From owner-chemistry@ccl.net Thu Mar 29 03:35:01 2007 From: "Jana Precechtelova janap- -ncbr.chemi.muni.cz" To: CCL Subject: CCL:G: interpretation of spin-spin couplings in g03 Message-Id: <-33923-070328111138-26191-13oPfKaJfIeO/iTHOycaNQ-,-server.ccl.net> X-Original-From: Jana Precechtelova Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 28 Mar 2007 12:54:39 +0200 (MEST) MIME-Version: 1.0 Sent to CCL by: Jana Precechtelova [janap]^[ncbr.chemi.muni.cz] Dear CCLers, does anybody know whether there are any means of interpretation of NMR spin-spin couplings implemented in Gaussian03 ? I just know about NBO, are there any other? Thanks, Jana ============================================================= Jana Precechtelova ------------------------------------------------------------- NMR Laboratory National Centre for Biomolecular Research (NCBR) Faculty of Science, Masaryk University Kamenice 3, 625 00 Brno, Czech Republic ============================================================= email: janap(0)ncbr.chemi.muni.cz ============================================================= From owner-chemistry@ccl.net Thu Mar 29 08:56:00 2007 From: "Ondrej Kroutil okroutil++gmail.com" To: CCL Subject: CCL:G: Lanthanocene optimization Message-Id: <-33924-070329082652-15822-pWuOQY6hNzcEJYDSBVGa7g+*+server.ccl.net> X-Original-From: "Ondrej Kroutil" Date: Thu, 29 Mar 2007 08:26:49 -0400 Sent to CCL by: "Ondrej Kroutil" [okroutil*o*gmail.com] Dear CLLers, could anybody help me with optimization of basic lanthanocenes? I'm beginner in this field... I try to optimize structure of Cp2SmH using Gaussian03, but still can't prepare proper input file. Could anybody send me any example file? Or correct this one: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ %Mem=15MW B3PW91/Gen Pseudo=Read Guess=Core Opt Pop=Reg Symm=(Int,Grad,Loose) Test Cp2SmH 0 1 C 1.180969 -1.653976 -1.527969 C -0.119446 -2.219391 -1.285202 .. C H 0 6-31G** **** Sm 0 MWB51 **** Sm 0 MWB51 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This is my trial input but it still doesn't work. End of output file looks like this: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Rotational constants (GHZ): 1.8924963 0.6838112 0.6519278 Basis read from rwf: (5D, 7F) Pseudo-potential data read from rwf file. There are 177 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 177 basis functions, 271 primitive gaussians, 180 cartesian basis functions 41 alpha electrons 41 beta electrons nuclear repulsion energy 597.4094037092 Hartrees. NAtoms= 22 NActive= 22 NUniq= 22 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F One-electron integrals computed using PRISM. 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 2850 NPrTT= 7563 LenC2= 2644 LenP2D= 5645. LDataN: DoStor=F MaxTD1= 6 Len= 172 LDataN: DoStor=T MaxTD1= 6 Len= 172 NBasis= 177 RedAO= T NBF= 177 NBsUse= 177 1.00D-06 NBFU= 177 Defaulting to unpruned grid for atomic number 62. Odd number of core electrons in MinBas. Error termination via Lnk1e in /software/g03-D.01/g03/l401.exe at Thu Mar 29 10:47:55 2007 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Can't find mistake...Maybe initial geometry is too far from minimum? Problem with multiplicity? Many thanx, Ondrej Kroutil okroutil%at%gmail.com VUT Brno, Purkynova 464/118 612 00 Brno From owner-chemistry@ccl.net Thu Mar 29 09:30:01 2007 From: "xue chun yu x_chy2002++sina.com" To: CCL Subject: CCL: Model interaction potentials for acetylene! Message-Id: <-33925-070329030544-639-woFbAniaeP+G+6KxLe01vg{=}server.ccl.net> X-Original-From: "xue chun yu" Date: Thu, 29 Mar 2007 03:05:39 -0400 Sent to CCL by: "xue chun yu" [x_chy2002]-[sina.com] hi, I want to calculate the adsoprtion curve of acetylene in zeolite. But i cann't find interaction potentilas for acetylene. Can you give me some reference articles for it? Thanks very much in advance! Best regards Xue Chunyu From owner-chemistry@ccl.net Thu Mar 29 10:23:01 2007 From: "Cory Pye cpye!A!crux.smu.ca" To: CCL Subject: CCL:G: Lanthanocene optimization Message-Id: <-33926-070329101559-30998-KFORwj1j1ucUP9+qDZm2qA%a%server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 29 Mar 2007 11:15:44 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye%crux.smu.ca] Hi, It appears that the Guess=core with the choice of the MWB51 ECP/basis combination might be causing your problems, as there would be an odd number of electrons for the guess, which the guess might not be able to handle. The input, pseudo and basis input appear reasonable. Try a calculation without the guess=core. Eventually you might wish to use a MWB28 (small-core ECP). -Cory On Thu, 29 Mar 2007, Ondrej Kroutil okroutil++gmail.com wrote: > > Sent to CCL by: "Ondrej Kroutil" [okroutil*o*gmail.com] > Dear CLLers, > could anybody help me with optimization of basic lanthanocenes? I'm beginner in this field... I try to optimize structure of Cp2SmH using Gaussian03, but still can't prepare proper input file. Could anybody send me any example file? Or correct this one: > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > %Mem=15MW > B3PW91/Gen Pseudo=Read Guess=Core Opt Pop=Reg Symm=(Int,Grad,Loose) Test > > Cp2SmH > > 0 1 > C 1.180969 -1.653976 -1.527969 > C -0.119446 -2.219391 -1.285202 > .. > > C H 0 > 6-31G** > **** > Sm 0 > MWB51 > **** > > Sm 0 > MWB51 > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > This is my trial input but it still doesn't work. End of output file looks like this: > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Rotational constants (GHZ): 1.8924963 0.6838112 0.6519278 > Basis read from rwf: (5D, 7F) > Pseudo-potential data read from rwf file. > There are 177 symmetry adapted basis functions of A symmetry. > Integral buffers will be 262144 words long. > Raffenetti 2 integral format. > Two-electron integral symmetry is turned on. > 177 basis functions, 271 primitive gaussians, 180 cartesian basis functions > 41 alpha electrons 41 beta electrons > nuclear repulsion energy 597.4094037092 Hartrees. > NAtoms= 22 NActive= 22 NUniq= 22 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F > One-electron integrals computed using PRISM. > 1 Symmetry operations used in ECPInt. > ECPInt: NShTT= 2850 NPrTT= 7563 LenC2= 2644 LenP2D= 5645. > LDataN: DoStor=F MaxTD1= 6 Len= 172 > LDataN: DoStor=T MaxTD1= 6 Len= 172 > NBasis= 177 RedAO= T NBF= 177 > NBsUse= 177 1.00D-06 NBFU= 177 > Defaulting to unpruned grid for atomic number 62. > Odd number of core electrons in MinBas. > Error termination via Lnk1e in /software/g03-D.01/g03/l401.exe at Thu Mar 29 10:47:55 2007 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Can't find mistake...Maybe initial geometry is too far from minimum? Problem with multiplicity? > > Many thanx, > > Ondrej Kroutil > okroutil%at%gmail.com > VUT Brno, Purkynova 464/118 612 00 Brno> > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye---crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Mar 29 10:55:00 2007 From: "Qian Wang xie.wang ~ gmail.com" To: CCL Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results? Message-Id: <-33927-070329103501-6909-VNfoYoQgE48Ubj/nU8KJtg * server.ccl.net> X-Original-From: "Qian Wang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 29 Mar 2007 10:34:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Qian Wang" [xie.wang%a%gmail.com] Dear all, Thank you all for your kind helps about the geometry optimization problem! The original question was why HF/6-31G structure is better compared with experimental (both X-ray and gas phase electron diffraction) structure than MP2/6-31G* structure is. In the first email I only mentioned X-ray structure, in the second one I added that HF structure is also closer to gas phase structrue than MP2 is (While X-ray structure is slightly more compact than gas phase structure, HF still compares better than MP2. HF bond length is slightly shorter than gas phase bond length, while MP2 bond lenght is a lot longer than gas phase bond length). Surely the gas phase optimization is better to be compared with gas phase experimental results. Sorry for the confusion! It looks now that Brian, Errol and Radoslaw are right: It is because of the small basis sets used. While in complete basis set limit MP2 should give better geometry than HF, the basis sets used here are far > from complete. I did a little more test and found that increasing the basis set in HF result in shorter bond length and further away from experimental results, while increasing basis set in MP2 could aim to the right direction. Special thanks to Brian Salter errol lewars Radoslaw Kaminski Dave Close. Marcel Swart Soren Eustis Best Regards, Qian From owner-chemistry@ccl.net Thu Mar 29 17:21:00 2007 From: "Karl Kirschner kkirschn/a\hamilton.edu" To: CCL Subject: CCL: Sixth MERCURY Conference on Undergraduate Computational Chemistry Message-Id: <-33928-070329110617-27789-SJ35gl5Imeg2A5y1+np5eA:_:server.ccl.net> X-Original-From: "Karl Kirschner" Date: Thu, 29 Mar 2007 11:06:14 -0400 Sent to CCL by: "Karl Kirschner" [kkirschn:_:hamilton.edu] Dear Colleagues: We are pleased to announce the Sixth MERCURY Conference on Undergraduate Computational Chemistry. The Conference will be held July 29-31, 2007, at Hamilton College, in Clinton, NY. The conference will feature plenary lectures by George Schatz, Northwestern University; Elfriede Kraka, University of the Pacific; Anne McCoy, Ohio State University; Erin Duffy, Rib-X Pharmaceuticals; Joseph Francisco, Purdue University; and Nigel Richards, University of Florida. In addition mainstays of the conference include an Undergraduate Poster Session and evening social sessions. This conference is an excellent forum for undergraduates to present their work and to learn from experts in the field, allowing them to put their own research in perspective. It is equally valuable as a network for faculty working with undergraduates. Undergraduates from all institutions are invited to come present their work. Conference Fees are 220 for faculty, postdocs, and graduate students, and 110 for undergraduates, and include registration, housing, and meals. Details of the conference and information on registration and submission of Abstracts can be found on our web site: http://mercury.chem.hamilton.edu/conference/2007/ George Shields & Karl Kirschner, on behalf of MERCURY, the Molecular Education and Research Consortium in Undergraduate computational chemistRY From owner-chemistry@ccl.net Thu Mar 29 17:57:00 2007 From: "Dennis G. Sprous dennis.sprous~!~redpointbio.com" To: CCL Subject: CCL: Ion channel recognition models Message-Id: <-33929-070329171111-11015-iOp7WLDunAWG1bU8y4Dvig/a\server.ccl.net> X-Original-From: "Dennis G. Sprous" Date: Thu, 29 Mar 2007 17:11:07 -0400 Sent to CCL by: "Dennis G. Sprous" [dennis.sprous%redpointbio.com] Dear All: For kinase and GPCR inhibitors, there has been success at developing focus libraries for screening. The success of these has been based on a variety of models trained over known inhibitors which then have successfully been applied to develop libraries with enhanced hit rates against the target protein class. I have not seen a good published example for this for the ion channels or subgroups of the ion channels (i.e., say ligand gated or NA+ specific...). If anyone can suggest a good published example for ion channel inhibitor library design or models developed to recognize ion channel inhibitors, I would be grateful for the reference. -- Dennis