molecular dynamics study of aqueous solutions in heterogeneous environments: water traces in organic...
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Molecular Dynamics Study of Aqueous Solutions in Heterogeneous 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 expect compared to bulk water Slow hydrogen bond
dynamics (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 vibration
of HOD/H2O in D2O FTIR spectroscopy to study hydroxyl and librational modes of
confined water in reverse micelles Output of experiments is usually a spectra, and in most cases it
is absorbance VS frequency, and dynamics are studied from the absorbance VS delay (signal)
Approachable time scales: Generally pico (10-12) seconds Sometimes 50-100 femto (10-15) seconds depending upon the
duration of probe pulses.
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Experiments with small traces of water in heterogeneous organic
solutions.2 (1:10:40) ratio of water, acetone and carbon tetrachloride
Assuming that water disperses
homogenously in solution
2 Dynamics of confined water molecules, Gilijamse et al, PNAS 2005, 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 in acetone/carbon tetrachloride system ?
Influence of water-water hydrogen bonds on dynamics of trapped water ?
Influence of water-acetone hydrogen bonds on dynamics of confined water ?
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Molecular Dynamics
Solving time dependent Newton’s equations of motion of all the particles in the system.
We use LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator ) developed by Steve Plimpton and his group of Sandia National Laboratories1.
LAMMPS employs spatial decomposition to load balance on the number of processors used.
Forces Computed: Inter-molecular (Van der Waal’s 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 point charge (SPC/E) potential.
Carbon tetrachloride with a fully flexible, non-polarizable five site model.
Acetone was modeled using united atom for methyl atoms and carbonyl (-C=O) group was explicitly modeled.
Ratio of water : acetone : carbon tetrachloride was maintained at 1:10:40 to mimic experimental conditions.
Initially 12 water molecules are used and all molecules 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 80 processors 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 (s
ec)
seaborg(375 MHz POWER3-II 64-)
topdawg (3.2 GHz, EM64T, 2 MB L2 cache)
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Results: I. Equilibrium structure
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.35
1 3 5 7 9 11 13 15 17 19 21 23 25
N
Po
pu
lati
on
Dis
trib
uti
on
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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01
23
4
0123
4
0.00
0.05
0.10
0.15
0.20
0.25
0.30
P
nw
na
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
AC
F
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OH-reorientational dynamics
OH reorientation ACF
u
Confined water
Bulk water
Pl is the legendre polynomial of order l
OH
-reo
rien
tati
on
AC
F
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Relaxation time constants
Relaxation times (ps)
Confined Water
Bulk Water Single Confined Water
(HB)(I)* 8.98 3.99
(HB)(I)(W-A)* 2.39 N/A N/A
(HB)(I)(W-A)* 0.92 @ N/A 0.31
(OH)** 0.91 1.22 0.28
HB
ttC exp
dttC OHOH )(0 ,2,2
**
* @ experimental value is 1.33 ps
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Conclusions Do traces of water completely disperse in acetone/carbon
tetrachloride system ? NO Influence of water-water hydrogen bonds on dynamics of
trapped water. MORE RESPONSIBLE FOR SLOW DYNAMICS
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 ?