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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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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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 ...
user1160
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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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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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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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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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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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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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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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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 ...
user28429
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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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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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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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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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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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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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Aromaticity-Bromonium Ion
Is the bridged ion intermediate aromatic or not?
What is the way to quickly identify aromaticity?
user14857
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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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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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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 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\},$$
where $\Delta G^\...
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Can AMBER as low-layer be used to model reaction mechanisms using ONIOM? If yes, do you need to parameterize the intermediates and Transition states?
I'm debating moving from (M06-2X:PM7:UFF) to (M06-2X:PM7:AMBER) for modelling a reaction mechanism in an enzyme. I've already examined the errors introduced by my partitioning and whether they cancel ...
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Is standard change in activation Gibbs free energy indepedent of pressure?
For a chemical reaction the activation volume is defined as:
$$Δ^{\ddagger}V={V^\ddagger}-V$$
where both $V^\ddagger$ and $V$ refer to standard states (I have omitted the symbol for simplicity). One ...
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Calculating pre-exponential factor using transition state theory
I would like to calculate the pre-exponential factor of a surface reaction using transition state theory. I've seen two ways to calculate it but I get different answers for each method (and I don't ...
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Why does transition state loses its ability to vibrate? (Transition State Theory)
In transition state theory, (according to my textbook) it is assumed that the the transition state loses its structure, and the ability to vibrate and rotate. If the transition state cannot vibrate, ...
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Kinetic vs thermodynamic control of HBr to 1,3-Butadiene
The author claims that the transition state leading to the formation of the 1,2 product from the allylic carbocation is lower in energy since the carbon (which is attached to Br in the 1,2 product) is ...
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Where does the RT term come from in the derivation for the activation enthalpy from the Eyring equation?
It is easy to show an Arrhenius-like equation from the Eyring equation, but if you do this, you get that the activation energy is about equal to the activation enthalpy. However, the real ...
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Is Gibbs Free Energy of formation equal to Gibbs Free Energy of transition state?
Is activation energy equivalent to Gibbs Free Energy of transition state as related by Eyring equation?
$$E_a=\Delta ^\ddagger G \, \, ?$$
Is Gibbs Free Energy of transition state defined by the ...
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In Statistical Transition State Theory, why is the concentration of the transition state for the forward and reverse reaction identical?
For example on Wikipedia, and also in my lecture notes, it is assumed that for a reaction
$$\ce{A + B<=> AB^{\ddagger} <=> P}$$
at equilibrium,
$$[\ce{AB^{\ddagger}_f}] = [\ce{AB^{\...
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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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