Using a semi-empirical molecular orbital method, we have studied the efficacy of magic numbers to predict the emergence of Y-aromaticity in specific compounds having a trifurcated structure, which we simply referred to as “n-Tridentene” in our previous report. In this study, we obtained computational results suggesting a tendency of increase in the HOMO–LUMO gap, relating to the kinetic stabilization, of n-Tridentene ions containing the same number of π electrons as the magic number. Furthermore, energetic and reaction kinetics considerations suggest the possible development of Y-aromaticity in the 6-Tridentene anion.
{"title":"Studies of Magic Numbers of Y-Aromaticity Using a Semi-Empirical Molecular Orbital Method","authors":"T. Ohmae","doi":"10.2751/jcac.20.18","DOIUrl":"https://doi.org/10.2751/jcac.20.18","url":null,"abstract":"Using a semi-empirical molecular orbital method, we have studied the efficacy of magic numbers to predict the emergence of Y-aromaticity in specific compounds having a trifurcated structure, which we simply referred to as “n-Tridentene” in our previous report. In this study, we obtained computational results suggesting a tendency of increase in the HOMO–LUMO gap, relating to the kinetic stabilization, of n-Tridentene ions containing the same number of π electrons as the magic number. Furthermore, energetic and reaction kinetics considerations suggest the possible development of Y-aromaticity in the 6-Tridentene anion.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69255956","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}
Hitoshi Yamano, Tomoyuki Miyao, N. Ono, Aki Morita, S. Kanaya
a Division of Information Sciences, Computational Systems Biology Lab., Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101 b Tokyo Ohka Kogyo Co., Ltd., Samukawa-machi Tabata 1590, Koza-gun, Kanagawa, Japan 253-0114 c Division of Materials Science, Data Driven Chemistry Laboratory, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101 d Data Science Center, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101
{"title":"[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Relationships of Polymer Properties and Predicting Polymer Properties Based on Monomer Structure Information","authors":"Hitoshi Yamano, Tomoyuki Miyao, N. Ono, Aki Morita, S. Kanaya","doi":"10.2751/jcac.20.84","DOIUrl":"https://doi.org/10.2751/jcac.20.84","url":null,"abstract":"a Division of Information Sciences, Computational Systems Biology Lab., Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101 b Tokyo Ohka Kogyo Co., Ltd., Samukawa-machi Tabata 1590, Koza-gun, Kanagawa, Japan 253-0114 c Division of Materials Science, Data Driven Chemistry Laboratory, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101 d Data Science Center, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara, Japan 630-0101","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69256393","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}
Amane Suzuki, Yuichiro Kikura, Kenichi Tanaka, K. Funatsu
{"title":"Solubility Prediction Using Neural Network and Chemical Explanation of Deep Learning Model","authors":"Amane Suzuki, Yuichiro Kikura, Kenichi Tanaka, K. Funatsu","doi":"10.2751/JCAC.19.1","DOIUrl":"https://doi.org/10.2751/JCAC.19.1","url":null,"abstract":"","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"3 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.19.1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69256101","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}
Fusako Sakata, Masaaki Kotera, Kenichi Tanaka, H. Nakano, M. Ukita, R. Shirasawa, S. Tomiya, K. Funatsu
{"title":"Developing Novel Descriptors to Predict Physical Properties of Inorganic Compounds from Compositional Formula","authors":"Fusako Sakata, Masaaki Kotera, Kenichi Tanaka, H. Nakano, M. Ukita, R. Shirasawa, S. Tomiya, K. Funatsu","doi":"10.2751/JCAC.19.7","DOIUrl":"https://doi.org/10.2751/JCAC.19.7","url":null,"abstract":"","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"19 1","pages":"7-18"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69256128","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}
In order to explain the strong basicity of guanidine, the concept of Y-aromaticity was proposed. As a typical compound of a Y-aromatic compound, a system in which three methylene of trimethylene methane is replaced by a chain conjugated system composed of n carbon atoms was proposed. The energy spectrum of the π-electron conjugated system of this compound was generally obtained within the Hückel approximation. The magic number of Y-aromatic compounds was determined by setting the conjugated system to a closed shell as a necessary condition for the energy stabilization of the system. The stabilization energies of several typical compounds were determined with the chain conjugated system as the reference system and the effectiveness of the magic number was investigated. The calculation of energy was done within the Hückel approximation. Although the tendency of magic number and energy stabilization did not perfectly agree, when the number of π electron system coincided with the magic number, energy destabilization tended to decrease.
{"title":"Study of Magic Number in Y-Aromaticity","authors":"T. Ohmae","doi":"10.2751/JCAC.19.19","DOIUrl":"https://doi.org/10.2751/JCAC.19.19","url":null,"abstract":"In order to explain the strong basicity of guanidine, the concept of Y-aromaticity was proposed. As a typical compound of a Y-aromatic compound, a system in which three methylene of trimethylene methane is replaced by a chain conjugated system composed of n carbon atoms was proposed. The energy spectrum of the π-electron conjugated system of this compound was generally obtained within the Hückel approximation. The magic number of Y-aromatic compounds was determined by setting the conjugated system to a closed shell as a necessary condition for the energy stabilization of the system. The stabilization energies of several typical compounds were determined with the chain conjugated system as the reference system and the effectiveness of the magic number was investigated. The calculation of energy was done within the Hückel approximation. Although the tendency of magic number and energy stabilization did not perfectly agree, when the number of π electron system coincided with the magic number, energy destabilization tended to decrease.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"19 1","pages":"19-25"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.19.19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69256118","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}
Mohammad Bozlul Karim, Nobutaka Wakamatsu, M. Altaf-Ul-Amin
Modern world is incorporating highly connected heterogeneous data due to information sharing through computer and communication technology. These data lead to a complex relation where drilling down and mining are needed for understanding the actual meaning of data. Today any modern computational technique uses graph clustering as a sophisticated technology for data analysis. In this paper we implement a generalized graph clustering algorithm DPClusO with easy operating procedure and clear visualization techniques. DPClusO is enhanced version of DPClus algorithm where overlapping property of clusters is taken into consideration along with density and periphery tracking. User can select different parameters and visualization attributes to render cluster set, single cluster, hierarchical graph etc. and save these data in image and text formats. This paper discusses step by step operation of the proposed software tool using an example network of metabolites collected from KNApSAcK database. This tool successfully generated cohesive groups of structurally similar metabolites. The tool can be used for analysis of network data of any field of studies.
{"title":"[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]DPClusOST: A Software Tool for General Purpose Graph Clustering","authors":"Mohammad Bozlul Karim, Nobutaka Wakamatsu, M. Altaf-Ul-Amin","doi":"10.2751/JCAC.18.76","DOIUrl":"https://doi.org/10.2751/JCAC.18.76","url":null,"abstract":"Modern world is incorporating highly connected heterogeneous data due to information sharing through computer and communication technology. These data lead to a complex relation where drilling down and mining are needed for understanding the actual meaning of data. Today any modern computational technique uses graph clustering as a sophisticated technology for data analysis. In this paper we implement a generalized graph clustering algorithm DPClusO with easy operating procedure and clear visualization techniques. DPClusO is enhanced version of DPClus algorithm where overlapping property of clusters is taken into consideration along with density and periphery tracking. User can select different parameters and visualization attributes to render cluster set, single cluster, hierarchical graph etc. and save these data in image and text formats. This paper discusses step by step operation of the proposed software tool using an example network of metabolites collected from KNApSAcK database. This tool successfully generated cohesive groups of structurally similar metabolites. The tool can be used for analysis of network data of any field of studies.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"18 1","pages":"76-93"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.18.76","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69256089","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":"[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Visualizing Individual and Region-specific Microbial–metabolite Relations by Important Variable Selection Using Machine Learning Approaches","authors":"Satoshi Tsutsui, Y. Date, J. Kikuchi","doi":"10.2751/JCAC.18.31","DOIUrl":"https://doi.org/10.2751/JCAC.18.31","url":null,"abstract":"","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"77 1","pages":"31-41"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.18.31","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69255375","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}
Ken Tanaka, Y. Horie, H. Nemoto, Hiroaki Kosaka, M. Jo, Y. Tezuka
In a previous paper, we analyzed the amounts of ferulic acid and its derivatives produced in the fermentation of brown rice and rice bran by Aspergillus oryzae (FBRA). Ferulic acid and its derivatives are considered to be biologically active constituents in FBRA and the amounts of these compounds increase remarkably depending on the fermentation time. Another benefit of fermentation is that it is considered to increase the nutritional value of the food. In this study, we examined changes in the nutritional components, such as dipeptides and the free forms of water soluble vitamins, in FBRA using LC-MS analysis.
{"title":"[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Analysis of Water-soluble Constituents in Fermented Brown Rice and Rice Bran by Aspergillus oryzae (FBRA)","authors":"Ken Tanaka, Y. Horie, H. Nemoto, Hiroaki Kosaka, M. Jo, Y. Tezuka","doi":"10.2751/JCAC.18.46","DOIUrl":"https://doi.org/10.2751/JCAC.18.46","url":null,"abstract":"In a previous paper, we analyzed the amounts of ferulic acid and its derivatives produced in the fermentation of brown rice and rice bran by Aspergillus oryzae (FBRA). Ferulic acid and its derivatives are considered to be biologically active constituents in FBRA and the amounts of these compounds increase remarkably depending on the fermentation time. Another benefit of fermentation is that it is considered to increase the nutritional value of the food. In this study, we examined changes in the nutritional components, such as dipeptides and the free forms of water soluble vitamins, in FBRA using LC-MS analysis.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"18 1","pages":"46-50"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.18.46","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69255427","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":"[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]The Effects of Age and Sex Difference on the Glucose Metabolism in the Hippocampus Using Positron Emission Tomography","authors":"Tetsuo Sato, T. Hoshida","doi":"10.2751/jcac.18.117","DOIUrl":"https://doi.org/10.2751/jcac.18.117","url":null,"abstract":"","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"18 1","pages":"117-123"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/jcac.18.117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69255219","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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