From owner-chemistry@ccl.net Fri Jun 29 06:01:02 2007 From: "Jens Spanget-Larsen spanget ~~ ruc.dk" To: CCL Subject: CCL: Change in dipole moment from ground state to excited state Message-Id: <-34601-070629044324-25772-evSruPNsywUXhpMfYYkt0w*_*server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 29 Jun 2007 10:10:22 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget=ruc.dk] Dear Sue, pay attention not only to the change in magnitude, but also to the possible change in direction of the dipole moment on electronic excitation. The solvent arrangement around the groundstate solute molecule will not change during vertical transition to the excited state. Hence, if the direction of the dipole moment is drastically changed in the excited state, fx pointing in the opposite direction (which is frequently the case), the interaction with the polar solvent molecules will tend to destabilize the solute species, leading to a blue shift of the vertical transition. Subsequently, the system will relax and the solvation will rearrange according to the charge distribution in the excited state. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget ~~ ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Sue Lam chsue2004===yahoo.com wrote: > Dear Marcel, > > Thank you for your information. I am looking the change in dipole > moment from ground state to excited state. I would like to study the > effect of the solvent on the energy of the transitions. Those should > be related to the dipole moment for the ground and excited states. If > an excited state has a larger dipole moment than a ground state, the > transition energy to that excited state will be red shifted from the > non-polar to polar solvent. > > "Marcel Swart marcel.swart _ icrea.es" > wrote: Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es] Dear > Sue, > > what do you mean ? The difference in dipole moment between ground > state and excited state, or the transition dipole moment ? > > Those are two different things, the latter should be given by > standard TD-DFT, while for the former you need to do finite field > calculations. How to obtain the dipole moment of the excited state > can be found in the following paper: > > "Excited state polarizabilities of conjugated molecules calculated > using time dependent density functional theory" F.C.Grozema, > R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders J. Chem. Phys. 115, > 2001, 10014-10021 > > On Jun 28, 2007, at 4:03 PM, Sue L chsue2004{}yahoo.com wrote: > > >> Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com] Hi >> >> Does anyone know how to calculate a change in dipole moment for >> transitions(ground state to excited state) in TDDFT calculation? >> >> Thank you very much! >> >> Sue From owner-chemistry@ccl.net Fri Jun 29 06:24:01 2007 From: "Pradipta Bandyopadhyay pradipta]=[iitg.ernet.in" To: CCL Subject: CCL: Boronic acid parameters ! Message-Id: <-34602-070629060025-1527-cbV0rbiQ1m7TA+HWI8aHlA]_[server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 29 Jun 2007 14:23:06 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta^iitg.ernet.in] Dear All, Does anyone have Boronic acid MM parameters compatible with AMBER force field? I got one paper but the parameters are given in Macromodel substructure format. Can anyone please help me with that format (I am not familiar with that format), so that I can get the parameters from that paper? thanks, Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta^iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm From owner-chemistry@ccl.net Fri Jun 29 10:10:00 2007 From: "Carsten Detering detering[a]biosolveit.de" To: CCL Subject: CCL: FlexX Release 2.2 out now Message-Id: <-34603-070629100537-7865-XF4pxY5lL6qDWJ/X00zYDw,,server.ccl.net> X-Original-From: "Carsten Detering" Date: Fri, 29 Jun 2007 10:05:32 -0400 Sent to CCL by: "Carsten Detering" [detering%biosolveit.de] Dear CClers, BioSolveIT is proud to announce the release of FlexX 2.2. This version comprises, among other novelties -A new placement algorithm (SIS) for docking into hydrophobic sites -Enhanced compatibility with MOE(R) by CCG We have a hassle-free FlexX download for evaluation from our web site, absolutely no paperwork involved: http://www.biosolveit.de/license/evaluation.html Aside of FlexX, we have also released FTrees 1.5.4 and CoLibri 1.1.1. More information can be found on our web site: www.biosolveit.com. Cheers, BioSolveIT -the developers of FlexX From owner-chemistry@ccl.net Fri Jun 29 12:07:00 2007 From: "=?iso-8859-1?Q?Jes=FAs_Orduna?= jorduna=-=unizar.es" To: CCL Subject: CCL:G: Change in dipole moment from ground state to excited state Message-Id: <-34604-070629080649-26495-xV//33lcnaCo7+sN/nVIHA]_[server.ccl.net> X-Original-From: =?iso-8859-1?Q?Jes=FAs_Orduna?= Content-Type: multipart/mixed; boundary="----=_NextPart_000_0001_01C7BA41.75BC1710" Date: Fri, 29 Jun 2007 11:34:14 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Jes=FAs_Orduna?= [jorduna%%unizar.es] This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C7BA41.75BC1710 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0002_01C7BA41.75BC1710" ------=_NextPart_001_0002_01C7BA41.75BC1710 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Calculation of the excited state dipole moments, and therefore dipole = moment changes, can be also performed in Gaussian 03 using the RHOCI Density.=20 Just choose the state of interest and the RHOCI density: = "TD=3D(root=3Dn) Density=3DRHOCI". =20 Maybe this calculation is not as precise as the finite field calculation = but it is simple enough and, in our experience, the obtained results are = often in a reasonable agreement with finite field calculations. See for = example "J. Am. Chem. Soc., 2006, 128, 12192-12204". =20 I hope this helps, =20 Jes=FAs =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Jesus Orduna Instituto de Ciencia de Materiales de Aragon Unidad de Nuevos Materiales Org=E1nicos Facultad de Ciencias CSIC-Universidad de Zaragoza E-50009 Zaragoza (Spain) Phone/FAX: +34 976 761194 e-mail: jorduna,+,unizar.es =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =20 _____ =20 De: owner-chemistry,+,ccl.net [mailto:owner-chemistry,+,ccl.net]=20 Enviado el: jueves, 28 de junio de 2007 21:41 Para: Orduna, Jesus Asunto: CCL: Change in dipole moment from ground state to excited state Dear Marcel, =20 Thank you for your information. I am looking the change in dipole moment > from ground state to excited state. I would like to study the effect of = the solvent on the energy of the transitions. Those should be related to the dipole moment for the ground and excited states. If an excited state has = a larger dipole moment than a ground state, the transition energy to that excited state will be red shifted from the non-polar to polar solvent.=20 "Marcel Swart marcel.swart _ icrea.es" = wrote:=20 Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es] Dear Sue, what do you mean ? The difference in dipole moment between ground state and excited state, or the transition dipole moment ? Those are two different things, the latter should be given by=20 standard TD-DFT, while for the former you need to do finite field calculations. How to=20 obtain the dipole moment of the excited state can be found in the following paper: "Excited state polarizabilities of conjugated molecules calculated using time dependent density functional theory" F.C.Grozema, R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders J. Chem. Phys. 115, 2001, 10014-10021 On Jun 28, 2007, at 4:03 PM, Sue L chsue2004{}yahoo.com wrote: > > Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com] > Hi > > Does anyone know how to calculate a change in dipole moment for=20 > transitions(ground state to excited state) in TDDFT calculation? > > Thank you very much! > > Sue > > > > -=3D This is automatically added to each message by the mailing=20 > script =3D- > To recover the email address of the author of the message, please=20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password:=20 > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20 > +-+-+ > > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart%a%icrea.es marcel.swart%a%udg.edu web http://www.icrea.es/pag.asp?id=3DMarcel.Swart http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt _____ =20 Be a better Globetrotter. Get better = travel answers from someone who knows. Yahoo! Answers - Check it out.=20 _____ =20 Estoy utilizando la versi=F3n gratuita de SPAMfighter para usuarios = privados. Ha eliminado 179 correos spam hasta la fecha. Los abonados no tienen este mensaje en sus correos. =A1Pruebe SPAMfighter gratis ya! ------=_NextPart_001_0002_01C7BA41.75BC1710 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Calculation of the excited state dipole = moments, and=20 therefore dipole moment changes, can be also performed in Gaussian 03 = using the=20 RHOCI Density.
Just choose the state of interest and the RHOCI = density:  "TD=3D(root=3Dn) Density=3DRHOCI".
 
Maybe this calculation is not as precise as the = finite=20 field calculation but it is simple enough and, in our experience, the = obtained=20 results are often in a reasonable agreement with finite field = calculations. See=20 for example "J. Am. Chem. Soc., 2006, 128, = 12192-12204".
 
I hope this helps,
 
Jes=FAs
 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Jes= us=20 Orduna
Instituto de Ciencia de Materiales de Aragon
Unidad de = Nuevos=20 Materiales Org=E1nicos
Facultad de Ciencias
CSIC-Universidad de=20 Zaragoza
E-50009 Zaragoza (Spain)
Phone/FAX: +34 976 = 761194
e-mail: jorduna,+,unizar.es
=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

 

De: owner-chemistry,+,ccl.net=20 [mailto:owner-chemistry,+,ccl.net]
Enviado el: jueves, 28 de = junio de=20 2007 21:41
Para: Orduna, Jesus
Asunto: CCL: = Change=20 in dipole moment from ground state to excited state

Dear Marcel,
 
Thank you for your information. I am looking the change in = dipole moment=20 > from ground state to excited state. I would like to study the effect of = the=20 solvent on the energy of the transitions. Those should be related to the = dipole=20 moment for the ground and excited states. If an excited state has a = larger=20 dipole moment than a ground state, the transition energy to that excited = state=20 will be red shifted from the non-polar to polar solvent.=20

"Marcel Swart marcel.swart _ icrea.es"=20 <owner-chemistry[a]ccl.net> wrote:=20

Sent=20 to CCL by: Marcel Swart [marcel.swart ~~ icrea.es]
Dear = Sue,

what do=20 you mean ?
The difference in dipole moment between ground state and = excited=20 state,
or the transition dipole moment ?

Those are two = different=20 things, the latter should be given by
standard TD-DFT,
while = for the=20 former you need to do finite field calculations. How to
obtain=20 the
dipole moment of the excited state can be found in the = following=20 paper:

"Excited state polarizabilities of conjugated molecules=20 calculated
using time dependent density functional = theory"
F.C.Grozema,=20 R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders
J. Chem. Phys. = 115, 2001,=20 10014-10021

On Jun 28, 2007, at 4:03 PM, Sue L = chsue2004{}yahoo.com=20 wrote:

>
> Sent to CCL by: "Sue L"=20 [chsue2004-x-yahoo.com]
> Hi
>
> Does anyone know = how to=20 calculate a change in dipole moment for
> transitions(ground = state to=20 excited state) in TDDFT calculation?
>
> Thank you very=20 much!
>
> Sue
>
>
>
> -=3D This is = automatically added to each message by the mailing
> script = =3D-
>=20 To recover the email address of the author of the message, please =
>=20 change> Conferences: http://server.ccl.net/chemistry/announcements/ =
> conferences/
>
> Search Messages:=20 http://www.ccl.net/htdig (login: ccl, Password:
> = search)>
>=20 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- =
>=20 = +-+-+
>
>
>

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
= dr.=20 Marcel Swart

ICREA researcher at
Institut de Qu=EDmica=20 Computacional
Universitat de Girona

Campus = Montilivi
17071=20 Girona
Catalunya=20 = (Spain)

fax
+34-972-418356
e-mail
marcel.swart%a%icrea.es=
marcel.swart%a%udg.edu
web
http://www.icrea.es/pag.asp?id=3DMar= cel.Swart
http://iqc.udg.edu/~marcel
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=


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<= /BLOCKQUOTE>

Be a better Globetrotter. Get=20 better travel answers from someone who knows.
Yahoo! Answers - = Check it=20 out.
Estoy utilizando la versi=F3n gratuita de SPAMfighter para usuarios=20 privados.
Ha eliminado 179 correos spam hasta la fecha.
Los = abonados no=20 tienen este mensaje en sus correos.
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------=_NextPart_001_0002_01C7BA41.75BC1710-- ------=_NextPart_000_0001_01C7BA41.75BC1710 Content-Type: text/x-vcard; name="=?iso-8859-1?Q?Jes=FAs_Orduna.vcf?=" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="=?iso-8859-1?Q?Jes=FAs_Orduna.vcf?=" BEGIN:VCARD VERSION:2.1 N:Orduna Catal=E1n;Jes=FAs;;Dr. FN:Jes=FAs Orduna ORG:ICMA. CSIC-Universidad de Zaragoza TITLE:Cient=EDfico Titular TEL;WORK;VOICE:976761194 TEL;WORK;FAX:976761194 ADR;WORK;ENCODING=3DQUOTED-PRINTABLE:;;Departamento de Qu=3DEDmica = Org=3DE1nica.=3D0D=3D0AFacultad de Ciencias. Universid=3D ad de Zaragoza.=3D0D=3D0APlaza San Francisco = s/n.;Zaragoza;Zaragoza;E-50009;Spai=3D n LABEL;WORK;ENCODING=3DQUOTED-PRINTABLE:Departamento de Qu=3DEDmica = Org=3DE1nica.=3D0D=3D0AFacultad de Ciencias. Universidad=3D de Zaragoza.=3D0D=3D0APlaza San Francisco s/n.=3D0D=3D0AZaragoza, = Zaragoza E-50009=3D =3D0D=3D0ASpain EMAIL;PREF;INTERNET:jorduna,+,unizar.es REV:20060111T082014Z END:VCARD ------=_NextPart_000_0001_01C7BA41.75BC1710-- From owner-chemistry@ccl.net Fri Jun 29 16:29:00 2007 From: "Xie Wang xie.wang]![gmail.com" To: CCL Subject: CCL:G: question about geometry optimization in PCM calculations (nonelectrost Message-Id: <-34605-070629162728-22710-mPaOqJp7fVO88Aub2xF8Lw(0)server.ccl.net> X-Original-From: "Xie Wang" Date: Fri, 29 Jun 2007 16:27:25 -0400 Sent to CCL by: "Xie Wang" [xie.wang++gmail.com] Dear all, When doing geometry optimization in PCM, is it a common practice to neglect the noelectrostatic contributions to the energy gradient? For example, in Gaussian manual: 'By default, non-electrostatic energy contributions are computed and printed, but they are not added into the energy and its derivatives during geometry optimizations. The keywords DDis, DRep, and DCav may be used to include them for the rare cases where the non-electrostatic energy terms are known to affect the geometry. Such cases will require care during optimization, and the optimization process may be trickier and more lengthy.' My question is: Do you know any publications that justify (or mention) the neglect of nonelectrostatic contribution in geometry opitimizations in PCM? When a paper said it did geometry optimization in PCM, but did not explicitly state how they treat nonelectrostatic terms, can I assume that they used the default (neglecting nonelectrostatic) ? Thanks in advance for any information you may provide! Best Regards, Qian From owner-chemistry@ccl.net Fri Jun 29 19:04:00 2007 From: "Qian Wang xie.wang.:.gmail.com" To: CCL Subject: CCL:G: question about geometry optimization in PCM calculations (nonelectrostatic contribution) Message-Id: <-34606-070629172103-16721-NH8x1V7EVdyEWGFmzTqLiw||server.ccl.net> X-Original-From: "Qian Wang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 29 Jun 2007 16:23:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Qian Wang" [xie.wang[-]gmail.com] Dear all, When doing geometry optimization in PCM, is it a common practice to neglect the noelectrostatic contributions to the energy gradient? For example, in Gaussian manual: 'By default, non-electrostatic energy contributions are computed and printed, but they are not added into the energy and its derivatives during geometry optimizations. The keywords DDis, DRep, and DCav may be used to include them for the rare cases where the non-electrostatic energy terms are known to affect the geometry. Such cases will require care during optimization, and the optimization process may be trickier and more lengthy.' My question is: Do you know any publications that justify (or mention) the neglect of nonelectrostatic contribution in geometry opitimizations in PCM? When a paper said it did geometry optimization in PCM, but did not explicitly state how they treat nonelectrostatic terms, can I assume that they used the default (neglecting nonelectrostatic) ? Thanks in advance for any information you may provide! Best Regards, Qian