カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.21, 10-19, by J-STAGE]
<Title:> 準結晶ペンローズタイルクラスタにおける周辺構造修飾と中心局在相
<Author(s):> 金崎　翼, 石井 　楽士, 武田　京三郎
<Corresponding author E-Mill:> takeda(at)waseda.jp
<Abstract:> 準結晶格子は短距離秩序と長距離非周期性という新たな構造的特質を有する．本研究ではこの格子の幾何的特質に依って生じ得る電子構造の特徴の抽出を試みた．具体的には典型的準結晶二次元格子であるペンローズタイル(PT)模様を想定し，そのクラスター化により対象系の簡素化を図った．さらに1格子原子1電子近似を行い，Harrison法とSlater-Koster法を組み合わせた強結合近似を用いて，当該系の電子構造を算出し，その体系化を行った． その結果，PTが有する5回回転対称短距離秩序と長距離非周期性により，クラスタ中心部位に強く局在する準位が発現する可能性を見出した．この準位はその中心局在性により，PTC外周辺部位に対し”構造鈍感”である．従って5回対称性を保持するように当該PTC類の周辺構造修飾(原子団の除去及び付加)を行えば，其れに伴う電子数の可変により，同準位のSOMO化が可能となる．こうして，短距離秩序と長距離非周期性という準結晶の幾何的特徴により，中心部位に局在かつ露出化された電子スピン状態の創出が期待できる事が明らかとなった．
<Keywords:> Penrose tile, clusters, quasicrystal, peripheral modification, central localization
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/1/21_2022-0006/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 20-32, by J-STAGE]
<Title:> モチーフコドン縮約表現に基づいた動的計画 (DP) 法によるゲノム機能部位推定システムの開発
<Author(s):> 大友　将宏, 小林　貴史, 加藤　博明
<Corresponding author E-Mill:> ohtomo(at)kuicr.kyoto-u.ac.jp
<Abstract:> 高等生物のゲノム配列にはタンパク質に翻訳されるエクソン領域とそれ以外のイントロン領域が存在し，その複雑な構造の中から機能部位を推定するのは一つの大きな課題である．一方，タンパク質アミノ酸配列にはその機能と密接な関係がある特徴的な配列パターンであるモチーフが保存され，遺伝子配列にもよく保存されていると考えられる．本研究ではコドン縮約表現とその近似表現を用いた，動的計画 (DP) 法によるゲノム機能部位推定システムを開発した．さらに，公共データベースのモチーフ辞書PROSITEのアミノ酸配列モチーフに対応する遺伝子配列を定量的に表現したコドン重み行列を基にした，モチーフコドン縮約表現を提案した．はじめに，HumanのTNNC1ゲノム配列に対してタンパク質のコーディング配列 (CDS) の推定実験を行った．次に，Humanをはじめとするいくつかのモデル生物種のTNNC1とHPCAゲノム配列に対してEF-handモチーフの推定実験を行い，システムの有用性を示した．
<Keywords:> codon reduced representation, dynamic programming, functional site estimation, PROSITE, protein-gene motif
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/1/21_2022-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 150-154, by J-STAGE]
<Title:> Effect of Pore Size of Carbon Support on Electrode Reaction Activity of Catalyst Layer in Polymer Electrolyte Fuel Cell: Reactive Molecular Dynamics Simulations
<Author(s):> Tetsuya NAKAMURA, Riku OTSUKI, Shuichi UEHARA, Yuta ASANO, Qian CHEN, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)tohoku.ac.jp
<Abstract:> For large output of polymer electrolyte fuel cells (PEFCs), the electrode reaction activity of the catalyst layer (CL) consisting of carbon supports, Pt nanoparticles, Nafion chains, and water should be improved. Experimentally, it is reported that when Ketjen black (KB) with meso pores is used as the carbon support, the output of PEFC increases and that the pore size of the KB support affects the electrode reaction activity of the Pt nanoparticles. Therefore, in the present study, to clarify the effect of pore size on the electrode reaction activity of the Pt nanoparticles, we constructed catalyst particle (CP) models in which the Pt nanoparticles are supported and Nafion chains are coated on the KB model and investigated the CP structures with a different pore size of the KB support by reactive molecular dynamics method. Regardless of the pore size, the Pt nanoparticles on the exterior of the pore are fully covered with the Nafion chains and the Pt nanoparticles in the interior of the pore are not covered with the Nafion chains. This result suggests that the Pt nanoparticles in the interior of the pore show high oxygen transport property that does not depend on the pore size. Furthermore, we evaluated the connectivity of the Nafion chains to H₂O molecules absorbed on the Pt nanoparticles on the exterior and in the interior of the pores because the Nafion chains conduct the protons to the H₂O molecules on the Pt nanoparticles. As the pore size increases, more Nafion chains penetrate the interior of the pore and contact with H₂O molecules on the Pt nanoparticles, because more Nafion chains are vertically distributed above the larger pore. Finally, these results propose that both high oxygen transport property and high electrode reaction activity are achieved over the Pt nanoparticles in the interior of the large pore of the KB support because the oxygen diffusion in the pore is not blocked by the Nafion chains and the large pore size promotes the formation of a proton conducting path composed of the Nafion chains, H₂O, and Pt nanoparticles.
<Keywords:> Reactive Molecular Dynamics, Polymer Electrolyte Fuel Cell, Catalyst Layer, Ketjen Black, Reaction Activity
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Relativistic DFT Calculations of Changes in NMR Chemical Shifts in Aqueous Solutions of Heavy-Metal Nitrates
<Author(s):> Yoshimitsu ASAKURA, Daisuke KUWAHARA, Naoya NAKAGAWA
<Corresponding author E-Mill:> kuwahara(at)uec.ac.jp
<Abstract:> The NMR chemical shifts for metal ions in aqueous solutions of inorganic salts often change with the solution concentration. These changes are referred to herein as dilution concentration (dc) shifts. For main-group elements, the dc shifts generally increase with increasing atomic number. We calculated the dc shifts for various metal and nonmetal ions in aqueous nitrate solutions of elements in periods 5 and 6 by the DFT method based on the spin orbit ZORA Hamiltonian. The calculation results revealed that the dc shifts of metal and nonmetal ions with the outermost shell electron configuration of 6s² are primarily determined by the changes in the spin orbit interaction terms of the shielding constants. Furthermore, the spin densities of the Pb(II) ions in aqueous lead nitrate solutions under an external magnetic field were calculated using the matrix/modified Dirac Kohn Sham Hamiltonian, which confirmed the presence of Fermi contacts between the spin-polarized electrons and the lead nucleus. When a suitable threshold for visualizing the spin density was set, there was no Fermi contact in the infinite dilution state, whereas the upward-spin electron was in Fermi contact with the lead nucleus in the saturation state. There have been few reports of the NMR chemical shifts of heavy atoms in terms of Fermi contacts with relativistically spin-polarized electrons. We succeeded in clarifying how the dc shifts occur on the hydrated ions of heavy atoms by visualizing the Fermi contact of spin-polarized electrons with heavy-metal nuclei.
<Keywords:> Spin orbit interaction, NMR, Density functional theory, Nitrates, Solvation, Hydration
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0048/_html

[Published online Journal of Computer Chemistry, Japan Vol.20, 129-131, by J-STAGE]
<Title:> 量子化学計算によるフェニルイソシアネート275 nm第一吸収帯の帰属
<Author(s):> 長沼　優人, 石橋　太祐, 奥山　克彦
<Corresponding author E-Mill:> okuyama.katsuhiko(at)nihon-u.ac.jp
<Abstract:> Abstract: Electronic spectra for the first 275-nm absorption system of phenyl isocyanate observed in a room temperature and in a jet were assigned with an assistance of quantum-chemistry calculation. All vibronic bands in a jet were diffuse with a width of 18 cm^-1, indicating the lower limit of the life time was 204 fs. A suitable pair of a theoretical method and a basis set was selected among combinations of B3LYP, CAM-B3LYP, and MP2 and 18 kinds of basis sets on the basis of molecular-orbital energies and the rotational constant spectroscopically observed. B3LYP/cc-pVTZ and B3YP/aug-cc-pVDZ gave us good results. Time-dependent calculation was performed by two pairs. It was found out that the 275-nm absorption system was assigned as the first ππ* and third excited state and that twonπ* states with a very small oscillator strength were lying in the infrared and visible region. The fast relaxation process observed in a jet was due to an internal conversion to two nπ* states.
<Keywords:> Phenyl isocyanate, Quantum-chemistry calculation, Supersonic-jet spectroscopy, Symmetry assignyment, Absorption system
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2021-0051/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 132-136, by J-STAGE]
<Title:> FMOプログラムABINIT-MPの整備状況2021
<Author(s):> 望月　祐志, 中野　達也, 佐藤　伸哉, 坂倉　耕太, 渡邊　啓正, 奥脇　弘次, 大島　聡史, 片桐　孝洋
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing the ABINIT-MP program for fragment molecular orbital (FMO) calculations over 20 years. In 2021, the Open Version 2 series has started for large scale systems consisting of more than ten thousand fragments. This letter describes the current status of ABINIT-MP, including the speed-up as well as the situation of distributions over supercomputing facilities in Japan.
<Keywords:> Fragment molecular orbital, FMO, ABINIT-MP, Supercomputer, A64FX, SX-Aurora TSUBASA
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0001/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 137-139, by J-STAGE]
<Title:> 第一原理計算によるカテキンの酸化還元電位の理論予測
<Author(s):> 段　練, 鷹野　優, 重田　育照
<Corresponding author E-Mill:> ytakano(at)hiroshima-cu.ac.jp
<Abstract:> Catechins are the main constituents in tea and have attracted attention due to their antioxidant properties. In this letter, the redox potential of single electron transfer and the pK_a of proton transfer in (+)-catechin has been calculated at the B3LYP/6-31++G (d, p) level of theory with a recently developed scheme to evaluate the standard hydrogen electrode potential and redox potential. Our computational scheme reproduced the experimental redox potential and pK_a value well.
<Keywords:> First-principles calculation, Catechin, Redox potential, Standard hydrogen electrode, p??i??K??/i????sub??a??/sub??
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0002/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 140-143, by J-STAGE]
<Title:> 動的分極率による励起状態計算へ向けた量子アルゴリズムqUCC-LR開発
<Author(s):> 高梨　倫哉, 吉川　武司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> In this study, we propose the quantum algorithm based on the unitary coupled cluster linear response theory for excited-state calculations with single and double excitations, denoted as qUCCSD-LR. Instead of the standard eigenvalue-problem-based scheme, the algorithm utilizes the dynamical-polarizability-based scheme, where the pole relative to the frequency of an external electric field corresponds to an excited state. Numerical applications of the qUCCSD-LR method to H₂ could reproduce the dynamical polarizabilities, excitation energies and oscillator strengths obtained by the standard CCSD-LR method. Furthermore, potential energy curves for the double bond rotation in the ground and excited states of C₂H₄ were accurately calculated by the proposed method.
<Keywords:> Quantum computer, Excited-state calculation, Unitary coupled cluster, Linear response, Dynamical polarizability
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0007/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 144-146, by J-STAGE]
<Title:> アミノ酸間相互作用ポテンシャルの類似度と分子構造の類似度の相関の解析
<Author(s):> 寺島　千絵子, 谷田　義明, 眞鍋　敏夫, 佐藤　博之
<Corresponding author E-Mill:> c.terashima(at)jp.fujitsu.com
<Abstract:> For middle molecule drug discovery, a coarse-grained model in which amino acid residues were treated with an amino acid pair interaction was investigated. To treat both natural and artificial types of amino acids and staples, new interaction potentials were developed by umbrella sampling. For any artificial types of amino acids, the amino acid its potential was similar enough was extracted by using our method applied the structure similarity.
<Keywords:> amino acid, Peptide, Coarse-grained model, Interaction potential, Molecular dynamics, Molecular similarity
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 126-128, by J-STAGE]
<Title:> 虚数時間発展法による電子状態計算手法の開発
<Author(s):> 王　欽林, 善甫　康成
<Corresponding author E-Mill:> qinlin.wang.3p(at)stu.hosei.ac.jp
<Abstract:> We have been studying the time-evolution technique in imaginary time. The electronic structure calculated in this technique is valid for the ground state, which is easily confirmed from the completeness of the wavefunction. However, the excited states can be also obtained by Gram-Schmidt orthogonalization technique. As a practical 3D calculation, we applied this technique to hydrogen atom and molecule systems. The results are in good agreement with their analytical solutions, including the excited states. The purpose of this study is to present the effectiveness of this technique for practical electronic structure calculations. To realize it, we will start to apply this to hydrogen and practical small molecule systems.
<Keywords:> Time-evolution technique, Imaginary time, Electronic structure calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0032/_article/-char/ja/