Workshop GWU, August 12 © SCM
Chemistry & Materials with the ADF modeling suite
workshop GWUScientific Computing & Modelling NVFedor Goumans [email protected] Carstensen [email protected]
Workshop GWU, August 12 © SCM
Outline• Background
• ADF– Spectroscopic properties– Bonding analysis
• BAND: periodic DFT
• DFTB: approximate DFT
• ReaxFF: reactive molecular dynamics
• COSMO-RS/SAC: fluid thermodynamics (logP, pKa, solubility, …)
• GUI demonstration, getting started
Workshop GWU, August 12 © SCM
Amsterdam Density Functional development
• Baerends group VU, Amsterdam (>1973) • Ziegler group, Calgary (>1975)• SCM: Spin-off company (1995)
• Currently 12 people (8 senior PhD’s) + EU fellows
• Many academic collaborators / EU networks
• Development, testing, debugging, optimizing, porting, documentation, support, ..– Implement what users want– New features from academia Tom Ziegler
(1945-2015)
Evert-Jan Baerends
Workshop GWU, August 12 © SCM
ADF modeling suite authors 2014E.J. Baerends, T. Ziegler, J. Autschbach, D. Bashford, A. Bérces, J.A. Berger, F.M. Bickelhaupt, C. Bo, P.L. de Boeij, P.M. Boerrigter, S. Borini, R. E. Bulo, L. Cavallo, D.P. Chong, L. Deng, R.M. Dickson, A. C. T. van Duin, D.E. Ellis, M. van Faassen, L. Fan, T.H. Fischer, C. Fonseca Guerra, M. Franchini, A. Ghysels, A. Giammona, S.J.A. van Gisbergen, M. Gorbani Asl, A.W. Götz, J.A. Groeneveld, O.V. Gritsenko, M. Grüning, S. Gusarov, F.E. Harris, T. Heine, P. van den Hoek, C.R. Jacob, H. Jacobsen, L. Jensen, E.S. Kadantsev, J.W. Kaminski, G. van Kessel, R. Klooster, F. Kootstra, A. Kovalenko, M.V. Krykunov, E. van Lenthe, J.N. Louwen, D.A. McCormack, E. S. McGarrity, A. Michalak, M. Mitoraj, S.M. Morton, J. Neugebauer, V.P. Nicu, L. Noodleman, V. P. Osinga, S. Patchkovskii, M. Pavanello, P.H.T. Philipsen, D. Post, C.C. Pye, W. Ravenek, M. de Reus, J.I. Rodríguez, P. Romaniello, P. Ros, R. Rüger, P.R.T. Schipper, H. van Schoot, G. Schreckenbach, J.S. Seldenthuis, M. Seth, D.G. Skachkov, J.G. Snijders, M. Solà, M. Swart, D. Swerhone, G. te Velde, P. Vernooijs, L. Versluis, L. Visscher, O. Visser, F. Wang, T.A. Wesolowski, E.M. van Wezenbeek, G. Wiesenekker, S.K. Wolff, T.K. Woo, A.L. Yakovlev
Workshop GWU, August 12 © SCM
Dr. Olivier Visser Dr. Erik van Lenthe Dr. Alexei Yakovlev Dr. Pier PhilipsenGUI, general ADF, ZORA, COSMO ADF, ReaxFF, DFTB BAND, periodic DFTB
MSc. Hans van Schoot MSc. Mirko Franchini Dr. Ole Carstensen ReaxFF, MD, GPUs ADF, BAND technical GUI, scripting, ReaxFF
SCM software development staffVac
ancy
Workshop GWU, August 12 © SCM
Dr. Stan van Gisbergen Dr. Fedor Goumans Dr. Sergio Lopez Lopez General Management Business Development Scientific Partner Manager Sales, Legal, Signatures Marketing, Technical Sales EU projects, collaborations
Mrs. Frieda Vansina Mrs. Kitty Kleinlein Office Manager Office ManagerLicense files, user interactions Bookkeeping, special projects
SCM staff – office / management / business
Workshop GWU, August 12 © SCM
ADF – molecular DFT
Workshop GWU, August 12 © SCM
ADF: strong points• User-friendly
– Easy install, integrated GUI, great support
• Accurate & Efficient– Slater orbitals, all-electron, all elements– heavy elements & transition metals: relativistic effects (ZORA)
• Spectroscopy– Many properties: NMR, IR, Raman, UV/Vis, X-Ray, EPR, (V)CD, ROA, ….– Advanced environment effects: FDE, RISM, (QM/MM – FlexMD)
• Chemical analysis– Energy decomposition, ETS-NOCV, charges, density properties, …
• Active developers worldwide– latest functionals, newest developments, user input
Workshop GWU, August 12 © SCM
User-friendly
"The support at SCM is truly top notch." Dr. K. Skinner, Top-10 US chemical company
"... I was very impressed by the quality of the support and their efficiency..." Mr. R. David, Director HPC, University of Strasbourg
Out-of-the-box parallel binariesMac, Windows, Linux/Unix
Integrated GUI for all modulesExpert support team
Workshop GWU, August 12 © SCM
ADFJobsJob type: double click to open input
Queue name
Job name
New input/Analyze output
Job status
The Graphical User Interface: key to usability
Workshop GWU, August 12 © SCM
Switch between codes Calculation options & details
Search
Molecule & periodic system building tools
ADFInput
The Graphical User Interface: key to usability
Workshop GWU, August 12 © SCM
Properties
The Graphical User Interface: key to usability
Workshop GWU, August 12 © SCM
Many Spectroscopic Properties• IR frequencies and intensities, VCD
–analytical and numerical• Time-Dependent DFT (+gradients and vibronic effects)
–Closed or open shell, spin-orbit coupled (also perturbatively)–Frequency dependent (hyper-) polarizabilities (NLO)–UV/Vis, X-ray absorption (NEXAFS/XANES)– (resonance) Raman, SE(H)RS, V(R)ROA –Circular dichroism (CD), optical rotation (ORD)–Core excitations, state-selected excitations–Lifetime effects, dispersion coefficients
• NMR – chemical shifts, spin-spin couplings, finite nucleus, paramagnetic, hybrids, SOC
• ESR–G-tensor, hyperfine interaction, D-tensor (SO part) – MCD
• Nuclear-quadrupole interaction (EFG: Q-tensors, NRVS)
Workshop GWU, August 12 © SCM
Insights in dinuclear metalloradical: VIS/NIR, EPR
E. F. van der Eide, P. Yang, E. D. Walter, T. Liu, and R. M. Bullock, Angew. Chem. Int. Ed. 51, 8361 (2012)
EPR
Workshop GWU, August 12 © SCM
Accurate NMR: all-electron, STOs, and ZORA
L. A. Truflandier, E. Brendler, J. Wagler, J. Autschbach, 29Si DFT/NMR Observation of Spin-Orbit Effect in Metallasilatrane Sheds Some Light on the Strength of the Metal→Silicon Interaction Alkyl Complexes Angew. Chem. Int. Ed. 50, 255 (2011)
29Si
- Heavy Atom effect on Light Atom Pt→Si
- Only Spin-Orbit Couplinggets NMR spectrum right
- NBO: dative, not covalent
Workshop GWU, August 12 © SCM
129Xe NMR: very sensitive probe
Bagno, Saielli (et al.) Chem. Eur. J. 18, 7341-7345 (2012); PNAS 109, 12393-12397 (2012)
Very strong deshielding by cryptophaneΔδobs = 277 ppm, Δδcalc = 281 ppm
1st spin-spin coupling via vdWJXe-H = -2.7 ± 0.6 Hz, calc. = -3.2 Hz
Workshop GWU, August 12 © SCM
Recent pNMR paper: Direct Detection of 17O in Gd(DOTA)] by NMR Spectroscopy, Chem. Eur. J. 21, 1955-1960 (2015)
Workshop GWU, August 12 © SCM
∆E = ∆Eprep + ∆Eint
∆Velstat + ∆EPauli + ∆Eoi
Analysis: Bond energy decomposition
Rev. Comput. Chem. 2000, 15, 1
Transition states/reaction pathways - activation strain theory (Bickelhaupt)
Extension: ETS-NOCV – orbital interactions + deformation densityM. Mitoraj, A. Michalak and T. Ziegler, J. Chem. Theor. Comput. 5, 962 (2009)
Periodic extension (Raupach, Tonner): molecule-surface interactions
Workshop GWU, August 12 © SCM
ETS-NOCV analysis of bonding interactionsAdenine-Thymine
kcal/mol,(BP86/TZ2P)
A-T
Etotal-exp. -12.1
Etotal -other theor. -13.2
Etotal -13.0
Eorb -22.0
EPauli 38.7
Eprep 2.1
Eelstat -31.9Eorb=-22.0
R. Kurczab, M. P. Mitoraj, A. Michalak,T. Ziegler
J. Phys. Chem. A,2010, 114, 8581.
Ns*(H-N)Os*(H-N)
See ETS-NOCV Webinar (Mitoraj)
Related: L. Guillaumes, S. Simon, and C. Fonseca Guerra, The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine–Thymine (AT) Base Pairs and Their Mimics, Chemistry Open, 4, 318-327 (2015)
Workshop GWU, August 12 © SCM
Modeling Organic Electronics with ADF
1) OLEDs: phosphorescence2) Charge mobility (e.g. OFETs)3) PVs/DSSC: singlet fission, excitation, e- injection, regenerationpublished papers & unpublished calcs by Mr. Mori, Ryoka Inc.
http://www.scm.com/OrganicElectronics
Workshop GWU, August 12 © SCM
Hartmut YersinHartmut YersinHartmut Yersin
Y. Suzuri et al., Sci. Technol. Adv. Mater. 15 (2014) 054202. doi:10.1088/1468-6996/15/5/054202
Organic Light-Emitting Diodes
Challenges:• Optimize triplet phosphorescence rate• Minimize triplet-triplet annihilation and triplet-polaron quenching• Optimize properties of host material (higher T energy)• Optimize mobility in electron / hole transport layers• Optimize out-coupling
Workshop GWU, August 12 © SCM
Phosphorescent OLED emitters: SOC-TDDFT with solvation compares well with Expt.
K. Mori, T. P. M. Goumans, E. van Lenthe, F. Wang, Phys. Chem. Chem. Phys. 16, 14523 (2014)
Workshop GWU, August 12 © SCM
Intersystem crossing through spin-orbit coupling in Os(II) complexes
Elise Yu-Tzu Li*, Tzung-Ying Jiang, Yun Chi and Pi-Tai Chou*. Semi-Quantitative Assessment of Intersystem Crossing Rate: An Extension of El-Sayed Rule to the Emissive Transition Metal Complexes. Phys. Chem. Chem. Phys. 16, 26184-26192 (2014)
lexc-dependent quantum yieldSOCME negligible for S1-Tn
ISC from higher Sn states
El-Sayed for organometallics: SOC is largest when:• both S (1dπ*) and T (3d’π*) are MLCT• different d-orbitals are involved (d ≠ d’).
Workshop GWU, August 12 © SCM
Vibronic fine structure OLED phosphor Pt complex: vibrational progression from T1 → S0 emission
Courtesy of Mr. Kento Mori, Ryoka, unpublished results
unpublished calcs by Mr. Mori, Ryoka Inc. on TSUBAME2.0, JACI
Workshop GWU, August 12 © SCM
h+
Methods to calculate charge mobilities • Hopping transport:
– Charge transfer integrals + other elements, directly printed– Electronic couplings from frozen-density embedding
• Band transport: effective mass tensors in BAND
• Non-equilibrium Green’s Function (NEGF)– transmission probabilities for single-molecule junctions– quick calculation: wide-band limit– also in BAND (periodic structures) and in DFTB (large systems) Q
Workshop GWU, August 12 © SCM
Hole / electron mobilities• Ordered crystals (low T) => band-like transport
• Amorphous materials: incoherent hopping
• Accoustic deformation potential
1 me
kk
m
k2
21 1
ii
ii k
kP
mc: the effective mass along the direction of transportmd: the density of states mass, (ma mb)1/2
ac: the acoustic deformation potential, V dEvbm/dVB: the elastic modulusLeff: the length of the p-bonded core of the molecule
dcBac
eff
mmTkBLe
2
3
Workshop GWU, August 12 © SCM
Effective transfer integral Jeff = electronic coupling V
• Definition of fragments • Matrix elements from ADF
C2HOMOks
C1HOMORP hJ
C2HOMO
C1HOMORP S
C1HOMOks
C1HOMORR hH
C2HOMOks
C2HOMOPP hH
extract dimer
Fragment C1
Fragment C2
Molecular crystal of pentacene
(a) “transfer integral”
(b) spatial overlap
(c) site energy
2RP
PPRRRPRP
12/
SHHSJV
orthogonalization
Workshop GWU, August 12 © SCM
Anisotropic hole mobilities in pentacene
S.-H. Wen et al., J. Phys. Chem. B 113, 8813 (2009)
Anisotropic mobility:
Workshop GWU, August 12 © SCM
Electronic couplings + environment with FDE:charge transfer, exciton, charge separation
Excitons: J. Chem. Phys. 138, 034104 (2013) Long range charge separation: J. Chem. Phys. 140, 164103 (2014) Charge transfer: J. Chem. Theory Comput. 10, 2546−2556 (2014)
Linear scaling, environment response, constrain charge/excitation/spin, ...
CDFT in trunk, to be extended to excited states (similar to CV-DFT)
Workshop GWU, August 12 © SCM
Exciton couplings with frozen-density embedding
C. König et al., Direct determination of exciton couplings from subsystem time-dependent density-functional theory within the Tamm-Dancoff approximation, J. Chem. Phys. 138, 034104 (2013).
C. König and J. Neugebauer, Exciton Coupling Mechanisms Analyzed with Subsystem TDDFT: Direct vs. Pseudo Exchange Effects, J. Phys. Chem. B 117, 3480 (2013).
Under development in DFTB: FDE-TDDFBT (Hernandez, Visser)
Workshop GWU, August 12 © SCM
Mechanism of DSSCs N3: Most typical dye
Three steps – all treated with ADF:1. Photoexcitation of dye
2. Electron injection from dye to TiO2
3. Dye regeneration
Workshop GWU, August 12 © SCM
Spin-orbit coupling increases dye efficiency
SOC-TDDFT: Incident photon to current efficiency (IPCE) of Ru sensitizer DX1 increased due to spectral broadening because of SOC
S. Fantacci, E. Ronca, and F. de Angelis, Impact of Spin–Orbit Coupling on Photocurrent Generation in Ruthenium Dye-Sensitized Solar Cells, J. Phys. Chem. Lett., 5, 375-380 (2014)
Workshop GWU, August 12 © SCM
Spin-orbit coupling increases dye efficiency
SOC indispensible to describe low-energy absorption bands of Os dyes
E. Ronca, F. de Angelis, and S. Fantacci, TDDFT Modeling of Spin-Orbit Coupling in Ru and Os Solar Cell Sensitizers, J. Phys. Chem. C, just accepted
[Os(dcbpy)2(SCN)2]4-
expSR-TDDFT
SOC-TDDFT
Workshop GWU, August 12 © SCM
Rational design of dyes for p-type DSSCLight-harvesting efficiency = 1 - 10-f
Charge-separation efficiency => increase hole-e- separation
Hole-injection efficiency, Koopman’s approximation:ERP = EHOMO(dye) - E(VB)(electrode)
J. Wang et al. J. Phys. Chem. C 117, 2245−2251 (2013)
Workshop GWU, August 12 © SCM
Rational design of dyes for p-type DSSC
J. Phys. Chem. C 117, 2245−2251 (2013)
Large separation e- - electrode
Alkyne-spaced-ligands (4,6) also have high f => high Light Harvesting EfficiencyHole-injection efficiency large for all ligands
Workshop GWU, August 12 © SCM
Other modules in the ADF modeling Suite
• Easy to learn / install:– Same GUI– Same binary– Re-use results
• BAND: Periodic DFT• DFTB: approximate DFT• ReaxFF: reactive MD• COSMO-RS: liquid properties
Workshop GWU, August 12 © SCM
BAND – periodic DFT
Workshop GWU, August 12 © SCM
BAND geometries, 1-, 2, and 3-dimensional
October 2010
N3 on TiO2 - surface
Solid - PyPySPyPy – OLED material - 584 atoms in unit cell
Nanotube- chain
Zeolite - solid
Workshop GWU, August 12 © SCM
BAND vs. Plane Wave codes• Atom centered basis functions, STO or NAO
– Compare cluster with periodic– No pseudopotentials, core spectrosopy– Easy (orbital) analysis– Fast for empty (1D, 2D, porous), slow for dense metallic
• True 2D surfaces:– No artifacts from 3D repetition (dipole across surface)– Continuum solvation above surface (COSMO, SM12…)– Homogeneous electric field (no sawtooth potential)– (2D-TDDFT – work in progress)
Workshop GWU, August 12 © SCM
Relativity makes your car start
R. Ahuja, A. Blomqvist, P. Larsson, P. Pyykkö, and P. Zaleski-Ejgierd, Phys. Rev. Lett. 106, 018301 (2011)
- Total and partial density of states (DOS) of lead in Lead (IV) oxide
- Strong relativistic shift inboth occupied and unoccupied Pb 6s states.
- Without relativity, 12V battery would be 2.4V!
Orange = lead 6s states, Green = lead 6p states.NR = nonrelativistic, SR = scalar relativistic, SOC = 2c spin orbit coupling
SOC
Workshop GWU, August 12 © SCM
Closing 2D band gaps in MoWSeS monolayers
3 eV/Å
Electron transport in MoWSeS monolayers in the presence of an external electric field, Phys. Chem. Chem. Phys. (2014)
Workshop GWU, August 12 © SCM
DFT-D3 XC functionals in ADF&BAND
S.Grimme, J. Antony, S. Ehrlich, and H. Krieg: J. Chem. Phys. 132, 154104 (2010).
- Less empirical than earlier DFT-D-
- Asymptotically correct
- Available for elements Z = 1-94
- Dispersion coefficients and cutoff radii computed explicitly
- Dispersion coefficients independent of connectivity
- Similar or better accuracy for light elements, better for heavy ones
Workshop GWU, August 12 © SCM
CH4 and H2 dissociation on Ni/γ-Al2O3
• Dissociation at interface preferred: polarization• Aluminum acts as electron donor
Li, Croiset, Ricardez-Sandoval, J. Phys. Chem. C 2013, 117, 16907
Workshop GWU, August 12 © SCM
Visualization ELF• Electron Localization Function
CO on Cu(100)
Workshop GWU, August 12 © SCM
STM visualization with/without bias• STM images (Tersoff-Hamann): LDOS
bias = 0.1bias = 0 Pt Ge(100)
Workshop GWU, August 12 © SCM
Smooth band structure with interpolation points
Workshop GWU, August 12 © SCM
Kohn-Sham gap ≠ fundamental gap => DFT underestimates band gap- underlying problem: integer derivative discontinuity in vxc
- Egap = I – A + Δxc
Possible ‘solutions’- many-body perturbation (GW) - (screened) hybrids- LDA/GGA + U (localize d, f electrons in TMO)- OEP-like exchange:
- TB-mBJ (fitted to band gaps)- GLLB-sc (includes explicit Δxc)
Fixing the band gap ‘problem’ in DFT
Workshop GWU, August 12 © SCM
Accurate Band Gaps of Semiconductors and Insulators with a Semilocal Exchange-Correlation Potential Phys. Rev. Lett. 102, 226401
(2009).
Tran & Blaha’s modified Becke-Johnson (TB-mBJ)
Workshop GWU, August 12 © SCM
Kohn-Sham potential with discontinuity for band gap materials M. Kuisma, J. Ojanen, J. Enkovaara, & T. T. Rantala Phys. Rev. B 82, 115106 (2010)
GLLB-sc: good band gaps for the ‘right reason’?
GLLB-sc can also be applied to 2D, 1D
Workshop GWU, August 12 © SCM
PBE 1.898GLLB-sc 3.201 (Δxc = 0.92)
TB-mBJ 3.296
Non-relativistic:TB-mBJ/NR 3.494GLLB-sc/NR 3.487
Smaller basis:GLLB-sc/TZP 3.253
Exp: 3.2 eV
Fixing the GaN band gap with model potentials
(SR-TZ2P-AE, k=5 (75 k-points), acc=5)
Experimental gap
Workshop GWU, August 12 © SCM
Approximate Quantum-based methods
51
DFTB ReaxFF
COSMO-RS
Workshop GWU, August 12 © SCM
Density-functional Based Tight-Binding (DFTB)Fast, approximate DFT => ideal for large systems• dynamics (limited to a few elements)• electronic properties
Workshop GWU, August 12 © SCM
DFTB: current capabilities• Second-order or third-order self-consistent charges (SCC, DFTB3)• Molecules, polymers, surfaces, bulk• Geometry and transition state optimization• IR, UV/VIS, 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)
Workshop GWU, August 12 © SCM
Time-dependent DFTB: excitation of a protein
Rüger, R., van Lenthe, E., Lu, Y., Frenzel, J., Heine, T. and Visscher, L., Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding, J. Chem. Theory Comput. 11, 157−167 (2015)
Workshop GWU, August 12 © SCM
DFTB EU projects: Propagate, MoWSeS• PROPAGATE:
– 3 PhD students Bremen-VU-SCM– MD for ground & excited states– QM/MM, QM/QM’ development– Excited state gradients (FCFs)
• MoWSeS: multi-partner ITN, 2 post-docs @ SCM– 2D systems: charge transport & optical properties
S1 (v)→S0 (v’)
Workshop GWU, August 12 © SCM
Semi-automated electronic DFTB parameters
SCM & Jacobs U, J. Chem. Theory Comput. 9, 4006−4017 (2013)
Repulsive parameters in progress…
GeSi (zinc blende)- DFT (PBE/TZP)●-DFTB
Workshop GWU, August 12 © SCM
Repulsive DFTB parameters (single-atom exp.)
Oliveira et al., JCTC, submittedMore repulsive parameters in progress…
Workshop GWU, August 12 © SCM
Other fast approximate methods with our GUI• MOPAC: Stewart’s semi-empirical AM1, PM3, PM6, PM6-DH, …
• molecules, periodic systems (gamma point only)• 70 atoms parametrized (up to Bi, lanthanides with ‘Sparkles’)• MOPAC2012: PM7 (more accurate, esp. for solids)
• UFF: Universal Force Field: all elements; molecules & periodic
Workshop GWU, August 12 © SCM
ReaxFF
Workshop GWU, August 12 © SCM
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 plantPre-oxidized Al-tube with ethylene/O2/ozone mixture
…require atomistic-scale solutions
Ni-particle reacting with propene at T=1500KFuel cell
Workshop GWU, August 12 © SCM
Force field methods
©2005 Markus Buehler, MIT
b
- Empirical, we need to derive values for the force field parameters (intuition, compare to experiment, compare to QM)
- MUCH faster than QM; can be applied to bigger systems
Workshop GWU, August 12 © SCM
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)
Ene
rgy
(kca
l/mol
)
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
Workshop GWU, August 12 © SCM
ReaxFF Computational expense
0.01
0.1
1
10
100
1000
10000
100000
1000000
0 100 200 300 400
ReaxFF
QM (DFT)
Nr. of atoms
Tim
e/ite
ratio
n (s
econ
ds)
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 most QM-methods (NlogN for ReaxFF, N3 or worse for many QM)
- (linear scaling for DFT, too)
Workshop GWU, August 12 © SCM
ReaxFF integration into ADF with GUI
Integration team:Olivier Visser, Alexei Yakovlev (SCM)- Mike Russo, Kaushik Joshi (Penn State)
Collaboration van Duin group – SCM• Serial speed-ups• Parallelization• Remove bottle-
necks
Workshop GWU, August 12 © SCM
Examples of parallel ADF/ReaxFF simulations
Pyrolysis of an Illinois coal sample (Combustion & Flame 2012)
Coal combustion on MoNi slab (Vasenkov et al., J. Appl Phys. 2012)
Hexane cracking on a Fe/H-ZSM5 catalyst (Fe/O: Aryanpour et al., JPC-A 2010)
Water onTiO2 surfaces(J. Phys. Chem. C 2013)
Workshop GWU, August 12 © SCM
TiO2 nanoparticle aggregation
Temperature- 1100KBox size- 125 Å x 325 Å x 125 ÅNumber of atoms- 10904Number of Water molecules- 1800ADF/ReaxFF
Time=0 ns
NVT simulation at 1100KNanoparticles and water molecules are placed randomly, no bias or restraints
Nano Lett. 14, 1836−1842 (2014)
Workshop GWU, August 12 © SCM
Anatase (112) to Anatase (112)
Time=93.75 psTime=125 ps
Time = 187.5ps
Time=250 ps
Workshop GWU, August 12 © SCM
Teflon coating reduces Li-S battery electrolyte decomposition
M. M. Islam, V. S. Bryantsev, and A. C. T. van Duin, ReaxFF Reactive Force Field Simulations on the Influence of Teflon on Electrolyte Decomposition during Li/SWCNT Anode Discharge in Lithium-Sulfur Batteries, J. Electrochem. Soc. 161, E3009-E3014 (2014).
Teflon coating acts as buffer, reducing thermal electrolyte decomposition
Temperature profile at 10ps after discharge from Li-SWCNT electrode(blue 60 K, red >1000 K).
Workshop GWU, August 12 © SCM
ReaxFF: Reactions in large, dynamical systems
Large part of periodic table covered, including metalsEnables dynamics studies of reactions in material science & biochemistry
Adri van Duin, Goddard, and coworkers (expanding network)Work in progress: semi-automated optimization (genetic algorithms, MMC)RxFF_consulting: spin-off Adri
not currently described by ReaxFF
Workshop GWU, August 12 © SCM
Semi-automatic parametrization: MMC-SA
E. Iype, M. Hutter, A. P. J. Jansen, S. V. Nedea, C. C. M. Rindt, J. Comp. Chem. 34, 1143–1154 (2013)
Caveat: training set is important!
Workshop GWU, August 12 © SCM
COSMO-RS
Workshop GWU, August 12 © SCM
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
• solubilities, partition coefficients (log P), VLE, LLE, boiling points• pKa
• Database of 1892 precalculated molecules, including many solvents• Easy to calculate more compounds with ADF• Database and COSMO-RS GUI included in license • Also implemented COSMO-SAC (Sandler) and COSMO-SAC-3D (Delft,
DSM, to be published)
Workshop GWU, August 12 © SCM
COSMO-RSConductor-like Screening Model for Real Solvents
Calculation of the chemical potentials-profile: charge density on COSMO ( = ) surfacepair-wise interaction between moleculesstatistical thermodynamics
Workshop GWU, August 12 © SCM
s-profiles
charge density averaged over rav
red curve: waterblue curve: methanolgreen curve: benzene
Workshop GWU, August 12 © SCM
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
Workshop GWU, August 12 © SCM
Partition coefficients (log P)log PA/B = log {[solute]A/[solute]B}
Experimental values taken from: A. Klamt et al., J. Phys. Chem. A 102 (1998) 5074
Octanol/water Hexane, Benzene, Ethoxyethane/water
Workshop GWU, August 12 © SCM
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-RSFitting 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
Workshop GWU, August 12 © SCM
Vapor pressure ternary mixture Methanol, Acetone. Chloroform at 330K
VLE data can be much improved by exp. Antoine parameters (DIPPR)
Workshop GWU, August 12 © SCM
COSMO-RS: Gas solubility in ionic liquids
Z. Lei, C. Dai, and B. Chen, Gas Solubility in Ionic Liquids, Chem. Rev., 114, 1289−1326 (2014).
• Prediction beyond parametrization (opposed to UNIFAC)
• Works well for SO2 solubilities• Improvements needed for CO2
Workshop GWU, August 12 © SCM
• ADF & BAND: all-electron, relativistic, spectroscopy, analysis• BAND unique: Proper 2D: COSMO, E-field
• Approximate Quantum-based methods:• DFTB: larger systems, ReaxFF: reactive molecular dynamics
limited by parameters - work in progress to automate further development of analysis tools and integration into suite• COSMO-RS/SAC: VLE, LLE, logP, …
Summary
Workshop GWU, August 12 © SCM
• Download binary (www.scm.com/Downloads/2014)user name: u17253 password: 73!Yp76a• Install • Run ADFJobs, enter password details to get license
Suggested exercises:• www.scm.com/Workshops/GWUWorkshop.html• Feel free to try out your own examples and ask usSupport after today: [email protected]
Try out ADF on Crunchyard (cloud)? email [email protected] to enter 2000-h prize draw
Getting started