral >> molecule. How can I do that? >> >> Thanks. >> >> >> >> Serdar Badogluhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>>> >> > > > > -- > Best regards, >   Serge Gorelsky>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>> > -- Best regards,   Serge Gorelskyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========