From owner-chemistry@ccl.net Mon Sep 6 02:35:01 2010 From: "Dr.Wolfgang Quapp quapp]~[rz.uni-leipzig.de" To: CCL Subject: CCL: 6 degree of freedom for linear molecule ?????? Message-Id: <-42702-100906023329-32430-dK3k6wTOvEc5LPW4t+vWmg- -server.ccl.net> X-Original-From: "Dr.Wolfgang Quapp" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 06 Sep 2010 08:33:21 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr.Wolfgang Quapp" [quapp{}rz.uni-leipzig.de] Zitat von "ABHISHEK SHAHI shahi.abhishek1984!A!gmail.com" : > Dear All > Here optimization give a linear geometry but on frequency calculation, > Job gives 6(translational+rotational) frequencies and they are negative > enough to make any sense.My route section is "# MP2=full/aug-cc-PVTZ > opt=(verytight,maxcycle=100) nosymm freq=noraman > scf=(xqc,vshift=150,tight)".And same problem is faced by me several other > complexes.Please help me in this problem.your suggestions are valuable for > me. > > Full mass-weighted force constant matrix: > Low frequencies -378.7133 -378.7122 -215.1945 -215.1944 0.0043 0.0046 > Low frequencies 0.0060 714.7626 2094.2659 > Molecule is linear but NTrRo=6. > Error termination via Lnk1e in /home/pkg/lic/g09/em64t/g09/l716.exe at Fri > Sep 3 19:32:28 2010. > Job cpu time: 0 days 3 hours 7 minutes 24.7 seconds. > Dear ABHISHEK SHAHI, first of all, there are 7 interesting frequencies. Three zeros for translation are o.k. My be that the 2 lowest are from a saddle of index 2? But opt searches for a minimum? Dr.Wolfgang Quapp ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Mon Sep 6 03:17:00 2010 From: "Andreas Klamt klamt**cosmologic.de" To: CCL Subject: CCL:G: Gsolv - pKa - Frequency Message-Id: <-42703-100906030718-17267-CsH4m55u+UQcb7P3ZcTjkQ() server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 06 Sep 2010 09:07:10 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt,+,cosmologic.de] Hi all together, I think that Chris is quite right in most of his arguments, and definitely Mike is right as well in saying that the partial molar entropy is thermodynamically well defined and that it can be considerably different in solution compared to the ideal gas. But this difference is to first order already implicitly parameterized into every continuum solvation model that is parameterized versus exp. dG_solv. data. Since these data do include the entropy change, the latter is also implicitly included into the parameterized solvation models, not based on a frequency change, but via surface proportional corrections. If you try to add the same via frequency based corrections (which are not well defined, as I mentioned earlier and as Chris mentioned in detail), you can only make things worse! In a solvation model which takes into account temperature dependence, as in COSMO-RS, you can quantify the included partial molar entropy of solvation based on the temperature derivative of dG_solv. If you would like to develop a solvation model which is open for the explicit addition of solvation entropy, you would have to do that based on the the enthalpy (heat) of solvation, but there are much less exp. data available for dH-solv than for dG_solv, and few people are interested in dH_solv. The only situation for which lots of well measure dG_solv ad dH_solv data are available, is self-solvation, which is nothing else than free energy of vaporization (i.e. ln(vapor pressure) and heat of vaporization). It should be noted that COSMO-RS describes dG_vap and dH_vap consistently as self-solvation. Regarding your pKa problem (as for any reaction calculation) this means: - Do the best gas phase calculation as you can afford, incl. gas-phase entropy change, and then add the solvation free energies of educts and products (with the right sign). - Or use a parameterized pKa model directly based on the solution phase energy difference of protonated and deprotonated species. Hope this helps. Andreas Am 05.09.2010 14:57, schrieb W Flak williamflak- -yahoo.com: > Sent to CCL by: "W Flak" [williamflak]![yahoo.com] > Dear CCL > I got some questions about pKa calculation hoping to get a help here. > * First of all, on G03 help page, it says Gsolvation=EPCMEgas, but if I > compared delta Gsolv obtained by SCFVAC with those obtained by carrying out two > separate jobs, I'd get difference. Why? > Example: > by SCFVAC > DeltaG (solv) (kcal/mol) = -10.26 > By two separated jobs: > deta Gsolv = Epcm - Egas = -15.49 > > * Is the entropy of a molecule in gas phase different from that in a solution? > if yes, please direct me to the undergraduate book I should read > > * I read many posts on pKa calculation and found some people (as Andreas > Klamt,2006) recommended not to include frequency in pKa calculation, and the > others include it. What do you recommend? > > * In G.A.A. Saracino et al. / Chemical Physics Letters 373 (2003) 411415 > Gibbs energies have been estimated by single point HF/6-31+G(d,p) calculations > at geometries optimised in aqueous solution at the PBE0/6-31+G(d,p) level. How > they calculated frequency at level differs from the optimization level? > > Any kind of help would be appreciated > W. Flak> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt{}cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Mon Sep 6 03:52:01 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis]~[borealisgroup.com" To: CCL Subject: CCL:G: Potential energy scans on Gaussian - Possible From Initial Geometry? Message-Id: <-42704-100906015539-26175-ExrwO94reD1H7Xp5+p4BGg#%#server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 6 Sep 2010 07:55:26 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis[#]borealisgroup.com] Jeffrey Hi If I understood your question correctly you need to perform a "rigid PES", which means that you will calculate single point energies for the structure that you have at each run of your scan. That means that if you change the angles you are interested in the rest of the geometry will remain unchanged (in comparison with your initial structure). Is this what you're looking for or I misunderstood your question? I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com%%ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com%%ccl.net] On Behalf Of Jeffrey Mo jdmo . mit.edu Sent: Saturday, September 04, 2010 4:29 AM To: Gkourmpis, Thomas Subject: CCL:G: Potential energy scans on Gaussian - Possible From Initial Geometry? Sent to CCL by: "Jeffrey Mo" [jdmo]=[mit.edu] Hi everyone, My first post! Hopefully I'll get some help from you guys and be able to give some help in the future too. I'm trying to perform a potential energy scan (PES) on short-chain alkyl/alkenyl radical transition states right now, and am running into a problem. Gaussian starts each new optimization in the scan from the previous geometry; therefore, when I get all the way around (360 degrees) a dihedral, for instance, I often don't end up at the same geometry. Is there a way that I can ask Gaussian to perform each new optimization from the initial geometry? That is, let's say we're on scan job #19 of a 36-point dihedral scan (where each scan increments by 10 degrees) -- then, I just want to change the relevant dihedral by 180 degrees from the initial geometry, not by 10 degrees from the geometry of scan job #18. Thanks in advance! Jeffrey Mo MIT Chemical Engineering Doctoral Candidate jdmo-x-mit.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Sep 6 04:27:00 2010 From: "Stan van Gisbergen vangisbergen]*[scm.com" To: CCL Subject: CCL: Antiferromagnetism and multiplicity Message-Id: <-42705-100906032911-27656-rTEd6iMaa+auc+9fsk6PFw.@.server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-39-508291981 Date: Mon, 6 Sep 2010 09:29:29 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen,,scm.com] --Apple-Mail-39-508291981 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Sayed, Generating broken symmetry solutions is easy with ADF. The code has some special keywords for this purpose, which enable you to perform calculations with appropriate starting spin densities and potentials, ensuring that the proper broken symmetry solution will be obtained. ADF has been used extensively for this purpose by Lou Noodleman and coworkers, who pioneered the broken symmetry approach for ferromagnetic / antiferromagnetic coupling. Our ADF-GUI tutorial 11 shows step-by-step how to perform such calculations in the tricky case of an Fe4S4 cluster (iron-sulfur cubane). http://www.scm.com/Doc/Doc2009.01/ADFGUI/ADFGUI_tutorial/page141.html In case you want to give it a try yourself: http://www.scm.com/ SCMForms/TrialRequest.jsp Best regards, Stan van Gisbergen On Sep 3, 2010, at 7:18 PM, Nuno A. G. Bandeira nuno.bandeira[a] ist.utl.pt wrote: > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira() ist.utl.pt] > On 03-09-2010 16:05, Sayed Mesa elsayed.elmes- -yahoo.com wrote: >> Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] >> Dear CCL community >> I measured experimentally the magnetic properties of some >> dinuclear transition-metal complexes for example [Co2L]4+ where L >> is macrocyclic ligand. I found most of them exhibit >> "Antiferromagnetic character". I want to optimize the geometries >> of these complexes but I am confused how can I define the >> multiplicity in such case? It is worth mentioned that the total >> number of electrons for the complex or for the ligand is even. > > The multiplicity is always singlet but you should attempt use what > is called the broken symmetry technique (Google or WoK it for the > relevant literature). > > Tipically you start with the highest multiplicity and then mix the > SOMOs to produce the singlet. > > > -- > Nuno A. G. Bandeira, AMRSC > Laboratoire de Chimie LR6 > Ecole Normale Superieure de Lyon > 46, Allee d'Italie > 69364 Lyon Cedex 07 - France > http://cqb.fc.ul.pt/intheochem/nuno/ > -- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen#,#scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-39-508291981 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII

Dear Sayed,

Generating broken symmetry = solutions is easy with ADF. The code has some special keywords for this = purpose, which enable you to perform calculations with appropriate = starting spin densities and potentials, ensuring that the proper broken = symmetry solution will be obtained. ADF has been used extensively for = this purpose by Lou Noodleman and coworkers, who pioneered the broken = symmetry approach for ferromagnetic / antiferromagnetic = coupling.

Our = ADF-GUI tutorial 11 shows step-by-step how to perform such calculations = in the tricky case of an Fe4S4 cluster (iron-sulfur = cubane).

http://www.scm.com/Doc/Doc2009.01/ADFGUI/ADFGUI_tutorial/page141.html=

In case you want to give it = a try yourself: http://www.scm.com/S= CMForms/TrialRequest.jsp

Best = regards,

Stan van = Gisbergen

On Sep 3, = 2010, at 7:18 PM, Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt = wrote:

Sent to CCL by: "Nuno A. G. Bandeira" = [nuno.bandeira() ist.utl.pt]
On 03-09-2010 16:05, Sayed = Mesa elsayed.elmes- -yahoo.com wrote:

Sent to CCL by: "Sayed Mesa" = [elsayed.elmes_-_yahoo.com]

Dear CCL = community

I measured experimentally the = magnetic properties of some dinuclear transition-metal complexes for = example [Co2L]4+ where L is macrocyclic ligand. I found most of them = exhibit "Antiferromagnetic character". I want to optimize the geometries = of these complexes but I am confused how can I define the multiplicity = in such case? It is worth mentioned that the total number of electrons = for the complex or for the ligand is even.

The = multiplicity is always singlet but you should attempt use what is called = the broken symmetry technique (Google or WoK it for the relevant = literature).

Tipically you start with the highest multiplicity = and then mix the SOMOs to produce the singlet.

Nuno A. G. Bandeira, AMRSC

Laboratoire de Chimie LR6

Ecole Normale Superieure de Lyon

46, Allee d'Italie

69364 = Lyon Cedex 07 - France

http://cqb.fc.ul.pt/intheoch= em/nuno/

-=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 change

the strange characters on the top line to the #,# = sign. You can also

look up the = X-Original-From: line in the mail header.

E-mail to = subscribers: CHEMISTRY#,#ccl.net = or use: