カテゴリー: 未分類

[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/

[Published online Journal of Computer Chemistry, Japan Vol.23, 40-43, by J-STAGE]
<Title:> The Analysis of Defect Structure of Sn-based Perovskite Solar Cell Materials Using First-principles Calculations
<Author(s):> Mai OTAKE, Suzune OMORI, Sana KOGURE, Masanori KANEKO, Koichi YAMASHITA, Azusa MURAOKA
<Corresponding author E-Mill:> muraokaa(at)fc.jwu.ac.jp
<Abstract:> While Sn-based perovskite solar cells have photoelectronic properties comparable to those of lead halide perovskites, their low photoelectric conversion efficiency is a problem. The main cause of this problem is the defect level caused by the presence of defects in the crystal. In this study, we analyzed the defect structures in FASnI₃ and MASnI₃ perovskites using first-principles calculations and focused on the correlation between the photoelectric conversion efficiency and defect levels.In both structures, the defect formation energy of V_Sn was low and tin tended to be easily removed. In FASnI₃, by changing the chemical potential to the Sn-rich, I-poor condition, the defect levels that were easy to form in the Sn-poor, I-rich condition became defect levels that were hard to form. It was also found that MASnI₃ has a wide range of thermodynamically stable regions with no defect levels that are prone to form under any chemical potential condition. Therefore, from the viewpoint of structural stability and structural defects, MA is preferable to FA as the A-site cation of Sn-based perovskite.
<Keywords:> Sn-based perovskite, Lead-free perovskite, Defect, Deep levels, Defect formation energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/1/23_2024-0010/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 33-36, by J-STAGE]
<Title:> ポテンシャルエネルギー曲面の新記述子:反応経路地図のパーシステント・ホモロジー
<Author(s):> 村山　武来, 小林　正人, 青木　雅允, 石橋　卓, 齋藤　琢弥, 中村　壮伸, 寺本　央, 武次　徹也
<Corresponding author E-Mill:> k-masato(at)sci.hokudai.ac.jp
<Abstract:> A reaction route map (RRM), which is a collection of elementary reaction pathways, contracts the potential energy surface (PES) with 3N – 6 variables (N: the number of atoms) into a weighted graph representation. Although the automated construction of RRMs has greatly contributed to the accurate understanding of chemical reaction mechanisms, only a small fraction of networks with low activation energies are relevant to actual chemical reactions, and thus studies focusing on the entire RRM have not been conducted. In this letter, we summarize our recent approach to applying the persistent homology (PH) analysis to the graph structure of an RRM.
<Keywords:> Keywords Potential energy surface, Reaction route map, Persistent homology
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/1/23_2024-0007/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 37-39, by J-STAGE]
<Title:> Oxaza[7]dehydrohelicene誘導体における円偏光二色性と円偏光発光に関する理論的研究
<Author(s):> 藤原　正也, 藤波　美起登, Salem　Mohamed S. H., 滝澤　忍, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Circularly polarized luminescence (CPL) materials have the potential for application in advanced optical devices. Oxaza[7]dehydrohelicene is a helicene-like organic molecule exhibiting CPL property for which an efficient synthesis method has been established. Although the correlation between circular dichroism (CD) and CPL for helicene systems is known and utilized for the screening of CPL materials, it is unclear whether the correlation exists for oxaza[7]dehydrohelicene derivatives. In this study, we conducted a comprehensive calculation of CD and CPL for up to three-substituted oxaza[7]dehydrohelicene derivatives. Numerical results demonstrated that the correlation between CD and CPL decreases as the molecule becomes more complex. The changes in the orbital distribution of S₀ and S₁ optimized structures lead to the gap between CD and CPL.
<Keywords:> キーワード Circularly polarized luminescence, Molecular design, Excited-state calculation, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/1/23_2024-0009/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 27-29, by J-STAGE]
<Title:> アルキル鎖長が異なる有機半導体の電子物性差異に関する分子動力学および量子化学計算
<Author(s):> 岡田　智悠, 鈴木　朝香, 井上　悟, 長谷川　達生, 松井　弘之
<Corresponding author E-Mill:> t221488d(at)st.yamagata-u.ac.jp
<Abstract:> The experimental mobilities of organic semiconductors, 2-C_n-BTNT (Figure 1), depend on the alkyl chain length n, while the mechanism is unclear. In this study, we elucidate the relationship between alkyl chain length and carrier mobility by classical force field (FF) and density functional theory (DFT) calculations. We analyzed the interactions between an alkyl chain and surrounding molecules and executed NVT molecular dynamics simulations at room temperature and ambient pressure by FF calculations. Transfer integrals were calculated using the DFT method with the coordinates after NVT simulations. As a result, alkyl chain length affects the lattice constant, thermal motion of the alkyl chain and transfer integrals and gives the difference of mobilities.
<Keywords:> キーワード Organic Semiconductors, Molecular Dynamics, Density Functional Theory, Transfer Integrals, Mobility
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/1/23_2024-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 24-26, by J-STAGE]
<Title:> 開始剤ラジカルの極性パラメータの算出
<Author(s):> 川内　進
<Corresponding author E-Mill:> skawauchi(at)quemix.com
<Abstract:> This paper describes a method for calculating the intrinsic e parameter of initiator radicals by applying the intrinsic Q-e scheme to the addition reaction between initiator radicals and monomers. Furthermore, DFT calculations show that there is a good relationship between the intrinsic e-value of initiator radicals and their electronegativity and Hammett constant, indicating that the e-value is a suitable parameter to describe the polar effect of initiator radicals.
<Keywords:> キーワード Radical polymerization, Initiator radical, Q-e value, polarity parameter, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/1/23_2024-0003/_article/-char/ja/