From owner-chemistry@ccl.net Fri Jul 6 04:26:01 2007 From: "Arvydas Tamulis tamulis]*[mserv.itpa.lt" To: CCL Subject: CCL:G: Problems with oscillator strengths in TDDFT Message-Id: <-34674-070706035451-12371-LnQr5Pgk1qXtSiQI0Y5rVQ_+_server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 6 Jul 2007 10:54:30 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis() mserv.itpa.lt] Good morning, The same reversible oscillator strengths for those two singlet transitions we obtaining not only for D3 symmetry Ru(bpy)32+ but also for [Ru(bpy)2(4-4'-Me2-2,2'-bpy)]2+ derivative where is breaking the D3 symmetry. While those two singlet transitions are from Ru to ligand in all two cases. Best regards, Arvydas On Thu, 5 Jul 2007, Sue Lam chsue2004#,#yahoo.com wrote: > Hi. Is the calculated oscillator strengths for those two singlet transitions the same, if you break down the symmetry of the [Ru(bpy)3]2+ molecule? > > Best regards, > Sue > > > "Arvydas Tamulis tamulis_._mserv.itpa.lt" wrote: > > Sent to CCL by: Arvydas Tamulis [tamulis.:.mserv.itpa.lt] > > Dear Colleagues, > > We have calculated spectrum and oscillator strengths of D3 symmetry > complex [Ru(bpy)3]2+ using TDDFT B3LYP with the LanL2DZ > basis set and IEFPCM or COSMO water solvent shell models in > Gaussian03 or ORCA program packages. We have received two > singlet-E lines: 456.18 nm (0.0140 oscillator strength) and > 435.61 nm (0.1373 oscillator strength). > Experiment of [Ru(bpy)3]2+ derivatives gives two peaks: > one at about 450 nm (intensity 1.0 arbitrary units) and the > other near 430 nm (intensity 0.6 arbitrary units) > therefore the values of our calculated intensities are reversible in > comparison with experiment. > Oscillator strength calculations done by G03 and > ORCA are exactly the same wrong calculating with PBEPBE potential > using 6-311G* basis set. > My impression is that it is something wrong in B3LYP, PBEPBE potentials > when calculating oscillator strengths by Gaussian03 and ORCA programs > of the D3 symmetry complexes and their derivatives > while the values of spectral lines are exactly good. > It is interesting that even ZINDO gives the right intensities in > comparison with experiment but the values of spectral lines are > shifted strongly. Maybe you can advise some good program with DFT > potential/basis set for the calculations of right oscillator strengths of > the D3 symmetry complexes and their derivatives? > > In the case if you are far from the field of calculations of oscillator > strengths in G03 or ORCA, would you please to forward my question to > developers of program packages who are working on subroutine > of calculations of oscillator strengths in G03, ORCA or people who > possesses the good subroutine. > > For regular organic compounds the oscillator strengths obtained by > TDDFT in G03 and ORCA are good. > More about our research you can see in our website > www.itpa.lt/~tamulis/ and press on button > For PACE project WEBsite > > With best regards, > Arvydas Tamulishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- > Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. From owner-chemistry@ccl.net Fri Jul 6 06:17:03 2007 From: "andras.borosy:-:givaudan.com" To: CCL Subject: CCL: Converting structures to IUPAC names Message-Id: <-34675-070706044237-24350-85SrheIaI6XdYE4GVF//aA###server.ccl.net> X-Original-From: andras.borosy/./givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002FD17FC1257310_=" Date: Fri, 6 Jul 2007 10:42:17 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy]~[givaudan.com This is a multipart message in MIME format. --=_alternative 002FD17FC1257310_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Arnab, Yes, I know it. We have ChemOffice but, I have not found out, if it worked = in batch mode. It seems to be not. Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Arnab Chakrabarty r.arnab,,gmail.com" =20 Sent by: owner-chemistry]-[ccl.net 05/07/2007 17:50 Please respond to "CCL Subscribers" To Andras Borosy/U/Givaudan]-[Givaudan cc Subject CCL: Converting structures to IUPAC names Sent to CCL by: Arnab Chakrabarty [r.arnab,+,gmail.com] Hi, I guess ChemOffice=20 (http://www.cambridgesoft.com/software/ChemOffice/) has that=20 functionality. Thanks Arnab andras.borosy/./givaudan.com wrote: > > Dear Colleagues, > > Does anyone know an application which is capable to convert structures=20 > to IUPAC names of a larger database? > > Best regards, > > Dr. Andr=E1s P=E9ter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = > - Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 002FD17FC1257310_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Arnab,

Yes, I know it. We have ChemOffice b= ut, I have not found out, if it worked in batch mode. It seems to be not.

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com


"Arnab Chakrabar= ty r.arnab,,gmail.com" <owner-chemistry]-[ccl.net>
Sent by: owner-chemistry]-[ccl.net

05/07/2007 17:50
Please respond to
"CCL Subscribers" <chemistry]-[ccl.net>
To
Andras Borosy/U/Givaudan]-[Givaudan
cc
Subject
CCL: Converting structures to IUPAC names






Sent to CCL by: Arnab Chakrabarty [r.arnab,+,gmail.com]
Hi,
     I guess ChemOffice
(http://www.cambridgesoft.com/software/ChemOffice/) has that functionality.=

Thanks
Arnab

andras.borosy/./givaudan.com wrote:
>
> Dear Colleagues,
>
> Does anyone know an application which is capable to convert structures
> to IUPAC names of a larger database?
>
> Best regards,
>
> Dr. Andr=E1s P=E9ter Borosy
> Scientific Modelling Expert
> Fragrance Research
> Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  C= H-8600  -  D=FCbendorf
>  -  Switzerland
> T:+41-44-824 2164  -  F:+41-44-8242926    -  = http://www.givaudan.com



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--=_alternative 002FD17FC1257310_=-- From owner-chemistry@ccl.net Fri Jul 6 06:18:02 2007 From: "andras.borosy[#]givaudan.com" To: CCL Subject: CCL: Converting structures to IUPAC names, check and size Message-Id: <-34676-070706045820-31659-x+6Rmy6ORdbaFLdSqYo6OQ%a%server.ccl.net> X-Original-From: andras.borosy{}givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00314278C1257310_=" Date: Fri, 6 Jul 2007 10:58:01 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy===givaudan.com This is a multipart message in MIME format. --=_alternative 00314278C1257310_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, If a Name to Structure converter were also available, it would be quite=20 simple. One should compare the original database to the results of=20 Structure-Name-Structure conversion by using a smaller but representative=20 database. Here "larger" means: ~100,000. Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com >=20 > And how does one verify that the conversions are done "correctly"? >=20 > Richard >=20 >=20 >=20 >=20 > ---------------------------------------- > > From: owner-chemistry_+_ccl.net > > To: rwoodphd_+_msn.com > > Subject: CCL: Converting structures to IUPAC names > > Date: Thu, 5 Jul 2007 17:47:18 +0200 > >=20 > >=20 > > Sent to CCL by: Alain Borel [alain.borel() epfl.ch] > > andras.borosy/./givaudan.com wrote: > > >=20 > > > Dear Colleagues, > > >=20 > > > Does anyone know an application which is capable to convert=20 structures=20 > > > to IUPAC names of a larger database? > >=20 > > ACD/Name comes to mind: > >=20 > > http://www.acdlabs.com/products/name=5Flab/name/ > >=20 > > But what do you mean by "of a larger database"? > >=20 > > --=20 > > Alain Borel > > Biblioth=E8que Scientifique Commune UNIL-EPFL > > BCH > > EPFL - SB - SCGC-BCH > > 1015 Lausanne, Switzerland. > >=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, please=20 change> >=20> > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage > >=20> > http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage > >=20 > > Subscribe/Unsubscribe:=20 > > http://www.ccl.net/chemistry/sub=5Funsub.shtml > >=20> >=20 > > Job: http://www.ccl.net/jobs=20 > > Conferences:=20 http://server.ccl.net/chemistry/announcements/conferences/ > >=20 > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password:=20 search) > >=20> >=20> >=20 > >=20> >=20 > >=20 > >=20 >=20 > =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F > Don't get caught with egg on your face. Play Chicktionary! =20 > http://club.live.com/chicktionary.aspx?icid=3Dchick=5Fwlmailtextlink --=_alternative 00314278C1257310_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Colleagues,

If a Name to Structure converter were also available, it would be quite simple. One should compare the original database to the results of Structure-Name-Structure conversion by using a smaller but repre= sentative database.

Here "larger" means: ~100,000.

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com

>
> And how does one verify that the conversions are done "correctly&= quot;?
>
> Richard
>
>
>
>
> ----------------------------------------
> > From: owner-chemistry_+_ccl.net
> > To: rwoodphd_+_msn.com
> > Subject: CCL: Converting structures to IUPAC names
> > Date: Thu, 5 Jul 2007 17:47:18 +0200
> >
> >
> > Sent to CCL by: Alain Borel [alain.borel() epfl.ch]
> > andras.borosy/./givaudan.com wrote:
> > >
> > > Dear Colleagues,
> > >
> > > Does anyone know an application which is capable to convert structures
> > > to IUPAC names of a larger database?
> >
> > ACD/Name comes to mind:
> >
> > http://www.acdlabs.com/products/name=5Flab/name/
> >
> > But what do you mean by "of a larger database"?
> >
> > --
> > Alain Borel
> > Biblioth=E8que Scientifique Commune UNIL-EPFL
> > BCH
> > EPFL - SB - SCGC-BCH
> > 1015 Lausanne, Switzerland.
> >
> >
> >
> > -=3D This is automatically added to each message by the mailing script =3D-
> >
> >
> >
> >
> >
> >       http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5F= message
> >
> >
> >       http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5F= message
> >
> >
> >       http://www.ccl.net/chemistry/sub=5Funsub.sht= ml
> >
> >
> >
> >
> > Conferences: http://server.ccl.net/chemistry/announcements/confer= ences/
> >
> > Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
> >
> >
> >      
> >
> >
> >
> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+
> >
> >
> >
>
> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
> Don't get caught with egg on your face. Play Chicktionary!  =
> http://club.live.com/chicktionary.aspx?icid=3Dchick=5Fwlmailtextlink --=_alternative 00314278C1257310_=-- From owner-chemistry@ccl.net Fri Jul 6 08:03:00 2007 From: "Joe Kwiatkowski jk905[*]imperial.ac.uk" To: CCL Subject: CCL: Grazing Incidence X-Ray Diffraction Message-Id: <-34677-070706074207-9147-DMaBY7VuaJZ0VAMhiq/Tog:_:server.ccl.net> X-Original-From: Joe Kwiatkowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Jul 2007 11:57:24 +0100 MIME-Version: 1.0 Sent to CCL by: Joe Kwiatkowski [jk905[]imperial.ac.uk] Dear CCL'ers. Is anybody aware of any software that can predict grazing incidence X-ray diffraction patterns for a given structure? Many thanks in advance, Joe Kwiatkowski Physics, Imperial College London From owner-chemistry@ccl.net Fri Jul 6 09:27:00 2007 From: "Brian Salter-Duke brian.james.duke+/-gmail.com" To: CCL Subject: CCL:G: CASSCF not giving ground state even though orbitals are correct Message-Id: <-34678-070706062203-23799-Lm5wtjObSnVrqOX+nYP6fA*server.ccl.net> X-Original-From: "Brian Salter-Duke" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 6 Jul 2007 19:26:35 +1000 MIME-Version: 1.0 Sent to CCL by: "Brian Salter-Duke" [brian.james.duke%x%gmail.com] I have been doing a simple CASSCF(6,8)/STO-nG calculation on the triplet groundstate of B2. I wanted to confirm that Gaussian agreed with GAMESS(US) and with the CASVB(6,8) method in the VB program VB2000. Gaussian kept giving me what was clearly an excited state. Finally I added FullDiag to the CASSCF command and it worked but the time in one case went from 3 secs to 3 mins. In every case I was doing a double job - ROHF followed by CASSCF and the ROHF had no problem with the correct orbitals - 2-sigma^2, 4-sigma^2, pi-x^1, pi-y^1 for the 6 electrons. Clearly without the FullDiag (which is default for 6 or less orbitals but not 8), the initial vector was wrong. Has anyone found this before and is there any solution to it? This occurred with G98 and G03. It sort of confirmed my preference for GAMESS for CASSCF, but I would like to understand the Gaussian use as well. Brian. -- Brian Salter-Duke (aka Brian Duke) Brian.James.Duke#,#gmail.com From owner-chemistry@ccl.net Fri Jul 6 10:02:01 2007 From: "Daniel Bonniot dbonniot(0)chemaxon.com" To: CCL Subject: CCL: Converting structures to IUPAC names Message-Id: <-34679-070706023857-2707-D100UJstY9LGziXnscK5lQ]~[server.ccl.net> X-Original-From: "Daniel Bonniot" Date: Fri, 6 Jul 2007 02:38:52 -0400 Sent to CCL by: "Daniel Bonniot" [dbonniot=-=chemaxon.com] You can use ChemAxon's IUPAC name generator: http://www.chemaxon.com/marvin/doc/user/iupacnaming.html For naming a large database, you will want to look at the batch tools in Marvin Beans (cxcalc, molconvert) or at Instant JChem 2: http://www.chemaxon.com/instantjchem/ijc_2_0/ijc_2_0.html Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html Best regards, Daniel Bonniot From owner-chemistry@ccl.net Fri Jul 6 12:04:00 2007 From: "errol lewars elewars]^[trentu.ca" To: CCL Subject: CCL:G: Basis sets with B3LYP Message-Id: <-34680-070706091825-9791-ItWG7Zx/wQL/p5x9Oqw60A#%#server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 06 Jul 2007 09:18:33 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars=trentu.ca] 2007 July 6 Occasionally a structure will oscillate on attempted geometry optimization because the initial hessian is unsatisfactory. For example, starting with an AM1 geometry for equatorial t-butylcyclohexane an attempted B3LYP/6-31G* opt failed with an MNDO hessian, but using a molecular mechanics hessian an optimized geometry was quickly obtained. Of course there are other sources of oscillation problems. E. Lewars ==== Michael Edmund Miller mill*|*pica.army.mil wrote: >Sent to CCL by: "Michael Edmund Miller" [mill- -pica.army.mil] >Dear all, >In gaussian 03, I am trying to run a B3LYP/6-31g(d) optimization of an open-ended nanotube consisting of 68 carbon and 2 boron atoms. Using HF optimized coordinates, I am not able to optimize at 6-31g(d) or even 3-21g using B3LYP (It appears to me that energy oscillations are occurring; also, as Gaussview shows me, the structure moves away from the local minimum and is not intact after a number of iterations). HOWEVER, I can optimize using STO-3G within B3LYP! The STO-3G optimized coordinates are as follows: > > >Optimization of C68B2 singlet using B3LYP/STO-3G optimized coor. > >0 1 >C1 -0.359613 -2.837234 0.030572 >C2 -1.822764 -2.846306 0.021630 >C3 0.366023 -2.620439 1.264848 >C4 0.350332 -2.550359 -1.206821 >C5 -2.572745 -2.552803 1.249363 >B1 -0.375396 -1.828130 2.322287 >C6 -2.515863 -2.555305 -1.210819 >C7 -0.360745 -1.763614 -2.198134 >C8 1.798604 -2.554804 -1.215518 >C9 1.809377 -2.575825 1.244195 >C10 -1.894237 -1.797746 2.269146 >C11 0.367210 -0.624769 2.877461 >C12 -1.805928 -1.767020 -2.205730 >C13 0.358588 -0.630281 -2.747865 >C14 -4.071224 -2.533801 1.193287 >C15 -3.998586 -2.567003 -1.250738 >C16 2.522275 -1.761316 2.238739 >C17 2.521863 -2.833380 0.014918 >C18 2.510926 -1.765512 -2.198179 >C19 -2.582264 -0.638069 2.778289 >C20 -0.358588 0.630179 -2.747888 >C21 -2.520623 -0.632966 -2.753789 >C22 -0.367210 0.624875 2.877438 >C23 -4.684785 -2.925720 -0.043346 >C24 -4.692631 -1.777887 2.221492 >C25 -4.630420 -1.828206 -2.301963 >C26 4.007116 -1.781453 2.215869 >C27 1.828055 -0.619929 2.820655 >C28 4.011574 -2.834800 -0.009767 >C29 3.992633 -1.774873 -2.217515 >C30 1.804093 -0.630848 -2.750662 >C31 -1.804093 0.630747 -2.750686 >C32 0.360745 1.763533 -2.198200 >B2 0.375396 1.828216 2.322219 >C33 -1.828055 0.620033 2.820632 >C34 -4.079738 -0.603691 2.731481 >C35 -4.007741 -0.627743 -2.767577 >C36 4.613723 -2.673463 1.272282 >C37 4.658889 -2.630781 -1.273259 >C38 4.626844 -0.662011 -2.854232 >C39 2.520624 0.632864 -2.753812 >C40 2.582264 0.638172 2.778266 >C41 4.694009 -0.685756 2.827634 >C42 -0.350332 2.550314 -1.206915 >C43 -0.366023 2.620486 1.264751 >C44 -2.510926 1.765430 -2.198245 >C45 -2.522275 1.761399 2.238674 >C46 -4.626844 0.661905 -2.854257 >C47 -4.694008 0.685860 2.827609 >C48 4.007741 0.627641 -2.767600 >C49 1.805928 1.766938 -2.205795 >C50 4.079738 0.603792 2.731458 >C51 1.894237 1.797830 2.269080 >C52 -1.798604 2.554758 -1.215613 >C53 0.359613 2.837235 0.030467 >C54 -1.809377 2.575871 1.244100 >C55 -3.992633 1.774791 -2.217581 >C56 -4.007116 1.781536 2.215803 >C57 4.630419 1.828121 -2.302030 >C58 2.515863 2.555260 -1.210914 >C59 2.572745 2.552850 1.249268 >C60 4.692630 1.777969 2.221426 >C61 -2.521863 2.833381 0.014814 >C62 -4.658889 2.630734 -1.273356 >C63 -4.613724 2.673510 1.272183 >C64 3.998586 2.566957 -1.250833 >C65 4.071224 2.533846 1.193193 >C66 1.822764 2.846307 0.021525 >C67 -4.011574 2.834800 -0.009871 >C68 4.684786 2.925718 -0.043455 > > > >Any comments/assistance on why a minimal basis set works, and yet all the split basis sets I've tried do not? >Thank you. >Mike> > > > > From owner-chemistry@ccl.net Fri Jul 6 12:57:00 2007 From: "Arvydas Tamulis tamulis]^[mserv.itpa.lt" To: CCL Subject: CCL:G: Problems with oscillator strengths in TDDFT Message-Id: <-34681-070706125244-7186-bdq0JDAV4heSV8GMhZU1Bw!^!server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 6 Jul 2007 19:52:25 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis%a%mserv.itpa.lt] Dear Colleagues, Enclosed please find summary of your answers to my request: Problems with oscillator strengths in TDDFT. Thank you very much for your advises! Best regards, Arvydas Tamulis ********************************************* Date: Wed, 4 Jul 2007 12:50:30 +0200 > From: Filipp Furche To: Arvydas Tamulis Subject: Re: Problems with oscillator strengths in TDDFT Dear Professor Tamulis, Thanks for your message. I would recommend to re-do the calculations without symmetry, and see if the results are identical to the D3 case. LanL2DZ is a small basis set. Reinhart Ahlrichs and Florian Weigend have recently developed triple and quadruple zeta basis sets for heavy elements with small-core pseudopotentials [Phys. Chem. Chem. Phys. 7 (2005), 3297]. You may want to use those for comparison. I personally think it's possible that the oscillator strengths of the two lines are reversed in TDDFT. The relative intensities depend strongly on the coupling between the two states, which is very sensitive to inaccuracies of the functional but also to basis set error or solvent effects. If you are interested in an efficient TDDFT code I recommend TURBOMOLE: www.turbomole.com. I am attaching a review that contains some benchmark data. Sincerely, Filipp Furche PD Dr. Filipp Furche Institut fr Physikalische Chemie Lehrstuhl fr Theoretische Chemie Universitt Karlsruhe (TH) Kaiserstrae 12 D - 76128 Karlsruhe Germanyphone: +49/721/608-7227 fax : +49/721/608-7225 email: Filipp.Furche-#-chemie.uni-karlsruhe.de ************************************************ Date: Wed, 04 Jul 2007 13:24:07 +0200 > From: Mark E. Casida To: Arvydas Tamulis Cc: Mark E. Casida Dear Arvydas, As is often the case when questions are sent to me regarding real or supposed failures of TDDFT, the information you are sending me leaves me perhaps as confused as you are yourself. You tell me that you have done the same calculation with 2 program packages and gotten the same answer and then ask me what is wrong with the programs!!?? Permit me to say that I am confused. It would seem that this is just one more indication that the programs are performing correctly and that the problem is in the exchange-correlation (xc) functional. Oscillator strengths are more sensitive than are excitation energies. We talk about oscillator strengths from TDDFT in [CS00] Mark E. Casida and Dennis Salahub, J. Chem. Phys. 113, 8918 (2000). "Asymptotic correction approach to improving approximate exchange-correlation potentials: Time-dependent density-functional theory calculations of molecular excitation spectra" I have attached the PDF file of the article. The point is that what you can expect to get right in the TDDFT adiabatic approximation when Exc is exact is the polarizability. Assuming that the dynamic polarizability is right means that the global distribution of oscillator strengths is about right given the calculated excitation energies. However nearby states (or states missed because of the adiabatic approximation) can lead to variations in the exact distribution of oscillator strengths. This is why in any method (not just TDDFT) it is very difficult to calculate accurate absolute oscillator strengths. (By the way it is also very difficult to determine accurate absolute oscillator strengths experimentally, which is why we were so careful in our article to chose good experimental data.) You might want to just convolute your TDDFT stick spectrum with a suitable broadening function and see how it compares with the experimental spectrum. Below I will ask you a few other questions ... > > We have calculated spectrum and oscillator strengths of D3 symmetry > complex [Ru(bpy)3]2+ using TDDFT B3LYP with the LanL2DZ > basis set and IEFPCM or COSMO water solvent shell models in > Gaussian03 or ORCA program packages. We have received two > singlet-E lines: 456.18 nm (0.0140 oscillator strength) and > 435.61 nm (0.1373 oscillator strength). > Experiment of [Ru(bpy)3]2+ derivatives gives two peaks: > one at about 450 nm (intensity 1.0 arbitrary units) and the > other near 430 nm (intensity 0.6 arbitrary units) > therefore the values of our calculated intensities are reversible in > comparison with experiment. > Oscillator strength calculations done by G03 and > ORCA are exactly the same wrong calculating with PBEPBE potential > using 6-311G* basis set. If G03 and ORCA give the same thing with the same basis and functional then that is NOT wrong. Rather it is just what TDDFT gives you. And as you say it is different from the official interpretation of the experiment (which to be perfectly rigorous would involve a vibronic calculation which was probably not done.) > My impression is that it is something wrong in B3LYP, PBEPBE potentials > when > calculating oscillator strengths by Gaussian03 and ORCA programs > of the D3 symmetry complexes and their derivatives > while the values of spectral lines are exactly good. Your impression is probably right that the problem is the xc functional. But : 1) How did you make the correspondance between the calculated and measured spectra? Did only one set of peaks come out of the theory and only one set could be identified in the experiment? 2) Why the association with D3 symmetry? Do you think that something is going on that has to do with degeneracy? > It is interesting that even ZINDO gives the right intensities in > comparison with experiment but the values of spectral lines are > shifted strongly. 3) What is the character of the ZINDO excitations? Do they have important charge transfer or 2-electron excitation character? ZINDO neglects Rydberg-type excitations. I wouldn't expect these to be too important in the species you are studying but do Rydberg-type excitations appear in your TDDFT calculations? > Maybe you can advise some good program with DFT > potential/basis set for the calculations of right oscillator strengths of > the D3 symmetry complexes and their derivatives? The programs you are working with should be fine. > > In the case if you are far from the field of calculations of oscillator > strengths in G03 or ORCA, would you please to forward my question to > developers of program packages who are working on subroutine > of calculations of oscillator strengths in G03, ORCA or people who > possesses the good subroutine. If the programs are correct, then why should I bother the developers ... ? Or are you saying that developers of xc functionals should be contacted? > > For regular organic compounds the oscillator strengths obtained by > TDDFT in G03 and ORCA are good. That is fine. > More about our research you can see in our website > www.itpa.lt/~tamulis/ and press on button > For PACE project WEBsite Looks like very nice work. Best wishes, Mark Mark E. CASIDA "Improving theory for better chemistry." Professeur, chimie theorique Laboratoire de Chimie Theorique Departement de Chimie Molecularie (DCM, UMR CNRS/UJF 5250) Institut de Chimie Moleculaire de Grenoble (ICMG, FR-2607) Universite Joseph Fourier (Grenoble I) 301 rue de la Chimie, BP 53 F-38041 Grenoble Cedex 9 FRANCE tel: 04.76.63.56.28 (from/de France) 011.33.4.76.63.56.28 (from/de Canada or/ou USA) mailto:Mark.Casida-#-UJF-Grenoble.FR web page: http://dcm.ujf-grenoble.fr/PERSONNEL/CT/casida *************************************** Date: Wed, 4 Jul 2007 09:41:52 -0500 > From: Jim Chelikowsky To: Arvydas Tamulis Dear Arvydas, Thank you for your interest in our work. I believe you can show that the oscillator sum should work with TDDFT. As such, I believe it is likely that the codes you mention may not be converged or TDDFT may not describe transition metal states properly. I do not think it is a matter of which functional you use. This said, I have not run either of these codes and cannot speak directly to the matter. (I do know with our code that we have computed static polarizabilities with finite field differences and with TDDFT. These numbers agree to within 1%. This is a good test on the oscillator strength, at least the sum of them. If you could, you might try a similar test for the system of your (if it is feasible).) I will forward your email to my former student, Igor Vasiliev. He may know more. Best regards, Jim Chelikowsky ************************************** Date: Thu, 5 Jul 2007 13:18:37 +0100 > From: Noel O'Boyle To: tamulis-#-mserv.itpa.lt I've done this calculation too at the B3LYP/LanL2DZ level of theory. Two points: (1) Experiment is in solution. Try a solvent model (note that some solvent models have no effect on symmetric molecules, I seem to recall). (2) Experiment has a band comprising multiple overlapping transitions. Try convoluting the experimental results (with 40 or so calculated transitions) with something like GaussSum, and see what happens. Noel O'Boyle (Formerly Han Vos Research Group, DCU) ********************************************* On Wed, 4 Jul 2007, Arvydas Tamulis tamulis_._mserv.itpa.lt wrote: > > Sent to CCL by: Arvydas Tamulis [tamulis.:.mserv.itpa.lt] > > Dear Colleagues, > > We have calculated spectrum and oscillator strengths of D3 symmetry > complex [Ru(bpy)3]2+ using TDDFT B3LYP with the LanL2DZ > basis set and IEFPCM or COSMO water solvent shell models in > Gaussian03 or ORCA program packages. We have received two > singlet-E lines: 456.18 nm (0.0140 oscillator strength) and > 435.61 nm (0.1373 oscillator strength). > Experiment of [Ru(bpy)3]2+ derivatives gives two peaks: > one at about 450 nm (intensity 1.0 arbitrary units) and the > other near 430 nm (intensity 0.6 arbitrary units) > therefore the values of our calculated intensities are reversible in > comparison with experiment. > Oscillator strength calculations done by G03 and > ORCA are exactly the same wrong calculating with PBEPBE potential > using 6-311G* basis set. > My impression is that it is something wrong in B3LYP, PBEPBE potentials when > calculating oscillator strengths by Gaussian03 and ORCA programs > of the D3 symmetry complexes and their derivatives > while the values of spectral lines are exactly good. > It is interesting that even ZINDO gives the right intensities in > comparison with experiment but the values of spectral lines are > shifted strongly. Maybe you can advise some good program with DFT > potential/basis set for the calculations of right oscillator strengths of > the D3 symmetry complexes and their derivatives? > > In the case if you are far from the field of calculations of oscillator > strengths in G03 or ORCA, would you please to forward my question to > developers of program packages who are working on subroutine > of calculations of oscillator strengths in G03, ORCA or people who > possesses the good subroutine. > > For regular organic compounds the oscillator strengths obtained by > TDDFT in G03 and ORCA are good. > More about our research you can see in our website > www.itpa.lt/~tamulis/ and press on button > For PACE project WEBsite > > With best regards, > Arvydas Tamulishttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Fri Jul 6 18:03:00 2007 From: "Yubo Fan yubofan]*[mail.chem.tamu.edu" To: CCL Subject: CCL: count hbond number Message-Id: <-34682-070706160248-25946-vwfZl1HNQJqJYsgQ95bsMA a server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0035_01C7BFD5.C7E48510" Date: Fri, 6 Jul 2007 13:58:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan%mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0035_01C7BFD5.C7E48510 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, everyone, I'm wondering if it's possible to count the number of H-Bonds for every = water molecules in each frame of the amber trajectory files. I tried the = command hbond in ptraj but it did not give me what I need. Any advice? = Thanks in advance. Yubo =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=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan^-^mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =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=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0035_01C7BFD5.C7E48510 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello, everyone,
 
I'm wondering if it's possible to count = the number=20 of H-Bonds for every water molecules in each frame of the amber = trajectory=20 files. I tried the command hbond in ptraj but it did not give me = what I=20 need. Any advice? Thanks in advance.
 
Yubo
=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=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan^-^mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=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=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
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