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 hydration 1 water 1
Experiments Femto second mid-infrared pump-probe measurements Water in Dimethylsulfoxide Water in acetone/carbon tetrachloride Vibrational Echo Spectroscopy for HOD in H 2 O Ultra-fast Infrared Spectroscopy to study OH stretch vibration of HOD/H 2 O in D 2 O 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 ( ) seconds Sometimes femto ( ) 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,
Typical output from femto second mid- infrared pump-probe measurements 2 Absorbance VS frequency ln(T/T o ) 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 Laboratories 1. 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,
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 each ‘O’, Radius of A o and charge of
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”
Results: I. Equilibrium structure Population distribution of cluster sizes at 300 K
Visualization of temporal breaking and forming of H-bonds
Probability P for one water molecule of being hydrogen bonded to n w water molecules and n a acetone molecules
Probability (P) of finding the water molecule hydrogen bonded to ‘n a ’ 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. Confined water Bulk water HB ACF
OH-reorientational dynamics OH reorientation ACF uu Confined water Bulk water P l is the legendre polynomial of order l OH-reorientation ACF
Relaxation time constants Relaxation times (ps) Confined Water Bulk WaterSingle Confined Water (HB) (I) * (HB) (I)(W-A) * 2.39N/A (HB) (I)(W-A) * N/A0.31 (OH) ** ** 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 ?