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

Importance of confined water Experiments used to study confined water Motivation for doing simulations Simulation details Findings from simulation study

OUTLINE

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

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.

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

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

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 ?

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

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

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)

Energy Curve ( indication to equilibrium)

Transformation from NVT to NPT ensemble with 12 water molecules in simulation box

Movie of 96 water molecules in the simulation box

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)

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)

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

Visualization of temporal breaking and forming of H-bonds

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

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).

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

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

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

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.

Acknowledgements

Dr. Henry Neeman OSCER, University of Oklahoma NERSC, Berkeley, CA Oklahoma State Reagents for Higher Education Department of Energy

QUESTIONS ?