Computational structure characterization tools in application to ordered and disordered porous materials
Lev Sarkisov and Alex Harrison
Institute for Materials and Processes, School of Engineering, University of Edinburgh, EH9 3JL,UK
Abstract
In this article we present a set of computational tools for systematic characterization of ordered and disordered porous materials. These tools include calculation of the accessible surface area and geometric pore size distribution, analysis of the structure connectivity and percolation analysis of the porous space. We briefly discuss the algorithms behind these calculations. To demonstrate the capabilities of the tools and the type of insights that can be gained from their application we consider a series of case studies. These case studies include small molecular fragments, several crystalline metal-organic materials, and variants of these materials with induced defects and disorder in their structure. The simulation package is available upon request.
Supplemental Information
I. Molecular visualizations of IRMOF-1, 10, 16 materials (from left to right, respectively). IRMOF-1 and IRMOF-10 feature two types of cavities, depending on the orientation of the paddlewheel linkers. The tangent orientation (with respect to the inscribed sphere) leads to a cavity with a larger characteristic size of the pore as measured by the inscribed sphere (yellow sphere). The inward orientation of the paddlewheels leads to a smaller effective size of the cage (blue sphere). IRMOF-16 features only one type of cage as a result of the aromatic rings within the linker being in various orientations.
II. Examples of the input files for the computational tools:
A. Accessible surface area
DREIDING.atoms ! file containing the atom types
IRMOF.xyz ! file containing the coordinates of adsorbent
3.314 ! probe size in Å
500 ! number of trials
25.83200 25.83200 25.83200 ! dimensions of the unitcell
90.00000 90.00000 90.00000 ! unit cell angles yz, xz, yx
0.593 ! crystal density in g / cm3
pot ! type of surface:
! hs - probed with a hard sphere probe
! pot - probed at the potential minimum distance (2**1/6 sigma)
1938098 ! random number seed
1 ! surface visualization option (1: yes; 0: no)
B. Geometric pore size distribution
DREIDING.atoms ! file containing the atom types
IRMOF.xyz ! file containing the coordinates of adsorbent
5000 ! number of trials
0.2 ! lower limit on the diameter of the probe
0.2 ! increment of the probe diameter
40 ! maximum probe diameter
25.83200 25.83200 25.83200 ! dimensions of the unit cell
90.00000 90.00000 90.00000 ! unit cell angles yz, xz, yx
328420 ! random seed number
1 ! logical variable: 1 if you want to save coordinates of the probes of specific diameter, 0 - no
13.0, 14.0 ! probe diameter range within which to save the coordinates
C. Structure connectivity
IRMOF.xyz ! file containing the coordinates of adsorbent
25.83200 25.83200 25.83200 ! dimensions of the unit cell
90.000 90.000 90.000 ! unit cell angles yz, xz, yx
2.00 ! distance between the two connected particles Å
D. Pore space connectivity
DREIDING.atoms ! file containing the atom types
IRMOF.xyz ! file containing the coordinates of adsorbent
4.0 ! lower limit on the probe size
0.50 ! probe size increment
7.00 ! upper probe size limit
0.5 ! grid spacing
25.83200 25.83200 25.83200 ! dimensions of the unit cell
90.000 90.000 90.000 ! unit cell angles yz, xz, yx
Dm. Pore space connectivity for a molecular probe
DREIDING.atoms ! file containing the atom types
IRMOF.xyz ! file containing the coordinates of adsorbent
Benzene.mol ! file containing the geometry of the probe
0.5 ! grid spacing
25.83200 25.83200 25.83200 ! dimensions of the unit cell
90.000 90.000 90.000 ! unit cell angles yz, xz, yx
21908391 ! random seed
III. Computer visualization of the percolated pathway accessible to a benzene molecule in IRMOF-1.
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