Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.23, 71-74, by J-STAGE]
<Title:> 分子動力学計算を用いたNa₂O-K₂O-SiO₂系ガラスにおける混合アルカリ効果の再現
<Author(s):> 吉本　直樹, 澤口　直哉
<Corresponding author E-Mill:> nasawa(at)muroran-it.ac.jp
<Abstract:> Molecular dynamics simulation of y{(1-x)Na₂O-xK₂O}-(1-y)SiO₂ glasses used an improved interatomic potential was performed to investigate the mixed alkali effect. The relation of self-diffusion coefficient of potassium and of sodium was improved, but the trend with x of the self-diffusion coefficient of potassium has become worse than the previous work.
<Keywords:> Keywords Molecular dynamics, Silicate glass, Mixed-Alkali Effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/3/23_2024-0025/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 68-70, by J-STAGE]
<Title:> 実時間TDDFTの時系列データに関する特異スペクトル解析
<Author(s):> 谷　直樹, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> naoki.tani.7x(at)stu.hosei.ac.jp
<Abstract:> Optical spectrum prediction based on first-principles calculations is important for the development of optical materials. In particular, Time Dependent Density Functional Theory (TDDFT) in real-time is one of the most widely used calculation methods. In real-time TDDFT, the dynamic dipole moment is used to obtain the polarizability by Fourier transform (FT). The optical spectrum can be obtained from this polarizability. However, if the time length is not sufficient, the spectrum becomes ambiguous. To solve this problem, we introduced singular spectrum analysis (SSA), which decomposes time series data into multiple orthogonal oscillations. By extracting only the main components related to the peak of interest, the corresponding time series data is reproduced. In this process, high-frequency oscillations recognized as noise are removed. We applied this method to TDDFT time-series data for ethylene and small molecules of benzene, naphthalene, anthracene and tetracene. We focused on band edges, which are important for understanding optical properties, to clarify the signals. Even when the time-series data is insufficient, we found that it is possible to obtain time-series data of sufficient time length by isolating the oscillation components contributing to the band edges and expanding and complementing them with time-series prediction.
<Keywords:> Keywords TDDFT, Singular Spectrum Analysis (SSA), Fourier Transform (FT)
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/3/23_2024-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 65-67, by J-STAGE]
<Title:> ポリスチレン解重合のシミュレーション方法の検討
<Author(s):> 三枝　俊亮
<Corresponding author E-Mill:> mieda.sd(at)om.asahi-kasei.co.jp
<Abstract:> To verify the possibility to simulate depolymerization, simulations of the depolymerization of polystyrene were performed. Molecular Dynamics simulations (MD) using neural network potentials were found to be similar in accuracy to MD using density functional theory calculations. It was also found that long-time simulations using neural network potential-MD predicted styrene monomer yields close to those obtained experimentally, and that the monomer yields tended to decrease with increasing pressure.
<Keywords:> Key words depolymerization of polystyrene, long-time simulation using NNP-MD, ReaxFF, DFT-MD, Neural Network Potential
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/3/23_2024-0017/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 59-61, by J-STAGE]
<Title:> Wulffの定理と第一原理計算を用いた金属クラスターの構造予測
<Author(s):> 大西　未優, 大野　彰太, 中田　彩子, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Metal nanoparticles are useful as catalysts having specific reactivity owing to highly reactive site and strong size dependency. Structural information of metal nanoparticles is essential for interpretation and prediction of their reactivity. Wulff theorem predicts the equilibrium structures of crystals by using the surface energies of plane indices such as (111), (110), and (100). In this study, we evaluated the surface energies of well-defined Rh surfaces by the first principles calculations, followed by systematically constructing various sizes of Rh nanoparticles based on the Wulff theorem. For small nanoparticles with radii of 2 nm or less, only the (111) and (100) planes were present. On the other hand, high index surfaces appeared at large nanoparticles, of which the radii were more than 2.5 nm.
<Keywords:> Metal nanoparticle, Wulff construction, First principles calculation, Surface energy, Plane index
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/3/23_2024-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 62-64, by J-STAGE]
<Title:> 動的分極率を用いた励起状態計算における励起配置解析
<Author(s):> 西村　龍星, 吉川　武司, 坂田　健, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We previously proposed an excitation configuration analysis for the divide-and-conquer (DC)-based excited-state calculation method using dynamical polarizability to interpret the nature of excited states [J. Chem. Phys. 160, 244103 (2024)]. This article reviews the proposed DC-based excitation configuration analysis and applies the natural transition orbital analysis based on the (de-)excitation coefficients obtained from the proposed method to the lowest excited state of tris-triphenylacetylammonia. The singular values of excitation coefficients were matched to the results of the TDHF method. Also, the shapes of the natural transition orbitals coincided as well.
<Keywords:> Excited-state calculation, Time-dependent Hartree Fock/density functional theory, Divide-and-conquer, Dynamical polarizability
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/3/23_2024-0027/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.10, -, by J-STAGE]
<Title:> Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation
<Author(s):> Tatsuya NAKANO, Yoshio OKIYAMA, Katsunori SEGAWA, Yoshiro SAITO, Yuji MOCHIZUKI, Yuto KOMEIJI
<Corresponding author E-Mill:> y-komeiji(at)aist.go.jp
<Abstract:> The fragment molecular orbital (FMO) method is an efficient quantum chemical method suitable for calculating the electronic structures of large molecular systems. FMO can be accelerated by several approximations, an important one being the approximation to the environmental electrostatic potential (ESP) exerted on the fragment monomers or dimers. The environmental ESP is often approximated using the Mulliken atomic orbital charge (AOC) for proximal fragment dimers (ESP-AOC approximation) and the Mulliken point charge (PTC) for distant dimers (ESP-PTC approximation). Recently, another approximation method based on Cholesky decomposition with adaptive metric has been proposed for environmental ESP (ESP-CDAM, Okiyama et al., Bull. Chem. Soc. Jpn., 2021, 94, 91). In the current article, the energy gradient is derived under the ESP-CDAM approximation and implemented in FMO-based molecular dynamics (FMO-MD). Several test FMO-MD simulations are performed to compare the accuracy of the ESP-CDAM approximation with that of the conventional methods. The results show that ESP-CDAM is more accurate than ESP-AOC.
<Keywords:> Fragment molecular orbital method (FMO), Cholesky decomposition with adaptive metric (CDAM), Molecular dynamics, FMO-MD, ABINIT-MP
<URL:> https://www.jstage.jst.go.jp/article/jccjie/10/0/10_2023-0038/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.10, -, by J-STAGE]
<Title:> Dependence of Substituents on UV-vis Spectra and Solvent Effect of Anthocyanins by Quantum Chemical Approach
<Author(s):> Kazuaki KUWAHATA, Yukio KAWASHIMA, Atsushi FUKUSHIMA, Masanori TACHIKAWA, Miyako KUSANO
<Corresponding author E-Mill:> tachi(at)yokohama-cu.ac.jp
<Abstract:> Plants can produce anthocyanins to survive their given environments. A model plant Arabidopsis thaliana (Arabidopsis) accumulates the 11 anthocyanins (A1 A11) with various substitutions to their basic structure. However, it is difficult to detect all 11 anthocyanins in every analysis using conventional analytical techniques. In this study, we predicted ultraviolet visible (UV-vis) absorption spectra of A1 A11 by an ab initio calculation based on density functional theory. We could identify substituents attached to the basic structure of anthocyanins from the predicted absorption peaks. We found that glucose substitution significantly reduced the solvation free energy due to five hydroxyl groups, whereas sinapoyl substitution increased the solvent effect due to the methyl group in a sinapoyl moiety. Our findings may explain the antioxidant capacity of each anthocyanin by comparing the predicted UV-vis absorption spectra with the measured UV-vis spectra. These outcomes can provide clues to uncover anthocyanin biosynthesis in different stress conditions/tissues.
<Keywords:> Anthocyanin, Arabidopsis, Ultraviolet visible absorption, Quantum chemical prediction, Solvent effect.
<URL:> https://www.jstage.jst.go.jp/article/jccjie/10/0/10_2023-0045/_html

[Published online Journal of Computer Chemistry, Japan Vol.23, 45-49, by J-STAGE]
<Title:> FMODBからのデータ取得用Pythonスクリプトの開発
<Author(s):> 松岡　壮太, 柿沼　紗也果, 奥脇　弘次, 土居　英男, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> フラグメント分子軌道(FMO)計算による相互作用解析は，特に理論創薬の分野でよく使われており，計算結果をデータベース化したFMODBも整備・公開されている．本論文では，FMODBにアクセスしてデータを取得するPythonツールを開発した．取得データをscikit-learnなど機械学習のツールで処理することも可能である．
<Keywords:> Fragment molecular orbital, FMO, FMODB, Python, Machine learning
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/2/23_2023-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.10, -, by J-STAGE]
<Title:> Reconstruction of Four-Body Statistical Pseudopotential for Protein-Peptide Docking
<Author(s):> Tae YAMAMOTO, Yasuhiro IKABATA, Hitoshi GOTO
<Corresponding author E-Mill:> gotoh(at)tut.jp
<Abstract:> We constructed the four-body statistical pseudopotential proposed by Krishnamoorthy and Tropsha, which is a type of coarse-grained potential previously used for protein-peptide docking, using different data sets. The first data set is composed of crystal structures of proteins that satisfy the conditions specified using PISCES, a protein sequence culling server. The second data set consists of crystal structures of protein-protein complexes obtained from the PDBbind-CN database. The four-body potential has 44275 patterns of scores, depending on the type of amino acid in the quadruplet of residues and the continuity of amino acid in the sequence of protein or peptide. While the PISCES-based data set covers almost all patterns, docking simulations revealed that both potentials provided comparable accuracy in reproducing experimentally determined peptide binding poses.
<Keywords:> Docking simulation, Protein-peptide complex, Four-body statistical pseudopotential, Coarse-grained potential, Peptide binding pose
<URL:> https://www.jstage.jst.go.jp/article/jccjie/10/0/10_2023-0039/_html

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> FMODBからのデータ取得用Pythonスクリプトの開発
<Author(s):> 松岡　壮太, 柿沼　紗也果, 奥脇　弘次, 土居　英男, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> フラグメント分子軌道(FMO)計算による相互作用解析は，特に理論創薬の分野でよく使われており，計算結果をデータベース化したFMODBも整備・公開されている．本論文では，FMODBにアクセスしてデータを取得するPythonツールを開発した．取得データをscikit-learnなど機械学習のツールで処理することも可能である．
<Keywords:> Fragment molecular orbital, FMO, FMODB, Python, Machine learning
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2023-0040/_article/-char/ja/