We present a cluster model for the active site of oxidized azurin, and investigate the electronic structure of the active site of oxidized azurin by using density functional calculations with polarizable continuum model. The singly occupied molecular orbital (SOMO) and spin density in the model widely distribute around the Cu 3d x 2 −y 2 and S(Cys112) 3p orbitals. The dependency of electronic properties such as partial charge density and spin density on the dielectric constant is discussed. We find that partial spin density and charge density on the copper ion become larger, when the dielectric constant increases.

ABSTRACT:We investigate multiphoton processes in diatomic molecules. We adopt the Morse oscillator model for the vibrational state of molecules and simulate the population transfer between vibrational levels caused by molecule-laser interaction. The ground-state energy is calculated by the quadratic configurational interaction (QCISD) level ab initio molecular orbital calculation, and the potential energy curve of the ground state is fitted by the Morse potential curve to evaluate the discrete vibrational levels. An intense laser field generally causes the nonlinear optical processes in molecules, such as multiphoton excitation and ionization. We investigate the 1-, 2-, 3-, and 4-photon absorption processes in H 2 and OH molecules in relation to the laser intensity in the picosecond (ps) regime. We also apply the stimulated Raman adiabatic passage (STIRAP) method to the efficient generation of the highly vibrational excited state, using a couple of the simultaneous 2-photon absorption processes as the Stokes and pump processes.

ABSTRACT:We present two cluster models of the active site of azurin. These models are determined by two stable configurations during our molecular dynamics (MD) simulation. In MD simulation, we find two stable configurations connected by the "jump motion" of Met121. One configuration is similar to the crystal structure by X-ray analysis, and the other is not the same. We perform density functional calculations for these two models and investigate physical properties such as total energy, singly occupied molecular orbital (SOMO), and spin density for each model. We find the difference in the shape of SOMO each other. We also estimate the reduction potential for each model and discuss the reduction potential and solvent effect of each model in relation to the electron transfer, which is one of the functionality of azurin.

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ABSTRACT:One of the phospholipids, sphingomyelin (SM, is the most abundant component of mammalian membranes in brain, nervous tissues, and human ocular lens. It plays an important role for apoptosis, aging, and signal transduction. Recently, Yappert and coworkers have shown that human lens sphingomyelin and its hydrogenated derivative, dihydrosphingomyelin (DHSM) are interacted with Ca 2ϩ ions to develop human cataracts. Previously, we have investigated conformational differences between an isolated SM/DHSM molecule and Ca 2ϩ -coordinated form by using density functional theory (DFT) for geometry optimization and normal mode analysis. As a result, one of stable conformers of SMs has a hydrogen bonding between hydroxyl group and phosphate group, whereas another conformer has a hydrogen bonding between hydroxyl and phosphate amide group. In this study, 31 P-Nuclear Magnetic Resonance (NMR) shielding constants of the obtained conformers are investigated by using ab initio and DFT with NMR-gauge invariant atomic orbitals (NMR-GIAO) calculations. The experimental 31 P-NMR chemical shifts of SMs and DHSMs have significant small value around 0.1 ppm. We consider the relative conformational changes between SMs and DHSMs affect the slight deviations of 31 P-NMR chemical shifts, and discuss intramolecular hydrogen bondings and the solvent effect in relation to NMR experimental reference.