Hello everyone,
I am pretty new to avogadro. And I am tryingto generate inp files for chemical reactions involving catalyst. For example acetic acid + ethanol in presence of Sulphuric acid. I can model the reactant and product in separate files but when I do simulate the reaction with orca , the intermediate steps are weird like the H of H3O is bonded to another H . I don’t know if this is what is expected or am I doing something wrong.
Any suggestion would be very helpful.
Thank you.
It would help to have a bit more detail, for example one of the files or a screenshot.
Quantum chemical programs like ORCA just output a set of atoms and coordinates. So “bonds” are perceived by Avogadro as atoms being within a distance of overlapping covalent radii.
Apologies for the delayed response. This is how my reactant file looks like :
And here is the orca input :
! B97-3c TightSCF NEB
%pal
nprocs 24
end
%maxcore 3000
%scf
MaxIter 250
SOSCFStart 30
end
%cpcm
smd true
SMDsolvent “water”
end
%neb
NImages 13
NEB_END_XYZFILE “P1.xyz”
PreOpt_Ends false
CI true
MaxIter 300
end
Generally looks okay. Just remember that the bonds drawn in visualization are based on distances.
My general advice would be to use 1.103 or a continuous release from https://two.avogadro.cc/ and use the animation tool with “dynamic bonds” when you’re viewing the NEB trajectory. That will attempt to redraw the bonds for every frame.
But there’s no surprise if near the transition state, you have something where a hydrogen is shared to multiple species. If you’re watching a proton transfer, there will obviously be some point in which the hydrogen is halfway between.
