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I want to use FAS (fluoroalkylsilane) in my molecular dynamics study. How can I find it's real structure? So that I can find proper forcefield for simulating the molecule. It would be very nice if you mention a better method for simulating this molecule. Like making a initial configuration in a software and then optimizing the geometry. I don't know about DFT so much, but can I use that somehow?

FAS17:

Best,

-Kazem

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  • $\begingroup$ fluoroalkilsilanes are a family of compounds. You need specific name. $\endgroup$ – permeakra Aug 8 '14 at 18:39
  • $\begingroup$ I added a picture to question (FAS17), that's what I want to simulate, and the chain containing F atoms will be smaller like FAS9 or FAS7, ... $\endgroup$ – Ghartal Aug 8 '14 at 19:11
  • $\begingroup$ It seems like you are just looking for a very qualitative picture (not knowing about the level of theory you want to apply). Also you need to mention what property you are looking for! 'Simulating' can mean just anything! DFT is a QM method calculated from first principles, which cannot be combined with Molecular dynamics simulations. You can try minimizing the energy using Chem3D, which has a good GUI. You can use UFF (universal force field) that has parameters for almost all atoms available in it. If you could rephrase your question a little clearer, I could help you more. $\endgroup$ – user3786990 Aug 20 '14 at 2:03
  • $\begingroup$ I want to study adsorption of FAS-9 on quartz 001 surface, I have made my quartz surface using CLAYFF and a vacuum slab on it, but I'm stuck with adding FAS-9 to the vacuum slab, and also I don't know what forcefield is proper for FAS-9 and interaction of FAS-9 with quartz surface. $\endgroup$ – Ghartal Aug 21 '14 at 10:36

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