2CSCS-2013-Jaksic-electroImagneticCeramics

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ON MODELING OF ADSORPTIONOF LARGE MOLECULES

ON CRYSTALLINE CERAMIC SURFACES

Olga Jaki, Danijela Randjelovi,Dana Vasiljevi-Radovi, Zoran Jaki

[email protected]

IHTM Centre of Microelectronic Technologies andSingle Crystals, University of Belgrade, Serbia

The Second Conference of the

Serbian Ceramic Society


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2CSCS 2013On modeling of adsorption of largemolecules on crystalline ceramic surfaces

Outline:

Parameters in theoretical models

Experimental data: pro et contra

Computer aided solutions & software

Our choice and our procedure

Examples


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AD processes / modeling

3

,

,, , ,

a i

d i

k

g i f i a ikA A A

,

, , , , ,

d

d

a i

a i g i f i d i a i

N

k N N k N t

, , 0, , , , ,1

d

d

ra i

a i i a i a j d i a i

j

Nk N N M N k N

t

Multicomponent adsorption

Ar

O2

H2

C6H6

a)

b)

c)

Binding site

Adsorption

Desorption He

buthow

tomodel

M?

www.research.che.tamu.edu


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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 ofthe same gas have different molecular projected areas onthe surface, depending on their orientation at the momentof adsorption on the surface

4

NO2 SO2

Single-site adsorption/of large molecules


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5www.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 showingthe planar arrays of corner linked TiO6

octahedra and the A-site cations.

Adsorption centre /vs. adsorption site


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Surface density/experimental

Photograph of the (3x3)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.


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Model/...more than just a picture

The Nobel Prize in Chemistry 1998was 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. Popleconducted

important theoretical research

that enabled

mathematical articulation ofmolecular structure

and evoked a plethora of software solutions

and great development in cheminformatics


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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 FlashMolecular EditorOnline editors (jsMolEditor, Ketcher, Chem Doodle Web Components)Java scripts that run on all platforms, iPad, iPhone, Android...

OLN JSDraw...Android applications

ChemDoodle MobilePart/basis for some of these routines: Jmol


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Jmol/http://jmol.sourceforge.net/


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Motivational example/Janocchio

Custom upgrade routine: Nuclear overhouser effect constants and

coupling copnstants for nuclear magnetic resonance


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Our choice /our procedure

Marvin 5.9.3, 2012 (http://www.chemaxon.com),

Not a free software, there is an academic institutions licencePubChem (http://pubchem.ncbi.nlm.nih.gov/) Substance and Compound online databaseThe procedure

The molecule structure is obtained using the chemicalstructure information available in the PubChem Substanceand Compound database through the unique chemicalstructure identifier CID.

molecular projected surface area was obtained using Marvin5.9.3, 2012

molecular projected surface areas were corrected beforebeing inversed in order to give the number of adsorptioncenters per unit area for that species

The results were compared with available literature data


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Example /trimethyl phosphate on minerals

P. Mkie, G. Westin, P. Persson, L. Osterlund, Adsorption of Trimethyl Phosphate on Maghemite, Hematite, andGoethite NanoparticlesThe Journal of Physical Chemistry A. 115 (2011) 89488959.


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Example /trimethyl phosphate on minerals

P. Mkie, G. Westin, P. Persson, L. Osterlund, Adsorption of Trimethyl Phosphate on Maghemite, Hematite, andGoethite NanoparticlesThe Journal of Physical Chemistry A. 115 (2011) 89488959.


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MATLAB /IHTM-CMTM custom designed routines

visualization

System parameters

Deterministic solutionsStochastic analysis


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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 (platformindependent)

Our choises: Jmol, Janocchio. The influence of the

molecular size to adsorption on crystalline ceramics has

been assessed using the ChemAxon's Marvin softwareand the PubChemdatabase.

A simplified but still accurate numerical model connecting

adsorption kinetics with measurable variables is proposed.15


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Acknowledgments

This work has been supported by the Serbian

Ministry of Education and Science through the

project TR 32008.

16http://nanosys.ihtm.bg.ac.rs/

+381 11 2638 188 Director's Office

+381 11 2628 587 MEMS & NEMS Lab

+381 11 2630 757 Transmitter Lab

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 standard9 gasses...

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SIDE EFFECTS /numerical errors, constraints

MATLAB Manual solving and thenMATLAB or Mathematica

There are situations that sdoftware cant do.

2CSCS-2013-Jaksic-electroImagneticCeramics

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