Help: Suggestion for gaussian calculation setup involving nanoparticles and DNA

rpestana94

Greetings, I want to use gaussian to see the interaction between DNA and nanoparticles(NPs) of gold and silver, for these, I was thinking on calculate the binding energy between the DNA and the NPs and also make a cytosine(C)-guanine(G) and put one NPs in different places and measure the binding energy between C-G. For this, the cluster of gold and silver were made by putting some atoms and do an optimization using Lanl2dz, the C-G was optimized using B3LYP.

I'm not pretty sure how to calculate the energy between the C-G and the NPs, maybe using Gen keyword or even if this kind of approximation makes sense, so I open to suggestions, changes in calculation, improvement, advice, etc.

Thanks in advance.

sobereva

You can refer to the binding energy calculation for benzene - Ag surface described in this post: http://bbs.keinsci.com/thread-16532-1-1.html
The difference is that you may want to use a spherical metal cluster instead of a finite slab model.

The binding energy can be calculated as E(GC-NP) - E(GC) - E(NP). For optimization purpose, Lanl2DZ for Au/Ag and 6-31G* for C-G is acceptable, however for evaluating binding energy, better basis set should be used, for example, SDD for Au/Ag and 6-311+G** for C-G, and its is best to consider Counterpoise correction. The recommended DFT functional for this case is PBE0-D3(BJ). B3LYP without dispersion correction should never be used for evaluating the binding energy because it is well known that B3LYP completely fails to represent dispersion effect.

wzkchem5

Please note that LANL2DZ is a basis set while B3LYP is a functional. Every calculation requires both a functional and a basis set, so sentences like "do an optimization using Lanl2dz, the C-G was optimized using B3LYP" don't really make sense. Functionals are global, so one cannot specify different functionals for different atoms, but it is possible to assign different basis sets to different atoms.

rpestana94

sobereva 发表于 2020-11-12 17:52
You can refer to the binding energy calculation for benzene - Ag surface described in this post: htt ...

Thanks, I will try it and let you know, any suggestion to create the spherical metal cluster?

rpestana94

wzkchem5 发表于 2020-11-12 21:50
Please note that LANL2DZ is a basis set while B3LYP is a functional. Every calculation requires both ...

Thanks, you're right, I apologize I check and we use pbepbe/def2sv for both, the C-G and the metal cluster.

wzkchem5

rpestana94 发表于 2020-11-21 00:46
Thanks, you're right, I apologize I check and we use pbepbe/def2sv for both, the C-G and the metal ...

def2sv is too small a basis set to be of publication quality, because it doesn't have any polarization functions. If you want to stick to the def2 series, you should use at least def2svpp.

sobereva

rpestana94 发表于 2020-11-21 00:40
Thanks, I will try it and let you know, any suggestion to create the spherical metal cluster?

You can use VMD program to dig out a spherical cluster from supercell of metal

rpestana94

sobereva 发表于 2020-11-12 17:52
You can refer to the binding energy calculation for benzene - Ag surface described in this post: htt ...

Prof Sob, for this question about the nanoparticle, following the tutorial you suggest and what you comment here, should I use this approximation?
! PBE0 D3 def2-TZVP(BJ) def2-SV(P) RIJCOSX opt noautostart miniprint nopop

Using the same functional for optimization and for single point calculation? That is publication quality? In my case is a nanoparticle I think I don't need to freeze atoms as you do in the tutorial but not totally sure.

sobereva

rpestana94 发表于 2021-3-30 06:02
Prof Sob, for this question about the nanoparticle, following the tutorial you suggest and what yo ...

Your keywords are incorrect.

If your nanoparticle is very large, due to consideration of computational cost, I suggest using pure DFT functional, it is significantly cheaper than hybrid-functional in ORCA when RI approximation is employed.

I suggest using the following keywords for optimization:
! PBE D3 def2-SVP def2/J noautostart miniprint nopop opt

For single point calculation:
! PBE D3 def2-TZVP def2/J noautostart miniprint nopop

Probably there are better choices, but I cannot give you more suggestion without detailed information of your nanoparticle (number of atoms, element...) and your computational resource.

wzkchem5

rpestana94 发表于 2021-3-30 06:02
Prof Sob, for this question about the nanoparticle, following the tutorial you suggest and what yo ...

BJ is a modifier of D3, not a modifier of the basis set. Writing BJ directly after the basis set is a syntax error. On the other hand, however, ORCA automatically uses D3BJ when you write D3, so that's why Sob omitted the BJ altogether.

rpestana94

sobereva 发表于 2021-3-29 23:52
Your keywords are incorrect.

If your nanoparticle is very large, due to consideration of comput ...

Prof Sob, the nanoparticle is about 43 Au atoms, the two DNA pair each one has around 29 to 32 atoms, so in the system, I will have the nanoparticle and a base pair of DNA, (43+32+32=107), this kind of calculation is suitable for this system, I think is a little big or what you recommend?

rpestana94

wzkchem5 发表于 2021-3-30 04:03
BJ is a modifier of D3, not a modifier of the basis set. Writing BJ directly after the basis set i ...

I see, thanks, I didn't know that, I'm really new in this kind of calc and still is a bit confusing to me

sobereva

rpestana94 发表于 2021-3-30 21:35
Prof Sob, the nanoparticle is about 43 Au atoms, the two DNA pair each one has around 29 to 32 ato ...

My recommendation of keywords works for your system.

rpestana94

sobereva 发表于 2021-3-30 08:42
My recommendation of keywords works for your system.

thanks

rpestana94

sobereva 发表于 2021-3-30 08:42
My recommendation of keywords works for your system.

Prof Sob another question, make sense to optimize the nanoparticle by it self and the optimize again with the base pair or just optimize the base pair with the nanoparticle immediately? I get the base pair using gaussian (gauss view) and the nanoparticle was made using charm-gui