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Journal of Computer Aided Chemistry最新文献

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Solvatochromism of 4-(diethylamino)-4’-nitroazobenzene: explanation based on CNDO/S calculation results 4-(二乙胺)-4′-硝基偶氮苯的溶剂致变色:基于CNDO/S计算结果的解释
Pub Date : 2021-01-01 DOI: 10.2751/jcac.22.8
Tomoya Takada, H. Tachikawa
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引用次数: 0
A method to search the most stable reaction pathway and its application to the Pinner Pyrimidine Synthesis reaction 寻找最稳定反应途径的方法及其在平纳嘧啶合成反应中的应用
Pub Date : 2021-01-01 DOI: 10.2751/jcac.22.1
Eri Maeyama, Toru Yamaguchi, Michinori Sumimoto, K. Hori
The development of synthetic routes for functional chemicals has been heavily depending on experience and intuition of synthetic organic chemists. In case that target molecules have complex structures, there are many possible synthetic routes, and it is often difficult to determine which one should be adopted. In order to decrease synthesis routes for experiments, we introduced “in silico screening” which requires to search TSs for synthesis routes, we have proposed a method to locate the new TS structure of a target reaction by using TS structures in TSDB. However, this method seldom gives the most stable TS structure within possible conformers. That is, the stability of transition states (TS), reactants and products is highly dependent on initial structures used for optimization. Therefore, this method is likely to give inadequate data to compare calculated and measured values of other synthetic reactions. For these purposes, we have to find reaction mechanisms with the most stable TS and molecules involved in the reactions. In this paper, we proposed a method to search the most stable reaction pathway and applied it to the Pinner Pyrimidine reaction of ethyl 3-oxobutanoate and 3-ethoxypropanimidamide.
功能化学品合成路线的发展在很大程度上依赖于合成有机化学家的经验和直觉。当目标分子结构复杂时,有许多可能的合成路线,往往难以确定应该采用哪一种。为了减少实验合成路线,我们引入了通过搜索TS来寻找合成路线的“In silico screening”,我们提出了一种利用TSDB中的TS结构来定位目标反应的新TS结构的方法。然而,这种方法很少在可能的构象中给出最稳定的TS结构。也就是说,过渡态(TS)、反应物和产物的稳定性高度依赖于用于优化的初始结构。因此,这种方法可能不能提供足够的数据来比较其他合成反应的计算值和测量值。为了达到这些目的,我们必须找到最稳定的TS和参与反应的分子的反应机制。本文提出了一种寻找最稳定反应途径的方法,并将其应用于3-氧丁酸乙酯与3-乙氧基丙酰胺的平纳嘧啶反应。
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引用次数: 0
Extended Regression Modeling of the Toxicity of Phenol Derivatives to Tetrahymena pyriformis Using the Electronic-Structure Informatics Descriptor 基于电子结构信息描述符的苯酚衍生物对梨形四膜虫毒性的扩展回归模型
Pub Date : 2021-01-01 DOI: 10.2751/jcac.22.17
Algafari Bakti Manggara, M. Sugimoto
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引用次数: 0
Prediction of Compound Cytotoxicity Based on Compound Structures and Cell Line Molecular Characteristics 基于化合物结构和细胞系分子特性的化合物细胞毒性预测
Pub Date : 2020-01-01 DOI: 10.2751/jcac.21.1
T. Nakano, J. B. Brown
In parallel to developments in Next-Generation Sequencing for cancer patient therapy decision making, personalized approaches to chemotherapy selection are also becoming desired. In an ideal situation, an individual's genomic, transcriptomic, and tumor-specific in-vitro response to chemical perturbation would be combined, and the US National Cancer Institute NCI-60 project has systematically screened a large chemical library against a variety of cell lines from various tumor types. Therefore, chemoinformatics approaches to make effective use of this data and identify the chemical and biological factors are of value. In this work, we investigate the impact of both chemical and biological descriptions of tumor response to chemical inhibition, and assess how well modeling approaches can predict tumor inhibition response on external datasets. We find that external datasets in both the classification and regression problems are reasonably well addressed, with the impact of chemical description outweighing the contribution from transcriptome or genome descriptions of tumors.
与用于癌症患者治疗决策的新一代测序技术的发展同时,个性化的化疗选择方法也越来越受欢迎。在理想的情况下,个体的基因组、转录组学和肿瘤特异性对化学扰动的体外反应将被结合起来,美国国家癌症研究所NCI-60项目已经系统地筛选了一个大型化学文库,针对来自各种肿瘤类型的各种细胞系。因此,化学信息学方法有效地利用这些数据并识别化学和生物因素是有价值的。在这项工作中,我们研究了肿瘤对化学抑制反应的化学和生物学描述的影响,并评估了建模方法在外部数据集上预测肿瘤抑制反应的效果。我们发现,分类和回归问题中的外部数据集都得到了很好的解决,化学描述的影响超过了肿瘤转录组或基因组描述的贡献。
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引用次数: 3
Prediction of Fish Acute Ecotoxicity of Inorganic and Ionized Chemical Substances by Machine Learning 用机器学习预测鱼类对无机和电离化学物质的急性生态毒性
Pub Date : 2019-01-01 DOI: 10.2751/jcac.20.104
Michiyoshi Takata, B. Lin, A. Terada, M. Hosomi
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引用次数: 0
[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Automatic Drawing of Orbital Correlation Diagrams. A Computational Tool for Electronic-Structure Informatics [船松木东教授荣誉奖特刊]轨道相关图的自动绘制。电子结构信息学的计算工具
Pub Date : 2019-01-01 DOI: 10.2751/jcac.20.56
M. Sugimoto, Takafumi Inoue
Finding direct correlations between electronic structures of molecules and their properties, which we call “electronic-structure informatics”, is one of the challenging issues in chemoinformatics because the electronic degree of freedom is an essential factor determining the chemical characteristics. Herein we develop computational methods to automatically draw two types of orbital correlation diagrams. They are expected useful to perform machine learning including electronic degrees of freedom. In the present approach, we focus on electronic similarity called orbital similarity whose score is defined as spatial overlap between two molecular orbitals (MOs) enclosed with their iso-value surfaces. The similarity scores are also used to derive another orbital correlation diagram called “orbital interaction diagram”. This diagram is to relate MOs of a target molecule with those of its fragments. Through applications to benzene derivatives, these diagrams are shown to be reasonable, indicating potential usefulness of the present method in machine learning for quantitative predictions of molecular properties and chemical reactivities.
寻找分子的电子结构与其性质之间的直接关系,我们称之为“电子结构信息学”,是化学信息学中具有挑战性的问题之一,因为电子自由度是决定化学特性的重要因素。本文提出了自动绘制两种轨道相关图的计算方法。它们有望用于执行包括电子自由度在内的机器学习。在目前的方法中,我们关注的是称为轨道相似性的电子相似性,其分数被定义为两个分子轨道(MOs)之间的空间重叠,它们的等值表面被包围。相似度分数还用于推导另一种称为“轨道相互作用图”的轨道相关图。这张图将目标分子的MOs与其片段的MOs联系起来。通过对苯衍生物的应用,这些图被证明是合理的,表明本方法在机器学习中对分子性质和化学反应性的定量预测的潜在有用性。
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引用次数: 0
[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Kimito Funatsu – The Driving Force of Chemoinformatics in Japan [荣誉奖特刊-献给木藤Funatsu教授]木藤Funatsu -日本化学信息学的驱动力
Pub Date : 2019-01-01 DOI: 10.2751/jcac.20.32
J. Gasteiger
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引用次数: 0
Predicting the Fish Chronic Ecotoxicity of Chemical Substance with New Ecotoxicity Fingerprint and Stacked Ensemble Method on Machine Learning 基于机器学习的新型生态毒性指纹和堆叠集成方法预测化学物质对鱼类的慢性生态毒性
Pub Date : 2019-01-01 DOI: 10.2751/jcac.20.111
Michiyoshi Takata, B. Lin, A. Terada, Masaaki Hosomia
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引用次数: 0
[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Chemoinformatics Approach for Estimating Recovery Rates of Pesticides in Fruits and Vegetables [船松教授荣誉奖特刊]估算蔬果中农药回收率的化学信息学方法
Pub Date : 2019-01-01 DOI: 10.2751/jcac.20.92
T. Serino, Yoshizumi Takigawa, Sadao Nakamura, Ming Huang, N. Ono, Altaf-Ul-Amin, S. Kanaya
{"title":"[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Chemoinformatics Approach for Estimating Recovery Rates of Pesticides in Fruits and Vegetables","authors":"T. Serino, Yoshizumi Takigawa, Sadao Nakamura, Ming Huang, N. Ono, Altaf-Ul-Amin, S. Kanaya","doi":"10.2751/jcac.20.92","DOIUrl":"https://doi.org/10.2751/jcac.20.92","url":null,"abstract":"","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":"69256401","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
A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA) 共享键分离原子(BDA)碎片间相互作用能(IFIE)的径向修正
Pub Date : 2019-01-01 DOI: 10.2751/JCAC.20.1
T. Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, C. Watanabe
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引用次数: 1
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Journal of Computer Aided Chemistry
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