From owner-chemistry@ccl.net Wed Apr 23 04:09:00 2008 From: "Lekpa Duukori duukori:+:gmail.com" To: CCL Subject: CCL:G: problems with a transition state Message-Id: <-36820-080423035814-19070-wVy+niNOuqFBnw2vsON/jQ_._server.ccl.net> X-Original-From: "Lekpa Duukori" Content-Type: multipart/alternative; boundary="----=_Part_9794_12638561.1208937474243" Date: Wed, 23 Apr 2008 09:57:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Lekpa Duukori" [duukori|-|gmail.com] ------=_Part_9794_12638561.1208937474243 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello David, Rainer and Alex I am trying out some of your suggestions. I will report what I get. Regards Lekpa On Tue, Apr 22, 2008 at 4:49 PM, Rainer Koch rainer.koch . uni-oldenburg.de< owner-chemistry!A!ccl.net> wrote: > > Sent to CCL by: Rainer Koch [rainer.koch^uni-oldenburg.de] > Dear Lepka, > > did you try to read in the force constants of your successful PM3 job into > the subsequent optimisations (opt(readfc))? This can help a lot as you now > already follow the "correct" mode. > > Cheers, > > Rainer. > > Lekpa Duukori duukori*gmail.com schrieb: > > Hello Everyone > > > > I am having some problems with a transition state optimization using > > Gaussian 03. > > > > I am working with fairly large silicate species of about 60 atoms. I > > did a transition state scan at PM3 level due to size and successfully > > obtained the TS points ( checked by frequency calculation at PM3 level). > > Subsequent optimizations at HF and B3LYP levels of theory however failed to > > locate this transition state. B3LYP/6-31+G(d) calculations at best get a > > negetive frequency corresponding to hydrogen tail wag. > > > > Does any one have some ideas of where to go from here? > > > > Thanks > > > > Lekpahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_9794_12638561.1208937474243 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello David, Rainer and Alex

I am trying out some of your suggestions. I will report what I get.

Regards

Lekpa

On Tue, Apr 22, 2008 at 4:49 PM, Rainer Koch rainer.koch . uni-oldenburg.de <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: Rainer Koch [rainer.koch^uni-oldenburg.de]
Dear Lepka,

did you try to read in the force constants of your successful PM3 job into the subsequent optimisations (opt(readfc))? This can help a lot as you now already follow the "correct" mode.

Cheers,

       Rainer.

Lekpa Duukori duukori*gmail.com schrieb:

Hello Everyone

I am having some problems with a transition state optimization using Gaussian 03.

I am working with fairly large silicate species  of about 60 atoms.  I did a transition state scan at PM3 level due to size and successfully obtained the TS points ( checked by frequency calculation at PM3 level). Subsequent optimizations at HF and B3LYP levels of theory however failed to locate this transition state. B3LYP/6-31+G(d) calculations at best get a negetive frequency corresponding to hydrogen tail wag.

Does any one have some ideas of where to go from here?

Thanks

Lekpa




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------=_Part_9794_12638561.1208937474243-- From owner-chemistry@ccl.net Wed Apr 23 04:44:00 2008 From: "Herbert Fruchtl herbert.fruchtl-x-st-andrews.ac.uk" To: CCL Subject: CCL:G: Gaussian 03 SCF converge problem. Message-Id: <-36821-080423042951-31657-r8LTHNWz8Xpd1vUHsYy0Fw^-^server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Apr 2008 09:29:04 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl**st-andrews.ac.uk] Dear Shentan, Transition metals are always difficult, due to the many orbitals close to the Fermi surface. Try SCF=XQC. That's slower, but more likely to converge. If it doesn't work, get another program. ORCA is good for transition metals. Doesn't do ECP's, but has a very fast RI-DFT, so you can do all-atom calculations (although you might get problems with relativistic effects for the heavier atoms). Herbert shentan chen modigger###gmail.com wrote: > > Sent to CCL by: shentan chen [modigger ~~ gmail.com] > Dear All, > > I am running DFT calculations on three organometallic ions(LnCr, LnMo > and LnW, where Ln are the same ligands) using Gaussian 03. All the > calculations were run under C3v symmetry. Only the job of Cr can be done > normally and the jobs of Mo and W always ended with SCF converge > failure. Why is that? How to solve this problem? > Thanks for your help, > shentan > > The following are parts of my input and output: > > Input > # opt freq pw91pw91 genecp > title > 1 2 > W > N,1,B1 > > Output: > ........... > EnCoef did 100 forward-backward iterations > Rare condition: small coef for last iteration: 0.625D-15 > EnCoef did 100 forward-backward iterations > EnCoef did 100 forward-backward iterations > Restarting incremental Fock formation. > ............ > EnCoef did 1 forward-backward iterations > Matrix for removal 9 Erem= -466.949785517310 Crem= 0.000D+00 > Density matrix is not changing but DIIS error= 1.16D-02 CofLast= 1.00D-04. > The SCF is confused. > Error termination via Lnk1e in /usr/local/g03d01/g03/l502.exe at Mon Apr > 21 17:49:22 2008.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed Apr 23 08:59:00 2008 From: "grog]![netsons.org" To: CCL Subject: CCL: Linear dependency in TurboMole Message-Id: <-36822-080423071010-31868-guteVaMOawWJie7H0rW++g%server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 23 Apr 2008 12:10:59 +0200 MIME-Version: 1.0 Sent to CCL by: [grog-.-netsons.org] Hi, trying to run dscf in TM with the fairly big aug-cc-pVTZ basis set. SCF convergence incredibly slow in some cases, in others strange oscillations during scf. With smaller basis sets scf converges in very few steps. I suspect linear dependency problems with the aug-cc-pVTZ basis set. Two small questions: 1) How to check for this in TM ? 2) How to solve it in TM ? TIA, jack -- Powered by http://www.netsons.org From owner-chemistry@ccl.net Wed Apr 23 10:16:01 2008 From: "TJ O Donnell tjo!A!gnova.com" To: CCL Subject: CCL: How to implement your own Daylight or MACCS fingerprint? Message-Id: <-36823-080422105339-18842-tW8WOWA/Ydc5Hs5mjX/cyA**server.ccl.net> X-Original-From: "TJ O Donnell" Date: Tue, 22 Apr 2008 10:53:35 -0400 Sent to CCL by: "TJ O Donnell" [tjo(0)gnova.com] You can generate path-based fingerprints (ala Daylight) using OpenBabel or FROWNS, both available as open source. The 166 MACCS keys can be expressed in SMARTS and those same 2 toolkits can be used to create a key-based fingerprint (ala MACCS), although you'd have to do a bit more programming. I've described both methods for fingerprinting in a new book, Design and Use of Relational Databases in Chemistry. It's due to be published this Fall. The gNova CHORD product can generate both types of fingerprints as well. I'ts free to academics. TJ -- TJ O'Donnell, Ph.D. President, gNova, Inc. http://www.gnova.com Tiejun Cheng tjcheng.:.mail.sioc.ac.cn wrote: > Sent to CCL by: "Tiejun Cheng" [tjcheng:_:mail.sioc.ac.cn] > Hi all, > > Anyone know or any clue on how to implement the Daylight or MACCS fingerprint? These two are very useful. > > Sincerely, > > Jay > From owner-chemistry@ccl.net Wed Apr 23 11:29:00 2008 From: "Ross Walker ross*rosswalker.co.uk" To: CCL Subject: CCL:G: UV-Vis spectra prediction Message-Id: <-36824-080423005003-25677-pLqRcnHTSUQpYoTFrPWzfg..server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 22 Apr 2008 21:45:29 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross!^!rosswalker.co.uk] Hi Nancy, You might also want to refer to the following publications which detail a method for predicting UV vis absorption and emission spectra along with line shapes and widths using a combination of molecular dynamics and QM/MM excitation calculations: Walker, R.C., Klug, D.A. et al., J. Phys. Chem. B., 2002, 106, p11658-11665 and Mercer, I.P, Gould, I.R., Klug, D.A., J. Phys. Chem. B., 1999, 103, p7720-7727 All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross * rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] > Sent: Friday, April 18, 2008 05:41 > To: Walker, Ross > Subject: CCL:G: UV-Vis spectra prediction > > > Sent to CCL by: "Nancy A Neale" [nealen:_:mail.nih.gov] > Dear David Gallagher, > > I am interested in this subject area as well. Please, may I > also have a copy of your presentation? > > Thank you, > > Nancy Neale > email: nneale-.-mail.nih.gov > > > "Sue Lam chsue2004#yahoo.com" wrote: > > > > Sent to CCL by: Sue Lam [chsue2004|-|yahoo.com] > > --0-2006443586-1208406809=:8689 > > Content-Type: text/plain; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > > Dear David Gallagher, > > > > I am also interested in that topic. Could I have a copy > of your powerpoint? > > > > Thanks, > > Sue > > > > "David Gallagher gallagher.da{=}gmail.com" > wrote: > > Bonjour Jerome, > > > > The band-width is related to the gradient of the excited > state at the transition, i.e. a high gradient allows access > to more vibrational levels > from the ground state and hence, > a higher band-width, conversely a low gradient gives a narrow > peak. I have some Powerpoint slides on UV-spectra that I put > together a few years ago explaining the concept . Please let > me know if you want a copy of them. > > > > Regards, > > David Gallagher > > CACheResearch.com > > > > At 05:16 AM 4/16/2008, Jerome Kieffer > Jerome.Kieffer{=}terre-adelie.org wrote: > > Dear CCLers, > > > > I am trying to reproduce experimental UV-spectra of organic > molecules : > > > > After the conversion wavelength (nm) -> energy (cm-1) of > the experimental spectrum, I deconvoluted it by a sum of > gaussian functions (using FitYK). It fits well. > > > > Transitions I obtained using TDDFT are pretty good compared > with the center of the gaussian deconvolution, but the FWHM > of the experimental spectrum's gaussian varies from 2000 to 8000 cm-1. > > > > So my question is: is it possible to calculate the > broadening of an absorption band ? some software like > gausssum suggest a FWMH of arround 3000cm-1 > > Thank you for your help > > > > Regards > > > > --------------------------------- > > Jrme Kieffer > > http://www.terre-adelie.org > > > > > > --------------------------------- > > Be a better friend, newshound, and know-it-all with Yahoo! > Mobile. Try it now. > > --0-2006443586-1208406809=:8689 > > Content-Type: text/html; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > >
Dear David Gallagher,
 
I > am also interested in that topic. Could I have a copy of your > powerpoint?
 
Thanks,
>
Sue

"David Gallagher > gallagher.da{=}gmail.com" > <owner-chemistry,ccl.net> wrote:
>
Bonjour > Jerome,

The band-width is related to the gradient of > the excited state at the transition, i.e. a high gradient > allows access to more vibrational levels > from the ground > state and hence, a higher band-width, conversely a low > gradient gives a narrow peak.  I have some Powerpoint > slides on UV-spectra that I put together a few years ago > explaining the concept . Please let me know if you want a > copy of them.

Regards,
David > Gallagher
CACheResearch.com

At 05:16 AM 4/16/2008, > Jerome Kieffer Jerome.Kieffer{=}terre-adelie.org wrote:
> >
Dear > CCLers,

I am trying to reproduce experimental > UV-spectra of organic molecules :

After the conversion > wavelength (nm) ->  energy (cm-1)  of the > experimental spectrum,  I deconvoluted it by a sum of > gaussian functions (using FitYK). It fits > well.

Transitions I obtained using TDDFT are pretty > good compared with the center of the gaussian > deconvolution,  but the FWHM of the experimental > spectrum's gaussian varies from 2000 to 8000 cm-1.

So > my question is: is it possible to calculate the broadening of > an absorption band ? some software like gausssum suggest a > FWMH of arround 3000cm-1   
Thank you for > your help

Regards
Jrme Kieffer
href="http://www.terre-adelie.org/" > eudora="autourl">http://www.terre-adelie.org >

> > > >

Be a better friend, newshound, and > > know-it-all with Yahoo! Mobile. href="http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.co m/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ "> Try it now. > > --0-2006443586-1208406809=:8689-- > > > > > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > > From owner-chemistry@ccl.net Wed Apr 23 13:04:01 2008 From: "Gonzalo Jimenez-Oses gjimenez+/-unizar.es" To: CCL Subject: CCL: low-spin versus high-spin complexes --SUMMARY-- Message-Id: <-36825-080423130222-2716-35fPAQyuEpBo8i2akzbSsg-*-server.ccl.net> X-Original-From: "Gonzalo Jimenez-Oses" Date: Wed, 23 Apr 2008 13:02:18 -0400 Sent to CCL by: "Gonzalo Jimenez-Oses" [gjimenez(0)unizar.es] Dear CCL'ers, Dear All, This is to gratefully thank the precise answers pointed out by Frank Nesse Luca Bertini and Marcel Swart. All the comments seem to go in the same direction, being the following the most remarkable ideas: - The energy comparison of low- and high-spin states for TM complexes is not an easy task. Although the high/low-spin values are comparable, whether one should discard one solution or not is system dependent. - In most cases DFT tends to overstabilize low spin states but this tends to be critically dependent on the amount of HF exchange - the "optimal value" of %HF exchange - unfortunately - depends on the system. HF itself hugely overstabilizes high spin states. For instance, Reiher and co-workers recommend 15% HF exchange in B3LYP instead of the usual 20% for Fe(II). Some useful references are: - M. Reiher, O. Salomon, B. A. Hess, Reparametrization of hybrid functionals based on energy differences of states of di erent multiplicity, Theor. Chem. Acc. 107 2001, 48 - Bertini, L.; Bruschi, M.; De Gioia, L.; Fantucci, P.;J. Phys. Chem. A.; (Article); 2007; 111(48); 12152-12162). - Fouqeau, A.; Casida, M.E.; Lawson, L.M.; Hauser, A.; Neese, F. (2005) Comparison of Density Functionals for Energy and Structural Differences Between the High-[5T2g: (t2g4)(eg2)] and Low-[1A1g: (t2g6)(eg0)] Spin States of Iron(II) Coordination Compounds : II. Comparison of Results for More than Ten Modern Functionals with Ligand Field Theory and Ab Initio Results for Hexaquoferrous Dication, [Fe(H2O)6]2+ and Hexaminoferrous Dication [Fe(NH3)6]2+, J. Chem. Phys., 122, 044110/1-13 - Fouqueau, A.; Mer, S.; Casida, M.E.; Daku, L.M.L.; Hauser, A.; Mieva, T.; Neese, F. (2004) Comparison of Density Functionals for Energy and Structural Differences between the High [5T2g: t2g4eg2] and Low [1A1g: t2g6] Spin States of the Hexaquo-Ferrous Ion, [Fe(H2O)6]2+, J. Chem. Phys., 120, 9473-9486 In my particular case, I was interested in octahedral Co(II) complexes and, like in the case of tetrahedral ones, high-spin seens to be the chemically sensible multiplicity. Concerning the Cu(I)/Cu(II) question, Prof. Nesse pointed out that the difference between the two energies for Cu(II) and Cu(I) at the same geometry represents the vertical ionization potential and at individually optimized geometries the adiabatic ionization potential. In reality these complexes exist in solution and will have very different solvatization energies. If one would calculate this perfectly one would obtain as the difference in free energy the redox potential of the Cu(II)/Cu(I) couple. I really appreciate this clarification. The solution that I tried was to calculate the following "isodemic" equation to evaluate the relative stability of different Cu(I)/Cu(II) species, given that I was not able to properly reproduce the redox potential of each isolated complex: Cu(I)-ligand_A + Cu(II)-ligand_B --> Cu(II)-ligand_A + Cu(I)-ligand_B Thanks, Gonzalo From owner-chemistry@ccl.net Wed Apr 23 19:34:00 2008 From: "Oluwakemi.Oloba:-:mail.uh.edu" To: CCL Subject: CCL:G: basis set Message-Id: <-36826-080423154022-9650-beJZc+Pasg1+Vp2shwhUaQ:_:server.ccl.net> X-Original-From: Oluwakemi.Oloba:-:mail.uh.edu Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_YkSFI+Wkqbqo/O1DUHuTug)" Date: Wed, 23 Apr 2008 13:48:16 -0500 MIME-version: 1.0 Sent to CCL by: Oluwakemi.Oloba~!~mail.uh.edu This is a multi-part message in MIME format. --Boundary_(ID_YkSFI+Wkqbqo/O1DUHuTug) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline what program are you using. for gaussian03 try using the gen keyword http://www.gaussian.com/g_ur/k_gen.htm ----- Original Message ----- =46rom: "Ioana Sovago isovago]*[chem.ubbcluj.ro" Date: Tuesday, April 15, 2008 4:37 pm Subject: CCL: basis set To: "Oloba, Kemi A " >=20 > Sent to CCL by: "Ioana=A0 Sovago" [isovago^chem.ubbcluj.ro] > Who cand help me how to write un input using 2 different baisis= =20 > set?=A0 For more details pleas send me an email. >=20 > Best regards, Ioana S >=20 >=20 >=20 > -=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,=20 > please change>=20> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message > Subscribe/Unsubscribe:=20 > =A0=A0=A0=A0=A0=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig=A0 (login: ccl,=20 > Password: search) >=20> =A0=A0=A0=A0=A0>=20>=20 >=20 > --Boundary_(ID_YkSFI+Wkqbqo/O1DUHuTug) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline what program are you using. for gaussian03 try using the gen keyword<= br>http://www.gaussian.com/g_ur/k_gen.htm

----- Original Messa= ge -----
From: "Ioana Sovago isovago]*[chem.ubbcluj.ro" <owner-= chemistry,ccl.net>
Date: Tuesday, April 15, 2008 4:37 pm
Sub= ject: CCL: basis set
To: "Oloba, Kemi A " <ooloba,uh.ed= u>

>
> Sent to CCL by: "Ioana  Sovago" [isov= ago^chem.ubbcluj.ro]
> Who cand help me how to write un input u= sing 2 different baisis
> set?  For more details pleas se= nd me an email.
>
> Best regards, Ioana S
>
&g= t;
>
> -=3D This is automatically added to each message= by the mailing
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