From owner-chemistry@ccl.net Fri Dec 5 06:41:01 2014 From: "Peter Kraus p.kraus12^imperial.ac.uk" To: CCL Subject: CCL:G: Rates of multiwell reactions Message-Id: <-50793-141205063819-28072-3u75LiEG5MHT0i7ESU46DA_-_server.ccl.net> X-Original-From: "Peter Kraus" Date: Fri, 5 Dec 2014 06:38:18 -0500 Sent to CCL by: "Peter Kraus" [p.kraus12||imperial.ac.uk] Dear CCL subscribers, I'm trying to obtain a pair of forward and reverse chemical reaction rates for what is esentially a recombination reaction. The details are as follows: One of the reactants contains platinum. I have optimised structures (using DFT in G09) of : 1) reactant pair (separate files) 2) first intermediate (seems to be a barrierless process) 3) first TS (between intermediate 1 and 2) 4) second intermediate 5) second TS 6) product I have performed IRC calculations from the TS's to confirm they are indeed the correct TS's All structures are converged using "tight" criteria, all structures have had their frequencies calculated. My question is, how do I get a reaction rate going from reactant to product? I've been told I can use chemrate, polyrate or mesmer, but as I'm completely new to this, I'd like some pointers. I'd prefer to use the obtained gaussian logfiles (without having to recalculate the structures), if at all possible. Thanks in advance! Peter From owner-chemistry@ccl.net Fri Dec 5 10:07:01 2014 From: "Robin Shannon R.Shannon(-)leeds.ac.uk" To: CCL Subject: CCL:G: Rates of multiwell reactions Message-Id: <-50794-141205091504-3690-gb9EHjL0WCtMD5NZ66Sw1w . server.ccl.net> X-Original-From: Robin Shannon Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Dec 2014 14:14:55 +0000 MIME-Version: 1.0 Sent to CCL by: Robin Shannon [R.Shannon]_[leeds.ac.uk] Dear Peter A master equation simulation in MESMER will give you pressure dependent rate coefficients for all the different channels, the difficulty will be in obtaining high pressure limiting rate coefficients for the barrierless process. To calculate the this from an a priori perspective you would need to use polyrate but such calculations require a large amount of potential energy information and as such can be non trivial to perform. Sums of states from polyrate calculations could then be read into MESMER. An alternative and simpler approach would be to assume the high pressure limit of the barrierless process to be described by a given Arrhenius form and the ILT method in MESMER will convert these k(T)'s to k(e)'s. The Arrhenius form can be guessed using simple capture type expressions or using chemical intuition. You can translate your Gaussian log files into MESMER input using open babel. Feel free to contact me directly and I can offer more help with getting you started in MESMER. Best wishes Robin ________________________________________ > From: owner-chemistry+chmrsh==leeds.ac.uk__ccl.net [owner-chemistry+chmrsh==leeds.ac.uk__ccl.net] On Behalf Of Peter Kraus p.kraus12^imperial.ac.uk [owner-chemistry__ccl.net] Sent: 05 December 2014 11:38 To: Shannon, Robin J Subject: CCL:G: Rates of multiwell reactions Sent to CCL by: "Peter Kraus" [p.kraus12||imperial.ac.uk] Dear CCL subscribers, I'm trying to obtain a pair of forward and reverse chemical reaction rates for what is esentially a recombination reaction. The details are as follows: One of the reactants contains platinum. I have optimised structures (using DFT in G09) of : 1) reactant pair (separate files) 2) first intermediate (seems to be a barrierless process) 3) first TS (between intermediate 1 and 2) 4) second intermediate 5) second TS 6) product I have performed IRC calculations from the TS's to confirm they are indeed the correct TS's All structures are converged using "tight" criteria, all structures have had their frequencies calculated. My question is, how do I get a reaction rate going from reactant to product? I've been told I can use chemrate, polyrate or mesmer, but as I'm completely new to this, I'd like some pointers. I'd prefer to use the obtained gaussian logfiles (without having to recalculate the structures), if at all possible. Thanks in advance! Peterhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Dec 5 11:47:01 2014 From: "Ambrish K. Srivastava ambrishphysics- -gmail.com" To: CCL Subject: CCL:G: Please read before you become the next.. Message-Id: <-50795-141205113525-28944-7AjbaxRlI7Fw6JMwVhMRsQ---server.ccl.net> X-Original-From: "Ambrish K. Srivastava" Date: Fri, 5 Dec 2014 11:35:24 -0500 Sent to CCL by: "Ambrish K. Srivastava" [ambrishphysics[#]gmail.com] Dear CCL subscribers, I'm not sure whether it is fair to someone to share it publicly, but I'm quite sure it will be in the welfare of many more. So, let me start the story which begins with the invitation by ABC (I don't want to quote the name but sorry, the truth can't be hidden) to co-operate in a joint article on CCL on 20th of October. "Dear Colleagues, Would you please to calculate and visualize ten frontier HOMO and LUMO orbitals of large bioorganic system by using DFT method. I will provide you with optimized geometry Cartesian coordinates.." "I can try if you provide me optimized geometry of your systems.", I replied on CCL. > From this reply, he started personal communication with me. Below, I present our communications along with timeline- 21st Oct: "I need to draw HOMO, LUMO and electron density transfer pictures of two micelles system in certain excited states for our joint article. Would you please to take the attached coordinates in inputFile_2.doc and run single point calculation. This file is prepared for Gaussian program package." [Few mails are removed due to space limit] 3rd Nov: "your job is successfully running. We'll let you know soon once it is finished." 3rd Nov: "Thank you for your promising letter." He replied. [No Communication] 28th Nov: "We are pleased to tell you that your job has been finished successfully at PBEPBE/6-311++G** level of computation. Now, as per your requirement, we can provide you MOs..." 28th Nov: "Thank you for your finished work on optimization geometry by PBEPBE/6-311++G**. Would you please to send your optimized resulting file to my server. My ftp server is accessible by such a way:... ..... Would you please to draw frontier orbitals... Please use the JPG format..." 4th Dec: "Let me first apologize for the delayed response. This is due to the fact that we were facing some technical problem in generating the required images from the Gaussian Output. We have tried Gauss View program many times to generate HOMOs and LUMOs but each time it failed with some unexpected error. Then, we turned to Avogadro and succeeded in generating few HOMOs and LUMOs (which are attached herein, along with Gaussian Output (.log) file). However, It provided only first five HOMOs/ LUMOs and not beyond it (There is no technical error, It is simply not providing.). We hope that these will work for you. Finally, we have tried to connect to your FTP server. But perhaps our institute does not permit us. So, I am providing everything required via e-mail. Waiting for your response..." I mailed him. 4th Dec: "I see that you did not optimized geometry of given supramolecular geometry. In the keywords row I do not see the keyword opt, please look to your calculations: #pbepbe/6-311++g** test SP pop=none scf=qc Without optimization of geometry all other further procedures are meaningless..." He replied. 4th Dec: "Below I paste your proposal: [I remembered him his requirement and ask..] What's wrong here? Please clarify..." 5th Dec (Today): "Nothing wrong was done from your side. I requested you to calculate this task at the end of October and supplied you with optimized coordinates which were done by PM3 method. Other colleagues during the last month calculated single point DFT job and drawn 11 HOMO and 11 LUMO orbitals very quickly. Now they already done PM6 optimization of this system and 50 steps of DFT geometry optimization and drawn 11 HOMO and 11 LUMO orbitals. Therefore I wrote you today that your drawn 5 HOMO and 5 LUMO become not actual just because other colleagues done this with higher accuracy of optimization and drawn 11 HOMO and 11 LUMO orbitals. But do not worry so much about this, just American supercomputers working significantly faster. We have to think now what good jobs you can to do in my proposed project in order to be coauthor of our joint paper? Please write your opinion..." This was his final reply. I am NOT telling the moral of this story. Because you all are definitely superior than me so can better decide it. I shared it with the hope that what happened with me, should not repeat and nor happen with you. Thanks for the reading... With kind regards, Ambrish K. Srivastava Senior Research Fellow (CSIR) Department of Physics, University of Lucknow E-mail: ambrishphysics : gmail.com