a Fortran code for topological and crystallographic tetrahedral sites analysis in zeolites and zeotypes

Written by:
German Sastre (Instituto de Tecnologia Quimica, Valencia, Spain)
Julian D. Gale (Curtin University of Technology, Perth, Australia)

Fragment of the CHA zeotype showing a tetrahedral central atom (pink), and its first (blue) and second (green) T-neighbours.

1. Introduction to zeoTsites

The catalytic function in zeolites and zeotypes is strongly determined by their microporous structure. Microporosity is oftenly viewed only as the size and shape of the microchannels and microcavities present in these materials and in this way we are only focusing on the void space. Such void space is the consecuence of the of the actual directionality taken by the T-O (T=tetrahedral atom) bonds in the three dimensional topology of the solid

and forming the void space usually means a deviation of a more stable topology such as -for example- that present in high density phases of silicates of equivalent chemical composition. Still less intuitive is to focus on the connectivity sequence of each particular structure although some consequences for the catalytic activity may also arise from it.

Exploring the topology and geometry of three-dimensional four-connected nets is the aim of the zeoTsites Fortran code. For the sake of clarity, the program, apart from calculating every single T-O and T-O-T units, also performs averages. Averages are considered from two viewpoints: T atoms are grouped by their coordination sequence and by their (crystallographic) label. This allows easy comparison between geometry variations related to topology and/or crystallographic site. The program can also be used to analyse geometries of a zeotype in which an isomorphic substitution has been performed and then the response of the framework to the substitution in the different parts of the structure can be analysed.

In the same way, NMR signals coming from different T sites can be classified according to their corresponding average T-O-T angles, or T-T distances, whose values are provided by the code. Any other external perturbation in the zeotype framework by any physical or chemical influence can be analysed by the code if the corresponding geometries are previously provided. In this sense the code can be a useful tool to be utilised after a given computer simulation.

2. Copyright notice

zeoTsites is available free of charge to academic and research institutions and non-commercial establishments only. Copies should be obtained from the authors only and should not be distributed in any form by the user to a third party without the express permission of the authors.

No claim is made that the program is free from errors and no liability will be accepted for any loss or damage that may result. The users are responsible for checking the validity of their results.

3. Getting zeoTsites

A tar file (zeots-x.y.tar, where x.y is the version number) can be obtained
from any of the authors by e-mail.
The unix installation proceeds as follows:
(i) untar the original file zeots-1.2.tar by typing:
'tar xvf zeots-1.2.tar'
(ii) type: 'make'
As to the use of the code:
(i) execute by typing: './zeots'
(ii) you will then be prompted twice as follows:
- "What is the zeotype ?"
you have to provide a name (no more than 20 characters) which
will be appended to the output files

- "Input file ?"
just give the complete name of the input file (.xtl format)

4. Input and output files

zeoTsites is provided with some sample input files (in .xtl format), and it produces 4 output files:

- "Connecty_of_filename"
this contains the coordination sequence of each T-atom in the unit cell (up to the 13th shell), and it classifies each topologically distinct atom with a number (in the column labelled "T-type")

then the vertex symbol of each T-atom is printed. For 4-connected atoms, this consists of 6 symbols corresponding to the rings found in the: O1-T-O2, O1-T-O3, O1-T-O4, O2-T-O3, O2-T-O4, O3-T-O4 directions. Each index indicates the number of T atoms in the ring, and the sub-index indicates the number of them. The vertex symbols are ordered (for 4-connected atoms) according to: ring size, opposite angles, and ring multiplicity. Opposite angles are defined (for 4-connected atoms) as: 1-4 and 2-3; 1-3 and 2-4; 1-2 and 3-4. For connectivities other than 4, the opposite angle criterion is not taken into account when ordering the vertex symbols.

then it prints the "Geometry analysis:" with the characteristics of all the T-O-T units in the unit cell (T-type, atom numbers, T-O-T angle, T-O and T-T distances, and atom labels). Atoms are renumbered: first all T-atoms, and then all O-atoms. The same numbering is followed in the "output_filename.xtl" file

then the "Average topological geometry analysis:" is printed which consists on averages over T-T types and T-types. The number under the column "Number" indicates the corresponding multiplicity

finally the "Average label geometry analysis:" is printed and these averages are referred to the label of the T-atoms in the input file. These averages can be particularly useful if the T and O atoms are labelled according to their crystallographic positions. Averages include T-O, T-T, T-O-T, and T averages

- "T1_sites_of_filename"
for each T-atom in the unit cell its T-first-neighbours are output by indicating: atom number, atom label, cell code

atoms connected to a given atom can be in one of the adjacent unit cells. the initial cell code is referred to as "0 0 0". the other cells are indicated by numbers of relative shifts to the central cell in the directions of the x,y,z axis respectively. i.e. the contiguous cell at the right would be "1 0 0"

- "T2_sites_of_filename"
for each T-atom in the unit cell its T-second-neighbours are output by indicating: atom number, atom label, cell code

T1_ and T2_ files can be useful for NMR applications. Complex unit cells with a given distribution of Si,Al,P atoms can be used as input files in order to find the neighbourhood of each T-atom

- "output_filename.xtl"
this is a .xtl file with the same input structure which contains the topological T-type (divided by 1000) in the column corresponding to the charges. This is useful for visual identification of the T-types when using a visualisation software such as Cerius2

5. Current limitations

(i) T-T connectivity is calculated through distance checks and confirmed by label check. Non connected T-T atoms in the range indicated by the parameters (adist1,adist2) will be identified as connected and the program will fail

(ii) cations must be cleared from input file as they do not contribute to the framework connectivity and they are not taken into account in the geometry analysis. Otherwise some cations may be interpreted as bonded to some of the framework atoms thus flawing the corresponding connectivity and spoiling the geometry analysis

6. More information

See the following paper:
Title: ZeoTsites: a code for topological and crystallographic tetrahedral
sites analysis in zeolites and zeotypes
Authors: G. Sastre, J.D. Gale
Journal: Microporous and Mesoporous Materials
Year: 2001
Volume: 43
Issue: 1
Pages: 27-40