t-young31
commented
3 months ago Hi @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 ade
ade.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"))8
r.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 0.722198
p.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 0.43597A 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.
Geert38
Hi,
I am new to autodE. Many reactions work really smoothly sur as dehydration, hydration, deamination and ring closures. Others are more tricky. I am trying to get decarboxylation reactions to work with little success. I have tried many different. Here is my code for the decarboxylation of acetic acid. Now this reaction is supposed to be difficult with a high activation energy. I suspect that there is something more going on than just a difficult reaction. You say you are interested in a test case, so here is one. Is is possible that there is a thing going on with CO2?
import autode as ade ade.Config.n_cores = 1 AceticAcid = ade.Reactant(smiles='CC(=O)O') Methane = ade.Product(smiles='C') CO2 = ade.Product(smiles='O=C=O') rxn = ade.Reaction(AceticAcid, Methane, CO2, solvent_name='water', name='AA-Decarboxilation') rxn.calculate_reaction_profile(free_energy=True) 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")) print("∆G_r (kcal mol-1) = ", rxn.delta("G").to("kcal mol-1")) print("∆G‡ (kcal mol-1) = ", rxn.delta("G‡").to("kcal mol-1")) print("TS imaginary freq = ", rxn.ts.imaginary_frequencies[0])
The energy E is nicely calculated but it does not calculate the free energy G. Actually it gives a value of 4 for dGts. The graph shows a warning that it assumes a barrierless reaction. When trying to read the value of the imaginary frequency it crashes, as it probably does not exist. I suspect that it has not located the transition state. I have tested a variety of techniques, Orca, Gaussian, B3LYP, MP2, HF, solvent or not, but it never works. The same is true for decarboxilation of formic acid (half of the WGS reaction), glycine, malonic acid and that of glutamic acid. Malonic acid is supposed to be easy to decarboxylate.
I work with Python 3.9 on Windows10 Orca 5.04, Gaussian09 autodE version 1.4.1 rdkit version 223.9.5
Any thoughts ? It looks like autodE does not like CO2 as most other reactions work fine. CO2 probably does not react well to the search of confomers. Would this be a problem in the search for a TS?
Thanks in advance.