From owner-chemistry@ccl.net Thu Feb 27 11:34:00 2014 From: "Adam Tenderholt atenderholt+/-gmail.com" To: CCL Subject: CCL: Enthalpy vs free energy of activation? Message-Id: <-49812-140227112210-27918-bnBpSQAMm6G0KeDIeSZD9Q+*+server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=089e0153873e05c6a104f365b773 Date: Thu, 27 Feb 2014 08:21:13 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt#,#gmail.com] --089e0153873e05c6a104f365b773 Content-Type: text/plain; charset=ISO-8859-1 Hi Andrew, In my experience with reaction coordinate calculations for oxo transfer to/from Mo dithiolene complexes (refs below), I generally saw good agreement between calculated and experimental enthalpies of activation but poor agreement for the entropies of activation. I believe the discrepancies for the entropies are due to calculations at a single transition state structure, and thus, the entropic effects due to the conformational space (i.e. orientation of substrate relative to Mo complex at TSs) are not fully captured. Perhaps others have work confirming or disproving this idea? Tenderholt, A. L., Hodgson, K. O., Hedman, B., Holm, R. H., & Solomon, E. I. (2012). Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites. *Inorganic Chemistry*, *51*(6), 3436-3442. doi:10.1021/ic2020397. Tenderholt, A. L., Wang, J.-J., Szilagyi, R. K., Holm, R. H., Hodgson, K. O., Hedman, B., & Solomon, E. I. (2010). Sulfur K-edge X-ray absorption spectroscopy and density functional calculations on Mo(IV) and Mo(VI)=O bis-dithiolenes: insights into the mechanism of oxo transfer in DMSO reductase and related functional analogues. *Journal of the American Chemical Society*, *132*(24), 8359-8371. doi:10.1021/ja910369c. Adam On Wed, Feb 26, 2014 at 7:17 PM, Andrew Yeung andrew.yeung%x%chem.tamu.edu < owner-chemistry . ccl.net> wrote: > > Sent to CCL by: Andrew Yeung [andrew.yeung : chem.tamu.edu] > Hi all > > I recall that some authors recommend that enthalpy of activation be used, > instead of free energy of activation. > > Does anybody have a reference handy? Thanks! > > -- > Andrew Yeung > Donald J. Darensbourg Research Group > Department of Chemistry, Texas A&M University > 3255 TAMU > College Station, TX 77843-3255 > > Tel: 979 845 4837 > Fax: 979 845 0158http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > > --089e0153873e05c6a104f365b773 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Andrew,

In my experience with reacti= on coordinate calculations for oxo transfer to/from Mo dithiolene complexes= (refs below), I generally saw good agreement between calculated and experi= mental enthalpies of activation but poor agreement for the entropies of act= ivation. I believe the discrepancies for the entropies are due to calculati= ons at a single transition state structure, and thus, the entropic effects = due to the conformational space (i.e. orientation of substrate relative to = Mo complex at TSs) are not fully captured. Perhaps others have work confirm= ing or disproving this idea?

Tenderholt, A. L., Hodgson, K. O., Hedman, B., Holm, R.= H., & Solomon, E. I. (2012). Substrate and Metal Control of Barrier He= ights for Oxo Transfer to Mo and W Bis-dithiolene Sites. Inorganic Chemi= stry, 51(6), 3436–3442. doi:10.1021/ic2020397.

Tenderholt, A. L., Wang, J.-J., Szilagyi, R. K., Holm, = R. H., Hodgson, K. O., Hedman, B., & Solomon, E. I. (2010). Sulfur K-ed= ge X-ray absorption spectroscopy and density functional calculations on Mo(= IV) and Mo(VI)=3DO bis-dithiolenes: insights into the mechanism of oxo tran= sfer in DMSO reductase and related functional analogues. Journal of the = American Chemical Society, 132(24), 8359–8371. doi:10.1021= /ja910369c.

Adam



On Wed, Feb 26, 2014 at 7:17 PM= , Andrew Yeung andrew.yeung%x%chem.tamu.ed= u <owner-chemistry . ccl.net> wrote:

Sent to CCL by: Andrew Yeung [andrew.yeung : chem.tamu.edu]
Hi all

I recall that some authors recommend that enthalpy of activation be used, i= nstead of free energy of activation.

Does anybody have a reference handy? Thanks!

--
Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158



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--089e0153873e05c6a104f365b773-- From owner-chemistry@ccl.net Thu Feb 27 14:48:01 2014 From: "Mike Towler mdt26-x-cam.ac.uk" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL differences - summary + QMC request Message-Id: <-49813-140227120446-20116-BEMFt2Tywl98zxlaI/Z2OQ()server.ccl.net> X-Original-From: "Mike Towler" Date: Thu, 27 Feb 2014 12:04:45 -0500 Sent to CCL by: "Mike Towler" [mdt26_-_cam.ac.uk] Dear all, About a week ago I asked a question about why GAUSSIAN, GAMESS, MOLPRO, and CRYSTAL were giving very different answers in test calculations for a methane molecule, using basis sets consisting only of functions of a particular high angular momentum (f functions only, in the example I presented). I just wanted to summarize the responses, and to make an additional request. Many thanks for all the replies, especially to Susi Lehtola, Mikael Johansson, William McDonald, Raghu, and in particular to Wenli (Zork Zou?), who all gave helpful responses leading to the right answer, which was that GAUSSIAN and CRYSTAL manage to produce lower-energy symmetry-broken solutions all by themselves, whereas GAMESS and MOLPRO require specific keyword incantations to kick them off a saddle point into the broken-symmetry state: MOLPRO: {hf;noenest;occ,1,2,1,1} GAMESS: $GUESS ORDER=1 IORDER(2)=6,3,4,5,2 $END Some people also suggested that I was using a poor quality basis set, and I needed to include s,p,d functions etc.. As any fule kno, this is quite true, and would be a concern if my aim were to calculate some property of the methane molecule. However, as I said in my original mail, these calculations are being done to check the correctness of the interface between our quantum Monte Carlo code 'CASINO' and various other quantum chemistry codes such as the four mentioned here. For a number of reasons, these interfaces are very easy to screw up for higher angular momentum Gaussians, and it's very helpful to check each value of L individually (and also to have all the MO coefficients having non-zero values, which is why I chose the tetrahedral symmetry..). Even though it's helpful for comparison purposes that GAUSSIAN, GAMESS etc. all end up in same state, it doesn't matter overall what state we end up in (e.g. the broken symmetry state, or the symmetric one); any state represents some many-body wave function which can be communicated to CASINO. The formula for the expectation value of the energy can then be numerically integrated by evaluating the wave function at random points in the configuration space (Monte Carlo integration). Hopefully this will give the same answer as the initial code running in HF mode. (Once that is verified, propagation in imaginary time will 'improve' the wave function and massage it towards the true ground state, but that's another story). Speaking of interfaces, here's my additional request, which concerns the new public release of CASINO which we're hoping will appear in a few weeks time. We're hoping to offer support for a wider range of quantum chemistry codes, and to this end Mike Deible of the University of Pittsburgh has very kindly written a conversion utility which converts output in the standard MOLDEN format (produced by many different quantum chemistry codes..) into the trial many-body wave function format required by CASINO. Using our standard tests, Mike is currently verifying that this works for the MOLPRO, CFOUR, PSI4, and TURBOMOLE packages (NB: certain issues can arise, depending on how the code chooses to write the MOLDEN FILE - and so e.g. it doesn't work for CFOUR - see the PS below my signature for the boring reasons why). Now, according to this page: http://www.cmbi.ru.nl/molden/others.html many other codes such as ACESII, MOLCAS, DALTON, Jaguar, CADPAC, GEOMOP, ORCA, and HONDO have some kind of support for the MOLDEN format. If any people with a professional interest in these or other MOLDEN-supporting codes would like to do QMC calculations, it should be possible quite quickly to verify that this general interface to CASINO works, and to add the code in question to the list of 'supported software' that we maintain here: http://vallico.net/casinoqmc/interfaces/ So if you would like to do that, please let me know. A good start would be for you to produce input files for the d-ane, f-ane, and g-ane molecules in a format suitable for your code (you may base these on the GAUSSIAN, GAMESS, MOLPRO, CRYSTAL examples for f-ane given in the links below; similar d-ane and g-ane files with suitable Gaussian exponents can be supplied on request). You should then send me those inputs plus the corresponding Hartree-Fock outputs with the wave function in MOLDEN format. We can then run Mike's converter on the MOLDEN file, and I can then do quick QMC Hartree-Fock calculations with CASINO; if it produces the same answer as you to within statistical error bars for all three cases (and for any one standard molecule with a 'normal basis' including s and p functions), then your code will be 'officially supported'. http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess_new.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro_new.txt Please address any general queries to me (mdt26 at cam.ac.uk) and specific technical queries about the MOLDEN interface to Mike Deible (mjd87 at pitt.edu). Best wishes, Mike PS: Just to give you an idea of the kind of problem that can arise - the problem with CFOUR according to Mike D. appears to be as follows. It normalizes the basis set before the calculation (like most codes), then does the HF calculation. It prints the orbitals to the MOLDEN file, but the basis set that it prints is not the normalized basis set that it used for the calculation, it is the basis set from the initial input. The CFOUR output prints the normalization constant it uses for each contraction for each atom, but because these aren't in the MOLDEN file and are different for each atom, there is no straightforward way to renormalize the contraction coefficients. MOLPRO prints to the MOLDEN file the normalized basis set that it uses, so it only needs to multiplied by some factor to be accepted by CASINO - hopefully this issue can therefore be fixed..