Publications (167)565.94 Total impact
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ABSTRACT: Theoretical and computational studies on the mechanisms of ligand exchange reaction (LER) and ligand coupling reaction (LCR) of hypervalent pentacoordinate Sb and tetracoordinate Te compounds were carried out. Contrary to the previous suggestion from experimentalists, the lone pair electrons of Te do not participate in LER. Also, LER of R5Sb proceeds via a similar mechanism to that of R4Te. As for the LCR of R5Sb, the apicalequatorial coupling mechanism was suggested.  [Show abstract] [Hide abstract]
ABSTRACT: The photoisomerisation dynamics following excitation to the S1 electronic state of two structurally related heterocyclic molecules, αpyrone and coumarin, in acetonitrile solution have been probed by timeresolved vibrational absorption spectroscopy. Following irradiation at 310 nm, αpyrone relaxes rapidly from its initially excited state, with a quantum yield for parent molecule reformation of 68%. Probing the antisymmetric ketene stretch region between 2100 cm(1) and 2150 cm(1) confirms the presence of at least two isomeric ringopened photoproducts, which are formed highly vibrationally excited and relax on a picosecond timescale. Following vibrational cooling, a secondary, thermally driven, isomerisation is observed with a 1.8(1) ns time constant. In contrast, coumarin reforms the parent molecule with essentially 100% efficiency following excitation at 330 nm. The conical intersections driving the nonradiative relaxation of αpyrone have been investigated using an automated search algorithm. The two lowest energy conical intersections possess remarkably similar structures to the two energetically accessible conical intersections reported previously for coumarin, suggesting that the differing photochemistry is the result of dynamical effects occurring after passage through these intersections.  [Show abstract] [Hide abstract]
ABSTRACT: Markovian dynamics on complex reaction networks have been one of the most in triguing subjects in a wide range of research elds such as chemical reactions, biological physics, and ecology. To represent the global kinetics, for example, from a node (cor responding to a basin on an energy landscape) to another, requires the information of multiple pathways to directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discretetime Markov chain (DTMC) derived from rst order rate equations. The TSs can naturally take into account the multiple path ways connecting any pair of nodes. We also propose a new type of disconnectivity graph to capture the hierarchical organization of dierent timescales of reactions. The graph can suggest how the network becomes simplied by changing the timescale of observation. The crux is the introduction of the minimum conductance cut (MCC) in graph clustering, corresponding to a dividing surface across the network having the \smallest" transition probability between two disjoint subnetworks (superbasins on the energy landscape) in the network. We present a new combinatorial search algorithm for searching this MCC. We apply our method to a reaction network of Claisen rear rangement of allyl vinyl ether (AVE) that consists of 23 nodes and 66 links (saddles on the energy landscape) connecting them. We compare the kinetic properties of our disconnectivity graph to those of the transition matrix of the rate equations, and show that our graph can properly reveal the hierarchical organization of timescales in a network.  [Show abstract] [Hide abstract]
ABSTRACT: The significance of kinetic analysis as a tool for understanding the reactivity and selectivity of organic reactions has recently been recognized. However, conventional simulation approaches that solve rate equations numerically are not amenable to multistep reaction profiles consisting of fast and slow elementary steps. Herein, we present an efficient and robust approach for evaluating the overall rate constants of multistep reactions via the recursive contraction of the rate equations to give the overall rate constants for the products and byproducts. This new method was applied to the Claisen rearrangement of allyl vinyl ether, as well as a substituted allyl vinyl ether. Notably, the profiles of these reactions contained 23 and 84 local minima, and 66 and 278 transition states, respectively. The overall rate constant for the Claisen rearrangement of allyl vinyl ether was consistent with the experimental value. The selectivity of the Claisen rearrangement reaction has also been assessed using a substituted allyl vinyl ether. The results of this study showed that the conformational entropy in these flexible chain molecules had a substantial impact on the overall rate constants. This new method could therefore be used to estimate the overall rate constants of various other organic reactions involving flexible molecules.  [Show abstract] [Hide abstract]
ABSTRACT: The ligand coupling reaction (LCR) of hypervalent pentacoordinate antimony compounds (Ar(n)Tol(5n)Sb; Ar = ptrifluoromethylphenyl, Tol = pmethylphenyl; n = 05) was analyzed via the longrangecorrected density functional theory. Although previous experimental or computational investigations have suggested apical apical or equatorial equatorial coupling of Ar(n)Tol(5n)Sb compounds, the present results lead to apical equatorial coupling. The biased experimental ratios of the coupling products, which were grounds for apical apical coupling, can be explained by the stability of the transitionstate (TS) structure for the apical equatorial coupling, where npi* interaction plays an important role to the stabilization. We further investigated the potential energy surface of H5Sb, for which the intrinsic reaction coordinate (IRC) from the TS structure for LCR indicates the equatorial equatorial coupling. It is found that the valleyridge transition occurs along the IRC near the TS structure and the transverse vibrational mode with imaginary frequency, orthogonal to the IRC, directs to the reactant structure corresponding to the apical equatorial coupling.  [Show abstract] [Hide abstract]
ABSTRACT: The existence of a valleyridge transition (VRT) point along the intrinsic reaction coordinate does not always indicate the existence of two minima in the product side, but VRT is a sign of bifurcating nature of dynamical trajectories running on the potential energy surface. It is demonstrated by molecular dynamics simulations.  [Show abstract] [Hide abstract]
ABSTRACT: A new type of reaction pathway which involves a nontotally symmetric trifurcation was found and investigated for a typical SN 2type reaction, NC() + CH3 X → NCCH3 + X() (X = F, Cl). A nontotally symmetric valleyridge inflection (VRI) point was located along the C3 v reaction path. For X = F, the minimum energy path (MEP) starting from the transition state (TS) leads to a secondorder saddle point with C3 v symmetry, which connects three product minima of Cs symmetry. For X = Cl, four product minima have been observed, of which three belong to Cs symmetry and one to C3 v symmetry. The branching path from the VRI point to the lower symmetry minima was determined by a linear interpolation technique. The branching mechanism is discussed based on the reaction path curvature and net atomic charges, and the possibility of a nonotally symmetric nfurcation is discussed. © 2015 Wiley Periodicals, Inc.  [Show abstract] [Hide abstract]
ABSTRACT: In 2005, Surján showed two explicit formulas for evaluating the secondorder Møller–Plesset perturbation (MP2) energy as a functional of the Hartree–Fock density matrix $$\varvec{D}$$D (Chem Phys Lett 406:318, 2005), which are referred to as the $$\Delta E_\text {MP2}[\varvec{D}]$$ΔEMP2[D] functionals. In this paper, we present the finitetemperature (FT) MP2 energy functionals of the FT Hartree–Fock density matrix. There are also two formulas for the FTMP2, namely the conventional and renormalized ones; the latter of which has recently been formulated by Hirata and He (J Chem Phys 138:204112, 2013). We proved that there exists onetoone correspondence between the formulas of two FTMP2 and the $$\Delta E_\text {MP2}[\varvec{D}]$$ΔEMP2[D] functionals. This fact can explain the different behavior of two $$\Delta E_\text {MP2}[\varvec{D}]$$ΔEMP2[D] functionals when an approximate Hartree–Fock density matrix is applied, which was previously investigated by Kobayashi and Nakai (Chem Phys Lett 420:250, 2006). We also applied the FTMP2 formalisms to the linearscaling divideandconquer method for improving the accuracy with tiny addition of the computational efforts.  [Show abstract] [Hide abstract]
ABSTRACT: Enhanced luminescence properties of mononuclear lanthanide complexes with asymmetric sevencoordination structures are reported for the first time. The lanthanide complexes are composed of a lanthanide ion (EuIII or TbIII), three tetramethyl heptanedionato ligands, and one triphenylphosphine oxide ligand. The coordination geometries of the lanthanide complexes have been evaluated by using singlecrystal Xray analyses and shapemeasurement calculations. The complexes are categorized to be sevencoordinate monocapped octahedral structures (point group C3v). The sevencoordinate lanthanide complexes show high intrinsic emission quantum yields, extralarge radiative rate constants, and unexpected small nonradiative rate constants. The brilliant luminescence properties have been elucidated in terms of the asymmetric coordination geometry and small vibrational quanta related to thermal relaxation.  [Show abstract] [Hide abstract]
ABSTRACT: Bottomup strategies can be effectively implemented for the fabrication of atomically precise graphene nanoribbons. Recently, using 1010'dibromo99'bianthracene (DBBA) as a molecular precursor to grow armchair nanoribbons on Au(111) and Cu(111), we have shown that substrate activity considerably affects the dynamics of ribbon formation, nonetheless without significant modifications in the growth mechanism. In this paper we compare the onsurface reaction pathways for DBBA molecules on Cu(111) and Cu(110). Evolution of both systems has been studied via a combination of corelevel Xray spectroscopies, scanning tunneling microscopy and theoretical calculations. Experimental and theoretical results reveal a significant increase in reactivity for the open and anisotropic Cu(110) surface in comparison with the closepacked Cu(111). This increased reactivity results in a predominance of the molecularsubstrate interaction over the intermolecular one, which has a critical impact on the transformations of DBBA on Cu(110). Unlike DBBA on Cu(111), the Ullmann coupling cannot be realized for DBBA/Cu(110) and the growth of nanoribbons via this mechanism is blocked. Instead, annealing of DBBA on Cu(110) at 250 ˚C results in the formation of a new structure  quasizerodimensional flat nanographenes. Each nanographene unit has dehydrogenated zigzag edges bonded to the underlying Cu rows and oriented with the hydrogenterminated armchair edge parallel to the [110] direction. Strong bonding of nanographene to the substrate manifests itself in high adsorption energy of 12.7 eV and significant charge transfer of 3.46 e from the copper surface. Nanographene units coordinated with bromine adatoms are able to arrange in highly regular arrays potentially suitable for nanotemplating.  [Show abstract] [Hide abstract]
ABSTRACT: Minimum energy conical intersection (MECI) geometries were searched for polycyclic aromatic hydrocarbons (PAHs) consisting of up to 26 atoms. The energy barriers to the obtained MECIs showed a correlation with their fluorescence quantum yields. This provides a theoretical rationale for the size dependence of the fluorescence quantum yields seen in these PAHs.  [Show abstract] [Hide abstract]
ABSTRACT: A global reaction route map is generated for Au 5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N − 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valleyridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed.  [Show abstract] [Hide abstract]
ABSTRACT: Using 42nm high harmonic pulses, the dissociation dynamics of 1,2butadiene was investigated by timeresolved photoelectron spectroscopy (TRPES), enabling us to observe dynamical changes of multiple molecular orbitals (MOs) with higher temporal resolution than conventional light sources. Since each lowerlying occupied MO has particular spatial electron distribution, the structural dynamics of photochemical reaction can be revealed. On the femtosecond timescale, a shortlived excited state with a lifetime of 37 ± 15 fs and the coherent oscillation of the photoelectron yield stimulated by HertzbergTeller coupling were observed. Ab initio molecular dynamics simulations in the electronically excited state find three relaxation pathways from the vertically excited structure in S1 to the ground state and one of them is the dominant relaxation pathway, observed as the shortlived excited state. On the picosecond timescale, the photoelectron yields related to the C−C bond decreased upon photoexcitation, indicating C−C bond cleavage.  [Show abstract] [Hide abstract]
ABSTRACT: Theoretical and experimental studies have been conducted to elucidate the mechanism of the formal nucleophilic boryl substitution of aryl and alkyl bromides with silylborane in the presence of potassium methoxide. Density functional theory was used in conjunction with the artificial force induced reaction method in the current study to determine the mechanism of this reaction. The results of this analysis led to the identification of a unique carbanionmediated mechanism involving the halogenophilic attack of a silyl nucleophile on the bromine atom of the substrate. These calculations have therefore provided a mechanistic rationale for this counterintuitive borylation reaction. Furthermore, the good functional group compatibility and high reactivity exhibited by this reaction towards sterically hindered substrates can be understood in terms of the low activation energy required for the reaction of the silyl nucleophile with the bromine atom of the substrate, and the subsequent rapid and selective consumption of the carbanion species by the in situ generated boron electrophile. The results of an experimental study involving the capture of the anion intermediate provided further evidence in support of the generation of a carbanion species during the course of this reaction. The anomalous formal nucleophilic borylation mechanism reported in this study could be used to provide new insights in silicon and boron chemistry.  [Show abstract] [Hide abstract]
ABSTRACT: The matrix shifts of the HXe stretching frequency of noblegas hydrides, HXeCCH, HXeBr, and HXeI in various noblegas matrices (in Ne, Ar, Kr, and Xe matrices) are investigated via the hybrid quantumclassical simulations. The order of the HXe stretching frequencies is found to be ν(gas) < ν(Ne) < ν(Xe) < ν(Kr) < ν(Ar) for HXeCCH and HXeBr, while it is ν(gas) < ν(Ne) < ν(Xe) < ν(Ar) < ν(Kr) for HXeI. This order is anomalous with respect to the matrix dielectric constants, and the calculated results reproduce the experimentally observed shifts quite successfully. We also find that the matrix shifts from the gasphase values are Δν(HXeCCH) ≈ Δν(HXeCl) < Δν(HXeBr) < Δν(HXeI) in the same noblegas matrix environments, which implies that the weakly bound molecules exhibit large matrix shifts. The local trapping site is analyzed in detail, and it is shown that a realistic modeling of the surrounding matrix environments is essential to describe the unusual matrix shifts accurately. 
Article: From Roaming Atoms to Hopping Surfaces: Mapping Out Global Reaction Routes in Photochemistry
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ABSTRACT: The photodissociation of small molecules occurs upon irradiation by ultraviolet or visible light and it is a very important chemical process in Earth's atmosphere, the atmospheres of other planets, and in interstellar media. Photodissociation is an important method used to thoroughly investigate the fundamental issues of chemical reactivity. Photodissociation involves molecules and reaction fragments moving over ground and exited state potential surfaces (PESs). Molecules can move on a single PES (adiabatic pathway) and they can also cross over from one PES to another in nonadiabatic pathways. For a full theoretical understanding of a photodissociation mechanism, all the important nonadiabatic and adiabatic pathways must be determined. This is not an easy task. We have developed an efficient computational method referred to as the global reaction route mapping (GRRM) strategy that allows for a theoretical exploration of ground and excited state PESs and their crossing seams in an automatic manner. In this article, we summarize our approaches and present examples of the application together with newly determined chemical insights. These include the complex photodissociation mechanism of the formaldehyde H2CO molecule, the exclusive excited state roaming dynamics of the nitrate NO3 radical, and all product channels and conformational memory in the photodissociation of the formic acid HCOOH molecule. Finally, perspectives for the theoretical design of photofunctional molecules are discussed.  [Show abstract] [Hide abstract]
ABSTRACT: Experimental and theoretical studies of HXeI and HXeH molecules in Ar, Kr, and Xe matrices are presented. HXeI exhibits the HXe stretching bands at 1238.0 and 1239.0 cm(1) in Ar and Kr matrices, respectively, that are blueshifted from the HXeI band observed in a Xe matrix (1193 cm(1)) by 45 and 46 cm(1). These shifts are larger than those observed previously for HXeCl (27 and 16 cm(1)) and HXeBr (37 and 23 cm(1)); thus, the matrix effect is stronger for less stable molecules. The results for HXeI are qualitatively different from all previous results on noblegas hydrides with respect to the frequency order between Ar and Kr matrices. For previously studied HXeCl, HXeBr, and HXeCCH, the HXe stretching frequency is reliably (by >10 cm(1)) higher in an Ar matrix than in a Kr matrix. In contrast, the HXe stretching frequency of HXeI in an Ar matrix is slightly lower than that in a Kr matrix. HXeH absorbs in Ar and Kr matrices at 1203.2 and 1192.1 cm(1) (the stronger band for a Kr matrix), respectively. These bands are blueshifted from the stronger band of HXeH in a Xe matrix (1166 cm(1)) by 37 and 26 cm(1), and this frequency order is the same as observed for HXeCl, HXeBr, and HXeCCH but different from HXeI. The present hybrid quantumclassical simulations successfully describe the main experimental findings. For HXeI in the 〈110〉 (double substitution) site, the order of the HXe stretching frequencies (ν(Xe) < ν(Ar) < ν(Kr)) is in accord with the experimental observations, and also the frequency shifts in Ar and Kr matrices from a Xe matrix are well predicted (30 and 34 cm(1)). Both in the theory and experiment, the order of the HXe stretching frequencies differs from the case of HXeCl, which suggests the adequate theoretical description of the matrix effect. For HXeH in the 〈100〉 (single substitution) site, the order of the frequencies is ν(Xe) < ν(Kr) < ν(Ar), which also agrees with the experiments. The calculated frequency shifts for HXeH in Ar and Kr matrices with respect to a Xe matrix (36 and 23 cm(1)) are in a good agreement with the experiments. The present calculations predict an increase of the HXe stretching frequencies in the noblegas matrices with respect to vacuum.  [Show abstract] [Hide abstract]
ABSTRACT: This work present results of a systematic investigation of adsorption and dissociation of H2 on the neutral, positively, and negatively charged gold clusters Aunq (n = 2–11; q = 0, ±1) using the global reaction route mapping (GRRM) technique combined with the anharmonic downward distortion following (ADDF) and the artificial forceinduced reaction (AFIR) methods. An exhaustive search for H2 dissociation pathways is performed not only on the most stable cluster structures but also on the large number of lowenergy isomers, allowing structural transformations between them. The present strategy can automatically identify the structuredependent lowest transition states (TS) for H2 dissociation with a systematic procedure in the regime of the structural fluxionality of gold clusters at finite temperature. Temperature effects, cluster isomerization, and influence of the charge state of gold clusters on H2 adsorption and dissociation are studied. It is demonstrated that the most stable structures of the gold clusters are not always highly reactive, and an ensemble of isomeric structures must be taken into account for adequate description of the reaction rates at finite temperatures. The proposed approach can serve as a promising tool for a systematic analysis and prediction of reactivity of small metal clusters.  [Show abstract] [Hide abstract]
ABSTRACT: The enthalpies of formation for some selected oxygenates have been calculated by the atomisation energy approach using B3LYP, BHandHLYP, MPW3LYP, MPW1K, MPWB1K, BB1K, MPW1B95, BMK, and longrange corrected (LCωPBE, LCBOP, LCgauBOP, LCBOP12, LCgauB97) density functionals, as well as the composite CBSQB3 method. Compared with experiment, BMK, LCωPBE, LCgauBOP, LCBOP12, LCgauB97, MPW195, MPW3LYP functionals and CBSQB3 give root mean square errors (RMSE) in enthalpies of formation no greater than 4 kcal/mol, whilst MPW1K and BHandHLYP show much worse performance (RMSE of 20–40 kcal/mol). The B3LYP, MPWB1K, and BB1K results fall between the two extremes. Energy barriers for the dominant paths in the unimolecular decomposition of simple esters (HCO2CH3, C2H5CO2C2H5), C1–C3 acids, and 1butanol are reproduced well by CBSQB3, BMK, BB1K, LCgauB97, and PW1B95 (RMSE = 1–2 kcal/mol), while other LC methods (LCωPBE, LCBOP, LCgauBOP, and LCBOP12) show a deviation of up to 4 kcal/mol. For the ionisation potentials, calculated from Koopman's theorem, all of the investigated LCmethods give good results compared with other density functional theory functionals with a maximum deviation of 0.4 eV, except for LCgauB97, which has an RMSE of 0.7 eV.  [Show abstract] [Hide abstract]
ABSTRACT: This article gives a comprehensive review of the anharmonic downward distortion following (ADDF) method. The ADDF method has been developed as an automated reaction path search method. This method follows the anharmonic downward distortion (ADD) toward transition states and dissociation channels starting from a local minimum on the potential energy surface (PES). Systematic applications of the ADDF method to all local minima provide a global network of reaction pathways on the PES of given chemical formulas. Various extensions have been proposed and applied to many interesting chemical problems such as elucidation of photodissociation mechanisms, structure prediction of Hbonded clusters, mechanistic studies of organometallic catalysis, design of generationconversion routes of amino acid molecules, and so on. It has also been employed in efficient construction of anharmonic PESs for highly accurate vibrational analysis. These developments and applications are illustrated with some representative results.
Publication Stats
3k  Citations  
565.94  Total Impact Points  
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Institutions

20052015

Hokkaido University
 • Division of Chemistry
 • Graduate School of Science
Sapporo, Hokkaido, Japan


19992008

Ochanomizu University
 • Department of Chemistry
 • Graduate School of Humanities and Sciences
Tōkyō, Japan


20012002

University of Cambridge
 Department of Chemistry
Cambridge, England, United Kingdom


19932001

The University of Tokyo
 Department of Applied Chemistry
Tōkyō, Japan


1996

Iowa State University
 Department of Chemistry
Ames, Iowa, United States
