Modeling Water Cluster Anions

A quantum Drude oscillator model was developed by our group to describe excess electrons interacting with water clusters1. This approach uses quantum Drude-oscillators to account for polarization and dispersion interactions between the excess electron and the water molecules. In the present work, the quantum Drude model£¬combined with a modified Thole-type water model with dipole point polarizability, denoted DPP, is used to investigate the (H2O)7- cluster. Several low-energy isomers were characterized, and the finite-temperature properties of the cluster was investigated by means of parallel tempering Monte Carlo simulations

Hydrophobic hydration driven self-assembly of Curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting strongly with hydrophilic groups at the surface of curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer.Comment: 31 pages, 9 figure

Role of Rotations on Surface Diffusion of Water Trimers on Pd\{111\}

Diffusion barriers for a cluster of three water molecules on Pd(111) have been estimated from ab-initio Density Functional Theory. A model for the diffusion of the trimer based in rotations yields a simple explanation of why the cluster can diffuse faster than a single water molecule by a factor $\approx 10^{2}$. This model is based on the differences between the adsorption geometry for the three monomers forming the cluster. One member interacts strongly with the surface and sits closer to the surface (d) while the other two interact weakly and stay at a larger separation from the surface (u). The trimer rotates nearly freely around the axis determined by the d monomer. Translations of the whole trimer imply breaking the strong interaction of the d monomer with the surface. Alternatively, thermal fluctuations exchange the actual monomer sitting closer to the surface with a lower energetic cost. Rotations around different axis introduce a diffusion mechanism where a strong interaction is kept along the diffusion path between the water molecule defining the axis of rotation and the Pd underneath.Comment: water ; monomer ; trimer ; water clusters ; diffusion ; rotation assisted ; Pd\{111\} ; ab-initio ; density functional theor

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes, but decrease slightly with increasing cluster size

Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria

Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria

Mn oxide as a kinetically dominant “true” catalyst for water oxidation

Nature uses an Mn cluster for water oxidation, and thus, water oxidation using Mn clusters is interesting when used in artificial water-splitting systems. An important question is whether an Mn cluster is a true catalyst for water oxidation or not. Herein, an Mn–K cluster was investigated for electrochemical water oxidation to find the true and the kinetically dominant catalyst using X-ray absorption spectroscopy, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and electrochemical methods. The experiments showed that conversion into nanosized Mn oxide occurred for the cluster, and the nanosized Mn oxides are the true catalyst for water oxidation