Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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Fast approximate methods for global chemical insight:
DFTB, COSMO-RS, ReaxFF
Fedor GoumansScientific Computing & Modelling NV
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
continuum methodsCOSMO-RS
mesoscale methods
molecular dynamicskinetic Monte Carlo
ReaxFF
semi-empiricalDFTB
Computational Chemistry: time & length scales
(fs) 10-15
(ps) 10-12
(ns) 10-9
(s) 10-6
(ms) 10-3
(s) 100
(My) 1012
……
(nm) 10-9
time (s)
(m) 10-6 (mm) 10-3 (m) 100 (AU) 109
length (m)
ab initioDFT
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
Density-functional Based Tight-Binding (DFTB)
Fast and efficient approximated DFT: ideally suited for large systems
Precomputed pairwiseHamiltonian/OverlapMolecular System
H S
Charges/Energy / Orbitals
• from DFT calcs.• includes vdW, relativistic• need for each A-B pair• highly transferable• tedious work – automate
QUASINANO project SCM – Heine group
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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)
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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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.
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
• 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)
QUASINANO (EU project), DFTB: outlook
Broad applicability depends on (automatic) generation of reliable DFTB parameters for large part of periodic table
COF-5
COFB. 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.
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
COSMO-RS
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012October 2010
COSMO-RS
Conductor-like Screening Model for Real Solvents
Calculation of the chemical potential-profile: charge density on COSMO ( = ) surfacepair-wise interaction between moleculesstatistical thermodynamics
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
Solvation energies, activity coefficients, solubility
Water is the solventExperimental values taken from: • A. Klamt et al., J. Phys. Chem. A 102 (1998) 5074• J. Li et al., Analytical Chemistry 65 (1993), 3212• Wikipedia
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
Vapor pressure ternary mixture Methanol, Acetone. Chloroform at 330K
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
ReaxFF
Engineering challenges….
- Higher efficiency- Lower exhaust- Higher combustion temperature - Need new materials that can sustain higher temperatures and oxidation chemistry
- Higher efficiency- Longer lifetime- Cheaper- Need new, cheap catalyst materials that are resistant to poisoning
Coal power plant
Fuel cell
Pre-oxidized Al-tube with ethylene/O2/ozone mixture
…require atomistic-scale solutions
Ni-particle reacting with propene at T=1500K
0.01
0.1
1
10
100
1000
10000
100000
1000000
0 100 200 300 400
ReaxFF
QM (DFT)
Nr. of atoms
Tim
e/it
era
tion
(se
con
ds)
ReaxFF Computational expense
x 1000,000
-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
0
15
30
1.25 1.5 1.75
DFT
ReaxFF
Harmonic
0
100
200
1 1.5 2 2.5 3 3.5 4
DFT
ReaxFF
Harmonic
C-C bond length (Å)
En
erg
y (k
cal/m
ol)
C-C bond stretching in Ethane
Around the equilibrium bond length Full dissociation curve
C-C bond length (Å)-ReaxFF employs a bond length/bond order relationship-All connectivty-dependent-parameters bond-length dependent
Failure of the harmonic model
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
ReaxFF integration into graphical user interface
Integration team:Olivier Visser, Alexei Yakovlev (SCM)- Mike Russo, Kaushik Joshi (Penn State)
Collaboration van Duin group - SCM
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 metalsEnables dynamics studies of reactions in material science
Adri van Duin, Goddard, and coworkers
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
• 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?)
ReaxFF parameter files
Water/TiO2
ReaxFF for water
Cu/Zn oxides
Pt/Ni fuel cells
Phosphates/sulfonates
Nafion fuel cell
Enzymes/DNA/
organic catalysis
Dendrimers/metal cations
Jahn-Teller distorted Cu(H2O)6
2+-cluster
MP2/6-31G(**)ReaxFF
+10.4
+4.1
-3.3
-7.7
MP2/6-31G(**)ReaxFF
+10.4
+4.1
-3.3
-7.7
ZnO/H2OPartially hydroxyl covered surface
With Raymand & Hermannsson (Uppsala)
With Ram Devanathan (PNNL))
With Ramie & Doren(Delaware)
MD(300K)
Aqueous phase reactions and surface chemistry
With Kim & Kubicki (PSU)
Proteins
Zeolite growth5Si(OH)4+OH- Si5O15H9+6H2O
With Thuat Trinh (Eindhoven)
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
Examples of recent parallel ReaxFF simulations
Pyrolysis of an Illinois coal sample (Kamat, Russo, Mathews and van Duin, in print)
Cu-metal particle on a ZnO-support with water vapor (Zn/O: Raymand et al., Surf. Sci. 2010)
Hexane cracking on a Fe/H-ZSM5 catalyst (Fe/O: Aryanpour et al., JPC-A 2010)
Noble gas accommodation coefficients on a graphene wafer (Kamat et al., submitted)
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
• 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
Summary
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
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Thank you!
Questions?
http://www.scm.com/News/ResearchHighlights
E-mail: [email protected]
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
Smooth QMMM transition molecules passing the QM/MM boundary.
T-region
A-regionE-region
R2
R1
New python tool: PyMD
t=∆
t=2∆
t=N∆
MetadynamicsAdaptive QM/MM
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012
DFTB features (April 2011)
-DFTB with Self Consistent Charge (SCC)-London Dispersion correction for vdWaals interactions-Single Point, Geometry Optimization, Transition State Optimization-Vibrational Frequencies, Molecular Dynamics-non-Periodic and Periodic systems, with multiple k-points-Optimization of geometry and/or lattice parameters-Molecular Dynamics with Simple Scaling and Berendsen Thermostats-Support for restarting in MD simulations-Interfaced with ADF-GUI (input set up, visualization results)
Copyright © 2012, SCM. ADF seminar UD, 23 March 2012October 2010
-profiles
charge density averaged over rav
red curve: waterblue curve: methanolgreen curve: benzene