We estimated surface energies of all flat surfaces of forsterite within the framework of density functional theory. We found that surface energy of (120) surface is the lowest and those of (010), (130) and (112) surfaces are followed subsequently. Morphology of forsterite at 0 K is predicted. Calculated Si K-edge XANES spectra of silicon in forsterite are consistent with experiments.
Enumeration of the conformers and conformational analysis were successfully conducted for an octahedral [M(ABC)6] complex. In this report the methods and results were briefly described. In the enumeration, 7173 conformers were found by the computational group theory method, and among them, 130 conformers were found to have stable M(AB)6 cores of S6 symmetry. The structures of the 130 conformers of [Zn(DMSO)6]2+ (DMSO: dimethylsulfoxide) were optimized by the DFT method, and the most stable conformer was obtained.
Mechanistic studies for linear cross-dimerization between 2,3-dimethylbuta-1,3-diene and 2,5-dihydrofuran by a Ru(0) complex, Ru(η6-naphthalene) (η4–1,5-COD), were performed computationally. The rate-determining steps of main and side reactions are different mechanisms, and correspond to the reductive elimination step and the oxidative coupling step, respectively. This suggests that the yield of the main product may be improved by modification of the heterocyclic compound or catalyst structure. In addition, the computational studies predicted that cross-dimerization between 2,3-dimethylbuta-1,3-diene and 2,5-dihydropyrrole may occur via a similar reaction mechanism.
Thermal conductivity of 4-n-alkyl-4'-cyanobiphenyl (nCB) simulated by using molecular dynamics method. We modified the dihedral angle parameter and the LJ parameters of the original AMBER Force Field for nCB. The dihedral angle parameter was corrected by using quantum chemical calculation, and the LJ parameters were fitted to reproduce the experimental data. Thermal conductivity was calculated by Green-Kubo Method. MD calculation using the corrected force field gave good thermal conductivity close to experimental value and successfully reproduced the anisotropy of thermal conductivity in the liquid crystal phase.
As an attempt at the electronic structure calculations of the B-type model-DNA, (poly-(guanine) poly-(cytosine)) model polymers is performed by means of ab initio crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and ions are included in the calculations. Energy band structures are calculated at 3-21G and 6-31G levels. The effective mass of hole shows a relatively large value while that of electron shows a smaller value which suggests electron conduction in the DNA backbones.
Plumbing stains grow up from invisible attachment of urea and urolith in the molecular level to biofilms in which bacteria adsorb such nutrients and secrete extracellular polymer substances. In order to understand and control such biofilm growth, we have developed a multiscale simulation that can analyze from adhesion of stains on the molecular scale to accumulation of biofilm on actual scale. In the present study, the biofilm growth and peeling by shear flow was successfully simulated for the condition of typical toilet use.
Aromatic molecules form stable charge-transfer complexes with quinones, tetracyanoethylene or halogen molecules. The charge-transfer interaction (orbital-orbital interaction) was believed to be the source of the attraction in the complexes. However, the contributions of other intermolecular interactions (dispersion, electrostatic etc.) to the attraction in the complexes are not well understood. The total interaction energy and contributions of electrostatic, induction, dispersion and orbital-orbital (exchange-repulsion and charge-transfer) interactions in the benzene-p-benzoquinone complex were studied by ab initio molecular orbital calculations. The analysis shows that the dispersion interaction is the major source of the attraction in the complex and that the orbital-orbital interaction is not attractive but even repulsive.
The mechanism of rolling frictions of wheel is discussed in relation with movement of Reuleaux-pentagons. In fact, driving and braking processes lead us to the suggestion that hysteresis-energy loss model is naturally obtained. In addition to this, the combined model of hysteresis-energy loss and differential-slip mechanisms is proposed so as to promote the computational investigations for rolling frictions of wheel.
A smartphone application for observating atmospheric state and visualizing suspended particle matter (SPM) was developed. By using the ratio of B/R, G/R and B/G, it was confirmed that the nonlinearity in the developed image can be canceled and the distribution of scattered light in the atmosphere can be observed.
As a refinement of the fluid mosaic model for explaining cell membrane functions, membrane-skeleton fence model and anchored membrane protein picket model have been proposed according to the tracing experiment of a single molecule in plasma membrane. In addition, the experimental observation that the diffusive motion of a transmembrane protein in plasma membrane leads to a normal diffusion through two-step relaxation has suggested that there are two types of nested compartments, large and small. In this paper, we propose a virtual nested two-dimensional lattice model that can express a nested compartment structure of plasma membrane using three parameters in order to represent such a single molecule diffusion movement. Using this 2D lattice model, various diffusive motion simulations of one particle random walks were performed and their trajectories were analyzed by Detrended fluctuation analysis. As a result, we have confirmed that both plasma membrane models, "fence" and "picket," can be represented by our virtual nested 2D lattice model.
The existence of an energy field that dominates the physiological mechanism of incorporating O2 in the atmosphere into the human body and excreting it outside the body as CO2 was investigated using computational chemistry techniques based on quantum theory. As a result, it was revealed that the binding, transportation, and metabolism of gas molecules depend on the weak magnetic energy induced by the earth's magnetic field (H0 = 4.5 × 10−5 T). Finally, it was concluded that the mechanism of oxygen transport and Christian Bohr's proposed”Bohr effect” depend on magnetic coupling between biomolecules.
Recently, studies of solar cells have been conducted actively. Especially, organic thin film solar cells are attracting attention for use as a next-generation flexible substrate material. The reasons include the recent advent of bulk heterojunction structures. Nevertheless, bulk heterojunction solar cells exhibit only about 10% conversion efficiency. They have remained in the study phase. One reason for their low conversion efficiency is that a bulk heterojunction conductive mechanism is so complicated that its fundamental electronic properties have not been elucidated well. This letter describes an examination of the excited state of the bulk heterojunction structure and evaluates its electronic properties. Charge densities are computed for excited and ground states. Then absorbance is computed and examined. Results suggest that the electronically excited state might come to differ from the electronic ground state in a phthalocyanine–fullerene bimolecular system. Moreover, we infer that this behavior brings about energy level change and subsequent variation in absorbance.
A numerical model, called the interaction energy projection method (IEPM), is suggested to evaluate electronic similarity among protein-ligand complexes. Herein we apply the method by referring to the "inter-fragment interaction energy (IFIE)," calculated using the fragment molecular orbital (FMO) method, in two human estrogen receptor complexes.
The N-N bond breaking of the N2 molecule on a metal surface is the key process in the ammonia synthesis using heterogeneous catalysts. Herein we discuss electronic factors in the bond cleavage on the basis of electronic-structure calculations. It is shown that the hydrogenation of the end-on coordinated N2 molecule may play an important role, which may be accompanied by electron transfer from the catalyst to N2.
We examine the effect of polarity of a ZnO substrate on the crystal growth process in physical vapor deposition via molecular dynamics simulation. First, we irradiate ZnO molecules at a velocity of 900 m/s on O-polar, Zn-polar, and nonpolar ZnO substrates and evaluate the crystallinity of the formed ZnO thin film. In the formed thin films on the O-polar and Zn-polar substrates, 8-membered rings are partly observed, while a normal ZnO crystal consists of only 6-membered rings. Thus, the formed thin films on the O-polar and Zn-polar substrates have O and Zn atomic defects. On the other hand, the formed thin film on the nonpolar substrate consists of only 6-membered rings and does not have the atomic defects. We reveal the crystal growth process of ZnO thin films at atomic scale and find that high-quality thin film is formed on the nonpolar substrate.