Journal of Computer Aided Chemistry最新文献_第9页

Predicting Rank of Japanese Green Teas by Derivative Profiles of Spectra Obtained from Fourier Transform Near-Infrared Reflectance Spectroscopy 利用傅里叶变换近红外反射光谱导数曲线预测日本绿茶的等级

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.37

T. Ikeda, M. Altaf-Ul-Amin, A. Parvin, S. Kanaya, T. Yonetani, E. Fukusaki

引用次数: 3

Monte Carlo Simulation Using Quantum Mechanical Calculations (QM/MC Simulation). An Application to Alkaline Hydrolysis of Methylacetate 蒙特卡罗模拟使用量子力学计算(QM/MC模拟)。在醋酸甲酯碱性水解中的应用

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/jcac.9.62

Toru Yamaguchi, Michinori Sumimoto, K. Hori

{"title":"Monte Carlo Simulation Using Quantum Mechanical Calculations (QM/MC Simulation). An Application to Alkaline Hydrolysis of Methylacetate","authors":"Toru Yamaguchi, Michinori Sumimoto, K. Hori","doi":"10.2751/jcac.9.62","DOIUrl":"https://doi.org/10.2751/jcac.9.62","url":null,"abstract":"Although it is possible to analyze chemical reactions in detail using molecular orbital (MO) and Density Functional Theory (DFT) calculations, these results simulate reactions at 0 K in the vacuum. Usual organic reactions proceed in solvents such as water, acetnitrile, alcohol and so on. In order to simulate the reactions in solution, it is necessary to investigate the mechanisms including solvent effects. The SCRF calculations have been used for this purpose while the method regards solvents as simple dielectric constants, and then, it is impossible to analyze the role of each solvent molecule for the reactions. Molecular dynamic (MD) calculations and Monte Carlo (MC) simulations have been used for calculating difference in free energy solvation. These theories usually use classical force fields so that it is very difficult to obtain good parameters for organic solvents used in organic synthesis. We have been developing Monte Carlo simulations using quantum mechanical calculations, called the QM/MC simulations. This approach makes it possible to analyze solvent effects from the quantum chemical view point. As an example of the simulation, we adopted alkaline hydrolysis of methyl acetate. A combination of ab initio calculations at the MP2/6-31++G** level of theory for analyzing the reaction mechanisms in the vacuum and the MC simulations using the PM3 method produced results consistent with experimental results very much.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/jcac.9.62","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257179","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}

引用次数: 0

Molecular Mechanics and Molecular Orbital Simulations on The Specific Interactions between Lactose Repressor Protein and Its Inducer and Anti-Inducer Molecules 乳糖抑制蛋白与诱导剂和抗诱导剂分子特异性相互作用的分子力学和分子轨道模拟

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.17

Shin Nishikawa, Shinsaku Kozakai, Y. Sengoku, N. Kurita

{"title":"Molecular Mechanics and Molecular Orbital Simulations on The Specific Interactions between Lactose Repressor Protein and Its Inducer and Anti-Inducer Molecules","authors":"Shin Nishikawa, Shinsaku Kozakai, Y. Sengoku, N. Kurita","doi":"10.2751/JCAC.9.17","DOIUrl":"https://doi.org/10.2751/JCAC.9.17","url":null,"abstract":"転写制御タンパク質であるラクトースリプレッサー(LacR)は、Ligand依存型タンパク質であり、結合するLigandの種類に依存してDNAの転写を抑制あるいは促進する。本研究では、Ligandの結合によりLacRの構造と電子状態がどのように変化するかを、古典分子力学計算、及び半経験的分子軌道計算により解析し、Ligand結合によりLacRとDNAの結合が変化する原因の解明を試みた。具体的には、LacR単体の構造、インデューサであるIPTGが結合したLacR-IPTG複合体構造、アンチインデューサであるONPFが結合したLacR-ONPF複合体構造を、古典分子力場AMBERを用いて水中で最適化し、最適化した構造の電子状態を半経験的分子軌道計算により解析した。その結果、LacRとLigandの結合にはLigand周辺の結晶水が重要な働きをしていることが明らかになった。また、LigandがLacRに結合することにより、LacRのDNA結合部位の構造が変化し、LacRとDNA間の結合エネルギーが変化することも明らかになった。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"9 1","pages":"17-29"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257549","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}

引用次数: 2

Theoretical Study on Emission Spectra of Bioluminescent Luciferases by Fragment Molecular Orbital Method 片段分子轨道法研究生物发光荧光素酶的发射光谱

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.47

Ayumu Tagami, Nobuhiro Ishibashi, D. Kato, Naoki Taguchi, Y. Mochizuki, Hirofumi Watanabe, Mika Ito, S. Tanaka

{"title":"Theoretical Study on Emission Spectra of Bioluminescent Luciferases by Fragment Molecular Orbital Method","authors":"Ayumu Tagami, Nobuhiro Ishibashi, D. Kato, Naoki Taguchi, Y. Mochizuki, Hirofumi Watanabe, Mika Ito, S. Tanaka","doi":"10.2751/JCAC.9.47","DOIUrl":"https://doi.org/10.2751/JCAC.9.47","url":null,"abstract":"フラグメント分子軌道（FMO）法は、生体高分子をフラグメントに分割することにより計算時間を大幅に短縮し、タンパク質やDNAなどの巨大分子系全体を量子論的に扱う計算方法として近年注目を集めている。本研究ではその中の1手法である多層FMO（MLFMO）を用いて、ホタルルシフェラーゼの励起状態計算を行った。計算に用いた構造は、野生型（緑色に発光）と橙色、赤色に発光する変異体の計4つである。発光体オキシルシフェリンと活性中心を含む比較的小規模な系で計算を行い、その結果4つの構造に対する発光エネルギーを実験値と相関して再現することに成功した。タンパク質の全体構造においても励起状態計算を行い、実験値と計算値の差を比較したところ、4つの構造において最大でも0.27eVの差と、実験値を定量的に再現することにも成功した。本報告ではその詳細と、発光色制御における周辺環境場の重要性について述べる。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"9 1","pages":"47-54"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257619","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}

引用次数: 2

Development of Evaluation Model for Strategic Sites in Synthetic Route Design System AIPHOS 综合路线设计系统AIPHOS中战略站点评价模型的建立

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.81

A. Tanaka, T. Kawai, Tsutomu Matsumoto, T. Takabatake, Hideho Okamoto, K. Funatsu

引用次数: 0

Parallelization of Crystal Calculation for Large-Scale Molecular Crystal Structure Analysis 大尺度分子晶体结构分析中晶体计算的并行化

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.8

S. Obata, H. Goto

{"title":"Parallelization of Crystal Calculation for Large-Scale Molecular Crystal Structure Analysis","authors":"S. Obata, H. Goto","doi":"10.2751/JCAC.9.8","DOIUrl":"https://doi.org/10.2751/JCAC.9.8","url":null,"abstract":"計算化学技術による結晶構造解析は、機能材料や医薬品の開発など広範囲な研究分野において重要な役割が期待されている。一般に結晶計算では、計算対象となる結晶モデルを大きくするとより実在系に近づき、より高精度な計算結果を期待できるが、それに伴う分子間相互作用の計算量は爆発的に増加する。このため、利用可能な計算機の演算性能に応じて計算できる結晶モデルの大きさは制限されてしまう。そこで本研究では、我々が開発してきた結晶構造最適化プログラムKESSHOUの結晶計算法を、汎用分子計算プログラムCONFLEXに導入したCONFLEX/KESSHOUにおいて、分子間相互作用の計算部分に並列分散処理技術を適用することによって、結晶構造のエネルギー計算や構造最適化の効率的な高速化を実現した。また、結晶モデルの大規模化に伴う分子間相互作用エネルギーの加算誤差を最小限に抑えるため、Kahanの加算アルゴリズムを適用した。並列分散計算環境を利用して、アスピリン結晶の構造最適化を行なったところ、その並列化効率が90％以上に達することを確認した。また、結晶モデルの大きさ（有効結晶半径）に依存した結晶エネルギー揺らぎを調べたところ、有効結晶半径80A以上の結晶モデルの結晶エネルギーは10-3 kcal/mol以内の精度で求められることが分かった。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"9 1","pages":"8-16"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257192","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}

引用次数: 9

Rough Set Theoryによるルールマイニングと構造活性相関への応用 Rough Set Theory对规则挖掘和结构活性相关的应用

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.1

清長谷川, 倫央光山, 正幹荒川, 公人船津

{"title":"Rough Set Theoryによるルールマイニングと構造活性相関への応用","authors":"清長谷川, 倫央光山, 正幹荒川, 公人船津","doi":"10.2751/JCAC.9.1","DOIUrl":"https://doi.org/10.2751/JCAC.9.1","url":null,"abstract":"本論文では、ルールマイニング手法として知られているRough Set Theory (RST)を構造活性相関に応用することで、高活性に必要なルールが導けるかどうかを検証した。これまでルールマイニング手法としては、Inductive Logic Programming (ILP)が知られているが、学習の準備、特に、background knowledgeを事前に作成することが大変で、実際の応用は限定されていた。RSTはあいまいなものや粗いデータなどの不正確、不完全なものを類別するための理論である。これをルールマイニングの手法として用いる事で、あるサンプルと別のサンプルを区別するのに必要最小限の変数セット(reduct)を選択し、選択されたセットからルールを導くことが出来る。構造活性データとしては、Dihydrofolate reductase (DHFR)阻害剤を利用した。このデータセットは、これまで数多く解析され、構造要求性がよく知られている。得られたルールは、この構造要求性と類似しており、RSTの有効性を証明することができた。今回、母核構造が一定で活性値が定量的なデータで検証したが、多様な化合物を含むデータや活性値が不正確なデータへの応用も期待できる。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"9 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.9.1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257537","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}

引用次数: 2

Automatic Generation of Structure of Phospholipids 磷脂结构的自动生成

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.55

H. Horai, T. Nishioka

引用次数: 0

Development of Fingerprint Verification Type Self-Organized Map Applied to Profiling Seized Methamphetamine 指纹验证型自组织图谱在查获甲基苯丙胺定性分析中的应用

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.30

Rika Nishikiori, Y. Makino, Yukino Ochi, Noriyuki Yamashita, Kousuke Okamoto, N. Kawashita, J. Takahara, T. Yasunaga, T. Takagi, M. Kawase

{"title":"Development of Fingerprint Verification Type Self-Organized Map Applied to Profiling Seized Methamphetamine","authors":"Rika Nishikiori, Y. Makino, Yukino Ochi, Noriyuki Yamashita, Kousuke Okamoto, N. Kawashita, J. Takahara, T. Yasunaga, T. Takagi, M. Kawase","doi":"10.2751/JCAC.9.30","DOIUrl":"https://doi.org/10.2751/JCAC.9.30","url":null,"abstract":"In a previous study {Takagi, T. et al., Chem. Pharm. Bull., 52(12), 1427-1432 (2004)}, we applied a slightly revised neural Independent Component Analysis (ICA) for profiling illegally distributed methamphetamine. Using ICA and an hourglass type Hierarchical Neural Network (HNN), we obtained better classification results than by using Principal Component Analysis (PCA), CATegorical PCA (CATPCA) and the MultiDimensional Scaling method (MDS). The HNN is a nonlinear machine learning method, and the ICA applied in that study exhibited nonlinear characteristics. The results indicated that nonlinear analysis is more efficient than linear analysis for profiling confiscated methamphetamine. Consequently, in this study, we applied Self-Organizing Maps (SOMs) to impurity profiling of methamphetamine. While SOM is currently a frequently employed nonlinear classification method, the ordinary SOM uses only that information contained by the winner neuron for classification and the information of other grid points is neglected. We therefore attempted to simultaneously utilize the information of loser neurons in order to avoid information loss. First, we visualized the resultant reference vectors using a contour map of each sample. Although considerable information can be visually compared using the SOM contour maps, metric comparisons are difficult. We therefore used MDS to construct a similarity matrix using the data of the resultant reference vectors to visualize metric data. To assess the results, we assumed that there are four synthetic routes (Nagai, Leuckart, Emde and reductive amination methods), and that each of these can be identified by comparing route-specific impurities.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"9 1","pages":"30-36"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69257560","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}

引用次数: 1

Development of Drug-likeness Model and Its Visualization 药物相似模型的发展及其可视化

Journal of Computer Aided Chemistry Pub Date : 2008-01-01 DOI: 10.2751/JCAC.9.70

Masamoto Arakawa, Tomoyuki Miyao, K. Funatsu

引用次数: 6