研究者業績

星野 忠次

ホシノ チュウジ  (Tyuji Hoshino)

基本情報

所属
千葉大学 大学院薬学研究院 准教授
学位
博士(工学)(早稲田大学)

J-GLOBAL ID
200901091415976961
researchmap会員ID
1000169674

外部リンク

論文

 157
  • Taichi Kamo, Keiichi Kuroda, Saki Nimura, Yan Guo, Shota Kondo, Michiyoshi Nukaga, Tyuji Hoshino
    Biochemistry 63(10) 1278-1286 2024年5月21日  
    Metallo-β-lactamases (MBL) deactivate β-lactam antibiotics through a catalytic reaction caused by two zinc ions at the active center. Since MBLs deteriorate a wide range of antibiotics, they are dangerous factors for bacterial multidrug resistance. In this work, organic synthesis, computational design, and crystal structure analysis were performed to obtain potent MBL inhibitors based on a previously identified hit compound. The hit compound comprised 3,4-dihydro-2(1H)-quinolinone linked with a phenyl-ether-methyl group via a thiazole ring. In the first step, the thiazole ring was replaced with a tertiary amine to avoid the planar structure. In the second step, we virtually modified the compound by keeping the quinolinone backbone. Every modified compound was bound to a kind of MBL, imipenemase-1 (IMP-1), and the binding pose was optimized by a molecular mechanics calculation. The binding scores were evaluated for the respective optimized binding poses. Given the predicted binding poses and calculated binding scores, candidate compounds were determined for organic syntheses. The inhibitory activities of the synthesized compounds were measured by an in vitro assay for two kinds of MBLs, IMP-1 and New Delhi metallo-β-lactamase (NDM-1). A quinolinone connected with an amine bound with methyl-phenyl-ether-propyl and cyclohexyl-ethyl showed a 50% inhibitory concentration of 4.8 μM. An X-ray crystal analysis clarified the binding structure of a synthesized compound to IMP-1. The δ-lactam ring of quinolinone was hydrolyzed, and the generated carboxyl group was coordinated with zinc ions. The findings on the chemical structure and binding pose are expected to be a base for developing MBL inhibitors.
  • Kouichi Kitamura, Tyuji Hoshino, Atsushi Okabe, Masaki Fukuyo, Bahityar Rahmutulla, Nobuko Tanaka, Sohei Kobayashi, Tomoaki Tanaka, Takashi Shida, Mashiro Ueda, Toshinari Minamoto, Hisahiro Matsubara, Atsushi Kaneda, Hideshi Ishii, Kazuyuki Matsushita
    International journal of molecular sciences 24(24) 2023年12月11日  
    The interaction between mRNA and ribosomal RNA (rRNA) transcription in cancer remains unclear. RNAP I and II possess a common N-terminal tail (NTT), RNA polymerase subunit RPB6, which interacts with P62 of transcription factor (TF) IIH, and is a common target for the link between mRNA and rRNA transcription. The mRNAs and rRNAs affected by FUBP1-interacting repressor (FIR) were assessed via RNA sequencing and qRT-PCR analysis. An FIR, a c-myc transcriptional repressor, and its splicing form FIRΔexon2 were examined to interact with P62. Protein interaction was investigated via isothermal titration calorimetry measurements. FIR was found to contain a highly conserved region homologous to RPB6 that interacts with P62. FIRΔexon2 competed with FIR for P62 binding and coactivated transcription of mRNAs and rRNAs. Low-molecular-weight chemical compounds that bind to FIR and FIRΔexon2 were screened for cancer treatment. A low-molecular-weight chemical, BK697, which interacts with FIRΔexon2, inhibited tumor cell growth with rRNA suppression. In this study, a novel coactivation pathway for cancer-related mRNA and rRNA transcription through TFIIH/P62 by FIRΔexon2 was proposed. Direct evidence in X-ray crystallography is required in further studies to show the conformational difference between FIR and FIRΔexon2 that affects the P62-RBP6 interaction.
  • Kazunori Miwa, Yan Guo, Masayuki Hata, Yoshinori Hirano, Norio Yamamoto, Tyuji Hoshino
    Chemical and Pharmaceutical Bulletin 71(12) 897-905 2023年12月1日  
  • Yuma Ito, Huiyan Lu, Mariko Kitajima, Hayato Ishikawa, Yoshihiro Nakata, Yasumasa Iwatani, Tyuji Hoshino
    Journal of natural products 86(11) 2487-2495 2023年11月24日  
    The emergence of drug-resistant viruses is a serious concern in current chemotherapy for human immunodeficiency virus type-1 (HIV-1) infectious diseases. Hence, antiviral drugs aiming at targets that are different from those of approved drugs are still required, and the RNase H activity of HIV-1 reverse transcriptase is a suitable target. In this study, a search of a series of natural compounds was performed to identify the RNase H inhibitors. Three compounds were found to block the RNase H enzymatic activity. A laccaic acid skeleton was observed in all three natural compounds. A hydroxy phenyl group is connected to an anthraquinone backbone in the skeleton. An acetamido-ethyl, amino-carboxy-ethyl, and amino-ethyl are bound to the phenyl in laccaic acids A, C, and E, respectively. Laccaic acid C showed a 50% inhibitory concentration at 8.1 μM. Laccaic acid C also showed inhibitory activity in a cell-based viral proliferation assay. Binding structures of these three laccaic acids were determined by X-ray crystallographic analysis using a recombinant protein composed of the HIV-1 RNase H domain. Two divalent metal ions were located at the catalytic center in which one carbonyl and two hydroxy groups on the anthraquinone backbone chelated two metal ions. Molecular dynamics simulations were performed to examine the stabilities of the binding structures. Laccaic acid C showed the strongest binding to the catalytic site. These findings will be helpful for the design of potent inhibitors with modification of laccaic acids to enhance the binding affinity.
  • Sohei Kobayashi, Takaki Hiwasa, Kouichi Kitamura, Masayuki Kano, Tyuji Hoshino, Sho Hirano, Mayuko Hashimoto, Masanori Seimiya, Hideaki Shimada, Fumio Nomura, Hisahiro Matsubara, Kazuyuki Matsushita
    Journal of clinical laboratory analysis e24978 2023年11月14日  
    BACKGROUND: At different stages of the disease, biomarkers can help to determine disease progression and recurrence and provide a personalized indicator of therapeutic effectiveness. The serological identification of antigens by recombinant cDNA expression cloning (SEREX) has identified five SEREX antigens. RESULTS: Compared with healthy donors, anti-FIRΔexon2 and anti-SOHLH antibodies (Abs) in the sera of patients with colorectal cancer (CRC) were markedly higher. Furthermore, no correlation was noted between five SEREX antigens and the three tumor markers (CEA, CA19-9, and anti-p53 Abs), indicating that anti-FIRΔexon2 Abs are an independent candidate marker for patients with CRC. Generally, the levels of anti-FIRΔexon2 Abs combined with clinically available tumor markers were determined to be significantly higher compared with CEA, CA19-9. Moreover, in early-stage CRC, the levels of anti-FIRΔexon2 Abs combined with existing tumor markers were higher than those of CEA, CA19-9. CONCLUSION: Due to the highly heterogeneous nature of CRC, a single tumor marker is unlikely to become a standalone diagnostic test due to its commonly insufficient sensitivity and/or specificity. Using a combination antibody detection approach of tumor markers for CRC diagnosis has the potential to be an effective approach. Therefore, the use of serum protein biomarker candidates holds promise for the development of inexpensive, noninvasive, and inexpensive tests for the detection of CRC.

MISC

 209
  • J. Phys. Chem. B 107, 10274-10283 2003年  
    Y.Fujii, N.Okimoto, M.Hata, T.Narumi, K.Yasuoka, R.Susukita, A.Suenaga, N.Futatsugi, T.Koishi, H.Furusawa, A.Kawai, T.Ebisuzaki, S.Neya, T.Hoshino : Molecular dynamics study on Class A β-lactamase: The hydrogen bond network among the functional groups the penicillin G and the side chains of the conserved residues in the active site
  • 藤井 康之, 沖本 憲明, 畑 晶之, 星野 忠次
    日本コンピュータ化学会年会講演予稿集 2002(1) 1P25 2002年7月3日  
  • 田中 良和, 藤井 康之, 畑 晶之, 星野 忠次
    日本コンピュータ化学会年会講演予稿集 2002(1) 1P27 2002年7月3日  
  • 畑晶之, 京田直子, 田中良和, 刑部泰輔, 幸瞳, 石井伊都子, 北田光一, 星野忠次, 根矢三郎
    日本生物物理学会年会講演予稿集 40th 2002年  
  • Kenichi Mori, Masayuki Hata, Saburo Neya, Tyuji Hoshino
    Chem-Bio Informatics Journal 2(4) 147-155 2002年  
    Ras protein is a kind of small G protein that functions as a molecular switch or a timer alternating between the inactive GDP-bound and active GTP-bound form. Ras requires Mg2+ as a cofactor for its full activity. Recently, in another small G protein family, the release of Mg 2+ coordinated by GDP was found to play an important role in binding the guanine nucleotide exchanging factor (GEF) that promotes the GDP/GTP exchange reaction. Here we calculated Mg2+-bound and Mg 2+-unbound conformations of the GDP-bound Ras by molecular dynamics (MD) simulation. In the Mg2+-unbound conformation, significant conformational changes in the switch 1 region were observed, in which the switch region opened to expose the nucleotide-binding site. The distance between the switch 1 and switch 2 regions increased, resulting in the appearance of a groove. These conformations of the switch regions were very similar to that of Ras bound to its GEF: SOS (Son Of Sevenless). These structural changes were not observed in the Mg2+-bound conformation. These results demonstrate the regulatory role of Mg2+ in GEF binding and suggest that the GDP dissociation occurs by a stepwise mechanism (1) Releasing of Mg2+ (2) Conformational changes of the switch regions (semi-open form) (3) GEF binding (complete-open form) and (4) GDP dissociation. We suggest that the concentration of Mg2+ ions may regulate the binding between small G-proteins and GEFs. Copyright 2002 Chem-Bio Informatics Society.
  • 村田 克美, 星野 忠次, 佐藤 慶治, 畑 昌之, 津田 穣
    Chem-Bio Inform. J., 2, 97-103 95-101 2002年  
    バクテリオロドプシンのL→M→N反応において、プロトンの移動が、通常とは逆の方向にも起こりやすい構造を見い出す研究をab initio 計算によって行った。その一例は、シッフ塩基に直結している水分子のO 原子と、シッフ塩基のN原子とを結ぶ直線が対称面に含まれる場合に、Asp85とAsp96とがCs対称を満たしている構造である。この構造では、L→M→N反応とN→M→L逆反応の可逆的なプロトン移動が容易に起こり得る。
  • M Hata, Y Hirano, T Hoshino, M Tsuda
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 123(26) 6410-6416 2001年7月  
    The substrate oxygenation mechanism by an ultimate species in monooxygenation by cytochrome P-450 (compound I) was investigated by the density functional theory method. An initial model compound was constructed from a structure obtained by 300-ps molecular dynamics simulation of compound I-formed P-450cam under physiologic conditions, and it consisted of porphine for protoporphyrin IX, S--CH3 for the side chain of Cys357 of the fifth ligand of heme, a methane molecule for the substrate, a heme iron, and an oxygen atom of the sixth ligand of heme. The results of the calculation revealed that the substrate oxygenation mechanism had four elementary processes, i.e., (1) formation of [FeOH](3+) and a substrate radical by hydrogen atom abstraction from the substrate caused by FeO](3+), (2) rotation of the OH group of the sixth ligand of FeOH](3+) produced by process 1. (3) substrate radical binding with the [FeOH](3+), and (4) elimination of the oxygenated substrate formed at the sixth ligand binding site. The rate-determining step is process 1, hydrogen atom abstraction from the substrate, and the activation energy was determined to be about 15 kcal/mol. For this reason, it is thought that this reaction occurs in vivo.
  • T Hoshino, M Hata, M Tsuda
    SURFACE SCIENCE 481(1-3) 205-214 2001年6月  
    Quantum chemical calculations were performed to indicate the lowest energy path and the activation energy for Si adatom diffusion on a Si(1 1 1) surface and to evaluate the dependency of the activation energy on strains imposed on the Si surface. The activation energy barrier for the adatom diffusion was estimated to be 0.8 eV for a non-strained surface. The energy barrier increases on Si surfaces under compressive strain and, conversely, decreases under tensile strain. However, the energy variations are only within 0.1 eV under strains ranging between +/-1%. The influence of strain on the 7 x 7 reconstruction is discussed in light of these theoretical results. (C) 2001 Elsevier Science B.V. All rights reserved.
  • N Okimoto, K Kitayama, M Hata, T Hoshino, M Tsuda
    JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 543(1-3) 53-63 2001年6月  
    We carried out molecular dynamics (MD) simulations of the HIV-1 protease (HIV-1 PR)-substrate complex and examined the efficiency of the catalytic activity in terms of the difference in the structures of the substrates. Four kinds of substrates were used in this work: three substrate peptides composed of the sequence of the natural cleavage site by HIV-I PR (Ac-Gln-Asn-Tyr-Pro-Ile-Val-NMe, Ac-Ser-Gln-Asn-Tyr-Pro-Ile-Val-NMe, and Ac-Val-Ser-Gln-Asn-Tyr-Pro-Ile-Val-Gln-Nme) and another substrate peptide in which Leu is substituted at the P4 position (Ac-Val-Leu-Gln-Asn-Tyr-Pro-Ile-Val-Gln-Nme). simulations revealed that the first three kinds of the HPV-I PR-substrate complexes maintain a specific conformation for initiating catalytic reaction, but the last HIV-I PR-substrate complex does not. Our results suggest that the first three substrate peptides are hydrolyzed when the respective ES complexes were formed. In contrast, a catalytic reaction seldom occurs for the last substrate peptide, even if it combined with HIV-I PR. (C) 2001 Elsevier Science B.V. All rights reserved.
  • T Hoshino, M Hirokami, M Hata, M Tsuda
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS SHORT NOTES & REVIEW PAPERS 40(3B) 1906-1910 2001年3月  
    Quantum chemical calculations have been performed to investigate changes in total energy and charge population of metal microclusters under various conditions for electric charging. This information would be helpful in the design of single-electron devices in which charge confinement in a quantum dot is essential to achieve device action. Total energies suggest that storage of electric charge is allowed within +/- 2e at normal device voltage for an At I,, cluster whose diameter is 3.8 nm in the planar structure. Less charge confinement (+/-e) is permitted for smaller cluster size. Charge populations show a difference between atoms located at the inner and outer parts of the Cluster. The total amount of electrons in the inner part is almost constant in spite of the variation of electric charging conditions. In contrast. the Outer part is significantly involved in storing or releasing electrons.
  • T Hoshino, K Murata, K Mizutani, M Hata, M Tsuda
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS SHORT NOTES & REVIEW PAPERS 40(1) 276-280 2001年1月  
    Stable structures of Al clusters grown on completely or incompletely H-terminated diamond (111) surfaces have been determined by first principles quantum chemical calculations. When Al atoms are deposited on the completely H-terminated diamond surface, planar stable structures are possibly formed as well as nonplanar ones. On the other hand, only nonplanar type Al clusters are grown on the partly H-removed surface losing three H atoms from the complete H-termination, and those nonplanar Al clusters have the structure of a single Al crystal. The result suggests the possibility uf. an epitaxial growth of Al metals on the diamond(111) substrate.
  • K Murata, Y Fujii, N Enomoto, M Hata, T Hoshino, M Tsuda
    BIOPHYSICAL JOURNAL 79(2) 982-991 2000年8月  
    The mechanism of proton transport around the Schiff base in bacteriorhodopsin was investigated by ab initio molecular orbital (MO) calculations. Computations were performed for the case where there is a water molecule between the Schiff base and the Asp residue and for the case where there is no water molecule. Changes in the atomic configuration and potential energy through the proton transport process were compared between two cases. In the absence of water, the protonated Schiff base was not stable, and a proton was spontaneously detached from the Schiff base, On the other hand, a stable structure of the protonated Schiff base was obtained in the presence of water. This suggests that the presence of a water molecule is required for stability in the formation of a protonated Schiff base.
  • T Hoshino, A Sekino, M Hata, M Tsuda
    APPLIED SURFACE SCIENCE 162 435-439 2000年8月  
    Quantum theoretical calculations have been performed to obtain the lowest energy reaction path for the oxidation of an Al micro-cluster with an O-2 molecule. In reactions with a ground state O-2 molecule(spin triplet state), a very low potential energy barrier of 0.2 eV exists for the adhesion of an O-2 molecule to an Al cluster and the stabilization energy of the final product is 3.0 eV. In reactions with an electronically excited O-2 molecule (spin singlet state), no energy barrier exists during the reaction and the oxidation of the Al cluster proceeds spontaneously, giving a stabilization energy of 7.7 eV. Since the ground electronic state of the initial reactant is the triplet state and the most stable final product is the singlet state, an inter-system crossing from the triplet to the singlet state is expected to occur during the oxidation process. (C) 2000 Elsevier Science B.V. All rights reserved.
  • J Ueno, T Hoshino, M Hata, M Tsuda
    APPLIED SURFACE SCIENCE 162 440-444 2000年8月  
    Ab initio theoretical calculations have been performed to obtain the stable structures for clusters consisting of a small number of Al atoms. Geometry optimization has revealed that there exists a stable planar structure for Al, clusters. The electron density distributions in the planar structures were examined for the electrically neutral, negative, and positive conditions of the Al clusters. Charge population maps suggested that the outer Al atoms of the cluster play a major role in the storage of extra electrons. In addition to the planar structure, nonplanar structures have been obtained for Al clusters. However, the configuration of these structures is much different from that of Al crystals. (C) 2000 Elsevier Science B.V. All rights reserved.
  • N Okimoto, T Tsukui, K Kitayama, M Hata, T Hoshino, M Tsuda
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 122(23) 5613-5622 2000年6月  
    Several molecular dynamics (MD) simulations of HIV-1 protease (HIV-1 PR)-substrate complex were performed. The initial structure of the enzyme-substrate (ES) complex was constructed based on the X-ray crystallographic structure of the HIV-1 PR-inhibitor (JG-365) complex. First, we investigate which of Asp25 and Asp25' at the catalytic site (two catalytic Asp residues) is protonated in the ES complex. These MD simulations have revealed that the protein hydrolysis mechanism is initiated from the ES complex in which Asp25' is protonated. This protein hydrolysis mechanism was already studied using quantum chemical calculations, which suggested that the specific conformation of the ES complex was essential for enzymatic activity. Next, we investigate the mechanism for the maintenance of specific conformation of the ES complex. The MD simulations suggest that two water molecules at the loop structures of the active site have a substantial role in maintaining the specific conformation for initiation of the enzyme reaction. This indicates that the enzymatic activity of HIV-1 PR cannot be induced by only the protease encoded by the RNA gene of HIV-1, but this also requires the incorporation of water molecules into the active site.
  • T Hoshino, Y Nishioka
    PHYSICAL REVIEW LETTERS 84(20) 4633-4636 2000年5月  
    Cluster computations with the density functional theory were performed to clarify the diffusion mechanism of an O atom adsorbed on a Si surface. The activation energy required for the oxygen diffusion into the Si substrate is estimated to be 1.6 eV, which is fairly small compared to oxygen diffusion within a Si crystal. The presence of a surface dangling bond is responsible for the lowering of the activation energy, assisting the generation of an intermediate which is involved in the rearrangement of the Si-O connections. Adsorption of another O atom on the Si surface appears to further enhance the inward oxygen diffusion.
  • M Hata, Y Fujii, M Ishii, T Hoshino, M Tsuda
    CHEMICAL & PHARMACEUTICAL BULLETIN 48(4) 447-453 2000年4月  
    The tetrahedral intermediate formation process, which is the first step in the deacylation reaction by class A beta-lactamase, was investigated by the ab initio molecular orbital method. In this study, benzyl penicillin was used as the substrate. From the results of our molecular dynamics study of the structure of beta-lactam antibiotics-beta-lactamase complex, the substrate, Ser70, Lys73, Ser130, Glu166 and a water molecule for the deacylation reaction were considered for construction of a model for calculation. The calculation results indicated that Glu166 plays a role in holding a water molecule, which is necessary for the deacylation reaction, and that the hydrogen bond network among Lys73N zeta, Ser130O gamma, and the carboxyl group of the beta-lactam antibiotics was formed by the uptake of beta-lactam antibiotics by beta-lactamase, The activation energy for this reaction was 33.3 kcal/mol, and it is very likely that the reaction occurred at body temperature, Subsequent calculation results obtained by using the model excluding Ser130 and the carboxyl group of the substrate indicated that the activation energy for this reaction was 40.8 kcal/mol, which is 7.5 kcal/mol higher than that of the previous reaction, It was found that the hydrogen bond network plays an important role in decreasing the activation energy for the tetrahedral intermediate formation reaction. Lys73N zeta, which is located at the edge of the hydrogen bond network, played a role in forming a hydrogen bond with Glu166O epsilon in order to help the deacylation reaction. The role of amino acid residues around the active site of class A beta-lactamase was also discussed.
  • M Hata, T Hoshino, M Tsuda
    CHEMICAL COMMUNICATIONS 20(20) 2037-2038 2000年  
    We propose a structure for the ultimate species which gives a straightforward explanation of the major results in the oxidation of hydrocarbons by cytochrome P-450 where the stereochemistry is retained and the isotope effect is small.
  • SHIMADA K, ISHIMARU T, WATANABE T, YAMAWAKI T, OSUKA M, HOSHINO T, OHDOMARI I
    Physical Review B 62(4) 2546-2551 2000年  
  • Yoshinori Hirano, Norihito Ohmori, Noriaki Okimoto, Masayuki Hata, Tyuji Hoshino, Minoru Tsuda
    Journal of Photopolymer Science and Technology 13(4) 503-506 2000年  
  • ISHIMARU T, HOSHINO T, SHIMADA K, YAMAWAKI T, OHDOMARI I
    Physical Review B 61(23) 15577-15580 2000年  
  • Hirano Yoshinori, Hata Masayuki, Hoshino Tyuji, Tsuda Minoru
    JCPE Journal 12(2) 119-128 2000年  
    Quantum chemical calculations have been performed to clarify the function of the active catalytic subunit (C-subunit) of cAMP-dependent protein kinase (cAPK) that plays an important role in the regulation of blood glucose. It was found that the phosphorylation of Ser residue by cAPK proceeds via two elementary reactions; (i) an intermediate is formed from the enzyme-substrate complex (ES-complex), and (ii) the phosphorylated Ser is released from the active site. In the intermediate between the two elementary reactions, the Ser of the substrate is attached to the γ-phosphoric acid of the ATP, and the γ-phosphorus atom has a five-coordinated structure. The former elementary reaction is the rate-determining step, and the activation energy required for this phosphorylation reaction has been estimated to be 29.04kcal/mol. Hence, this phosphorylation reaction is expected to proceed at a body temperature of about 310K.
  • H Morinaga, T Hoshino, Y Omura, M Kitagawa, M Aoki
    CLEANING TECHNOLOGY IN SEMICONDUCTOR DEVICE MANUFACTURING 99(36) 585-592 2000年  
    It is found that metallic impurities such as Al, Fe and Zn are more likely to adhere onto SiO2 surfaces than bare Si surfaces in both neutral and alkali solutions. Speculating that "mechanism of metal adhesion in alkali solution is caused by the dehydration reaction between OH-terminated Si surface and OH bound with metals': authors tried quantum chemical calculation of potential energy change during the reaction, and found that calculated results were in good agreement with experimental results and adhesion models. Use of chelate-added alkali cleaning solution significantly reduces metal adhesion from cleaning solution. This will lead to improvement of Si surface cleanliness and cost reduction.
  • HOSHINO T, NISHIOKA Y
    Physical Review B 61(7) 4705-4713 2000年  
  • N Futatsugi, M Hata, T Hoshino, M Tsuda
    BIOPHYSICAL JOURNAL 77(6) 3287-3292 1999年12月  
    Quantum chemical computations using the ab initio molecular orbital (MO) method have been performed to investigate the molecular switching mechanism of Pas protein p21, which has an important role in intracellular signal cascades. Lys(16) was demonstrated to be crucial to the function of Pas p21, and the hydrolysis of GTP to GDP was found to be an one-step reaction. The potential energy barrier of this hydrolysis reaction from GTP to (GDP + P) was calculated to be similar to 42 kcal/mol. The role of GAP (GTPase-activating protein) was also discussed in terms of the delivery of the water molecules required for the hydrolysis.
  • T Hoshino, Y Nishioka
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS SHORT NOTES & REVIEW PAPERS 38(12A) 6855-6859 1999年12月  
    Energy changes during the conversion reaction among OH-, F-, and H-terminated Si surfaces have been evaluated by first-principles calculations with the density functional theory and the reaction field method for solvent effect. First, the reaction paths for the conversion of surface terminating species were examined in terms of the interactions with HF or H2O and, next, the potential energy curves were estimated, incorporating the effect of the solvent. It was suggested that the OH-termination is easily converted into the F-termination and the reverse reaction also possibly occurs at room temperatures, whereas the conversion between the H- and OH-terminations is not probable. The replacement of F by H is not favorable, and instead, Si etching would be required for the generation of the H-terminated surface.
  • H Hayashi, S Morishita, T Tatsumi, Y Hikosaka, S Noda, H Nakagawa, S Kobayashi, M Inoue, T Hoshino
    JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A-VACUUM SURFACES AND FILMS 17(5) 2557-2571 1999年9月  
    To investigate the mechanism of C4F8 dissociation in parallel-plate-type plasma, we used several of the latest diagnostic tools and. made extensive measurements of electrons, radicals, and ions under conditions that greatly suppressed the effects of plasma-surface interaction. These measurements showed that the amount of light fluorocarbon radicals and ions increased with increasing electron density. The dissociation of C4F8 was analyzed by using rate equations, after confirming the stability and uniformity of the plasma. The total dissociation rate coefficient of C4F8 was 1 x 10(-8) cm(3)/s, and, CF2 radicals were mainly generated from products of C4F8 dissociation. F was mainly generated from CF2 by electron-impact dissociation and lost by pumping. We could estimate that the C2F4 density was roughly comparable to the densities of CF and CF3, and that the surface loss probability of C2F4, increased with increasing electron density. C2F4 might play an important role in the etching because of its rich polymerization characteristics. (C) 1999 American Vacuum Society., [S0734-2101(99)00905-7].
  • T Ishimaru, K Shimada, T Hoshino, Ohdomari, I
    SURFACE SCIENCE 433 401-404 1999年8月  
    During in situ scanning tunneling microscopy (STM) observations of quenched Si(111) surfaces at a temperature around 400-500 degrees C, the structure with the adatom arrangement which is not coincident with the normal dimer-adatom-stacking fault (DAS) structure was often observed. The flipping between this structure and the normal DAS stacking fault (SF) half unit frequently occurred. From the adatom arrangement and the strong preference of the adatoms for the sites adjacent to the dimers, it has been concluded that the dimers in the DAS structures are rearranged frequently during the flipping, (C) 1999 Elsevier Science B.V. All rights reserved.
  • N Okimoto, T Tsukui, M Hata, T Hoshino, M Tsuda
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 121(32) 7349-7354 1999年8月  
    The protein hydrolysis mechanism by the HIV-1 protease (HIV-1 PR) was studied using ab initio molecular orbital calculations with a model compound. The initial model compound was constructed based on the result of a 100 ps molecular dynamics (MD) simulation of the enzyme-substrate (ES) complex under physiologic conditions, and consists of an acetate/acetic acid pair for the two catalytic-site Asp residues, a water molecule acting on the hydrolysis, and a dimethylacetamide for the substrate. This study suggests that the hydrolysis mechanism of the Phe-Propeptide bond specific to the HIV-1 PR consists of three elementary reactions: first, the reaction of the formation of the amide hydrate intermediate; second, the reaction of the protonation of the proline nitrogen of the substrate; and third, the reaction of the C-N bond cleavage of the substrate. The rate-determining step is the protonation of the substrate proline nitrogen, and its activation energy is 23.95 kcal/mol. This result strongly suggests that protein hydrolysis by the HIV-1 PR occurs in vivo.
  • T Hoshino, Y Nishioka
    JOURNAL OF CHEMICAL PHYSICS 111(5) 2109-2114 1999年8月  
    Ab initio theoretical computations have been performed to reveal the mechanism of the etching reaction of silicon oxide (SiO2) by HF molecules. The probable reaction paths, in which the etching reaction proceeds through four sequential steps to remove a single fragment of SiO2, are presented with their potential energy curves. In every step, the insertion of an HF molecule into an Si-O bond leads to the dissociation of the Si-O connection. The potential energy barriers evaluated along the reaction paths suggest that the HF molecule has an ability to etch the SiO2 surface. The strong interaction among HF molecules, however, likely causes HF polymer formation, which is expected to reduce the reaction rate of SiO2 etching. (C) 1999 American Institute of Physics. [S0021-9606(99)71129-3].
  • T Watanabe, H Fujiwara, H Noguchi, T Hoshino, Ohdomari, I
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS 38(4A) L366-L369 1999年4月  
    A novel interatomic potential energy function is proposed for condensed systems composed of silicon and oxygen atoms, from SiO2 to Si crystal. The potential function is an extension of the Stillinger-Weber potential, which was originally designed for pure Si systems. All parameters in the potential function were determined based on ab initio molecular orbital calculations of small clusters. Without any adjustment to empirical data, the order of stability of five silica polymorphs is correctly reproduced. This potential realizes a large-scale modeling of SiO2/Si interface structures on average workstation computers.
  • T Hoshino, T Ishimaru, H Kawada, Ohdomari, I
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS SHORT NOTES & REVIEW PAPERS 38(4A) 1858-1862 1999年4月  
    The decomposition process of silicon islands deposited on 7 X 7 reconstructed and "1 X 1" disordered areas of Si(111) surfaces was observed with an in situ scanning tunneling microscope (STM). We successfully monitored silicon islands on the 7 X 7 area gradually decomposing through the loss of a few adatoms with every STM scan. The smallest island just before the complete decomposition always has a corner hole configuration where Si adatoms are arranged in a ring-shaped formation. Corner holes are also observed for silicon islands deposited on the disordered "1 X 1" area. The corner hole is maintained even on the "1 X 1" area until the last moment before the complete decomposition of the silicon island.
  • T Hoshino, Y Nishioka
    JOURNAL OF CHEMICAL PHYSICS 110(14) 6947-6953 1999年4月  
    First-principles quantum chemical calculations have been performed to reveal the reaction mechanisms of HF molecules with metal impurities (Al or Cu) on Si surfaces. The lowest energy paths of this HF attack reaction have been obtained in two situations when a metal atom adheres to a Si surface with and without an O atom incorporated between the metal atom and the surface. The potential energy changes along these reaction paths were evaluated. It was revealed that a HF molecule has the ability to etch an Al monoxide on the Si surface. On the other hand, HF is not effective in the etching of a metal atom (Al or Cu) which has directly bonded to a Si surface. (C) 1999 American Institute of Physics.
  • T Hoshino, K Okano, N Enomoto, M Hata, M Tsuda
    SURFACE SCIENCE 423(1) 117-126 1999年3月  
    Ab-initio quantum chemical calculations by density functional theory have been performed to investigate the migration process of an Al adatom on the Si(111) surface. The most stable adsorption site of a single Al adatom has been confirmed to be the T-4, site, and the Al adsorption on the H-3, site is also demonstrated to be a stable structure. In order to determine the probable Al migration path on the 1 x 1 area of the Si(111) surface, the potential energy changes during the movement of an Al adatom have been calculated. Computational results have clarified that the shortest path connecting the T-4 site with the H-3 site is the lowest potential energy route for Al diffusion. The activation energy barrier along this path has been estimated to be 0.9 eV. (C) 1999 Elsevier Science B.V. All rights reserved.
  • Yoshinori Hirano, Norihito Ohmori, Masayuki Hata, Tyuji Hoshino, Minoru Tsuda
    Journal of Photopolymer Science and Technology 12(4) 637-640 1999年  
  • ISHIMARU T, SHIMADA K, HOSHINO T, YAMAWAKI T, OHDOMARI I
    Physical Review B 60(19) 13592-13597 1999年  
  • HOSHINO T, YAMAZAKI K, SAGIYAMA S, HATA M, TSUDA M
    Physical Review B 60(7) 4810-4815 1999年  
  • T Hoshino, N Enomoto, M Hata, M Tsuda
    JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS SHORT NOTES & REVIEW PAPERS 38(1B) 487-490 1999年1月  
    Ab initio quantum chemical calculations using density functional theory have been performed to investigate the migration process of an Al adatom on the partly H-terminated Si(lll) surfaces. The diffusion of an Al adatom from the H-terminated monohydride area to the nonterminated bare Si area has been examined with two types of computational cluster models, both of which consistently indicate similar potential energy changes. It has been revealed that the transfer of a single Al adatom from the H-terminated to the nonterminated area spontaneously proceeds without any activation energy barrier, and results in a very stable adhesion to the Si surface with an energy stabilization by 3.3 eV.
  • 榎本 展之, 畑 晶之, 星野 忠次, 津田 穣
    生物物理 38(2) S45 1998年9月7日  
  • 二木 紀行, 畑 晶之, 星野 忠次, 津田 穣
    生物物理 38(2) S44 1998年9月7日  
  • T Ishimaru, K Shimada, T Hoshino, H Kawada, Ohdomari, I
    APPLIED SURFACE SCIENCE 130 18-22 1998年6月  
    The formation and the annihilation rates of stacking fault (SF) half-units were precisely determined from the high-temperature scanning tunneling microscopy (STM) observation of dimer-adatom-stacking-fault (DAS) domains gown on quenched Si(111) surface at 485 degrees C, as a function of the number of corner holes shared by a preexisting large domain and a newly born single SF triangle. In contrast to the general nucleation and growth with a single atom as a building unit, in the nucleation and growth of a n X n DAS domain with a single SF half-unit as a building unit, Gibbs free energy as a function of the number of SF half-units has discrete values. This feature is reflected in the behavior of a newly born SF half-unit adjacent to a larger DAS domain. For the SF half-units sharing one corner hole, the formation rate was lower than the annihilation rate due to the greater contribution of periphery strain to the increase in the Gibbs free energy than that of area increase. For the formation of the SF half-unit sharing two corner holes, the annihilation rate was negligibly small, suggesting that the addition of this single SF triangle increases the domain area keeping the periphery length constant, which results in Gibbs free energy reduction. (C) 1998 Elsevier Science B.V. All rights reserved.
  • T Watanabe, T Handa, T Hoshino, Ohdomari, I
    APPLIED SURFACE SCIENCE 130 6-12 1998年6月  
    Time-independent and -dependent Monte Carlo simulations of a two-dimensional lattice gas were performed to investigate the effect of fixed particles on periodic adatom arrangements on Si(111) 1 X 1 surfaces. In both the simulations introducing fixed particles, domains of the periodic structures were divided into small fragments around them. This can be explained by the fixed particles reducing the degree of freedom of the adatom configurations so the number of ways of reaching the uniform configuration is highly restricted. Based on the simulations, we predict that a large 1 X 1 region without any obstacle impurities is desirable to obtain a large periodic structure of Si adatoms. (C) 1998 Elsevier Science B.V. All rights reserved.
  • N Enomoto, T Hoshino, M Hata, M Tsuda
    APPLIED SURFACE SCIENCE 130 237-242 1998年6月  
    Ab initio quantum chemical calculations with density functional theory have been performed to investigate the migration process of Al adatom on the partially H-terminated Si(111) surfaces. The transfer of Al adatom from H-terminated to bare Si area has been revealed to proceed spontaneously. The potential energy barrier during the Al migration on the H-terminated monohydride Si(111) surface has been confirmed to be extremely small. Further, the potential energy monotonously decrease without any activation energy barrier as transferring of Al adatom from the H-terminated to the bare area on Si(111) surface. The stabilization energy due to the Al adatom migration from H-terminated area to the T(4) site on bare Si area is estimated to be 3.6 eV. (C) 1998 Elsevier Science B.V. All rights reserved.

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