We examined the published data for the binding affinity of typical ligands to the α-subtype of the human estrogen receptor with use of an approximate molecular orbital method applicable to interacting molecular clusters. An ab initio procedure for “molecular fragments” proposed recently to deal with such macromolecules as proteins was applied to the molecular orbital calculations. The receptor ...

So far, we still lack a clear molecular mechanism to explain the protein-ligand interaction on the basis of electronic structure of a protein. By combining the calculation of the full electronic structure of a protein along with its hydrophobic pocket and the perturbation theory, we found out two rules on the protein-ligand interaction. One rule is that the interaction only occurs between the l...

Thin films of vapor-deposited Ni(II) and Co(II) complexes of tetraphenylporphyrin (NiTPP and CoTPP) were studied supported on gold and embedded in Al-Al(2)O(3)-MTPP-Pb tunnel diodes, where M = Ni or Co. Thin films deposited onto polycrystalline gold were analyzed by ultraviolet photoelectron spectroscopy (UPS) using He I radiation. Scanning tunneling microscopy (STM) and orbital-mediated tunnel...

We present our perspective and goals on highperformance computing for nanoscience in accordance with the global trend toward “peta-scale computing.” After reviewing our results obtained through the grid-enabled version of the fragment molecular orbital method (FMO) on the grid testbed by the Japanese Grid Project, National Research Grid Initiative (NAREGI), we show that FMO is one of the best c...

Density functional theory is applied to the computation of the adsorption energy (DEads) for a series of molecules on c-Al2O3. Three different cluster models are used to represent the c-Al2O3 surface. The molecules of interest all contain a phosphonyl (P@O) functional group and adsorb via formation of a donor bond between the O atom and a threefold-coordinated tetrahedral Al [Al(Td)] surface si...

Molecular crystals from thiophene molecules can be doped with TCNQ-F4 molecules for use in all-organic optoelectronic and semiconductor devices. The charge transfer and the molecular orbital energy level formation in between these two organic molecules are investigated here by density functional theory calculations. The isolated molecules are calculated nonbonded and bonded together, forming a ...

Herein, the interaction of hydrogen sulfide with inside and outside single-wall carbon nanotube of (5,0) and (5,5) is investigated using density functional theory at B3LYP/6-31G* level of theory in the gaseous phase by Gaussian 09. The adsorption energies, thermodynamic properties, highest occupied molecular orbital, lowest unoccupied molecular orbital, energy gaps, and partial charges of the i...

Molecular dynamics (MD) simulation and Density functional theory (DFT) methods were applied to the two thiocarbohydrazides derivatives (T1 and T2) as corrosion inhibitors for carbon steel in aqueous phase. Experimental results have shown that the corrosion rate follows the below order: T1>T2. Quantum chemical parameters such as hardness (η), electrophilicity (ω),polarizability (α), dipole momen...

Density functional theory (DFT) calculations were performed to investigate adsorptions of vitamin C (Vit) on the surface a fullerene structure (Ful) in gaseous and water–solvated systems. Two models of Vit including OVit and MVit were created based on the original structure of Vit for OVit and methylation of all hydroxyl groups for MVit. All singular and hybrid structures were optimized and the...