カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.21, 106-110, by J-STAGE]
<Title:> FMOプログラムABINIT-MPの整備状況2022
<Author(s):> 望月　祐志, 中野　達也, 坂倉　耕太, 渡邊　啓正, 佐藤　伸哉, 奥脇　弘次, 秋澤　和輝, 土居　英男, 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. Several improvements for accelerated processing were made after the release of Open Version 2 Revision 4 at September 2021. Functionalities were enhanced as well. In this short report, we summarize such developments toward the next release of Revision 8.
<Keywords:> Fragment molecular orbital, FMO, ABINIT-MP, Supercomputer, A64FX, SX-Aurora TSUBASA
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2022-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 103-105, by J-STAGE]
<Title:> 分子軌道エネルギーを説明変数とした機械学習
<Author(s):> 寺前　裕之, 玄　美燕, 高山　淳, 岡﨑　真理, 坂本　武史
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> The values of the DPPH free radical scavenging ability values (IC₅₀) of ferulic acid and its derivatives have been estimated by machine learning with only molecular orbital (MO) energies as the explanatory variables. We use four machine learning regression methods, Partial Least Square (pls), Random Forest (rf), Multi-Layer Perceptron Neural Network with Optional Monotonicity Constraints (monmlp) and eXtreme Gradient Boosting with Linear model (xgbLinear), using R-package caret. We use 22 molecules for the training set and 6 molecules for the test set. The root mean square (RMS) errors of predicted values for the test set are used for estimating the precision of the training. The best result is obtained by xgbLinear just using two MO energies (HOMO and LUMO). It has been proved that the IC₅₀ values can be predicted by the molecular orbital energies only.
<Keywords:> Antioxidant effect, Radical scavenging ability, Equilibrium geometries, Eigenvalues of molecular orbital, Machine learning
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0001/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 99-102, by J-STAGE]
<Title:> 分子集合体の弾性体モデルにもとづく粗視化剛性行列の力学的解釈
<Author(s):> 北條　博彦, 中嶋　紘大, 岡村　彰太, 菊岡　龍太郎
<Corresponding author E-Mill:> houjou(at)iis.u-tokyo.ac.jp
<Abstract:> We have been developing a method for coarse-graining the low-frequency vibration modes of molecular assemblies, which affords a numerical representation of the down-sized stiffness matrix. In this study, we present an analytical representation of the stiffness matrix based on the elastic-body modeling of molecular assemblies. Comparison between the numerical and analytical data allows the 13 parameters regarding the dimension and mechanical properties of the putative elastic body. The results for 57 molecular dimers with various hydrogen-bond multiplicity demonstrate that the obtained parameters were physically reasonable and well-reproduced the wavenumbers of normal-mode vibrations.
<Keywords:> Intermolecular stiffness, Normal-mode analysis, Elastic-body mechanics, Finite element method, Trans-scale simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0006/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 87-89, by J-STAGE]
<Title:> 積層芳香族性を有するπスタック単分子接合の伝導特性に関する理論的研究
<Author(s):> 岡澤　一樹, 辻　雄太, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> π-stacked single-molecule junctions stacked with π-conjugated molecules have the potential to be used as building blocks for single-molecule scale three-dimensional integrated circuits. In this study, we investigate the relationship between π-stacking distance and conductance in face-to-face π-stacked single-molecule junctions with benzene as the monomer unit using the non-equilibrium Green’s function (NEGF), which combines the H ckel molecular orbital (HMO) and density functional theory (DFT) methods. As the π-stack distance between two benzene molecules decreases, the pseudo-para junction, which is insulating, turns conductive. Furthermore, it was found that the cause of this change can be explained by orbital interactions.
<Keywords:> Single-molecule junction, π-conjugated system, Stacked aromaticity, Frontier orbital, H ckel method
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0002/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.9, -, by J-STAGE]
<Title:> Lattice Folding Simulation of Peptide by Quantum Computation
<Author(s):> Rui SAITO, Koji OKUWAKI, Yuji MOCHIZUKI, Ryutaro NAGAI, Takumi KATO, Kenji SUGISAKI, Yuichiro MINATO
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> Computational protein folding has attracted considerable interest over the years, including molecular simulations and artificial intelligence assisted methods. On the other hand, research and development of quantum computer hardware and software have been thriving recently. In this paper, we report a case study of peptide (PSVKMA) folding based on a two-dimensional lattice model, by using both the blueqat quantum simulator (called AutoQML) and the IonQ quantum device. As a result, it was found that the actual device was still susceptible to noises.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccjie/9/0/9_2022-0036/_html

[Published online Journal of Computer Chemistry, Japan Vol.21, 80-81, by J-STAGE]
<Title:> 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
<Author(s):> 渡辺　七都稀, 庄司　光男, 堀　優太, 重田　育照
<Corresponding author E-Mill:> watanabe.natsuki.sm(at)alumni.tsukuba.ac.jp
<Abstract:> Racemization of amino acid catalyzed by aldehyde and carboxylic acid has been proposed and widely used. Herein, we investigated the detailed racemization mechanism of alanine catalyzed by salicylaldehyde and acetic acid. Quantum chemistry calculations based on the density functional theory demonstrated that the dehydration reaction is the rate-determining step, and this dehydration step is enhanced by surrounding water molecules. We also discussed the dependence of the reaction rates on the type of amino acid.
<Keywords:> Racemization reaction, Organocatalytic reaction, Amino acid, Alanine, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0004/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 77-79, by J-STAGE]
<Title:> Theoretical Characterization of the Electronic and Spin Structures for Iron Sulfur Cubane in Reduced High-Potential Iron Sulfur Proteins Using Density Functional Theory
<Author(s):> Yuta HORI, Ayaka SATO, Yasuteru SHIGETA
<Corresponding author E-Mill:> hori(at)ccs.tsukuba.ac.jp
<Abstract:> In this work, density functional theory and natural bond orbital analysis are used to investigate the electronic structures of the [4Fe-4S] cluster in reduced high-potential iron sulfur proteins. Calculated 3d-orbital occupancies of Fe atoms in the [4Fe-4S] cluster revealed a spin structure with two ferromagnetically coupled [2Fe-2S]⁺ subclusters that are antiferromagnetically coupled to each other. In addition, the chemical bonds between S Fe were found to form primarily through the donation of electrons from S to Fe atoms.
<Keywords:> [4Fe-4S] cluster, High-potential iron sulfur protein, Natural bond orbital, Density functional theory, Electronic structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 85-86, by J-STAGE]
<Title:> Keggin型ポリオキソタングステートの合成経路に関する研究
<Author(s):> 石上　快, 大堺　利行, 中嶋　隆人, 枝　和男
<Corresponding author E-Mill:> 212s203s(at)stu.kobe-u.ac.jp
<Abstract:> Synthetic pathways of Keggin-type polyoxotungstates (POTs), which are expected to catalyze multi-electron transfer reactions, were investigated by first-principles calculations. The reaction pathways for the formation of new Keggin-type POTs from existing ones via ion exchange were explored by the Nudged Elastic Band (NEB) method, and the effects of the kind of heteroatom and the relative permittivity of the solvent were discussed.
<Keywords:> Keggin, Polyoxometalates, Polyoxotungstates, First-principles calculations, NEB method
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 77-79, by J-STAGE]
<Title:> Theoretical Characterization of the Electronic and Spin Structures for Iron Sulfur Cubane in Reduced High-Potential Iron Sulfur Proteins Using Density Functional Theory
<Author(s):> Yuta HORI, Ayaka SATO, Yasuteru SHIGETA
<Corresponding author E-Mill:> hori(at)ccs.tsukuba.ac.jp
<Abstract:> In this work, density functional theory and natural bond orbital analysis are used to investigate the electronic structures of the [4Fe-4S] cluster in reduced high-potential iron sulfur proteins. Calculated 3d-orbital occupancies of Fe atoms in the [4Fe-4S] cluster revealed a spin structure with two ferromagnetically coupled [2Fe-2S]⁺ subclusters that are antiferromagnetically coupled to each other. In addition, the chemical bonds between S Fe were found to form primarily through the donation of electrons from S to Fe atoms.
<Keywords:> [4Fe-4S] cluster, High-potential iron sulfur protein, Natural bond orbital, Density functional theory, Electronic structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 82-84, by J-STAGE]
<Title:> 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
<Author(s):> 宗井　陽平, 堀　優太, Hengphasatporn　Kowit, 原田　隆平, 重田　育照
<Corresponding author E-Mill:> shigeta(at)ccs.tsukuba.ac.jp
<Abstract:> Metalloproteins such as 4-hydroxyphenylpyruvate dioxygenase (HPPD) and Cytochrome P450 are important for agrochemical research. In classical mechanics, to reproduce the metal-coordination environment of metalloproteins, various models (Nonbonded model, Bonded model, Nonbonded/Bonded Hybrid model etc.) for metal complexes have been developed. In this study, we built force field parameters for the molecular dynamics simulation of HPPD and evaluated the Fe²⁺-coordination environment. The result revealed that the hybrid model is suitable for the simulation of HPPD and able to simulate the metal-ligand (water) exchange process.
<Keywords:> Molecular dynamics, Metalloprotein, Force field, 4-Hydroxyphenylpyruvate dioxygenase, Agrochemical
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0003/_article/-char/ja/