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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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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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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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1answer
184 views

Explain the difference between reaction intermediate and reactive intermediate

Wikipedia definitions of the terms: Reaction intermediate: https://en.m.wikipedia.org/wiki/Reaction_intermediate Reactive intermediate: https://en.m.wikipedia.org/wiki/Reactive_intermediate What ...
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Why some reaction have no transition state?

All stationary point are local minimum, if any parameters changed the energy should be increase. There is no way for a stationary point that energy go straight down to reach another. I was told that ...
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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 ...
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1answer
584 views

Kinetic vs thermodynamic control of HBr to 1,3-Butadiene

The author claims that the transition state leading to the formation of the 1,2 product from the allylic carbocation is lower in energy since the carbon (which is attached to Br in the 1,2 product) is ...
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2answers
173 views

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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Why only molecules with three or more atoms undergo unimolecular reaction?

Only molecules with three or more atoms undergo unimolecular reactions. A diatomic molecule cannot dissociate in this way because it has a single mode of vibrational freedom. If this mode is excited ...
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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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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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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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1answer
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Explaining boiling using internal energy

Internal energy is summation of potential and kinetic energies of a substance Using this interpretation of internal energy, how can I explain boiling? Kinetic remains constant. Potential should ...
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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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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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2answers
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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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1answer
400 views

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 ...
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Transition state - multidimensional surfaces

I've been reading an explanation about transition states in Smith's Organic Synthesis: A transition state is an energy maximum along the reaction coordinate. However, a chemical reaction where ...
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1answer
366 views

References for Transition State Theory and Quantum Transtion State Theory

Having asked recently this, I started to look for good references and notes on Transition State Theory and, also, modern versions of it including things like tunneling (which isn't taken into account ...
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50 views

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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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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287 views

Aromaticity-Bromonium Ion

Is the bridged ion intermediate aromatic or not? What is the way to quickly identify aromaticity?
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If Gibbs energy of activation is positive, how is the change to the transition state possible?

The Gibbs energy increases from the reactants to the transition state, but according to the Second Law of Thermodynamics, entropy of the universe can only increase. Why is the transition state ...
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1answer
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How is the energy of reactants in a chemical reaction found ?

A pretty rudimentary question, but I'm reviewing the concept of energy diagrams and activation energy and I'm curious to know how chemists find the energy of reactants and of a transition state in a ...
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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 ...
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Transition state and free energy

We have products $\ce{A + B}$ combining to form $\ce{C + D}$ through the transition state $\ce{X}$. Are all reactions at least virtually reversible? Is the difference between a reversible reaction ...