From chemistry-request#* at *#server.ccl.net Thu Mar 23 12:24:35 2000 Received: from oulu.fi (root:~at~:ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26553 for ; Thu, 23 Mar 2000 12:24:29 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id TAA07739 for ; Thu, 23 Mar 2000 19:24:15 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id TAA19024510 for ; Thu, 23 Mar 2000 19:24:14 +0200 (EET) Date: Thu, 23 Mar 2000 19:24:14 +0200 From: Atte Sillanpaa X-Sender: asillanp#* at *#paju.oulu.fi To: chemistry(+ at +)ccl.net Subject: Summary of activation free energy In-Reply-To: <862568AB.00469176.00 $#at#$ unomail.unomaha.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII First of all thanks for everyone who replied. From the responses I gather that searching for a free energy maximum based on potential energy surface even if there is no extremum on the PES is a sound approach. The program POLYRATE, which Jordi suggested, gives possibility to use more sophisticated theories to calculate rate constants. As another alternative Cory Pye suggested the thermodynamic integration scheme from constrained molecular dynamics. The responses (slightly edited to save space) were: --------8<------------------------- From: Cory Pye On Wed, 15 Mar 2000, Atte Sillanpaa wrote: > Hello CCLers, > I'm trying to calculate the free energy of activation for a process where > there is no minimum on the potential energy surface (PES). The (ethene > polymerisation termination) reaction begins with > a beta elimination from an alkyl group to the metal center. This forms a > fairly unstable metal hydride and a hapto2-alkene. The PES for scanning > the alkene away from the metal increases monotonically approaching the > separated products value. The free energy of separated products is readily > calculated, and is naturally much lower relative to PE. However, as the > alkene recedes from the metal it gradually gains the translational and > rotational degrees of freedom and its free energy drops, but there is a > maximum at some point. > > The question is that if I calculate the free energy with the harmonic > approximation at some (ambigious) constrained geometry (distance from the > metal) is it of any approximate value for the free energy of activation? If you use this approach, you would probably have to select some "reaction coordinate" and calculate the free energy at some selected points along your coordinate, say every 0.5 angstroms, to roughly locate your Free energy transition structure. Then you could refine the region near the maximum. > > Is there some other method for calculating the free energy of activation > in this kind of PES? > Another way is to calculate the free energy using constrained molecular dynamics with a DFT energy. Tom Ziegler's group at the U of Calgary has done these types of simulations (I was a post-doc there with him on a different project). Check out: 1) JACS 118 4434-4441 (1996) - Cp2Zr(C2H5)+ + C2H4 2) JACS 118 13021-13030 (1996) - (CpSiH2NH)TiR+ + C2H4 I. 3) Organometallics 16 3454-3468 (1997) - "" II. 4) JACS 119 6177-6186 (1997) - Ni(II)-diimine + C2H4 5) JPC B 101 7877-7880 (1997) - NI(II)-diimine + C2H4 6) JACS 120 2174-2175 (1998) - Ti(IV)-H2 7) "Transition State Modelling for Catalysis", D. G. Truhlar and K. Morokuma, (eds), ACS Symp. Ser. 721, ACS, Washington, D.C. (1999), p173-186 8) Catalysis Today 50 479-500 (1999) - overview ************* ! Dr. Cory C. Pye ***************** ! Assistant Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye(+ at +)crux.stmarys.ca http://husky1.stmarys.ca/cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) ----8<----------------------- From: Jordi =?iso-8859-1?Q?Vill=E0?= Dear Atte, take a look at GAUSSRATE (http://comp.chem.umn.edu/sds/), which you can use for calculating the free energy profile for your reaction using Variational Transition State Theory (VTST), even if you don't have any maximum on the PES. In principal you have two general approaches to use for solving your problem using VTST. The first is the use of the geometries generated by an intrinsic reaction path (IRC) calculation and the second is using a simple distinguished reaction coordinate (DCP). Both of these possibilities can be readily explored using GAUSSRATE (for automatically calculate the needed structures if you have Gaussian installed in your computer) or its father POLYRATE (if you have previously calculated those paths and you kept first and second derivatives along them) Jordi -- Jordi Villa i Freixa Department of Chemistry, University of Southern California 3620 S McClintock Av. #418; Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 jorgevil _-at-_)usc.edu http://laetro.usc.edu/jorgevil ----------8<----------------------- From: michael braunschweig hi atte, to obtain an trasition state try to calculate a first order saddle point on the pes without making any constrains. to find the start structure make a quadratic synconous transit. to be sure this is a valid transition state make a frequency calculation (one imaginary frequency) and compute an irc-run. in g98 the keywords are: opt=qst2 (or qst3), opt=ts and irc. hope this will help michael braunschweig university of dortmund department of chemistry germany atte.sillanpaa ^at^ oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 Oulun Yliopisto FINLAND | Entropy requires no maintenance. |