{"title":"Molecular Mechanics and Molecular Orbital Simulations on Specific Interactions between Peroxisome Proliferator-Activated Receptor PPAR and Plasticizers","authors":"Shingo Iwabuchi, Tomohiko Nakagawa, Haruhiko Nakamura, Yoko Yamaguchi, Tamie Nasu, N. Kurita","doi":"10.2751/JCAC.8.1","DOIUrl":"https://doi.org/10.2751/JCAC.8.1","url":null,"abstract":"ペルオキシゾーム増殖剤活性化受容体(Peroxisome proliferator-activated receptor : PPAR)は、リガンド依存的転写因子であり、最近の医学的研究により、多くの病気に関与することが明らかになっている。また、プラスチック類の可塑剤として使用されるフタル酸ジ-2-エチルヘキシル(DEHP)などのフタル酸エステル類は、PPARを誘導し、様々な毒性を発揮することが生理医学的研究により分かっている。本研究では、PPARのサブタイプであるPPARαとプラスチック可塑剤の特異的相互作用機構を原子・電子レベルで解明することを目的とし、PPARαとフタル酸エステル類及びアジピン酸エステルとの複合体の安定構造を、古典分子力場AMBERを用いて求めた。また、安定構造に対し、半経験的分子軌道法MOPACを用いて電子状態を計算した。これらの結果を基に、PPARαとフタル酸エステル類及びアジピン酸エステルの結合特性を解析し、マウスを用いた実験結果と比較した。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257354","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}
Motoki Nakajima, Y. Sakuratani, Y. Noguchi, J. Yamada, Kenji Hori
我々は,化審法における生分解性予測に新たな視点を加えるため,その変化物生成の主たる要因の一つである加水分解予測に,量子化学計算による反応解析から得られる活性化エネルギーを判断指標の一つとして用いることを検討している。この過程において,MOPACベースでの平易な活性化エネルギーの算出を可能とするインタフェースとして,加水分解予測システムを開発した。このシステムでは,遷移状態付近の構造探索を効率的に行うために,過去の計算結果を利用する置換基法を,加水分解反応に特化して応用しシステム化した。その結果,エステル酸加水分解反応について,市販の量子化学計算ソフトウェアのみを用いた反応解析に比べ,大幅に計算時間を短縮しつつ,MOPACベースでの活性化エネルギー計算結果が得られることが判明した。今後,DFT計算やab initio MO計算といった上位の計算手法との併用も視野に入れ,生分解性予測へ活用することを検討している。
我们为了对化审法的生物可降解性预测增加新的视角,对导致变化物生成的主要因素之一的水解预测,研究将通过量子化学计算的反应分析得到的活化能作为判断指标之一。在此过程中,作为能够基于MOPAC简单计算活化能的接口,开发了水解预测系统。该系统为了有效地搜索过渡状态附近的结构,将利用过去计算结果的取代基法专门应用于水解反应,实现了系统化。结果表明,与仅使用市面上销售的量子化学计算软件进行的反应分析相比,酯酸水解反应可大幅缩短计算时间,同时可获得基于MOPAC的激活能量计算结果。今后还将考虑与DFT计算和ab initio MO计算等上层计算方法同时使用,并研究将其应用于生物可分解性预测。
{"title":"Development of Hydrolysis Prediction System Using Reaction Analysis with Quantum Chemical Calculation","authors":"Motoki Nakajima, Y. Sakuratani, Y. Noguchi, J. Yamada, Kenji Hori","doi":"10.2751/JCAC.8.103","DOIUrl":"https://doi.org/10.2751/JCAC.8.103","url":null,"abstract":"我々は,化審法における生分解性予測に新たな視点を加えるため,その変化物生成の主たる要因の一つである加水分解予測に,量子化学計算による反応解析から得られる活性化エネルギーを判断指標の一つとして用いることを検討している。この過程において,MOPACベースでの平易な活性化エネルギーの算出を可能とするインタフェースとして,加水分解予測システムを開発した。このシステムでは,遷移状態付近の構造探索を効率的に行うために,過去の計算結果を利用する置換基法を,加水分解反応に特化して応用しシステム化した。その結果,エステル酸加水分解反応について,市販の量子化学計算ソフトウェアのみを用いた反応解析に比べ,大幅に計算時間を短縮しつつ,MOPACベースでの活性化エネルギー計算結果が得られることが判明した。今後,DFT計算やab initio MO計算といった上位の計算手法との併用も視野に入れ,生分解性予測へ活用することを検討している。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"103-113"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257364","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. Hori, Hirotaka Sadatomi, Katsuhiko Okano, Michinori Sumimoto, Atsuo Miyamoto, S. Hayashi, Hidetoshi Yamamotoa
In synthesizing target compounds, synthetic chemists search for and examine papers concerning syntheses to create their own synthetic routes. Synthetic route design system programs such as AIPHOS and EROS can also create many synthetic routes for targets compounds. However, it takes a long time to experimentally test all the routes created by these programs. Therefore, computational chemistry has been used to investigate mechanisms of chemical reactions which have already been examined experimentally. It is feasible to consider theoretical methods as effective in examining whether or not synthetic routes from chemoinformatics can be used practically for synthesizing target compounds. There are many difficulties associated with the aforementioned application, because theoretical calculations have to be done without information from experimental works. In the present study, we proved that this concept works well for synthetic routes of benzyl methacrylate, created from the KOSP and TOSP programs.
{"title":"An Attempt Method for Developing New Synthetic Routes by Fusing Computational Chemistry and Chemoinformatics: Syntheses of Ethyl and Benzyl Methacrylates","authors":"K. Hori, Hirotaka Sadatomi, Katsuhiko Okano, Michinori Sumimoto, Atsuo Miyamoto, S. Hayashi, Hidetoshi Yamamotoa","doi":"10.2751/jcac.8.12","DOIUrl":"https://doi.org/10.2751/jcac.8.12","url":null,"abstract":"In synthesizing target compounds, synthetic chemists search for and examine papers concerning syntheses to create their own synthetic routes. Synthetic route design system programs such as AIPHOS and EROS can also create many synthetic routes for targets compounds. However, it takes a long time to experimentally test all the routes created by these programs. Therefore, computational chemistry has been used to investigate mechanisms of chemical reactions which have already been examined experimentally. It is feasible to consider theoretical methods as effective in examining whether or not synthetic routes from chemoinformatics can be used practically for synthesizing target compounds. There are many difficulties associated with the aforementioned application, because theoretical calculations have to be done without information from experimental works. In the present study, we proved that this concept works well for synthetic routes of benzyl methacrylate, created from the KOSP and TOSP programs.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257424","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}
化学反応に及ぼす溶媒効果は,溶媒の物理的性質である誘電率や溶解パラメータで説明されているが,非プロトン性溶媒とプロトン性溶媒の溶媒効果を同時に説明できない場合が多く生じる。そのため,経験的溶媒パラメータが多数提唱されている。そのなかでGutmann et al. のdonor number (DN)とacceptor number (AN) は溶媒の電子授受性の尺度と考えられている。したがって,溶媒のHOMOおよびLUMOのエネルギー値との間に相関があると見なされ,8種類の溶媒 (DMSO, DMF, AN, Ac, EtOH, MeOH, FA, H2O ) の値がすでに計算されてANとの相関が調べられている。今回,さらにそれらの溶媒を加えて31種類の溶媒についてab initio法によりEHOMOおよびELUMOの値を求めて検討した。その結果,プロトン性溶媒で, ELUMO値が大きくなり,電子受容能が低下しAN 値の間で逆の相関が成立しているのが認められ,予想と反対の結果となった。そこで,31P NMR化学シフトに基づく経験的溶媒パラメータAN値の基準標準物質であるtriethylphosphine oxide(Et3PO)と溶媒(S)の1:1溶媒和構造を半経験的方法とab initio 法で計算を行い,Et3PO のPおよびOの電子電荷分布,P-O距離,Et3POとSの間の水素結合距離を求めた。AN値は溶液(溶媒(S))中で得られた値であり,気相中の計算結果との比較は興味が持たれる。溶媒は非プロトン性溶媒とプロトン性溶媒に大別されるが,さらに極性の大小により分けられる。AN値が10以下の溶媒は極性の小さい非プロトン性溶媒,10から20までの間に極性の大きい非プロトン性溶媒,20以上に極性を持つプロトン性溶媒が位置している。したがって,各グループからよく使用される溶媒を20種類選択した。その結果,極性の小さい非プロトン性溶媒と水以外のプロトン性溶媒は,ほぼ1:1溶媒和錯体で相関関係(R=0.79-0.88)がよく,溶液中においても気相計算から得られた構造に基づくことが示唆された。一方,10から20までの間の非プロトン性極性溶媒と54.8の水がAN値との相関関係から大きくずれた。10から20までの非プロトン性極性溶媒(DMF,DMA, DMSO 等)は双極子モーメントが大きく,溶媒の液体構造が発達した構造 (aggregation) を形成している。また,水は水素結合形成による液体構造(cluster)を形成している。したがって,これらの溶媒中では,aggregationまたはcluster 化した複数の溶媒分子が溶媒和に関与しており,このことがずれの原因であると見なされる。
对化学反应产生的溶剂效果通过溶剂的物理性质即介电常数和溶解参数进行了说明,但经常出现不能同时说明非质子性溶剂和质子性溶剂的溶剂效果的情况。因此,很多人提出了经验性溶剂参数。其中Gutmann et al.的donor number (DN)和acceptor number (AN)被认为是溶剂的电子授受性的尺度。因此,认为与溶剂的HOMO和LUMO能量值相关,已经计算出8种溶剂(DMSO、DMF、AN、Ac、EtOH、MeOH、FA、H2O)的值,并研究其与AN的相关性。此次又增加了这些溶剂,对31种溶剂通过ab initio法求出EHOMO和ELUMO的值进行了研究。结果发现,质子性溶剂的ELUMO值变大,电子接受能力下降,AN值之间的反向相关成立,结果与预想相反。于是,基于31p NMR化学位移的经验溶剂参数AN值的基准标准物质triethylphosphine oxide (Et3PO)和溶剂(S)的1:1溶剂和结构的半经验方法和ab利用initio法进行计算,求出了Et3PO的P和O的电子电荷分布、P-O距离、Et3PO和S之间的氢键结合距离。AN值是在溶液(溶剂(S))中得到的值,与气相中的计算结果比较很有趣。溶剂可分为非质子性溶剂和质子性溶剂两大类,还可根据极性大小进行区分。AN值在10以下的溶剂是极性小的非质子性溶剂,极性大的非质子性溶剂在10到20之间,极性在20以上的是具有极性的质子性溶剂。因此,各组选择了20种常用的溶剂。结果表明,极性小的非质子性溶剂和水以外的质子性溶剂几乎是1:1的溶剂和配合物,具有良好的相关关系(R=0.79-0.88),即使在溶液中也是基于气相计算得到的结构。另一方面,从10到20之间的非质子极性溶剂和54.8的水与AN值的相关性出现了较大偏差。从10到20的非质子极性溶剂(DMF、DMA、DMSO等)的偶极矩大,形成了溶剂液体结构发达的结构(aggregation)。另外,水通过氢键形成液体结构(cluster)。因此,在这些溶剂中,aggregation或cluster化的多个溶剂分子参与了溶剂和,这被认为是发生偏差的原因。
{"title":"Triethylphosphine Oxideと溶媒分子の1:1溶媒和に関する理論的研究 - 31P NMR化学シフトに基づく経験的溶媒パラメータANとの間の相関関係 -","authors":"阿部 百合子, 千尋 日下部, 中尾 いずみ, 裕美 田中, 信一 山邊","doi":"10.2751/JCAC.8.59","DOIUrl":"https://doi.org/10.2751/JCAC.8.59","url":null,"abstract":"化学反応に及ぼす溶媒効果は,溶媒の物理的性質である誘電率や溶解パラメータで説明されているが,非プロトン性溶媒とプロトン性溶媒の溶媒効果を同時に説明できない場合が多く生じる。そのため,経験的溶媒パラメータが多数提唱されている。そのなかでGutmann et al. のdonor number (DN)とacceptor number (AN) は溶媒の電子授受性の尺度と考えられている。したがって,溶媒のHOMOおよびLUMOのエネルギー値との間に相関があると見なされ,8種類の溶媒 (DMSO, DMF, AN, Ac, EtOH, MeOH, FA, H2O ) の値がすでに計算されてANとの相関が調べられている。今回,さらにそれらの溶媒を加えて31種類の溶媒についてab initio法によりEHOMOおよびELUMOの値を求めて検討した。その結果,プロトン性溶媒で, ELUMO値が大きくなり,電子受容能が低下しAN 値の間で逆の相関が成立しているのが認められ,予想と反対の結果となった。そこで,31P NMR化学シフトに基づく経験的溶媒パラメータAN値の基準標準物質であるtriethylphosphine oxide(Et3PO)と溶媒(S)の1:1溶媒和構造を半経験的方法とab initio 法で計算を行い,Et3PO のPおよびOの電子電荷分布,P-O距離,Et3POとSの間の水素結合距離を求めた。AN値は溶液(溶媒(S))中で得られた値であり,気相中の計算結果との比較は興味が持たれる。溶媒は非プロトン性溶媒とプロトン性溶媒に大別されるが,さらに極性の大小により分けられる。AN値が10以下の溶媒は極性の小さい非プロトン性溶媒,10から20までの間に極性の大きい非プロトン性溶媒,20以上に極性を持つプロトン性溶媒が位置している。したがって,各グループからよく使用される溶媒を20種類選択した。その結果,極性の小さい非プロトン性溶媒と水以外のプロトン性溶媒は,ほぼ1:1溶媒和錯体で相関関係(R=0.79-0.88)がよく,溶液中においても気相計算から得られた構造に基づくことが示唆された。一方,10から20までの間の非プロトン性極性溶媒と54.8の水がAN値との相関関係から大きくずれた。10から20までの非プロトン性極性溶媒(DMF,DMA, DMSO 等)は双極子モーメントが大きく,溶媒の液体構造が発達した構造 (aggregation) を形成している。また,水は水素結合形成による液体構造(cluster)を形成している。したがって,これらの溶媒中では,aggregationまたはcluster 化した複数の溶媒分子が溶媒和に関与しており,このことがずれの原因であると見なされる。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"59-68"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257480","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. Ikenaga, M. Hanaki, Michinori Sumimoto, Hiroshi Shigi, T. Nagaoka, K. Hori
{"title":"A Chemoinformatics Approach for Enantioseparation Mechanism of Amino Acids by Micellar Electrokinetic Chromatography Using Bile Acids","authors":"Y. Ikenaga, M. Hanaki, Michinori Sumimoto, Hiroshi Shigi, T. Nagaoka, K. Hori","doi":"10.2751/JCAC.8.69","DOIUrl":"https://doi.org/10.2751/JCAC.8.69","url":null,"abstract":"","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"69-74"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.8.69","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257495","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. Sengoku, Shin-ichiro Miyahara, Hajime Wakabayashi, H. Sekino
The Fragment-Molecular-Orbital (FMO) method is an approximate quantum chemical method for huge systems like biological macromolecules and is known to provide not only an accurate total energy but also properties of the system with sufficient precision compared with conventional first principle methods. In the present study we report the spectroscopic properties such as dipole moment, polarizability and their derivatives by the FMO in order to examine the accuracy of the method in predicting IR and Raman spectroscopies of biological macromolecules. The results show the promising features of the method as a theoretical tool in the spectroscopic study of large bio-systems.
{"title":"The Predictive Accuracies of Spectroscopic Parameters in Biological Macromolecules by Fragment MO Method","authors":"Y. Sengoku, Shin-ichiro Miyahara, Hajime Wakabayashi, H. Sekino","doi":"10.2751/JCAC.8.85","DOIUrl":"https://doi.org/10.2751/JCAC.8.85","url":null,"abstract":"The Fragment-Molecular-Orbital (FMO) method is an approximate quantum chemical method for huge systems like biological macromolecules and is known to provide not only an accurate total energy but also properties of the system with sufficient precision compared with conventional first principle methods. In the present study we report the spectroscopic properties such as dipole moment, polarizability and their derivatives by the FMO in order to examine the accuracy of the method in predicting IR and Raman spectroscopies of biological macromolecules. The results show the promising features of the method as a theoretical tool in the spectroscopic study of large bio-systems.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"85-91"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257516","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":"Structure Optimization of Gas Separation Membrane Module","authors":"Takuro Nishimura, K. Funatsu","doi":"10.2751/JCAC.8.92","DOIUrl":"https://doi.org/10.2751/JCAC.8.92","url":null,"abstract":"ガスの膜透過現象を扱えるように拡張された数値流体力学(CFD)による、分離膜モジュールの性能シミュレーションシステムを開発した。このシステムでは、分離膜面積に依存した性能予測だけではなく、分離膜表面での濃度分極や、モジュール内部のガスの流動状態を反映させた性能評価により、分離膜モジュールの構造パラメータによる分離モジュールの性能比較が可能となった。その結果、分離膜モジュールの分離性能は、分離膜エレメントの配置パターンの影響が大きいことが明らかとなり、分離膜面積が比較的小さい場合でも、分離モジュールの体積を小さくコンパクトにした分離モジュールの中に、分離効率に優れたモジュールが存在することを確認した。さらに、分離エレメントの太さと分離エレメントの配置間隔の関係が、分離モジュールの性能に及ぼす影響も明らかとなった。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"92-102"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257528","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 the hydrogen production through the steam reforming reaction of the methane, the technology of the separation and purification influences the production cost of hydrogen directly. We have developed the simulation system concerning the structure design of the separation module in order to take out hydrogen with high purity. This system uses computational fluid dynamics (CFD) engine developed for the simulation of gas permeation through membranes. It can simulate the performance of the separation membrane module by considering the calculated gas stream with the aid of CFD at the stage of complex modular design. The purpose of this system is to propose the modular structure parameter set in order to attain the best separation performance of the module at the design stage of the separation membrane module. The calculated results showed that the optimization of the structural parameter combined with CFD simulation was important for the design of the separation membrane module with high efficiency.
{"title":"Simulation System for Structure Optimization of Hydrogen Separation Membrane Module","authors":"Takuro Nishimura, K. Funatsu","doi":"10.2751/JCAC.8.50","DOIUrl":"https://doi.org/10.2751/JCAC.8.50","url":null,"abstract":"In the hydrogen production through the steam reforming reaction of the methane, the technology of the separation and purification influences the production cost of hydrogen directly. We have developed the simulation system concerning the structure design of the separation module in order to take out hydrogen with high purity. This system uses computational fluid dynamics (CFD) engine developed for the simulation of gas permeation through membranes. It can simulate the performance of the separation membrane module by considering the calculated gas stream with the aid of CFD at the stage of complex modular design. The purpose of this system is to propose the modular structure parameter set in order to attain the best separation performance of the module at the design stage of the separation membrane module. The calculated results showed that the optimization of the structural parameter combined with CFD simulation was important for the design of the separation membrane module with high efficiency.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"50-58"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257475","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":"Analysis of Cancer Invasion Mechanism by Cellular Simulation","authors":"Keisuke Nagase, Hiroshi Kobayashi, Noboru Nagata, F. Yamamoto, T. Natsume, Kenichi Dedachi, T. Tsukamoto, N. Kurita","doi":"10.2751/JCAC.8.75","DOIUrl":"https://doi.org/10.2751/JCAC.8.75","url":null,"abstract":"癌細胞の浸潤には様々な蛋白質分解酵素が関与している。本研究では、これらの酵素の役割を明確にするため、細胞シミュレータ E-CELL を用いて、癌浸潤機構のモデルを新たに開発した。このモデルを用いて、5種類の癌細胞の浸潤特性を解析し、実験結果と定性的に一致する結果を得た。その結果、癌細胞の浸潤には、癌細胞が産生する urokinase-type plasminogen activator ( uPA )と癌細胞膜上に存在する活性型受容体 uPA receptor の結合が重要であることが、明らかになった。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"75-84"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257506","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}
Hiroyuki Matsuda, H. Yamamoto, Kiyofumi Kurihara, K. Tochigi
Predictive models for representing the ionic conductivity and viscosity of ionic liquids (ILs) were constructed using a polynomial expansion model, coupled with descriptors of group contribution type. These equations could be applied to cations of alkyl amine, pyrole, piperidine, pyridine, imidazole and pyrazole, with the following anions: TFSI, Br, Cl, PF6, BF4, CF3SO3, CF3BF3, and C2F5BF3. To determine coefficients in non-linear equations, genetic algorithms were adapted. Calculated results gave good correlation accuracy of ionic conductivity and viscosity. An examination of the predictive performance was also attempted by comparing the calculated with experimental values not used for the determination of the parameters.
{"title":"Prediction of The Ionic Conductivity and Viscosity of Ionic Liquids by QSPR Using Descriptors of Group Contribution Type","authors":"Hiroyuki Matsuda, H. Yamamoto, Kiyofumi Kurihara, K. Tochigi","doi":"10.2751/JCAC.8.114","DOIUrl":"https://doi.org/10.2751/JCAC.8.114","url":null,"abstract":"Predictive models for representing the ionic conductivity and viscosity of ionic liquids (ILs) were constructed using a polynomial expansion model, coupled with descriptors of group contribution type. These equations could be applied to cations of alkyl amine, pyrole, piperidine, pyridine, imidazole and pyrazole, with the following anions: TFSI, Br, Cl, PF6, BF4, CF3SO3, CF3BF3, and C2F5BF3. To determine coefficients in non-linear equations, genetic algorithms were adapted. Calculated results gave good correlation accuracy of ionic conductivity and viscosity. An examination of the predictive performance was also attempted by comparing the calculated with experimental values not used for the determination of the parameters.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"8 1","pages":"114-127"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.8.114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257419","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}