oksupercompsymp2006 talk tummala
TRANSCRIPT
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Molecular Dynamics Study of
Aqueous Solutions inHeterogeneous Environments:
Water Traces in Organic Media
Naga Rajesh Tummala and Alberto Striolo
School of Chemical, Biological and Materials Engineering
University of Oklahoma
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Importance of confined water
Experiments used to study confined water
Motivation for doing simulations Simulation details
Findings from simulation study
OUTLINE
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CONFINED WATER
Where do we find ?
protein hydration
various biochemical
processes
ionic channels
Differences we expectcompared to bulk water
Slow hydrogen bonddynamics (time scales ?)
Slow reorientation times
Ion channels
hydrophobic
solvent
water
Protein hydration1
water
1
http://www.lsbu.ac.uk/water/protein.html
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Experiments
Femto second mid-infrared pump-probe measurements Water in Dimethylsulfoxide
Water in acetone/carbon tetrachloride
Vibrational Echo Spectroscopy for HOD in H2O
Ultra-fast Infrared Spectroscopy to study OH stretch vibrationof HOD/H2O in D2O
FTIR spectroscopy to study hydroxyl and librational modes ofconfined water in reverse micelles
Output of experiments is usually a spectra, and in most cases itis absorbance VS frequency, and dynamics are studied fromthe absorbance VS delay (signal)
Approachable time scales: Generally pico (10-12) seconds
Sometimes 50-100 femto (10-15) seconds depending upon theduration of probe pulses.
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Experiments with small traces of
water in heterogeneous organicsolutions.2 (1:10:40) ratio of water,
acetone and carbon tetrachloride
Assuming that water
disperseshomogenously in
solution
2 Dynamics of confined water molecules, Gilijamse et al, PNAS2005, 102, 3202-3207
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Typical output from femto second mid-
infrared pump-probe measurements2
Absorbance VS frequency ln(T/To) VS delay
Experimentally it was found that the energy transfer in
confined water is more than 20 times slower than bulk water
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MOTIVATION
To answer following questions
Do traces of water completely disperse inacetone/carbon tetrachloride system ?
Influence of water-water hydrogen bonds ondynamics of trapped water ?
Influence of water-acetone hydrogen bonds on
dynamics of confined water ?
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Molecular Dynamics
Solving time dependent Newtons equations of motion of all theparticles in the system.
We use LAMMPS (Large-scale Atomic/Molecular MassivelyParallel Simulator ) developed by Steve Plimpton and his group
of Sandia National Laboratories1
.
LAMMPS employs spatial decomposition to load balance on thenumber of processors used.
Forces Computed: Inter-molecular (Van der Waals forces, Coulombic forces) Intra-molecular (bond, angle, dihedral and improper forces)
1 Large-scale Atomic/Molecular Massively Parallel Simulator , Fast Parallel
Algorithms for Short- Range Molecular Dynamics, S. J. Plimpton, J. Comp. Phys. 1995,117, 1-19 . http://www.cs.sandia.gov/~sjplimp/lammps.html
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Simulation Details
Water modeled with extended simple pointcharge (SPC/E) potential.
Carbon tetrachloride with a fully flexible,non-polarizable five site model.
Acetone was modeled using united atom formethyl atoms and carbonyl (-C=O) groupwas explicitly modeled.
Ratio of water : acetone : carbontetrachloride was maintained at 1:10:40 tomimic experimental conditions.
Initially 12 water molecules are used and allmolecules were placed in a lattice.
H, effectively zero
radius and charge of
+ 0.4238 each
O, Radius of 3.166 Ao
and charge of -0.8476
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1 ns at 1000 K
Cooling at 100 K every 300 ps
Equilibration for 1.5 ns at 300 K
NVT (constant (#
of atoms, volume
and temperature))
simulation
NPT (constant (#
of atoms,
pressure and
temperature))
simulation
Simulation box replicated twice
in X,Y and Z directions
Equilibration for 375 ps at 300 K
Production phase for 300 ps at
300 K with output every 100 fs for
only water and acetone
time step
1 fs
SIMULATION
METHODOLOGY
(1:10:40)
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Energy Curve ( indication to equilibrium)
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Transformation from NVT to NPT ensemble
with 12 water molecules in simulation box
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Movie of 96 water molecules in the
simulation box
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Computational Expenses
System with 12 water molecules takes ~8 hrs on 20
processors to simulate 300ps (2916 atoms)
System with 96 water molecules takes ~2days on 80processors to simulate 300 ps (23328 atoms)
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Performance comparison of SEABORG and
TOPDAWG
0
20000
40000
60000
80000
0 64 128 192 256 320 384 448 512
# of processors
t(sec)
seaborg(375 MHz POWER3-II 64-)
topdawg (3.2 GHz, EM64T, 2 MB L2 cache)
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Results: I. Equilibrium structure
0 . 0 0
0 . 0 5
0.10
0.15
0 . 2 0
0 . 2 5
0 . 3 0
0 . 3 5
1 3 5 7 9 11 13 15 17 19 21 23 25
N
PopulationDistribution
Population distribution of cluster sizes at 300 K
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Visualization of temporal breaking and
forming of H-bonds
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0 12
34
01
23
4
0.00
0.05
0.10
0.15
0.20
0.25
0.30
P
nwna
Probability P for one water molecule of being
hydrogen bonded to nw water molecules and na
acetone molecules
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0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0 1 2na
P
Probability (P) of finding the water molecule hydrogen bonded to na
acetone molecules within the system of molecular composition
(1:120:480).
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Results II. Hydrogen Bond Dynamics
Intermittent auto correlation functions for
water-acetone hydrogen bonds.
0)()0(
)(h
thhtC
"!
Confined water
Bulk water
HB
ACF
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OH-reorientational dynamics
OH reorientation ACF
uE
Confined water
Bulk water
Pl is the legendrepolynomial of order l
OH-reorientation
ACF
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Relaxation time constants
Relaxation times
(ps)
Confined
Water
Bulk Water Single Confined
Water
X(HB)(I)* 8.98 3.99
X
(HB)(I)(W-A)*
2.39 N/A N/A
X(HB)(I)(W-A)* 0.92 @ N/A 0.31
X(OH)** 0.91 1.22 0.28
HBttC X} exp
dttCOHOH
)(0
,2,2 g
!X**
* @ experimental valueis 1.33 ps
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Conclusions
Do traces of water completely disperse in acetone/carbontetrachloride system ? NO
Influence of water-water hydrogen bonds on dynamics of
trapped water. MORE RESPONSIBLE FOR SLOWDYNAMICS
Influence of water-acetone hydrogen bonds on dynamics of
confined water. ~ EQUIVALENT TO BULK WATER
We cannot neglect water-water hydrogen bonds which are
responsible for slow dynamics of trapped water.
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Acknowledgements
Dr. Henry Neeman
OSCER, University of Oklahoma
NERSC, Berkeley, CA Oklahoma State Reagents for Higher Education
Department of Energy
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QUESTIONS ?