カテゴリー: 未分類

[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/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Analyses of Optical Gains and Oscillation Wavelengths for Quantum Cascade Lasers Using the Nonequilibrium Green’s Function Method
<Author(s):> Hirotaka TANIMURA, Shigeyuki TAKAGI, Tsutomu KAKUNO, Rei HASHIMOTO, Kei KANEKO, Shinji SAITO
<Corresponding author E-Mill:> takagisgyk(at)stf.teu.ac.jp
<Abstract:> We have succeeded in improving the gain of the base quantum cascade laser (QCL) through experiments and device simulations using the nonequilibrium Green’s function (NEGF) method, and we investigate the factor that increases the gain by reducing the thickness of the barrier by 10%. Specifically, we analyzed the minibands (Wannier Stark states), density of states (DOS), and electron density that contribute to the emission. The results show that the gain enhancement is due to the increase in the electron density of the quantum wells in the active region and the increase in the oscillator strength between the minibands that contribute to the emission. Quantum mechanical calculation like the NEGF method is very effective for mesoscopic systems such as the active layer of QCL.
<Keywords:> Nonequilibrium Green’s function, Quantum cascade laser, Optical gain, Electroluminescence, Current voltage characteristic, Oscillation wavelength, Density of states, Electron density, Oscillator strength
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0024/_html

[Published online Journal of Computer Chemistry, Japan Vol.20, 123-125, by J-STAGE]
<Title:> マイクロ波帯の交番電磁界印加における分子運動のシミュレーション
<Author(s):> 杉山　順一, 米谷　慎
<Corresponding author E-Mill:> sugiyama-j(at)aist.go.jp
<Abstract:> Molecular dynamics calculations were performed to consider the peculiarities of microwave chemistry. The temperature rise curve obtained without using the parameters of permittivity and conductivity showed the rise due to the traveling energy in addition to the accumulation of thermal energy in the periodic application of the electric field. We showed that the non-thermal effects of microwave chemistry might be caused by this traveling energy.
<Keywords:> Microwave heating, Molecular dynamics, Traveling energy, Conductive loss, Dielectric loss
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 106-111, by J-STAGE]
<Title:> 機械学習QSARの整数計画法に基づく逆解析法
<Author(s):> 仁 永持, 見深 朱, Naveed Ahmed AZAM, 和也 原口, 亮 趙, 達也 阿久津
<Corresponding author E-Mill:> nag(at)amp.i.kyoto-u.ac.jp
<Abstract:> We have developed a novel framework for inferring a chemical graph. Given an ANN that maps a feature vector x = f ( G ) of a chemical graph G to a predicted value η ( x ) of a chemical property to G, we formulate an integer program that simulates the functions f and η. Given a target value y*, we can infer a chemical graph G such that η ( f ( G ) ) = y * by solving the integer program.
<Keywords:> Machine learning, Integer programming, Chemical graphs, QSAR/QSPR, Molecular design
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 112-115, by J-STAGE]
<Title:> 数学・数理科学からのアプローチによる分子動力学計算
<Author(s):> 深作　亮也, 溝口　佳寛, 檜貝　信一
<Corresponding author E-Mill:> higai(at)ark-i.com
<Abstract:> In the present report, we introduce our new three approaches based on the mathematics / mathematical sciences to the classical molecular dynamics calculations; 1) the approach by the analytical mechanics instead of the classical mechanics; 2) the approach to the periodic boundary condition by the torus model; 3) the approach by the mathematics-based programming substituting for the procedural (imperative) programming. Then, we found that these approaches are very effective to make calculations simpler, more compact, steadier, and firmer. Thus, it was concluded that the mathematical / mathematical scientific approaches are the promising ones to overcome various problems that we confront in the computational chemistry.
<Keywords:> Analytical mechanics, Periodic boundary condition, Torus model, Mathematics-based programming, Molecular dynamics calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0043/_article/-char/ja/