Activities of the tiny science lab for school kids, called “Fukurou-jyuku”, established in Sendai several years ago, are reported by the author who had long been involved in molecular spectroscopic studies. Examples of the unique programs and efforts for the hands-on science experiments are given, as well as interesting episodes related to the activities of the lab and personal events in the author’s past that led him to become a scientist.
We have developed a quantum molecular dynamics simulation method which can widely search hydrogen systems from an isolated hydrogen molecule to condensed phase hydrogens exhibiting strong nuclear quantum effects such as zero-point energy and nuclear delocalization. We will briefly summarize derivations and advantages of our method and report our recent results on liquid, solid and supercooled hydrogens, suggesting new molecular pictures and guiding insights useful for future experiments of these mysterious quantum molecules.
Vibrational spectroscopy is a viable tool to reveal the mechanism of various molecular systems at the atomic and molecular resolution; yet the interpretation of the observed spectrum is often non-trivial and requires a theoretical assistance. Although it is rather common to calculate the vibrational spectrum based on the harmonic approximation, anharmonicity plays a crucial role, in particular, for the OH and NH stretching vibrations that lie in a high frequency region. In this article, recent advances in the vibrational structure theory are reviewed regarding: (1) The generation of anharmonic potential energy surface by the electronic structure calculation, (2) An efficient solver of vibrational Schrödinger equation by the vibrational quasi-degenerate perturbation theory based on variationally optimized coordinates, (3) A weight average approach to simulate the vibrational spectrum of condensed phase systems.
Microbial rhodopsin is a photo-receptive membrane protein of micro-organisms. The most ubiquitous microbial rhodopsins are light-driven ion pumps which actively transport H+ or Cl- against membrane chemical potential. In 2013, we reported a new class of ion pump rhodopsin, sodium pump rhodopsin (KR2) which outwardly transports Na+ ion by the use of light energy. The mechanism of Na+ transport by KR2 was investigated in spectroscopic and crystallographic studies. The results showed that the H+ transfer between photoisomerized retinal Schiff base and its counter ion, Asp116, is a critical process for the Na+-transport function. After this H+ transfer, the protonated Asp116 sequesters the H+ from the ion-transport pathway, and then immediately Na+ is taken up from the cytoplasmic side. The Na+ binds to the site composed of Asn112 and Asp251, and simultaneously H+ goes back to the retinal Schiff base. Then, positive charge of the reprotonated retinal Schiff-base prevents the back flow of Na+ to the cytoplasmic side. Finally, the Na+ is released to the extracellular side. Furthermore, on the basis of structural insights about KR2, we have succeeded to develop new artificial K+ and Cs+ pumping KR2 mutants, KR2K+ and KR2Cs+, respectively. Wildtype KR2 and these mutants are expected to provide new ways of the application to optogenetics.
Dynamics of solvent molecules around a solute molecule plays a crucial role in chemical and biological processes, such as chemical reactivity, biological recognition, and hydrophobic interaction. Though extensive studies on the solvation dynamics have been carried out, the single molecular level information about the dynamics is hard to obtain in the condensed phase suffered by averaging effects over solvent molecules in various environments. In this study, gas phase hydrated clusters, for which size and orientation of hydration can be specifically defined, are utilized as a model system to elucidate the solvation dynamics in a molecular specific fashion by complementary use of picosecond time resolved IR spectroscopy and on-the-fly DFT MD simulation. An ionization induced CO → NH water reorientation in the CO bound acetanilide-water cluster was investigated as the first example of solvent reorientation. The time resolved IR spectra revealed that the reaction has an intermediate and takes ca. 6 ps to finish the reorientation. The MD simulation showed that the reaction is composed of two different channels; one is a fast channel in which the water molecule travels around the CH3 group and the other is a slow channel in which water molecule once stays above the molecular plane. This detailed information about the water reorientation dynamics is first obtained by introducing a new dimension, i.e. time, into the established method of determining static cluster structures, IR spectroscopy + quantum chemical calculations. This concept would open a new stage to study dynamic processes in the molecular level using gas phase solvated clusters.
We performed femtosecond reflection spectroscopy on a series of perovskite-type cobalt oxide, RBaCo2O6-δ (R = Sm, Gd, and Tb). The transient reflectivity as well as the optical conductivity just after photoirradiation shows ultrafast change within the time resolution (ca. 120 fs) at room temperature, implying appearance of a hidden state different from the high temperature phase. The transferred spectral weight in the optical conductivity by the photoexcitation sensitively depends on the R-species. i.e., transfer of the d electron. Recent theoretical treatment which quantitatively succeeded in reproducing the transfer dependence of the excited state indicates that the photoirradiation causes locally ferromagnetic state via double-exchange interaction between the injected hole and spins of Co ion, which can be viewed as a novel example of photoinduced phase transition.
Gas-phase clusters isolated in vacuum have been studied intensively as a model system of heterogeneous catalysts. Recently, reactivity of clusters in thermal conditions attracts much attention, as catalysts operate in thermal conditions. In this review, a new experimental method to observe reactions of thermalized clusters, gas-phase temperature-programmed desorption (TPD), is introduced. As a typical example, redox reactions of cerium oxide clusters have been revealed using this method. Oxygen storage capacity of cerium oxide clusters was confirmed, i.e., cerium oxide clusters can release and extract oxygen. Oxidation reactions of CO and NO by cerium oxide clusters were observed, and detailed processes of these reactions were analyzed by gas-phase TPD.