Biomedical subjects

Hiroki Nakamura

Publications and source records attributed to Hiroki Nakamura.

14 recordsLinked to original sources

PubMed2006

Dynamics of nonadiabatic chemical reactions.

New methods are proposed to treat nonadiabatic chemical dynamics in realistic large molecular systems by using the Zhu-Nakamura (ZN) theory of curve-crossing problems. They include the incorporation of the ZN formulas into the Herman-Kluk type semiclassical wave packet propagation method and the trajectory surface hopping (TSH) method, formulation of the nonadiabatic transition state theory, and its application to the electron transfer problem. Because the nonadiabatic coupling is a vector in multidimensional space, the one-dimensional ZN theory works all right. Even the classically forbidden transitions can be correctly treated by the ZN formulas. In the case of electron transfer, a new formula that can improve the celebrated Marcus theory in the case of normal regime is obtained so that it can work nicely in the intermediate and strong electronic coupling regimes. All these formulations mentioned above are demonstrated to work well in comparison with the exact quantum mechanical numerical solutions and are expected to be applicable to large systems that cannot be treated quantum mechanically numerically exactly. To take into account another quantum mechanical effect, namely, the tunneling effect, an efficient method to detect caustics from which tunneling trajectories emanate is proposed. All the works reported here are the results of recent activities carried out in the author's research group. Finally, the whole set of ZN formulas is presented in Appendix.

Chemical Phenomena↗

PubMed2006

Laser control of reactions of photoswitching functional molecules.

Laser control schemes of reactions of photoswitching functional molecules are proposed based on the quantum mechanical wave-packet dynamics and the design of laser parameters. The appropriately designed quadratically chirped laser pulses can achieve nearly complete transitions of wave packet among electronic states. The laser parameters can be optimized by using the Zhu-Nakamura theory of nonadiabatic transition. This method is effective not only for the initial photoexcitation process but also for the pump and dump scheme in the middle of the overall photoswitching process. The effects of momentum of the wave packet crossing a conical intersection on the branching ratio of products have also been clarified. These control schemes mentioned above are successfully applied to the cyclohexadiene/hexatriene photoisomerization (ring-opening) process which is the reaction center of practical photoswitching molecules such as diarylethenes. The overall efficiency of the ring opening can be appreciably increased by using the appropriately designed laser pulses compared to that of the natural photoisomerization without any control schemes.

Journal Article↗

PubMed2006

Semiclassical treatment of thermally activated electron transfer in the intermediate to strong electronic coupling regime under the fast dielectric relaxation.

The generalized nonadiabatic transition-state theory (NA-TST) (Zhao, Y.; et al. J. Chem. Phys. 2004, 121, 8854) is used to study electron transfer with use of the Zhu-Nakamura (ZN) formulas of nonadiabatic transition in the case of fast dielectric relaxation. The rate constant is expressed as a product of the well-known Marcus formula and a coefficient which represents the correction due to the strong electronic coupling. In the case of general multidimensional systems, the Monte Carlo approach is utilized to evaluate the rate by taking into account the multidimensionality of the crossing seam surface. Numerical demonstration is made by using a model system of a collection of harmonic oscillators in the Marcus normal region. The results are naturally coincident with the perturbation theory in the weak electronic coupling limit; while in the intermediate to strong electronic coupling regime where the perturbation theory breaks down the present results are in good agreement with those from the quantum mechanical flux-flux correlation function within the model of effective one-dimensional mode.

Journal Article↗

PubMed2006

Tunneling splitting of energy levels and rotational constants in the vinyl radical C2H3.

The instanton theory newly implemented by two of the authors (G.V.M. and H.N.) is applied to hydrogen tunneling transfer in a vinyl radical. The converged instanton trajectory is found on the CCSD(T)/aug-cc-pVTZ level of an ab initio potential energy surface. The calculated ground-state energy splitting agrees with the recent high-resolution experimental data within 3% of discrepancy. The semiclassical wave function is used to estimate the splitting of the principal rotational constants of the radical.

Journal Article↗

PubMed2006

HOCl Ro-vibrational bound-state calculations for nonzero total angular momentum.

The Lanczos homogeneous filter diagonalization method has been employed to compute the HOCl ro-vibrational states for a range of total angular momenta (J = 0, 1, 5, 10, 11, 20, 30) on a newly developed ab initio potential energy surface by Nanbu et al. (J. Theor. Comput. Chem. 2002, 1, 263). For such computationally challenging calculations, a parallel computing strategy has been incorporated into our method to perform the matrix-vector multiplications. For the computed low bound states, a spectroscopic assignment has been made and the widely used approximate adiabatic rotation method has been tested for the broad range of total angular momenta for this deep-well system. Comparison of experimental results with exact quantum mechanical calculations for the selected far-infrared transitions involving the range of total angular momenta has been made possible for the first time.

Computer Simulation↗

PubMed2006

Generalized trajectory surface hopping method based on the Zhu-Nakamura theory.

We present a generalized formulation of the trajectory surface hopping method applicable to a general multidimensional system. The method is based on the Zhu-Nakamura theory of a nonadiabatic transition and therefore includes the treatment of classically forbidden hops. The method uses a generalized recipe for the conservation of angular momentum after forbidden hops and an approximation for determining a nonadiabatic transition direction which is crucial when the coupling vector is unavailable. This method also eliminates the need for a rigorous location of the seam surface, thereby ensuring its applicability to a wide class of chemical systems. In a test calculation, we implement the method for the DH(2) (+) system, and it shows a remarkable agreement with the previous results of C. Zhu, H. Kamisaka, and H. Nakamura, [J. Chem. Phys. 116, 3234 (2002)]. We then apply it to a diatomic-in-molecule model system with a conical intersection, and the results compare well with exact quantum calculations. The successful application to the conical intersection system confirms the possibility of directly extending the present method to an arbitrary potential of general topology.

Journal Article↗

PubMed2006

Ab initio nonadiabatic quantum dynamics of cyclohexadiene/hexatriene ultrafast photoisomerization.

Reaction mechanisms of the ultrafast photoisomerization between cyclohexadiene and hexatriene have been elucidated by the quantum dynamics on the ab initio potential energy surfaces calculated by multireference configuration interaction method. In addition to the quantum wave-packet dynamics along the two-dimensional reaction coordinates, the semiclassical analyses have also been carried out to correctly estimate the nonadiabatic transition probabilities around conical intersections in the full-dimensional space. The reaction time durations of radiationless decays in the wave-packet dynamics are found to be generally consistent with the femtosecond time-resolution experimental observations. The nonadiabatic transition probabilities among the ground (S0), first (S1), and second (S2) excited states have been estimated by using the semiclassical Zhu-Nakamura formula considering the full-dimensional wave-packet density distributions in the vicinity of conical intersections under the harmonic normal mode approximation. The cyclohexadiene (CHD) ring-opening process proceeds descending on the S1(1 1B) potential after the photoexcitation. The major part of the wave-packet decays from S1(1 1B) to S1(2 1A) by the first seam line crossing along the C2-symmetry-breaking directions. The experimentally observed ultrafast S1-S0 decay can be explained by the dynamics through the S1-S0 conical intersection along the direction toward the five-membered ring. The CHD: hexatriene (HT) branching ratio is estimated to be approximately 5:5, which is in accordance with the experiment in solution. This branching ratio is found to be mainly governed by the location of the five-membered ring S1-S0 conical intersection along the ground state potential ridge between CHD and HT.

Journal Article↗

PubMed2005

Incorporation of nonadiabatic transition into wave-packet dynamics.

Nonadiabatic wave-packet dynamics is factorized into purely adiabatic propagation and instantaneous localized nonadiabatic transition. A general formula is derived for the quantum-mechanical local nonadiabatic operator which is implemented within the framework of the R-matrix method. The operator can be used for incorporating the nonadiabatic transition in semiclassical wave-packet dynamics.

Journal Article↗

PubMed2005

Instanton theory for the tunneling splitting of low vibrationally excited states.

We develop the instanton theory for calculating the tunneling splitting of excited states. For the case of low vibrational quantum states we derive a canonically invariant formula which is applicable to a multidimensional system of arbitrary Riemannian metric. The effect of multidimensionality in relation to the vibrational excitation is explained in terms of the effective frequencies along the instanton trajectory. The theory is demonstrated to work well by taking HO2 molecule as an example.

Free Radicals↗

PubMed2005

Laser control of electronic transitions of wave packet by using quadratically chirped pulses.

An effective scheme is proposed for the laser control of wave packet dynamics. It is demonstrated that by using specially designed quadratically chirped pulses, fast and nearly complete excitation of wave packet can be achieved without significant distortion of its shape. The parameters of the laser pulse can be estimated analytically from the Zhu-Nakamura theory of nonadiabatic transition. If the wave packet is not too narrow or not too broad, then the scheme is expected to be utilizable for multidimensional systems. The scheme is applicable to various processes such as simple electronic excitation, pump-dump, and selective bond breaking, and it is actually numerically demonstrated to work well by taking diatomic and triatomic molecules (LiH, NaK, H(2)O) as examples.

Journal Article↗

PubMed2004

Evaluation of canonical and microcanonical nonadiabatic reaction rate constants by using the Zhu-Nakamura formulas.

We consider a problem of calculating both thermal and microcanonical rate constants for nonadiabatic chemical reactions. Instead of using the conventional transition state theory, we use a generalized seam surface and introduce a concept of a coordinate dependent effective nonadiabatic transition probability based on the Zhu-Nakamura theory which can treat the nonadiabatic tunneling properly. The present approach can be combined with Monte Carlo method so as to be applicable to chemical reactions in complicated systems. The method is demonstrated to work well in wide energy and temperature range. Numerical tests also show that it is very essential for accurate evaluation of the thermal rate constant to use the generalized seam surface and take into account the nonadiabatic tunneling effect.

Journal Article↗

PubMed2004

Simple and accurate method to evaluate tunneling splitting in polyatomic molecules.

A practical and accurate semiclassical method for calculating the tunneling splitting of the ground state in polyatomic molecules is presented based on a recent version of the instanton theory [J. Chem. Phys. 115, 6881 (2001)]. The method uses ab initio quantum chemical data for the potential energy surface without any concomitant extrapolation and requires only a small number of ab initio data points to get convergence even for large molecules. This enables one to use an advanced level of electronic structure theory and achieve a high accuracy of the result. The method is applied to the 9-atomic malonaldehyde molecule by making use of the potential energy surface at the level of CCSD(T) with the hybrid basis set of aug-cc-pVTZ (for oxygen atoms and the transferred hydrogen atom) and cc-pVTZ (for other atoms).

Journal Article↗

PubMed2004

Clinical impact of strip biopsy for early gastric cancer.

BACKGROUND: The impact of EMR (strip biopsy method) on the selection of subsequent treatment for early gastric cancer was analyzed retrospectively. METHODS: A total of 163 consecutive patients with gastric epithelial tumors (186 lesions) underwent strip biopsy. On the basis of pretherapeutic findings, the indications for strip biopsy were classified into 4 groups: benign-malignant borderline group (93 lesions), curative indication group (65), diagnostic indication group (22), and palliative indication group (6). The clinical impact of the strip biopsy result on the subsequent treatment strategy was assessed. RESULTS: Of the lesions in the benign-malignant borderline group, 36.6% were intramucosal cancer. In the curative indication group, the results of strip biopsy differed from the pretherapeutic findings for 7.7% of the lesions. Strip biopsy was effective treatment for all lesions in the benign-malignant borderline group and for 92.3% of those in the curative indication group. Strip biopsy avoided unnecessary surgery in 50% of patients in the diagnostic indication group and 16.7% of those in the palliative indication group. After the strip biopsy results were explained, 50% of the patients in the palliative indication group reversed their initial decision and opted for surgery. Strip biopsy results reversed the decision for surgery, which had been based on inaccurate pretherapeutic information, in 20% of cases of early gastric cancer. CONCLUSIONS: Strip biopsy has a major clinical impact, because it provides an accurate diagnosis, aids in the selection of an appropriate treatment strategy, and reduces unnecessary surgery.

Biopsy↗

PubMed2004

Molecular epidemiologic analysis of hepatitis C virus infection in injecting drug users with acute hepatitis C in Japan.

BACKGROUND AND AIM: The aim of this study was to examine whether particular hepatitis C virus (HCV) subtypes are spreading among injecting drug users (IDUs) in Yamaguchi prefecture, on the south-western tip of the island of Honshu in Japan, as found in European countries. METHODS: We prospectively enrolled acute hepatitis C patients from January 2001 to March 2003. E2 gene sequences of HCV isolates from IDUs with acute hepatitis C were phylogenetically compared to those from 30 chronic hepatitis C patients with the same HCV subtypes who had or did not have a history of intravenous drug use. RESULTS: Nine of 11 patients (82%) with acute hepatitis C were IDUs. The HCV subtypes were 2a in four and 2b in five, which contrasted with the high prevalence of subtype 1b in patients with chronic liver diseases in Japan. IDUs with acute hepatitis C (22.0 +/- 2.4 years old) were significantly younger than those with chronic hepatitis C (49.5 +/- 9.5 years old) for subtype 2a (P = 0.0005), but not for subtype 2b (25.6 +/- 5.4 vs 28.1 +/- 2.4 years old). Some HCV isolates of subtype 2b from IDUs with acute hepatitis C were phylogenetically related to those from IDUs with chronic hepatitis C. By contrast, there was no phylogenetic segregation of HCV in IDUs with subtype 2a. HCV isolates from non-IDUs were genetically divergent from each other and those from IDUs, irrespective of the HCV subtype. CONCLUSION: Hepatitis C virus of the non-1b subtype, particularly subtype 2b, seemed to be transmitted between IDUs very recently in Yamaguchi prefecture, Japan.

Adult↗