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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1answer
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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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3answers
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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 ...
14
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1answer
2k 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 ...
12
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1answer
223 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 ...
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3answers
622 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 ...
9
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1answer
254 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 ...
9
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1answer
800 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}\...
7
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4answers
420 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 ...
7
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2answers
237 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
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1answer
504 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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0answers
549 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: ...
5
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2answers
271 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
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2answers
685 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
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2answers
278 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 ...
4
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1answer
590 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 ...
4
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2answers
530 views

Aromaticity-Bromonium Ion

Is the bridged ion intermediate aromatic or not? What is the way to quickly identify aromaticity?
4
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1answer
123 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 ...
4
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2answers
220 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?
3
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1answer
114 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
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1answer
174 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^\...
3
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0answers
53 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
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0answers
296 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 ...
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3answers
337 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, ...
2
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1answer
1k 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 ...
2
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1answer
66 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 ...
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1answer
99 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 ...
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1answer
70 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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1answer
306 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 ...
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92 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\...
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1answer
465 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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1answer
81 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 ...
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0answers
39 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 ...
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0answers
46 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 ...
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0answers
45 views

Primary kinetic isotope effect

Why does the transition state in both protonated and deuterated molecules have the same energy? My textbook assumes that during transitional state the isotopic bond is half-broken or on its way to ...
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0answers
42 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 ...
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0answers
44 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 + ...
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0answers
44 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 ...
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0answers
48 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 ...
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0answers
86 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
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1answer
116 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 ...
0
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1answer
488 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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0answers
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?
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Endothermic and Exothermic [closed]

I was doing a CHEM112LAB Assignment when I saw this question and I will like answers to help me solving future problems related to it. Distinguish between heat of I combustion heat of fusion.