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Fast approximate methods for global chemical insight: DFTB, COSMO-RS, ReaxFF

Fast approximate methods for global chemical insight: DFTB, COSMO-RS, ReaxFF. Fedor Goumans Scientific Computing & Modelling NV goumans@scm.com. Computational Chemistry: time & length scales. time (s). continuum methods COSMO-RS. (My) 10 12. ……. mesoscale methods. (s) 10 0.

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Fast approximate methods for global chemical insight: DFTB, COSMO-RS, ReaxFF

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  1. Fast approximate methods for global chemical insight: DFTB, COSMO-RS, ReaxFF Fedor GoumansScientific Computing & Modelling NVgoumans@scm.com

  2. Computational Chemistry: time & length scales time (s) continuum methods COSMO-RS (My) 1012 …… mesoscale methods (s) 100 molecular dynamics kinetic Monte Carlo ReaxFF (ms) 10-3 (ms) 10-6 semi-empirical DFTB (ns) 10-9 (ps) 10-12 ab initio DFT (fs) 10-15 length (m) (nm) 10-9 (mm) 10-6 (mm) 10-3 (m) 100 (AU) 109

  3. H S Density-functional Based Tight-Binding (DFTB) Fast and efficient approximated DFT: ideally suited for large systems Molecular System Precomputed pairwise Hamiltonian/Overlap • from DFT calcs. • includes vdW, relativistic • need for each A-B pair • highly transferable • tedious work – automate • QUASINANO project • SCM – Heine group Charges/Energy / Orbitals

  4. DFTB: current capabilities • Second-order or third-order self-consistent charges (SCC, DFTB3) • Molecules, polymers, surfaces, bulk • Geometry and transition state optimization • Frequencies, phonons, (P)DOS, band structure, Mulliken analysis • Molecular Dynamics: velocity Verlet, Scaling or Berendsen thermostat • Fully integrated in GUI (pre-optimization/Hessian re-use ADF/BAND)

  5. DFTB - tensile simulations of MoS2 nanotubes Harmonic behaviour until rupture! Harmonic behaviour until rupture! I. Kaplan-Ashiri, S. R. Cohen, K. Gartsman, R. Rosentsveig, V. Ivanovskaya, T. Heine, G. Seifert, H. D. Wagner, and R. Tenne, Proc. Natl. Acad. Sci. USA 103 (2006), 523-528.

  6. QUASINANO (EU project), DFTB: outlook • Automated ADF + BAND parameter generation for DFTB • Future work (2 years): • Parametrization for large part of periodic table • Properties (reuse ADF code ..) • Hybrid DFT / DFTB method (nontrivial) COF-5 B. Lukose, A. Kuc, T. Heine, Chemistry Eur. J. 2011, 17, 2388-2392; B. Lukose, A. Kuc, J. Frenzel, T. Heine, Beilstein J. Nanotechnology 2010, 1, 60-70. COF Broad applicability depends on (automatic) generation of reliable DFTB parameters for large part of periodic table

  7. Other fast approximate methods with our GUI • MOPAC2009: Stewart’s semi-empirical PM3, PM6, PM6-DH, … • molecules, periodic systems (gamma point only) • 70 atoms parametrized (up to Bi, but no lanthanides) • UFF: Universal Force Field: all elements; molecules & periodic

  8. COSMO-RS

  9. COSMO-RS (COnductor-like Screening Model for Realistic Solvents) • Quantum-based (post-SCF) thermodynamic properties liquids • Original: Dr. Klamt (J. Phys. Chem. A 102 (1998) 5074; book) • ADF: reparametrized by Pye, Ziegler, van Lenthe, Louwen • 216 molecules against 642 exp. data: • vapor p: ~0.2 log, partition coeff.: ~0.35 log, hydration ~0.37 kcal/mol • Instantaneous prediction of thermodynamic properties of mixed liquids: • activity coefficients, solvent free energies • excess energies for mixing GE, HE, TSE • boiling points, solubilities, partition coefficients, vapor-liquid equilibria • pKa • Database of 1892 precalculated molecules, including many solvents • Easy to calculate more compounds with ADF • Database and COSMO-RS GUI included in license

  10. COSMO-RS • Conductor-like Screening Model for Real Solvents • Calculation of the chemical potential • -profile: charge density on COSMO ( = ) surface • pair-wise interaction between molecules • statistical thermodynamics

  11. Solvation energies, activity coefficients, solubility • Water is the solvent • Experimental values taken from: • A. Klamt et al., J. Phys. Chem. A 102 (1998) 5074 • J. Li et al., Analytical Chemistry 65 (1993), 3212 • Wikipedia

  12. pKa values (acid) AH (aq) + H2O (l) → H3O+ (aq) + A- (aq) (base) BH+ (aq) + H2O (l) → H3O+ (aq) + B (aq) Empirical fitting as in [1], different parameters used for ADF COSMO-RS Fitting calculated Δgdiss against experimental pKa (acid) pKa = 0.62 ΔGdiss/(RT ln(10)) + 2.10 (base) pKa = 0.67 ΔGdiss/(RT ln(10)) - 2.00 Experimental values taken from [1] F. Eckert, M. Diedenhofen, A. Klamt, Mol. Phys. 108 (2010) 229

  13. Vapor pressure ternary mixture Methanol, Acetone. Chloroform at 330K

  14. ReaxFF

  15. Engineering challenges…. • Higher efficiency • Lower exhaust • Higher combustion temperature • Need new materials that can sustain higher temperatures and oxidation chemistry Pre-oxidized Al-tube with ethylene/O2/ozone mixture Coal power plant • Higher efficiency • Longer lifetime • Cheaper • Need new, cheap catalyst materials that are resistant to poisoning Ni-particle reacting with propene at T=1500K …require atomistic-scale solutions Fuel cell

  16. ReaxFF Computational expense 1000000 • ReaxFF allows for reactive MD-simulations on systems containing more than 1000 atoms • ReaxFF is 10-50 times slower than non-reactive force fields • Better scaling than QM-methods (NlogN for ReaxFF, N3 (at best) for QM 100000 10000 x 1000,000 1000 Time/iteration (seconds) QM (DFT) 100 ReaxFF 10 1 0.1 0.01 0 100 200 300 400 Nr. of atoms

  17. Failure of the harmonic model C-C bond stretching in Ethane Around the equilibrium bond length Full dissociation curve Energy (kcal/mol) C-C bond length (Å) C-C bond length (Å) • ReaxFF employs a bond length/bond order relationship • All connectivty-dependent-parameters bond-length dependent

  18. ReaxFF in ADF - collaboration van Duin • Improved usability • Geometry builder • Input set up, output visualization • Speed: • Serial speed-ups • parallelized version • removed memory bottlenecks (now 100,000 atoms on laptop) • Combinations with ADF: • Transition State search using ADF’s algorithms • Also geometry optimization, numerical frequencies, .. • Future: QM/MM? Not trivial

  19. ReaxFF integration into graphical user interface Collaboration van Duin group - SCM Integration team: Olivier Visser, Alexei Yakovlev (SCM) - Mike Russo, Kaushik Joshi (Penn State)

  20. ReaxFF: Reactions in large, dynamical systems not currently described by ReaxFF YSZ/Ni/butane interface simulation at T=750K Large part of periodic table covered, including metals Enables dynamics studies of reactions in material science Adri van Duin, Goddard, and coworkers

  21. ReaxFF parameter files • Standard force field parametrizations in ADF2012: • (H/O/N/B) Ammonia Borane • Al-water: (AL/H/O) - unpublished • AuO: (Au/O) • CHO: (C/H/O) Hydrocarbon oxidation • Cu-water: (Cu/H/O) • FeOCH: (Fe/O/C/H) • HE: (C/H/O/N) RDX/High Energy • NaH: (Na/H) • NiCH: (Ni/C/H/O/N/S/F/Pt/Cl) • VOCH: (V/O/C/H) • ZnOH: (Zn/O/H) • Additional standard force fields to follow gradually • Tools to make new parametrization available in the code, BUT currently too hard for non-expert • Semi-automated approach using Genetic Algorithms (ADF2013?)

  22. Aqueous phase reactions and surface chemistry Cu/Zn oxides Zeolite growth Water/TiO2 MD(300K) Si5O15H9+6H2O 5Si(OH)4+OH- With Kim & Kubicki (PSU) With Thuat Trinh (Eindhoven) Partially hydroxyl covered surface ZnO/H2O Pt/Ni fuel cells ReaxFF for water With Raymand & Hermannsson (Uppsala) Dendrimers/metal cations Nafion fuel cell Phosphates/sulfonates Enzymes/ DNA/ organic catalysis Proteins With Ramie & Doren(Delaware) Jahn-Teller distorted Cu(H2O)62+-cluster With Ram Devanathan (PNNL))

  23. Examples of recent parallel ReaxFF simulations Hexane cracking on a Fe/H-ZSM5 catalyst (Fe/O: Aryanpour et al., JPC-A 2010) Cu-metal particle on a ZnO-support with water vapor (Zn/O: Raymand et al., Surf. Sci. 2010) Pyrolysis of an Illinois coal sample (Kamat, Russo, Mathews and van Duin, in print) Noble gas accommodation coefficients on a graphene wafer (Kamat et al., submitted)

  24. Summary • DFT: accurate, static calcs of <1000 atoms • Semi-empirical programs (DFTB/MOPAC) for large approximate calculations of molecules & periodic systems • COSMO-RS for thermodynamic properties fluids/mixtures • ReaxFF for large-scale reactive molecular dynamics • ReaxFF, DFTB limited by parameters • Work in progress to automate • (Advanced MD / QM/MM) • Future: workflow to automate complex job set-ups

  25. Thank you!Questions?http://www.scm.com/News/ResearchHighlightsE-mail: goumans@scm.com

  26. New python tool: PyMD Adaptive QM/MM Metadynamics t=∆ T-region R2 R1 t=2∆ A-region t=N∆ E-region Smooth QMMM transition molecules passing the QM/MM boundary.

  27. DFTB features (April 2011) • DFTB withSelf Consistent Charge (SCC) • London DispersioncorrectionforvdWaalsinteractions • Single Point, GeometryOptimization, Transition State Optimization • VibrationalFrequencies, Molecular Dynamics • non-PeriodicandPeriodic systems, with multiple k-points • Optimization of geometryand/or lattice parameters • Molecular Dynamics with Simple Scalingand Berendsen Thermostats • Support forrestarting in MD simulations • Interfacedwith ADF-GUI (input set up, visualizationresults)

  28. -profiles charge density averaged over rav red curve: water blue curve: methanol green curve: benzene

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