Molecular dynamics simulations of structural disordering and forming defects in a milling process for selenium

In our previous paper, structural changes of selenium powders ground by a planetary ball mill at various rotational speeds were investigated for the nanostructural modification of particles using mechanical grinding process. The experimental results indicated that the amorphisation of Se by grinding accompanies lattice strain, and the lattice strain arises from impact energy which is more than an energy related to intermolecular interaction. In this paper, molecular dynamics simulations of selenium have been carried out under compressing conditions of various pressure strengths for obtaining information of the lattice strain at atomic level. Then, dynamical behaviour of atomic configuration has been discussed in this process. The structural disordering and formation of the structural defects were estimated by deviations of bond length and angle and the number of created defects before and after compressing from simulated results. The disordering took place during compressing at various pressure strengths, and the disordered atoms return to their initial positions at lower pressure. Stable disordered state and defects after the compression can however remain by compression at more than a certain pressure strength mainly associated with binding energy of selenium.     

Molecular dynamics simulations of the formation for NaCl cluster at the interface between the supersaturated solution and the substrate

Molecular dynamics simulations of supersaturated aqueous NaCl solution including the Pt(100) or NaCl(100) crystal surfaces have been performed at an average temperature of 298 K. The behavior of the NaCl cluster produced in the solution have been studied through the consideration of the water dielectric property near the crystalline surfaces for understanding the role of crystal growth on the surface. The surfaces in the solutions greatly influence heterogeneous nucleation in crystallization process. Density profile of the supersaturated solution and polarization of water molecules was calculated in order to describe the effect of the surfaces on the solution structure at the solid–liquid interfaces. The formation levels of NaCl clusters heavily depended on the water orientation at the interfaces. NaCl clusters were easily formed near the Pt(100) surface compared with the NaCl(100) surface owing to a different construction of water molecules between the platinum and NaCl surface.     

Aggregation modeling of calcium carbonate particles by Monte Carlo simulation

The mechanism on aggregation of spindle granular particles of calcite was investigated for the carbonation of calcium hydroxide in aqueous suspension for the purpose of controlling morphology of CaCO₃. The experimental carbonation process was carried out in a semi-batch bubble column reactor under different conditions. Although, fine rhombic nano-particles diameter ranged from 100 to 200 nm were obtained at 291 K, a higher temperature of 300 K provided spindle granular particles with a length of 1.0–1.5 μm and a width of 0.3–0.5 μm. The average crystallite size was 28 nm for the fine rhombic nano-particles and 43 nm for the spindle granules. Zeta potential measurement for the spindle granules indicated that the suspension tended to be aggregated during the carbonation process. The effect of the degree of particle aggregation on the shape of the obtained calcite particles was studied by Monte Carlo simulations. Our simulation results elucidated the dependence of aggregation on unit particles, i.e., primary particles, on the experiment carbonation condition where the spindle granules were formed out of the unit particles under the same condition as the experiments. In addition, the formation mechanism of the granules was investigated by applying classical nucleation theory to the present simulations.     

Mechanism of intramolecular electron transfer in the photoexcited Zn-substituted cytochrome c: theoretical and experimental perspective

Photoinduced electron transfer (ET) in zinc-substituted cytochrome c (Zn-cyt c) has been utilized in many studies on the long-range ET in protein. Attempting to understand its ET mechanism in terms of electronic structure of the molecule, we have calculated an all-electron wave function for the ground-state of Zn-cyt c on the basis of density functional theory (DFT). The four molecular orbitals (MOs) responsible for excitation by UV-vis light (Gouterman's 4-orbitals) are assigned on the basis of the excited states of chromophore model for Zn-porphine complex calculated with the time-dependent DFT method. ET rates between each Gouterman's 4-orbitals and other MOs were estimated using Fermi's golden rule. It appeared that the two occupied MOs of the 4-orbitals show exclusively higher ET rate from/to particular MOs that localize on outermost amino acid residues (Lys 7 or Asn 54), respectively, whereas ET rates involving the two unoccupied MOs of the 4-orbitals are much slower. These results imply that the intramolecular ET in photoexcited Zn-cyt c is governed by the hole transfer through occupied MOs. The couplings of MOs between zinc porphyrin core and specific amino acid residues on the protein surface have been demonstrated in Zn-cyt c immobilized on an Au electrode via carboxylic acid group-terminated self-assembled monolayer. The Zn-cyt c-modified electrode showed photocurrents responsible for photoillumination. The action spectrum of the photocurrent was identical with the absorption spectrum of Zn-cyt c, indicating photoinduced electron conduction via occupied MOs. The voltage dependence of the photocurrent appeared to be linear and bidirectional like a photoconductor, which strongly supports the intramolecular ET mechanism in Zn-cyt c proposed on the basis of the theoretical calculations.     

Mechanically Strain-Induced Modification of Selenium Powders in the Amorphization Process

For the fabrication of particles designed in the nanoscale structure, or the nanostructural modification of particles using mechanical grinding process, selenium powders ground by a planetary ball mill at various rotational speeds have been investigated. Structural analyses, such as particle size distributions, crystallite sizes, lattice strains and nearest neighbour distances were performed using X-ray diffraction, scanning electron microscopy and dynamical light scattering.By grinding powder particles became spherical composites consisting of nanocrystalline and amorphous phase, and had a distribution with the average size of 2.7 m. Integral intensities of diffraction peaks of annealed crystal selenium decreased with increasing grinding time, and these peaks broadened due to lattice strains and reducing crystallite size during the grinding. The ground powder at 200 rpm did not have the lattice strain and showed amorphization for the present grinding periods. It indicates that the amorphization of Se by grinding accompanies the lattice strain, and the lattice strain arises from a larger energy concerning intermolecular interaction. In this process, the impact energy is spent on thermal and structural changes according to energy accumulation in macroscopic (the particle size distribution) and microscopic (the crystallite size and the lattice strain) range.     

Dehydration process in NaCl solutions under various external electric fields

Ionic motions at solid-liquid interface in supersaturated NaCl solutions have been investigated by molecular dynamics (MD) simulation for understanding crystal growth processes. The density profile in the vicinity of the interfaces between NaCl(100) and the supersaturated NaCl solution was calculated. Diffusion coefficients of water molecules in the solution were estimated as a function of distance from the crystal interface. It turned out that the structure and dynamics of the solution in the interfaces was different from those of bulk solution owing to electric fields depending on the surface charge. Therefore, the electric field was applied to the supersaturated solutions and dehydration phenomenon occurring in the process of the crystal growth was discussed. As the electric field increased, it was observed that the Na⁺ keeping strongly hydration structure broke out by the electric force. In supersaturated concentration, the solution structure is significantly different from that of dilution and has a complicated structure with hydration ions and clusters of NaCl. If the electric fields were applied to the solutions, the breakout of hydration structure was not affected with increasing the supersaturated ratio. This reason is that the cluster structures are destroyed by the electric force. The situation depends on the electric field or crystal surface structure.