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Transition state - multidimensional surfaces

The picture below shows a simple potential energy surface with a transition state at the maximum point on the reaction path, which is at the 'saddle point'. The reaction path is the solid black line. (...
porphyrin's user avatar
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8 votes
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Finding chair and boat transition states during ring-forming reactions

As you have figured out, this is a non-trivial problem. It's okay to find a boat conformation that might be a bit higher in energy and see if it can map to a TS. Keep in mind that for 6-membered ...
Geoff Hutchison's user avatar
8 votes

How to estimate the temperature needed to overcome an activation energy barrier?

You could convert the rate constant($k$) to half-life($t_{1/2}$) which would give you an idea of the time scale required for the reaction to finish at a certain temperature. The equation to obtain ...
S R Maiti's user avatar
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8 votes

How to estimate the temperature needed to overcome an activation energy barrier?

From the Eyring equation, we can simply calculate the $k$ value for it. \begin{align} k &= \frac{k_\mathrm{b} T}{h}\exp\left(\frac{-\Delta G^\ddagger}{RT}\right)\\ k_\mathrm{b} &= \pu{1.38E-9 ...
M.L's user avatar
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7 votes
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When are transition state's energy barrier "reasonable" at a certain temperature?

Your question is really about what you consider to be a reasonable rate constant and so is somewhat subjective. The fastest a bimolecular reaction can be in solution is given by how fast the reactants ...
porphyrin's user avatar
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7 votes

Ambimodal transition states in some organic reaction pathways

Why do these ambimodal transition states occur? I don't know that there is a general reason for that. Potential energy surfaces are complicated. Very often, there is an abundance of local minima, ...
agaitaarino's user avatar
7 votes
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NMR and dienes to isolate certain isotopes?

There are at least two glaring problems: Look at the energy scales on which NMR operates (for example, take the resonance frequency $\nu$ and calculate the associated energy $h\nu$)... and compare it ...
orthocresol's user avatar
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5 votes
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References for Transition State Theory and Quantum Transtion State Theory

There are many sources that you can check out, in particular the reviews of Truhlar: Current Status of Transition-State Theory by Truhlar et al. This article was used in my undergraduate course of ...
user1420303's user avatar
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5 votes

Why some reaction have no transition state?

There is nothing special in having an activation barrier between reactants and products although, obviously, very many reactions do. But some reactions, such as electron transfer, are observed ...
porphyrin's user avatar
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4 votes
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Kinetic vs thermodynamic control of HBr to 1,3-Butadiene

A transition state does not ‘represent the energies of […] reactants and […] products’. A transition state is a certain arrangement of atoms somewhere between the most stable atom arrangement the ...
Jan's user avatar
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4 votes

Intrinsic Reaction Coordinate - Converting To Reaction Coordinate with Units of Distance

Intrinsic reaction coordinate (IRC) is not some internal coordinate of a molecular system (such as, bond length, bond angle, etc.), rather it is a curvilinear coordinate that describes the intrinsic ...
Wildcat's user avatar
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4 votes
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Transition state optimisation on the surface of periclase

To study surface reactions I recommend the growing string method (GSM) for surfaces. Here is a nice quote from the paper which developed it (Ref. 1) GSM’s efficacy was confirmed by comparison with ...
Cody Aldaz's user avatar
4 votes
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Why does transition state loses its ability to vibrate? (Transition State Theory)

Only some of the statements you quote are true, certainly a transition state cannot be isolated since it lasts for less than a picosecond. In fact there is hardly any direct measurement of transition ...
porphyrin's user avatar
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4 votes

NMR and dienes to isolate certain isotopes?

Look up the difference of the isotopic masses between hydrogen and deuterium (a factor of about 2),* and the two isotopes of uranium (difference here $\approx1.5\%$), e.g. in NIST's table of atomic ...
Buttonwood's user avatar
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3 votes

What is the reasoning behind the assumptions of Transition State Theory?

This is deeper discussed in Rate Constant Units and Eyring Equation, but I am going to post a very short take-home message here. First, the three assumptions you have cited are not complete. They ...
Martin - マーチン's user avatar
3 votes
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Where does the RT term come from in the derivation for the activation enthalpy from the Eyring equation?

Using vibrational partition functions to define the reaction rate constant produces an equation of the form $\displaystyle k=aT^be^{-\Delta U_0^\mathrm{O}/(RT)}$ where $a,b$ are constants independent ...
porphyrin's user avatar
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3 votes

Entropy of Activation and Temperature Dependence

The equation $$\ln\left(\frac{k}{T}\right) = \frac{-\Delta H^{\ddagger}}{RT} + \frac{\Delta S^{\ddagger}}{R} + \ln\left(\frac{k_\mathrm{B}}{h}\right)$$ does not assume that $\Delta S^{\ddagger}$ is ...
Buck Thorn's user avatar
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3 votes
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Explaining boiling using internal energy

You are wrong when you say the potential energy of particles decrease when they move apart. The forces between the particles are attractive not repulsive. Recall the definition of potential energy. ...
Mitchell's user avatar
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3 votes

Transition state - multidimensional surfaces

First, the question may pose itself why $3N-6$ at all? And for that, we should take a step back and ask ourselves: Why $3N$? These are the degrees of freedom of a molecule. If you break a molecule ...
Jan's user avatar
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3 votes

Unix/MobaXterm Project Assistence (Knowing the Error in my Output File)

I copied your input into a new file, added some empty lines at the end and changed the input line to be "#p opt=qst3 hf/6-31..." instead of redundant (and maybe erroneous(?) "opt ... opt=qst3"). I ...
pH13 - Yet another Philipp's user avatar
3 votes
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Unix/MobaXterm Project Assistence (Knowing the Error in my Output File)

I already tested the TS search calculation of this reaction based on your proposed structure coordinates. The calculation has been terminated quickly at link9999.exe sub-routine program in which its ...
High Performance Rangsiman's user avatar
3 votes

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

The statement is essentially correct. Unimolecular reactions refer to the Lindemann scheme and its improvements called RRKM theory. The Lindemann model is $\ce{A + M <=> A^* +M ;\; A^*\...
porphyrin's user avatar
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3 votes
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Why only molecules with three or more atoms undergo unimolecular reaction?

I'm guessing this quote is given in the context of classical transition rate theory. Although the statement may seem very strong at first, it is generally true but has some important caveats. Energy ...
user213305's user avatar
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3 votes

Transition state and free energy

First you are correct, there is no fundamental difference in reactions being described as reversible or irreversible, unlike in thermodynamics. A reaction will be called irreversible (a)if the product ...
porphyrin's user avatar
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2 votes
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Explain the difference between reaction intermediate and reactive intermediate

A reaction intermediate is nothing more than a plain old intermediate, which you probably understand. There is no stipulation as to how stable the intermediate must be. The IUPAC Gold Book defines ...
orthocresol's user avatar
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2 votes

In Statistical Transition State Theory, why is the concentration of the transition state for the forward and reverse reaction identical?

In transition state theory, it is assumed that the forward and the reverse reaction occur via the same transition state. This is implied by assuming a quasi-equilibrium between the reactants and the ...
Martin - マーチン's user avatar
2 votes

When are transition state's energy barrier "reasonable" at a certain temperature?

Using this website, input the activation energy and temperature and it gives half life. A reasonable half-life is up to the user, but more than 1 day is going to be super slow. Usually assume the ...
Cody Aldaz's user avatar
2 votes

When are transition state's energy barrier "reasonable" at a certain temperature?

If you don't have any idea what $k$ value would be appropriate, arguably the best option is to identify a catalyst that is experimentally verified to do the reaction of interest and is assumed to ...
Argon's user avatar
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2 votes
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Is Gibbs Free Energy of formation equal to Gibbs Free Energy of transition state?

The Arrhenius equation $$k=A\exp\left(-\frac{E_a}{RT}\right)$$ places all of the $T$-dependence in the exponential factor. The pre-exponential factor is not assumed to be temperature-dependent. By ...
Buck Thorn's user avatar
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2 votes

Can rate constant depend upon the concentration of reactants (or other species involved in the reaction)?

It seems possible that you mix the terms. There is the reaction rate constant -- in your equation $k_r$, and there is the rate of reaction -- in your equation $r$ and sometimes expressed by $v$. ...
Buttonwood's user avatar
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