PhD defence presentation

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My PhD defence on the Effective Fragment Molecular Orbital (EFMO) method

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PhD defence presentation

  1. 1. Department of ChemistryThe Effective Fragment Molecular Orbital Method: The development and application of a parameter free force fieldCasper SteinmannDepartment of ChemistryUniversity of Copenhagen Supervisor: Professor Jan H. JensenUniversity of Copenhagen, Feb. 12th, 2013Dias 1
  2. 2. Department of ChemistryOutline•  Motivation•  Current approaches to treat large systems•  My work •  Applications•  Conclusions and OutlookUniversity of Copenhagen, Feb. 12th, 2013Dias 2
  3. 3. Department of ChemistryMotivation•  Understand and improve enzyme catalysis•  Large systems are problematic in a computer•  Not one go-to program KE Ranaghan, AJ Mulholland (2010), Int. Rev. Phys. Chem.University of Copenhagen, Feb. 12th, 2013Dias 3
  4. 4. Department of ChemistryCurrent approaches to treat large systems QM/MM Fragment Based QM Method MM And the other ones …University of Copenhagen, Feb. 12th, 2013Dias 4
  5. 5. Department of ChemistryI want to study interaction energies …University of Copenhagen, Feb. 12th, 2013Dias 5
  6. 6. Department of ChemistryEffective Fragment Potential Method (EFP2)•  EFP2 is a model potential derived from first principles •  Multipole moments •  Dipole polarizability tensors •  Among others … doi: 10.1063/1.472045 doi: 10.1021/jp002747hUniversity of Copenhagen, Feb. 12th, 2013Dias 6
  7. 7. Department of ChemistryEffective Fragment Potential Method (EFP2) N N E EFP 2 =E HF − ∑ E = ∑ ( EIJ + EIJ + EIJ ) + Etot 0 I ES XR CT POL I IJUniversity of Copenhagen, Feb. 12th, 2013Dias 7
  8. 8. Department of Chemistry The Effective Fragment Potential Method (EFP2) N N E EFP 2 =E HF − ∑ EI = ∑ ( EIJ + EIJ + EIJ ) + Etot ES XR CT POL I IJMany-body polarization Computed classically using induced dipoles for entire system University of Copenhagen, Feb. 12th, 2013 Dias 8
  9. 9. Department of ChemistryI want interaction energies and internal energies …University of Copenhagen, Feb. 12th, 2013Dias 9
  10. 10. Department of ChemistryFragment Based Methods Fragment Molecular Orbital (FMO2) And most other fragmentation methods N N E FMO2 = ∑ EI + ∑ (EIJ − EI − EJ ) I IJUniversity of Copenhagen, Feb. 12th, 2013Dias 10
  11. 11. Department of Chemistry Fragment Based Methods Fragment Molecular Orbital (FMO2) And most other fragmentation methods N N E FMO2 = ∑ EI + ∑ (EIJ − EI − EJ ) I IJMany-body Polarization: Monomer SCF in the Coulomb field of all other monomers Iterated to self-consistency University of Copenhagen, Feb. 12th, 2013 Dias 11
  12. 12. Department of Chemistry Fragment Based Methods N N E FMO2 = ∑ EI + ∑ (EIJ − EI − EJ ) I IJNon-Coulomb effects: Dimer SCF in the Coulomb field of all other monomers Iterated to self-consistency University of Copenhagen, Feb. 12th, 2013 Dias 12
  13. 13. Department of Chemistry Fragment Based Methods N N E FMO2 = ∑ EI + ∑ (EIJ − EI − EJ ) I IJ Coulomb effects:Coulomb energy in the Coulomb field of all other monomers University of Copenhagen, Feb. 12th, 2013 Dias 13
  14. 14. Department of ChemistryFragment Based Methods•  The FMO2 method •  All monomers converge in the Coulomb field of all other monomers iteratively. •  Dimers converge in the static Coulomb fieldUniversity of Copenhagen, Feb. 12th, 2013Dias 14
  15. 15. Department of ChemistryI want interaction energies and internal energies … FASTUniversity of Copenhagen, Feb. 12th, 2013Dias 15
  16. 16. Department of Chemistry Fragment Based Methods N RI ,J ≤Rcut RI ,J >Rcut E EFMO = ∑ EI0 + ∑ (EIJ − EI0 − EJ0 − EIJ ) + 0 POL ∑ ES POL EIJ +Etot I IJ IJ Monomer SCF in the gas phase Extract multipoles,and dipole polarizabilities PLoS ONE 2012, 7:e41117 University of Copenhagen, Feb. 12th, 2013 Dias 16
  17. 17. Department of Chemistry Fragment Based Methods N RI ,J ≤Rcut RI ,J >Rcut E EFMO = ∑ EI0 + ∑ (EIJ − EI0 − EJ0 − EIJ ) + 0 POL ∑ ES POL EIJ +Etot I IJ IJMany-body polarization Computed classically using induced dipoles for entire system University of Copenhagen, Feb. 12th, 2013 Dias 17
  18. 18. Department of Chemistry Fragment Based Methods - EFMO N RI ,J ≤Rcut RI ,J >Rcut E EFMO = ∑ EI0 + ∑ (EIJ − EI0 − EJ0 − EIJ ) + 0 POL ∑ ES POL EIJ +Etot I IJ IJ Coulomb andNon-Coulomb effects dimer SCF in the gas phase University of Copenhagen, Feb. 12th, 2013 Dias 18
  19. 19. Department of ChemistryFragment Based Methods - EFMO N RI ,J ≤Rcut RI ,J >Rcut E EFMO = ∑ EI0 + ∑ (EIJ − EI0 − EJ0 − EIJ ) + 0 POL ∑ ES POL EIJ +Etot I IJ IJCoulomb effectsComputed usingstatic multipolesUniversity of Copenhagen, Feb. 12th, 2013Dias 19
  20. 20. Department of ChemistryFragment Based Methods - EFMO N RI ,J ≤Rcut E COR = ∑ EICOR + ∑ (EIJ − EICOR − EJ ) +0 COR COR I IJUniversity of Copenhagen, Feb. 12th, 2013Dias 20
  21. 21. Department of ChemistryCovalent Fragmentation - EFMOUniversity of Copenhagen, Feb. 12th, 2013 PLoS ONE 2012, 7:e41117Dias 21
  22. 22. Department of ChemistrySoftware to help setup calculations: FragIt•  Use SMARTS to find places to break bonds PLoS ONE 2012, 7:e44480University of Copenhagen, Feb. 12th, 2013Dias 22
  23. 23. Department of ChemistrySoftware to help setup calculations: FragIt•  Use SMARTS to find places to break bonds Chignolin (10 residues) PLoS ONE 2012, 7:e44480University of Copenhagen, Feb. 12th, 2013Dias 23
  24. 24. Department of Chemistry Fragment Based Methods - EFMO Gradients Trp cage (20 residues) 2 residues/fragment EFMO FMO2Error in energy -4.3 6.4 kcal/molMP2/6-31G(d) gradient 314 409 minutes20 cores(most time spent in MP2 dimers) PLoS ONE 2012, 7:e41117 University of Copenhagen, Feb. 12th, 2013 Dias 24
  25. 25. Department of ChemistryFragment Based Methods - EFMO QM/”MM” E EFMO = EA + EA / F + EF RA,J ≤Rcut RA,J >Rcut E EFMO =E + 0 A ∑ (E 0 AJ 0 0 −E −E −E A J POL AJ )+ ∑ ES POL E AJ + Etot J∈F J∈F Active FrozenUniversity of Copenhagen, Feb. 12th, 2013 arxiv.org/abs/1212.6172Dias 25
  26. 26. Department of Chemistry Proof of concept – chorismate mutaseONIOM: MP2/cc-pVDZ:EFMO-RHF/6-31G(d) 16 Å ΔH ≠ = 18 vs 13 (exp) kcal/mol University of Copenhagen, Feb. 12th, 2013 arxiv.org/abs/1212.6172 Dias 26
  27. 27. Department of ChemistryConclusion and Outlook•  Fast polarizable force field•  Applicable to any systemEFMO/PCMFully flexible EFPs N RI ,J ≤Rcut RI ,J >Rcut E FIEFMO = ∑E + 0 I ∑ 0 0 0 (E − E − E − E IJ I J POL IJ )+ ∑ ES CT XR Disp POL (EIJ + EIJ + EIJ + EIJ ) +Etot I IJ IJCombine MP2:RHF-D optimizationUniversity of Copenhagen, Feb. 12th, 2013Dias 27
  28. 28. Department of ChemistryAcknowledgements•  Jan Jensen•  Dmitri Fedorov, AIST, Japan•  Colleagues at the Department of Chemistry•  Friends and Family•  In silico Rational Engineering of Novel Enzymes (IRENE)University of Copenhagen, Feb. 12th, 2013Dias 28
  29. 29. Department of ChemistryUniversity of Copenhagen, Feb. 12th, 2013Dias 29
  30. 30. Department of Chemistry Thank you for listeningUniversity of Copenhagen, Feb. 12th, 2013Dias 30

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