chemistry & materials with the amsterdam modeling suite ... · • adf: powerful molecular dft...
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Fedor Goumans, [email protected] support: [email protected]
Chemistry & Materials with the Amsterdam Modeling Suite:
Polymers
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Polymers with AMS 2019 © SCM 2
Amsterdam Modeling Suite• ADF: powerful molecular DFT
o Spectroscopy: NMR, EPR, VCD, UV, XASo Advanced solvation / environmentso Reactivity, Bonding analysis
• BAND: periodic DFTo (2D) Materials, spectroscopy, analysis
• Interface with and binaries for QE
• DFTB & MOPACfast electronic structure
• ReaxFF: Reactive MDo Dynamics of large complicated systems
• COSMO-RS: fluid thermodynamicso VLE, LLE, logP, solubility
• Integrated GUI: use out of the box
• AMSdriver: complex PES tasks
• PLAMS: python scripting workflows & automation
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Polymers with AMS 2019 © SCM 3
Background: SCM, ADF & AMS• ADF = first DFT code for chemistry (1970s)
Baerends@VU (>’73), Ziegler@Calgary(+) (>’75)
• SCM: Spin-off company 1995
• 20 people (10 senior PhD’s) + 3 EU fellows
• Many academic collaborators / EU networkso ~150 authorso New functionality
• SCM: development, debug, port, optimize, docs & support
articles &patents in materials science with“density functional theory”, Nat. Mat. 4619
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Polymers with AMS 2019 © SCM 4
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Polymers with AMS 2019 © SCM 5
ADF: Molecular DFTStrong & unique points
• All-electron Slaters, H-Og
• Relativity: ZORA (SR, SOC)
• Modern xc functionals
• Spectroscopyo EPR, NMR, IR (VCD), UVVIS, XAS
• Bonding analysis: o Fragment-based approacho ETS-NOCV, QTAIM, MO diagrams, NCI, ....o Activation strain modelo Transfer integrals
• Environmentso Subsystem DFT, DRF, QM/MMNMR calculations locate 13C di-Rh carbene
catalyst intermediate, Science, 342, 351 (2013)
Bonding analysis: Understanding Catalyst-Substrate Interactions Nature Chem. 2, 417 (2010)
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Polymers with AMS 2019 © SCM 6
BAND vs. Plane Wave codes (QE)• Atom centered basis functions, STO or NAO
o Compare cluster with periodico No pseudopotentials, all elementso Core spectroscopy (core holes)o Easy orbital analysis: pDOS, COOP, EDAo Fast for empty (1D, 2D, porous)o xc: SCAN, MN15-L, HSE06, GLLB-sc, D3(BJ), DFT-1/2o Self-consistent NEGF
• True 2D surfaces, 1D polymerso Solvation: COSMO, SM12o 2D electronics (homogeneous E field)o Nanotubes
• Integrated Graphical Interface: o Easy set up & analysiso Switch: ADF, BAND & Quantum Espresso
Polarizing 2D semiconductor (tutorial)
N. Zibouche et al. PCCP (2014)
periodic energy decomposition analysis (tutorial)
L. Pecher and R. TonnerWIREs CMS, (2018)
COOP in perovskites(tutorial)
Goesten & HoffmannJACS (2018)
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Polymers with AMS 2019 © SCM 7
DFTB: ‘fast DFT’ for molecules & periodicApproximated DFT• Nearest neighbor & minimal basis• Tabulated elec & rep. parameters:
o Grimme GFN-xTB (Z = 1-86)o QuasiNaNo & DFTB.org
Capabilities & Features• UV/VIS for molecules (fast!)• MOs, Band structures, DOS• Molecules, 1D polymers, bulk
DFTB & MOPAC + AMS driver • Geometries, frequencies, phonons• Stress tensors (optimize under p)• Advanced MD, PES scans• GCMC, molecule gun
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Polymers with AMS 2019 © SCM 8
ReaxFF: concept• Simulate complex systems at realistic scales
o Atomistic potentials – single atom type (reasonably transferable)o Update charges and bond orders at every step
A.C.T. van Duin et al ,J. Phys. Chem. A 2001 , 105, 9396-9409.
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Polymers with AMS 2019 © SCM 9
ReaxFF: applications
Pd-catalysed CO oxidation GCMC+ReaxFFJ. Chem. Phys., 139 044109 (2013)
Hydrogen embrittlement of steels Phys. Chem. Chem. Phys. 18 761 (2016)
Li battery discharge: J. Electrochem. Soc. 161, E3009 (2014); PCCP, 17, 3383 (2015), tutorial
Crystallization TiO2 nano-particles in waterNano Lett. 14, 1836-1842 (2014)
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Polymers with AMS 2019 © SCM 10
ReaxFF tools in Amsterdam Modeling Suite
GCMC: speed up thermo
fbMC, CVHD, PRD?: speed up kinetics
ChemTraYzer: Automated rates & pathwaysNew: Analyze surface reactions
Molecule gun: depositing molecules on surfaces
CMA-ES ReaxFFforce field
(re)parameterization
bond boostbuild polymers
T-NEMD, local T:heat transport
eReaxFF: include e-
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Polymers with AMS 2019 © SCM 11
Epoxy polymers: structure & properties• Understand & predict how cross-linking effects mechanical properties
o Exp = slow: minutes to hours to reach ~80% cross-linkingo ReaxFF: simulate few ns => accelerate kinetics to get highly xlinked structures
Modulus, yield pointJ. Polym. Sci. B 2018, 56, 255
epoxy + amine
polymer
glass transition Tg
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Polymers with AMS 2019 © SCM 12
Accelerating dynamics with Bond Boost• Track distances; add ‘boost’ potential if within mask
o Sample dynamics with sufficient energy to surmount barrierso Reactions can fail:
§ Steric hindrance§ Unfavorable approach path
• Overcome slow kineticso Get to end resulto No mapping to real time
van Duin et al. J. Phys. Chem. A, 122, 6633 (2018), cf. Miron & Fichthorn JCP 119, 66210 (2003)
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Polymers with AMS 2019 © SCM 13
Properties of cross-linked epoxy polymers• Good predictions: densities & Tg
• Aliphatic amine => lower Tg
Polymer 158, 354 (2018)
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Polymers with AMS 2019 © SCM 14
Properties of cross-linked epoxy polymers• Coefficients of thermal expansion too low
o Reparameterize ReaxFF?
• Modulus: good linear fit (calc = high strain)o bulk stress tensors = faster
§ ReaxFF, DFTB
Polymer 158, 354 (2018)
From Stress-Strain:• Yield point(s)• Strain ratios
Odegard groupJ. Polym. Sci. B, 56, 255-264 (2018)
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Polymers with AMS 2019 © SCM 15
Degradation of polymers in space• Atomic Oxygen bombardment studying low earth orbit conditions• Silica is high initial resilience, Teflon lowest erosion rate
o Good heat transfer properties can help; Kapton can be stabilized with silica.
J. Phys. Chem. A, 2014, (118), 2780
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Polymers with AMS 2019 © SCM 16
Quantum Chemistry & QSPR for quick property predictionsCOSMO-RS/SAC: thermodynamic properties of fluids
COntinuum Solvation MOdel + RS (Klamt), SAC (Sandler)chemical potential => activity coefficients => instantaneous properties
• Solvation & excess energies, pKa• Solubilities, LLE, VLE, boiling points• Optimize mixtures: solubility, LLE• Polymers: Flory-Huggins X
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Polymers with AMS 2019 © SCM 17
COSMO-RS reaction ratesCopolymer composition is solvent-dependent
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Polymers with AMS 2019 © SCM 18
COSMO-RS reaction ratesCopolymer composition is solvent-dependent
Gas phase
Reactants stabilized by solvation
TS stabilized by solvation
New J.Chem., 38, (2014) 170
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Polymers with AMS 2019 © SCM 19
Polymer mixture design with COSMO-RS • COSMO-RS: mixture thermodynamics
§ Liquid-activity coefficient § Fit to experimental data (predictability outside fit) § Pseudo-chemical potential from quantum mechanics (surface charges)
• Existing design approaches focus on property targeting (QSPR)• Mixing => requires free energies, activities
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Polymers with AMS 2019 © SCM 20
Flory-Huggins from COSMO-RS
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Polymers with AMS 2019 © SCM 21
QSPR predictions with sigma-moments
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Polymers with AMS 2019 © SCM 22
1 GUI: build, run & analyze
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Polymers with AMS 2019 © SCM 23
The AMS driver: decouple from Engine• Frequencies (+ analysis) & phonons• Stress & elastic tensors• Scan (multiple) coords, any periodicity • Geometries, TS, IRC• Advanced Molecular Dynamics• (Grand Canonical) Monte Carlo
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Polymers with AMS 2019 © SCM 24
PLAMS: python scripting
Links all modules + various tools→ workflows & screening→ (custom) post-processing→ rapid prototyping
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Polymers with AMS 2019 © SCM 25
ReaxPro: Reactive Process Design as a Multi-scale / Multi-equation Problem
kMC: Zacros, CFD: Catalytic FOAM
EU project 2019-2023 Industrial partners: BASF, JM, DowDuPont, Shell