月別: 2023年4月

[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