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19

The reaction coordinate is the progress of a reaction from reactants to products with various intermediates and transition states in between. It is an abstraction. It has no relation to time. Rather it is the progress of bond-forming and bond-breaking reaction steps. The free energy change of partially formed and partially broken bonds cannot be measured. ...


13

The order of a reaction is an experimentally determined quantity and can be positive, negative or fractional. The order need not be related to the stoichiometric coefficients, although sometimes it is. In some reactions it is not possible to define an order. There seems to be no reason therefore why the order cannot be greater than three; the iodate-iodine ...


6

Various criteria may be applied in order to ascertain the connectivity of structures. A common solution is a path generated by requiring it to be a Newton path on the potential energy surface (E): $$ (\nabla\nabla^\ast E(x))^{-1}\nabla E(x) = -\frac{dx}{dt} $$ Two points $x_0$ and $x_1$ are connected only if $\exists x:\mathbb{R}\to\Omega,\tau_0, \tau_1\in \...


5

IRC is a gradient following algorithm that tries to follow the imaginary mode. Check the algorithm (several one implemented, so really depends on which you are talking about) and you will see that unlike in optimisation algorithms, there is a big emphasis on following the real gradient (and not just jump to the endpoint as fast as possible). It works well ...


5

Be sure you have really obtained TS, that means stationary point, i.e. all gradients are zero. Than, you should have one imaginary frequency corresponding to the motion along the reaction coordinate. If this is true and you still get both IRCs going to same minimum, your assumptions regarding the shape of Potential Energy Surface (PES) could be wrong. It is ...


5

Equation (1) is an empirical one that does not consider entropy. If you substitute it for the Eyring equation (considering free energy of activation $\Delta G^\ddagger$) you end up with equation (6) as expected, not equation (5). Wikipedia has a nice section on the relationship of activation energy and Gibbs energy of activation: Although the equations ...


4

Single molecule reaction Some diagrams refer to a single molecule reacting. If that is the case, several quantities are not defined or ill-defined: pressure entropy of mixing temperature In those diagrams, the best label would be potential energy, and the energy difference between reactant and transition state should be labeled activation energy. ...


4

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 reaction path (IRP), which is the reaction path along the direction of the gradient. Only for some simple reactions one can visually (and approximately) identify ...


4

I think what you are fundamentally saying is you are trying to relate classical thermodynamics to the molecular properties. It is best to have some firm familiarity with classical thermodynamics before attempting this. Classical thermodynamics does not require a molecular interpretation at all! (It helps a lot but is by no means necessary)!. I personally ...


3

(1) There are several web sites giving details of this reaction and so this need not be copied out here. (2,3) Rather than describe a complex reaction scheme it is easier to understand a generic autocatalytic reaction. The general autocatalytic reaction of species A with catalyst B has the form $\ce{A + B $\to$ P + 2B}$ and the rate equation is deceptively ...


3

I think the description you lay out in your question has it basically right. MEPs, IRCs, etc. all assume that the geometric rearrangements that occur over the course of a reaction strictly follow the gradient uphill from reactants to transition state, and then downhill from TS to products (or intermediates). Energetically, this provides the "path of least ...


3

The IRC algorithm usually follows the gradient from TS to product state B and by definition has to go always downhill in energy. In best case, it treats the Potential Energy Surface (PES) around the given point as quadratic and just integrates Newtonian equation of motion and does it until it reaches local minimum. This procedure is different from geometry ...


2

The "packet" of energy exchanged fall into one of three forms: heat, work, or electromagnetic radiation. The first two are kinetic energy phenomena. Expanding on Aesin's answer about potential and kinetic energy. Reactions that are exothermic convert potential energy into kinetic energy. The potential energy is the energy stored in the chemical bonds (...


2

Essentially yes - if you consider the two particles colliding into a potential well, the kinetic energy associated with each will (depending on the angular specifics) be apportioned into rotational, vibrational, and even occasionally electronic excitations. So, the two particles collide, and are then vibrating and/or rotating about each other with all the ...


2

It could also be the case (impossible to tell, as you haven't told us what molecules you are using) that the two minima are equivalent by symmetry.


2

The answer is (b). The initial step of the reaction should take energy. Otherwise the reactant molecule itself is unstable. The very initial portion of the curve in (c) is downward-sloped, which doesn't make sense. If the reacting alkene could relax to a different conformation without any activation barrier, then it would do so. But the fact that the ...


2

Following is an example of Reaction Coordinate Diagram. I labelled all necessary details for your convenient. Please note that the Blue path is for the same reaction when catalyst is involved. The difference is the activation energy, which is lower in the presence of a catalyst.


2

When two species $A$ and $B$ react, $A + B \to product$, the rate of reaction is $k\mathrm{[A][B]}$ where $k$ is the rate constant and $\mathrm{[A]}$ and $k\mathrm{[B]}$ the concentrations at any time during the reaction, which clearly change with time. To work out what happens in each small time interval means calculating the change in the number of ...


1

I just figured out that there is a way to do this. Though its not that clean I think. I can define the initial structure where x3 = (x1+x2)/2 and then freeze the following expression using gic. x3 - (x1+x2)/2


1

Firstly, since $\overline{\mu_\alpha} = \overline{g_\alpha}$, the two approaches that you propose are basically the same: $\overline{\mu_\ce{CO2}}-\overline{\mu_\ce{CO}} -\frac{1}{2}\overline{\mu_\ce{O2}}$ is the same as the change in $G$ per mol of forward reactions. Let's suppose that we can calculate the true, absolute value of the molar Gibbs energy at ...


1

The Law of Mass action states: The rate of a reaction is directly proportional to the concentration of reactants raised to powers equal to their stoichometric coefficients This is only valid for elementary reactions since they happen in a single step. As a result, such simple relations hold good. But what about the more complicated ones. Certain ...


1

When I generate an IRC from a TS - using GAMESS (US) software - I calculate the IRC for the forward direction and the IRC for the backwards direction using MacMolPlt. Is it possible you've stitched together two forward (or two backward) direction IRCs by accident? Also, I once tried to calculate and IRC from a TS but both the forward and backward IRCs went ...


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