normal Platinum bead

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3 months 17 hours ago #7694 by Rajat Desikan
Rajat Desikan created the topic: Platinum bead
Dear Martini experts,

I am looking at parameterizing organometallic molecules with platinum in it. Typically, the Pt atom forms 4 coordinate bonds with oxygen or nitrogen atoms around it. Can I get suggestions on how I can proceed with parameterization? Thank you for your time.

Warm regards,
Rajat

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3 months 16 hours ago #7695 by riccardo
riccardo replied the topic: Platinum bead
What do you need the model for? If it is for modeling a cofactor in a protein, you may find some inspiration in this publication:

D.H. de Jong, N. Liguori, T. van den Berg, C. Arnarez, X. Periole, S.J. Marrink. Atomistic and coarse grain topologies for the cofactors associated with the photosystem II core complex. JPCB, 119:7791–7803, 2015

Otherwise, note that metal-organic interactions are not in the realm of things which the Martini model is used for -- please see also this thread:

cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np

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3 months 16 hours ago #7696 by Rajat Desikan
Rajat Desikan replied the topic: Platinum bead
Hi Riccardo,
Thank you for the quick reply. I plan to look at drug encapsulation within liposome nanoparticles. There are no proteins in my system at present.

I took a look at the paper above and saw that ions were modelled as charged particles (Q). I wonder if the same approach may work here as well. Your thoughts?

Regards,
Rajat

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2 months 4 weeks ago #7698 by riccardo
riccardo replied the topic: Platinum bead
Let me rephrase my question. Where does the Pt come into play?

My point, which I also try to make in this older post ( cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np ) is that if the metal that you want to describe is buried (for example, a gold nanoparticle which is functionalized with organic molecules, or a metal which is part of a heme group which is constrained on a pocket of a protein), the metal-organic interactions won't be critical. The interactions will be taking place between, say, the organic molecules on the surface of the metal nanoparticle and the environment. The metal-organic interactions are frozen to a certain configuration and, indeed, you may think to describe a metal center with a charge assuming that a metal in that particular environment is charged.

However, if your metal is "naked", and you want to be able to describe metal-organic interactions (you were talking about coordination shells of Pt) in a dynamic way, I do not think that Martini is the tool for that.

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2 months 4 weeks ago - 2 months 4 weeks ago #7699 by Rajat Desikan
Rajat Desikan replied the topic: Platinum bead
Thank you for such a clear reply, Riccardo. I shall use a martinized version of my molecule for self-assembly and membrane insertion simulations where the hydrophobic organic moieties are important and not the metal.

I had another question. The atomic weight of Pt2+ is 195 and its vdw radius is 0.175 nm, which is very different from that of a Q particle. Any thoughts on how to proceed? I don't think that I can randomly change the attributes of a Q bead and expect Martini to behave normally.

Regards,
Rajat
Last Edit: 2 months 4 weeks ago by Rajat Desikan.

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2 months 3 weeks ago #7701 by riccardo
riccardo replied the topic: Platinum bead
Definitely randomly changing the parameter of a Q bead won't lead you to a Pt bead, I agree :-) So, I don't have direct experience with that. I think you better first check the references you find at www.cgmartini.nl/index.php/62-about/gallery/277-nano like [Langmuir, 27:8323–8332, 2011], etc.. to see how people dealt with (gold) nanoparticles and the parametrization of the Au beads. Sorry but I can't be of more help for now.

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