=0A

Dear Eliac;

=0A

Are you sure&nb= sp;that your binding energy calculation is based on the truely optimiz= ed structure? Have you checked its IR frequencies?

=0A

Regard= s

=0A

Mehdi

=0A

---------------= ---------------------------------------------------------------------------= ------------------------------------

=0A

`The man who makes no mistakes does not usua= lly make anything.'

=0A

= &nb= sp; Edward John Phelp= s (1822-1900)

=0A

-----------------------------------------= ---------------------------------------------------------------------------= ----------
Mehdi D. Esrafil= i

=0A

Assistanc= e Professor of Physical Chemistry
Current address: = ;Department of Chemistry= ,

=0A

Faculty = of Basic Sciences, University of Maragheh

=0A

Margheh, Iran.

=0A

Tel.: (+098) 021-82883488
Fax:= (+098) 021 88009730
E-mail 1: m_esrafili*yahoo.com
E-m= ail 2: es= rafili*maragheh.ac.ir

=0A

------------------------------------------------------------= ------------------------------------------------------------------ <= /DIV>=0A

=0A

=0A<= HR SIZE=3D1>=0AFrom: Pedro = Silva pedros[-]ufp.edu.pt <owner-chemistry*ccl.net>
To: "Esrafili, Mehdi D " <m_es= rafili*yahoo.com>
Sent: Wed, December 22, 2010 7:36:42 PM
ufp.edu.pt]
You should not expect very reliable data from semi-em= prirical computations ;-)

On Sun, Dec 19, 2010 at 10:07 PM, Eliac Br= own Eliacbrown|-|yahoo.com
<owner-chemistry^_^ccl.net> wrote:
&= gt;
> Sent to CCL by: "Eliac Brown" [Eliacbrown%%yahoo.com]
= > Dear All
> According to my semiempirical calculations using PM3 = and AM1, the distance
> between two molecules is less than the sum of= vdw radii by around 0.3 ang., but
> when I calculated the binding energies I got a posit= ive energy difference.
> Have any body got this observation before? o= r is there something wrong with my
> data?
> Merry xmas
>= Eliac> http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age> http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e> http://www.ccl.net/chemistry/sub_unsub.shtml&= gt; http://www.ccl.net/spammers.txt>
>
>=

--
Pedro J. Silva
Associate Professor
Universidad= e Fernando Pessoa
Porto - Portugal
http://www2.ufp.pt/~pedros/science= /science.htm

-=3D This is automatically added to each messag= e by the mailing script =3D-
To recover the email address of the author = of the message, please changelook up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY*ccl.net or use:
= ; http://www.ccl.net/cgi-bin/ccl/send_ccl_message
E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or = use
http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e
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Before posting, check wait time at:= http://www.ccl.net

Search M= essages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your = mail bounces from CCL with 5.7.1 error, check:
http://www.ccl.net/= spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instruc= tions/

=0A=0A --0-1383476510-1293044868=:9946-- From owner-chemistry@ccl.net Wed Dec 22 15:35:00 2010 From: "Mehdi Esrafili m_esrafili^^yahoo.com" To: CCL Subject: CCL: Semiempirical energies Message-Id: <-43445-101222143020-17263-sXWv6zCFLUbBRLDabqUdVw a server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="0-2009928354-1293046213=:70669" Date: Wed, 22 Dec 2010 11:30:13 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili!A!yahoo.com] --0-2009928354-1293046213=:70669 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Eliac;=0AAre you sure=A0that your=A0binding energy calculation is base= d on the truely =0Aoptimized structure?=A0Have you checked its IR frequenci= es?=0ARegards=A0=0AMehdi=0A=0A---------------------------------------------= ---------------------------------------------------------------------------= ------=A0=A0=0A=0A`The man who makes no mistakes does not usually make anyt= hing.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John Phelps (1822-1900)=0A--------= ---------------------------------------------------------------------------= -------------------------------------------=0A =0AMehdi D. Esrafili=0AAssis= tance Professor of Physical Chemistry=0ACurrent address:=A0Department of Ch= emistry, =0AFaculty of Basic Sciences, University of Maragheh=0AMargheh, Ir= an. =0ATel.: (+098) 021-82883488=A0=0AFax: (+098) 021 88009730 =0AE-mail 1:= m_esrafili*yahoo.com=0AE-mail 2: esrafili*maragheh.ac.ir=0A----------------= ---------------------------------------------------------------------------= -----------------------------------=0A=0A=0A --0-2009928354-1293046213=:70669 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A
Dear Eliac;
=0A
Are you sure tha= t your binding energy calculation is based on the truely optimized= structure? Have you checked its IR frequencies?
=0A
Regards&= nbsp;
=0A
Mehdi
=0A

=0A
-----------------= ---------------------------------------------------------------------------= ----------------------------------
=0A
`The man who makes no mistakes does not usuall= y make anything.'
=0A
&n= bsp; = ; Edward John Phelps (1822-1900)
=0A
-------= ---------------------------------------------------------------------------= --------------------------------------------
Mehdi D. Esrafili
=0A
Assistance Professor of Physical Chemistry
Current address: Department = of Chemistry,
=0A
Faculty of Basic Sciences, University of Maragheh
=0A
<= FONT face=3D"arial, helvetica, sans-serif">Margheh, Iran.
=0A
Tel.: (+098) 021-82883488
Fax: (+098) 02= 1 88009730
E-mail 1: m_esrafili*yahoo.com
E-mail 2: esrafili*maragheh.ac.ir
=0A
-------------------------------------------------= ---------------------------------------------------------------------------= --
=0A

<= br>=0A=0A --0-2009928354-1293046213=:70669-- From owner-chemistry@ccl.net Wed Dec 22 16:21:00 2010 From: "Jamin Krinsky krinsky.jamin * gmail.com" To: CCL Subject: CCL:G: Calculation absorption spectrum using Gaussian G03 Message-Id: <-43446-101222161945-31906-+Jz+BZrWVeGatbrXdvS2mQ,,server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Dec 2010 13:19:38 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin|,|gmail.com] Hi Pilar, First of all, a gold atom is d9 so it cannot have odd multiplicity, if the ground state is low spin than it will be a doublet. So maybe you are talking about the cation? You also stated that you did a geometry optimization so we are all probably a little puzzled. You didn't specify what method you are using for the excitations, but generally speaking a negative excitation energy means your reference electronic state is not the ground state. If the excitation energies are VERY small then it might be just noise. A single atom obviously has lots of symmetry, and G03 will not use this full symmetry, so you might be stuck at a state that is the ground state for a lower-symmetry system (I might be wrong about this). You could try adding the keyword "nosymm" to your input and see if that changes things, or also you could run a stability calculation specifying "stable=opt" in your input, the first part of that calculation being related to your excitation calculation (it finds negative excitations and tries to decide the cause, then the opt option tries to get rid of the instability). However do not assume that you are done just because the stability calculation tells you that you have a stable state. If you start with an excited-state configuration (by accident) and your method is TD-DFT, you will get an answer but I'm not sure if it would have any meaning. This is because only the ground state in a given irreducible representation is defined for "normal" DFT, and you need a reliable ground state in order to have reliable TD-DFT results. Regards, Jamin On Wed, Dec 22, 2010 at 8:59 AM, Pilar Constanza Suarez pcs_3++hotmail.com wrote: > > Sent to CCL by: "Pilar Constanza Suarez" [pcs_3::hotmail.com] > Dear All. > > We try to calculate the UV-VIS absorption spectra of one gold atom whit > multiplicities 1 (ground state),3 y 5 using Gaussian 03 (Geometry optimization > of these molecules was obtained using b3pw91 method). > > The simulations to calculate absorption spectrum finished without errors but > when I checked the output files with AGUI the excitation energy values for gold > atom with multiplicities 3 and 5 are NEGATIVES. > > So I would like to know why these values are negatives and what it means? > > Also what happens if the calculation (UV-VIS absorption spectra) starts from an > excited open shell state? > > Thank you. > > Pilar.> 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> > > From owner-chemistry@ccl.net Wed Dec 22 17:23:00 2010 From: "Loan Huynh huynhkl2000 _ yahoo.ca" To: CCL Subject: CCL: calculation of logP using atom contribution Message-Id: <-43447-101222153210-19989-pn+ZGqAgxEFDqIVJSDK/rA_+_server.ccl.net> X-Original-From: Loan Huynh Content-Type: multipart/alternative; boundary="0-659394555-1293049899=:65619" Date: Wed, 22 Dec 2010 12:31:39 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000],[yahoo.ca] --0-659394555-1293049899=:65619 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0ADear CCL,=20 =0A =0AI am currently calculating the logP values using the atom contribution b= y Grosh=0Aand Crippen ( J. Computational Chemistry, 1988, 9, p.80-90). =0A= =0A=A0=0A=0AI have done quite a lot of searching on calculating the=0Aoxida= tion state of carbon. However, I have trouble calculating the formal=0Aoxid= ation number of various hybridization carbons. =A0For example, for H attach= ed to sp carbon, I=0Acannot obtain the formal charge of 3 for sp carbon.=A0= =0A=0A=A0=0A=0AIs there any document that shows the calculation of oxidati= on=0Anumber for sp carbon?=A0 =0A=0A=A0=0A=0AThank you very much for your h= elp,=0A=0A=A0=0A=0ALoan=0A=0A =0A=0A --0-659394555-1293049899=:65619 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A
Dear CCL,
=0A
=0AI am currently calculating the logP values usin= g the atom contribution by Grosh=0Aand Crippen ( J. Computational Chemistry= , 1988, 9, p.80-90).
=0A=0A

=0A=0A
I have done quite a lot of searching on calculating the= =0Aoxidation state of carbon. However, I have trouble calculating the forma= l=0Aoxidation number of various hybridization carbons. &nb= sp;For example, for H attached to sp carbon, I=0Acannot obtain the f= ormal charge of 3 for sp carbon.
=0A=0A
=0A=0A
Is there any do= cument that shows the calculation of oxidation=0Anumber for sp carbon?
=0A=0A

=0A=0A=
Thank you very much for your help,
=0A=0A

=0A=0A
Loan
=0A=0A=

--0-659394555-1293049899=:65619-- From owner-chemistry@ccl.net Wed Dec 22 17:57:00 2010 From: "PILAR SUAREZ MARTINEZ pcs_3]*[hotmail.com" To: CCL Subject: CCL:G: Calculation absorption spectrum using Gaussian G03 Message-Id: <-43448-101222173228-9553-UhJXj1FH2e9dgkpGShV3xA|*|server.ccl.net> X-Original-From: PILAR SUAREZ MARTINEZ Content-Type: multipart/alternative; boundary="_d60797ea-2cd9-4493-a7b9-e3cfd00bbeac_" Date: Wed, 22 Dec 2010 17:32:17 -0500 MIME-Version: 1.0 Sent to CCL by: PILAR SUAREZ MARTINEZ [pcs_3__hotmail.com] --_d60797ea-2cd9-4493-a7b9-e3cfd00bbeac_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Jamin Thank you. I 'll try those keyword that you suggested me.Sorry I made a mis= take when I wrote the multiplicities. The correct values are m=3D2 (ground = state)=2C 4 and 6. The excitation energy values for gold atom with multipli= cities 4 and 6 are NEGATIVES. PILAR CONSTANZA SUAREZ MARTINEZ CHEMICAL ENGINEER > From: owner-chemistry.:.ccl.net > To: pcs_3.:.hotmail.com > Subject: CCL:G: Calculation absorption spectrum using Gaussian G03 > Date: Wed=2C 22 Dec 2010 13:19:38 -0800 >=20 >=20 > Sent to CCL by: Jamin Krinsky [krinsky.jamin|=2C|gmail.com] > Hi Pilar=2C >=20 > First of all=2C a gold atom is d9 so it cannot have odd multiplicity=2C i= f > the ground state is low spin than it will be a doublet. So maybe you > are talking about the cation? You also stated that you did a geometry > optimization so we are all probably a little puzzled. >=20 > You didn't specify what method you are using for the excitations=2C but > generally speaking a negative excitation energy means your reference > electronic state is not the ground state. If the excitation energies > are VERY small then it might be just noise. A single atom obviously > has lots of symmetry=2C and G03 will not use this full symmetry=2C so you > might be stuck at a state that is the ground state for a > lower-symmetry system (I might be wrong about this). You could try > adding the keyword "nosymm" to your input and see if that changes > things=2C or also you could run a stability calculation specifying > "stable=3Dopt" in your input=2C the first part of that calculation being > related to your excitation calculation (it finds negative excitations > and tries to decide the cause=2C then the opt option tries to get rid of > the instability). However do not assume that you are done just because > the stability calculation tells you that you have a stable state. >=20 > If you start with an excited-state configuration (by accident) and > your method is TD-DFT=2C you will get an answer but I'm not sure if it > would have any meaning. This is because only the ground state in a > given irreducible representation is defined for "normal" DFT=2C and you > need a reliable ground state in order to have reliable TD-DFT results. >=20 > Regards=2C > Jamin >=20 >=20 >=20 > On Wed=2C Dec 22=2C 2010 at 8:59 AM=2C Pilar Constanza Suarez > pcs_3++hotmail.com wrote: > > > > Sent to CCL by: "Pilar Constanza Suarez" [pcs_3::hotmail.com] > > Dear All. > > > > We try to calculate the UV-VIS absorption spectra of one gold atom whit > > multiplicities 1 (ground state)=2C3 y 5 using Gaussian 03 (Geometry opt= imization > > of these molecules was obtained using b3pw91 method). > > > > The simulations to calculate absorption spectrum finished without error= s but > > when I checked the output files with AGUI the excitation energy values = for gold > > atom with multiplicities 3 and 5 are NEGATIVES. > > > > So I would like to know why these values are negatives and what it mean= s? > > > > Also what happens if the calculation (UV-VIS absorption spectra) starts= from an > > excited open shell state? > > > > Thank you. > > > > Pilar.> http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemis= try/sub_unsub.shtml> > > > > >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_d60797ea-2cd9-4493-a7b9-e3cfd00bbeac_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =3BJamin

Thank you. I 'll try those keyword that yo= u suggested me.
Sorry I made a mistake when I wrote the multiplic= ities. The correct values are m=3D2 (ground state)=2C 4 and 6. =3BThe e= xcitation energy values for gold =3Batom with multiplicities 4 and 6 ar= e NEGATIVES.

PILAR CONSTANZA= SUAREZ MARTINEZ
CHEMICAL ENGINEER<= /b>

>=3B From: owner-chemistry.:.ccl.net
&= gt=3B To: pcs_3.:.hotmail.com
>=3B Subject: CCL:G: Calculation absorptio= n spectrum using Gaussian G03
>=3B Date: Wed=2C 22 Dec 2010 13:19:38 -= 0800
>=3B
>=3B
>=3B Sent to CCL by: Jamin Krinsky [krinsky= .jamin|=2C|gmail.com]
>=3B Hi Pilar=2C
>=3B
>=3B First of a= ll=2C a gold atom is d9 so it cannot have odd multiplicity=2C if
>=3B = the ground state is low spin than it will be a doublet. So maybe you
>= =3B are talking about the cation? You also stated that you did a geometry>=3B optimization so we are all probably a little puzzled.
>=3B >=3B You didn't specify what method you are using for the excitations= =2C but
>=3B generally speaking a negative excitation energy means you= r reference
>=3B electronic state is not the ground state. If the exci= tation energies
>=3B are VERY small then it might be just noise. A sin= gle atom obviously
>=3B has lots of symmetry=2C and G03 will not use t= his full symmetry=2C so you
>=3B might be stuck at a state that is the= ground state for a
>=3B lower-symmetry system (I might be wrong about= this). You could try
>=3B adding the keyword "nosymm" to your input a= nd see if that changes
>=3B things=2C or also you could run a stabilit= y calculation specifying
>=3B "stable=3Dopt" in your input=2C the firs= t part of that calculation being
>=3B related to your excitation calcu= lation (it finds negative excitations
>=3B and tries to decide the cau= se=2C then the opt option tries to get rid of
>=3B the instability). H= owever do not assume that you are done just because
>=3B the stability= calculation tells you that you have a stable state.
>=3B
>=3B I= f you start with an excited-state configuration (by accident) and
>=3B= your method is TD-DFT=2C you will get an answer but I'm not sure if it
= >=3B would have any meaning. This is because only the ground state in a>=3B given irreducible representation is defined for "normal" DFT=2C an= d you
>=3B need a reliable ground state in order to have reliable TD-D= FT results.
>=3B
>=3B Regards=2C
>=3B Jamin
>=3B
&= gt=3B
>=3B
>=3B On Wed=2C Dec 22=2C 2010 at 8:59 AM=2C Pilar Co= nstanza Suarez
>=3B pcs_3++hotmail.com <=3Bowner-chemistry^ccl.net&g= t=3B wrote:
>=3B >=3B
>=3B >=3B Sent to CCL by: "Pilar Consta= nza Suarez" [pcs_3::hotmail.com]
>=3B >=3B Dear All.
>=3B >= =3B
>=3B >=3B We try to calculate the UV-VIS absorption spectra of o= ne gold atom whit
>=3B >=3B multiplicities 1 (ground state)=2C3 y 5 = using Gaussian 03 (Geometry optimization
>=3B >=3B of these molecule= s was obtained using b3pw91 method).
>=3B >=3B
>=3B >=3B The = simulations to calculate absorption spectrum finished without errors but>=3B >=3B when I checked the output files with AGUI the excitation ene= rgy values for gold
>=3B >=3B atom with multiplicities 3 and 5 are N= EGATIVES.
>=3B >=3B
>=3B >=3B So I would like to know why the= se values are negatives and what it means?
>=3B >=3B
>=3B >= =3B Also what happens if the calculation (UV-VIS absorption spectra) starts= from an
>=3B >=3B excited open shell state?
>=3B >=3B
>= =3B >=3B Thank you.
>=3B >=3B
>=3B >=3B Pilar.>=3B = =3B =3B =3Bhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message>=3B = =3B =3B =3Bhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message&g= t=3B =3B =3B =3Bhttp://www.ccl.net/chemistry/sub_unsub.shtml= >=3B =3B =3B =3Bhttp://www.ccl.net/spammers.txt>=3B
&= gt=3B >=3B
>=3B >=3B
>=3B
>=3B
>=3B
>=3B -= =3D This is automatically added to each message by the mailing script =3D-<= br>>=3B To recover the email address of the author of the message=2C plea= se change
>=3B the strange characters on the top line to the .:. sign. Y= ou can also
>=3B=
>=3B
>=3B
&= gt=3B
>=3B
&= gt=3B
>=3B =
>=3B
>=3B =
>=3B http://www.ccl.net/chemistry/sub_un= sub.shtml
>=3B
>=3B Before posting=2C check wait time at: http:/= /www.ccl.net
>=3B
>=3B
>=3B C= onferences: http://server.ccl.net/chemistry/announcements/conferences/
&= gt=3B
>=3B Search Messages: http://www.ccl.net/chemistry/searchccl/in= dex.shtml
>=3B
>=3B If your mail bounces from CCL with 5.7.1 err= or=2C check:
>=3B
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= >=3B
>=3B =
>=3B
= --_d60797ea-2cd9-4493-a7b9-e3cfd00bbeac_-- From owner-chemistry@ccl.net Wed Dec 22 18:32:00 2010 From: "Serge Gorelsky gorelsky=-=gmail.com" To: CCL Subject: CCL:G: Calculation absorption spectrum using Gaussian G03 Message-Id: <-43449-101222175248-3434-8lIYfrNdvhtHlwjf2AkuRA(!)server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 22 Dec 2010 17:52:41 -0500 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky]=[gmail.com] Negative excitation energies in TD-DFT calculations mean that there are lower energy electronic states relative to the "reference" electronic state. This is one of the tests to determine whether or not the reference state is the true ground state: if there are negative excitation energies, the reference state is NOT the ground state. On Wed, Dec 22, 2010 at 11:59 AM, Pilar Constanza Suarez pcs_3++hotmail.com wrote: > > Sent to CCL by: "Pilar Constanza Suarez" [pcs_3::hotmail.com] > Dear All. > > We try to calculate the UV-VIS absorption spectra of one gold atom whit > multiplicities 1 (ground state),3 y 5 using Gaussian 03 (Geometry optimization > of these molecules was obtained using b3pw91 method). > > The simulations to calculate absorption spectrum finished without errors but > when I checked the output files with AGUI the excitation energy values for gold > atom with multiplicities 3 and 5 are NEGATIVES. > > So I would like to know why these values are negatives and what it means? > > Also what happens if the calculation (UV-VIS absorption spectra) starts from an > excited open shell state? > > Thank you. > > Pilar.> Â Â Â http://www.ccl.net/cgi-bin/ccl/send_ccl_message> Â Â Â http://www.ccl.net/cgi-bin/ccl/send_ccl_message> Â Â Â http://www.ccl.net/chemistry/sub_unsub.shtml> Â Â Â http://www.ccl.net/spammers.txt> > > -- Best regards, Â Serge Gorelsky