From owner-chemistry@ccl.net Wed Jul 20 13:31:01 2016 From: "Jim Kress jimkress35^^gmail.com" To: CCL Subject: CCL:G: 0. Basics,1. Biradicals, Guidance. 2. Connectivity Problems Message-Id: <-52319-160720103441-19233-5vKyCiQ684sKE273CwxLpQ() server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Jul 2016 10:34:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35%x%gmail.com] I'd use Orca. The user manual not only tells you how to use the program but clearly explains the answers to your questions as a part of describing how to do the calculations. https://orcaforum.cec.mpg.de/portal.php Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com-x-ccl.net [mailto:owner-chemistry+jimkress35==gmail.com-x-ccl.net] On Behalf Of Daniel Morales Salazar danielmoralessalazar91]![gmail.com Sent: Tuesday, July 19, 2016 8:17 PM To: Kress, Jim Subject: CCL:G: 0. Basics,1. Biradicals, Guidance. 2. Connectivity Problems Sent to CCL by: "Daniel Morales Salazar" [danielmoralessalazar91---gmail.com] Dear CCL Members, First of all, thank you very much for your input in my previous questions, which was always thorough and proactive. 0. This time I prepared the question by mainly glancing through: Abe, Manabu. "Diradicals." Chemical reviews 113.9 (2013): 7011-7088, Chapters 3 and 4 of, Datta, Sambhu N., Carl Trindle, and Francesc Illas. Theoretical and computational aspects of magnetic organic molecules, Imperial College Press, Hackensack, NJ;London; 2014., both a bit overwhelming for the amount of time I currently have, I also looked at some of my undergraduate textbooks and online .pdf files, but I am still struggling with some trivial and not-so trivial details. Trivial things such as terminology like the difference between a "triplet ground state" and "triplet excited state" are not very clear to me yet, what is simple and correct way of thinking about the difference of these two? it seems as if in most of my reading I keep finding that T1 is a triplet excited state, so is the "triplet ground state" a "T0"? and computationally (DFT), what is the difference? is it that one calculates a "triplet ground state" using (U)DFT and the "triplet excited state" using (R)TD-DFT? I am getting too long now so I would appreciate some feedback on the following mostly: 1. I am interested in calculating the energies and properties of neutral mesomeric systems (C, H, N, P, S) containing 25 to 60 atoms, which may or may not exist as open shell singlet biradicals in their ground state, and/or have interesting singlet triplet gaps and this type of "theoretical business" :) where can I find a good "step by step" kind of reference for an experimentalist who is learning theoretical aspects of biradicals? and which functionals do you advice me to try? I have read there may be better functionals than B3LYP for pi-conjugated systems in which the "radicals" are separated yet part of a delocalized system, in my cases they are anywhere > from 7 to 13 bonds apart. 2. I am optimizing the geometry of a system (C46H43Br2PSi2) with the following input route: #p opt=tight pm6 geom=connectivity gfinput gfprint int=fine iop(6/7=3) Item Value Threshold Converged? Maximum Force 0.000001 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.000047 0.000060 YES RMS Displacement 0.000009 0.000040 YES Predicted change in Energy=-4.577343D-12 However, the connectivity of the final structure significantly differs > from the initial one. I see some sort of 2+2 cycloaddition product, which is definitely not what I expected since I used the "geom=connectivity" keyword as read online. I am trying to optimize this same compound using B3LYP/6-311G** from my initial ("correct") geometry, and I see the same type of "cycloaddition" or "erroneous" intermediates after a number of cycles. How can I force Gaussian to keep the bonding situation exactly as given in the input, or is this a Molden/GaussView problem? ... I doubt the latter one because some bonds I find are really longer than what they would be if they were double bonds for example. I hope the question serves to other people with similar problems.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt