{"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}
K. Somekawa, T. Ueda, T. Yoshidome, Takeshi Ishikawa, Hisashi Nishikori
{"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}
Tetsuya Nakamura, Riku Otsuki, S. Uehara, Y. Asano, Qian Chen, Yusuke Ootani, N. Ozawa, M. Kubo
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.
为了实现聚合物电解质燃料电池(PeFCs)的大产量，需要提高由碳载体、铂纳米颗粒、钠离子链和水组成的催化剂层(CL)的电极反应活性。实验结果表明，以具有介孔的ketjen black (kb)作为碳载体时，PeFC的产量增加，kb载体的孔径大小影响Pt纳米颗粒的电极反应活性。因此，在本研究中，为了阐明孔径对Pt纳米颗粒电极反应活性的影响，我们构建了在KB模型上负载Pt纳米颗粒和包覆Nafion链的催化剂颗粒(CP)模型，并通过反应分子动力学方法研究了不同孔径KB载体的CP结构。无论孔大小如何，孔外部的Pt纳米颗粒都被Nafion链完全覆盖，而孔内部的Pt纳米颗粒则没有被Nafion链覆盖。这一结果表明，Pt纳米颗粒在孔隙内部表现出高氧输运特性，而这种输运特性与孔隙大小无关。此外，由于Nafion链将质子传导到Pt纳米颗粒上的h2o分子上，我们评估了Nafion链与Pt纳米颗粒外部和内部吸收的h2o分子的连通性。随着孔尺寸的增大，更多的Nafion链穿透孔内部，与Pt纳米颗粒上的h2o分子接触，因为更多的Nafion链垂直分布在较大孔的上方。最后，这些结果表明，在KB载体的大孔内部，Pt纳米颗粒获得了高氧传输性能和高电极反应活性，因为孔中的氧扩散不会被Nafion链阻断，而且大孔径促进了由Nafion链、h2o和Pt纳米颗粒组成的质子传导路径的形成。
{"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}
C. Handa, Tomonaga Ozawa, Kaori Fukuzawa, E. Yonemochi
{"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}
Masato Kobayashi, Toshikazu Fujimori, T. Taketsugu
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.
{"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}
Y. Tanida, Hiroyuki Sato, Toshio Manabe, Chieko Terashima
{"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}
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.
{"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}
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.
{"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}
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