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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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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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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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 ...
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Why does alpha-carbon substituents increase the rate of E2 reactions?
The reason for more reactivity of more substituted alkyl halides for E2 Reaction is said to be due to the more stability of its more substituted alkene character having transition state but here (...
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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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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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NMR and dienes to isolate certain isotopes?
I am looking to achieve isotope separation using transition states.
In the rxn of dienes with halogens, based on the temperature, the dienes can create a thermodynamic product or a kinetic product. ...
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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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Why is the transition state the highest energy point? [closed]
If partial bonds form during transition state, it means some energy is released, so how can it have the highest energy? Shouldn't the point before transition state be highest energy? (the point where ...
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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 ...
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Can rate constant depend upon the concentration of reactants (or other species involved in the reaction)?
Transition state theory tells us that the rate constant of an elementary step is $$k_\mathrm{r} = \frac{\kappa k_\mathrm{B}T}{h}\exp\left\{\frac{- \Delta G^\ddagger}{RT}\right\},$$
where $\Delta G^\...
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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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What is the reasoning behind the assumptions of Transition State Theory?
We were told in a first year introductory Thermodynamics and Kinetics lecture, and also from Wikipedia, that there are 3 main assumptions for the derivations used in Transition State Theory, but I'm ...
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Understanding transition state theory
Let's say we have standard chemical reaction given by
$$A-B + C \leftrightharpoons [A\cdot\cdot B\cdot\cdot C]^{\dagger} \rightarrow A +B-C$$
I want to estimate the pre-exponential factor of this ...
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Entropy of Activation and Temperature Dependence
I am trying to understand the extrapolation of enthalpy $\Delta H^{\ddagger}$ and entropy of activation $\Delta S^{\ddagger}$ from the Eyring equation. It's typically cast as:
$$\ln\left(\frac{k}{T}\...
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Transition State search
I've been trying to find a transition state for the reaction of Pd + F2 with no luck. Has anyone ever tried a similar reaction, have they managed to get the TS? The reaction proceeds from the ...
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Where does the RT term come from in the derivation for the activation enthalpy from the Eyring equation?
It is easy to show an Arrhenius-like equation from the Eyring equation, but if you do this, you get that the activation energy is about equal to the activation enthalpy. However, the real ...
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Transition state optimisation on the surface of periclase
I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT.
I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC).
The ...
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When are transition state's energy barrier "reasonable" at a certain temperature?
Every computational chemist who does a little bit of mechanistic studies has asked himself this question. When you obtain your first transition state and look at the activation barrier needed to ...
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Stabilizing donor-acceptor interaction between orthogonal orbitals in the SN2 transition state?
For the $\mathrm{S_N2}$ reaction between chloroacetone and iodide, my professor has drawn a donor-acceptor interaction between the iodine lone pair attacking the Cl-substituted carbon and the π ...
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Investigating the effect of solvents (protic vs aprotic) on the alkaline hydrolysis of ethyl acetate using a conductivity meter
What different areas about solvents can be explored with the conductivities collected of the alkaline hydrolysis of ethyl acetate in propanone and ethanol?
$$\ce{CH3COOC2H5 + NaOH -> CH3COONa + ...
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Is Gibbs Free Energy of formation equal to Gibbs Free Energy of transition state?
Is activation energy equivalent to Gibbs Free Energy of transition state as related by Eyring equation?
$$E_a=\Delta ^\ddagger G \, \, ?$$
Is Gibbs Free Energy of transition state defined by the ...
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Units of rate constant (cycles per second vs radians per second) in Eyring equation
In the Eyring equation (EE),
$$k = \frac{k_\mathrm B T}{h} \exp\left(\frac{-\Delta G_{\mathrm f}}{RT}\right),$$
the units of $k$ are $\mathrm{s^{-1}}$. However, in general rate constants are usually ...
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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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Solids to liquids process
Melting point is the critical point at which a solid starts to be transformed into a liquid? Does this mean that the geometric lattice of a solid is broken?
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Why does transition state loses its ability to vibrate? (Transition State Theory)
In transition state theory, (according to my textbook) it is assumed that the the transition state loses its structure, and the ability to vibrate and rotate. If the transition state cannot vibrate, ...
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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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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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In Statistical Transition State Theory, why is the concentration of the transition state for the forward and reverse reaction identical?
For example on Wikipedia, and also in my lecture notes, it is assumed that for a reaction
$$\ce{A + B<=> AB^{\ddagger} <=> P}$$
at equilibrium,
$$[\ce{AB^{\ddagger}_f}] = [\ce{AB^{\...
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