Norifumi Yamamoto

Norifumi Yamamoto
Chiba Institute of Technology · Faculty of Engineering

PhD
Computational Chemist at Chiba Institute of Technology

About

46
Publications
1,758
Reads
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613
Citations
Citations since 2017
10 Research Items
229 Citations
2017201820192020202120222023010203040
2017201820192020202120222023010203040
2017201820192020202120222023010203040
2017201820192020202120222023010203040
Introduction
I’m working on the analysis and design of functional materials and biomolecules using various methods of Computational Chemistry such as Quantum Chemistry (QC), Molecular Dynamics (MD), and Machine Learning (ML). My current research interests are Aggregation Induced Emission (AIE), Virus Drug Resistance, Metal Organic Framework (MOF), and Chemical Education.
Additional affiliations
April 2012 - present
Chiba Institute of Technology
Position
  • Professor (Assistant)
April 2012 - March 2016
Chiba Institute of Technology
Position
  • Professor (Assistant)

Publications

Publications (46)
Article
A mixture of ferrous ions and hydrogen peroxide, known as Fenton's reagent, is an effective oxidant and has been widely used in various industrial applications; however, there is still controversy about what the oxidizing agents are and how they are produced. In this study, we have determined minimum free-energy paths (MFEPs) from Fenton's reagent...
Article
In this study, the aggregation-induced emission (AIE) of a cyanostilbene derivative, called CN-MBE, was investigated using molecular simulations. The E-form of CN-MBE has been known to exhibit AIE, which is non-emissive in dilute solutions but becomes highly emissive in aggregated states, while its Z-form is non-emissive even in its crystalline for...
Article
An approach to quantitatively analyze the factors contributing to the activation of aggregation-induced emission (AIE) of a molecule is proposed using molecular simulations. A cyanostilbene derivative, 1-cyano-1,2-bis-(4′-methylbiphenyl)ethylene (CN-MBE), has two isomers, E and Z forms. The E-form of CN-MBE exhibits AIE, and is non-emissive in dilu...
Article
An improved understanding of the contributions of various factors to aggregation-induced emission (AIE) is required to advance the development and application of highly efficient AIE luminogens. Herein, the AIE of diphenyldibenzofulvene (DPDBF), which is nonemissive in dilute solutions but becomes highly emissive in aggregated states, was investiga...
Article
Full-text available
The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl...
Article
Full-text available
The substitution of Ile to Val at residue 117 (I117V) of neuraminidase (NA) reduces the susceptibility of the A/H5N1 influenza virus to oseltamivir (OTV). However, the molecular mechanism by which the I117V mutation affects the intermolecular interactions between NA and OTV has not been fully elucidated. In this study, we performed molecular dynami...
Article
CO2 hydrates are ice‐like substances in which CO2 molecules are encapsulated in water and are known to reduce the rate at which CO2 dissolves in water. It is believed that the thickness of the hydrate film is dominant in the dissolution rate. In this study, we have developed a model that takes into account two factors: the permeation of H2O molecul...
Article
Full-text available
Background Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated. Methods In this study, we used dynamic residue interaction network (dRIN) analys...
Article
Pin1 enzyme protein recognizes specifically phosphorylated serine/threonine (pSer/pThr) and catalyzes the slow interconversion of the peptidyl-prolyl bond between cis and trans forms. Structural dynamics between the cis and trans forms are essential to reveal the underlying molecular mechanism of the catalysis. In this study, we apply the weighted...
Preprint
Full-text available
This study develops a model to predict the CO2 hydrate layer thickness. As to achieve this, we need the mass transfer coefficients at the interface between water phase and CO2 hydrate layer and the diffusion coefficients in CO2 hydrate. Firstly, we conducted the visualization experiment of CO2 hydrate layer dissolution behavior. From the experiment...
Article
The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located...
Article
The effect of intermolecular interactions on excited-state intramolecular proton transfer (ESIPT) in 4'-N,N-dimethylamino-3-hydroxyflavone (DMHF) doped in acetonitrile crystals was investigated by measuring its temperature dependence of steady-state fluorescence excitation and fluorescence spectra and picosecond time-resolved spectra. The relative...
Article
1-Cyano-trans-1,2-bis-(4’-methylbiphenyl)ethylene (CN-MBE) is a prototypical molecule that exhibits aggregation-induced emission (AIE), however there is very little information about the molecular structure. Viscosity-dependence of fluorescence excitation and fluorescence spectra, fluorescence quantum yield, and fluorescence lifetime were recorded...
Conference Paper
In the present study, we analytically tackle the development of a prediction model with the experiment as a counterpart. The model separate two stages: (i) CO_2 hydrate is generated from at the interface, and propagated of hydrate under CO_2 hydrate without condition and ; (ii) CO_2 hydrate grew for the case that the hydrate exists. In developing t...
Article
The effect of intermolecular interaction on excited-state intramolecular proton transfer (ESIPT) in 4′-N,N-dimethylamino-3-hydroxyflavone (DMHF) doped in acetonitrile crystals was investigated by measuring the temperature dependence of fluorescence excitation and fluorescence spectra. A solid/solid phase transition of DMHF-doped acetonitrile crysta...
Article
The external field effects on the steady-state electronic spectra and fluorescence dynamics were investigated for 4'-N,N-dimethylamino-3-hydroxyflavone (DMHF) in a poly(methyl methacrylate) (PMMA) film. In the steady-state spectrum, dual emission was observed from the excited states of the normal (N*) and tautomer (T*) forms. Application of an exte...
Article
The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing β-sheet expansion facilitates the formation of a...
Article
Infrared (IR) spectra of the enol and keto forms of 4-amino-6-oxopyrimidine (AOP) isolated in a low-temperature Xe matrix were recorded, where the change from the keto to the enol form was found to be induced by UV irradiation (λ > 270 nm). On the other hand, the hydrated crystal of AOP exhibited a similar IR spectrum to the anhydrous crystal by de...
Article
For the purpose of providing a realistic description of the reaction mechanisms in large molecular systems, we propose a quantum mechanical/molecular mechanical (QM/MM) method combined with the ab initio fragment molecular orbital (FMO) method, i.e., the ab initio FMO-QM/MM method. By connecting a molecular dynamics (MD) program AMBER with an FMO p...
Article
Crystal structures of polymorphs of 2-(2'-hydroxyphenyl)benzimidazole (HPBI), Forms α and β, are analyzed by X-ray crystallography. The fluorescence excitation (FE) and fluorescence spectra of the polymorphs are separately observed at temperatures 77-298 K. It has been found that the electronic spectra of the two crystal forms are significantly dif...
Article
Electroabsorption and electrophotoluminescence spectra were investigated for 2-(2′-hydroxyphenyl)benzimidazole in PMMA, and the results were compared with quantum chemical calculations. The electroabsorption spectrum of the enol form was ascribed to a change in the molecular polarizability following photoexcitation. On the other hand, the electroph...
Article
To obtain the energy gradient of a specific region in a large molecule, we defined a partial energy gradient (PEG) based on the fragment molecular orbital (FMO) method. The suitability of PEG was examined by performing geometry optimizations of model systems, and we found that optimization with PEG could provide almost the same geometry obtained wi...
Article
A peptide fragment of human prion protein, HuPrP(106–126), has been reported to mimic the pathological features underlying prion diseases. Although the actual neurotoxic mechanism of HuPrP(106–126) has not been elucidated, several hypotheses has been proposed based on the role for copper. In this study, to understand the toxic function of HuPrP(106...
Article
Prion diseases result from the conformational conversion of a normal prion protein (PrPC) into an abnormal isoform (PrPSc). Recently, we discovered an anti-prion compound GN8 to interfere with the pathological conversion of prion protein; however, the mechanisms underlying the anti-prion activity remained unresolved. In this study, we provide the f...
Article
Although some antiprion compounds have been shown to interfere with the pathological conversion of prion protein into a misfolded isoform, the actual mechanism has not been elucidated. In this study, we compared different conformations of prion protein with and without ligand binding, based on molecular dynamics simulations, to clarify the role of...
Article
We studied the redox behavior of copper-binding sites in prion protein (PrP) to clarify copper's role in the pathological mechanism underlying prion diseases. We investigated the coordination structures, binding affinities, and redox potentials of copper-binding peptide fragments derived from the N-terminal domain of PrP by density functional theor...
Article
We investigated the structures and redox properties of copper-chelating cuprizone using DFT-B3LYP calculations to gain insights into its toxicity causing neurodegeneration similar to lesions in prion diseases. We found that the copper-cuprizone complex has redox potentials of the Cu(III)/Cu(II) couple that range from −0.05 to +0.98V (vs. normal hyd...
Article
Full-text available
The N2(+) states lying in the ionization region of 26-45 eV and the dissociation dynamics are investigated by high-resolution threshold photoelectron spectroscopy and threshold photoelectron-photoion coincidence spectroscopy. The threshold photoelectron spectrum exhibits several broad bands as well as sharp peaks. The band features are assigned to...
Article
Intramolecular vibrational energy redistributions of the O-H stretching (nuOH) vibration for the methanol monomer and its water complex, the methanol-water dimer, are investigated by using ab initio full-dimensional classical trajectory calculations. For the methanol monomer, in the high-energy regime of the 5nuOH overtone, the time dependence of t...
Article
Ab initio classical trajectory calculations have been applied to the intramolecular vibrational energy redistribution process of an O-H stretching vibration for phenol cation, [phenol]+, and its hydrogen-bonded water complex, [phenol-water]+. In phenol cation, a single narrow peak in the power spectrum, obtained by Fourier transformation of the aut...
Article
In a previous paper we reported a study of the electronic structures of inner valence states of O(2) (+) and the dissociation process, where there remained some questions as to the origins of the dissociation fragment formation of the O+((2)D)+O((3)P) limit in observed spectra. In this paper, we present the results of calculations of the nonadiabat...
Article
High-resolution threshold photoelectron spectroscopy has been used to study O 2 in the 24–50 eV photon energy region, where several broad bands with superimposed fine peaks are observed. Theoretical calculations on the basis of the state-averaged complete-active-space self-consistent-field method followed by the second order configuration interacti...
Article
Infrared photodissociation spectra of [aniline−(H2O)n]+ (n = 1−8) are measured in the 2700−3800 cm-1 region. The spectra are interpreted with the aid of density functional theory calculations. The n = 1 ion has an N−H···O hydrogen bond. The spectrum of the n = 2 ion demonstrates a large perturbation to both of the NH oscillators, indicating the 1−1...
Article
Pulsed field ionization (PFI)-zero-kinetic-energy (ZEKE) photoelectron spectra are measured for 4-aminobenzonitrile (4ABN) and “NH2-donor isomer” of 4ABN–H2O 1 : 1 complex in which the oxygen atom of water is bonded to the amino hydrogen (K. Sakota, N. Yamamoto, K. Ohashi, H. Sekiya, M. Saeki, S. Ishiuchi, M. Sakai and M. Fujii, Chem. Phys. Lett.,...
Article
The OH stretching vibrations of phenol (Ph), phenol cation ([Ph]+), phenol–water complex (Ph–H2O) and phenol–water cationic complex ([Ph–H2O]+) are investigated theoretically in terms of ab initio potential energy surfaces, vibrational wavefunctions, and infrared absorption intensities. It was found that the anharmonic coupling between the hydrogen...
Article
To elucidate the relative stability of various structures of the benzene dimer cation radical, $ (\C_6 \H_6)^{+}_2 $ in its ground and low-lying excited states, ab initio complete active space self-consistent field (CASSCF), multi-reference singly and doubly excited configuration interaction (MRSDCI), and multi-reference coupled pair approximation...
Article
The IR-dip spectra and IR–UV hole-burning spectra of jet-cooled 4-aminobenzonitrile–water 1:1 complex have been measured to investigate the effects of the introduction of two substituents into the aromatic ring on the hydrogen-bonding interaction and stable structures of the complex. We have obtained a clear evidence for the observation of three st...
Article
The structures of aniline dimer cation are investigated by the density functional theory calculations at the B3LYP/cc-pVDZ level. We obtained two stable conformational isomers which have `NH⋯N' or `NH⋯π' hydrogen bond. The NH⋯N isomer is more stable by 2.50kcalmol−1. The calculated infrared spectra suggest that the NH stretching vibrations due to t...
Article
The hole-burning, fluorescence excitation, and dispersed fluorescence spectra of jet-cooled tropolone (TRN)–(CO2)n (n=1,2) complexes are measured to investigate the structures of the complexes and the effects of intermolecular interaction on proton tunneling in TRN. The electronic transitions of TRN–(CO2)n (n=1,2) are well separated in the hole-bur...
Article
The mass-resolved spectrum indicates that only one conformation contributes to sharp peaks observed in the S-1 <-- S-0 resonance two-photon ionization (R2PI) spectrum. However, geometry optimizations at the MP2/cc-pVDZ level suggest that two conformational isomers are stable: a head-to-head conformation with a single NH . . .N hydrogen bond and a h...
Article
The electronic and infrared spectra of jet-cooled 4-aminobenzonitrile–(H2O)1 (4ABN–(H2O)1) hydrogen-bonded complex have been measured by the resonance-enhanced multiphoton ionization (REMPI) and infrared-dip (IR-dip) spectroscopy. Both the amino and cyano groups form intermolecular hydrogen bond with water, providing two stable isomers. It has been...
Article
Structures of (aniline–benzene)+ and (aniline)2+ are re-investigated by electronic spectroscopy in the near-infrared region and vibrational spectroscopy in the NH stretching region. The spectra of (aniline–benzene)+ indicate a structure including a hydrogen bond between an NH bond of the ionic aniline and the π-electrons of the neutral benzene. Two...

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Project (1)
Project
The goal of this project is to elucidate the molecular mechanism of Aggregation-Induced Emission (AIE) using computational chemistry methods such as the QM/MM Free-Energy Perturbation (FEP) method.