月別: 2024年10月

[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