From owner-chemistry@ccl.net Sun Feb 24 03:39:00 2008 From: "Andreas Klamt klamt{:}cosmologic.de" To: CCL Subject: CCL: Self Consistent Reaction Field Message-Id: <-36368-080224033400-615-WH5Ot1LEgx23bcA5RJ0LNw:_:server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 24 Feb 2008 09:33:46 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt]^[cosmologic.de] Sina, you are absolutely right. Such coordinated solvent molecules must be=20 treated explicitly, expecially for Me atoms, because SCRF methods do not = include the orbital interactions between the solute and solvent. Anyway, = I doubt that there are any well proven radii available for such metal=20 atoms in SCRF methods, just for the same reason. Andreas Sina T=FCreli sinatureli[#]gmail.com schrieb: > I would like to ask one more question if possible. Suppose that I am=20 > calculating the spectra of chlorophyll molecules in 1:1 solution and=20 > in solution due to energetic differences it is possible that its Mg=20 > atom is 5 coordinated by the solvent molecule. When doing spectra=20 > calculations on this molecule using SCRF solvent method, should I also = > include the coordinating (sat H2O) solvent molecule in the calculation = > or exclude it from the model (I ofcourse included in the geometry=20 > optimizations I performed, here I am talking about spectra=20 > calculations)? Although I am still not very knowledable on the issue=20 > my opinion is that I should since SCRF is not a method to calculate=20 > the effect of individual solvent molecules on the Mg atom. > > Thanks > > On Fri, Feb 22, 2008 at 9:23 AM, Andreas Klamt klamt^cosmologic.de=20 > > wrote: > > > Sent to CCL by: Andreas Klamt [klamt^^cosmologic.de > ] > Sina, > > your problem is complicated. It must be split into two parts. > 1) What is the right way to represent the ground-state of your > molecule > in the protein environent, > and > 2) What is the best way to represent the the excitation in the > presence > of the protein environment. > > to 1a) I doubt that dielectric solvation models are capable of doin= g > this. If you are able to do good Force-Field calculations on the > protein-ligand complex, perhaps do such first. > 1b) Now could construct the ligand cavity of an SCRF model, remove = the > ligand, use eps=3Dinfinity, i.e. a conductor, and calculate the > screening > charges of the exterior field. > 1c) Now do the quantum chemical groundstate calculation of the > ligand in > the presence of these fixed screening charges. Since these screeni= ng > charges represent the electrostatics of the protein exerted on the > ligand, this corresponds to a ground state calculation in the prese= nce > of the protein field. > > 2) Now you can do the calculation of the UV spectrum by taking into= > account the electronic polarizability of the protein represented by= > eps=3Dn**2 which roughly is 2. Please note, that solvation by the > electronic polarizability - and only by the electronic polarizabili= ty) > is only required for the electronic density change by excitation, n= ot > for the ground state density, because the slow reorientational degr= ees > of freedom cannot follow a fast electronic excitation as it is > considered in an UV spectrum. For more details on this see > "Calculation of UV/Vis Spectra in Solution", A. Klamt, /J. Phys. > Chem./ > 3349-3353 (1996). > > The problem is that this workflow is most likely nowhere > implemented as > software. TURBOMOLE allows you do the excitation in the presence > of the > frozen solute groundstate polarization charges, but step 1b) is not= > supported and would have to be done externally (which is doable, > because > the cavity and A-matrix are written to a file.) It might also be > doable > with some MOPAC versions. Unfortunately, the last public domain > versions > did not contain any robust COSMO implementation, nor the > UV-extension. I > have a locally modified version of MOPAC7 which could do that. Perh= aps > the new MOPAC2007 from Jimmy Stewart > (http://www.cacheresearch.com/mopac.html) can do it, but I do not k= now > exactly. > > As you see, this is real new research, not a standard application o= f > SCRF. Perhaps someone else has a simpler idea, but I doubt that the= > problem can be casted into a simple SCRF problem. > > Andreas > > > Sina T=FCreli sinatureli-x-gmail.com > schrieb: > > I just wanted to bring up my question once more since it was not > > answered. > > > > On Mon, Feb 18, 2008 at 5:17 AM, Sina T reli > sinatureli-,-gmail.com > > > > >> wrote: > > > > > > Sent to CCL by: "Sina T reli" [sinatureli\a/gmail.com] > > Greetings, > > > > I have a question about scrf. While calculationg UV-spectrum = of > > molecules, if we take them to be inside protein enviroment > ligated > > to some protein side-chain, is it a good idea to use scrf and= if > > it is what should be the index of refraction and dielectric > > constant to be used? Since it is burried inside the protein I= > > assume a dielectric constant of 4-6 would be okay but I am no= t > > sure about the refractive index. > > > > Thanks... > > > > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY^-^ccl.net > > > or use:> > > E-mail to administrators: CHEMISTRY-REQUEST^-^ccl.net > > > > or use> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: > > search)> > > > > > > > -- > -------------------------------------------------------------------= ---------- > Dr. habil. Andreas Klamt > COSMOlogic GmbH&CoKG > Burscheider Str. 515 > 51381 Leverkusen, Germany > > Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 > e-mail: klamt() cosmologic.de > web: www.cosmologic.de > -------------------------------------------------------------------= ---------- > COSMOlogic > Your Competent Partner for > Computational Chemistry and Fluid Thermodynamics > -------------------------------------------------------------------= ---------- > > > > - This is automatically added to each message by the mailing script= - > > > > E-mail to subscribers: CHEMISTRY{=3D}ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST{=3D}ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > --=20 -------------------------------------------------------------------------= ---- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt::cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------= ---- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------= ---- From owner-chemistry@ccl.net Sun Feb 24 06:28:01 2008 From: "Barabara Jagoda-Cwiklik barbara,,fh.huji.ac.il" To: CCL Subject: CCL:G: cc-pvDZ for K Message-Id: <-36369-080224061758-29369-klLzgQ8t/R86nwJL4UpC3w__server.ccl.net> X-Original-From: "Barabara Jagoda-Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 24 Feb 2008 12:20:41 +0200 MIME-Version: 1.0 Sent to CCL by: "Barabara Jagoda-Cwiklik" [barbara%a%fh.huji.ac.il] Dear CCLers, I am looking for a correlation consistent pvDZ basis set for potassium (it is not available on EMSL), preferably in Gaussian94 format. I found that it was mentioned, for instance, in ChemPhysLett 430 (2006) 459 (doi:10.1016/j.cplett.2006.09.029) Thank you for any help! Best regards, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara],[fh.huji.ac.il