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me_inspired1me_inspired1 

ZIF-8/PDMS membrane

Dear experts,
please have a look into the link

http://iopscience.iop.org/article/10.1088/1361-651X/aa584f/meta
 Actually i want to make membrane using ZIF-8 with PDMS polymer. 

I created a polymer structure using build module with 25 repeating uints and from CCDC website i downloaded the ZIF-8 structure as mentioned in the above paper. the author used different number of zif-8 atoms with PDMS to make a membrane. my question is how can we use specific number of atoms from structure downloaded from CCDC website? 

i tried to make structure P1 then copy the number of atoms i needed but when i do optimization of those atoms it fails . i tried to contact the author but author isn't responding me.

i hope i am able to make you guys understand what i want to know and what problem i am facing.

in brief, i want to make PDMS membrane in which specific percentages of ZIF-8 i want to use.????

looking for proper guide line from the experts 

thank you 

 

me_inspired1me_inspired1
No expert here is willing to help me out? :( 
Jason DeJoannisJason DeJoannis
Can you upload your structure?
me_inspired1me_inspired1

Dear Jason thank you for your reply and also accept my apologize for the late reply.

Well let me explain you again what i am asking.

in the link i mentioned there is paper in which the author has used ZIF-8 with PDMS to make a membrane. author downloaded the structure from the Cambridge Data base. 

in this paper he mentioned that he used different proportions of ZIF-8 with PDMS. (Please see the attach table) 

I also wanted to do the same i.e to use different number of atoms say 92, 180 and 272 for my different compositions of PDMS to make different membranes.

for this i made PDMS polymer with 25 repeating units. then ZIF-8 structure which i also downloaded form CCDC, i made it P1 so that i can use Zif-8 parts (not the entire unit cell) for different membranes as i mentioned above.User-added imageWhen I try to copy some part of ZIF-8 and make another xsd so that i can use it with PDMS to make AC. 

to optimize the selected part of Zif-8 using COMPASS i used the Forcite module-> Geo.optimization-> Energy (COMPASS), Charge-> Force field assigned 

Summation methods to Atom based/ group based but when i hit the run button i get the error.  
User-added imageand if do optimization by unchecking the calculate force field automatically then i get freaking structure like 

User-added image
then i tried another thing i.e after calculating the force field manually i deleted the bonds n then run optimization but after the optimization i could not able to make bonds again ....... :(  

 i am totally stuck brother just at the start even i tried to approach the author but didnt get any kind of a response.

me_inspired1me_inspired1
User-added image
me_inspired1me_inspired1
The above structure is the ZIF-8 downloaded from CCDC
Jason DeJoannisJason DeJoannis
Can you post the ZIF-8 structure? What element is that? It might be causing the problem. Maybe COMPASS does not have coverage of that element.
me_inspired1me_inspired1

Dear Jason

I already uploaded the structure just above your comment.

It consists of Zn, N, C and H.

I also mentioned that in paper (The link I have posted in the Question) the author has also used the COMPASS force field but haven't provide enough info in the paper. 

Please also tell me about the steps i did? to select some part of zif-8 from the unit cell did i follow the right path? and further process which i did is that the right way or not?

Jason DeJoannisJason DeJoannis
Hi me_inspired1,

In the above post, I only see two screenshots of structures, but I do not see any attached structure files (XSD). 

The COMPASS forcefield does not have a forcefield-type for this kind of zinc atom. I attempted to manually assign zn2o (meant for zinc oxides) but naturally it does not have bond parameters. That is why you are seeing those long stretched bonds after optimization.

Your best bet for quick results is to use the Universal forcefield.

Best,
Jason
me_inspired1me_inspired1

dear jason, 

attach is the cif. file of zif-8.

what you did i also did the same and got the same results as you....... yeah also have tried universal force field and it does work in optimization but in creating the AC it fails due to the fragments issues according to software. 

anyways if you suggest me to with the universal forcefield then ill ask you a question" if COMPASS isnt applicable in MOF's specially in ZIF-8 case then how the author and other authors are applying this force field on these things ? " 

Anyways I am really thankful to you for looking into this matter.

VickylsimplVickylsimpl
Try pcff or cvff forcefield
me_inspired1me_inspired1

Dear Vicky

thanks for your reply

I also tried both the force fields i.e pcff and cvff but problem stays.

so I think its not the force field which is causing an issue,  Metal organic framework (MOF) is the main issue and I think all of us are missing some trick to deal with the MOF's.

Almost every author used COMPASS force field so there is some trick  

Jason DeJoannisJason DeJoannis
Here is an excerpt from the paper:
Since the bond and cross-coupling energy do not exist between ZIF-8 and PDMS matrix, the non-bond terms were mainly used to investigate the interaction energy in our study, which include a LJ 6-9 function for the van der Waals interaction and a Coulombic function for the electrostatic interaction.

I'm not sure what that means -- perhaps they ignored the issue and/or used constraints/restraints? You could try contact the authors.

I tried your structure with COMPASS (zn2o) and Universal. The Universal option appears to be far better at keeping the shape of the MOF.
User-added image
me_inspired1me_inspired1

Dear Jason,

Thank you for your kind response.

There is must be some trick involve for the case of MOFs, I also try to contact the Author but the Author isn't responding me i wonder why infect i contacted few other authors as well who used MOFs with the same force field but unfortunately non of them have replied me anyways I appreciate your efforts Sir.

Thank you again