安藤 耕司

Molecular dynamics (MD) simulations were used to analyze the effect of the odorant molecule eugenol on the olfactory receptor protein mOR-EG and the dynamic correlation between amino acid residues around the binding site due to ligand binding. When eugenol hydrogen-bonded with Ser 113 of mOR-EG, the dynamic correlation with amino acid residues 213-218 on the adjacent α-helix increased within 10 ps. In particular, the correlation between Ser 113 and Leu 217 showed characteristic oscillations between 10 ps and 30 ps. The correlation with Leu 217 shifted toward residues closer to the G protein over time. Correlation with amino acids on the other side of the membrane was also observed, suggesting the contribution of collective protein motion.

High-harmonic generation (HHG) spectrum from a LiH molecule induced by an intense laser pulse is computed and analyzed with potential energy surfaces for electron motion (ePES) constructed from a model of localized electron wave packets (EWP) with valence-bond spin-coupling. The molecule has two valence ePES with binding energies of 0.39 hartree and 1.1 hartree. The HHG spectrum from an electron dynamics on the weaker bound valence ePES, virtually assigned to Li 2s, exhibits a dominant peak at the first harmonic without plateau and cut-off. This compares with the free electron spectrum under oscillating laser field and is comprehensive with the shape and depth of the ePES. The other valence ePES, assingned to H 1s, is deeper bound such that the overall profile of the wave function is well approximated by a Gaussian of the width comparable to the Li-H bond length. However, a small fraction, less than $10^{-3}$, of the probability density amplitude tunnels out from the bound potential with high wave number, and spreads over tens of nm's with parts recombining to the molecule due to the laser field oscillation. This minor portion of the electronic wave function is the major origin of the HHG extending up to 50 harmonic orders. Nonlinear dynamics within the potential well induced by the laser field oscillation also contributes to the HHG up to 30 harmonic orders.

<p>The recently developed quantum molecular dynamics method including nuclear quantum effects demonstrated that supercooled hydrogens exhibit intrinsic properties including a precursor of superfluidity which neither normal hydrogen liquid nor solid possesses.</p>

A new computational scheme to analyze electron transfer (ET) pathways in large biomolecules is presented with applications to ETs in bacterial photosynthetic reaction center. It consists of a linear combination of fragment molecular orbitals and an electron tunneling current analysis, which enables an efficient first-principle analysis of ET pathways in large biomolecules. The scheme has been applied to the ET from menaquinone to ubiquinone via nonheme iron complex in bacterial photosynthetic reaction center. It has revealed that not only the central Fe2+ion but also particular histidine ligands are involved in the ET pathways in such a way to mitigate perturbations that can be caused by metal ion substitution and depletion, which elucidates the experimentally observed insensitivity of the ET rate to these perturbations.

A mixed quantal-semiquantal theory is presented in which the semiquantal squeezed-state wave packet describes the heavy degrees of freedom. We first derive mean-field equations of motion from the time-dependent variational principle. Then, in order to take into account the interparticle correlation, in particular the 'quantum backreaction' beyond the mean-field approximation, we introduce the stochastic particle description for both the quantal and semiquantal parts. A numerical application on a model of O2 scattering from a Pt surface demonstrates that the proposed scheme gives correct asymptotic behavior of the scattering probability, with improvement over the mixed quantum-classical scheme with Bohmian particles, which is comprehended by comparing the Bohmian and the stochastic trajectories.

The initial-value representation (IVR) of semiclassical propagator for the semiquantal (SQ) squeezed-state wave packet (WP) is examined. The SQ IVR is derived naturally from the coherent-state path-integral theory, in which similarity and difference from the conventional semiclassical methods are transparent. The accuracy of SQ IVR is assessed numerically on assorted schemes of treating the WP width. It is found to yield accurate wave function propagation when the WP width is optimized initially on the SQ potential and its dynamical motion is frozen or damped. (C) 2013 Elsevier B.V. All rights reserved.

Intermolecular interactions in molecular crystal of 5-bromo-9-hydroxyphenalenone are analyzed by means of Bader's theory of atoms in molecules. A set of criteria to ascertain the presence of a hydrogen bond is applied to two candidates of intermolecular contacts suggested by our previous work [Otaki and Ando, Phys. Chem. Chem. Phys. 2011, 13, 10719]. It is shown that they almost satisfy the criteria to confirm the existence of intermolecular C?H center dot center dot center dot O hydrogen bond. In addition to the hydrogen bonding, other types of interactions, such as H center dot center dot center dot H and H center dot center dot center dot Br, are found in one of the candidates. The discussions are extended to explain how the molecular dipole moment is induced by surrounding molecules. It is also found that the bias in the atomic charges due to the electrophilicity of the oxygen atom is strongly correlated with the induced dipole moment. (c) 2012 Wiley Periodicals, Inc.

A semiquantal (SQ) molecular dynamics (MD) simulation method using spherical Gaussian wave packets (WPs) is applied to a microscopic analysis of hydrogen-bond (H-bond) exchange dynamics in liquid water. We focus on the molecular jump mechanism of H-bond reorientation dynamics proposed from a classical MD simulation by Laage and Hynes (Science 2006, 311, 832). As a notable quantum effect, broadenings of both the oxygen and hydrogen WPs of jumping water are observed associated with the H-bond switching events. Nonetheless, quantum effects on averaged trajectories of structural parameters measured with respect to the WP centers are rather minor. A 1/f fluctuation of local H-bond number is observed in both SQ and classical simulations. This is obtained straightforwardly from the real-time trajectories, in contrast with the originally found 1/f fluctuation (Sasai et al., J. Chem. Phys. 1992, 96, 3045) of the total potential energies collected at quenched inherent structures. The quantum effects are found to accelerate the relaxation of H-bond number fluctuation, which is reflected in the region near the lower bound of the 1/f behavior in the power spectra. New developments in the implementation of SQMD simulations including all atoms are also described. (c) 2012 Wiley Periodicals, Inc.

A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed Gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many-body molecular systems in which the local anisotropic fluctuations of nuclear WPs play an essential role. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4762840]

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling T-DA and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (H-L) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe2+ and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe2+ ion, its replacement by Zn2+, or its removal are found to affect the T-DA value by factors within 2.2. The calculated T-DA values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments.

We have developed an efficient theoretical framework of a non-Born-Oppenheimer (non-BO) nuclear and electron wave packet (NWP and EWP) method and applied it to intra- and intermolecular energies of a hydrogen dimer. The energy surface functions were derived at low computational cost. In contrast with the ordinary BO nuclear quantization on a given energy surface that reduces the effective barrier, non-trivial non-BO interactions between the EWPs and NWPs resulted in increases of intermolecular rotational and translational barriers. A direct comparison demonstrated that the non-BO effect on the intermolecular energy is significant. (c) 2012 Elsevier B.V. All rights reserved.

A simple wave packet (WP) modeling of electrons in chemical bonding is examined. It is found that floating and breathing minimal Gaussian WPs with fully non-orthogonal perfect-pairing valence-bond spin coupling yield the ground state potential energy surfaces of LiH, BeH2, CH2, and H2O molecules of comparable quality to a high-level ab initio electron-correlated calculations. A simple form of core pseudopotential with two parameters is shown to give proper modeling of core-valence interactions. (C) 2011 Elsevier B. V. All rights reserved.

The vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to a harmonic bath are examined to assess the applicability of the time correlation function (TCF), the response function, and the semiclassical frequency modulation (SFM) model to the calculation of infrared (IR) spectra. These three approaches are often used in connection with the molecular dynamics simulations but have not been compared in detail. We also analyze the vibrational energy relaxation (VER), which determines the line shape and is itself a pivotal process in energy transport. The IR spectra and VER are calculated using the generalized Langevin equation (GLE), the Gaussian wavepacket (GWP) method, and the quantum master equation (QME). By calculating the vibrational frequency TCF, a detailed analysis of the frequency fluctuation and correlation time of the model is provided. The peak amplitude and width in the IR spectra calculated by the GLE with the harmonic quantum correction are shown to agree well with those by the QME though the vibrational frequency is generally overestimated. The GWP method improves the peak position by considering the zero-point energy and the anharmonicity although the red-shift slightly overshoots the QME reference. The GWP also yields an extra peak in the higher-frequency region than the fundamental transition arising from the difference frequency of the center and width oscillations of a wavepacket. The SFM approach underestimates the peak amplitude of the IR spectra but well reproduces the peak width. Further, the dependence of the VER rate on the strength of an excitation pulse is discussed. (C) 2011 American Institute of Physics. [doi:10.1063/1.3594093]

By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T-DA of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T-DA. Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T-DA for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3594100]

The molecular mechanisms in both vibrational relaxation and proton transfer (PT) associated with infrared (IR)-induced PT in a dilute hydrofluoric acid solution at ambient temperature are studied by molecular dynamics (MD) simulations with the multistate empirical valence bond model. To investigate the solvation dynamics, a collective solvent coordinate and its perpendicular bath modes are defined from the diabatic energy gap and their motions are examined by the generalized Langevin equation (GLE) formalism. The GLE analysis using the equilibrium MD simulation shows that the major solvent reorganizations in the PT are represented by the libration and hindered translation. In particular, the libration gives the stronger coupling to the solvent reorganization and the faster relaxation. The nonequilibrium MD simulation demonstrated that both the HF stretching vibration and the solvent reorganization relax on a similar time scale and thus compete in the PT. It also supported the "presolvation mechanism" for the PT in this system.

We have performed the multistate empirical valence bond (MS-EVB) molecular dynamics simulations of a dilute hydrofluoric acid solution at ambient temperature to study the hydration structure associated with its weak acidity. The developed MS-EVB model showed reasonable agreement with experimental and previous ab initio molecular dynamics and reference interaction site model self-consistent field simulations for the free energy and structural properties. The local tetrahedral and translational order parameters around the fluorine atom significantly increase in the transition and product states of the HF dissociation reaction. This indicates that the angular and translational rearrangements of the hydrogen-bond topology are necessary especially around the fluorine atom. At the transition state of the proton transfer, the tetrahedral order parameters are very large, whereas the translational order parameters are not. This suggests that for the proton transfer to occur the large angular rearrangements of the hydrogen-bond topology are more necessary than the translational ones.

We present a novel pathway analysis of super-exchange electronic couplings in electron transfer reactions using localized molecular orbitals from multi-configuration self-consistent field (MCSCF) calculations. In our analysis, the electronic coupling and the tunneling pathways can be calculated in terms of the configuration interaction (CI) Hamiltonian matrix obtained from the localized MCSCF wave function. Making use of the occupation restricted multiple active spaces (ORMAS) method can effectively produce the donor, acceptor, and intermediate configuration state functions (CSFs) and CIs among these CSFs. In order to express the electronic coupling as a sum of individual tunneling pathways contributions, we employed two perturbative methods: Lowdin projection-iteration method and higher-order super-exchange method. We applied them to anion couplings of butane-1,4-diyl and pentane-1,5-diyl. The results were (1) the electronic couplings calculated from the two perturbative methods were in reasonable agreement with those from a non-perturbative method (one-half value of the energy difference between the ground and first excited states), (2) the main tunneling pathways consisted of a small number of lower-order super-exchange pathways where bonding, anti-bonding, or extra-valence-shell orbitals were used once or twice, and (3) the interference among a huge number of higher-order super-exchange pathways significantly contributed to the overall electronic coupling, whereas each of them contributed only fractionally. Our method can adequately take into account both effects of non-dynamical electron correlation and orbital relaxation. Comparing with the analyses based on the Koopmans' theorem (ignoring both effects) and the ORMAS-CIs from frozen localized reference orbitals (ignoring the effect of orbital relaxation), we discuss these effects.

Dielectric properties of the hydrogen-bonded material, 5-bromo-9-hydroxyphenalenone (C13H7O2Br; BrHPLN), are investigated theoretically by means of electronic structure calculations and Monte Carlo simulations. The density functional calculations of BrHPLN crystals have revealed that the polarization per one molecule can be about 1.7 times larger than that of the isolated monomer. It is also found that there exists significant electron density (0.01 e bohr(-3)) in an intermolecular C-H center dot center dot center dot O region, which, together with the interatomic distances of 2.39 angstrom for H center dot center dot center dot O and 3.34 angstrom for C center dot center dot center dot O, suggests the existence of intermolecular weak hydrogen bonding that may enhance the molecular polarization. The induced polarization effects in various intermolecular configurations are evaluated with the Fragment Molecular Orbital method. In addition to the pi-pi stacking interactions, two types of "in plane'' intermolecular weak hydrogen-bonding configurations are found to affect the molecular dipole moment most significantly. These effects are efficiently included in a Monte Carlo simulation method in terms of "dipole corrections'' as functions of both the intermolecular arrangements and the intramolecular proton configurations. The application to the dielectric phase transition of a BrHPLN crystal shows that the dipole corrections almost double the transition temperature, toward better agreement with experiments, and qualitatively affect the temperature dependence of the dielectric constant. Discussions are given to support that the results will remain adequate and consistent even after explicit inclusion of the quantum tunneling effects.

Structural and energetic reorganizations in redox reaction of type 1 copper proteins are studied by density functional and ab initio molecular orbital calculations. Model complexes of the active site with varying number of ligands, from Cu(SCH3)(0/+) to Cu(SCH3)(Im)(2)(S(CH3)(2))(0/+), where Im denotes imidazole, are investigated. Following the findings of structural instability in Cu(I) X(SCH3)(Im)(2) and its stabilization by the addition of the axial methionine (Met) ligand model, the structure and energetics are examined as functions of the Cu-S-Met distance in the range of 2.1-3.3 angstrom. The reorganization energies in both redox states exhibit a minimum at the Cu-S-Met distance of similar to 2.4 angstrom, whereas the ionization potential increases monotonically. The changes of reorganization energies correlate well with one of the Cu-N-His distances rather than the Cu-S-Cys distance. The estimated Arrhenius factor for oxidation of plastocyanin by P700(+) (in photosystem I) changes by an order of magnitude when the Cu-S-Met distance fluctuates between 2.4 and 3.0 angstrom, whereas the factor for reduction of plastocyanin by cytochrome f is nearly constant. Together with the data from our previous classical molecular dynamics simulation of solvated protein, we argue that the electron transfer rate is affected, and thus may be controlled, by the fluctuation of a weakly bound axial Met ligand. We also present the assessment of various exchange-correlation functionals, including those with the long-range correction, against the CCSD(T) reference and on the basis of a perturbative adiabatic connection model. For Cu(SCH3) and Cu(SCH3)(Im), simple correlations have been found between the reorganization energies and the amount of Hartree-Fock exchange. (C) 2010 American Institute of Physics. [doi:10.1063/1.3495983]

Quantum effects such as zero-point energy and delocalization of wave packets (WPs) representing water hydrogen atoms are essential to understand anomalous energetics and dynamics in water. Since quantum calculations of many-body dynamics are highly complicated, no one has yet directly viewed the quantum WP dynamics of hydrogen atoms in liquid water. Our semiquantum molecular dynamics simulation made it possible to observe the hydrogen WP dynamics in liquid water. We demonstrate that the microscopic WP dynamics are closely correlated with and actually play key roles in the dynamical rearrangement in the hydrogen-bond network (HBN) of bulk water. We found the quantum effects of hydrogen atoms on liquid water dynamics such as the rearrangement of HBN and the concomitant fluctuation and relaxation. Our results provide new physical insights on HBN dynamics in water whose significance is not limited to pure liquid dynamics but also a greater understanding of chemical and biological reactions in liquid water. (C) 2010 American Institute of Physics. [doi:10.1063/1.3397809]

A semiquantal wave packet modeling of electrons in chemical bonding is presented. It is based on the valence bond (VB) theory with non-orthogonal floating and breathing spherical Gaussian orbitals, simplified to treat many electrons by decoupled electron pair approximations (DPA) and core pseudopotentials (CPP). The extended Hamiltonian formalism offers pictorial interpretation and analysis in the extended phase space of the wave packet center and width coordinates. The numerical calculations are demonstrated on the ground state potential energy surfaces of H-2, LiH, and BeH2. For LiH, the perfect-pairing VB (VB-PP) calculation with the minimal orbitals gives an accurate potential energy curve of comparable quality with a correlated ab initio calculation. The two-electron VB calculation with a CPP underestimates the binding energy but gives qualitatively correct potential energy curves. For BeH2, the VB-PP with CPP gives reasonably accurate potential energy surface along both the stretching and bending coordinates. A few versions of DPA are developed and assessed, aiming toward large scale dynamic simulations. A scaling ansatz is introduced and examined on the bonding potential energy surfaces. The efficacy of the theory for studying linear and nonlinear electronic polarizations is also illustrated via an analysis of potential energy surfaces in the extended phase space.

Semiquantum liquid water molecular dynamics simulation was developed using the time-dependent Hartree approach. The classical intra- and intermolecular potential functions of water were extended to describe the wave packet (WP) hydrogen atoms. The equations of motion with an extended phase space including auxiliary coordinates and momenta representing the hydrogen WP widths were derived and solved. The molecular dynamics simulation of semiquantum water demonstrated that the semiquantum hydrogen atoms make the liquid water less structured and the hydrogen bonds weakened. The poor structurization in liquid water was inferred from the increased mobility of a water molecule and the redshift of OH stretching frequency. The zero-point energy introduced by the semiquantum hydrogens enhances the anharmonic potential effects and contributes to the redshifted OH stretching vibration. We found a significant peak around 4400 cm(-1) in the absorption spectrum resulting from the energy exchange between the WP width dynamics and the coupling of the OH stretching mode and the rotational motion of each water. We proposed that a liquid free energy landscape is smoothed due to semiquantum hydrogen atoms, and influences the liquid structure and dynamics.

Equilibrium and nonequilibrium dynamics of a blue copper protein plastocyanin in an oxidized state are studied by molecular dynamics (MD) simulation. Potential energy functions of the lowest seven electronic states, including ligand-to-metal charge-transfer (LMCT) and copper d -&gt; d excited states, were taken from our previous work (Ando, K. J. Phys. Chem. B 2004, 108, 3940), which employed ab initio molecular orbital and density functional calculations on the active-site model. The equilibrium MD simulations in the ground state indicate that ligand motions coupled to transition from the ground state to the LMCT state are mostly represented by stretching and bending vibrations of the Cu-S(Cys) distance, N-delta(His)-Cu-N-delta(His) angle, and S(Cys)-Cu-[N-delta(HiS)](2) trigonal pyramid structure. The nonequilibrium dynamics on the LMCT potential exhibit rapid decays in which surface crossings to the d -&gt; d and the first excited states occur in 70-80 fs. The crossing dynamics mostly correlate with cleavage of the Cu-S(Cys) bond and the associated response in the N-delta(His)-Cu-N-delta(His) moiety. The average dynamics of the vertical energy gap coordinates exhibit an overdamped decay with a recurrence oscillation in 500 fs, which shows clear coherence surviving after the ensemble averaging. This oscillation stems mostly from the recoiling motion of the N-delta(His)-Cu-N-delta(His) part. The dynamics of the energy gaps after this coherent oscillation are randomized such that the ensemble average yields flat profiles along time, although each single trajectory exhibits fluctuations with amplitudes large enough to reach surface crossings. These indicate that the relaxation from the LMCT state first occurs via ballistic and coherent potential crossings in 70-80 and 500 fs, followed by thermally activated random transitions.

The semiquantal time-dependent Hartree (SQTDH) theory is applied to the coupled Morse and modified Lippincott-Schroeder (LS) model potentials of hydrogen bond. The structural correlation between the heavy atoms distance and the proton position, the geometric isotope effect, the energy of hydrogen bond formation, and the proton vibrational frequency shift are examined in a broad range of structural parameters. In particular, the geometric isotope effect is found to depend notably on the choice of the potential model, for which the LS potential gives the isotope shift of the heavy atoms distance in the range of 0.02-0.04 angstrom, in quantitative agreement with the experimental findings from assortment of hydrogen bonding crystals. The fourth-order expansion approximation to the semiquantal extended potential was confirmed to be highly accurate in reproducing the full SQTDH results. The approximation is computationally efficient and flexible enough to be applied to general models of hydrogen bond. (c) 2006 American Institute of Physics.

The structural correlation and the geometric isotope effects in hydrogen-bond crystals are studied by the semiquantal time-dependent Hartree (SQTDH) approach recently developed [K. Ando, J. Chem. Phys. 121, 7136 (2004)]. The theory is demonstrated to provide accurate ground state wave functions for both weak and strong hydrogen bonds via a simple potential minimization procedure in an extended phase space of the variational parameters. It is shown that the asymmetry of the potential energy surface plays a significant role in affecting the correlation between A-H and A(...)B distances in A-(HB)-B-... hydrogen bonds in such a way as to explain the observed variation of experimental data from a variety of compounds. The calculated geometric isotope effect on the A(...)B distance induced by deuteration is 0.02 angstrom or less, in agreement with experiments on normal compounds. The origin of the exceptionally large geometric isotope effects observed in some crystals having zero dimensional hydrogen-bond network is discussed on the basis of the present results.