Questions tagged [transition-state-theory]
Questions related to explanations of the reaction rates of elementary chemical reactions. The theory assumes a special type of chemical equilibrium (quasi-equilibrium) between reactants and activated transition state complexes.
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Calculation of rate constant for bimolecular reaction from Gaussian DFT calculations
I am working with a bimolecular reaction for which I have computed the energy profile. I have output files for TS and reactants which I intend to use for rate constant calculations. From TST we have:
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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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Is standard change in activation Gibbs free energy indepedent of pressure?
For a chemical reaction the activation volume is defined as:
$$Δ^{\ddagger}V={V^\ddagger}-V$$
where both $V^\ddagger$ and $V$ refer to standard states (I have omitted the symbol for simplicity). One ...
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Calculating pre-exponential factor using transition state theory
I would like to calculate the pre-exponential factor of a surface reaction using transition state theory. I've seen two ways to calculate it but I get different answers for each method (and I don't ...
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Gibbs free energy of transition and activation energy
Let's consider a reaction A (reactant) -> B(product) and activated complex is denoted by C.
This graph ( potential energy vs reaction coordinate ) tells us that reactant need some amount of ...
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rate constant via flux-flux correlation function for linear potential energy surface
How does one calculate fully quantum mechanical rate ($\kappa$) in the golden-rule approximation for two linear potential energy surfaces?
Attempt:
Miller (83) proposes $\kappa=\int{Tr[\exp{(-\beta\...
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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 ...
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Can there be two transition states (first order saddle point) connecting the same pair of minimas on a potential energy surface?
This is a purely hypothetical question. Consider a pair of local minimas A and B on a multi dimensional potential energy surface. Can there be two first saddle points (IE two different configurations) ...
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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 ...
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Stabilizing donor-acceptor interaction between orthogonal orbitals in the SN2 transition state?
For the $\mathrm{S_N2}$ reaction between chloroacetone and iodide, my professor has drawn a donor-acceptor interaction between the iodine lone pair attacking the Cl-substituted carbon and the π ...
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Investigating the effect of solvents (protic vs aprotic) on the alkaline hydrolysis of ethyl acetate using a conductivity meter
What different areas about solvents can be explored with the conductivities collected of the alkaline hydrolysis of ethyl acetate in propanone and ethanol?
$$\ce{CH3COOC2H5 + NaOH -> CH3COONa + ...
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Intuition of following the lowest curvature mode to find a saddle point on a PES
In this paper A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives, it is mentioned that
The saddle point is a maximum along the lowest ...
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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 ...
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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 ...
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What is the Best Transition State Search Method
I want to find transition states (TS) on the potential energy surface (PES) of small/medium reactions with sinle-ended methods. For example the reaction network from here. I've been looking at ...
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