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Various studies are conducted to examine the above-threshold dissociation on diatomic molecules by using nonresonant intense laser pulses. Various new methods for controlling the spectrum peaks are also discussed.

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ−phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond. [ABSTRACT FROM PUBLISHER]

We study the structures of the Hras-GTP complex and the Hras-GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras-GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg2+. Our simulations show that the averaged structure differences between the Hras-GTP complex and Hras-GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α2 -helix of Hras-GDP is shorter than the α2 -helix of Hras-GTP. The averaged number of water molecules in the first hydration sphere in Hras-GDP complex is larger than that in Hras-GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras-GTP and in Hras-GDP. In Hras-GDP complex, β-phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras-GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state, of the molecules through nuclear-electron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital, density functional theory, and other empirical strategies. The Born-Oppenheimer approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion. In this study, we introduce Morse anharmonic oscillator model to calculate average internuclear distance of diatomic molecules having X-H bonding and X-D bonding. Morse parameters are determined by fitting to potential energy surface of molecular orbital and/or density functional calculations, and then the average distance are obtained as the expectation value of the analytical Morse vibrational wavefunction. Nuclear magnetic resonance shielding constants of the H/D isotopomer are calculated again on the average distance by using GIAO with B3LYP and CCSD calculation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

We investigate multiphoton absorption, including the dissociation process in the OH molecule by means of wavepacket dynamics. The time-development scheme is the so-called split-operator method, which conserves the norm of the state vector. The resultant wavepacket involves the information of all discrete vibrational states and the dissociative continuum state substantially, so we are able to treat all the bound–bound, the bound–continuum and the continuum–continuum transitions. The energy spectra of the system under the strong laser pulse can also be obtained by the spectrum method, where the autocorrelation function of the wavepacket under consideration is Fourier transformed. First, we discuss the field intensity dependence of the population and the competition between dissociation and absorption processes in multiphoton processes of above-threshold dissociation (ATD). Then, we analyze the above-threshold dissociation due to the continuum–continuum transition in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [ABSTRACT FROM AUTHOR]

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 H2 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. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]

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. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]