Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be reweighted to yield results consistent with the original, unmodified potential. In conventional AMD the reweighting procedure has an inherent statistical problem in systems with large acceleration, where the points with the largest biases will dominate the reweighted result and reduce the effective number of data points. We propose a replica exchange of various degrees of acceleration (REXAMD) to retain good statistics while achieving enhanced sampling. The REXAMD method is validated and benchmarked on two simple gas-phase model systems, and two different strategies for computing reweighted averages over a simulation are compared

On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations.

We use thermodynamic integration (TI) and explicit solvent molecular dynamics (MD) simulation to estimate the absolute free energy of host-guest binding. In the unbound state, water molecules visit all of the internally accessible volume of the host, which is fully hydrated on all sides. Upon binding of an apolar guest, the toroidal host cavity is fully dehydrated; thus, during the intermediate λ stages along the integration, the hydration of the host fluctuates between hydrated and dehydrated states. Estimating free energies by TI can be especially challenging when there is a considerable difference in hydration between the two states of interest. We investigate these aspects using the popular TIP3P and TIP4P water models. TI free energy estimates through MD largely depend on water-related interactions, and water dynamics significantly affect the convergence of binding free energy calculations. Our results indicate that wetting/dewetting transitions play a major role in slowing the convergence of free energy estimation. We employ two alternative approaches-one analytical and the other empirically based on actual MD sampling-to correct for the standard state free energy. This correction is sizable (up to 4 kcal/mol), and the two approaches provide corrections that differ by about 1 kcal/mol. For the system considered here, the TIP4P water model combined with an analytical correction for the standard state free energy provides higher overall accuracy. This observation might be transferable to other systems in which water-related contributions dominate the binding process

Magnetoelectrically driven catalytic degradation of organics

Here, we report the catalytic degradation of organic compounds by exploiting the magnetoelectric (ME) nature of cobalt ferrite-bismuth ferrite (CFO-BFO) core-shell nanoparticles. The combination of magnetostrictive CFO with the multiferroic BFO gives rise to a magnetoelectric engine that purifies water under wireless magnetic fields via advanced oxidation processes, without involvement of any sacrificial molecules or co-catalysts. Magnetostrictive CoFe2O4 nanoparticles are fabricated using hydrothermal synthesis, followed by sol-gel synthesis to create the multiferroic BiFeO3 shell. We perform theoretical modeling to study the magnetic field induced polarization on the surface of magnetoelectric nanoparticles. The results obtained from these simulations are consistent with the experimental findings of the piezo-force microscopy analysis, where we observe changes in the piezoresponse of the nanoparticles under magnetic fields. Next, we investigate the magnetoelectric effect induced catalytic degradation of organic pollutants under AC magnetic fields and obtained 97% removal efficiency for synthetic dyes and over 85% removal efficiency for routinely used pharmaceuticals. Additionally, we perform trapping experiments to elucidate the mechanism behind the magnetic field induced catalytic degradation of organic pollutants by using scavengers for each of the reactive species. Our results indicate that hydroxyl and superoxide radicals are the main reactive species in the magnetoelectrically induced catalytic degradation of organic compounds

PHOTOCHEMICAL RING-OPENING IN meso-CHLORINATED CHLOROPHYLLS

Irradiation of 20-chloro-chlorophylls of the a-type with visible light produces long-wavelength shifted photoproducts, which transform in the dark to linear tetrapyrroles (bile pigments). The possible significance for chlorophyll degradation is discussed

Energetics of the primary electron transfer reaction revealed by ultrafast spectroscopy on modified bacterial reaction centers

The modification of reaction centers from Rhodobacter sphaeroides by the introduction of pheophytins instead of bacteriopheophytins leads to interesting changes in the primary photosynthetic reaction: long-living populations of the excited electronic state of the special pair P* and the bacteriochlorophyll anion B−A show up. The data allow the determination of the energetics in the reaction center. The free energy of the first intermediate P+B−A, where the electron has reached the accessory bacteriochlorophyll BA lies ≈ 450 cm−1 below the initially excited special pair P*

Single step electrosynthesis of NiMnGa alloys

An electrochemical synthesis route for NiMnGa alloys is presented. Thin films of NiMnGa were fabricated by single step electrodeposition from aqueous electrolytes using direct current over a range of current densities. By electrolyte tuning, homogeneous films with high Ga and Mn content could be achieved at current densities as high as -400 mA cm-2. Detailed compositional analysis of the alloys showed that growth was homogeneous and oxygen content was minimized. Films plated at very low current densities were found to be nanocrystalline/amorphous. In order to obtain fully crystalline samples, thermal annealing was carried out. Mechanical characterization was assessed by nanoindentation, and the effect of Ga content on mechanical properties was investigated