Computational structure characterization tools for the era of material
informatics
Lev Sarkisov1,* and Jihan Kim2
1Institute
for Materials and Processes, School of Engineering, The University of Edinburgh, Edinburgh, United
Kingdom
2Department
of Chemical and Biomolecular Engineering, KAIST, South Korea
*Corresponding author (Lev.Sarkisov@ed.ac.uk)
ABSTRACT: Current advances in synthesis of new porous materials outpace our ability to test
them in real adsorption applications. This situation is particularly evident in the area of metalorganics frameworks (MOFs), where hundreds of new MOFs are reported every year and the
number of possible MOFs is virtually infinite. How to make sense out of this vast number of
existing and possible structures?
In this article, we will review the application of computational structure characterization tools for
systematic description and classification of porous materials and their adsorption properties.
Using examples from recent research in our groups and others, we will discuss how the
information obtained from computational characterization can be used in screening protocols to
identify the most promising materials for a specific application before any costly and time
consuming experimental effort is committed. We will finally touch upon the need for the tools to
systematically organize the information generated in computational studies. These tools
combined with the recent impressive advances in synthesis of porous materials may
fundamentally change the way we approach material discovery, starting the era of material
informatics.
Supplemental Information file:
1. Parameters of the Poreblazer v3.0.2 structural characterization analysis:
2.58, 10.22, 3.314, 298: Helium atom sigma (Å), helium atom epsilon (K), nitrogen atom sigma
(Å), temperature (K)
12.8, 1.122, 500: Cutoff distance (Å), accessible surface area coefficient (1.0 for hard sphere
1
surface, 1.122 for potential minimum surface), number of trials for surface area calculation
0.2: Cubelet size (Å)
20.0, 0.25: Largest anticipated pore diameter (Å), size of the bin for PSD (Å)
21908391: Random number seed
2. Simulation parameters for the results described in Section 4 of the article and related to
the breath analysis application
All molecular species are considered as rigid structures. Interaction of a single molecule with
the atoms of the structure involves van der Waals and Coulombic components. The van der
Waals interactions are described using the Lennard-Jones potential. Lennard-Jones parameters in
this study for both MOFs and adsorbates are obtained from the DREIDING (1) and UFF (2) force
fields, as described below. All partial charges on atoms are obtained from the B3LYP (3,4)
density functional theory calculations using the ChelpG method (5). For MOFs partial charges
are taken from the literature (6).
All density functional calculations are carried out using
Gaussian 09 (7). The adsorbate-adsorbent Coulombic interactions are calculated using a variant
of the Wolf pair-wise summation method, proposed by Fennell and Gezelter (8). For both
Lennard-Jones and Coulombic interactions the cut-off radius is taken to be 13.0 Å in this work.
In the calculation of Henry’s constants of adsorption, the grid size is 0.1 Å and 50 rotations of a
rigid molecule per cubelet are tried. The variation of the logarithm of the Henry’s constant with
the reciprocal temperature provides a well known route to the isosteric heat of adsorption, or
more appropriately, to the differential enthalpy of adsorption:
  ln K H 
h   R 

 (1 / T )  N a
2
where Na corresponds to the amount adsorbed. In experiments, it is the excess amount adsorbed
that is measured, whereas in simulations the absolute amount adsorbed is calculated. In principle,
an appropriate conversion from the absolute to excess values must be applied in order to compare
the differential enthalpy and other properties obtained in simulations to those in experiments.
However, at very low pressures and loadings (the regime of interest here), the difference between
the excess and absolute amounts adsorbed is negligible.
2.1 Interaction parameters for atoms of MOFs and adsorbates
Name
C
O
H
Zn
V
Cu
σ, Å
3.480
3.034
2.850
2.462
2.801
3.114
ε, K
41.00
39.90
7.64
62.38
8.05
2.51
Forcefield
DREIDING
DREIDING
DREIDING
UFF
UFF
UFF
All adsorbates are treated as rigid.
3. Molecular species and charges from B3LYP/CHELPG
x, Å
Benzaldehyde
C
C
C
C
C
C
C
H
O
H
H
H
H
H
y, Å
z, Å
q, e
14
0
-1.03935
-0.73823
0.60028
1.63871
1.33841
-0.30373
0.5783
-1.44911
-2.06491
-1.53779
0.83198
2.6721
2.13671
0.57872
-0.37071
-1.73207
-2.15469
-1.2145
0.14998
2.0199
2.68734
2.50103
-0.01693
-2.46574
-3.21523
-1.54535
0.88785
0
0
0
0
0
0
0
0
0
0
0
0
0
0
-0.02762
-0.02427
-0.11473
-0.05039
-0.06629
-0.14916
0.43664
-0.01302
-0.47229
0.09361
0.09997
0.08818
0.09349
0.10588
13
-1.39421
-1.04324
-0.09635
-0.30874
Btanone
C
3
C
C
O
C
H
H
H
H
H
H
H
H
-0.56773
0.82862
-0.99856
1.87392
-0.81569
-2.29253
-1.68988
1.08028
0.84421
2.87517
1.8856
1.6577
0.20983
0.04143
1.33133
-0.1999
-1.82039
-0.81109
-1.45594
0.95837
-0.79624
-0.30077
0.64099
-1.11418
0.10534
0.68612
-0.21123
-0.42955
-0.6105
-0.67129
0.87775
1.22912
1.39447
0.00197
-1.13058
-0.9945
0.59862
-0.11535
-0.53137
-0.04698
0.08662
0.09238
0.0803
0.04462
0.02097
0.03548
0.03505
0.00841
12
1.9113
0.52251
-0.60715
-1.86133
2.05524
2.70283
2.05524
0.40413
0.40413
-0.53489
-0.53489
-2.62112
0.13512
-0.5218
0.50089
-0.24124
0.76612
-0.62201
0.76612
-1.16616
-1.16616
1.1464
1.1464
0.37394
0
0
0
0
-0.88625
0
0.88625
0.87998
-0.87998
-0.88977
0.88977
0
-0.27843
0.0784
0.37272
-0.76465
0.0588
0.07761
0.0588
0.01507
0.01507
-0.0396
-0.0396
0.44584
32
-5.79404
-4.49383
-3.22725
-1.91978
-0.65366
0.65366
1.91977
3.22726
4.49381
5.79406
-6.6775
-5.85262
-5.85262
-4.47572
-4.47572
-3.24453
-3.24453
-1.90363
-1.90363
-0.6697
-0.28815
0.53193
-0.34336
0.46928
-0.4064
0.40645
-0.46924
0.34338
-0.53195
0.28808
0.36081
-0.93361
-0.93361
1.19245
1.19245
-1.00457
-1.00457
1.13037
1.13037
-1.06746
0
0
0
0
0
0
0
0
0
0
0
0.88556
-0.88556
-0.87957
0.87957
0.88029
-0.88029
-0.8803
0.8803
0.88029
-0.18735
0.13464
0.01704
-0.05052
0.06945
0.06943
-0.05051
0.01705
0.13463
-0.18735
0.04319
0.03949
0.03949
-0.02614
-0.02614
-0.00694
-0.00694
0.00094
0.00094
-0.02058
Propano
l
C
C
C
O
H
H
H
H
H
H
H
H
Decane
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
4
H
H
H
H
H
H
H
H
H
H
H
H
-0.6697
0.66971
0.66971
1.90361
1.90361
3.24456
3.24456
4.47568
4.47568
6.67749
5.85267
5.85267
-1.06746
1.0675
1.0675
-1.13033
-1.13033
1.00458
1.00458
-1.19246
-1.19246
-0.36092
0.93353
0.93353
-0.88029
-0.88029
0.88029
-0.8803
0.8803
0.88029
-0.88029
0.87957
-0.87957
0
0.88556
-0.88556
-0.02058
-0.02058
-0.02058
0.00094
0.00094
-0.00694
-0.00694
-0.02614
-0.02614
0.04319
0.03949
0.03949
16
0
1.34258
1.66795
0.65337
-0.68737
-1.01072
-0.28376
-1.48574
2.13467
2.70953
0.90137
-1.48051
-2.05419
0.60467
-2.42134
-1.57213
0.56233
0.13273
-1.22651
-2.18951
-1.77963
-0.42219
2.00866
2.60773
0.87665
-1.53241
-3.2461
-2.521
-0.12458
2.64016
2.05639
3.68919
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.24701
-0.23453
-0.03385
-0.13303
-0.05652
-0.18704
-0.18549
-0.28253
0.11224
0.08559
0.09729
0.08624
0.11474
0.12045
0.12219
0.12724
Syrene
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
(1)
Mayo, S. L.; Olafson, B. D.; Goddard, W. A. Journal of Physical Chemistry 1990, 94,
8897
(2)
Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. Journal of the
American Chemical Society 1992, 114, 10024.
(3)
Becke, A. D. Journal of Chemical Physics 1993, 98, 5648.
(4)
Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Journal of Physical
Chemistry 1994, 98, 11623.
(5)
Breneman, C. M.; Wiberg, K. B. Journal of Computational Chemistry 1990, 11, 361.
(6)
Yazaydin, A. O.; Benin, A. I.; Faheem, S. A.; Jakubczak, P.; Low, J. J.; Willis, R. R.; R.
Q. Snurr, Chemistry of Materials 2009, 21, 1425-1430.
(7)
Gaussian09.
(8)
Fennell, C. J.; Gezelter, J. D.; Journal of Chemical Physics, 2006, 124, 234104.
5