Membrane proteins are indispensable for cell signaling, bioenergetics, and transportation. Atomic structures of membrane proteins have been elucidated by methods in structural biology (e.g. X-ray crystallography). Structural changes of them in action should be investigated to improve the understanding of the molecular mechanisms in more detail. Infrared spectroscopy is a powerful method to analyze structural changes of protein by combining it with various kinds of stimulus-induced difference spectroscopic techniques. In this review article, my recent studies on microbial rhodopsin, ion channel and ion pump proteins are summarized. Light-induced difference infrared spectroscopy revealed the hydrogen-bonding change of Thr204 in pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore, which turned out to be a key residue for the signal transduction. Attenuated total reflection (ATR) method was applied on the studies of ion-protein interaction of a potassium channel, KcsA, and a sodium pump, V-type ATPase. Finally, development of a rapid-buffer exchange apparatus for time-resolved ATR infrared spectroscopy is introduced, which would be a powerful technique for investigating ion- and ligand-binding reactions of membrane proteins.
A major challenge in molecular electronic structure theory arises from chemical systems where the mean-field picture based upon a single electronic configuration fails to properly describe mechanics of many electrons. Such complex electronic states should be accounted for using a correlated superposition of multiple determinants and are referred to as multireference in quantum chemistry. Application domain of traditional multireference methods is severely limited to systems containing a small number of correlated electrons because of their exponential complexity. In recent years, much attention has been drawn to the density matrix renormalization group (DMRG) theory as a promising alternative. It has been introduced in ab initio quantum chemistry calculations and shown to be a highly-scalable multireference method that can handle full quantum degrees of freedom for the strongly-correlated wavefunction with unprecedented large configuration space. In this article, we provide an explicative introduction to the underlying theory and formalism built into the DMRG method and give a brief overview of our methodological extensions that combine DMRG and active-space correlation models.
Liquid interfaces play ubiquitous roles in many fields of chemistry and related sciences, though molecular-level understandings of liquid interfacial phenomena are still far from complete. Main obstacles for the further advances are (i) scarcity of experimental probe techniques with sufficient surface sensitivity and selectivity and (ii) lack of reliable analysis methods of the experimental observables about liquid interfaces. In the present review we summarize our recent efforts to overcome the above difficulties, by combination of vibrational sum frequency generation spectroscopy and molecular simulation. Close collaboration of these methods has shed light on clear understanding of the liquid interfaces.
Excited-state double-proton transfer (ESDPT) in the coplanar 7-azaindole dimer (7AI2) has been studied as a model base pair. Concerted and stepwise mechanisms were proposed for ESDPT in 7AI2. In the concerted mechanism, two protons transfer concertedly on the excited-state potential energy surfaces where a local minimum does not exist. On the other hand, an intermediate state exists in the stepwise mechanism. Therefore, after one single-proton transfer, the second single-proton transfers via the intermediate state. Numerous spectroscopic and theoretical studies were conducted to determine the mechanism of ESDPT of 7AI2. This review focuses on the ESDPT mechanisms in the gas phase. A prologue and epilogue of the concerted and stepwise mechanism controversy are presented. Spectroscopic experiments in the condensed phase and theoretical calculations related to the potential energy surfaces are important for deriving a final conclusion. In addition, some significant results are comparatively discussed.
Atacama Large Millimeter/submillimter Array (ALMA) is a large aperture-synthesis radio telescope constructed in northern Chile by international collaboration among east Asia, north America, and Europe. It observes spectral line emission/absorption of molecules and thermal emission of dust particles in various kinds of astronomical objects with much higher sensitivity and much higher angular resolution than conventional radio telescopes in the world. ALMA has started its early science operation from 2011, and chemical processes during star and planet formation are being explored in detail. Even in the early science operation, many surprising results are coming out. In this article, I would like to highlight some of them in particular emphasis on possible relation to molecular science.
Photoirradiation and application of electric field give a powerful method to examine electronic structure of molecules and molecular systems and to control excitation dynamics, material function and biological function. Electric dipole moment in the excited state as well as in the ground state of molecules and molecular systems can be determined using Stark quantum beat spectroscopy in vapor phase and using electroabsorption (E-A) and electrophotoluminescence (E-PL) spectroscopy in condensed phase. Electric field effects on photoexcitation dynamics in organic photoinduced electron transfer systems, π-conjugated polymers and semiconductor quantum dots, which play an important role in optoelectronic devices, have been elucidated, based on the measurements both of the E-A and E-PL spectra and of the field-induced change in emission decay profile. Electrical conductivity in organic conductors can be controlled by photoirradiation and application of pulsed electric field, that is, tuning of electrical conductivity among insulator, metal and superconductor is possible with photoirradiation and application of electric field. Intracellular function is affected by application of short-pulsed electric field, that is, electric-field-induced apoptosis has been confirmed. It is also proposed that fluorescence lifetime microscopy is applicable to evaluate the local electric field in cells, which seems to be one of the vital factors that control the reactions in biological systems.