著者

諸熊 奎治

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.1, no.1, pp.A0003-A0003, 2007-06-15 (Released:2007-06-29)

著者

保木 邦仁

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.6, no.1, pp.A0050, 2012 (Released:2012-06-21)

参考文献数

16

---

This article reviews recent advances in computer games. It is explained that methods famous in computational chemistry have enhanced the performance of Go and shogi programs. A history of the grand challenge in computer science that aims to defeat human experts in games is briefly summarized.

著者

鈴木 俊法

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.10, no.1, pp.A0082, 2016 (Released:2016-08-29)

著者

安積 徹

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.AC0005, 2011 (Released:2011-06-14)

---

注釈:この講義ノート前編は 2007年11月に発表され,元となる講義ノートについては分子科学会のhttp://j-molsci.jp/archives/index.htmlの頁にて公開している。

著者

諸熊 奎治

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.8, no.1, pp.A0065, 2014 (Released:2014-09-04)

参考文献数

18

著者

志賀 基之

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.A0038, 2011 (Released:2011-06-04)

参考文献数

81

---

Nuclear quantum effects, such as zero-point vibration and tunneling, are important aspect in molecular systems containing light atoms like hydrogen, and it is considered to have substantial influence on their chemical behavior and physical properties. In this report, I will describe the basic idea of path integral molecular dynamics simulations which enables one to compute nuclear quantum effects in complex many-body systems. When the method is combined with ab initio electron structure calculations, the whole molecular entity composed of electrons and nuclei is treated quantum mechanically based on first principles within the framework of Born-Oppenheimer approximation. Using this technique, the quantum nature of strong hydrogen bonds in protonated and deprotonated water clusters have been studied, with a focus on the geometrical isotope effect.

著者

安積 徹

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.AC0008-AC0008, 2011 (Released:2011-06-14)

---

注釈:この講義ノート後編は 2008年1月に発表され,元となる講義ノートについては分子科学会のhttp://j-molsci.jp/archives/index.htmlの頁にて公開している。

著者

神取 秀樹

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.A0043, 2011 (Released:2011-05-26)

参考文献数

99

被引用文献数

1 1

---

Rhodopsins contain a retinal molecule, and convert light into chemical energy or signal. The chromophore of visual or microbial rhodopsins is a retinal Schiff base of the 11-cis or all-trans form, respectively, where specific chromophore-protein interaction determines their colors. Upon light absorption, ultrafast photoisomerization initiates protein structural changes, leading to each functional expression. By use of spectroscopic methods, we have been studying how rhodopsins respond to light. Ultrafast spectroscopy of visual rhodopsin revealed that cis-trans isomerization is the primary event in our vision, which is optimized in protein environment. Fourier-transform infrared (FTIR) spectroscopy of visual and microbial rhodopsins provides various important vibrational bands related to structural changes of these proteins. Detection of protein-bound water molecules is one of the research highlights, and the comprehensive FTIR study has shown that a strongly hydrogen-bonded water molecule is the functional determinant of light-driven proton pump proteins. Here I review our spectroscopic challenge for > 25 years, particularly focusing our recent findings.

著者

杉本 敏樹

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.14, no.1, pp.A0112, 2020 (Released:2020-08-27)

参考文献数

75

被引用文献数

1

---

Interfacial phenomena, in which water molecules are deeply involved, are critical subjects in basic and applied research in a wide range of fields, including physics, chemistry, and biology. In the symmetry-breaking interfacial systems, molecular orientation is key structural parameter that determines the functional properties of water molecules. However, orientation of water molecules, i.e. configuration of hydrogens, in the interfacial hydrogen-bond network has been extremely difficult to be investigated by traditional structure-analysis techniques such as electron diffraction, grazing X-ray scattering and even scanning probe microscopy, because hydrogen has only a single electron and responds extremely weakly to the probes of these techniques; thus, the determination of molecular orientation of interfacial water systems has been an experimental challenge. We have recently tackled the challenges of elucidating the orientational structures of water molecules on metal surfaces by using cutting-edge nonlinear optical spectroscopy, i.e. heterodyne-detected sum-frequency generation (HD-SFG) spectroscopy. In this review article, brief descriptions of the basic concept of SFG spectroscopy as a hydrogen-configuration sensitive probe are followed by overviews of our current understanding of the adsorption geometry and rotational ordering of water molecules on representative metal surfaces and ice-film surfaces.

著者

関谷 博 迫田 憲治

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.8, no.1, pp.A0071, 2014 (Released:2014-09-04)

参考文献数

67

---

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.

著者

春田 正毅

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.6, no.1, pp.A0056, 2012 (Released:2012-06-21)

参考文献数

36

被引用文献数

1

---

Although gold (Au) in bulk is almost inert as a catalyst, it turns to be active for many reactions when deposited as nanoparticles (NPs) and clusters on base metal oxides. They are characterized by three features; active at low temperatures, enhanced by water, and uniquely selective. Over supported Au NPs CO adsorbs on the Au surfaces and O2 is activated at the perimeter interfaces around Au NPs. Both the two adsorbates react with each other at the perimeter interfaces. Gold clusters are expected to exhibit unique selectivity through the precise control of the number of atoms and the selection of appropriate support materials.

著者

大野 公一 前田 理

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.A0042, 2011 (Released:2011-06-04)

参考文献数

83

被引用文献数

2 2

---

It has been a long standing problem to answer the following fundamental questions in chemistry; (1) what kinds of chemical compounds (isomers) can be produced from a set of atoms given by a chemical formula, such as H4C2O2, (2) how the isomers can be converted to one another, (3) how they are decomposed into smaller species, or conversely (4) how they are made of smaller species. Although this problem can be solved theoretically if all minima and pathways among them via saddles could be searched on the potential energy hypersurface, it has been believed to be impossible, when the number of atoms exceeds four in the target chemical formula. A very simple tool like a compass for voyage could be discovered for global reaction route mapping (GRRM) in the chemical world. That is the anharmonic downward distortion (ADD) which enables one to follow all reaction pathways from an equilibrium (EQ) point toward structures of transition states (TS) surrounding the EQ point. Subsequent downward followings from already found TSs can easily be made as conventional intrinsic reaction coordinate (IRC) followings to reach some EQ points and dissociation channels (DC). Further quests around newly found EQs will yield many more reaction pathways via many other TSs. Such one-after-another procedures will continue until no new EQ could be found, and finally one can obtain a global reaction route map of the chemical formula as well as the answers to the fundamental questions in chemistry. Now, one should step into the new era of chemical problems to perform a perfect microscopic control of chemistry involved in the stereo reaction dynamics of atoms and molecules, based on leading information on typical trajectories searched by the automated exploration of chemical reaction pathways.

著者

杉田 有治 優 乙石 Michael Feig

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.11, no.1, pp.A0094, 2017 (Released:2017-08-31)

参考文献数

36

被引用文献数

2

---

Atomic structures of proteins, nucleic acids, and their complexes are determined using X-ray crystallography, NMR, or cryo-Electron Microscopy. These structures are essential to understand their structure-function relationships. However, the experimental conditions are totally different from the actual cellular environments and it is hard to understand how biomolecules behave in such cellular environments, just using the atomic structures. We have recently built protein crowding systems in computers and carried out all-atom molecular dynamics (MD) simulations of the systems to understand biomolecular dynamics in the crowded environments. The largest simulations we have ever performed were the all-atom MD simulations of a bacterial cytoplasm using K computer. By analyzing the simulation trajectories, we observed that non-specific protein-protein and protein-metabolite interactions play important roles in biomolecular dynamics and stability in a cell. The new insight from the simulations is useful not only for basic life science in molecular and cellular biology but also drug discovery in future for introducing the effect of non-specific protein-drug interactions.

著者

秋元 肇

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.9, no.1, pp.A0079, 2015 (Released:2015-08-31)

参考文献数

71

---

In recent years much of interest in atmospheric chemistry has been focused on atmospheric aerosols. In this article, laboratory kinetic studies and related quantum chemical theoretical studies on typical processes of formation and transformation of organic aerosols have been reviewed. Specifically, it targets on the topics of heterogeneous reactions of atmospheric O3 and OH with organic compounds at the surface of aerosols, and aqueous-phase reactions of dialdehydes (glyoxal and methylglyoxal) in cloud and aerosol particles. In order to attain better understanding on such processes, fundamental studies based on molecular science are needed, and closer collaboration between atmospheric chemistry and theoretical computational chemistry is proposed.

著者

柳井 毅

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.8, no.1, pp.A0069, 2014 (Released:2014-09-04)

参考文献数

35

---

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.

著者

長坂 将成

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.12, no.1, pp.A0096, 2018 (Released:2018-08-27)

参考文献数

55

---

Soft X-ray absorption spectroscopy (XAS) is an element specific method to reveal local structures of liquid samples since soft X-ray below 1 keV has chemically important absorption edges such as C, N, and O K-edges, and L-edges of transition metals. In aqueous solutions, interactions of organic molecules are measured in C and N K-edges and solvent water is separately observed in O K-edge. However, it is difficult to measure XAS of liquid in transmission mode since the thickness of a liquid layer should be less than 1 µm due to large soft X-ray absorption coefficient of liquid. We have successfully developed a liquid flow cell for XAS in transmission mode, where the absorbance of liquid samples can be easily optimized by controlling the liquid thickness. In this review, we report on the temperature dependent change of hydrogen bond in liquid water by O K-edge XAS and intermolecular interactions of pyridine with water in aqueous pyridine solutions at different molar fractions by using XAS in C, N, and O K-edges. For the operando observation of electrochemical reaction, we have developed an electrochemical cell with built-in electrodes and measured Fe L-edge XAS of aqueous iron sulfate solutions during electrochemical reaction under the same scan rate as in cyclic voltammetry. For understanding the phase transition mechanism, not only the mixed phase but also liquid-liquid interfaces after phase transition should be investigated by spatially resolved XAS. We have developed a liquid flow cell that is set in a scanning transmission X-ray microscope. The mechanism of a lower critical solution temperature in aqueous triethylamine solution is studied by spatially resolved XAS of the liquid-liquid interfaces between triethylamine and water phases with the spatial resolution of 140 nm.

著者

中迫 雅由

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.2, no.1, pp.A0022, 2008 (Released:2008-03-12)

参考文献数

20

被引用文献数

3

---

Water is a mother liquid of life. To understand why water is indispensable to life, I have been investigating the structures and interactions at protein-water interface, i.e. the hydration structures of proteins, by cryogenic X-ray crystallography and molecular dynamics simulation. Through developing devices and experimental techniques in cryogenic X-ray diffraction experiments, I realized that cryogenic X-ray crystallography is one of techniques effectively observe hydration structures of proteins surface. In addition, the author developed a novel calculation codes to characterize systematically hydration structures of the protein structures determined at around 100 K, as to the amount of water molecules, the hydrogen-bond geometries, the local and the global distribution of them on the surface of proteins. The standard tetrahedral hydrogen bonds of water molecules in bulk water were retained in the hydration structures and contributed to extend three-dimensional network of hydrogen bonds among hydration water molecules and oxygen and nitrogen atoms of protein surface. In cryo-crystallography of multi-subunit or multi-domain proteins, the reorganization of hydration structure occurred with the dynamical motions of proteins. In that, water molecules act as inhibitors for protein motions, glue to stabilize the higher-order structures or lubricant to realize conformational changes by utilizing its tetrahedral arms of hydrogen bonds. Thus, hydration water molecules must have great influences on the dynamics and functions of proteins in aqueous solution.

著者

三上 直彦

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.10, no.1, pp.A0083, 2016 (Released:2016-08-29)

参考文献数

20

---

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.

著者

山本 智

出版者

Japan Society for Molecular Science

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.8, no.1, 2014

---

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.

著者

田隅 三生

出版者

分子科学会

雑誌

Molecular Science (ISSN:18818404)

巻号頁・発行日

vol.5, no.1, pp.A0036-A0036, 2011 (Released:2011-05-26)

参考文献数

28