Tutorial 16 | How to Calculate Binding and Interaction Energies with Gaussian | Dr M A Hashmi

In this video, I describe the calculation of binding energy for the attachment of oxygen to myoglobin.
www.rcsb.org/3...
Also the difference between Interaction energy and Binding energy is described.
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Email: muhammad.hashmi [at sign] ue.edu.pk

[@AuthenticEducationChannel]

what is relationship between binding energy and physisorption as well as chemisorption.what is normal range of binding energy for chemisorption and physisorption.kindly clear this with reference

[@Learning432]

It's really helpful dear sir , thanks

[@WisdomCenter]

Most welcome

[@foundationsofchemistryscc-2640]

This is a great video and very helpful in clarifying the difference between interaction and binding energies. I do have a couple of questions about your energies though. Why are they positive for the myoglobin and oxymyoglobin? In my experience the total energy calculated in Gaussian is always negative. Does it depend on the method used? Or is it because these are electronic energies only? Did you subtract out the nuclear contribution manually or take something other than the total energy in the results summary? Thanks again for the great video!

[@WisdomCenter]

Thank you for your comment. I didn't actually notice this about positive values of electronic energy. I believe using a sophisticated method would give you negative energies. It should be the method in this case

[@anandhu_g_nair]

Sir can you please kindly tell me a reference for this binding energy. Thanks for your time and consideration

[@easyphysicsinmalayalamandt1230]

Thank you so much sir

[@WisdomCenter]

Most welcome

[@muralidharpandey6074]

How we can calculate the binding and interaction energy in between perticular amino acid of protein and DNA residue?

[@muralidharpandey6074]

How we can calculate the binding and interaction energy in between perticular amino acid of protein and DNA residue

[@hanamutiara4742]

Thank you, it's really helpful, can i ask why you set the multiplicity into 2 in the complex optimization?

[@WisdomCenter]

Welcome. I did not set the multiplicity to 2 myself. It was automatically done by the software as there would be one unpaired electron in this molecular system.

[@nawalguebbai4015]

Hello pr how about adsorption energy and especially with BSSE energy thanks

[@user-rp8pc9pl2v]

Hi sir, I have a question regarding to interaction energy. If you don't optimize the Mon 1 and Mon 2, how did you have the energy? It is very depending on how to draw the structures of each Mon. I am so confused. Can you please clearly explain? Thank you so much.

[@WisdomCenter]

You don't need an optimization for energy. You can calculate single point energy and it will give you the energy without optimizing.

[@user-rp8pc9pl2v]

@@WisdomCenter I am confused. If you don't optimize, how can you get Emom1 and Emom2 (not Eoptmom1 or Eopt mom2). Did you just draw the molecule and do energy calculation? If so, the energy is depending on how you drew the molecules. If possible, can you please do a video how to calculate the INTERACTION energy? I tried to find but I could not get it anywhere. Thank you.

[@WisdomCenter]

@@user-rp8pc9pl2v chemistry.stackexchange.com/questions/24326/what-tools-can-be-used-to-estimate-binding-energies See this link. It has a very good explanation

[@user-rp8pc9pl2v]

@@WisdomCenter Thank you for sharing the link. I read the link and I understand. However, my question is "How did you have the value of Emon1 and Emon2". If you only draw the molecule and calculate the energy to obtain the energy, I think 10 people will have 10 different values of energy because they have different ways to draw the molecule. Can you please explain how you did that? I appreciate if you can. Thank you.

[@wishabc6465]

How to calculate the chemical potential of atom?

[@TALKyLIKEENGLISH]

Thank you, prof. My question is when we compare 2 different complexes' interaction energies, less Eint better binds or more Eint better binds?

[@WisdomCenter]

More value with negative sign

[@TALKyLIKEENGLISH]

@@WisdomCenter thanks 😊

[@hemillyoliveira7426]

MUITO OBRIGADA!

[@WisdomCenter]

Você é bem vindo

[@jabirhussain1713]

Thanku soo much sir.please i am.confused in case of alkaline earthide what we consider for Eopt.dimerr in case of interaction energy and binding energy sir

[@WisdomCenter]

The question is not clear

[@jabirhussain1713]

Sir how can we calculate interaction energy in case of alkaline earthide

[@faiqasfoodandvlogs9908]

Assalam-o-Alaikum Sir can you make a video on that how to find charge transport hole values using Gaussian software?

[@WisdomCenter]

W.salam I am sorry I do not know about this topic.

[@umeshchandramakwana806]

Excellent!

[@WisdomCenter]

Many thanks!

[@maryamdaneen7190]

If the monomers are identical then we have to optimise them only once??

[@WisdomCenter]

Yes

[@ahmedlakhani7839]

Thank you!!

[@WisdomCenter]

You're welcome!

[@mazharuddinquazi2959]

Sir, I am using Quantum espresso to determine binding energy and interaction energy but I am facing a problem that I don't know whether I should take the same dimension of the unit cell for all species or be different with vacuum. Can you please guide me? I am new to this field.

[@WisdomCenter]

I am sorry I never used any solid state software (like Quantum Espresso)

[@mazharuddinquazi2959]

@@WisdomCenter Its okay sir. thank you for your reply. Your channel contents are really helpful.

[@kapofimweuhala8984]

The video is very informative Sir, Thank you., I have a question regarding interaction and binding energy of doped clusters by transition metals, provide me your email Sir

[@WisdomCenter]

My email address is given in my recent videos description.

[@kapofimweuhala8984]

@@WisdomCenter I will appreciate if you share it Prof.

[@mustafakhan6701]

Hello sir Sir can you please tell me that how to find interaction energy ? According to formula E= Eopt dimer --(E mon1 + E mono2), if I'm optimized the dimer and put it's energy it's ok but from where we can put the energy or value of E mono1 E mono2??

[@WisdomCenter]

You can take the energy of the monomers the same way as you do for the dimer.

[@mustafakhan6701]

@@WisdomCenter sir you mean that in the same way we can calculate and optimize the energy of monomer 1 and Monomor 2?

[@yoboyj7678]

Thank for the video can tell me how to run dft calculation ?

[@WisdomCenter]

It has already been told. Please go through the playlist and you 'll find it. kzbin.info/www/bejne/p3S0fH-rgMaXrpY

[@PoojaKumari20]

please give lectures on coupling reaction optimisation

[@WisdomCenter]

Will try

[@misslojyn2829]

How can I calculate the interaction energies of 1 complexes in oniom method

[@WisdomCenter]

I don't yet have experience with ONIOM method

[@romanrains8091]

Hello Sir, I have been using Gauusian 09 on a Windows 10 laptop, having Ryzen 4600h processor with 8gb Ram, I am working with Atrazine molecule and trying to compute it's interaction energy with a set of monomers .the computing time for a system of 55 atoms and 228 electrons is coming out to be 7+ hours. Any suggestions how I can optimize the Gaussian software so as to better utilise my PC. I am using DFT with WB97XD levels and DEF2TZVP basic set

[@WisdomCenter]

You better email me a file and I can reply you with the tweaked file and guidline. It is hard to write all in a comment.

[@pavangutti7808]

Sir , can u please make video on interaction energies ( Eint)

[@WisdomCenter]

I have already explained this in this video

[@guttipavan9306]

@@WisdomCenter Yes sir, but sir i could not understand, how can i different Eopt_mon and E mon

[@enseignante6444]

how I can calculate Interaction energy on ONIOM method please

[@WisdomCenter]

I don't yet have experience with ONIOM method

[@05_FuNnY_cArToOn]

Please make a video in drawing myoglobin molecule

[@WisdomCenter]

You do not need to draw it as you can easily download its structure from pdb database.

[@05_FuNnY_cArToOn]

@@WisdomCenter and sir for porphyrin structure it can be download from pdb database too ?

[@WisdomCenter]

@@05_FuNnY_cArToOn Porphyrin structure isn't that complex so drawing it shouldn't be a problem too

[@05_FuNnY_cArToOn]

@@WisdomCenter yeah sir it's not too complicated to draw by self so I have draw it by my self Thanks for the reply😊

[@PoojaKumari20]

Sir can you please teach how to create energy profile diagram.

[@WisdomCenter]

I don't understand what do you want to ask? Energy profile of what?

[@PoojaKumari20]

I wanted to learn how to create energy profile diagram for transition states in guassian

[@PoojaKumari20]

Basically want to learn optimising transition states

[@WisdomCenter]

@@PoojaKumari20 There are tools for it but I do it manually using ChemDraw. I 'll try to make a video about it

[@WisdomCenter]

@@PoojaKumari20 I already have videos about TS See them at: kzbin.info/www/bejne/i5SumKCMoJKoZtU and kzbin.info/www/bejne/d3iUdaaQaZJ3esU

[@sharesomecryocoininfor4718]

no entropy

[@anisaju-jx1yr]

Thanks for your great video. Sir will you send your mail id

[@WisdomCenter]

Check description. Its given in all the new videos