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.
46
questions
0
votes
1
answer
104
views
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 (...
2
votes
0
answers
273
views
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 ...
1
vote
0
answers
46
views
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) ...
3
votes
2
answers
222
views
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. ...
3
votes
0
answers
49
views
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 ...
1
vote
0
answers
159
views
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 ...
4
votes
2
answers
1k
views
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 ...
4
votes
1
answer
556
views
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 ...
3
votes
0
answers
61
views
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 ...
3
votes
1
answer
534
views
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^\...
1
vote
1
answer
206
views
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 ...
1
vote
0
answers
57
views
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 ...
2
votes
1
answer
205
views
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 ...
1
vote
0
answers
56
views
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 ...
2
votes
1
answer
276
views
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 ...
1
vote
0
answers
50
views
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 + ...
3
votes
0
answers
641
views
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 ...
0
votes
0
answers
17
views
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?
2
votes
3
answers
797
views
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, ...
5
votes
0
answers
856
views
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:
...
1
vote
0
answers
56
views
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 ...
1
vote
0
answers
74
views
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 ...
7
votes
4
answers
1k
views
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 ...
0
votes
1
answer
987
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 ...
4
votes
1
answer
1k
views
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 ...
12
votes
1
answer
283
views
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 ...
2
votes
1
answer
2k
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 ...
5
votes
2
answers
338
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 ...
4
votes
2
answers
381
views
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 ...
26
votes
2
answers
1k
views
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 ...
9
votes
1
answer
1k
views
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}\...
1
vote
0
answers
100
views
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 ...
0
votes
1
answer
152
views
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 ...
2
votes
0
answers
105
views
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 $\kappa=\int{Tr[\exp{(-\beta\...
9
votes
1
answer
280
views
Transition state optimisation on the surface of periclase
I want to model a reaction catalysed by periclase ($\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 ...
4
votes
2
answers
342
views
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?
1
vote
1
answer
531
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 ...
7
votes
2
answers
428
views
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 ...
7
votes
1
answer
757
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 ...
2
votes
1
answer
135
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,
$$[\ce{AB^{\ddagger}_f}] = [\ce{AB^{\...
9
votes
3
answers
720
views
Units of rate constant (cycles per second vs radians per second) in Eyring equation
In the Eyring equation (EE),
$$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 ...
4
votes
2
answers
693
views
Aromaticity-Bromonium Ion
Is the bridged ion intermediate aromatic or not?
What is the way to quickly identify aromaticity?
2
votes
1
answer
467
views
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 ...
4
votes
1
answer
139
views
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 ...
14
votes
1
answer
3k
views
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 ...
14
votes
3
answers
6k
views
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 ...