From owner-chemistry@ccl.net Wed Aug 27 05:41:01 2014 From: "Mariusz Radon mariusz.radon[A]gmail.com" To: CCL Subject: CCL: Solvation Free Energy of Proton in THF Message-Id: <-50446-140827053826-28532-5fcYL6ycLPzbIjAF125eVQ],[server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 27 Aug 2014 11:38:16 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon::gmail.com] On 08/25/2014 08:23 PM, BUSRA DERELI bsradereli++gmail.com wrote: > Sent to CCL by: "BUSRA DERELI" [bsradereli::gmail.com] > Hello, > > I am trying to calculate pKa values of two systems, one is anionic and the > other is cationic copper systems. I got so weird numbers not close to the > experimental values when I computed the free energy of proton in THF which is > the solvent of interest. I use M11-L local functional with SDD basis set on Cu > atom and 6-31G(d) on all other atoms in the system. Thus, I want to compare the > computed solvation free energy of proton in THF with the experimental value. In > some literature reports, I have seen absolute solvation free energy of proton > in a couple of solvents but not in THF. > > Thanks, > Busra Dereli > Dear Busra: Not very strange that you get weird number for solvation energy of proton which (unlike other ions) is just a point charge! As far as I know, it is extremely difficult to reproduce solvation energy of proton in such calculations. If your goal is to compare acidity of two substances, you are probably more interested in the difference of their pKa values, than in the individual pKa values. The point is that when you compute the difference, the (huge) error on the proton solvation energy cancels out exactly. Alternatively, you can compute relative pKa values of both substances with respect to some other chemical, treated as reference, whose actual pKa you take from experiment. That is much easier than trying to reproduce absolute pKa values. Best regards, Mariusz Radon -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Wed Aug 27 07:39:01 2014 From: "Andreas Klamt klamt/./cosmologic.de" To: CCL Subject: CCL: Solvation Free Energy of Proton in THF Message-Id: <-50447-140827073330-28890-QWU6x1Tvs+R6UKNCO20a9w:-:server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 27 Aug 2014 13:33:32 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^^cosmologic.de] Dear Busra, obviously Mariusz is absolutely right. If you really should like to try to calculate absolute pKa, then you should get aware that the state of the proton in THF surely is not an isolated proton, but a protonated THF. As in water you have H3O+. But I also would not expect that you can get an accurate prediction of the total free energy of the protonated H3O+ with a continuum model. Best regards Andreas Am 27.08.2014 11:38, schrieb Mariusz Radon mariusz.radon[A]gmail.com: > Sent to CCL by: Mariusz Radon [mariusz.radon::gmail.com] > On 08/25/2014 08:23 PM, BUSRA DERELI bsradereli++gmail.com wrote: >> Sent to CCL by: "BUSRA DERELI" [bsradereli::gmail.com] >> Hello, >> >> I am trying to calculate pKa values of two systems, one is anionic and the >> other is cationic copper systems. I got so weird numbers not close to the >> experimental values when I computed the free energy of proton in THF which is >> the solvent of interest. I use M11-L local functional with SDD basis set on Cu >> atom and 6-31G(d) on all other atoms in the system. Thus, I want to compare the >> computed solvation free energy of proton in THF with the experimental value. In >> some literature reports, I have seen absolute solvation free energy of proton >> in a couple of solvents but not in THF. >> >> Thanks, >> Busra Dereli >> > Dear Busra: > > Not very strange that you get weird number for solvation energy of > proton which (unlike other ions) is just a point charge! As far as I > know, it is extremely difficult to reproduce solvation energy of proton > in such calculations. > > If your goal is to compare acidity of two substances, you are probably > more interested in the difference of their pKa values, than in the > individual pKa values. The point is that when you compute the > difference, the (huge) error on the proton solvation energy cancels out > exactly. Alternatively, you can compute relative pKa values of both > substances with respect to some other chemical, treated as reference, > whose actual pKa you take from experiment. That is much easier than > trying to reproduce absolute pKa values. > > Best regards, > Mariusz Radon > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt+/-cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Aug 27 16:12:00 2014 From: "Susi Lehtola susi.lehtola%alumni.helsinki.fi" To: CCL Subject: CCL: Derivative of overlap integral for Slater orbital Message-Id: <-50448-140827144739-11125-0z2cWblRgW9YatZV2gO1pA:_:server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 27 Aug 2014 11:47:25 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola#alumni.helsinki.fi] On 08/26/2014 09:34 AM, sudipta sudipta.mml]=[gmail.com wrote: > Hi All, > > Does anyone have solution for the derivative of overlap integral for > Slater orbital. For the sake of simplicity, I don't need the angular > part of it. If anyone have solution or reference for the radial part of > Slater orbital, please share with me. > > Thanks in advance Your question is nonsensical. The overlap integral is an integral over R^3, yielding a number. There *is* no angular part. Spending two seconds typing "slater overlap integral" into google, in the third result I found analytic expressions for the overlap integal in the general case. http://journals.aps.org/pra/pdf/10.1103/PhysRevA.48.243 The result is pretty hairy (as usually is for non-single center integrals involving Slater functions), but taking its derivative with respect to R should be trivial. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola()alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Aug 27 19:22:01 2014 From: "Andrey.Bliznyuk-#-anu.edu.au" To: CCL Subject: CCL: Derivative of overlap integral for Slater orbital Message-Id: <-50449-140827191233-13198-NObekvkw8PtvcC2CnVWvvw,,server.ccl.net> X-Original-From: Andrey.Bliznyuk:_:anu.edu.au Content-description: Mail message body Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII Date: Thu, 28 Aug 2014 09:12:21 +1000 MIME-Version: 1.0 Sent to CCL by: Andrey.Bliznyuk..anu.edu.au Hi, > > Does anyone have solution for the derivative of overlap integral for > > Slater orbital. For the sake of simplicity, I don't need the angular > > part of it. If anyone have solution or reference for the radial part of > > Slater orbital, please share with me. Probably the simplest form can be found on page 261 in J. Lipinski and J. Leszczynski, Int. J. Quant. Chem, 1982, v22, pp253-263, where the derivative of the overlap integral is expressed as a sum of 3 integrals with different quantum numbers. Best wishes, Andrey From owner-chemistry@ccl.net Wed Aug 27 21:29:01 2014 From: "Marysue Noble office__q-chem.com" To: CCL Subject: CCL: Series of Webinars on Electronic Structure: A Useful Resource Message-Id: <-50450-140827212745-2113-uOoOD51suN1oDCLbTydlDw*|*server.ccl.net> X-Original-From: "Marysue Noble" Date: Wed, 27 Aug 2014 21:27:44 -0400 Sent to CCL by: "Marysue Noble" [office],[q-chem.com] Series of Webinars on Electronic Structure: A Useful Resource Colleagues, As the new academic year rolls in, I wanted to bring to you attention a useful educational resource -- series of webinars on different aspects of electronic structure calculations available from the Q-Chem website: http://www.q-chem.com/qchem-website/ws_sch4.html The topics range from introductory to advanced. Each webinar is about 1 hour long; most include both theoretical background and tutorial materials. Below please find a complete list: Presentation by Prof. Anna Krylov, Prof Daniel Lambrecht, Prof. John Herbert and Dr. Zhengting Gan: "Q-Chem 4.2: An Engine for Innovation" Presentation by Dr. Andreas Dreuw, University of Heidelberg:, "ADC in Q-Chem: A Versatile Module for Excited, Ionized and Electron-Attached States" Presentation by Abir Ganguly, University of Illinois at Urbana-Champaign: "Exploring Reaction Pathways using Quantum Mechanical/Molecular Mechanical Free Energy Simulations with Q-Chem and CHARMM: Application to Biochemical Reactions" Presentation by Prof. Ryan P. Steele, University of Utah: "Beyond Critical Points: Ab initio dynamics and sampling in Q-Chem" Presentation by Prof. Nick Besley, University of Nottingham: "Studying X-ray Absorption Spectroscopy With Q-Chem" Presentation by Prof. Martin Head-Gordon, University of California at Berkeley: "What's New in Q-Chem?" Presentation by Prof. Roi Baer, Hebrew University of Jerusalem, and Dr. Tamar Stein, Rice University: "Tune your range separated hybrid and breathe life into your orbital energies" Presentation by Dr. Emil Proynov, Senior Scientist at Q-Chem, Inc.: "Free Ride Through Some Aspects of Density Functional Theory" Presentation by Dr. Lee Woodcock of University of South Florida: "The Q-Chem/Charmm Interface for QM/MM Studies" Presentation by Dr. Roberto Peverati of University of California at Berkeley: "An Overview of the Minnesota Exchange-Correlation Functionals for DFT Calculations with Q-Chem" Presentation by Prof. Daniel Lambrecht, University of Pittsburgh: "MP2 Methods in the Q-Chem Software Package" Presentation by Dr. Cherri Hsu, Academia Sinica (Taipei, Taiwan): "The Electronic Couplings in Electron Transfer and Excitation Energy Transfer" Presentation by Prof Alan Aspuru-Guzik, Harvard University: "The Harvard Clean Energy Project" Presentation by Prof. John Herbert, Ohio State University: "Exploring solvation effects with polarizable continuum solvation models" Presentation by Prof. Anna Krylov, University of Southern California: "Studying excited states and open-shell species with Q-Chem" Presentation by Andrew Gilbert: "Using the IQmol interface to Q-Chem" Presentation by Martin Head-Gordon: "Exploring Reaction Paths Using the Freezing String Method"