From owner-chemistry@ccl.net Thu May 10 02:54:00 2007 From: "Frank Neese neese+*+thch.uni-bonn.de" To: CCL Subject: CCL:G: hyperfine coupling constans fo transition metals Message-Id: <-34231-070510025219-26882-sHq9EuynC+sl2JkXaX00lA**server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 10 May 2007 08:51:35 +0200 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese|thch.uni-bonn.de] Dear Sibel, the ORCA program has special features to calculate transition metal hyperfine couplings. In particular, for transition metals you need a spin orbit correction that may become pretty large and you need to simultaneously include the spin polarization. Since the ORCA program has an accurate spin orbit operator implemented and does all parts of the hyperfine it will probably be your code of choice. We have also defined a "core properties" basis set for transition metals that is adequate for hyperfine calculations. You will find the program, detailed documentation and references to original work under http://www.thch.uni-bonn.de/tc/orca/ All the best, Frank At 10:59 09.05.2007, you wrote: >Sent to CCL by: "Sibel Tokdemir" [sozturk!A!gyte.edu.tr] >Hello, >I have experience on calculating hyperfine coupling constant for >organic molecules using Gaussian program. I want to do same thing >for first raw transition metals. As far as I read I saw that people >used ADF program for transition metals.I wonder if anyone used >Gaussian98(or 03) for this purpose. Which basis set will be >appropriate for DFT method for Sc-Zn? > >thanks > >Sibel Tokdemir/ sozturk(!)gyte.edu.tr From owner-chemistry@ccl.net Thu May 10 04:08:00 2007 From: "David Cornil cornildavid#yahoo.fr" To: CCL Subject: CCL: Steele_potential Message-Id: <-34232-070510040623-24998-vj/eRwjKxq4DW6CL7oabVw!=!server.ccl.net> X-Original-From: "David Cornil" Date: Thu, 10 May 2007 04:06:20 -0400 Sent to CCL by: "David Cornil" [cornildavid:+:yahoo.fr] Dear CCL's users, I'm actually focusing on the effective potentials for interaction between isolated atom (or molecules) and a perodic metal surface. I see that the potential commonly using in the litterature is the [10-4-3] Steele potential in the Fourier serie form [see Steele, Surface Science 36 317 (1973)]. My question is : Are they other ways to resolve the problem of pair-wise interaction between an atom an a surface or is the Steele's scheme the standard procedure for it? Thanks in advance for reply David Ph Student University of Mons-Hainaut Belgium From owner-chemistry@ccl.net Thu May 10 06:29:00 2007 From: "Georg Lefkidis lefkidis-.-physik.uni-kl.de" To: CCL Subject: CCL:G: SAC-CI and spin-density Message-Id: <-34233-070510062215-2093-UNx87URgxW7cVfCZQnK2iA{:}server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="windows-1250" Date: Thu, 10 May 2007 11:49:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis ~ physik.uni-kl.de] Dear CCLers, I am trying to calculate spin-density for SAC-CI states (triplets) in Gaussian03, and I get the error message "Sorry, spin-density calculation is for KSTATE >= 3." Any idea what KSTATE is, and how to change it? Cheers George ------------------------------------------------------------------------ -- Dr. Georg Lefkidis E-mail:lefkidis(at)physik(dot)uni-kl(dot)de University of Kaiserslautern Tel. +49 631 205 3207 Department of Physics Fax: +49 631 205 3907 PO Box 3049 67653 Kaiserslautern Germany ------------------------------------------------------------------------ --- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.467 / Virus Database: 269.6.6/795 - Release Date: 09/05/07 15:07 From owner-chemistry@ccl.net Thu May 10 10:03:00 2007 From: "Deskins, Nathaniel A nathaniel.deskins]_[pnl.gov" To: CCL Subject: CCL: Surface Coverage Calculations Message-Id: <-34234-070509172637-20720-QuKSqZxmP6eNBtpAg4VqBg^server.ccl.net> X-Original-From: "Deskins, Nathaniel A" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 May 2007 13:26:12 -0700 MIME-Version: 1.0 Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins-x-pnl.gov] A typical approach is to choose one atom (in your case Al) as the basis and use this to determine the coverage. For example, if your Al(111) 3x3 surface has 9(?) atoms, then 3 Si atoms on the surface would give 3/9 = 0.333 coverage. Of course, the coverages that come from experimental results may or may not agree with this definition of coverage. Aaron -----Original Message----- > From: owner-chemistry,,ccl.net [mailto:owner-chemistry,,ccl.net] Sent: Tuesday, May 08, 2007 5:52 AM To: Deskins, Nathaniel A Subject: CCL: Surface Coverage Calculations Sent to CCL by: "soumya s" [soumya_samineni|a|rediffmail.com] I have generated Al(111) 3X3 surface with slab depth of 4 layers. Can you please suggest me how can i now generate monolayers of additional atoms (like Si) with different surface overages ..? 0.25ML, 0.5 ML and 1 ML . thanx in advace soumya From owner-chemistry@ccl.net Thu May 10 15:25:00 2007 From: "Sengen Sun sengensun/./yahoo.com" To: CCL Subject: CCL: The Kuhn dilemma and a possible solution Message-Id: <-34235-070510151840-24798-debSR5paiocSWWZKWnc0PQ[-]server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 10 May 2007 11:18:11 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun a yahoo.com] I came across the following web page when I searched the internet: http://jonathankerr.spaces.live.com/Blog/cns!19311A7F1792DA1C!329.entry Thanks for the comment there. One thing that that site tells me is the contrast difference between the young and the well-established scientists. A young scientist is eager to think something new and wish to make changes for better science. A well-established scientist tends to maintain what he/she has already achieved. Such a dilemma was well described by Kuhn (not Kohn :-) http://www.des.emory.edu/mfp/Kuhn.html Kuhn recognized that a significant (or important) paradigm shift in scientific theories is generally made by a younger scientist, and is strongly resisted by the established scientific community, as shown by the history. But a young scientist also tends to make naive mistakes in theoretical science, complicating the standout of a true theoretical revolution. I would like to call this dilemma between the young and the established as the Kuhn dilemma. What is an appropriate solution for the Kuhn dilemma then? How about to establish an award for theoretical paradigm shift? That would be really a good intention worth praising. But who should be the judges? Such an award would create another philosophical dilemma on the top of the Kuhn dilemma. If the established community (where the judges from) are eager to award (not to resist) a significant and important paradigm shift in theoretical science, Kuhn's theory and reasoning are wrong! Actually, I think that the Kuhn dilemma has been solved for nearly two decades due to human's civilization in the Internet communications, which will make the resistance (to the new theoretical discovery) powerless or very short-lived. The youngers instead of the established will be the ultimate judges of scientific theories. As soon as we have a global community of free, open, equal, and professional discussions on science, a scientific truth will be eventually a scientific truth. Any naive mistakes will be mistakes and cannot be helped by the internet. The Internet communications are profoundly changing a world community of political correctness in theoretical chemistry, a world community of blind trust, and a world community of fear to speak the correct science. The Nobel foundation and Nobel laureates are not super-human but all normal human beings who make errors here and there. The Internet communications are changing the absolute control of the scientific discussions by Nobel foundation-authorized scientific giants. That web site by Kerr also tells me that some younger computational and theoretical chemists are not quite familiar with famous philosophers in science such as Popper (not Pople :-) Kuhn and Popper's philosophies are closedly related to CCLers. Kuhn was more accurate in account of historical evolution of scientific theories. Popper is a figure of vigorously logical reasoning: http://plato.stanford.edu/entries/popper/ Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu May 10 21:03:01 2007 From: "Maurizzio m.argonni^^gmail.com" To: CCL Subject: CCL: Tunnels in proteins Message-Id: <-34236-070510202921-13084-Kr20jGp+aWmT3wIi3h8WRQ_-_server.ccl.net> X-Original-From: Maurizzio Content-Type: multipart/alternative; boundary="----=_Part_39751_18545635.1178839874069" Date: Thu, 10 May 2007 19:31:14 -0400 MIME-Version: 1.0 Sent to CCL by: Maurizzio [m.argonni-x-gmail.com] ------=_Part_39751_18545635.1178839874069 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello to all, I was wondering if anyone is aware of a web server or free software able to find tunnels in proteins. The problem I want to solve is the following: given the location of the active site in a protein I would like to know the possible routes for substrates to get there from the exterior. Any clues are greatly appreciated. Thanks, Maurizzio ------=_Part_39751_18545635.1178839874069 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello to all,
 
I was wondering if anyone is aware of a web server or free software able to find tunnels in proteins.
The problem I want to solve is the following: given the location of the active site in a protein I would like to know the possible routes for substrates to get there from the exterior.
Any clues are greatly appreciated. Thanks,
 
Maurizzio
 
------=_Part_39751_18545635.1178839874069-- From owner-chemistry@ccl.net Thu May 10 21:38:00 2007 From: "Venkataramanan NS venkataramananns!=!gmail.com" To: CCL Subject: CCL: Vertical IP for triplet Message-Id: <-34237-070510210529-19298-DgO5EvwhqLcQx0gI6Pa8xw%a%server.ccl.net> X-Original-From: "Venkataramanan NS" Date: Thu, 10 May 2007 21:05:26 -0400 Sent to CCL by: "Venkataramanan NS" [venkataramananns:+:gmail.com] Dear CCL users, Do any one have idea, how to calculate the vertical IPs for the triplet systems. If "Yes" explain and please provide me with a reference. Thanks in advance Venkataramanan