I have a bare metal oxide nanoparticle (wire/rod-shaped). I already have experimental characterization data like UV-Vis, TEM, XRD, XPS, FTIR, SEM, and Raman. I want to simulate the nanoparticle to find its binding with some receptor protein whose PDB file is also available. Finally, I want to perform docking of the nanoparticle with the proteins.
First you can have Suspension of iron nanoparticle until to molecular docking.
dear Das,
try this site: https://zhanglab.dcmb.med.umich.edu/IonCom/ or http://bioinfo.cmu.edu.tw/MIB/
The attached site is useful to this subject>
https://zhanglab.dcmb.med.umich.edu/IonCom/ or http://bioinfo.cmu.edu.tw/MIB/
Salafranca, Juan, Jaume Gazquez, Nicolás Pérez, Amílcar Labarta, Sokrates T. Pantelides, Stephen J. Pennycook, Xavier Batlle, and Maria Varela. "Surfactant organic molecules restore magnetism in metal-oxide nanoparticle surfaces." Nano letters 12, no. 5 (2012): 2499-2503.
Bodhisatwa Das
To predict (simulate) the interaction of nanoparticles with proteins, the chemical properties of functional groups of the protein and the surface of nanoparticles are used. For example, gold nanoparticles interact well with protein thiol groups. The nanoparticles will attach to the place of the protein where there are thiol groups.
Theoretically:
From XRD patterns as follows:
Variations in the height of the specimen in its holder, whether increasing or decreasing, cause XRD peaks to change from their original location.
Important and useful pathways are connected to the XRD Curve:
Scherrer’s equation:
Particle Size, D = (0.9 x λ)/ (d cosθ)
λ = 1.54060 Å (in the case of CuKa1) so, 0.9 x λ = 1.38654
Θ = 2θ/2 (in the example = 20/2)
d = the full width at half maximum intensity of the peak (in Rad) – you can calculate it using Origin software.
To convert from angle to rad
Rad = (22 x angle) / (7 x 180) = angle x 0.01746
Example: if d = 0.5 angle (θ)
= (22 x 0.5)/ (7x 180) = 0.00873 rad
Then
Delta=1/D^2
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