ON MODELING OF ADSORPTION

OF LARGE MOLECULES
ON CRYSTALLINE CERAMIC SURFACES
Olga Jaki, Danijela Randjelovi,
Dana Vasiljevi-Radovi, Zoran Jaki
olga@nanosys.ihtm.bg.ac.rs
IHTM Centre of Microelectronic Technologies and
Single Crystals, University of Belgrade, Serbia
The Second Conference of the
Serbian Ceramic Society
2CSCS 2013
On modeling of adsorption of large
molecules on crystalline ceramic surfaces
Outline:
Parameters in theoretical models
Experimental data: pro et contra
Computer aided solutions & software
Our choice and our procedure
Examples
2CSCS 2013
AD processes / modeling
3
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+

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d
d
a i
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,
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Multicomponent adsorption

Ar
O
2

H
2

C
6
H
6

a)
b)
c)
Binding site
Adsorption
Desorption
He
but
how
to
model
M?
www.research.che.tamu.edu
2CSCS 2013
Are there prefferable orientations?
Different gases with complex non-spherical molecules
have different molecular projected area on the surface.
But it is also true that complex non-spherical molecules of
the same gas have different molecular projected areas on
the surface, depending on their orientation at the moment
of adsorption on the surface
4
NO2 SO2
Single-site adsorption/ of large molecules
2CSCS 2013
5
www.research.che.tamu.edu
The surface is also not simple, one molecule = one adsorption site
Even monoatomic molecules may multisite.
The (110) structure of zirconolite-2M. The
interlayer Ca (large) and Zr (small) cations
are shown between the planar octahedral
Ti layers.
The (110) structure of pyrochlore showing
the planar arrays of corner linked TiO6
octahedra and the A-site cations.
Adsorption centre / vs. adsorption site
2CSCS 2013
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Surface density/ experimental
Photograph of the (\3x\3)R30
structure formed bymolecular
hydrogen adsorbed on a
graphite surface. The H-
induced extra spots have a
much lower intensity than the
graphite spots and are hardly
visible. After (Seguine and
Suzanne, 1982)
Landolt-Brnstein series
K. Christmann, 3.4.1 Adsorbate properties of hydrogen on solid surfaces, in: H.P. Bonzel
(Ed.), Adsorbed Layers on Surfaces. Part 5: Adsorption of Molecules on Metal,
Semiconductor and Oxide Surfaces, Springer Berlin Heidelberg, 2006: pp. 1130.
Most literature data refer to
surface density of adsorbate molecules in equilibrium !!!
Lab work is expensive end cumbersome.
We need a RELIABLE theoretical model.
2CSCS 2013
Model/...more than just a picture
The Nobel Prize in Chemistry 1998 was divided equally between
Walter Kohn "for his development of the density-functional
theory" and John A. Pople "for his development of computational
methods in quantum chemistry".
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1998/
Walter Cohn and John A. Pople
conducted
important theoretical research
that enabled
mathematical articulation of
molecular structure
and evoked a plethora of software solutions
and great development in cheminformatics
2CSCS 2013
Chemical software/free, more than modeling
Standalone progams for different platforms
Chem Tool, Smormo-Ed, Bioclipse, Ascalaph, Avogadro,
BKchem, molsKetch, SketchEI, XDrawChem, Zem,
BALLView, JChemPaint
Applets
JME molecular editor, SketchEI,Chemis3D, FlaME Flash
Molecular Editor
Online editors
(jsMolEditor, Ketcher, Chem Doodle Web Components)
Java scripts that run on all platforms, iPad, iPhone, Android...
OLN JSDraw...
Android applications
ChemDoodle Mobile
Part/basis for some of these routines: Jmol
2CSCS 2013
Jmol/ http://jmol.sourceforge.net/
2CSCS 2013
Motivational example/ Janocchio
Custom upgrade routine: Nuclear overhouser effect constants and
coupling copnstants for nuclear magnetic resonance
2CSCS 2013
Our choice / our procedure
Marvin 5.9.3, 2012 (http://www.chemaxon.com),
Not a free software, there is an academic institutions licence
PubChem (http://pubchem.ncbi.nlm.nih.gov/)
Substance and Compound online database
The procedure
The molecule structure is obtained using the chemical
structure information available in the PubChem Substance
and Compound database through the unique chemical
structure identifier CID.
molecular projected surface area was obtained using Marvin
5.9.3, 2012
molecular projected surface areas were corrected before
being inversed in order to give the number of adsorption
centers per unit area for that species
The results were compared with available literature data
2CSCS 2013
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Demonstrative examples are given for
adsorbates like aromatic hydrocarbons or
trimethyl phosphate on crystalline
structures of mineral particles like
maghemite, hematite and goethite.
Example / trimethyl phosphate on minerals
P. Makie, G. Westin, P. Persson, L. Osterlund, Adsorption of Trimethyl Phosphate on Maghemite, Hematite, and
Goethite NanoparticlesThe Journal of Physical Chemistry A. 115 (2011) 89488959.
2CSCS 2013
13
Demonstrative examples are given for
adsorbates like aromatic hydrocarbons or
trimethyl phosphate on crystalline
structures of mineral particles like
maghemite, hematite and goethite.
Example / trimethyl phosphate on minerals
P. Makie, G. Westin, P. Persson, L. Osterlund, Adsorption of Trimethyl Phosphate on Maghemite, Hematite, and
Goethite NanoparticlesThe Journal of Physical Chemistry A. 115 (2011) 89488959.
2CSCS 2013
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MATLAB / IHTM-CMTM custom designed routines
visualization
System parameters
Deterministic solutions
Stochastic analysis
2CSCS 2013
Conclusion
Modelling of AD processes on crystalline minerals
within the context of software usage is addressed
A review of different free software solutions is given
Standalone programs (for different platforms)
Applets , online editors, java scripts (platform
independent)
Our choises: Jmol, Janocchio. The influence of the
molecular size to adsorption on crystalline ceramics has
been assessed using the ChemAxon's Marvin software
and the PubChem database.
A simplified but still accurate numerical model connecting
adsorption kinetics with measurable variables is proposed.
15
2CSCS 2013
Acknowledgments
This work has been supported by the Serbian
Ministry of Education and Science through the
project TR 32008.
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2CSCS 2013
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2 gasses / MATLAB, time evolutions
This solution is unusable: no distinguishable transients&stationary state
Medical gasses 5 gasses
Natural gas standard 9 gasses...

2CSCS 2013
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SIDE EFFECTS / numerical errors, constraints
MATLAB
Manual solving and then
MATLAB or Mathematica
There are situations that sdoftware cant do.