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Towards Understanding Heterogeneous Processes

I-Feng W. Kuo, Christopher J. Mundy, Matthew J. McGrath, J. Ilja Siepmann, Shawn M. Kathmann, Marcel D. Baer, Douglas J. Tobias, Courtney Stanton, and Ken N. Houk. Towards Understanding Heterogeneous Processes.

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Towards Understanding Heterogeneous Processes

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  1. I-Feng W. Kuo, Christopher J. Mundy, Matthew J. McGrath, J. Ilja Siepmann, Shawn M. Kathmann, Marcel D. Baer, Douglas J. Tobias, Courtney Stanton, and Ken N. Houk Towards Understanding Heterogeneous Processes

  2. Unified approach to understanding heterogeneous systems: The use of first principles simulation techniques as a predictive tool. Ion Interactions Air-Water Interface Surface Water Proteins

  3. Applying First Principles Simulation Technique with tera-scale computing to study complex heterogeneous systems. • First principles molecular dynamics simulation • Solves Newton’s Equation of Motion • Interaction via KS-DFT • Computationally expensive • CPMD (plane-waves) • www.cpmd.org • 1440 CPU’s • 60% parallel efficiency • 0.7 million CPU hours (21 days) • CP2K (plane-waves + Gaussian type orbitals) • cp2k.berlios.de • 96 CPU’s • 15X reduction in computational cost with same computational accuracy Diagram test system 71Å ~ 35Å 216 H2O BLYP and 70Ry 7ps simulated 15Å

  4. First Attempt at Looking at Heterogeneous system: Structure Air/water Interface Marx, Science303, 634 (2004) • Validate NEXAFS and XAFS experiments • Single donor hydrogen bond species • Surface expansion of water • Surface contraction of methanol Kuo and Mundy Science 303, 658 (2004) Kuo et. al. JPC-B 110, 3738 (2006) Wick et. al. JCTC 3, 2002 (2007)

  5. Surface Potential and Polarization at the Air/water Interface • Experiment is limited but progress continues to be made • Theoretical results can vary depending on the precise model for the charge distribution • Electrostatic potential determined by core and electronic charge distribution • We will directly examine the effects of a smeared charge distribution using DFT • 6000 frames (128CPUs for 2 hour) • Surface potential  = -18 mV with • Interfacial electric field of 8.9x107 V/m Kathmann, Kuo, and Mundy submitted.

  6. New insight into cause of high catalytic activity at the liquid-vapor interface of sea-salt particles A new “conventional wisdom” is emerging regarding ions at the liquid-vapor interface • Preferential adsorption of polarizable ions at the liquid/vapor interface • Implications towards heterogeneous chemistry!!! Jungwirth and Tobias, J. Phys. Chem B106, 6361 (2002) Jungwirth and Tobias, J. Phys. Chem. B 105, 10468 (2001) B.Garrett, Science Feb 20 2004: 1146-1147 • Results obtained using polarizable force fields parameterized for bulk!!! • Experiments are difficult to perform and hard to interpret.

  7. Computational prediction of ion concentration: Potential of Mean Force (PMF) of ions through the interface • PMF is a technique to compute the free energy for movements of ions across a domain. • Utilizes umbrella sampling or constraint for sampling. • In practice, can take advantage of parallelization and compute all <Fz> simultaneously. • Accuracy • dz =1Å •  ~ 10ps • Answer question regarding ion concentration at the interface. • Each ion requires 25 independent simulations • 96CPUs (71 Hours per picosecond) Progressive increase in simulation time

  8. Computational prediction of ion concentration:Are F- or ClO4- surface enhanced? ClO4- F- No surface enhancement which confirms experimental findings. Predicts large surface enhancement.

  9. Application of First Principles simulation to enzymology:Orotidine 5'-monophosphate Decarboxylase (ODCase) Most proficient enzyme known (Radzicka and Wolfenden Science 1995, 267, 90) Average proficiency is 1016 M-1 Uncatalyzed reaction half-time is 78 million years Mechanism still unknown Reviews: Miller and Wolfenden Ann. Rev. Biochem. 2002, 71, 847. Houk et al. Top. Curr. Chem. 2004, 238, 1. Lee and Tantillo J. Adv. Phys. Org. Chem. 2003, 38, 183. Need a unified approach to look at all possible reactions on a equal footing.

  10. Ambiguous Results from Previous Studies Small model systems and ab initio calculations O4 protonation favored over O2 protonation Lee and Houk Science 1997, 276, 942 Base protonation mechanisms favored over direct decarboxylation Lundberg et al. J. Mol. Model. 2002, 8, 119 Enzyme system, QM/MM calculations, and direct decarboxylation Using QM regions composed of substrate only or substrate plus one Lys gives predictions within 4 kcal/mol higher than experiment Wu et al. PNAS 2000, 97, 2017 Warshel et al. Biochemistry 2000, 39, 14728 Using larger QM regions composed of substrate plus Asp-Lys-Asp-Lys tetrad gives a predicted barrier 7 kcal/mol higher than experiment Lundberg et al. Top. Curr. Chem. 2004, 238, 79 Raugei et al. JACS 2004, 126, 15730 Empirical force-field methods, e.g. CHARMM High level electronic methods, e.g. density functional theory

  11. Ambiguous Results from Previous Studies cont… Problem solved? Raugei, S.; Cascella, M.; Carloni, P. J. Am. Chem. Soc. 2004, 126, 15730-15737. • CPMD QM/MM, BLYP/plane wave basis set, multiple steering MD ΔG±enzyme = 21 kcal/mol ΔG±sol = 44 kcal/mol ΔΔG±comp = 23 kcal/mol ΔΔG±exp = 22 kcal/mol

  12. ODCase with inhibitor (1DQX) Is a Larger QM Region Better? QM/MM of ODCase with BMP 125 QM atoms 58 QM atoms Snapshot of system after equilibration using different QM subsystem.

  13. OMP Decarboxylation (Solution) 103 QM atoms, 5800 total atoms 128 CPUs 432 hours ΔG±sol = 40 ± 1.6 kcal/mol ΔG±sol,exp = 39 kcal/mol

  14. OMP Decarboxylation 127 QM atoms, 29,000 total atoms 128 CPUs 2000 CPU hours ΔG±enz = 33 ± 1.1 kcal/mol ΔG±enz,exp = 17 kcal/mol

  15. System Size Effects and ΔΔG±enz Small QM subsystem (60 QM atoms) Large QM subsystem (127 QM atoms) Our study:ΔΔG±enz,sm = 24 kcal/mol Carloni study:ΔΔG±enz = 22 kcal/mol Experiment:ΔΔG±enz,exp = 23 kcal/mol Our study:ΔΔG±enz,lg = 7 kcal/mol Solution Reaction Our study: 40 kcal/mol Carloni Study: 44 kcal/mol Experiment: 39 kcal/mol

  16. Future Direction: Use of first principles simulation to explore other hypothesized mechanisms.

  17. Conclusions • Surface Potential and Electric Field • Resolve experimental uncertainly about the magnitude and sign. • Enhancement of Ion Concentration at Interface • First principles simulation techniques can be used to predict ion concentration at the interface. • Verify no surface enhancement of F- • Predicts surface enhancement of ClO4- • Generation of new and better transferable polarizable force field • ODCase • We have shown that the direct decarboxylation of OMP in solution and ODCase is not a viable mechanism as believed. • Use of large QM region is essential for predictive enzyme mechanisms.

  18. Dr. Christopher Mundy Dr. Matthew McGrath Prof. Ilja Siepmann Dr. Jochen Schmidt Dr. Shawn Kathmann Marcel Baer Prof. Douglas J. Tobias Prof. Juerg Hutter Dr. Sutapa Ghosal Dr. Courtney Stanton Prof. Ken Houk CPMD Consortium CP2K Mannschaft N. Goldman L. Fried C. Westbrook S. Futral G. Tomaschke R. Springmeyer D. Dannenberg A. Moody M. Wolfe C. Shereda Everybody at LC Acknowledgements

  19. Generation of new transferable Polarizable force field for interface ClOx- Radial Distribution Function Ion Concentration Using previous first principles PMF calculations as a training data set, we can now parameterized and obtain a highly accurate polarizable force field.

  20. Metadynamics: A method to compute free energy surface for chemical reactions. Laio and Parrinello PNAS2002, 99, 12562 Proton transfer in malonaldehyde is a rare event[GTS~4 kcal/mol] • Self-adaptive sampling: • Need to choose a (set) of collective variables {sa} • distance • coordination number • {sa} integrated via an extended Lagrangian • Addition of history dependent potential V(t,s) = • F(s) = V(t,s) Free energy surface Coord. # GTS >> kT Coord. #

  21. 1.023 1.023 1.293 1.263 1.410 1.432 1.089 1.091 1.400 1.418 1.398 1.397 1.424 1.415 1.404 1.406 1.459 1.471 1.234 1.240 1.264 1.271 ODCase with inhibitor (1DQX)Is a larger QM Region Better? B Intramolecular Distances A C Distance from possible proton source A ~4Å 1.74Å B 1.83Å 1.96Å 2.96Å C ~7Å Systematic difference in intra/intermolecular structure with different QM subsystems.

  22. Substitution of BMP with OMP in ODCase follow by geometry optimization Gray denotes the changes in 3D structure of ODCase BMP colored BLUE and OMP in RED 1. No observable change in tertiary structure near enzymatic pocket with insertion of OMP. 2. OMP orientation in the pocket perfectly overlays that of BMP from crystal structure.

  23. Validation/Calibration of DFT:Phase Equilibra of Liquid Water Liquid/vapor coexistence at 473K We combine the Gibbs Ensemble technique with QUICKSTEP Liquid box Vapor box T1 = T2 V1 + V2 = V m1 = m2 McGrath et. al. Mol. Phys. 104, 3619 (2006) McGrath et. al. JPC-A 110, 640 (2006)

  24. BLYP summary Tc=550K Boiling Point = 350K First Principles Water contains a stable liquid phase. • No difference in VLCC from 32-256 molecules using TIP4P • Boiling Point = 365K

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