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VIBE Calculations of Vibrational modes Using Siam Quantum

VIBE Calculations of Vibrational modes Using Siam Quantum . A full-feature presentation by Nanta Sophonrat Adviser: Dr.Teepanis Chachiyo. Computational Physics @ KKU Date : May 7,2010. Outlines. Introduction Theoretical Background Programming Results Discussion Conclusion.

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VIBE Calculations of Vibrational modes Using Siam Quantum

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  1. VIBECalculations of Vibrational modes Using Siam Quantum A full-feature presentation by NantaSophonrat Adviser: Dr.TeepanisChachiyo Computational Physics @ KKU Date : May 7,2010

  2. Outlines • Introduction • Theoretical Background • Programming • Results • Discussion • Conclusion

  3. Introduction: Ab initio Quantum Chemistry program using Hartree-Fock method to determine energy and wave function of molecule Input: Structure file + basis set file Output : Ground state energy + wave function http://www.physics.kku.ac.th/sq/ http://www.physics.kku.ac.th/Computational_physics/?q=node/33

  4. Introduction: Vibrational modes IR Spectroscopy ?  What theory lies beneath these tools? What do we use to identify molecules? http://webbook.nist.gov/chemistry http://www.physics.kku.ac.th/raman/ Raman Spectroscopy

  5. Introduction • Normal mode OR Vibrational mode • a pattern of motion in which all parts of the system oscillate with the same frequency • The frequency is called • “Natural frequency” What about molecules? http://en.wikipedia.org/wiki/Normal_mode

  6. Theoretical background molecular system Coordinate mass particle A particle B cartesian coordinate coordinate @ equilibrium

  7. Theoretical Background • Lagrange equation Generalized coordinate Mass-Weighted Hessian Lagrangian Kinetic energy Taylor’s expansion @ equilibrium ( ) Potential energy

  8. Theoretical Background 3N equations Differential Equation Eigenvalue equations = angular freq. Ref: Lecture on molecular vibration, Dr.TeepanisChachiyo (http://www.physics.kku.ac.th/computational_physics/)

  9. VIBEProgramming Flowchart start read structure file (@ equilibrium) + basis file find Mass-Weighted Hessian Solve eigenvalue equation eigenvalue = eigenvector = write file to animate each mode end

  10. Programming find Mass-Weighted Hessian from Siam Quantum x y z • Using Finite Different method A B case case for VIBE

  11. Programming H = mass-weighted hessian C = eigenvector E = eigenvalue S = overlap matrix (in this case = identity) Solve eigenvalue equation • in the form HC = ESC • using LAPACK eigenvalue = eigenvector = In case , we let it equal to zero. angular frequency is natural frequency.

  12. Programming write file to animate each mode • reposition by eigenvector T= no. of frame=50 t = 0,1,..,T suitable coefficient optional

  13. Programming • VIBE : usage http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

  14. Result1 : H2O (9 normal modes) mode 1 mode 3 mode 5 Torsion modes Rotational modes

  15. Result1 : H2O (9 normal modes) mode 2 mode 4 mode 6 OH stretching mode

  16. Result1 : H2O (9 normal modes) • Significant mode mode 9 mode 7 mode 8 OH symmetric Stretching mode OH antisymmetric Stretching mode Bending mode

  17. Result2 : H2O2 (12 normal modes) mode 2 mode 3 mode 1 Torsion Rotation Torsion

  18. Result2 : H2O2 (12 normal modes) mode 5 mode 6 mode 4 OH stretch + Rotation OH stretch OH stretch

  19. Result2 : H2O2 (12 normal modes) mode 7 (321) mode 7(631) mode 8 OH stretching OH stretching OO stretch

  20. Result2 : H2O2 (12 normal modes) mode 9 mode 10 Antisymmetric bending Symmetric bending

  21. Result2 : H2O2 (12 normal modes) mode 11 mode 12 OH antisymmetric stretching OH symmetric stretching

  22. Result Comparing • Vibe VS Gaussian • Example : H2O + basis 321G Gaussian 03W Vibe

  23. Result Comparing • Vibe VS Experiment • Example : H2O Vibe

  24. Table1 H2O : Vibe VS Gaussian

  25. Table2 H2O : Vibe&Gaussian VS Experiment

  26. Table3 H2O2: Vibe VS Gaussian

  27. Result Comparing • Experimental data: H2O2

  28. Table4 H2O2: Vibe&Gaussian VS Experiment

  29. Discussion • Over estimate approximation • From table 2 and 4, we can see that all of the error is positive. That is Vibe results is larger than experimental value. • Since the results of Vibe are corresponded to those of Gaussian as seen in table 1and 3; we can conclude that error is not from our algorithm. • In the nut shell, the error is due to Hartree-Fock methods itself that it is not taking Coulomb correlations into account. (for more info. please see Thijsen,Computational Physics,2007)

  30. Conclusion • Vibe is a program created to calculate natural frequency and vibrational modes which can be visualized using VMD. We use two molecules to test the accuracy of Vibe: H2O and H2O2.The results are compared with experimental data and with the results from Gaussian. The error compared with Gaussian is in the range of 0.16 – 3.99% which is acceptable; while the error compared with experimental data is in the range of 1.91 – 31.58%. We note that the all of the frequencies obtained from Vibe and also from Gaussian are larger than those from experiment. This is due to the limit of Hartree-Fock method used to calculated Energy in Siam Quantum and Gaussian.

  31. QUESTIONS THE END THANK YOU

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