From owner-chemistry@ccl.net Sat Nov 12 01:28:00 2005 From: "Alan Shusterman alan\a/reed.edu" <owner-chemistry:server.ccl.net> To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-29950-051111214725-3302-6WkL0TEU5CnYbBHk0CZeRw:server.ccl.net> X-Original-From: Alan Shusterman <alan-,-reed.edu> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 Nov 2005 18:07:39 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan=reed.edu] Some years ago, I posted a question to CCL about homonuclear diatomics, Li2 thru F2. Hartree-Fock calculations with modest basis sets (6-311+G*) sometimes gave different orbital orderings from what appeared in intro chem (and inorganic chem) textbooks. Since I hadn't reached the HF limit, I wondered why this discrepancy existed. Was it the textbook or was it my limited basis set? After some CCL discussion and literature research, I arrived at a similar conclusion as Wayne Steinmetz's: qualitative/textbook MO theory is a sort 'swindle'; the discussion in the book often delivers less than meets the eye. How did the books get so screwed up? Because, in the many decades before high-level calcs became available, chemists used experimental data (like PES) and some approximate theories (like Koopmans) to develop ideas regarding MO properties (shapes, orbital energy orderings, etc.). The 'swindle' becomes obvious when we do the calculations. Experiment-based MO properties do not always match calculated MO properties. My teaching approach today treats qualitative MO theory as a different kind of computational method from Hartree-Fock calculations. The former is useful for mental and back-of-the-envelope calculations. The latter is useful when adequate computational resources are available. They need not agree with each other. When they don't, I prefer the latter (up to a point). You may find this article useful: Non-Koopmans' Molecules Brian J. Duke and Brian O'Leary Journal of Chemical Education 72(6), 501-504 [1995] -Alan Eric Scerri scerri__chem.ucla.edu wrote: >Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu] > > > >In teaching qualitative molecular orbital theory one encounters the >question of the crossing of the sigma 2p and pi 2p bonding orbitals >in homonuclear diatomics. > > >This is such that N2 has the pi orbitals of lower energy than sigma >whereas for O2 the energies are reversed. > >But what about heteronuclear diatomics where each of the atoms ? > > >The ordering given in general chemistry textbooks shows a wide >variation. See for example Oxtoby, Zumdahl or Olmsted and Williams, >all three of which contradict each other. > >Herzberg's, Spectra of Diatomic Molecules specifically states the >configurations of CO and NO. > >For CO the ordering is as in the case of N2 whereas for NO the >ordering is as in O2. > >However Herzberg's book is now a little out of date (1950). > >Do more recent calculations on these two molecules suggest anything >different? Would anyone be prepared to run these calculations and >tell me the results? > >How about experimental evidence such as PES on CO and NO? > > > >regards, >eric scerri> > > > > -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://academic.reed.edu/chemistry/alan/ "Yield and overcome; Bend and be straight." Lao Tzu 22 From owner-chemistry@ccl.net Sat Nov 12 02:03:01 2005 From: "Starr Hazard hazards+*+musc.edu" <owner-chemistry()server.ccl.net> To: CCL Subject: CCL: AutoDock3 and shuffled peptide sequences Message-Id: <-29951-051111165714-12908-ocJHkatGDOQhb0/7z2zEGA()server.ccl.net> X-Original-From: Starr Hazard <hazards|-|musc.edu> Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 11 Nov 2005 16:27:36 -0500 MIME-Version: 1.0 Sent to CCL by: Starr Hazard [hazards|-|musc.edu] Folks, I am examining the docking of a hexapeptide to a protein with AutoDock3. I generated some initial results and sought to examine specificity. I shuffled the sequence (ie left amino acid content constant and altered the sequence order) and tried to AutoDock3 again. In many cases the shuffled sequences show better scores than the original sequences. The shuffled and "wildtype" sequences were docked under similar ie mostly default conditions. Have I shown that the binding is none specific or have just got a sampling error? Starr Starr From owner-chemistry@ccl.net Sat Nov 12 02:38:00 2005 From: "Starr Hazard hazards---musc.edu" <owner-chemistry : server.ccl.net> To: CCL Subject: CCL: autodock3 and SYBYL mol2 files Message-Id: <-29952-051111165717-12951-T79+31KDHsUPoTN12efp0w : server.ccl.net> X-Original-From: Starr Hazard <hazards+*+musc.edu> Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 11 Nov 2005 16:12:53 -0500 MIME-Version: 1.0 Sent to CCL by: Starr Hazard [hazards*o*musc.edu] Folks, I wish to run AutoDock3 to dock a sixmer peptide to a modest little target protein. I create my sixmer ligand(all standard amino acids) with SYBYL 7.0 where I add charges (AMBER FF99) and hydrogens. I use "deftors sixmer.mol2" to create the ligand pdbq file. In the error file I see : REMARK *** ERROR 1 *** Non-integral total charge (0.300) for residue PVA- ! REMARK *** ERROR 1 *** Non-integral total charge (-0.305) for residue VAL- 1! REMARK *** ERROR 1 *** Non-integral total charge (-0.351) for residue SER- 6! REMARK *** ERROR 2 *** Non-integral total charge (0.350) for residue PSE- ! "PVA" and "PSE" are not residues in the sixmer. Am I correct in assuming that AutoDock3 is misinterpreting the sybyl mol2 file? Thanks, Starr From owner-chemistry@ccl.net Sat Nov 12 13:13:00 2005 From: "Marcelo Zaldini zaldini*_*ufpe.br" <owner-chemistry%%server.ccl.net> To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29953-051112093040-11046-0pRNtpmVmiiEIaAkZNSlPw%%server.ccl.net> X-Original-From: "Marcelo Zaldini" <zaldini+/-ufpe.br> Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Sat, 12 Nov 2005 10:32:53 -0200 MIME-Version: 1.0 Sent to CCL by: "Marcelo Zaldini" [zaldini[a]ufpe.br] Dear Evgeniy You can take a look at: http://www.ufpe.br/farmacia/zaldini/agoa.html Regards. Marcelo. > On Fri, 11 Nov 2005, Evgeniy Gromov > Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de wrote: > >> Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] >> Dear All, >> >> Does someone know a soft which allows one to simulate >> solvent by explicitly setting up (coordinates of) certain >> number of solvent molecules (e.q. water molecules) surrounding >> a solute system. For instance I'd like to add say 10 water >> molecules around some other system. Is it possible to >> do this "automatically" using some soft? >> >> Thanks a lot, >> >> Evgeniy >> -- >> _______________________________________ >> Dr. Evgeniy Gromov >> Theoretische Chemie >> Physikalisch-Chemisches Institut >> Im Neuenheimer Feld 229 >> D-69120 Heidelberg >> Germany >> >> Telefon: +49/(0)6221/545263 >> Fax: +49/(0)6221/545221 >> E-mail: evgeniy**tc.pci.uni-heidelberg.de >> _______________________________________> > > > > From owner-chemistry@ccl.net Sat Nov 12 21:44:00 2005 From: "Jim Kress ccl_nospam-x-kressworks.com" <owner-chemistry**server.ccl.net> To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29954-051112145628-19211-qvzLbBg9RPrVNXllbakG3w**server.ccl.net> X-Original-From: "Jim Kress" <ccl_nospam###kressworks.com> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 12 Nov 2005 14:55:14 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam-,-kressworks.com] Gromacs provides a utility to do this. It adds the solvent molecules in an physically/ chemically intelligent way as opposed to some programs that just stuff them around the solute. I'd highly recommend it. http://www.gromacs.org Jim > -----Original Message----- > From: Marcelo Zaldini zaldini*_*ufpe.br > [mailto:owner-chemistry[A]ccl.net] > Sent: Saturday, November 12, 2005 1:23 PM > To: Kress, Jim > Subject: CCL: Soft for adding (solvent) molecules around some > other system > > Sent to CCL by: "Marcelo Zaldini" [zaldini[a]ufpe.br] Dear Evgeniy > > You can take a look at: > http://www.ufpe.br/farmacia/zaldini/agoa.html > > Regards. > Marcelo. > > > On Fri, 11 Nov 2005, Evgeniy Gromov > > Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de wrote: > > > >> Sent to CCL by: Evgeniy Gromov > >> [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > >> Dear All, > >> > >> Does someone know a soft which allows one to simulate solvent by > >> explicitly setting up (coordinates of) certain number of solvent > >> molecules (e.q. water molecules) surrounding a solute system. For > >> instance I'd like to add say 10 water molecules around some other > >> system. Is it possible to do this "automatically" using some soft? > >> > >> Thanks a lot, > >> > >> Evgeniy > >> -- > >> _______________________________________ > >> Dr. Evgeniy Gromov > >> Theoretische Chemie > >> Physikalisch-Chemisches Institut > >> Im Neuenheimer Feld 229 > >> D-69120 Heidelberg > >> Germany > >> > >> Telefon: +49/(0)6221/545263 > >> Fax: +49/(0)6221/545221 > >> E-mail: evgeniy**tc.pci.uni-heidelberg.de > >> _______________________________________> > > > > > > > > > > > > -= 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 [A] sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > >