Problem with decarboxylation reactions about autode HOT 4 CLOSED

On Sun, 31 Mar 2024 at 18:21, Tom Young ***@***.***> wrote: The library suggests that it is possible to make quantum chemistry simple, but this is deceptive, it will never be simple. Great quote. Should get it on a T-shirt! I did actually test the following, but I suspect this is also too complex: I'd suspect that too. A nano-reactor approach (e.g. 10.1021/acs.jctc.9b00143) is probably the best The thing is that the documentation is a bit on the light side for a complex tool Fair comment. Unfortunately writing documentation never reaches the top of the priority list. Contributions are very welcome! I asked for access to the slack some time ago without response Sorry for missing this. I'll dig it out — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

On Fri, 29 Mar 2024 at 13:40, Tom Young ***@***.***> wrote: Hi @Geert38 <https://github.com/Geert38> I've just tried it out and indeed autodE doesn't do a great job. Part of the problem is this early-stopping criteria on the initial path autode.log.log: WARNING Have a peak, products not made on isomorphism, but at least one of the distances is final. Assuming the peak is suitable which picks up a proton transfer across the carboxyl. We can force matters with a little manual intervention by creating reactant and products in the correct conformation import autode as adeade.Config.lcode = ade.Config.hcode = "orca" r = ade.Reactant("r.xyz")p = ade.Product("p.xyz")rxn = ade.Reaction(r, p, name='neb')rxn.optimise_reacs_prods()rxn.locate_transition_state()print("∆E_r (kcal mol-1) = ", rxn.delta("E").to("kcal mol-1"))print("∆E‡ (kcal mol-1) = ", rxn.delta("E‡").to("kcal mol-1")) 8r.xyz C -0.94699 -0.07829 -0.14189 C 0.49717 0.30811 -0.03089 O 0.96924 1.36670 -0.34881 O 1.23865 -0.68632 0.48331 H -1.51414 0.74203 -0.59422 H -1.34656 -0.30848 0.85676 H -1.04552 -0.99068 -0.74768 H 0.53828 -1.44002 0.72219 8p.xyz C -1.44659 -0.74815 0.05192 C 1.87467 0.88434 -0.02008 O 1.21899 1.79465 -0.43515 O 2.53012 -0.02628 0.39507 H -1.21104 0.26014 -0.34547 H -2.18369 -0.65644 0.87580 H -1.87258 -1.37341 -0.75929 H -0.51975 -1.22181 0.43597 A relevant aside: I'd be *very* surprised if this sort of decarboxylation is elementary with innocent solvent (consistent with the >60 kcal mol-1 barrier at DFT). I'd imagine some other acid/base or at least water mediated pathway is much more feasible. — Reply to this email directly, view it on GitHub <#331 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BG22KLWJ5HOAD3QY4GVL2LDY2VHKTAVCNFSM6AAAAABFMXTQP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRXGE4DQOJUGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>