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:
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A. Accessible surface area
DREIDING.atoms
IRMOF.xyz
3.314
500
25.83200
90.00000
0.593
pot
25.83200
90.00000
! file containing the atom types
! file containing the coordinates of adsorbent
! probe size in Å
! number of trials
25.83200 ! dimensions of the unit cell
90.00000 ! unit cell angles yz, xz, yx
! crystal density in g / cm3
! type of surface:
! hs - probed with a hard sphere probe
! pot - probed at the potential minimum distance (2**1/6 sigma)
1938098
1
! random number seed
! 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
IRMOF.xyz
4.0
! file containing the atom types
! file containing the coordinates of adsorbent
! lower limit on the probe size
2
0.50
7.00
0.5
25.83200
90.000
25.83200
90.000
! probe size increment
! upper probe size limit
! grid spacing
25.83200 ! dimensions of the unit cell
90.000
! unit cell angles yz, xz, yx
Dm. Pore space connectivity for a molecular probe
DREIDING.atoms
IRMOF.xyz
Benzene.mol
0.5
25.83200
25.83200
90.000
90.000
21908391
! file containing the atom types
! file containing the coordinates of adsorbent
! file containing the geometry of the probe
! grid spacing
25.83200 ! dimensions of the unit cell
90.000
! unit cell angles yz, xz, yx
! random seed
III. Computer visualization of the percolated pathway accessible to a benzene
molecule in IRMOF-1.
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