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I have a substance, a Cu-bisphenanthroline complex, and I want to examine its adsorption on different materials. I am considering carbon and silica, and possibly something else like liposomes to discuss various options and choose the most suitable one.

The problem is that I have never worked with these materials before. My substance is spherical and quite large, as one might assume. Therefore, I doubt that a carbon layer would be a good choice and perhaps nanotubes would be better. The same goes for silica— instead of sticking with a single layer, I consider using pore of a mesoporous silica instead, given that tube-like shape might better accommodate the ligand.

Additionally, I am unsure which software to use for this analysis. I have been using Gaussian, but I’m wondering if it is the best choice for this type of study. Can anyone recommend more suitable software for this purpose or give general advices on the topic?

Thanks

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  • $\begingroup$ If you're still in the planning phase it might be difficult but some more detail would definitely be useful. Is it the 'binding' energy and/or orientation you're interested in? Something else? If this is to guide a synthetic effort do you know what surfaces you actually have available? I wouldn't recommend looking at nanotubes if you don't have access to any nanotubes in the lab for example. If the 'surfaces' are large you'll probably be looking for a mixed QM/MM type method I think... $\endgroup$
    – leeman
    Commented Aug 15 at 11:43
  • $\begingroup$ @leeman, My goal is to seek for the most plausible material I could use to deliver drug to the cell. I know this won’t be anchieved just with compchem but need to steer research into something before synthesising all the possibilities and then discarding 95% of them. There’s no problem with available surfaces so I am free to go with computations. That’s why I also asked what else should I consider and whether sheets are actually reasonable given spherical character of the substance that adsorbs (this naturally better fits to materials I mentioned, but maybe something else too?) cheers ! $\endgroup$
    – farmaceut
    Commented Aug 15 at 15:36

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I recommend you to use xTB software (site/docs, downloads).

It uses Semiempirical Tight Binding method, well tested against different system types with very good results.

The image below is the workflow I am using to study adsorption of small molecules on a surface. All the main calculations are done with xTB: single system/molecule optimization, complex formation (how your Cu-bisphenanthroline complex will be added to the carbon layer/nanotube), complex optimization, molecular dynamics, thermal stability, thermodynamic properties, infrared spectra, electron transfer, etc.

Using the wave function from xTB, you can use MultiWFN to study topology properties of your system (determining the bond critical points, LOL/ELF index, etc.) to characterize the type of interactions, etc.

enter image description here

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  • $\begingroup$ hi, @Camps ! Looks great; I know both software packages and while MultiWFN was obvious choice I wouldn’t consider XTB as the only software for my work; seemingly, I am not aware of it capabilities if only using it for confirmers generation. Do you mind sparing with me how you choose size of your surfaces and how you actually construct them? This is quite of my predominant interest now. Thanks ! $\endgroup$
    – farmaceut
    Commented Aug 15 at 15:32
  • $\begingroup$ Until know, I just worked with heavy metal/green house gases interacting with carbon/boron nitride nanotubes and with carbon/boron nitride nanobelts. Take a look at these papers: link1, link2 and link3. $\endgroup$
    – Camps ♦
    Commented Aug 16 at 2:14
  • $\begingroup$ + Anyway, I recommend that for choosing the surface size, you measure the size of your molecule (in the “bigger” direction) and add 20Angs (thinking that your molecule is at the center, you will have 10Angs for each side (when using periodic boundary conditions, this 10Angs will ensure that there aren't image-image interactions). $\endgroup$
    – Camps ♦
    Commented Aug 16 at 2:14

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