Dear Anam,

In order to calculate the rate of a reaction (activation energy of the rate limiting step) you should follow the following steps:

1-To search for the global minimum (GM) of the reactant, since the reactant can exist in a local minimum which leads to incorrect results.

To run frequency calculations: all frequencies for GM should be positive

2-To assign the transition state (TS) of the reaction; the TS for the rate-limiting step.

To run frequency calculations for TS; Only one negative frequency is allowed. If there are more than one negative frequency the geometry will be imaginary (not real).

The activation energy of the reaction will be:

Energy (enthalpy + entropy) of TS - Energy (enthalpy + entropy) of reactant.

For first order reaction:

ln k = - activation energy/RT

Where k is the reaction rate; R the gas constant and T the temperature in Kelvin.

Please note that the unit for the calculated enthalpy by G09 is in Hartree and you should convert it to kcal/mol.

In addition, you run optimization for the product in a similar manner to that of the GM.

In the input file you should specify the method to be used along with the basis set: an example B3LYP/6-31G (d,p), the charge and the multiplicity of the structure (compound).

The following link is gaussview and gaussian tutorial for computational chemistry

http://www.d.umn.edu/~psiders/courses/chem5650/gaussviewtutorial/tutorial.html

Hoping this will be helpful,

Rafik

Dear Anam,

In order to calculate the rate of a reaction (activation energy of the rate limiting step) you should follow the following steps:

1-To search for the global minimum (GM) of the reactant, since the reactant can exist in a local minimum which leads to incorrect results.

To run frequency calculations: all frequencies for GM should be positive

2-To assign the transition state (TS) of the reaction; the TS for the rate-limiting step.

To run frequency calculations for TS; Only one negative frequency is allowed. If there are more than one negative frequency the geometry will be imaginary (not real).

The activation energy of the reaction will be:

Energy (enthalpy + entropy) of TS - Energy (enthalpy + entropy) of reactant.

For first order reaction:

ln k = - activation energy/RT

Where k is the reaction rate; R the gas constant and T the temperature in Kelvin.

Please note that the unit for the calculated enthalpy by G09 is in Hartree and you should convert it to kcal/mol.

In addition, you run optimization for the product in a similar manner to that of the GM.

In the input file you should specify the method to be used along with the basis set: an example B3LYP/6-31G (d,p), the charge and the multiplicity of the structure (compound).

The following link is gaussview and gaussian tutorial for computational chemistry

http://www.d.umn.edu/~psiders/courses/chem5650/gaussviewtutorial/tutorial.html

Hoping this will be helpful,

Rafik

Thank you

Dear Anam,

You can calculate rate using Canonical Transition State Theory(CTST). The term involve in this equation can be obtained from frequency calculation results. Nowadays people are trying to report rate using polyrate sofware developed by  D. G. Truhlar. You can know about this from internet because it is free.

The Equation given above relating the rate constant (k) to activation energy (ln k = - activation energy/RT) is not correct.

If you compute the Gibbs free energies of the reactant(s) (Greact) and the product(s) (Gprod), then you can find the change in Gibbs free energy for the reaction simply as DeltaG = Gprod - Greact. Then you can obtain the Equilibrium Constant (Keq) for the reaction from

lnKeq = -DeltaG/RT

If you compute the Gibbs free energy of the transition state (Gts), then you can obtain the activation free energy simply as DeltaGdagger = Gts-Greact. To find the reaction rate constant (k), you can use the Eyring Equation

k = (kBoltz*T/h)exp(-Deltadagger/RT)

or in logarithmic form

lnk = ln(kBoltz*T/h) -DeltaGdagger/RT

kBoltz = Boltzmann's constant     T = absolute temp      h = Planck's constant

[Take a look at a decent P Chem book for more info on the validity of the Eyring Equation).]

Of course, the rate constants will be as inaccurate as the DeltaGdagger values they are derived from.  Comparing a series of related reactions is advisable, rather than expecting a single set of calculations to produce an accurate rate constant.

The Gibbs free energies necessary are all in the G09 output after the freq calculation.

Dear Prof Karsten Krogh-Jespersen , 

Thank you for your reply.  I am trying to perform transition state calculations. I followed a video available on youtube. I am also following the same procedure but I am getting error (Termination error).

The procedure is:

For a particular reaction A+B=> C + D

I am first optimizing individual geometries of reactants and products.

Then I am adding optimized geometries of A and B in the same window and performing TS calculations. (Here I am getting termination error).

Is it possible for you to figure out the reason? Or I am doing some mistake?

Please help me to solve this problem.

Regards

You have to break the overall reaction down to elementary steps. A+B => C+D is most likely a multi-step reaction. Split it up into elementary steps and focus on what you assume will be the rate-determining step. The TS concept only applies to elementary steps.

You are not providing any real infor regarding what you are doing, so it is near impossible for an outsider to analyze what is going wrong. What does your keyword line look like? Input file? There is most likely a semi-descriptive message associated with the termination error....What is it? (I grant you that G09 'explanatory messages' may not be easy to decode).

You would benefit from running an already published (simple) reaction on your computer first to convince yourself that you know what to do and that you can reproduce the published thermodynamics and kinetics (same method, basis set etc. as used in the publication). Practice makes perfect....

And then go back to your A+B reaction.

Dear Prof,

Thank you.  My system is rather simple. The equation is as follows:

Fe+2 + H2O2 => HO(rad) + HO-(ion) + Fe+3

I am obtaining the following error message:

C:\G09W\l502.exe

I need help.  I would like to send you detailed output file. However, it would possible for me to send you tomorrow from my workstation. 

I would really appreciate this favor

Thank you

ok----use [email protected]

Dear Prof,

Thank you so much. Thank you for the favor.

Regards

Anam

Hi

Can you please find the attached image that shows the equation I used during the calculation of reaction rate of conversion of butene

Have a very good day and best of luck

Hi when using Eyring equation, for enthalpy and entropy should I use sign like for exothermic enthaplpy change is negative

?