car-parrinello method and applications moumita saharay jawaharlal nehru center for advanced...
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Car-Parrinello Method and Car-Parrinello Method and ApplicationsApplications
Moumita SaharayJawaharlal Nehru Center for Advanced Scientific Research,
Chemistry and Physics of Materials Unit,
Bangalore.
Outline
Difference between MD and ab initio MDWhy to use ab initio MD ?Born-Oppenheimer Molecular DynamicsCar-Parrinello Molecular DynamicsApplications of CPMDDisadvantages of CPMDOther methodsConclusions
DFT, MD, and CPMD Properties of liquids/fluids depend a lot on configurational entropy
MD with improved empirical potentials
DFT calculation of a frozen liquid configuration
Configurational Entropy part of the free energy will be missing in that case.
Ab initio MD offers a path that mixes the goodness of both MD and of DFT
AIMD is expensive.
Molecular simulations Classical MD
Hardwired potential
No electronic degrees of freedom
No chemical reaction
Accessible length scale ~100 Å
Accessible time scale ~ 10 ns
Ab initio MDOn-the-fly potential
Electronic degrees of freedom
Formation and breaking of bonds
Accessible length scale ~ 20 Å
Accessible time scale ~ 10 ps
Livermore’s Nova Laser Sandia National Laboratories Z accelerators
A short intense shock caused the hydrogen to form a hot plasma and become a conducting metal
The experiments found different compressibilities which could affect the equation of state of hydrogen and its isotope
Quantum simulations could give the proper reasons for different results
Conditions of the Nova and Z flyer were different : Time scales of the pulse were different
Why ab Initio MD ?Chemical processes
Poorly known inter atomic interactions e.g. at high Pressure and/or Temperature
Properties depending explicitly on electronic states ; IR spectra, Raman scattering, and NMR chemical shift
Bonding properties of complex systems
Born-Oppenheimer approximation Electronic motion and nuclear motion can be
separated due to huge difference in mass Different time scale for electronic and ionic
motion Fast electrons have enough time to readjust
and follow the slow ions
Born-Oppenheimer MD Electron quantum adiabatic evolution and classical ionic dynamicsEffective Hamiltonian :
HoI → Ionic k.e. and ion-ion interaction
2nd term → Free energy of an inhomogeneous electron gas in the presence of fixed ions at positions (RI)
Electronic ground state – electron density ρ(r) – F({RI}) min
Born-Oppenheimer Potential Energy Surface
Born-Oppenheimer MDForces on the ions due to electrons in ground state
Ionic Potential Energy
Ψi (r) one particle electron wave function1st → Electronic k.e. ; 2nd → Electrostatic Hartree term
3rd → integral of LDA exchange and correlation energy density εxc
4th → Electron-Ion pseudopotential interaction ; 5th → Ion-Ion interaction
Born-Oppenheimer MD
Electronic density ; fi → occupation number
EeI → Electron-Ion coupling term includes local and nonlocal components
Kohn-Sham Hamiltonian operator
Time evolution of electronic variables
Time dependence of Hks ← slow ionic evolution given by Newton’s equations
Uks = minimum of Eks w.r.t. ψi-
Merits and Demerits of BOMDAdvantages Disadvantages
True electronic Adiabatic Evolution on the BO surface
Need to solve the self- consistent electronic-structure problem at each time step
Minimization algorithms require ~ 10 iterations to converge to the BO forces
Poorly converged electronic minimization → damping of the ionic motion
Computationally demanding procedure
Car-Parrinello MDCP Lagrangian
Ψi → classical fields μ → mass like parameter [1 Hartree x 1 atu 2 ]
4th → orthonormality of the wavefunctions
Constraints on the KS orbitals are holonomic No dissipation
Choice of μFolkmar Bornemann and Christof Schutte demonstrate
If the gap between occupied and unoccupied states = 0
If the gap between occupied and unoccupied states = 0
(Insulators and semiconductors)
(Metals)
Fictitious kinetic energy of the electrons grow without control
Use electronic thermostat
μ must be small → small integration time step
μ ~ 400 au , time step ~ 0.096x 10-15 s
CP Equations of motionEquations of motion from Lcp :
Ionic time evolution
Electronic time evolution
Constraint equation
Boundary conditions
Hellmann-Feynman TheoremIf Ψ is an exact eigenfunction of a Hamiltonian H, and E is the corresponding energy eigenvalue :
λ is any parameter occurring in H
For an approximate wavefunction Ψ
For an exact Ψ
I
I
REF
Force on Ions
GI → constraint force
+ GI
When, ψi is an eigenfunction
Force on the ions due to electronic configuration, when electronic wavefunction is an eigen function is zero
Constants of motion
Vibrational density of states of electronic degrees of freedom
Comparison with the highest frequency phonon mode of nuclear subsystem
Merits and Demerits of CPMD Advantages
Fast dynamics compared to BOMD
No need to perform the quenching of electronic wave function at each time step
DisadvantagesDynamics is different from the adiabatic evolution on BO surface
Forces on ions are different from the BO forces
Ground state
Ψi ≡ Ψksi → good agreement
with the BOMD
References R. Car and M. Parrinello; Phys. Rev. Lett. 55 (22), 2471
(1985) D. Marx, J. Hutter; http://www.fz-juelich.de/nic-series/ F. Buda et. al; Phys. Rev. A 44 (10), 6334 (1991) D.K. Remler, P.A. Madden; Mol. Phys. 70 (6), 921 (1990) B.M. Deb; Rev. Mod. Phys. 45 (1), 22 (1973) M. Parrinello; Comp. Chemistry 22, (2000) M.C. Payne et. al; Rev. Mod. Phys. 64 (4), 1045 (1992)
CPMDCPMD code is available at http://www.cpmd.org
Code developers : Michele Parrinello, Jurg Hutter, D. Marx, P. Focher, M. Tuckerman, W. Andreoni, A. Curioni, E. Fois, U. Roethlisberger, P. Giannozzi, T. Deutsch, A. Alavi, D. Sebastiani, A. Laio, J. VandeVondele, A. Seitsonen, S. Billeter and others
PWscf (Plane Wave Self Consistent field) http://www.pwscf.org
PINY-MD http://homepages.nyu.edu/~mt33/PINY_MD/PINY.html
Autoionization in Liquid Water
Chandler, Parrinello et. al Science 2001, 291, 2121
pH determination of water by CPMDIntact water molecules dissociate → OH- + H3O+ Rare event ~ 10 hours >>>> fs
Transition state separation between the charges ~ 6Å
Proposed theory → Autoionization occurs due to specific solvent structure and hydrogen bond pattern at transition state
Diffusion of ions from this transition state
Role of solvent structure in autoionization Diffusion of ions
Microsecond motion of a system as it crosses transition state can not be resolved experimentally
pH = - log [H+]
Nature of proton transfer in waterGrotthuss’s idea : Proton has very high mobility in liquid water which is due to the rearrangement of bonds through a long chain of water molecule; effective motion of proton than the real movement
+ +
Charge separation
Chandler, Parrinello et. al Science 2001, 291, 2121
1
Dissociation: Fluctuation in solvent electric field ; cleavage of OH bond
2
H3O+ moves by proton transfer within 30 fs
3
4
Conduction of proton through H-bond network 60 fs
5
Crucial fluctuations carries system to transition state ; breaking of H-bond : 30 fs
6
NO fast ion recombination
Order parameter for autoionizationFluctuations that control routes for proton :
No. of hydrogen bond connecting the ions : ℓ
ℓ = 2 ; recombination occurs within 100 fsreactant ℓ = 0 ; product ℓ ≥ 3
Critical ion separation is 6 Å
At ℓ = 2 , sometimes reactant basin ; Thus ℓ is not the only order parameter
Potential of proton in H-bonded wire → fluctuation
q → configuration description ; q = 1 neutral ; q = 0 charge separated
ΔE = E[r(1) – r(0)] → solvent preference for separated ions over neutral molecules
Potential of protons in hydrogen bonded wires connecting H3O+ and OH- ions
Chandler, Parrinello et. al Science 2001, 291, 2121
Neutral state, bond destabilizing electric field has not appeared
Electric field starts to appear ; metastable state w.r.t. proton motion ; 2kcal/mol higher than neutral state
Field fluctuations increase ; stable charge separated state ; 20kcal/mol more stable
Nature of the hydrated excess proton in liquid water
Two proposed theories : 1. Formation of H9O4+ (by Eigen)
2. Formation of H5O2+ (by Zundel)
Charge migration happens in a few picoseconds
Tuckermann, Parrinello et. al J. Chem. Phys. 1997, 275, 817
+ +
H9O4+
H5O2+
+
Hydrogen bonds in solvation shells of the ions break and reform and the local environment reorders
Ab initio calculations show that transport of H+ and OH- are significantly different
Proton transport
Tuckermann, Parrinello et. al Nature 1997, 275, 817
Proton diffusion does not occur via hydrodynamic Stokes diffusion of a rigid complex
Continual interconversion between the covalent and hydrogen bonds
Proton transportδ = ROaH - RObH
+Oa
ObH
For small δ ; equal sharing of excess proton → Zundel’s H5O2+
For large δ ; threefold coordinated H3O+ → Eigen’s H9O4+
Tuckermann, Parrinello et. al Nature 1997, 275, 817
ΔF(ν) = -kBT ln [ ∫ dROO P(ROO,ν) ]
Free energy :
H5O2+ : at δ = 0 ± 0.05Å, Roo ~ 2.46-2.48 ÅΔF < 0.15 kcal/mol, thermal energy = 0.59 kcal/mol
Numerous unclassified situations exists in between these two limiting structures
Breaking bonds by mechanical stress
Frank et. al J. Am. Chem. Soc. 2002, 124, 3402
Reactions induced by mechanical stress in PEG1. Formation of ions corresponds to heterolytic bond cleavage
2. Motion of electrons during the reaction Polymer is expanded with AFM tip
Unconstrained reactions can not be observed by classical MD
Quantum chemical approaches are more powerful in describing the general chemical reactivity of complex systems
H
H
C2
C C
C
O1
O2 H
H H H
H H H H
O
H
H
Solvent
Small piece of PEG in water
Breaking bonds by mechanical stress
Method ΔE (C-O) kcal/mol ΔE (C-C) kcal/mol
BLYP
Exp
83.979.1
85.0 83.0
Radicaloid bond breaking
After equilibration, distance between O1 and O2 was increased continuously by 0.0001 au/time
Reaction started at 250 K ; C2O1 ~ 3.2 Å
Snapshots of the reaction mechanisms
O
O
H
O
H
HO
H
H OH
+
-
OH
OH
O
H
O H
H
OH
O
O
H
O
H HO
HH
O
H
O
O
H
O
H H
O
H HO
H
OO
H
O
H
HO
H
H OH
+
-
O
OH
O
H
O H
H
OH
H
250 K
320 K
Frank et. al J. Am. Chem. Soc. 2002, 124, 3402
Hydrogen bond driven chemical reaction
Parrinello et. al J. Am. Chem. Soc. 2004, 126, 6280
Beckmann rearrangement of Cyclohexanone Oxime into ε-Caprolactam in SCW
SCW accelerates and make selective synthetic organic reactions
System description :
CPMD simulation , BLYP exchange correlation
MT norm conserving pseudo potential
Plane wave cut-off 70 Ry, Nose-Hoover thermostat
T = 673K, 300K
64 H2O + 1 solute, 18 ps analysis + 11 ps equil.
Disrupted hydrogen bond network of SCW alters the solvation of O and N
Problems Computationally costly
Can not simulate slow chemical processes that take place beyond time scales of 10 ps
Inaccuracy in the assumption of exchange and correlation potential
Limitation in the number of atoms and time scale of simulation
Inaccurate van der Waals forces, height of the transition energy barrier
BOMD not applicable for photochemistry; transition between different electronic energy levels
Other methods QM/MM – quantum mechanics / molecular
mechanics
Classical MD AIMD e.g. catalytic part in enzyme
Path-sampling approach combined with ab-initio MD for slow chemical processes Metadynamics, for slow processes
Conclusions CPMD : nuclear and electronic degrees of freedomInteraction potential is evaluated on-the-flyBond formation and breaking is accessible in CPMD : direct access to the chemistry of materialsTransferability over different phases of matterCPMD is computationally expensive