Fukui Institute for Fundamental Chemistry

Kyoto, Japan

Fukui Institute for Fundamental Chemistry

Kyoto, Japan
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Morokuma K.,Fukui Institute for Fundamental Chemistry
Journal of Computational Chemistry | Year: 2017

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.

Morokuma K.,Fukui Institute for Fundamental Chemistry
International Journal of Quantum Chemistry | Year: 2014

The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions. The IRC gives a unique connection from a given transition structure to local minima of the reactant and product sides. This allows for easy understanding of complicated multistep mechanisms as a set of simple elementary reaction steps. In this article, three topics concerning the IRC approach are discussed. In the first topic, the first ab initio study of the IRC and a recent development of an IRC calculation algorithm for enzyme reactions are introduced. In the second topic, cases are presented in which dynamical trajectories bifurcate and corresponding IRC connections can be inaccurate. In the third topic, a recent development of an automated reaction path search method and its application to systematic construction of IRC networks are described. Finally, combining these three topics, future perspectives are discussed. © 2014 Wiley Periodicals, Inc.

Morokuma K.,Fukui Institute for Fundamental Chemistry
Chemical Record | Year: 2016

In this account, a technical overview of the artificial force induced reaction (AFIR) method is presented. The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions. There are two modes in the AFIR method, i.e., a multicomponent mode and a single-component mode. The former has been applied to bimolecular and multicomponent reactions and the latter to unimolecular isomerization and dissociation reactions. Five numerical examples are presented for an Aldol reaction, a Claisen rearrangement, a Co-catalyzed hydroformylation, a fullerene structure search, and a nonradiative decay path search in an electronically excited naphthalene molecule. Finally, possible applications of the AFIR method are discussed. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Maegawa T.,Kyoto Institute of Technology | Irie Y.,Kyoto Institute of Technology | Imoto H.,Kyoto Institute of Technology | Fueno H.,Kyoto University | And 2 more authors.
Polymer Chemistry | Year: 2015

The selective introduction of functional groups at the para-position in mono-functionalized T8-caged silsesquioxanes would enable us to design new organic inorganic hybrid polymers. Here, a para-substituted bisvinylhexaisobutyl-T8 caged monomer was successfully synthesized via a selective corner-opening reaction of the vinylheptaisobutyl-T8 cage followed by a subsequent corner-capping reaction. © The Royal Society of Chemistry 2015.

Ichikawa M.,Kyoto University | Takabatake F.,Kyoto University | Miura K.,Kyoto University | Iwaki T.,Fukui Institute for Fundamental Chemistry | And 3 more authors.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2013

The photoinduced motion of an oil droplet on an aqueous solution under local irradiation by a green laser is reported. The results showed that a repulsive force is generated on pure water, while an attractive force is observed with an aqueous solution containing a surfactant. The driving force is discussed in terms of a thermal Marangoni effect. The switching on the photothermal effect is interpreted by taking into account the advection caused by the spatial gradient of the surface tension under local heating by a laser. A numerical model revealed that the geometrical profile of the surface tension around the droplet determines the mode of advection around the droplet and causes switching in the direction of migrations. © 2013 American Physical Society.

Pomogaeva A.V.,RAS Institute of Chemistry | Morokuma K.,Fukui Institute for Fundamental Chemistry | Timoshkin A.Y.,RAS Institute of Chemistry
Journal of Computational Chemistry | Year: 2016

A detailed first-principle DFT M06/6-311++G(d.p) study of dehydrogenation mechanism of trimeric cluster of lithium amidoborane is presented. The first step of the reaction is association of two LiNH2BH3 molecules in the cluster. The dominant feature of the subsequent reaction pathway is activation of H atom of BH3 group by three Li atoms with formation of unique Li3H moiety. This Li3H moiety is destroyed prior to dehydrogenation in favor of formation of a triangular Li2H moiety, which interacts with protic H atom of NH2 group. As a result of this interaction, Li2H2 moiety is produced. It features N--H+-H- group suited near the middle plane between two Li+ in the transition state that leads to H2 release. The transition states of association and hydrogen release steps are similar in energy. It is concluded that the trimer, (LiNH2BH3)3, is the smallest cluster that captures the essence of the hydrogen release reaction. © 2016 Wiley Periodicals, Inc.

Akagi K.,Kyoto University | Akagi K.,Fukui Institute for Fundamental Chemistry
Kobunshi | Year: 2015

The π-conjugated polymers bearing jt-electrons delocalized over the main chains are extensively investigated from viewpoints of fundamental and applied sciences because of their unique optoelectronic properties and functions. Nowadays it is further required for the conjugated polymers, as next-generation plastic electronics materials, to have newly designed polymer structures, novel functions and high performance in optoelectronic functions. Herein, we discuss helical rc-conjugated polymers with super-hierarchically controlled structures, by focusing on (i) optically active polymers with white colored circularly polarized luminescence (CPL) and intensity amplification of CPL via liquid crystalinity, (ii) external stimulus-responsive π-conjugated polymers and reversible switching in CPL, and (iii) interchain helically stacked assemblies consisting of cationic achiral π-conjugated polymers and anionic chiral molecules and the formation of spherulites based on the polymer assemblies.

Sakaki S.,Kyoto University | Ohnishi Y.-Y.,Fukui Institute for Fundamental Chemistry | Sato H.,Kyoto University
Chemical Record | Year: 2010

Theoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C-H σ-bond activation of benzene by Pd(II)-formate complex and that of methane by Ti(IV)-imido complex successfully disclosed that these reactions are under-stood to undergo heterolytic σ-bond activation and the driving force is the formation of strong O-H and N-H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of σ-bond activation by oxidative addition. The transmetallation, which is a key process in the cross-coupling reaction, is understood to be heterolytic σ-bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an SN2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substitutents which are replaced in the small model. Frontier-orbital-consistent quantum-capping potential (FOC-QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC-QCP was successfully applied to large systems including transition metal elements. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Chen Y.,Fukui Institute for Fundamental Chemistry | Sunada Y.,Japan Science and Technology Agency | Sunada Y.,Kyushu University | Nagashima H.,Japan Science and Technology Agency | And 3 more authors.
Chemistry - A European Journal | Year: 2016

Nanosheet compounds Pd11(SiiPr)2(SiiPr2)4(CNtBu)10 (1) and Pd11(SiiPr)2(SiiPr2)4(CNMes)10 (2), containing two Pd7(SiiPr)(SiiPr2)2(CNR)4 plates (R=tBu or Mes) connected with three common Pd atoms, were investigated with DFT method. All Pd atoms are somewhat positively charged and the electron density is accumulated between the Pd and Si atoms, indicating that a charge transfer (CT) occurs from the Pd to the Si atoms of the SiMe2 and SiMe groups. Negative regions of the Laplacian of the electron density were found between the Pd and Si atoms. A model of a seven-coordinated Si species, that is, Pd5(Pd-SiMe), is predicted to be a stable pentagonal bipyramidal molecule. Five Pd atoms in the equatorial plane form bonding overlaps with two 3p orbitals of the Si atom. This is a new type of hypervalency. The Ge analogues have geometry and an electronic structure similar to those of the Si compounds. But their formation energies are smaller than those of the Si analogues. The use of the element Si is crucial to synthesize these nanoplate compounds. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PubMed | Fukui Institute for Fundamental Chemistry and Kyushu University
Type: | Journal: Soft matter | Year: 2016

Active diffusion, i.e., fluctuating dynamics driven by athermal noise, is found in various out-of-equilibrium systems. Here we discuss the nature of the active diffusion of tagged monomers in a flexible polymer. A scaling argument based on the notion of tension propagation clarifies how the polymeric effect is reflected in the anomalous diffusion exponent, which may be of relevance to the dynamics of chromosomal loci in living cells.

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