Chemistry methods : new approaches to solving problems in chemistry最新文献

Front Cover: Stability of Information-Carrying DNA Origami Nanostructures During Repeated Freeze–Thaw Cycles (Chem. Methods 4/2026) 封面：携带信息的DNA折纸纳米结构在重复冻融循环中的稳定性（化学）。方法4/2026)

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-13 DOI: 10.1002/cmtd.70104

Xinyang Li, Lukas Rabbe, Jacqueline Linneweber, Guido Grundmeier, Adrian Keller

引用次数: 0

Global Lipidome Workflow for Mycobacterium tuberculosis Using High-Resolution Mass Spectrometry 使用高分辨率质谱分析结核分枝杆菌的全球脂质组工作流程

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-03 DOI: 10.1002/cmtd.202500143

Glenda Vasku, Nashied Peton, Evelyn Y.-W. Huang, Madison R. Nuske, Chai Xin Yu, Xiaoxu Chen, Anna K. Coussens, Ivanhoe K. H. Leung

{"title":"Global Lipidome Workflow for Mycobacterium tuberculosis Using High-Resolution Mass Spectrometry","authors":"Glenda Vasku, Nashied Peton, Evelyn Y.-W. Huang, Madison R. Nuske, Chai Xin Yu, Xiaoxu Chen, Anna K. Coussens, Ivanhoe K. H. Leung","doi":"10.1002/cmtd.202500143","DOIUrl":"10.1002/cmtd.202500143","url":null,"abstract":"The lipid-rich envelope of Mycobacterium tuberculosis (Mtb) is a defining feature that underpins its virulence, persistence and response to antibiotics. An understanding of this envelope would allow us to link its lipid composition to the bacterium's physiology and pathogenicity. However, the chemical diversity and structural complexity of the lipid components present a major challenge in obtaining a complete profile of the lipid classes within the envelope. Herein, we report our work in the development of a high-resolution mass spectrometry pipeline to profile the Mtb lipidome using Mtb H37Rv (mc2 6206) as a model. Lipids were separated using a reversed phase chromatography method and analysed in dual polarity with adduct awareness in tandem mass spectrometry. This workflow enables both the relative quantification and identification of the lipids present in the sample. We found that a brief, ice-cold cell homogenisation step before lipid extraction improved coverage and abundance of both the inner-membrane phospholipids, neutral glycolipids and envelope glycoconjugates. These indicate that mechanical disruption of the mycomembrane enhances solvent access ensuring a higher abundance of extracted lipids. Hence, this ‘homogenisation-first’ step serves as a practical optimisation to improve lipid yields in Mtb lipidomic analyses. Overall, this workflow establishes a robust foundation for investigating the lipid composition of Mtb.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202500143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668208","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

Optimised Sample Preparation for Metabolic Analysis of Cell Cultures Using DESI-MS 利用DESI-MS优化细胞培养物代谢分析的样品制备

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-03 DOI: 10.1002/cmtd.70095

Wei Chen, Chiara Urban, Hakan Taskiran, Chenyue Dai, Kıvanç Görgülü, Julia Jellusova, Nicole Strittmatter

{"title":"Optimised Sample Preparation for Metabolic Analysis of Cell Cultures Using DESI-MS","authors":"Wei Chen, Chiara Urban, Hakan Taskiran, Chenyue Dai, Kıvanç Görgülü, Julia Jellusova, Nicole Strittmatter","doi":"10.1002/cmtd.70095","DOIUrl":"10.1002/cmtd.70095","url":null,"abstract":"Desorption electrospray ionisation mass spectrometry (DESI-MS) can profile cultured cells with minimal sample preparation, but salt carryover and wash-induced leakage often reduce metabolite coverage and reproducibility. Using the non-adherent human Burkitt’s lymphoma B cell line Ramos, we evaluated different substrates. Reversed-phase C18 thin-layer chromatography (TLC) plates produced homogeneous and robust signals of the deposited cellular material, while enabling passive separation of soluble contaminants from the cell-dense region. We then optimised wash solvents and frequency. Ammonium acetate (AA) washes are frequently used by the community to replace phosphate-buffered saline (PBS) washes. However, we observed that repeated AA washes markedly reduced cell viability, whereas PBS washing left residual salts that suppressed ion signals. A single 1:1 PBS/AA wash best balances desalting with cell integrity and improved coverage and reproducibility across small polar metabolites and lipids. Finally, we applied the workflow to human pancreatic ductal adenocarcinoma cell line, PANC-1, treated with a glutaminase 1 inhibitor and captured glutamine accumulation with depletion of glutamate and downstream metabolites. This rapid, extraction-free molecular profiling approach supports high-throughput phenotyping and can help reveal metabolic diversity and candidate biomarkers across cell models. Repeated measurements on the same sample support screening-scale metabolic phenotyping and the recording of additional acquisition modes.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.70095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668206","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}

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Modular Access to Bridgehead Heterocycle-Substituted Bicyclo[1.1.0]butanes via Late-Stage Functionalization of Alkynylbicyclo[1.1.0]butanes 通过炔基双环[1.1.0]丁烷的后期功能化模块化制备桥头堡杂环取代双环[1.1.0]丁烷

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-03 DOI: 10.1002/cmtd.202500164

Yu-Jie Li, Quanxin Peng, Wen-Biao Wu, Jian-Jun Feng

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A Two-Stage Machine Learning Framework With Physically Inspired Descriptors for Efficient Prediction of Hydration Free Energies 具有物理启发描述符的两阶段机器学习框架用于有效预测水化自由能

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-02 DOI: 10.1002/cmtd.202500150

Luyang Jia, Zhan-Yun Zhang, Bin-Bin Xie, Lin Shen, Wei-Hai Fang

{"title":"A Two-Stage Machine Learning Framework With Physically Inspired Descriptors for Efficient Prediction of Hydration Free Energies","authors":"Luyang Jia, Zhan-Yun Zhang, Bin-Bin Xie, Lin Shen, Wei-Hai Fang","doi":"10.1002/cmtd.202500150","DOIUrl":"10.1002/cmtd.202500150","url":null,"abstract":"Hydration free energy is essential to understanding stability and reactivity in aqueous environments. Recently, we reported a machine learning model Mole2Solv to predict experimental hydration free energies of molecules (J. Phys. Chem. Lett., 2023, 14, 1877). Physically inspired descriptors such as electrostatic potential distribution around solute molecules were proposed instead of chemistry-specific input features, thus improving transferability of the prediction model when it meets new compounds. However, most of these descriptors require ab initio calculations on solute molecules in vacuum, which seriously hinders its application on large-scale molecular solvation modeling and high-throughput screening. To address this limitation, we propose a two-stage framework that combines Mole2Solv with DeepMoleNet, a multilevel attention-based graph neural network developed by Ma and coworkers (J. Chem. Inf. Model., 2021, 61, 1066). Using the DeepMoleNet, 13 physically inspired descriptors can be predicted based on chemical structures of solutes and then applied to the subsequent Mole2Solv regression model. Expensive electronic structure calculation is no longer necessary for generating descriptors. In comparison with our previous model, the proposed two-stage framework keeps the prediction accuracy while significantly reduces the computational cost. Additionally, the transferability of physically inspired descriptors to unseen chemical structures can be well preserved within the two-stage framework.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202500150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668168","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

Preserving DNAzyme Stability and Activity in Stool Samples for Clinical Diagnostics 保持粪便样品中DNAzyme的稳定性和活性用于临床诊断

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-04-01 DOI: 10.1002/cmtd.70099

Soyeon Lee, Jimmy Gu, Bruno J. Salena, Yingfu Li

{"title":"Preserving DNAzyme Stability and Activity in Stool Samples for Clinical Diagnostics","authors":"Soyeon Lee, Jimmy Gu, Bruno J. Salena, Yingfu Li","doi":"10.1002/cmtd.70099","DOIUrl":"10.1002/cmtd.70099","url":null,"abstract":"Stool is one of the most challenging biological matrices for functional nucleic acid–based diagnostics because of its high and variable nuclease activity. Here, we present a simple and robust strategy for stabilizing RNA-cleaving fluorogenic DNAzymes (RFD) while preserving their catalytic function in stool. Using RFD-CD3—a DNAzyme previously developed for Clostridioides difficile detection—as a model system, we evaluated two stabilization approaches. While nucleic acid competitors, including tRNA and salmon sperm DNA, provided only modest protection under alkaline conditions, heparin treatment combined with high-pH buffer conditions significantly enhanced DNAzyme stability without compromising catalytic activity. This approach proved effective in both pooled and individual stool samples. The generality of the strategy was further demonstrated using RFD-CD2, a sequence-divergent C. difficile-responsive DNAzyme, as well as RFD-EC1, which targets Escherichia coli K12. Across all tested DNAzymes, stabilization preserved both probe integrity and target-responsive catalytic function. Together, these findings establish a practical and broadly applicable platform for deploying DNAzyme-based diagnostics in complex clinical samples such as stool.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.70099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668088","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

Democratizing AI-Enhanced Experimental Optimization: An Accessible Workflow for Chemists 民主化人工智能增强实验优化：化学家可访问的工作流程

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-03-31 DOI: 10.1002/cmtd.202600004

Nicholas N. Dahlen, Tori Z. Forbes

{"title":"Democratizing AI-Enhanced Experimental Optimization: An Accessible Workflow for Chemists","authors":"Nicholas N. Dahlen, Tori Z. Forbes","doi":"10.1002/cmtd.202600004","DOIUrl":"10.1002/cmtd.202600004","url":null,"abstract":"Experimental optimization is a cornerstone of chemical research, driving the perpetual search for novel methods to accelerate the process. Statistical design of experiments (DoE) methodologies are tools designed to accelerate experimental optimization but traditionally struggle to incorporate the qualitative observational data that are often paramount to optimization. The rapid advancement of artificial intelligence (AI), particularly general-use large language models (LLMs), presents a new avenue to address this limitation. We present an iterative AI-enhanced DoE workflow that utilizes accessible AI tools available for minimal cost. In this workflow, an LLM digitizes handwritten lab notes into machine-readable Markdown format. NotebookLM then consolidates observational data and integrates them into a prompt used by an LLM to perform a retrieval-augmented generation (RAG) analysis. The result is a detailed research report grounded in the user-provided information to provide insight into the chemical space, relevant literature to investigate, and experimental suggestions toward the goal of optimization. Finally, a human-in-the-loop (HITL) review validates the AI-generated report to ensure accuracy, relevance, and chemical safety. This approach aims to effectively bridge the gap between statistical DoE and qualitative insights, democratizing access to AI-assisted experimental optimization.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202600004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668834","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

Small Molecule-Based Conditional Gene Regulation: Advances and Applications 基于小分子的条件基因调控：进展与应用

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-03-31 DOI: 10.1002/cmtd.202500137

Mohd Afaque Ansari, Riddhima Sharma, Priyanka Swami, Ambadas B. Rode

{"title":"Small Molecule-Based Conditional Gene Regulation: Advances and Applications","authors":"Mohd Afaque Ansari, Riddhima Sharma, Priyanka Swami, Ambadas B. Rode","doi":"10.1002/cmtd.202500137","DOIUrl":"10.1002/cmtd.202500137","url":null,"abstract":"The precise, temporal, and reversible control of gene expression using small molecule ligands is crucial for understanding complex cellular functions and is rapidly advancing the field of synthetic biology. Small molecule-mediated conditional gene regulation has widespread applications, including bio-manufacturing, cellular reprogramming, gene therapy, and genome editing. The conditional regulatory systems act as molecular switches where a small molecule ligand interacts with target biomolecules (DNA, RNA, or proteins) and either induces the dimerization or recruitment of components, causes steric hindrance to block a process, or allosterically alters the target's functional conformation to modulate the gene expression over orders of magnitude in optimized contexts. This review provides a comprehensive mechanistic survey of these systems at the transcriptional, post-transcriptional, translational, and post-translational levels, highlighting recent innovations and applications across bacteria to human cells. It also discusses key challenges, including achieving high ligand binding (affinity), effective delivery (permeability), minimal side effects (toxicity), and low background activity (leakiness), that need to be addressed to fully unlock the potential of these regulatory systems for biomedical applications.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202500137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668833","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

Thermo-Oxidative Stability of Materials: Assessment and Predictions 材料的热氧化稳定性：评估与预测

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-03-22 DOI: 10.1002/cmtd.202500147

Peter Šimon, Tibor Dubaj, Zuzana Cibulková

{"title":"Thermo-Oxidative Stability of Materials: Assessment and Predictions","authors":"Peter Šimon, Tibor Dubaj, Zuzana Cibulková","doi":"10.1002/cmtd.202500147","DOIUrl":"https://doi.org/10.1002/cmtd.202500147","url":null,"abstract":"This article summarizes our experience after more than 25 years‘ work in the field of thermooxidative stability of materials. Theory for kinetic description of induction periods of polymer oxidation is outlined. It is based on the isoconversional methods where the temperature function is expressed as the Berthelot–Hood equation. It is demonstrated here that this equation provides the best approximation of the apparent rate constant as well as the best lifetime extrapolations to application temperatures. A method of extrapolation based on the temperature function derived in our laboratory is presented as well. Dimensionless criteria have been listed enabling deeper and more synoptical analysis of the results of high-temperature thermooxidation tests. The theory is applicable for the lifetime estimation of the artifacts made of plastics and of the materials employed in the conservation of plastic artifacts. The stability assessments and predictions are experimentally studied by thermoanalytical methods. Applications of the theory for the study of thermooxidation of various polymer systems are reviewed. There are reviewed also applications for the study of artifacts. The theory outlined can be applied not only for polymers, but also for thermooxidation of other organic materials in condensed phase, and for other processes exhibiting the induction period.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202500147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147568118","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

Thermo-Oxidative Stability of Materials: Assessment and Predictions 材料的热氧化稳定性：评估与预测

IF 3.6

Chemistry methods : new approaches to solving problems in chemistry Pub Date : 2026-03-22 DOI: 10.1002/cmtd.202500147

Peter Šimon, Tibor Dubaj, Zuzana Cibulková

{"title":"Thermo-Oxidative Stability of Materials: Assessment and Predictions","authors":"Peter Šimon, Tibor Dubaj, Zuzana Cibulková","doi":"10.1002/cmtd.202500147","DOIUrl":"https://doi.org/10.1002/cmtd.202500147","url":null,"abstract":"This article summarizes our experience after more than 25 years‘ work in the field of thermooxidative stability of materials. Theory for kinetic description of induction periods of polymer oxidation is outlined. It is based on the isoconversional methods where the temperature function is expressed as the Berthelot–Hood equation. It is demonstrated here that this equation provides the best approximation of the apparent rate constant as well as the best lifetime extrapolations to application temperatures. A method of extrapolation based on the temperature function derived in our laboratory is presented as well. Dimensionless criteria have been listed enabling deeper and more synoptical analysis of the results of high-temperature thermooxidation tests. The theory is applicable for the lifetime estimation of the artifacts made of plastics and of the materials employed in the conservation of plastic artifacts. The stability assessments and predictions are experimentally studied by thermoanalytical methods. Applications of the theory for the study of thermooxidation of various polymer systems are reviewed. There are reviewed also applications for the study of artifacts. The theory outlined can be applied not only for polymers, but also for thermooxidation of other organic materials in condensed phase, and for other processes exhibiting the induction period.","PeriodicalId":72562,"journal":{"name":"Chemistry methods : new approaches to solving problems in chemistry","volume":"6 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cmtd.202500147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147568117","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