Qui ckTi me™ and a
TIFF (Uncompressed) decompressor
are needed to see this pictur e.
Fast approximate methods
for global chemical insight:
DFTB, COSMO-RS, ReaxFF
Fedor Goumans
Scientific Computing & Modelling NV
goumans@scm.com
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
Computational Chemistry: time & length scales
time (s)
continuum methods
COSMO-RS
(My) 1012
……
(s)
mesoscale
methods
100
molecular dynamics
kinetic Monte Carlo
ReaxFF
(ms) 10-3
(ms) 10-6
(ns) 10-9
(ps) 10-12
(fs) 10-15
semi-empirical
DFTB
ab initio
DFT
length (m)
(nm) 10-9 (mm) 10-6 (mm) 10-3 (m) 100
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
(AU) 109
Density-functional Based Tight-Binding (DFTB)
Fast and efficient approximated DFT: ideally suited for large systems
Precomputed pairwise
Hamiltonian/Overlap
Molecular System
H
S
Charges/Energy / Orbitals
Copyright © 2012, SCM.
• from DFT calcs.
• includes vdW, relativistic
• need for each A-B pair
• highly transferable
• tedious work – automate
QUASINANO project
SCM – Heine group
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
Qui ckTi me™ and a
TIFF (Uncompressed) decompressor
are needed to see this pictur e.
DFTB - tensile simulations of MoS2 nanotubes
Harmonic
Harmonic
behaviour
behaviour
until rupture!
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
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
COF
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.
Broad applicability depends on (automatic) generation of reliable
DFTB parameters for large part of periodic table
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)
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•
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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 2012
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
October 2010
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
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
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
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
Engineering challenges….
Coal power plant
- 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
Fuel cell
Pre-oxidized Al-tube with
ethylene/O2/ozone mixture
Ni-particle reacting with propene
at T=1500K
…require atomistic-scale solutions
ReaxFF Computational expense
1000000
Time/iteration (seconds)
100000
10000
x 1000,000
1000
100
QM (DFT)
10
ReaxFF
1
0.1
0.01
0
100
200
300
Nr. of atoms
400
-ReaxFF allows for
reactive MDsimulations on systems
containing more than
1000 atoms
- ReaxFF is 10-50
times slower than nonreactive force fields
- Better scaling than
QM-methods (NlogN
for ReaxFF, N3 (at
best) for QM
Failure of the harmonic model
Energy (kcal/mol)
C-C bond stretching in Ethane
Around the equilibrium bond length
30
Full dissociation curve
200
DFT
15
ReaxFF
DFT
100
ReaxFF
Harmonic
0
1.25
Harmonic
0
1.5
1.75
1
1.5
2
2.5
3
3.5
4
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
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
Collaboration
van Duin group - SCM
Integration team:
Olivier Visser, Alexei
Yakovlev (SCM)
- Mike Russo,
Kaushik Joshi (Penn
State)
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
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
ReaxFF parameter files
• Standard force field parametrizations in ADF2012:
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(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?)
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
Aqueous phase reactions and surface chemistry
MD(300K)
With Kim & Kubicki (PSU)
ZnO/H2O
Partially hydroxyl
covered surface
Water/TiO2
5Si(OH)4+OH-
Si5O15H9+6H2O
Zeolite growth
With Thuat Trinh (Eindhoven)
Cu/Zn oxides
With Raymand & Hermannsson (Uppsala)
ReaxFF for water
Dendrimers/metal
cations
Pt/Ni fuel cells
Nafion fuel cell
Enzymes/
Proteins DNA/
With Ramie & Doren(Delaware) organic
Phosphates/sulfonates
Jahn-Teller distorted
With
Ram
Devanathan (PNNL))
catalysis
Cu(H O) 2+-cluster
Examples of recent parallel ReaxFF simulations
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.
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)
ADF seminar UD, 23 March 2012
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
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
Qui ckTi me™ and a
TIFF (Uncompressed) decompressor
are needed to see this pictur e.
Thank you!
Questions?
http://www.scm.com/News/ResearchHighlights
E-mail: goumans@scm.com
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
New python tool: PyMD
Adaptive QM/MM
Metadynamics
T-region
R2
t=∆
R1
t=2∆
A-region
E-region
t=N∆
Smooth QMMM transition molecules
passing the QM/MM boundary.
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012
DFTB features (April 2011)
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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 2012
-profiles
charge density averaged over rav
red curve: water
blue curve: methanol
green curve: benzene
October 2010
Copyright © 2012, SCM.
ADF seminar UD, 23 March 2012