Thanks! Could you make a tutorial on how to approach finding TS/Intermediates that involve open shell species? E.g. classical oxidative addition vs radical halide abstraction.
Yes, actually I can. Let me find a good example and perhaps I will do a series, from drawing the initial structures to different strategies for getting the transition state. Do you have particular examples in mind? If you have a reference for something similar to what you want please copy the DOI in the comments and I will take a look and see if it's something feasible for me.
@@niconeuman 10.1016/j.jorganchem.2014.08.015 This would be an example of what I mean. For instance, in Fig 1, TS2 would be a classical 3-membered-ring TS polar oxidative addition, which I would know how to compute. But for TS1 (radical halide abstraction), leading to open shell radical intermediates, that then further recombine to give eventually closed-shell IN_1t, it goes over my head. If you could explain how to approach the calculations of such mechanism, focusing on the open shell INTs and comparing it to the closed-shell ones, it would be awesome. You're doing god's work with this channel!
ok let me take a look at it. it may take me a while because I need to finish some stuff for work. it looks to me that steps 1a and 1b require broken symmetry so you will get radicals on each site. another possibility would be to use fragments, which I think allow you to define the spin of each. the problem with this stuff is that on one side of the reaction you may have two radicals and on the other side a singlet species, so the transition state involves a change in spin. I've been told that that is tricky to compute, but I don't have particular experience with those cases. but usually energy differences between true and broken symmetry singlets are not that great so that they will significantly alter the transition state energy. I will read a little because this topic is interesting for my own work also. cheers
I use Chemcraft for visualisation. But it's not free. Avogadro is free and quite good and easy to use. But I prepare the input files in a normal text editor. I just draw or modify structures in the editor and manually copy the coordinates to the input file. I never generate input files directly from the visualisation program
@@niconeuman thanks. I am using Gaussian with GaussView but I have always been attracted towards Orca because of its simplicity and powerful engine. Will do it sir.
Thanks for your useful videos. Indeed I am looking for a way to calculate ESP charge of a molecule by ORCA. Any comments would be appreciated.
Thanks! Could you make a tutorial on how to approach finding TS/Intermediates that involve open shell species? E.g. classical oxidative addition vs radical halide abstraction.
Yes, actually I can. Let me find a good example and perhaps I will do a series, from drawing the initial structures to different strategies for getting the transition state. Do you have particular examples in mind? If you have a reference for something similar to what you want please copy the DOI in the comments and I will take a look and see if it's something feasible for me.
@@niconeuman 10.1016/j.jorganchem.2014.08.015 This would be an example of what I mean. For instance, in Fig 1, TS2 would be a classical 3-membered-ring TS polar oxidative addition, which I would know how to compute. But for TS1 (radical halide abstraction), leading to open shell radical intermediates, that then further recombine to give eventually closed-shell IN_1t, it goes over my head. If you could explain how to approach the calculations of such mechanism, focusing on the open shell INTs and comparing it to the closed-shell ones, it would be awesome.
You're doing god's work with this channel!
ok let me take a look at it. it may take me a while because I need to finish some stuff for work. it looks to me that steps 1a and 1b require broken symmetry so you will get radicals on each site. another possibility would be to use fragments, which I think allow you to define the spin of each. the problem with this stuff is that on one side of the reaction you may have two radicals and on the other side a singlet species, so the transition state involves a change in spin. I've been told that that is tricky to compute, but I don't have particular experience with those cases. but usually energy differences between true and broken symmetry singlets are not that great so that they will significantly alter the transition state energy. I will read a little because this topic is interesting for my own work also.
cheers
Sir, which software to use for visualization and prepare input???
I use Chemcraft for visualisation. But it's not free. Avogadro is free and quite good and easy to use. But I prepare the input files in a normal text editor. I just draw or modify structures in the editor and manually copy the coordinates to the input file. I never generate input files directly from the visualisation program
@@niconeuman thanks. I am using Gaussian with GaussView but I have always been attracted towards Orca because of its simplicity and powerful engine. Will do it sir.