Chemistry methods : new approaches to solving problems in chemistry最新文献_第9页

Reaction Impurity Prediction using a Data Mining Approach** 用数据挖掘方法预测反应杂质**

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-03-27 DOI: 10.1002/cmtd.202200062

Adarsh Arun, Dr. Zhen Guo, Dr. Simon Sung, Prof. Alexei A. Lapkin

{"title":"Reaction Impurity Prediction using a Data Mining Approach**","authors":"Adarsh Arun, Dr. Zhen Guo, Dr. Simon Sung, Prof. Alexei A. Lapkin","doi":"10.1002/cmtd.202200062","DOIUrl":"10.1002/cmtd.202200062","url":null,"abstract":"Automated prediction of reaction impurities is useful in early-stage reaction development, synthesis planning and optimization. Existing reaction predictors are catered towards main product prediction, and are often black-box, making it difficult to troubleshoot erroneous outcomes. This work aims to present an automated, interpretable impurity prediction workflow based on data mining large chemical reaction databases. A 14-step workflow was implemented in Python and RDKit using Reaxys® data. Evaluation of potential chemical reactions between functional groups present in the same reaction environment in the user-supplied query species can be accurately performed by directly mining the Reaxys® database for similar or ‘analogue’ reactions involving these functional groups. Reaction templates can then be extracted from analogue reactions and applied to the relevant species in the original query to return impurities and transformations of interest. Three proof-of-concept case studies (paracetamol, agomelatine and lersivirine) were conducted, with the workflow correctly suggesting impurities within the top two outcomes. At all stages, suggested impurities can be traced back to the originating template and analogue reaction in the literature, allowing for closer inspection and user validation. Ultimately, this work could be useful as a benchmark for more sophisticated algorithms or models since it is interpretable, as opposed to purely black-box solutions.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"3 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202200062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42101603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Plasmonic Scattering Microscopy for Label-Free Imaging of Molecular Binding Kinetics: From Single Molecules to Single Cells 等离子体散射显微镜用于分子结合动力学的无标记成像:从单个分子到单个细胞

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-03-27 DOI: 10.1002/cmtd.202200066

Dr. Pengfei Zhang, Xinyu Zhou, Prof. Shaopeng Wang

引用次数: 2

Ionic Liquid Modified Electrocatalysts: a STEM-EDX Approach for Identification of Local Distributions within Ionomer Containing Catalysts Layers 离子液体修饰的电催化剂:用STEM - EDX方法鉴定含离聚体催化剂层内的局部分布

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-03-27 DOI: 10.1002/cmtd.202200084

Kai Brunnengräber, Katharina Jeschonek, Michael George, Prof. Dr. Gui-Rong Zhang, Prof. Dr. Bastian J. M. Etzold

{"title":"Ionic Liquid Modified Electrocatalysts: a STEM-EDX Approach for Identification of Local Distributions within Ionomer Containing Catalysts Layers","authors":"Kai Brunnengräber, Katharina Jeschonek, Michael George, Prof. Dr. Gui-Rong Zhang, Prof. Dr. Bastian J. M. Etzold","doi":"10.1002/cmtd.202200084","DOIUrl":"10.1002/cmtd.202200084","url":null,"abstract":"Driven by the transition to a CO2-neutral energy economy, research on polymer electrolyte fuel cells gained much interest during the last decade, with researchers trying to overcome the sluggish kinetics of the oxygen reduction reaction (ORR) limiting their performance. Modification of existing ORR catalysts with small amounts of ionic liquids (IL) represents an innovative approach to altering the catalytic activity and stability. ILs are supposed to take effect by modifying the local microenvironment at electrochemical interfaces. Nevertheless, a thorough understanding about the local distribution of ILs over solid catalysts is still lacking, hindering the IL modification strategy to be a generic approach to rationally modulating the catalytic performance of a catalyst. In this study we employed STEM-EDS spectral imaging to locate the IL distribution on the catalyst in presence of NafionTM. To overcome the difficulties associated with low energy STEM-EDS we setup a sophisticated data processing routine based on machine learning.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"3 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202200084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42191618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cover Picture: (Chem. Methods 3/2023) 封面图片：（化学方法3/2023）

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-03-01 DOI: 10.1002/cmtd.202300010

引用次数: 0

Recent Progress in Artificial Structural Colors and their Applications in Fibers and Textiles 人造结构色及其在纤维和纺织品中的应用研究进展

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-02-13 DOI: 10.1002/cmtd.202200081

Run Li, Shiliang Zhang, Prof. Rufan Zhang

引用次数: 3

Cover Picture: (Chem. Methods 2/2023) 封面图片:(化学)方法2/2023)

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-02-07 DOI: 10.1002/cmtd.202300001

引用次数: 0

In Silico Design of Dihydroazulene/Vinylheptafulvene Photoswitches for Solar-Energy Storage Guided by an All-Around Performance Descriptor** 基于全方位性能描述符的太阳能储能用二氢偶氮烯/乙烯基七氟烯光开关的硅设计**

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-02-01 DOI: 10.1002/cmtd.202200060

Dr. Enrique M. Arpa, Prof. Bo Durbeej

{"title":"In Silico Design of Dihydroazulene/Vinylheptafulvene Photoswitches for Solar-Energy Storage Guided by an All-Around Performance Descriptor**","authors":"Dr. Enrique M. Arpa, Prof. Bo Durbeej","doi":"10.1002/cmtd.202200060","DOIUrl":"10.1002/cmtd.202200060","url":null,"abstract":"A major challenge in the development of molecular photoswitches capable of storing and releasing solar energy is to simultaneously realize many of the performance criteria required of the switches for such applications. Here, we take on this challenge by introducing an all-around performance descriptor that combines three key criteria (related to energy density, storage time and light-absorption characteristics), and by using density functional theory methods to calculate its values for 52 newly designed dihydroazulene/vinylheptafulvene (DHA/VHF) switches. Thereby, we are able to identify several switches with excellent overall properties that contain a structural motif absent in all DHA/VHF compounds previously considered for solar-energy storage. For some of these switches, we also provide retrosynthetic analyses and demonstrate that they form the energy-storing VHF isomer through a facile DHA→VHF photoisomerization reaction. All in all, we conclude that these switches show great promise for further development towards applications in solar-energy storage.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"3 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202200060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41858714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of Drug Metabolites with Infrared Ion Spectroscopy – Application to Midazolam in vitro Metabolism** 红外离子光谱法鉴定药物代谢产物——在咪唑安定中的应用体外代谢**

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-02-01 DOI: 10.1002/cmtd.202200068

Dr. Rianne E. van Outersterp, Dr. Jonathan Martens, Dr. Giel Berden, Arnaud Lubin, Dr. Filip Cuyckens, Prof. Dr. Jos Oomens

{"title":"Identification of Drug Metabolites with Infrared Ion Spectroscopy – Application to Midazolam in vitro Metabolism**","authors":"Dr. Rianne E. van Outersterp, Dr. Jonathan Martens, Dr. Giel Berden, Arnaud Lubin, Dr. Filip Cuyckens, Prof. Dr. Jos Oomens","doi":"10.1002/cmtd.202200068","DOIUrl":"10.1002/cmtd.202200068","url":null,"abstract":"The identification of biotransformation products of drug compounds is a crucial step in drug development. Over the last decades, liquid chromatography-mass spectrometry (LC-MS) has become the method of choice for metabolite profiling because of its high sensitivity and selectivity. However, determining the full molecular structure of the detected metabolites, including the exact biotransformation site, remains challenging on the basis of MS alone. Here we explore infrared ion spectroscopy (IRIS) as a novel MS-based method for the elucidation of metabolic pathways in drug metabolism research. Using the drug midazolam as an example, we identify several biotransformation products directly from an in vitro drug incubation sample. We show that IR spectra of the aglycone MS/MS fragment ions of glucuronide metabolites establish a direct link between detected phase I and phase II metabolites. Moreover, using quantum-chemically computed IR spectra of candidate structures, we are able to assign the exact sites of biotransformation in absence of reference standards. Additionally, we demonstrate the utility of IRIS for structural elucidation by identifying several ring-opened midazolam derivatives formed in an acidic environment.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"3 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202200068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43164388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

High-Throughput Experimentation as an Accessible Technology for Academic Organic Chemists in Europe and Beyond** 高通量实验是欧洲及其他地区学术有机化学家可获得的技术**

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-02-01 DOI: 10.1002/cmtd.202200059

Dr. Xisco Caldentey, Dr. Eugénie Romero

引用次数: 1

A Practice-Oriented Benchmark Strategy to Predict the UV-Vis Spectra of Organic Photocatalysts** 基于实践的有机光催化剂紫外可见光谱预测基准策略**

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2023-01-20 DOI: 10.1002/cmtd.202200069

Dr. Péter Pál Fehér, Dr. Ádám Madarász, Dr. András Stirling

{"title":"A Practice-Oriented Benchmark Strategy to Predict the UV-Vis Spectra of Organic Photocatalysts**","authors":"Dr. Péter Pál Fehér, Dr. Ádám Madarász, Dr. András Stirling","doi":"10.1002/cmtd.202200069","DOIUrl":"10.1002/cmtd.202200069","url":null,"abstract":"With this work, we wish to facilitate further developments in photocatalysis by proposing reliable methods for the computational pre-screening of potential photocatalysts. To this end, we have developed a new benchmark strategy, and we have applied it to evaluate the predictions given by two wavefunction and several density functional theory (DFT) methods for the UV-vis absorption spectra of recently developed organic photocatalyst molecules. The novelty in our benchmark framework is that it focuses on evaluating the real-world applicability of computational methods and does not penalize errors that do not contribute to spectral shapes. We employ a spectral fitting process where the calculated excitations are convoluted with Gaussians using two parameters for broadening and wavelength scaling. This way, most methods can sufficiently reproduce the experimental spectra, but they differ in how much adjustment they require from the parameters. Overall, the double hybrids (with the notable exception of DSD-BLYP) are the best functionals that offer the highest predictive power as they require practically no scaling. They are exceptionally good in estimating the excitation energies with almost 90 % of the fitted spectra falling into the ±10 % scaling window. This is the same level of accuracy as provided by the STEOM-DLPNO-CCSD correlated wavefunction method. In terms of cost efficiency, M06 emerges as the best functional. It compensates a slightly less consistent performance with lower computational demand and availability in nearly all computational codes. Therefore, we recommend the use of double-hybrid and M06 functionals for UV-vis spectrum prediction of novel organic photocatalysts, and we also highlight that M06 can be used as a black-box method even by those who are non-experts in computational chemistry. The developed protocol and a user-friendly notebook to assist the analysis are available on GitHub.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"3 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202200069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41902996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2