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

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

[email protected]


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


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


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)




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.


• 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.


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


COSMO-RS


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


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


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


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


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


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


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


• 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)


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)


• 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




Thank you!

Questions?

http://www.scm.com/News/ResearchHighlights

E-mail: [email protected]


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


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

Documents

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