Oksupercompsymp2006 Talk Tummala

8/3/2019 Oksupercompsymp2006 Talk Tummala

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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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