I am working on gaseous adsorption studies of some MOFs and I need to add MD simulation results to strengthen my findings. I know how to go about with the MD simulations but my challenge is how to modify some MOF such as: MOF-5 to IR-MOF-3 (amine functionalized MOF-5) using either VESTA or Material studio suit. Please I need assistance on this.
Thanks
Hi Shedrick,
would you please look at this attached file? I hope you will find a solution from it for the issue you mentioned. it is a very good tutorial manual for Material studio.
kind regards
Yosef
Dear Yosef Nikodimos , I have gone through your pdf upload. Thanks. However, I am still not able to perfectly introduce a functional group without collapsing the crystal, although I converted my structure from "PERIODIC" to "NON PERIODIC" even before I substituted functional groups (-NH2 or -COOH), but trying to form a crystal (periodic structure) again after introducing functional groups seem impossible. Please kindly help me out.
Thanks
Hi Shedrck Akpe
when you say periodic, do you want to create a super structure? for example extending in all dimensions like 2x2x2? If it is so, first add/substitute the functional group you want, the save it in the form of crystal information file (CIF). After that, you can use VESTA to visualize the structure as well as to make a super structure. Did I get your idea? I can help you what I can, don't hesitate to ask me. Thank you
Thanks once again for your response. Now this is what I meant. From the 2 images I uploaded, one is UiO-66 in a box(periodic structure), the other is UiO-66[+4NH2] not in a box (non periodic).
Before adding the NH2 groups to form the second structure, one must convert from periodic to non-periodic (by removing the box which made the structure a crystal). However, after adding the functional groups, I am not able to convert back to crystal (box-like structure called periodic) anymore. Whenever I try to, the crystal collapses. How do I do it? Or is there a better way of adding the functional groups without changing to a non-periodic structure? Hope you understand my plight better?
Shedrck Akpe, would you please follow the following steps,
"Build" > "Crystals" > "Build Crystal":
then under this you will find "enter group" and make it "1 P1" then press "Build"
Hopefully, you will resolve this issue using these steps. Right?
Wow! it worked!! Thanks a million Yosef Nikodimos . You've saved me. I indeed appreciate your guidance. Bless you brother!
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