From owner-chemistry@ccl.net Wed Jul 12 03:41:00 2006 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jvilla:-:imim.es" To: CCL Subject: CCL:G: How to calculate reaction rates without transition states? Message-Id: <-32113-060711120238-23996-XRBWfHmxKzbjvreLx3L6ZQ#%#server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Jul 2006 17:15:08 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jvilla|,|imim.es] Dear Zhe, it depends on what you call Transition State. If you have "just" problems locating the topological saddle point on the PES this does not necessarily imply the reaction does not have a transition state. You may still use some distinguished reaction coordinate that connects reactants and products and using software like, e.g., Polyrate you can generate the free energy profile for the reaction through this reaction coordinate. Polyrate will in principle take care of the appropriate projections of the given distinguished coordinate in order to build transition state hypersurfaces with the right properties to fullfill (variational) transition state theory. See the abundant literature by Truhlar's group on this issue. Hope this helps Jordi En/na Zhe Li lizhe3#%#mail.ustc.edu.cn ha escrit: > Sent to CCL by: "Zhe Li" [lizhe3(0)mail.ustc.edu.cn] > For example, a coordination reaction: PH3+Pd(PH3)->Pd(PH3)2, I can not find the transition state of this reaction, at least with Gaussian. Then how can I calculate the reaction rate?> > > > > -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Unit on Biomedical Informatics (GRIB) - IMIM/UPF/PRBB C/ Doctor Aiguader, 80; 08003 Barcelona (Spain) Tel: +34 93 221 1009 ext 2619 // Fax: +34 93 221 3237 e-mail: jvilla/a\imim.es http://diana.imim.es MSc on Bioinformatics for Health Sciences http://diana.imim.es/Bioinformatics From owner-chemistry@ccl.net Wed Jul 12 08:45:00 2006 From: "Carsten Detering detering*_*biosolveit.de" To: CCL Subject: CCL: 4th FlexX Training Workshop - Web Site Updated/Hotel list added Message-Id: <-32114-060712084251-14899-a2w7CLyZGNSYvIJ4aplLeg__server.ccl.net> X-Original-From: "Carsten Detering" Date: Wed, 12 Jul 2006 08:42:48 -0400 Sent to CCL by: "Carsten Detering" [detering() biosolveit.de] Dear CCLers, The 4th FlexX Training Workshop on Sept. 7/8 in Santa Clara, CA is approaching fast. This is why we have added a list of hotels on our workshop web site for your convenience. You can find it here: www.biosolveit.de/workshops/2006 For those of you who have not registered yet: register now to secure your spot in this premier event. This is your chance to become a FlexX master, as one of our former participants put it. We can only guarantee your spot if you have registered via our web site www.biosolveit.de/workshops/2006/registration.html and if the registration fee is paid in full. We are looking forward to seeing you in San Francisco! -BioSolveIT Your FlexX developers FlexX is exclusively available from BioSolveIT, the premier scientific solution provider. From owner-chemistry@ccl.net Wed Jul 12 09:19:00 2006 From: "Sergio Emanuel Galembeck segalemb__usp.br" To: CCL Subject: CCL: how to find out hybridization ? Message-Id: <-32115-060712083526-14167-FHIwgotlDKAzjE/ATwZh2Q\a/server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 12 Jul 2006 09:35:10 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb-.-usp.br] Dear Tapta, Putting pop=nbo you will find in NBO section the atomic hybridizations and the hybridization of each atom in one NBO. Hope this help you, Sergio Citando "Tapta K Roy ch05ph03-#-uohyd.ernet.in" : > Sent to CCL by: "Tapta K Roy" [ch05ph03%%uohyd.ernet.in] > Dear friend. > How to find out hybridization of an atom in a molecule by G-03. I have tried > with pop=nbo keyword in a optimised structure by B3lyp method, but couldn't > able to find out or calculate it from log file. > Thank you for your help. > Best regards, > Tapta K Roy > Hydrabad School of Chemistry > India> > > > From owner-chemistry@ccl.net Wed Jul 12 12:15:01 2006 From: "Igor Avilov avilovi*o*averell.umh.ac.be" To: CCL Subject: CCL: Electronic coupling depending on the level of theory Message-Id: <-32116-060712120844-25428-9p+OCi4bxVM16jdexBAppA=-=server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 12 Jul 2006 18:08:20 +0200 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi_._averell.umh.ac.be] Dear CCL-ers, I have the results on the performance of different theoretical methods in the calculation of electronic coupling matrix elements, which puzzle me. I study the properties of donor/acceptor complexes. To estimate the value of the charge transfer from donor to acceptor, the knowledge of electronic matrix element (electronic coupling) between the occupied orbitals of the donor and unoccupied orbitals of acceptor is crucial. To test the performance of different methods, I calculated electronic coupling between several pairs of donor/acceptor orbitals varying the geometry of the system. I used ZINDO/S, DFT with BHandHLYP functional and HF. The tendency in the variation of electronic coupling (depending on the geometry of the system) is the same, while the absolute values are largely different. And namely, the largest difference is obtained for HOMO (of the donor)/LUMO (of the acceptor) pair of orbitals. BHHLYP values are about 10 larger than those of ZINDO/S, while HF values are about 2 times larger than those of BHHLYP. Surprisingly, electronic matrix elements calculated for several other pairs of orbitals (for example, HOMO-1 (of the donor)/LUMO (of the acceptor)) have similar values according to all three methods. I used the same basis set 6-31G* for BHHLYP and HF calculations. So far I was not able to find any satisfactory explanation for such behaviour and I'd be very grateful for any hint from the quantum-chemical community. Best regards, Igor Avilov. From owner-chemistry@ccl.net Wed Jul 12 12:50:00 2006 From: "James N Scott scottjn],[gmail.com" To: CCL Subject: CCL: Freezing angles in GAMESS-UK/CHARMM QM/MM simulations? Message-Id: <-32117-060712121415-26092-KUSAd9aHk/yGBmbZ6io9sA===server.ccl.net> X-Original-From: "James N Scott" Date: Wed, 12 Jul 2006 12:14:14 -0400 Sent to CCL by: "James N Scott" [scottjn-$-gmail.com] Greetings CCLers. I am on the verge of purchasing GAMESS-UK in order to do some simple QM/MM simulations of different small molecules in water, with the goal of examining solvent effects on spectra. Is it possible to make constant an angle or bond length internal to the QM system of interest? For instance, can I fix a dihedral angle between two QM molecules embedded in MM water molecules, or a bond length within a single QM molecule? Thanks very much for any assistance! J. Nathan Scott From owner-chemistry@ccl.net Wed Jul 12 13:25:01 2006 From: "David A. Case case() scripps.edu" To: CCL Subject: CCL: accounting for counterions in implicit solvent? Message-Id: <-32118-060712123251-31485-IsH6p8pmmCic0hgdCNXfpw{}server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 12 Jul 2006 08:45:27 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case===scripps.edu] On Tue, Jul 11, 2006, Samuel C Flores samuel.flores^^yale.edu wrote: > > Is there an implicit solvent code available that takes into account the > effect of counterions? I have several positive charges in my protein, so if > I use plain vanilla implicit solvent models in TINKER, the protein denatures > slightly. I would prefer to use TINKER or CHARMm, but will consider other > academic codes. One simple approach to this problem is given here: %A J. Srinivasan %A M.W. Trevathan %A P. Beroza %A D.A. Case %T Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects %J Theor. Chem. Acc. %V 101 %P 426-434 %D 1999 This idea is implemented in Amber and NAB; it is also in CHARMM, but perhaps not yet in any released version. Since the idea is so simple, it is probably easy to add it to TINKER or to other implicit solvent codes. Note also that it has not really been critically tested: at best, it will mimic adding Debye-Huckel screening in a linearlized Poisson-Boltzman approach. So, use with caution. ...hope this helps...dave case From owner-chemistry@ccl.net Wed Jul 12 22:39:00 2006 From: "Hiro Maekawa hmaekawa*|*uci.edu" To: CCL Subject: CCL:G: Normal mode displacement in GAUSSIAN Message-Id: <-32119-060712163027-25413-PkvMr8611LRKpvyICSYVHw .. server.ccl.net> X-Original-From: "Hiro Maekawa" Date: Wed, 12 Jul 2006 16:30:23 -0400 Sent to CCL by: "Hiro Maekawa" [hmaekawa!A!uci.edu] Dear CCL, I have difficulty in understanding normal mode displacement obtained from GAUSSIAN03 package. I have read a paper in the GAUSSIAN website ("vibrational analysis in GAUSSIAN") and checked the CCL archive, but it is still not clear whether I am correct or not. I would like to get a matrix L which relates normal mode coordinate Q [angstrom*(amu)1/2] and cartesian coordinate x [angstrom] of 3N atoms, that is x=LQ. In the GAUSSIAN output file, you can get normal coordinate which does not have any unit as follows. incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: Atom AN X Y Z X Y Z X Y Z 1 6 0.00 0.00 0.00 0.00 0.00 0.03 0.00 0.00 0.07 2 8 0.00 0.00 0.04 0.00 0.00 0.06 0.00 0.00 0.03 3 7 0.00 0.00 -0.06 0.00 0.00 0.00 0.00 0.00 0.30 My concerns are... 1. These displacements are normalized by multiplying by square root of the reduced mass, and hence are dimensionless. I need to divide by it to obtain the original numbers. 2. The numbers I get after the process 1 are elements of the trasposed matrix of L (=tL), that is Q=(tL)x. If these are wrong, please tell me the correct. I appreciate your help. --------------------------------------- Hiro Maekawa hmaekawa(0)uci.edu Rowland Hall, Irvine, USA.