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Yu Harabuchi

Bio: Yu Harabuchi is an academic researcher from Hokkaido University. The author has contributed to research in topics: Conical intersection & Excited state. The author has an hindex of 17, co-authored 59 publications receiving 1053 citations. Previous affiliations of Yu Harabuchi include Reaction Design & National Presto Industries.


Papers
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Journal ArticleDOI
TL;DR: The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions as mentioned in this paper, which gives a unique connection from a given transition structure to local minima of the reactant and product sides.
Abstract: 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.

267 citations

Journal ArticleDOI
TL;DR: Investigation of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described.
Abstract: This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

133 citations

Journal ArticleDOI
TL;DR: 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.
Abstract: 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.

112 citations

Journal ArticleDOI
TL;DR: It is concluded that ππ*-excited cis-stilbene propagates primarily toward the twisted structural region due to dynamic effects, with partial branching to the DHP structural region via the flat-surface region around (S1)cis-min.
Abstract: On-the-fly dynamics simulations were carried out using spin-flip time dependent density functional theory (SF-TDDFT) to examine the photoisomerization and photocyclization mechanisms of cis-stilbene following excitation to the ππ* state. A state tracking method was devised to follow the target state among nearly degenerate electronic states during the dynamics simulations. The steepest descent path from the Franck–Condon structure of cis-stilbene in the ππ* state is shown to reach the S1-minimum of 4,4-dihydrophenanthrene (DHP) via a cis-stilbene-like structure (referred to as (S1)cis-min) on a very flat region of the S1-potential energy surface. From the dynamics simulations, the branching ratio of the photoisomerization is calculated as trans:DHP = 35:13, in very good agreement with the experimental data, trans:DHP = 35:10. The discrepancy between the steepest descent pathway and the significant trans-stilbene presence in the branching ratio observed experimentally and herein computationally is clarifie...

77 citations

Journal ArticleDOI
TL;DR: The present approach combines the seam model function approach with the recently proposed single-component artificial force induced reaction method to find MECIs systematically, and requires neither a Hessian nor a derivative coupling vector.
Abstract: Locating accessible conical intersections (CIs), especially minimum energy CI (MECI) structures, near the Franck–Condon (FC) region is one of the most important tasks in theoretical analyses of pho...

60 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

01 Feb 1995
TL;DR: In this paper, the unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio using DFT, MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set.
Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

1,652 citations

Journal ArticleDOI
TL;DR: An efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm is proposed and discussed, opening many possible applications in modern computational chemistry and drug discovery.
Abstract: We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.

671 citations

Journal ArticleDOI
TL;DR: The theory and fundamental principles of the spin-vibronic mechanism for ISC are presented, followed by empirical rules to estimate the rate of ISC within this regime.
Abstract: Intersystem crossing (ISC), formally forbidden within nonrelativistic quantum theory, is the mechanism by which a molecule changes its spin state. It plays an important role in the excited state decay dynamics of many molecular systems and not just those containing heavy elements. In the simplest case, ISC is driven by direct spin–orbit coupling between two states of different multiplicities. This coupling is usually assumed to remain unchanged by vibrational motion. It is also often presumed that spin-allowed radiationless transitions, i.e. internal conversion, and the nonadiabatic coupling that drives them, can be considered separately from ISC and spin–orbit coupling owing to the vastly different time scales upon which these processes are assumed to occur. However, these assumptions are too restrictive. Indeed, the strong mixing brought about by the simultaneous presence of nonadiabatic and spin–orbit coupling means that often the spin, electronic, and vibrational dynamics cannot be described independe...

505 citations