All Questions
Tagged with transition-state-theory computational-chemistry
13
questions
1
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0
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29
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Is the minimum energy pathway a geodesic in the potential energy surface?
I just finished NEB-TS calculation using Orca 4.2.1. One of the output file is the minimum energy pathway (MEP) data. Am I correct to interpret the MEP as the geodesic (path of minimum length) on the ...
- 283
3
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0
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50
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Can AMBER as low-layer be used to model reaction mechanisms using ONIOM? If yes, do you need to parameterize the intermediates and Transition states?
I'm debating moving from (M06-2X:PM7:UFF) to (M06-2X:PM7:AMBER) for modelling a reaction mechanism in an enzyme. I've already examined the errors introduced by my partitioning and whether they cancel ...
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4
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2
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1k
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How to estimate the temperature needed to overcome an activation energy barrier?
Trying to elucidate a reaction pathway, I calculated the energies for different transition states possible for that reaction (computational chem. DFT). I found activation free energies ranging from 29 ...
1
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0
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58
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Transition State search
I've been trying to find a transition state for the reaction of Pd + F2 with no luck. Has anyone ever tried a similar reaction, have they managed to get the TS? The reaction proceeds from the ...
- 41
1
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0
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77
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What is the intuition of using "dimer method" for searching transition states?
I learned dimer method for searching transition state in this paper:
A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives.
However, I still ...
- 273
12
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1
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286
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Finding chair and boat transition states during ring-forming reactions
Reactions that form 6 membered rings most commonly go via either boat or chair transition states but the products themselves do not necessarily adopt the same conformation as the TS.
I'm attempting ...
- 17.2k
5
votes
2
answers
345
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Unix/MobaXterm Project Assistence (Knowing the Error in my Output File)
I'm a student and I recieved a project in which I am supposed to simulate a transition state in an $\mathrm{S_N2}$ reaction.
The first instruction in this project is to use a benchmark reaction in ...
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26
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2
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1k
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Ambimodal transition states in some organic reaction pathways
In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
- 17.2k
1
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0
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101
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Should the normal mode of vibration leading to the transition state be removed?
I would like to know whether the normal mode of vibration of the reactant should be deleted when calculating $\Delta ZPE$ and $\delta G_{\text{corr}}(T)$, where $\Delta ZPE$ is the zero-point energy ...
- 339
9
votes
1
answer
283
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Transition state optimisation on the surface of periclase
I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT.
I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC).
The ...
- 2,883
4
votes
2
answers
346
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Can the number of intermediates for a reaction be more than the total number of transition states?
I'm getting results from a transition state guess software, in which the number of intermediates are two and there's only one transition state for a reaction, is that possible?
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1
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1
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534
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Intrinsic Reaction Coordinate - Converting To Reaction Coordinate with Units of Distance
I've located a transition state and ran two IRC calculations (one to get to the product and one to get to the reactant). Is there some type of way of approximating the IRC to something that has units ...
- 73
14
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1
answer
3k
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Why are the total energies of transition states so commonly corrected for zero-point vibrational energy?
So often I see total energies of transition states corrected for zero-point vibrational energy which always confuses me. Zero point energy is the lowest energy that a ground state minimum energy ...
- 4,629