application of gaussian package to chemical reaction studies

EGEE-II INFSO-RI-031688

Enabling Grids for E-sciencE

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Application of Gaussian package to chemical reaction studies

M. Sterzel1

T. Szepieniec1, W. Piskorz2, F. Zawada2

1ACC CYFRONET AGH2Depatment of Chemistry, Jagiellonian University

EGEE User Forum, Manchester 11th May 2007

Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 2



Outlook

• Aim of this talk– To demonstrate Grid application to chemical reaction studies

• Parts of the talk topics– Commercial Software on the Grid– Gaussian VO– Chemical reaction – basics– Sample calculations– Final Remarks




Commercial Software

• Commercial Software – why bother about it?– Used by majority of scientists to conduct research– Faster implementation of new computational methods– Better user support– More frequent bug fixes

• Why Gausian?– Large number of computational methods implemented– One of the first ab-initio codes– The most popular among communities– User friendly– Available on many platforms along with GUI




Gaussian VO

• Invented and operated by ACC CYFRONET• All license issues confirmed with Gaussian Inc,• Open for every EGEE user• Any compuing centre with proper Gaussian

license may support it (4 supporting centres, another 3 in the line)

• 20 users since the start in September 2006• VO manager – Mariusz Sterzel

([email protected])




Gaussian VO – participation

As a user:• Register at:

https://voms.cyf-kr.edu.pl:8443/vo/gaussian/vomrs

• Accept Gaussian VO license requirements• Wait for VOMRS admin acceptance• voms-proxy-init --vo gaussian and you are ready to use the

program...




Gaussian VO – participation

As a user:• Register at:

https://voms.cyf-kr.edu.pl:8443/vo/gaussian/vomrs

• Accept Gaussian VO license requirements• Wait for VOMRS admin acceptance• voms-proxy-init --vo gaussian and you are ready to use the

program...

As a participating centre:• Just sent an e-mail concerning participation to VO manager• After confirmation of the license status at your centre with

Gaussian Inc, detailed informations concerning set-up will be sent back to you




Becaming a user

gaussian VO Registration

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Welcome to the gaussian VO user registration phase I page.

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If you don't receive the confirmation email, please check youremail address in VOMRS and change it if necessary. If it wascorrect, contact the VO administrator .

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You are logged in as /C=XX/O=GRID/O=Important/CN=Jon Doe - Gaussian

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Future work

• Web portal with a plug-in for Gaussian

• Parallel version of the code

• Integration with other chemical packages




H—CN CN—H

Chemical reactions

... a process that results interconversion of molecules




Chemical reactions

Points of interest:– Structure of substrates and products– Structure of active complex at TS– Reaction path




Chemical reactions

Points of interest:– Structure of substrates and products– Structure of active complex at TS– Reaction path(s)

Reactionpath

substrate(s) product(s)

Transition State (TS)

Energy




Chemical reactions

Energy

substrate(s)product(s)

A+B C

DIntermediateproduct

TS1

TS2

E(TS1) > E(TS2)

Reactionpath




Chemical reactions

Energy

Possible reaction paths;More intermediate products

Reaction path




Chemical reactions

Main problem – TS determination




Chemical reactions





Chemical reactions


E

‘reaction coordinate’




Chemical reactions


‘reaction coordinate’

E




Chemical reactions

TS verification – vibrational analysis – one imaginary frequency!

i1203 cm-1




Sample calculations

N2O braking on oxide surfaces – possible mechanisms

• Electron transfer

6. (O-)--X+--(O-) X + O2

1. N2O + X 2. N2O(s) + X X+--N2O-

4. X+--N2O- X+--(O-) + N25. (O-)--X+--(O-)

e- transfer




Sample calculations

N2O braking on oxide surfaces – possible mechanisms

• An Oxygen transfer

1. N2O(g) N2O(s) 2. N2O(s) + X X--O--N2

4. O-X-O 5. O--O-X 6. X + O2

4. X-O




Sample calculations

Vac

uu

m

Oxi

de

slab

Adsorbed N2O

Slab construction

Oxi

de

slab

Matrix generation




Sample calculations

• Reaction paths:




Sample calculations

Computational details:– Gaussian 03 D.01– BP86 functional– Basis set of double-ζ quality

Timings:– CPU time for SP calculation – approx 7 hours– 15 paths – 10-50 energy points on each path– In total about 250 energy poits calcutated

Work still in progress...




Summary

• Chemical reaction studies require huge computational resources

• Data point on energy surfaces are collected separately

• With a little of work the whole process can be automated

application of gaussian package to chemical reaction studies

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