Japan Institute for Molecular Science

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Okazaki, Japan
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Abe M.,Hiroshima University | Abe M.,Japan Institute for Molecular Science | Abe M.,Japan Science and Technology Agency
Chemical Reviews | Year: 2013

Recent development in diradical chemistry are summarized in detail. Diradicals are long-known chemical species, but they continue to be fascinating molecules because of their inherently high reactivity and their potential molecular functions, which are mainly derived from their small HOMO-LUMO energy gaps. Kinetic stabilization and thermodynamic stabilization have made it possible to isolate diradical species. The terminology of singlet and triplet states in diradicals is derived from the number of energy level in diradicals under an external magnetic field. The triplet state is the ground-state spin multiplicity for diradicals in which a large overlap integral exists between the two energetically degenerate molecular orbitals that are occupied by two electrons. Localized diradicals are key intermediates in processes involving the homolytic bond-cleavage and -formation reactions of cyclic compounds.


Kurashige Y.,Japan Institute for Molecular Science | Chan G.K.-L.,Princeton University | Yanai T.,Japan Institute for Molecular Science
Nature Chemistry | Year: 2013

It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 1018 quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle. © 2013 Macmillan Publishers Limited. All rights reserved.


Feng X.,Japan Institute for Molecular Science | Feng X.,Beijing Institute of Technology | Ding X.,Japan Institute for Molecular Science | Jiang D.,Japan Institute for Molecular Science | Jiang D.,Japan Science and Technology Agency
Chemical Society Reviews | Year: 2012

Covalent organic frameworks (COFs) are a class of crystalline porous polymers that allow the atomically precise integration of organic units to create predesigned skeletons and nanopores. They have recently emerged as a new molecular platform for designing promising organic materials for gas storage, catalysis, and optoelectronic applications. The reversibility of dynamic covalent reactions, diversity of building blocks, and geometry retention are three key factors involved in the reticular design and synthesis of COFs. This tutorial review describes the basic design concepts, the recent synthetic advancements and structural studies, and the frontiers of functional exploration. This journal is © The Royal Society of Chemistry 2012.


Taira T.,Japan Institute for Molecular Science
Optical Materials Express | Year: 2011

Transparent laser ceramics have been demonstrated to offer tremendous processing and design advantages in the diode-pumped solidstate laser field. Successfully developed composite Nd:YAG/Cr:YAG ceramics realized a multi-megawatt three-beam output microchip laser for efficient engine ignition. After a progress review for Giant Micro-photonics, including their wavelength extension with micro-domain controlling, we'd like to discuss the next generation of high-brightness lasers based on anisotropic ceramics. The capability of transparent anisotropic ceramics, by using a new crystal orientation process based on large magnetic anisotropy induced by 4f electrons, offers extremely high-power laser materials such as RE:FAP and patterning process for multi-function integrated monolithic solid-state lasers. © 2011 Optical Society of America.


Sakamoto Y.,Japan Institute for Molecular Science | Suzuki T.,Japan Institute for Molecular Science
Journal of the American Chemical Society | Year: 2013

An aromatic saddle was designed from the hypothetical three-dimensional graphene with the negative Gaussian curvature (Schwarzite P192). Two aromatic saddles, tetrabenzo[8]circulene (TB8C) and its octamethyl derivative OM-TB8C, were synthesized by the Scholl reaction of cyclic octaphenylene precursors. The structure of TB8C greatly deviates from planarity, and the deep saddle shape was confirmed by single-crystal X-ray crystallography. There are two conformers with the S4 symmetry, which are twisted compared to the DFT structure (D2d). The theoretical studies propose that the interconversion of TB8C via the planar transition state (125 kcal mol-1) is not possible. However, the pseudorotation leads to a low-energy tub-to-tub inversion via the nonplanar transition state (7.3 kcal mol-1). The ground-state structure of TB8C in solution is quite different from the X-ray structure because of the crystal-packing force and low-energy pseudorotation. OM-TB8C is a good electron donor and works as the p-type semiconductor. © 2013 American Chemical Society.


Kurashige Y.,Japan Institute for Molecular Science
Molecular Physics | Year: 2014

Recent advances in quantum chemical density matrix renormalisation group (DMRG) theory are presented. The DMRG, originally devised as an alternative to the exact diagonalisation in condensed matter physics, has become a powerful quantum chemical method for molecular systems that exhibit a multireference character, e.g., excited states, π-conjugated systems, transition metal complexes, and in particular for large systems by combining it with conventional multireference electron correlation methods. The capability of the current quantum chemical DMRG is demonstrated for an application involving the potential energy curve of the chromium dimer, which is one of the most demanding multireference systems and thus requires the best electronic structure treatment for non-dynamical and dynamical correlation as well as large basis sets. © 2013 Taylor & Francis.


Xu Y.,Japan Institute for Molecular Science | Jin S.,Japan Institute for Molecular Science | Xu H.,Japan Institute for Molecular Science | Nagai A.,Japan Institute for Molecular Science | Jiang D.,Japan Institute for Molecular Science
Chemical Society Reviews | Year: 2013

Conjugated microporous polymers (CMPs) are a class of organic porous polymers that combine π-conjugated skeletons with permanent nanopores, in sharp contrast to other porous materials that are not π-conjugated and with conventional conjugated polymers that are nonporous. As an emerging material platform, CMPs offer a high flexibility for the molecular design of conjugated skeletons and nanopores. Various chemical reactions, building blocks and synthetic methods have been developed and a broad variety of CMPs with different structures and specific properties have been synthesized, driving the rapid growth of the field. CMPs are unique in that they allow the complementary utilization of π-conjugated skeletons and nanopores for functional exploration; they have shown great potential for challenging energy and environmental issues, as exemplified by their excellent performance in gas adsorption, heterogeneous catalysis, light emitting, light harvesting and electrical energy storage. This review describes the molecular design principles of CMPs, advancements in synthetic and structural studies and the frontiers of functional exploration and potential applications. © 2013 The Royal Society of Chemistry.


Xu H.,Japan Institute for Molecular Science
Nature Materials | Year: 2016

Progress over the past decades in proton-conducting materials has generated a variety of polyelectrolytes and microporous polymers. However, most studies are still based on a preconception that large pores eventually cause simply flow of proton carriers rather than efficient conduction of proton ions, which precludes the exploration of large-pore polymers for proton transport. Here, we demonstrate proton conduction across mesoporous channels in a crystalline covalent organic framework. The frameworks are designed to constitute hexagonally aligned, dense, mesoporous channels that allow for loading of N-heterocyclic proton carriers. The frameworks achieve proton conductivities that are 2–4 orders of magnitude higher than those of microporous and non-porous polymers. Temperature-dependent and isotopic experiments revealed that the proton transport in these channels is controlled by a low-energy-barrier hopping mechanism. Our results reveal a platform platform based on porous covalent organic frameworks for proton conduction. © 2016 Nature Publishing Group


Kurahashi T.,Japan Institute for Molecular Science | Fujii H.,Japan Institute for Molecular Science
Journal of the American Chemical Society | Year: 2011

Ligand radicals from salen complexes are unique mixed-valence compounds in which a phenoxyl radical is electronically linked to a remote phenolate via a neighboring redox-active metal ion, providing an opportunity to study electron transfer from a phenolate to a phenoxyl radical mediated by a redox-active metal ion as a bridge. We herein synthesize one-electron-oxidized products from electronically diverse manganese(III) salen complexes in which the locus of oxidation is shown to be ligand-centered, not metal-centered, affording manganese(III)-phenoxyl radical species. The key point in the present study is an unambiguous assignment of intervalence charge transfer bands by using nonsymmetrical salen complexes, which enables us to obtain otherwise inaccessible insight into the mixed-valence property. A d 4 high-spin manganese(III) ion forms a Robin-Day class II mixed-valence system, in which electron transfer is occurring between the localized phenoxyl radical and the phenolate. This is in clear contrast to a d 8 low-spin nickel(II) ion with the same salen ligand, which induces a delocalized radical (Robin-Day class III) over the two phenolate rings, as previously reported by others. The present findings point to a fascinating possibility that electron transfer could be drastically modulated by exchanging the metal ion that bridges the two redox centers. © 2011 American Chemical Society.


Aono S.,Japan Institute for Molecular Science
Advances in Microbial Physiology | Year: 2013

Sensor proteins play crucial roles in maintaining homeostasis of cells by sensing changes in extra- and intracellular chemical and physical conditions to trigger biological responses. It has recently become clear that gas molecules function as signalling molecules in these biological regulatory systems responsible for transcription, chemotaxis, synthesis/hydrolysis of nucleotide second messengers, and other complex physiological processes. Haem-containing sensor proteins are widely used to sense gas molecules because haem can bind gas molecules reversibly. Ligand binding to the haem in the sensor proteins triggers conformational changes around the haem, which results in their functional regulation. Spectroscopic and crystallographic studies are essential to understand how these sensor proteins function in these biological regulatory systems. In this chapter, I discuss structural and functional relationships of haem-containing PAS and PAS-related families of the sensor proteins. © 2013 Elsevier Ltd.

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