Framework Semi-Flexibility: pX in NU-2000

Introduction

• NU-2000 is a MOF with 3D-linkers that is highly-selective to para-xylene.
• Here we show an example of using semi-flexible framework representation, or namely linker rotation move for the adsorption of para-xylene and to explore how para-xylene pack within the channels of NU-2000 when the linkers can rotate.
• The linkers can rotate around its axis, the rotation is free, meaning that it can rotate to any random angle.
• The linkers can be processed in a linker definition file

simulation.input

Framework definition

• NumberofFrameworkComponents <size_t>
  • This keyword will dictate the number of framework components
  • by default, this number is 1
  • if more than 1, a component will be scrapped from the framework
  • The framework CIF file does not have to be a super cell, but has to be P1 symmetry
• Framework_Component_ <size_t>
  • Provide the definition for the scrapped framework component here
  • You can provide probabilities of MC moves for molecules in this component
  • The definition of the components needs to be provided elsewhere, explained here
  • NOTE: to distinguish this part from the adsorbate component, we add a "_" to the keyword
• In our example, this part looks like below :

  FrameworkName Al-Bicyclo-AddedH-P1-fix-PBC
  SeparateFrameworkComponents yes
    NumberofFrameworkComponents 2
  UnitCells 0 4 2 2
  
  Framework_Component_ 1
           TranslationProbability     0.0
           RotationSpecialProbability 1.0
  END_OF_Framework_Component_ 1
  

Framework Component file

• Provide the atom indices of the framework component in CIF file defined in simulation.input file
• The name of the example below is Framework_Component_1.def
  • The name has to match the component you mentioned in simulation.input file.
• NOTE: Make sure your framework molecules do not cross the periodic boundary (make sure they are not cut by the boundary)
• The example looks like below :

  #Note: The numbering here should match the numbering in your CIF FILE. P1 Symmetry is required.
  #YOU SHOULD have no issue making supercells with this list defined here, the numbers will be replicated accordingly.
  #Molecule index should match atom indices, also make sure your molecule do not across the pbc
  Framework_Component_Name: BiCyclo-Linker
  Number_of_Molecules_for_Framework_component: 4
  Number_of_atoms_for_each_molecule: 22
  Atom_Indices_for_Molecule 0: 5 6 7  8  9  10 11 12  13  14  15  16  17  18  20  21  22  23  25  26  27  28
  Atom_Indices_for_Molecule 1: 38 39 40 41 42 43 44 45  46  47  48  49  50  51  53  54  55  56  58  59  60  61
  Atom_Indices_for_Molecule 2: 67 68 69 70 71 72 73 74  75  76  77  78  79  80  82  83  84  85  86  87  88  89
  Atom_Indices_for_Molecule 3: 93 94 95 96 97 98 99 100 101 102 103 104 105 106 108 109 110 111 112 113 114 115
  

Other Usages: Extra-Framework Cations/Anions

• Similar setup can be used to simulate extra-framework cations/anions
• For example, we have an anionic framework with -12 e
• If the extra-framework cations are calcium, we need 6 Ca2+ per unit cell
• Here are the steps:
  1. We first add 6 Ca2+ in the CIF file, as follows
     • NOTE: the cations do not have to be in perfect locations, just don't create overlaps.

       Ca 1 0.5 0.5 0.5 Biso 1 Ca 1
       Ca 1 0.55 0.5 0.5 Biso 1 Ca 1
       Ca 1 0.6 0.55 0.5 Biso 1 Ca 1
       Ca 1 0.65 0.45 0.5 Biso 1 Ca 1
       Ca 1 0.45 0.65 0.5 Biso 1 Ca 1
       Ca 1 0.45 0.6 0.55 Biso 1 Ca 1
       

  2. Add the definition of these cation molecules in Framework_Component_1.def

     #Note: The numbering here should match the numbering in your CIF FILE. P1 Symmetry is required.
     #YOU SHOULD have no issue making supercells with this list defined here, the numbers will be replicated accordingly.
     #Molecule index should match atom indices, also make sure your molecule do not across the pbc
     Framework_Component_Name: Ca_Ion
     Number_of_Molecules_for_Framework_component: 6
     Number_of_atoms_for_each_molecule: 1
     Atom_Indices_for_Molecule 0: 306
     Atom_Indices_for_Molecule 1: 307
     Atom_Indices_for_Molecule 2: 308
     Atom_Indices_for_Molecule 3: 309
     Atom_Indices_for_Molecule 4: 310
     Atom_Indices_for_Molecule 5: 311
     

  3. in simulation.input file, add the following lines
     • NOTE: these two code blocks will tell gRASPA to separate atoms in CIF file into two (framework + cation) host components, and assign translation move to the cation.

       FrameworkName xxx
       SeparateFrameworkComponents yes
       NumberofFrameworkComponents 2
       

       and

       Framework_Component_ 1
           TranslationProbability     1.0
       END_OF_Framework_Component_ 1