Journal of Computer Chemistry-Japan最新文献

{"title":"Visualization of Orbitals (13) ― How the Orbital Hybridization Accounts for the Structure of Hydrocarbons: σ-bond and π-bond.","authors":"S. Tokita","doi":"10.2477/jccj.2022-0021","DOIUrl":"https://doi.org/10.2477/jccj.2022-0021","url":null,"abstract":"","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69049339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolving Society and Academy in Computational Chemistry and Expectations for Younger Generations","authors":"A. Miyamoto","doi":"10.2477/jccj.2020-0026","DOIUrl":"https://doi.org/10.2477/jccj.2020-0026","url":null,"abstract":"1945年8月15日の終戦を経て,1947年5月3日に,新 しい日本国憲法が施行されたが,それが自分の誕生日で もある.ベビーブーム (団塊 )世代であるので,憲法だけ でなく,様々な面で新しい制度とともに歩んだ.中学卒 業後に5年間学んだ国立鈴鹿工業高等専門学校もその一 つであった.5年間の一貫教育で,大学の工学部卒業レ ベルに到達させるべく,先生方もとても意欲的で,数学, 英語,ドイツ語,化学,物理,卒業研究などの教育を受 けたことは振り返ってみると貴重な体験であった. 鈴鹿高専での学習を通して,もっと深く勉強してみた いという気持ちをもっていた時に,東北大学工学部が編 入生を受け入れるという情報を得て,5年生の1月の編 入学試験を受け,高専から編入学1期生として東北大学 工学部3年生で学ぶ機会を得た.当時は何処の大学でも 学園紛争が盛んで,東北大学でも3年生の前期には,か なりの時間がストライキ,学生討論などが行われ,大学 に来たことを実感することになった.その中で語られる 様々な内容に興味をもち,歴史,経済,心理学,哲学, 数学,量子力学,相対性理論など社会の基礎,科学の基 礎をもっと深く勉強する機会を得たことは幸せなことで あった.研究室配属は,高専での経験もあり,触媒を専 門とされる荻野研究室を志望した.「液体金属の触媒作 用」という全く新しい研究テーマを頂き,主体的に,研 究手法,解析手法,実験装置の製作を行い,金属系,物 理系,東工大,北大,名大などの研究者,学生と交流し","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69047163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Simulation Analysis of Novel and Chiral Diels-Alder Reactions by Basic Catalysts","authors":"K. Somekawa, T. Ueda, T. Yoshidome, Takeshi Ishikawa, Hisashi Nishikori","doi":"10.2477/jccj.2021-0011","DOIUrl":"https://doi.org/10.2477/jccj.2021-0011","url":null,"abstract":"","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69047825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Pore Size of Carbon Support on Electrode Reaction Activity of Catalyst Layer in Polymer Electrolyte Fuel Cell: Reactive Molecular Dynamics Simulations","authors":"Tetsuya Nakamura, Riku Otsuki, S. Uehara, Y. Asano, Qian Chen, Yusuke Ootani, N. Ozawa, M. Kubo","doi":"10.2477/jccj.2022-0008","DOIUrl":"https://doi.org/10.2477/jccj.2022-0008","url":null,"abstract":"For large output of polymer electrolyte fuel cells (PeFCs), the electrode reaction activity of the catalyst layer (CL) consisting of carbon supports, Pt nanoparticles, Nafion chains, and water should be improved. Experimentally, it is reported that when ketjen black (kb) with meso pores is used as the carbon support, the output of PeFC increases and that the pore size of the KB support affects the electrode reaction activity of the Pt nanoparticles. Therefore, in the present study, to clarify the effect of pore size on the electrode reaction activity of the Pt nanoparticles, we constructed catalyst particle (CP) models in which the Pt nanoparticles are supported and Nafion chains are coated on the KB model and investigated the CP structures with a different pore size of the KB support by reactive molecular dynamics method. Regardless of the pore size, the Pt nanoparticles on the exterior of the pore are fully covered with the Nafion chains and the Pt nanoparticles in the interior of the pore are not covered with the Nafion chains. This result suggests that the Pt nanoparticles in the interior of the pore show high oxygen transport property that does not depend on the pore size. Furthermore, we evaluated the connectivity of the Nafion chains to H 2 O molecules absorbed on the Pt nanoparticles on the exterior and in the interior of the pores because the Nafion chains conduct the protons to the H 2 O molecules on the Pt nanoparticles. As the pore size increases, more Nafion chains penetrate the interior of the pore and contact with h 2 O molecules on the Pt nanoparticles, because more Nafion chains are vertically distributed above the larger pore. Finally, these results propose that both high oxygen transport property and high electrode reaction activity are achieved over the Pt nanoparticles in the interior of the large pore of the KB support because the oxygen diffusion in the pore is not blocked by the Nafion chains and the large pore size promotes the formation of a proton conducting path composed of the Nafion chains, H 2 O, and Pt nanoparticles.","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69048651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of Graph Convolutional Network in Ames Prediction of Drug Candidate Compounds","authors":"C. Handa, Tomonaga Ozawa, Kaori Fukuzawa, E. Yonemochi","doi":"10.2477/jccj.2020-0015","DOIUrl":"https://doi.org/10.2477/jccj.2020-0015","url":null,"abstract":"","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69046345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automatic Determination of Buffer Region in Divide-anc-Conquer Quantum Chemical Calculations","authors":"Masato Kobayashi, Toshikazu Fujimori, T. Taketsugu","doi":"10.2477/jccj.2021-0025","DOIUrl":"https://doi.org/10.2477/jccj.2021-0025","url":null,"abstract":"A scheme to automatically determine the buffer region in the divide-and-conquer (DC) large-scale quantum chemi cal method is introduced. The buffer region directly relates to the error introduced by the DC method. In the iterative DC Hartree-Fock procedure, the automatic scheme adopts two-layered buffer region and gradually enlarges the buffer region by evaluating the energy contribution from the outer buffer region and determining whether the buffer region should be enlarged or not based on the energy-based threshold. On the other hand, in the non-iterative DC second-order Møller-Plesset perturbation calculation, the energy contribution is approximately estimated for the atoms in the buffer region and only those atoms that contribute more than an energy-based threshold are left in the buffer region. We demonstrated that both methods achieve almost constant accuracy in the energy using only one energy-based threshold as a parameter.","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"36 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69047653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formulation of Phonon Band Calculation Scheme Using Intermolecular Stiffness Matrix Represented upon Coarse-grained Coordinate System.","authors":"H. Houjou, Yue Wang, Shota Okamura","doi":"10.2477/jccj.2022-0004","DOIUrl":"https://doi.org/10.2477/jccj.2022-0004","url":null,"abstract":"","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69048245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fast Conformation Search of Macrocyclic Peptides Using a Combination of Digital Annealer and REST2","authors":"Y. Tanida, Hiroyuki Sato, Toshio Manabe, Chieko Terashima","doi":"10.2477/jccj.2021-0036","DOIUrl":"https://doi.org/10.2477/jccj.2021-0036","url":null,"abstract":"","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69048365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Constructing Regression Models with High Prediction Accuracy and Interpretability Based on Decision Tree and Random Forests","authors":"Naoto Shimizu, H. Kaneko","doi":"10.2477/jccj.2020-0021","DOIUrl":"https://doi.org/10.2477/jccj.2020-0021","url":null,"abstract":"Models for predicting properties/activities of materials based on machine learning can lead to the discovery of new mechanisms underlying properties/activities of materials. However, methods for constructing models that exhibit both high prediction accuracy and interpretability remain a work in progress because the prediction accuracy and interpretability exhibit a trade-o ff relationship. In this study, we propose a new model-construction method that combines decision tree (DT) with random forests (RF); which we therefore call DT-RF. In DT-RF, the datasets to be analyzed are divided by a DT model, and RF models are constructed for each subdataset. This enables global interpretation of the data based on the DT model, while the RT models improve the prediction accuracy and enable local interpretations. Case studies were performed using three datasets, namely, those containing data on the boiling point of compounds, their water solubility, and the transition temperature of inorganic superconductors. We examined the proposed method in terms of its validity, prediction accuracy, and interpretability.","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69047149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Commentary toward the 20th Anniversary of the Society ofComputer Chemistry, Japan","authors":"H. Nakai","doi":"10.2477/jccj.2021-0020","DOIUrl":"https://doi.org/10.2477/jccj.2021-0020","url":null,"abstract":"The Society of Computer Chemistry, Japan (SCCJ) was established on January 1, 2002 by merging the Japan Chemistry Program Exchange (JCPE) and the Chemical Software Society of Japan (CSSJ), and will soon celebrate its 20th anniversary. This article looks back on the past 20 years of SCCJ by introducing literatures related to computer chemistry. First, the numbers of literatures are compared by individual research fields such as chemistry, physics, engi -neering, materials science, and biochemistry. Next, some of highly cited literatures with top 100 rankings are explained with categorizing into methodologies, software, database, and topics.","PeriodicalId":41909,"journal":{"name":"Journal of Computer Chemistry-Japan","volume":"1 1","pages":""},"PeriodicalIF":0.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69047571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}