A. Suenaga, Y. Komeiji, M. Uebayasi, T. Meguro, I. Yamato
a Department of Biological Science and Technology, Science University of Tokyo 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan *e-mail: yamato @yl05hp. tb. noda. sut. ac. jp (tel. +81-471-24-1501 ex.4405; fax. +81-471-25-1841) bSupermolecular Science Division , Electrotechnical Laboratory 1-1-4 Umezono, Tsukuba-shi, Ibaraki 305-0045, Japan c Specific Metabolism Laboratory, National Institute of Bioscience and Human Technology 1-1-3 Higashi, Tsukuba-shi, Ibaraki 305-0046, Japan
{"title":"Molecular dynamics simulation of unfolding of histidine-containing phosphocarrier protein in water.","authors":"A. Suenaga, Y. Komeiji, M. Uebayasi, T. Meguro, I. Yamato","doi":"10.2477/JCHEMSOFT.4.127","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.127","url":null,"abstract":"a Department of Biological Science and Technology, Science University of Tokyo 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan *e-mail: yamato @yl05hp. tb. noda. sut. ac. jp (tel. +81-471-24-1501 ex.4405; fax. +81-471-25-1841) bSupermolecular Science Division , Electrotechnical Laboratory 1-1-4 Umezono, Tsukuba-shi, Ibaraki 305-0045, Japan c Specific Metabolism Laboratory, National Institute of Bioscience and Human Technology 1-1-3 Higashi, Tsukuba-shi, Ibaraki 305-0046, Japan","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127930791","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}
Takeshi Uno, Haruhisa Hayashi, K. Yamana, H. Nakano
タンパク質立体構造表示プログラムであるModrast-Pの機能を拡張し、立体構造のデータをVirtual Reality Modeling Language (VRML) のデータ形式に変換する機能を加えた。この機能を使うことによって、Modrast-Pで表示されている分子模型をそのままVRML形式のデータに変換することができる。これにより、これまでいくつかの問題があったコンピュータネットワーク上での分子模型のやりとりがVRMLをもちいることによって簡単かつ迅速に行えるようになると期待される。
扩展蛋白质立体结构显示程序modust - p的功能，将立体结构数据Virtual Reality Modeling Language (VRML)的转换为数据格式的功能。通过使用该功能，可以将modust - p显示的分子模型直接转换成VRML格式的数据。通过VRML，一直以来存在诸多问题的计算机网络分子模型交换将变得简单快捷。
{"title":"A Display of Biopolymer Using Virtual Reality Modeling Language","authors":"Takeshi Uno, Haruhisa Hayashi, K. Yamana, H. Nakano","doi":"10.2477/jchemsoft.4.157","DOIUrl":"https://doi.org/10.2477/jchemsoft.4.157","url":null,"abstract":"タンパク質立体構造表示プログラムであるModrast-Pの機能を拡張し、立体構造のデータをVirtual Reality Modeling Language (VRML) のデータ形式に変換する機能を加えた。この機能を使うことによって、Modrast-Pで表示されている分子模型をそのままVRML形式のデータに変換することができる。これにより、これまでいくつかの問題があったコンピュータネットワーク上での分子模型のやりとりがVRMLをもちいることによって簡単かつ迅速に行えるようになると期待される。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131999770","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":"Exhaustive Parallel Conformational Search of Pyrethroids and Structure Similarity Study","authors":"H. Chuman, M. Karasawa, M. Sasaki, U. Nagashima","doi":"10.2477/JCHEMSOFT.4.143","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.143","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122002143","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 Measuring System for Hydrogen Ion Concentration in Rainfall","authors":"Takashi Tanaka","doi":"10.2477/JCHEMSOFT.4.113","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.113","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133340718","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}
MOLDA for Java, a platform-independent molecular modeling and molecular graphics program written in the Java language, is presented. The molecular coordinates in MOLDA, XMol and Protein Data Bank formats can be transferred to the VRML1.0/2.0 format le and can be viewed as a molecular model by using a VRML viewer on the World Wide Web. This program can also be used as an interface to the semi-empirical molecular orbital program MOPAC and the ab initio molecular orbital program GAUSSIAN 94.
介绍了用Java语言编写的独立于平台的分子建模和分子图形程序MOLDA for Java。MOLDA、XMol和Protein Data Bank格式的分子坐标可以转换为VRML1.0/2.0格式，并可以通过在万维网上使用VRML查看器来查看分子模型。该程序还可以作为半经验分子轨道程序MOPAC和从头算分子轨道程序高斯94的接口。
{"title":"MOLDA for Java-A Platform-independent Molecular Modeling and Molecular Graphics Program Written in the Java Language","authors":"H. Yoshida, H. Matsuura","doi":"10.2477/JCHEMSOFT.4.81","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.81","url":null,"abstract":"MOLDA for Java, a platform-independent molecular modeling and molecular graphics program written in the Java language, is presented. The molecular coordinates in MOLDA, XMol and Protein Data Bank formats can be transferred to the VRML1.0/2.0 format le and can be viewed as a molecular model by using a VRML viewer on the World Wide Web. This program can also be used as an interface to the semi-empirical molecular orbital program MOPAC and the ab initio molecular orbital program GAUSSIAN 94.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"401 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124323329","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}
Yuji Shinohara, T. Nakajima, Satoshi Suzuki, S. Mishima, H. Ishikawa
A computational chemical investigation has been made into the mechanisms of the dehydration and the dehydrogenation of ethanol on six oxide catalysts (SiO2, TiO2, ZnO, MnO, MgO and CdO) using the DV-Xα method. Transition state models of the consecutive mechanism including ethoxide formation and the concerted mechanism proposed by Eucken and Wicke were computed.By comparing the computed results with experimental ones published in the literature, it was concluded that the consecutive mechanism is more reasonable than the concerted one. It was also concluded that the rate-determing step of the ethanol dehydration is for a β-hydrogen shift to a surface oxide ion and that the ease of theshift is a factor controlling the dehydration/ dehydrogenation selectivities of oxide catalysts.
{"title":"A Computational Chemical Investigation of the Dehydration and Dehydrogenation of Ethanol on Oxide Catalysts","authors":"Yuji Shinohara, T. Nakajima, Satoshi Suzuki, S. Mishima, H. Ishikawa","doi":"10.2477/JCHEMSOFT.4.89","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.89","url":null,"abstract":"A computational chemical investigation has been made into the mechanisms of the dehydration and the dehydrogenation of ethanol on six oxide catalysts (SiO2, TiO2, ZnO, MnO, MgO and CdO) using the DV-Xα method. Transition state models of the consecutive mechanism including ethoxide formation and the concerted mechanism proposed by Eucken and Wicke were computed.By comparing the computed results with experimental ones published in the literature, it was concluded that the consecutive mechanism is more reasonable than the concerted one. It was also concluded that the rate-determing step of the ethanol dehydration is for a β-hydrogen shift to a surface oxide ion and that the ease of theshift is a factor controlling the dehydration/ dehydrogenation selectivities of oxide catalysts.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124337771","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":"Development of A File Conversion Program for Chemical Structure Data: MOLCONV. Traensplantation of the MOLCONV program from PC-9801 for IBM personal computer.","authors":"K. Hayami","doi":"10.2477/jchemsoft.4.119","DOIUrl":"https://doi.org/10.2477/jchemsoft.4.119","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132422303","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}
A program to construct a fundamental and original starting material library to embody starting material-oriented retrosynthetic analysis in the AIPHOS system has been developed. The data in the library can be registered automatically from ACD, a commercial chemical structure database, by utilizing this program. This program recognizes synthetic equivalents to categorize functional groups. The resultant library is made up of a hierarchical structure using abstract graphs. The structure, the constructing method of the starting material library for AIPHOS and the registration results of data selected at random from ACD are described. In addition, a brief outline of AIPHOS is included.
{"title":"Development of a Program for Construction of a Starting Material Library for AIPHOS","authors":"K. Satoh, S. Azuma, Hiroko Satoh, K. Funatsu","doi":"10.2477/JCHEMSOFT.4.101","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.101","url":null,"abstract":"A program to construct a fundamental and original starting material library to embody starting material-oriented retrosynthetic analysis in the AIPHOS system has been developed. The data in the library can be registered automatically from ACD, a commercial chemical structure database, by utilizing this program. This program recognizes synthetic equivalents to categorize functional groups. The resultant library is made up of a hierarchical structure using abstract graphs. The structure, the constructing method of the starting material library for AIPHOS and the registration results of data selected at random from ACD are described. In addition, a brief outline of AIPHOS is included.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129575080","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}
N. Ashida, Yoshihiro Aoyama, Tadayosi Yoshimura, B. T. Newbold
We have developed multimedia type chemistry CAL software by Netscape Navigator browser.We have converted CAL software, made by ExpandBook form, into HTML form, whose theme is for physical chemistry experiments. Multimedia type chemistry CAL material with video movie really helps students to visualize chemistry operations in practical experiments. Anyone can make a teaching document by HTML language easily if one memorizes a procedure. When we tried the intranet use of CAL software in a remote place (separate room) and video movies of CAL, it produced smooth movement and was useful for the learning student.
{"title":"Development and the Use of Chemistry Teaching Video Materials by Internet Browser","authors":"N. Ashida, Yoshihiro Aoyama, Tadayosi Yoshimura, B. T. Newbold","doi":"10.2477/JCHEMSOFT.4.51","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.51","url":null,"abstract":"We have developed multimedia type chemistry CAL software by Netscape Navigator browser.We have converted CAL software, made by ExpandBook form, into HTML form, whose theme is for physical chemistry experiments. Multimedia type chemistry CAL material with video movie really helps students to visualize chemistry operations in practical experiments. Anyone can make a teaching document by HTML language easily if one memorizes a procedure. When we tried the intranet use of CAL software in a remote place (separate room) and video movies of CAL, it produced smooth movement and was useful for the learning student.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"2016 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128943443","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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