The effect of the tube length on the thermodynamic stability and chemical reactivity of finite-length armchair carbon nanotubes (CNTs) were examined by means of topological resonance energy (TRE) and algebraic structure count (ASC), respectively. Oscillations with the period of 3 were found in TRE and ASC as the tube length increased It was also found that ”Clar type” armchair CNTs, which have been shown to have non-bonding molecular orbitals (NBMO) and zero HOMO-LUMO gaps at the level of HMO theory, have minimum values of TRE and ASC in each period of the oscillations.
A solution of 3d-Ising Model with boundary conditions was studied. Because of the lack of 3d-Pfaffian we used the symmetry of a cubic lattice to obtain the final results. We obtained 23% upper value of the transition point compared with the one which was given by Monte Carlo Method for a cubic lattice.
The double ionization energies of two-site double core-hole (tsDCH) states were calculated for dicyano molecules and disilyl compounds. For dicyano molecules, the interatomic relaxation energy increases monotonically from negative value toward zero with an increase in the length of the carbon chain. For disilyl compounds, the energy first decreases from positive to negative and then approaches zero with an increase in the length of the carbon chain. The results based on density functional theory agree with those based on Hartree-Fock theory for these systems. Furthermore, the double ionization energies of single-site DCH and tsDCH states were calculated for XHm-YHn (X,Y: C,N,O,F; m,n = 0–3) systems and their fluorine substituted compounds. Using Wagner plots, initial bonding and final relaxation effects were clearly visualized.
We have developed a mapping pipe line for RNA-seq data analysis. In the mapping pipe line, we combined Bowtie and TopHat to handle splicing and improve the number of unique reads. Furthermore, we have proposed a novel algorithm to define annotation of non-coding RNA, and we have developed a data processing program using a novel algorithm. Additionally, in order to find new functional genes, we have developed an analysis program for RNA expression in the intergenic region.
Since many fatal accidents were caused by legal intoxicants and synthetic cannabis, these drugs were re-named "dangerous drugs" in July 2014. The crackdown for the drugs has been enforcing. I made a web page which shows the structures of novel compounds made by manufacturers who have chemical knowledge, and their chemical bonding state to protein by Jmol (a molecular viewer). I will point out their problems continuously with appropriate latest news.
hA2AAR antagonists are developed as drugs for the treatment of neurodegenerative disorders. First, we generated the developed structures from a 1,2,4-triazole derivative by using transformation rules of StarDrop/Nova and BIOSTER. In one case, we got 73,452 compounds of the first and second generations by using all transformation rules. There were 4,069 compounds with more suitable ADME than the first compound. In another case, we generated structures of the first, second and third generations, selecting ADME score's top 300 compounds each generation. As a result, we got the compounds having the higher score of ADME with higher probability when we used all transformation rules. Next, we evaluated 325 compounds with suitable ADME by using Torch3D. Torch3D can compare the 3D compound with 2D compounds based on electrostatic/hydrophobic/aromatic/steric characters. Finally, we got the best compound with not only the higher score of ADME than the first one but also suitable 3D molecular characters for docking to hA2AAR.
We carried out ab initio fragment molecular orbital calculations for vitamin D receptor (VDR) mutants at the RI-MP2/cc-pVDZ level, to elucidate the mechanism of hereditary vitamin D-resistant rickets caused by mutant VDR. We calculated the energies of interactions between the residues of the ligand binding pocket in the VDR and its ligands by using inter-fragment interaction energy analysis based on the fragment molecular orbital method. In all mutants, the interaction energies of Y147, F150, and Q273 were decreased. These results indicate that these residues are key to ligand recognition.
We carried out ab initio fragment molecular orbital calculations for wild-type and halogenated glutathione S-transferase (GST) at the MP2/6-31G** level. To elucidate the mechanism of structural stability of the halogenated protein, we calculated the interaction energies for all residue pairs in GST by using inter-fragment interaction energy analysis based on the fragment molecular orbital method. We were able to evaluate electrostatic and van der Waals dispersion interaction energies separately and explicitly. Differences in interaction energies of each residue pair between the two structures were interpreted as the effect of halogenation. The results show that the local interaction around halogen atoms was enhanced. The enhanced interaction effects of Cl and Br were stronger than those of F and I.
Next-generation sequencers (NGS) have made it possible to analyze entire genome sequence. NGS can be used for the identification of genes associated with a wide variety of diseases. We investigate RNAs encoded by intergenic regions to identify novel genes that are involved in respiratory diseases. The respiratory tracts of mice were exposed to lipopolysaccharide to establish a model of respiratory disease. RNA expression levels in the mouse exosome were analyzed by NGS to identify genes involved in the development of respiratory diseases. Several disease-related regions exhibited altered expression levels of intergenic RNAs.
The refractory is used to protect the furnace and to improve the efficiency of a steel making process. Most of the refractories used in the Iron making process are the castable refractories that are primarily composed of Al2O3, MgO, or Cr2O3, etc. particles. By addition of Fumed Silica, which is amorphous silica micro-particle, to the castable, densification of the refractory is found at intermediate temperature range (e.g., 500 ˚C). However, the chemical principle of this densification is not known well yet. In this study, we aim to reveal qualitatively the chemical behavior of Fumed Silica in a castable refractory by using semi-empirical Molecular Orbital calculation. The result showed that Fumed Silica and Alumina does not react at room temperature, i.e., Al-O-Si bond is not formed. We also investigated the transition state of the Alumina-Silica reaction and its activation energy, and calculated the temperature corresponding to that energy.
The maximum entropy method (MEM) is one of the key techniques for spectral analysis. The main feature is to describe spectra in low frequency with short time-series data. We adopted MEM to analyze the spectrum from the dipole moment obtained by the time-dependent density functional theory (TDDFT) calculation in real time, which is intensively studied and applied to computing optical properties. In the MEM analysis, however, the maximum lag of the autocorrelation is restricted by the total number of time-series data. We proposed that, as an improved MEM analysis, we use the concatenated data set made from several-times repeated raw data. We have applied this technique to the spectral analysis of the TDDFT dipole moment of ethylene and oligo-fluorene with n = 8. As a result, higher resolution can be obtained, which is closer to that of FT with just raw data. The efficiency and the characteristic feature of this technique are presented in this paper.
Some iron(III) complexes, including [Fe2(μ-O)(nta)2(H2O)2]2– and [Fe2(μ-O)(ida)2(H2O)4], are considered to be significant carcinogens to cause renal injuries from the result of previous animal experiments. On the other hand, similar iron(III) complex [Fe2(μ-O)(pac)2(H2O)2] is not considered to be a carcinogen. In order to clarify the differences in carcinogenicity, conformational analyses have been conducted for four dinuclear iron(III) complexes, [Fe2(μ-O)(nta)2(H2O)2]2–, [Fe2(μ-O)(edda)2(H2O)2], [Fe2(μ-O)(ida)2(H2O)4], and [Fe2(μ-O)(pac)2(H2O)2], where nitrilotriacetate [(nta)3–], ethylenediamine-N,N'-diacetate [(edda)2–], iminodiacetate [(ida)2–], and N-(2-pyridylmethyl)iminodiacetate [(pac)2–] are the chelating ligands (chelators). Based on the DFT computation, two-point interaction with hydrogen peroxide or α-helix was found to be possible for carcinogenic iron(III) complexes, [Fe2(μ-O)(nta)2(H2O)2]2– and [Fe2(μ-O)(ida)2(H2O)4], whereas the interaction was not found to be possible for non-carcinogenic iron(III) complex, [Fe2(μ-O)(pac)2(H2O)2].
Previously, we demonstrated that Cs1-xNaxMnII(CN)3 prussian blue analog exhibits high-efficient cesium adsorption, through the ion-exchange between cesium and sodium ions under applied voltage. In this study, we investigated the superexchange interaction between manganese atoms via cyano-ligand, by the use of chemical bonding rule.
Misleading classification of isomeric and stereoisomeric relationships as well as the related misleading classification of isomers and stereoisomers are discussed in terms of equivalence relationships and equivalence classes, which have not been taken into consideration in the conventional terminology of modern stereochemistry.
GPU acceleration for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. We have developed a GPU-accelerated Fock matrix preparation routine without atomic operation and implemented it into the worker module of an OpenFMO program, which is parallelized in a master-worker programming model. The GPU-accelerated program shows 1.5× speedups from CPU only FMO-HF/6-31G (d) calculation with a direct SCF method for 642 atomic protein on 8 nodes of HA-PACS base cluster.
The local pseudopotential method (PS) has been implemented into real-space electronic structure calculations based on symmetric smoothed particle hydrodynamics (SSPH). As a simple example, we applied this SSPH to a simple atom such as H, He and Li. To evaluate SSPH with PS, the results are compared with those of the finite difference method (FD), the simple SSPH, and the usual atom calculation (AT). Similar results were obtained from both of FD and the simple SSPH. However, there are several differences between the results of the simple SSPH and that of AT. When we use SSPH with PS, the results can be controlled to those of AT, using appropriate parameters. We recognize that, in our previous study, the error between the simple SSPH and AT is mainly caused by the difference of the charge in the vicinity of the ion core. The discretization by the simple SSPH is not enough to describe the electronic structure, especially the Hartree term. Since the pseudopotential around the ion core is finite, this error reduces in our SSPH with PS. Our results show that SSPH with PS can be practically applied to electronic calculations, keeping high accuracy, SSPH with PS
Interaction energies of pyridine complexes with C6F5X (X = I, Br, Cl, F and H) were studied by ab initio molecular orbital calculations. The strength of the halogen bonds follow the order Cl < Br < I. The attraction in the halogen bond with the fluorine atom is negligible. The magnitude of the electrostatic interactions is the cause of the halogen dependence of the interaction energy. The magnitude of the directionality of the halogen bonds coincides with the magnitude of the attraction. The halogen bonds of I and Br are highly directional. On the other hand the directionality of the halogen bonds of Cl is low and that for F is negligible. The electrostatic interactions are mainly responsible for the directionality of the halogen bonds.
We observed scattering light of the atomosphere by using a digital camera on Marishiten peak on Mt. Norikura at Sept 11, 2013. The RGB brightness, B/R and G/R ratio of the pixels were analized. The optical character of the black mist layer was discussed. We also observed the distribution of dilute particules in the atmosphere and the difference between zodiacal light and city light.
To establish a system for the early diagnosis of respiratory diseases, we developed a method for analyzing RNA sequence data obtained by next-generation sequencer identify genes showing altered expression as biomarkers of respiratory tract infection. The respiratory tracts of mice were exposed to lipopolysaccharide to establish a model of respiratory disease. Twenty-five genes exhibited significantly altered RNA expression following exposure. We identified non-coding RNAs in five regions that could be candidate biomarkers of respiratory diseases.
For small memory communications in the exascale computing, we are developing an Advanced Communication Primitives (ACP) library based on one-sided communication. ACP library uses Global Address (GA) data for identifying a logical address of a process. We estimated memory requirements of ACP library for four communication patterns of the OpenFMO application. The maximum memory requirement of GAs is about 1 MByte for the master process of master-worker communications. This result shows the memory requirement of GAs is considerably smaller than the available memory size of one process of exascale computer.
Photomechanical materials in which the shape change of a high polymer is extracted as motion by photoirradiation are attracting attention lately. Nevertheless, details of the complicated mechanism of this photoirradiation-induced shape change have yet to be elucidated. Using molecular dynamics and the Monte Carlo method, we have conducted molecular simulations for a case in which a straight chain oligomer is irradiated by photons. Thereby, we have investigated the interaction between an oligomer and photon as the first step in elucidating photoirradiation-induced shape change. Results show that the oligomer's light absorption and the Compton effect between a photon and an oligomer cause a chemical energy change and bring about shape change. Furthermore, short-wavelength ultraviolet radiation has been found to cause greater shape change than infrared radiation does.