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What is the best way to attach ligand on the surface of gold nanoparicles?
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5 years 5 months ago - 5 years 5 months ago #7891
by Imamul
What is the best way to attach ligand on the surface of gold nanoparicles? was created by Imamul
Hi All,
I have used packmol script to attach the ligands on nanoparticles surface. The ligand start with sulfer (S) atoms which converted atomistic structure to coarse-grained using 1:1 mapping, likewise gold nanoparticles. Some of the previous literatures treated Au-S as rigid body by considering a harmonic bonds between them. I have used position restrained only to S atoms/beads of the ligands during simulations to fix its position near the surface atoms/beads of Au nanoparticles. I run a small equilibrations about 100ns and noticed everything is fine. Is this a right way to attach ligand? If it is okay than how many ligands should be wise to take for 3nm size (about 887 atoms/beads) nanoparticle?
Regards
Imamul
I have used packmol script to attach the ligands on nanoparticles surface. The ligand start with sulfer (S) atoms which converted atomistic structure to coarse-grained using 1:1 mapping, likewise gold nanoparticles. Some of the previous literatures treated Au-S as rigid body by considering a harmonic bonds between them. I have used position restrained only to S atoms/beads of the ligands during simulations to fix its position near the surface atoms/beads of Au nanoparticles. I run a small equilibrations about 100ns and noticed everything is fine. Is this a right way to attach ligand? If it is okay than how many ligands should be wise to take for 3nm size (about 887 atoms/beads) nanoparticle?
Regards
Imamul
Last edit: 5 years 5 months ago by Imamul.
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5 years 5 months ago #7895
by Pim
Replied by Pim on topic What is the best way to attach ligand on the surface of gold nanoparicles?
I would say position restraints are not the most elegant way, because it doesn't allow any movement of the sulfurs away from their starting coordinates (not even much in terms of equilibration), therefore the nanoparticle also can't move. If your nanoparticle uses position restraints also, I guess it doesn't matter very much.
Considering the Au-S bond is pretty much a covalent bond, I would have also gone for harmonic bonds like the literature. In that way you can at least have diffusion of your whole nanoparticle with ligands, but if that's not an issue both should work.
The number of ligands is not an easy question. Maybe you can find a literature value on the surface coverage of gold nanoparticles. I recently came across work from Rafal Klajn's group where they are pretty sure a 5.5 nm particle has 450 thiolate ligands. Probably they, or others, have also looked at 3 nm ligands.
Considering the Au-S bond is pretty much a covalent bond, I would have also gone for harmonic bonds like the literature. In that way you can at least have diffusion of your whole nanoparticle with ligands, but if that's not an issue both should work.
The number of ligands is not an easy question. Maybe you can find a literature value on the surface coverage of gold nanoparticles. I recently came across work from Rafal Klajn's group where they are pretty sure a 5.5 nm particle has 450 thiolate ligands. Probably they, or others, have also looked at 3 nm ligands.
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5 years 5 months ago #7905
by Imamul
Replied by Imamul on topic What is the best way to attach ligand on the surface of gold nanoparicles?
Thank you Pim for giving me an overall concept. Please let me clearify, I have NP with 3nm in size. I placed 100 dodecanethiol CG ligand on the surface of NP using packmol and then imposed position restraint only S beads during equlibration (100ns) of NP-ligand, water system. After 100ns equlibration, I took only the ligand coated NP and equilibrated further with lipid system for 100ns. This time I didn't apply any position restraint to any beads or molecules. After 100ns equlibration, I visualized the system and observed that the all ligands still coated the NP but not all the S beads are close to NP surface beads.
Now, If I want to create a harmonic bonds between Au-S, should I do it manually? I got the NP structure using openMD and then I converted it to CG. Is there any other way to create harmonic bonds except manual process?
Thanks in advance.
Regards
Imamul
Now, If I want to create a harmonic bonds between Au-S, should I do it manually? I got the NP structure using openMD and then I converted it to CG. Is there any other way to create harmonic bonds except manual process?
Thanks in advance.
Regards
Imamul
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5 years 5 months ago #7906
by Pim
Replied by Pim on topic What is the best way to attach ligand on the surface of gold nanoparicles?
Alright, so I'd argue that "ligands still coated the NP but not all the S beads are close to NP surface beads" is not sufficiently representing the Au-S linkage.
I'm not aware of any easy package that allows you to make the connection between a single S and the closest Au automatically. Maybe you could write a script, but it is probably easier and faster to do it manually once.
I'm not aware of any easy package that allows you to make the connection between a single S and the closest Au automatically. Maybe you could write a script, but it is probably easier and faster to do it manually once.
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5 years 5 months ago #7907
by Imamul
Replied by Imamul on topic What is the best way to attach ligand on the surface of gold nanoparicles?
Again THANKS for your advices. You are absolutely right, if we want to attacted dodecanethiol ligand then there be a harmonic bonds between Au-S.
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