From owner-chemistry@ccl.net Tue Oct 9 08:26:01 2007 From: "luca bertini luca.bertini(0)unimib.it" To: CCL Subject: CCL: a small imaginarily frequency Message-Id: <-35352-071008112214-18834-pV/M2LmPjW+uUIdnFgtE5Q:server.ccl.net> X-Original-From: "luca bertini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Mon, 08 Oct 2007 16:19:41 +0200 MIME-Version: 1.0 Sent to CCL by: "luca bertini" [luca.bertini##unimib.it] Dear Nuno, I think that your guideline for the imaginary normal model frequencies does not take into account the fact that rotations (when not sterically hindered) are characterize by low imaginary frequencies, and that in general B3LYP frequencies could be higher in frequency that those computed using GGA BP86, for example. I think that the real problem is how correct is the topology of the DFT PES, compared to that obtained at correlated level. In my experience I have seen real rotation TS with 20i imaginary frequency mode using BP86 (real means that the structure of the TS calculated likely correspond to that of the experiments, with computed barrier in agreement with the experiments like dynamical NMR). So, for me if the TS structure is reasonable, a imaginary frequency of 57i is enough to claim that on the DFT PES, this structure is really a TS. Finally, I'm very curious about the “minimum” with DFT frequency of 300i. Could you send me the reference? ciao, Luca On Mon, 08 Oct 2007 13:23:10 +0100 "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" wrote: > > Sent to CCL by: "Nuno A. G. Bandeira" >[nuno.bandeira|a|ist.utl.pt] > may abdelghani may01dz|*|yahoo.fr wrote: >> Sent to CCL by: "may abdelghani" [may01dz-x-yahoo.fr] >> dear CCLers >> A unique imaginarily frequency of -57 cm-1 is enough to >>say, that the >> corresponding structure is a transition states and not >>another local >> minima? The task was be a transition states search. > > If it's not a weak interaction you're dealing with then >I'd say it's a minimum. Just so you know there have been >"minima" reported in the literature with as much as -300 >cm-1. > > But the usual arbitrary guideline is discard imaginary >frequencies between 0 and -100 cm-1. They generally can >be put off as computational error within DFT. > > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, >Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student .. IST,Lisbon > -- > > > > -= This is automatically added to each message by the >mailing script =- > 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> > E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or >useConferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, >Password: search)> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/> > > From owner-chemistry@ccl.net Tue Oct 9 13:54:00 2007 From: "Kalju Kahn kalju*chem.ucsb.edu" To: CCL Subject: CCL: Drug design course Message-Id: <-35353-071008210617-13199-i/kfCa5cD/vluDe5p8mvbw[*]server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 8 Oct 2007 17:26:19 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] Omar, Some materials for the Drug Design course at UCSB are available via http://www.chem.ucsb.edu/~kalju/chem162/. The lecture notes are not publicly accessible with the exeption of one sample lecture but you can browse some computational drug discovery tutorials and assignments in the "Assignments" section. Students in our course work on individual drug design projects and guidelines on how to accomplish this are also freely available. There is not a single book that meets all the needs of our course but Silverman's "The Organic Chemistry of Drug Design and Drug Action" is very helpful when teaching ligand-based design approaches. However, most of our students have a strong chem/biochem background, and you may want to use some other text depending on the background of your pharmacy students. Best regards, Kalju > Dear CCL users, > I would like to give a drug design course to the 5th year Pharmacy > students. > I will appreciate any comments or suggestions concerning this course > including textbook, lecture notes, handouts, power point presentation, > excercises ...etc > > Thanks in advance > > Dr. Omar Deeb > Al-Quds University > Jerusalem > > > --------------------------------- > Tonight's top picks. What will you watch tonight? Preview the hottest > shows on Yahoo! TV. From owner-chemistry@ccl.net Tue Oct 9 15:13:00 2007 From: "CCL CCL computationalchemist===gmail.com" To: CCL Subject: CCL: Ag:Si(111) Surface Message-Id: <-35354-071009151104-31660-ISmGu4jlZYbxv+m8EApnPg]|[server.ccl.net> X-Original-From: "CCL CCL" Content-Type: multipart/alternative; boundary="----=_Part_7252_5988121.1191953435583" Date: Tue, 9 Oct 2007 19:10:35 +0100 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist*|*gmail.com] ------=_Part_7252_5988121.1191953435583 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Friends, I'm planning to make some DFT studies on Silver Terminated Silicon surface. Could any one please let me know, how a Ag:Si(111) surface look like. Any pointers or papers or suggestions are greatly welcome. Thanks in Advance. -- Regards, Dr. Sanjay Kalyani College of Engineering, India ------=_Part_7252_5988121.1191953435583 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Friends,
 
I'm planning to make some DFT studies on Silver Terminated Silicon surface.
 
Could any one please let me know, how a Ag:Si(111) surface look like.
 
Any pointers or papers or suggestions are greatly welcome.

Thanks in Advance.

--
Regards,
Dr. Sanjay
Kalyani College of Engineering,
India
------=_Part_7252_5988121.1191953435583-- From owner-chemistry@ccl.net Tue Oct 9 15:47:00 2007 From: "CCL CCL computationalchemist-#-gmail.com" To: CCL Subject: CCL: Ag:Si(111) Surface Message-Id: <-35355-071009151809-1482-kiEfkebHFd61QOx/G0NPzQ^server.ccl.net> X-Original-From: "CCL CCL" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 9 Oct 2007 20:11:45 +0100 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist^^gmail.com] Dear Friends, I'm planning to make some DFT studies on Silver Terminated Silicon surface. Could any one please let me know, how a Ag:Si(111) surface look like. Any pointers or papers or suggestions are greatly welcome. Thanks in Advance. -- Regards, Dr. Sanjay Kalyani College of Engineering, India From owner-chemistry@ccl.net Tue Oct 9 22:05:01 2007 From: "Steve Bowlus chezbowlus]^[comcast.net" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35356-071009220209-8300-CFYjEL0H+ZSG561nOz3BRg=-=server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 Oct 2007 19:00:49 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus*comcast.net] I don't know how newer or commercial versions of Mopac may have changed this, but for older versions (original 7)... For cartesian input, your options are only to freeze everything (_all_ flags 0) or optimize everything (all flags 1). You can get a mopac z-matrix by using the cartesian input and running 1SCF (so no geometry optimization occurs). Somewhere in the .out file there will be a z-matrix which can be edited into mopac input (.dat or .mop depending on whose version you use). As part of the editing process you can set the flags for individual distances/bond lengths, angles and dihedrals. In doing this be certain that mopac has defined all of these coordinates in a sensible (for your purposes) fashion. For example, a distance between two arbitrary atoms may be used as a first coordinate (which may be chemical nonsense) while you really want a bond distance between specific atoms to be fixed. Also, depending on what you are fixing, you may be able to use mopac symmetry definitions to speed things up (I never do). If you are not satisfied with mopac's translation, you can always build the matrix by hand (**gasp!**). Once you become accustomed to doing so, this is not onerous for reasonably sized molecules, and well worth the effort for the added control over the calculation. Many other programs do the converson (e.g Mol2Mol), but I can't say their translations will be superior to Mopac's. Cheers, Steve Sina T reli sinatureli|gmail.com wrote: > Sent to CCL by: "Sina T reli" [sinatureli-x-gmail.com] > Hello, > > I want to run a calculation with mopac in which I need to freeze some atoms. I was looking at the FAQ of mopac and it says in the z-matrix input format there are two types of information, one of which is the atomic coordinates which should supposedly be in the form: > > H -1.31 1 0.12 1 1.89 1 > > where if I change the 1's to 0's the atoms will be frozen. > > However the only information in the Z-matrix files are in the form of > > H 1.092 1 120.615 1 179.979 1 10 9 11 > > which state the bond distances, angles and dihedgral angles of the given atom to other atoms. I tried to create both z-matrix and xyz files using hyperchem and downloaded some samples from the website but none of them seems to contain the atoms coordinate in the form given (xyz does contain coordinates but then it is only a list of coordinates with nothing, no 0's or 1's near the coordinates). > > How can I create mopac input files in which I can freeze atoms by the form given above? > > Thanks alot...> > > >