Ultrafast optical Kerr effect spectroscopy of water confined in nanopores of the gelatin gel

Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study

Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.

Altered relaxation dynamics of excited state reactions by confinement in reverse micelles probed by ultrafast fluorescence up-conversion

Chemical reactions in confined environments are important in areas as diverse as heterogenous catalysis, environmental chemistry and biochemistry, yet they are much less well understood than the equivalent reactions in either the gas phase or in free solution. The understanding of chemical reactions in solution was greatly enhanced by real time studies of model reactions, through ultrafast spectroscopy (especially when supported by molecular dynamics simulation). Here we review some of the efforts that have been made to adapt this approach to the investigation of reactions in confined media. Specifically, we review the application of ultrafast fluorescence spectroscopy to measure reaction dynamics in the nanoconfined water phase of reverse micelles, as a function of the droplet radius and the charge on the interface. Methods of measurement and modelling of the reactions are outlined. In all of the cases studied (which are focused on ultrafast intramolecular reactions) the effect of confinement was to suppress the reaction. Even in the largest micelles the result in the bulk aqueous phase was not usually recovered, suggesting an important role for specific interactions between reactant and environment, for example at the interface. There was no simple one-to-one correspondence with direct measures of the dynamics of the confined phase. Thus, understanding the effect of confinement on reaction rate appears to require not only knowledge of the dynamics of the reaction in solutions and the effect of confinement on the medium, but also of the interaction between reactant and confining medium.

Isotope Effect in the Liquid Properties of Water Confined in 100 nm Nanofluidic Channels

Liquids confined in 10-100 nm spaces show different liquid properties from those in the bulk. Proton transfer plays an essential role in liquid properties. The Grotthuss mechanism, in which charge transfer occurs among neighboring water molecules, is considered to be dominant in bulk water. However, the rotational motion and proton transfer kinetics have not been studied well, which makes further analysis difficult. In this study, an isotope effect was used to study the kinetic effect of rotational motion and proton hopping processes by measurement of the viscosity, proton diffusion coefficient, and the proton hopping activation energy. As a result, a significant isotope effect was observed. These results indicate that the rotational motion is not significant, and the decrease of the proton hopping activation energy enhances the apparent proton diffusion coefficient.

Femtosecond optical Kerr effect setup with signal "live view" for measurements in the solid, liquid, and gas phases

We present the experimental setup constructed in our laboratory for measurement of the femtosecond optical Kerr effect. The setup allows measurements with high temporal resolution and acquisition speed. The high signal to noise ratio is obtained with use of a homemade balanced detector. Due to the high acquisition speed and good signal to noise ratio, it is possible to have a "live view" of the signal and to easily tune the sample position and orientation before the measurement. We show the example results obtained in the solid, liquid, and the gas phases and we use them in order to check on the precision of our setup. As the samples we have used a YAG crystal, liquid acetone, and atmospheric air. In the latter two cases, a good agreement with the literature data has been found. The measurements in the gas phase confirm that our setup, although utilizing low energy pulses from the sapphire oscillator, is able to acquire high quality rotational signal in a low density sample.

Carbohydrate Clustering in Aqueous Solutions and the Dynamics of Confined Water

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.