There are several formats to describe PDB structural data and I introduce them in this article. Each format file is available from the PDBj web site (Figure 1). The most historical format is PDB format (Figure 2). It is 80 columns fixed format and the included information is partial. Moreover it includes some free description sections and it is not suitable for computational processing. As it will be phased out in 2016, it is recommended to use the current canonical format PDBx/mmCIF (Figure 3). It is defined by the extension of STAR format, which can include flexible length of lines. wwPDB also provides XML translated format PDBML (Figure 4). One can use general XML purser for it, but the file size is larger than PDBx/mmCIF. In the PDBx/mmCIF and PDBML, two types of ids for items such as atoms and residues are defined. One is author-defined id, which is not always sequential and may include non-numerical strings. The other is defined by wwPDB, which follows the systematic rule.
Probability density distribution in the 3-dimensional representation of hydrogen 1s, 2s, and 3s orbitals in a 5 x 5 x 8 cm3 (Figure 4: top) or a 4 x 4 x 8 cm3 glass block (Figure 4: bottom) was developed . It was compared with 3-D isosurface models (Figure 3 (a-d)). Isosurface models can hardly show the entire region where an electron can be found. On the other hand, in the diagram of probability density distribution models, an electron is found everywhere around the nucleus. The density of the dots sculptured in the glass block shows the probability density of finding an electron, so the nodal plane is well described as spherical shell(s) where the dots cannot be found. In the diagram of probability density distribution model, we can compare the size of 1s orbital with that of 2s or 3s orbital from their distribution regions.
Some iron(III) complexes, including [Fe2(μ-O)(nta)2(H2O)2]2– (1), [Fe2(μ-O)(edda)2(H2O)2] (2), and [Fe2(μ-O)(ida)2(H2O)4] (3), are considered to be carcinogens causing renal injuries according to the results of previous animal experiments, where nitrilotriacetate [(nta)3–], ethylenediamine-N,N'-diacetate [(edda)2–], and iminodiacetate [(ida)2–] are the chelating ligands (chelators). On the other hand, a similar iron(III) complex [Fe2(μ-O)(pac)2(H2O)2] (4) is not considered to be a carcinogen, where N-(2-pyridylmethyl) iminodiacetate [(pac)2–] is the chelating ligand. In order to clarify the differences in carcinogenicity, the structures of complexes 1–4 were investigated based on the density functional theory (DFT) method, because the structures of complexes had not been clarified in solution. As a result, two-point interaction with hydrogen peroxide or α-helix was found to be possible for carcinogenic iron(III) complexes 1 and 3, whereas the interaction was found to be impossible for non-carcinogenic iron(III) complex 4.
The reaction mechanism of lutidine derivative formation, 3, 5-diacetyl-1, 4-dihydro-2, 6-Dimethylpyridine, 3, 5-dibenzoyl-1, 4-dihydro-2, 6-dimethylpyridine and 3, 5-dibenzoyl-1, 4-dihydro-2, 6-diphenyl-pyridine from the corresponding β-diketone is studied by using B3LYP/6-31G** level and partly MP2/6-31G** level. The optimized structures and the transition state structures of all the elementary reactions are calculated. The activation energy of the elementary reaction of the formation of reaction intermediate FLUORAL-P is greatly reduced from 47.15 kcal/mol to 25.35 kcal/mol at PCM MP2/6-31G** level when adding one H2O molecule.
After the accident of Fukushima's nuclear power plant, soil contamination was caused by radioactive cesium. In this study, the new cesium-adsorbent: Cs1-xNaxMnII(CN)3 Prussian blue analogue was theoretically designed to solve the problem. In Prussian blue (iron cyano-compound), both water defect and iron vacancy are closely related to cesium-adsorption. On the other hand, in Cs1-xNaxMnII(CN)3, the cesium-adsorption mechanism is completely different. Hybrid Kohn-Sham DFT calculations were performed to investigate the cesium-adsorption mechanism. It was concluded that more stable and efficient cesium-adsorption can be realized by the ion exchange between counter cations (between sodium and cesium ions), under applied voltage.