From owner-chemistry@ccl.net Thu Apr 26 08:19:01 2012 From: "Sotirios Baskoutas bask__upatras.gr" To: CCL Subject: CCL: JOURNAL OF ADVANCED PHYSICS_ CALL FOR PAPERS Message-Id: <-46797-120426051605-25986-hARNRsDRpKPnAIKV1zumsg|,|server.ccl.net> X-Original-From: "Sotirios Baskoutas" Date: Thu, 26 Apr 2012 05:16:04 -0400 Sent to CCL by: "Sotirios Baskoutas" [bask,upatras.gr] Dear Collegues I would like to invite you to submit an article for the upcoming journal "Journal of Advanced Physics". The deadline for the first issue is 30/5/2012. Authors will receive the following benefits: Fast reviews Rapid times to publication No page charges Free color where justified Distinguished editorial board Manuscripts must be prepared according to Journal's guidelines, available at http://www.aspbs.com/jap/ Submit your manuscript directly to Editor-in-Chief Dr. S. Baskoutas (editorjap(!)upatras.gr) Yours sincerely ------------------------------------------ Dr. Sotirios Baskoutas Department of Materials Science University of Patras 26504 Patras, Greece Editor-in-Chief: Journal of Advanced Physics http://www.aspbs.com/jap/ Email: editorjap(!)upatras.gr Tel.: 0030 2610 96 93 49 From owner-chemistry@ccl.net Thu Apr 26 10:05:00 2012 From: "Vera Cathrine vera.cathrine|,|yahoo.com" To: CCL Subject: CCL: G09: PES rigid scan in cartesian coorinate? Message-Id: <-46798-120426100207-4761-YRhPAYxm/xGGuQh9ZPYsiQ#,#server.ccl.net> X-Original-From: "Vera Cathrine" Date: Thu, 26 Apr 2012 10:02:04 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine_._yahoo.com] Hello CCLers, I want to perform a rigid PES scan along a bond distance using oniom method for a large molecule. The problem is that I have only the Cartesian coordinates for the system. It is very hard to work with Z-matrix created by Gaussview for this system. I know that opt or geom=modredundant are available for relaxed scan. However, I am not sure how we could define the scanning coordinate in the Cartesian for rigid scan? Any help is highly appreciated. Best regards, Vera From owner-chemistry@ccl.net Thu Apr 26 17:19:01 2012 From: "Christoher Kim ckim===deltacollege.edu" To: CCL Subject: CCL:G: Example Gaussian 09 Input File for UV/Vis spectrum calculation Message-Id: <-46799-120426141814-2010-PMHidxmoh1ORZpaU4oLamg a server.ccl.net> X-Original-From: "Christoher Kim" Date: Thu, 26 Apr 2012 14:18:13 -0400 Sent to CCL by: "Christoher Kim" [ckim- -deltacollege.edu] Hi All, I have been doing some reading and web searching for an example Gaussian 09 input file that would allow me to calculate the UV/Vis spectrum for aqueous solutions of transition metal complexes. I would love a system that would give me similar results for both experimental and calculated. Any help or suggestions would be greatly appreciated. I am quite new to all of this, so please me kind. Thanks, -Chris From owner-chemistry@ccl.net Thu Apr 26 17:54:01 2012 From: "Jason G. Gillmore gillmore : hope.edu" To: CCL Subject: CCL:G: Help please - CPCM with UAKS radii in Gaussian03 Message-Id: <-46800-120426155210-24684-XBT8h2NpYnYvnOzPtFlqxA:server.ccl.net> X-Original-From: "Jason G. Gillmore" Date: Thu, 26 Apr 2012 15:52:09 -0400 Sent to CCL by: "Jason G. Gillmore" [gillmore++hope.edu] Short questions: 1) In Gaussian03, when I do a molecular energy calculation with CPCM using radii=UAKS, does this include explicit spheres for hydrogen in creating the cavity (like UFF) or not (like UA0)? 2) Is there an appropriate reference to that fact I can cite in a paper? Jason Gillmore, gillmore^hope.edu Longer explanation behind question: We developped and published a method for predicting organic reduction potentials (JPCA 2008, 112, 5684)using single point calculations in G03 at B3LYP/6-31G(d) or /6-311+G(d,p) levels of theory with CPCM (in acetonitrile), with the then default UA0 radii. Later on, when we attempted to use this method on molecules that can have intramolecular hydrogen bonds, these jobs often failed to converge. On the basis of advice on the list (e.g., http://www.ccl.net/chemistry/resources/messages/2005/11/17.005-dir/) my student started using radii=UAKS for these jobs and they worked! We've since then greatly updated and expanded our correlations and tested several different variables, among them redoing all our correlations with both UAKS and UA0 radii, and are writing this up in another paper for submission to JPCA or possibly JOC. I'd like to be able to say something cogent about the difference between UAKS and UA0 and more behind out motivation of trying UAKS (besides the fact that in hindsight it worked.) The aforementioned post by Luis Simn Rubio leads the student to believe, that UAKS (like UFF) includes explicit hydrogens. The G03 users manual explcitly specifies that radii= UFF, Pauling, and Bondi, all do include explicit hydrogens, while not mentioning hydrogens for UA0, UAHF, or UAKS. This would imply to me that none of the United Atom Topological Model radii methods include explicity hydrogens. The G09 users manual, where UFF is now the default radii for SCRF PCM/CPCM calcs, explicitly notes that UA0 does not and UFF does include explicity hydrogens, but says nothing about explicit hydrogens for UAHF or UAKS (though again noting that BONDI and PAULING do include them.) Less clear. Can someone help clear this up for us, and ideally point us to a reference we can cite in our paper one way or the other? Gratefully, Jason G. Gillmore Associate Professor of Chemistry Hope College, Holland, MI USA gillmore^hope.edu From owner-chemistry@ccl.net Thu Apr 26 23:41:00 2012 From: "Matthew Reish mreish---chemistry.otago.ac.nz" To: CCL Subject: CCL: Raman Phonon Calculations Message-Id: <-46801-120426211551-13042-B+j1FtkIGhX3cjhaUGldng[a]server.ccl.net> X-Original-From: "Matthew Reish" Date: Thu, 26 Apr 2012 21:15:49 -0400 Sent to CCL by: "Matthew Reish" [mreish#,#chemistry.otago.ac.nz] General question but any help would be appreciated. I find myself needing to calculate Raman active phonon energies and intensities of crystalline benzoic acid and not sure how to get started. A google search makes it seem that using the VASP program to calculate force constants then export this into a separate program to calculate phonon modes is a common method used but seems fairly complex. Before I begin using the VASP method I want to make sure this is the best way for me to proceed. Any advice for a novice to calculating phonons would be helpful. Cheers, Matthew Reish Chemistry Department University of Otago Dunedin, New Zealand