A combined QM/MM and Classical Molecular Dynamics Study of [Ru(bpy)3]2+ in Water

The solvation of the Ru(bPy)(3) (bpy = 2,2'-bipyridyl) cation was studied by molecular dynamics simulations, using both a hybrid QM/MM Car-Parrinello scheme and a classical force field. The trajectory analysis reveals that the first solvation sphere consists of chains of H-bonded water molecules intercalating between the bpy ligands, which in turns induces an organization of the second solvation sphere. Comparison with a simple charged sphere model shows the influence of the geometry of the cation and its ligands on the surrounding water. A water residence time in the first solvation shell of Ru(bpy)(3) of 12.4 ps is computed, which is significantly larger than the value of 4.5 ps found in bulk water. On the other hand, due to the one-dimensional arrangement of hydrogen bonds, the dipole of the water molecules can easily reorient, providing a way to explain the fast solvent dependent relaxation dynamics observed following photoexcitation.

Towards a Composite Benchmark Method for the Aqueous Solvation Free Energies of Organic Compounds

Daniel David Sadowsky

Water is ubiquitous in the biosphere, and the difficulty of rigorously treating the effects of aqueous solvation currently limits the widespread use of computational methods in many areas of environmental chemistry. We propose an approach to benchmark calculations of aqueous free energies of solvation based on molecular dynamics simulation which is derived from first principles, statistical mechanically complete, and systematically improvable. The approach partitions the solvation free energy into the free energies of solvent density change, solvent cavity organization, and solvent-solute interaction, each of which is computed from first principles. A composite approach is considered for the calculation of the contributions of quantum nuclear effects to solvation free energies and the contributions of electron correlation and relativistic effects to solvent-solute interactions.

2015

Molecular insights in aqueous systems

Yixing Chen

The unique structure and dynamics of the water hydrogen (H)-bond network enable a multitude of structures and chemical reactions in both bulk solutions and at interfaces. The underlying molecular interactions between water and dissolved electrolytes, organic molecules, and nanoscale interfaces are difficult to study and hence not fully understood, especially when it involves interactions of length scales larger than one nanometer. In this thesis, we perform second order nonlinear light scattering experiments to investigate extended hydration shells (over one nanometer) and interfacial structures of buried aqueous interfaces that surround nanodroplets. We investigate the spatial range of ion-water interactions by probing the molecular structure of the water network in dilute electrolyte solutions. We find that electrolytes induce long-range, non-ion-specific orientational order in the H-bond network of water (over distances up to 70 hydration shells or 20 nm). These modifications in the water network start at electrolyte concentrations as low as 10 micromolar. The amount of induced orientational order and the concentration at which it occurs is different between light and heavy water. We link the observed ion induced changes in the bulk H-bond network of water to ion induced surface tension anomalies that occur in the same concentration range. We also study the same interactions in solutions with higher electrolyte concentrations focusing on cations. We observe specific ion effects in both the local charge distribution and water ordering in extended hydration shells of ions. Cations with larger charge densities induce larger changes in these two observables that follow a direct Hofmeister trend. The ion-induced structural changes in the water network are strongly correlated with the viscosity B-coefficient and hydration free energy of cations. These correlations facilitate constructing a better molecular model for specific ion effects in aqueous solutions. Next, we study the nanoscale hydrophobe/water interface and related interactions by probing the molecular structure of the interface formed with amphiphilic alkanols. We find that alkanols form a fluid film at the oil nanodroplet surface. Long chain alkanols show similar molecular structures and number densities at the interface. With increasing alkanol density, interfacial water loses its initial orientational alignment. The structure of interfacial oil molecules is more distorted for shorter alkanols. This interfacial structure differs significantly from those of macroscopic planar alkanol/water and alkanol/air interfaces and charged surfactant/oil/water interface, which can be explained by the balance between dispersive and H-bonding interactions. Finally, we develop a new membrane model system: 3D-lipid monolayers with tunable molecular structure on oil nanodroplets in water. This in-situ prepared system mimics the structure of lipid droplets in cells. The interfacial structure of lipids can be tuned from a tightly packed monolayer (liquid condensed phase) to a dilute one (liquid condensed/liquid expanded coexistence phase) by varying the lipid/oil/water ratio. The tunability of the chemical structure, the high surface-to-volume ratio, and the small sample volume make this system ideal for studies of molecular interactions of lipids in membranes.

EPFL2017

Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution

Frederico Alves Lima, Paul Beaud, Majed Chergui, Amal El Nahhas, Thomas James Penfold, Van Thai Pham, Ivano Tavernelli, Renske Marjan van der Veen

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L-1,L-3 edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I-/I-0(H2O)(n=1-4) clusters. The L-1 edge sub-picosecond spectra point to the existence of a transient species that is not present at SO ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I-0(OH2) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 Ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.

2011

Molecular insights in aqueous systems

Yixing Chen

EPFL2017