PRACE Scientific Seminar in KTH Stockholm
Feb. 21-23, 2011
Ab initio modeling of chemical reactions in aqueous
environment
Kari Laasonen, Physical Chemistry, Aalto University, Espoo, Finland
Chemistry is a science that study molecules and molecular reactions
NaCl(s) + H2O -> Na+(aq) + Cl-(aq)
nCO @ Fe -> CNT + CO2 + Fe(s) (CNT = Carbon NanoTube)
• Computational chemistry is a field that use quantum mechanical
methods to study molecules properties and reactions
• In most of the calculations the studied molecules are in vacuum
which is seldom the case with real molecules
• We need computational chemistry in realistic environment
• The molecules also moves so often we need to simulate the
molecular dynamics (MD)
• We heard the talk of Dr. Hess of empirical MD. I will focus on ab
initio MD.
• The main advantage of AIMD is that chemical reactions can be
studied.
Ab Initio Molecular Dynamics
• combining periodic DFT-GGA and MD.
• DFT = density functional theory, efficient quantum mechanical model for
several electrons (but not very accurate)
• nuclei are treated classically, F = ma, F = -<φ|H|φ>
• CPMD smooth effective core potentials and plane wave basis set
• CP2K hard effective core potentials and gaussian basis set. Time step
ca. 1 fs.
• accuracy of GGA is usually good – Van der Waals interactions are
missing. We use DFT + empirical corrections a la Grimme
• full arsenal of MD techniques and electronic structure analysis methods
are implemented – thermostats, constraints, thermodynamic integration,
Wannier functions, TD-DFT
Ab Initio Molecular Dynamics
• examples: Al2OnHmCl2 + 65 water, Al5OnHmClk+ 144 water, PBE-GGA
• various simulations, simulation time scale ca. 100 ps
• CPMD or CP2K code, computations with Cray XT5/XT4 (Louhi @CSC)
Ab initio molecular dynamics
aluminum oxide chemistry in aqueous solution
• Al oxides are widely used chemicals for water cleaning (coagulation)
• Not much are known of their formation chemistry
• We have a lot of new mass spectrometer data of these complexes which
needs computations to resolve the molecular structures
Ab initio molecular dynamics
aluminum oxide chemistry in aqueous solution
1.35 Å
1.48 Å
Time (ps) Time (ps)
Dis
tan
ce
(Å
)
Dis
tan
ce
(Å
)
loosely bound proton (acidic) normal proton (water)
The AIMD simulations time scale is few 100 ps but the chemical reaction time scale is almost always much longer than this. At room temperature the time scale of the reaction below is around 1 s.
We need methods to force the chemical reaction to happen -> Constrained MD simulation
Al - Cl
O
H
H
Al --- Cl
O
H
H
Constrained MD simulation
One can fix some geometrical parameters and compute the force to this constraint. MetaDynamics allows treatment of more complex reaction.
Free energy difference is an integral of this force
Tedious calculations since they need long simulation to get good averaging.The constraint can slowly grow or it can be fixed (the later turned out to be more efficient)
Constrained MD simulation
Test the hysteresis – grow and reduce the constraint. The
result should be the same
Constrained MD simulation
Also the static calculations need long simulations
fs
Aluminum oxide chemistry in aqueous solution
2.2 3.22.4 2.6 2.8 3.02.2 3.22.4 2.6 2.8 3.02.2 3.22.4 2.6 2.8 3.0
Distance [Å]
∆G
[k
Jm
ol-
1]
14 ± 3 kJ mol-1 40 ± 5 kJ mol-1
• reaction barriers
• very large ligand effect:
Al1ClOHw, Al2Clw2
• small barriers Cl’s will
dissociate
J. Saukkoriipi and K. Laasonen,
J. Phys. Chem. A, 112, 10873 (2008),
360 370 380 390 400 410 420 430 440
m/z
0
100
%
411
393
391
375373
369
367 371
377385
387
409
395
397
429
413427
415
431
433
Simulation of four chlorines
+ H2O
+ H2O + H2O
Mass spectra and Al5OnHmClk clusters in gas phase
Aluminum oxide chemistry in aqueous solution
+ H2O + H2O+
H2 O
+ H2O+ H2O
+ H2O
~ 1 ps ~ 2 ps~
3 p
s
~ 5 ps~ 9 ps
+ H2O + H2O+
H2 O
+ H2O+ H2O
+ H2O + H2O+
H2 O
+ H2O+ H2O
+ H2O
~ 1 ps ~ 2 ps~
3 p
s
~ 5 ps~ 9 ps
• The aluminum pentamer and spontaneous hydration reactions in water.Taken as a snapshots from AIMD trajectory (~ 27 ps).
xy+ 2H2O + 3H2O - H2O
x
y
Time [ps]
Bo
nd
le
ng
th [
Å]
Time [ps]
Bo
nd
le
ng
th [
Å]
*
10 20 30 35 4025150 5 10 20 30 35 4025150 5
1.5
2.0
2.5
3.0
3.5
4.0
4.5
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
• A surprising result: the ’nice’ and compact initial structures broke
up during the simulations
Bo
nd
le
ng
th [
Å]
Time [ps]
50 10 15 20 25 30
3.0
2.0
Bo
nd
le
ng
th [
Å]
Time [ps]
2.4
2.6
2.8
3.0
3.2
3.4
3.6
50 10 15 20 25 30
4.0
5.0
6.0
7.0
8.0
+ 2H2O+ 2H2O + H2O - Cl- and + H2O
Wet surfaces
Computational aspects – CP2K code
Developed mostly in Zurich, Prof. Hutter’s group
http://cp2k.berlios.de/
Free to download (from the address above)
Tutorials: 2nd CP2K Tutorial: Enabling the Power of Imagination in MD Simulations. www.cecam.org
Very complex code (600.000+ lines of code, Fortran 95)
Huge amount of features
Difficult to compile and difficult to learn to use
Important help from CSC (compilation)
Computational aspects – CP2K code
Efficient code but in normal application not very good parallel scaling.
We are interested of some simulation of 100-200 waters and around 100.000
MD steps. Each simulation will take around 1 month (wall clock time, Cray
XT5) and ca. 90.000 CPUh .
A supercomputer is essential
Good scaling up to 128 cores
(note: rather old version of the code)
Computational aspects – near future
The code is in continuous development (CVS)
Scientifically was are in a good spot – there are enormous amount of good problems that can be done with the present resources or somewhat larger computers.
Bottlenecks – the computations are still very slow and the scaling is not very good.
Farming – better project planning
Several new fileds – wet surfaces, electrochemistry – which would need a lot of resources.
Conclusions
• Of medium size molecules most of the reactions can be computed in
aqueous environment
• other solvents are much more time consuming
• Also surface reactions can be studied
• simple wet surfaces can be studied
