The information on protein molecule structure at atomic resolution is useful for various purposes such as understanding the mechanism of chemical reaction and developing medicines for therapy. We manage Protein Data Bank (PDB), the archive of such data. We receive the deposition of structural data determined by experimental method, and provide the archive which is accessible with no charge. PDB was established in 1971 with seven structures. Recently the number of entries increased dramatically by developing the experimental method and now we keep more than 100,000 PDB entries. PDB includes various structures such as myoglobin (PDB entry 1mbn (Figure 1), which is the first structure of the protein) and hemoglobin, which is composed of four myoglobin-like chains. We also provide interactive interface "Yorodumi"(Figure 2), which enables the operation of molecules by mouse action. Another feature of our site is a Japanese keyword search (Figure 3).
Computational group theory (CGT) method investigations have been conducted for a hexakis-methylamine nickel(II) complex cation [Ni(CH3NH2)6]2+ [hexakis(methylamine-κN)nickel(II) dication] to find 54 possible conformers. Considering all the conformers, six conformers have been finally obtained after optimization based on the Density Functional Theory (DFT) computations. The most stable conformer has been found to be a helical conformer (C1 symmetry), which is suitable for avoiding steric repulsion between adjacent ligands. A related zinc(II) complex ([Zn(CH3NH2)6]2+) has also been investigated, and the same conformer was found to be the most stable. Since the energy differences among the conformers have been found to be very small, the conformers are thought to be mixed at room temperature, and the dominant species are thought to be changeable by environment for both complexes.
Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Our work is the first development and application of the diagonal BO correction (DBOC) based on spin-free relativistic Hamiltonians. We used the second and infinite-order Douglas-Kroll-Hess Hamiltonians at their spin-free levels. Our test calculations of noble atoms (He – Xe) show that the DBOC energy (EDBOC) is approximately proportional to atomic number Z. Hence the BO correction generally increases when a molecule contains heavier atoms. We also computed the adiabatic corrections to the barrier heights for linearization of H2X molecules where X = O, S, Se, and Te, to discuss DBOC corrections for heavy elements.