IRC calculation path is reversed ?

More Shiv Pal's questions See All

Instead of Me4Sn , Could other compound be used as reference for 119Sn NMR

Hi everyone ! Is it possible to use other Sn compound like SnI2, SnCl2 or SnCl4 as reference compound for 119Sn NMR, since I dont have tetramethyltin right now and I need NMR spectrum urgently.

06 July 2017 7,987 5 View

Why , there is two Lp* on Ge atom while it have only one empty p orbital ?

I did a NBO calculation on molecule having Ge and N atom . I want to study donation of lone pair of N to empty orbital of Ge. Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis...

01 February 2016 3,708 0 View

Could anyone tell me correct syntax to use %CHOOSE keylist in NBO 3.1 ?

01 February 2016 3,238 2 View

NBO Summary is under two Molecular Unit. Why ?

11 December 2015 4,960 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How do I increase the yield of my PCR product?

Hello, We would like to increase the yield of our PCR product. We are running a series of PCR reactions that is targeting ~1.1kb sequence. We begin each reaction with ~400pg of template DNA...

02 March 2021 4,029 3 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Can thermal cycler machines be problematic during PCR?

Hi, my question is about the heating of thermal cycler machines and I hope some of you had experienced a similar thing previously. There are two thermal cycler machines in the lab(BioRad) and for...

26 February 2021 4,777 4 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Could not amplify CD28 and CD3z ectodomain from cDNA of Jurkat Cells ?

For my experiments, I have to express ectodomains of human CD28 and CD3z. As a source, I extracted RNA from Jurkat cells and verified the quality of RNA on the gel. I, then, prepared cDNA using...

23 February 2021 7,051 4 View

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View

A. Nijamudheen

Hi Shiv,

I think, it is fine, since the IRC connects TS with both the reactant and the products. The forward/reverse keyword can lead to the reactant/product side depending on the the direction of the imaginary mode of the TS.

regards,

Nijam

Shiv Pal

Dear Ahmad Alrawashdeh

Multiplicity of molecule is 1

Dear A. Nijamudheen

The IRC calculation connect the TS both side but forward calculations must leads to product. If this is the problem because of direction of imaginary mode, Is there any solution to change it ? or should i try to search other TS, however I have tried several time to search other TS.

Thank You for your suggestion.

Shubhajit Das

I agree with Nijam. Basically, when you run an IRC calculation in forward and reverse directions, you find out the respective minima. The forward calculation often follows the path towards the more deeper minimum i.e towards exothermic direction. This might be reversed in your perception since your description of the reactants and products are based on chemical intution which has nothing to do with the IRC calculatiom. As long as the two minima (obtained after IRC calculation) correspond to your reactant/product, it is fine and you have found the right transition state. Now, you should look at the energies of the minima and decide the exo/endothermic nature of your reaction.

Dear Shubhajit Das

Thank you for your suggestion ..

It might be possible that reaction may endothermic. I will check the energies for both the minima after running the job up to sufficient point. Could I personally email you regarding this calculation by sharing the output file ?

Thank You again