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TransPeakNet for solvent-aware 2D NMR prediction via multi-task pre-training and unsupervised learning.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-20 DOI: 10.1038/s42004-025-01455-9
Yunrui Li, Hao Xu, Ambrish Kumar, Duo-Sheng Wang, Christian Heiss, Parastoo Azadi, Pengyu Hong
{"title":"TransPeakNet for solvent-aware 2D NMR prediction via multi-task pre-training and unsupervised learning.","authors":"Yunrui Li, Hao Xu, Ambrish Kumar, Duo-Sheng Wang, Christian Heiss, Parastoo Azadi, Pengyu Hong","doi":"10.1038/s42004-025-01455-9","DOIUrl":"10.1038/s42004-025-01455-9","url":null,"abstract":"<p><p>Nuclear Magnetic Resonance (NMR) spectroscopy is essential for revealing molecular structure, electronic environment, and dynamics. Accurate NMR shift prediction allows researchers to validate structures by comparing predicted and observed shifts. While Machine Learning (ML) has improved one-dimensional (1D) NMR shift prediction, predicting 2D NMR remains challenging due to limited annotated data. To address this, we introduce an unsupervised training framework for predicting cross-peaks in 2D NMR, specifically Heteronuclear Single Quantum Coherence (HSQC). Our approach pretrains an ML model on an annotated 1D dataset of <sup>1</sup>H and <sup>13</sup>C shifts, then finetunes it in an unsupervised manner using unlabeled HSQC data, which simultaneously generates cross-peak annotations. Our model also adjusts for solvent effects. Evaluation on 479 expert-annotated HSQC spectra demonstrates our model's superiority over traditional methods (ChemDraw and Mestrenova), achieving Mean Absolute Errors (MAEs) of 2.05 ppm and 0.165 ppm for <sup>13</sup>C shifts and <sup>1</sup>H shifts respectively. Our algorithmic annotations show a 95.21% concordance with experts' assignments, underscoring the approach's potential for structural elucidation in fields like organic chemistry, pharmaceuticals, and natural products.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"51"},"PeriodicalIF":5.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Glucose-derived receptors for photo-controlled binding of amino acid esters in water.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-19 DOI: 10.1038/s42004-025-01445-x
Mario M Most, Linus B Boll, Peter Gödtel, Zbigniew L Pianowski, Bartosz Lewandowski
{"title":"Glucose-derived receptors for photo-controlled binding of amino acid esters in water.","authors":"Mario M Most, Linus B Boll, Peter Gödtel, Zbigniew L Pianowski, Bartosz Lewandowski","doi":"10.1038/s42004-025-01445-x","DOIUrl":"10.1038/s42004-025-01445-x","url":null,"abstract":"<p><p>Selective receptors of amino acids in aqueous media are highly sought after as they may enable the creation of novel diagnostic and sensing tools. Photoswitchable receptors are particularly attractive for such purposes as their response and selectivity towards bioanalytes can be modulated using light. Herein we report glucose-based photoswitchable receptors of amino-acid methyl esters and biogenic amines in water. The tetra-ortho-fluoroazobenzene unit in the receptors structure allows to control the distance between their binding sites using light. The Z-isomers of both receptors, having these sites in closer proximity, bind lysine, ornithine and arginine esters significantly stronger compared to E-isomers, where the binding sites are further apart.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"50"},"PeriodicalIF":5.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemical reactivity of RNA and its modifications with hydrazine.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-14 DOI: 10.1038/s42004-025-01444-y
Nur Yeşiltaç-Tosun, Yuyang Qi, Chengkang Li, Helena Stafflinger, Katja Hollnagel, Leona Rusling, Jens Wöhnert, Steffen Kaiser, Stefanie Kaiser
{"title":"Chemical reactivity of RNA and its modifications with hydrazine.","authors":"Nur Yeşiltaç-Tosun, Yuyang Qi, Chengkang Li, Helena Stafflinger, Katja Hollnagel, Leona Rusling, Jens Wöhnert, Steffen Kaiser, Stefanie Kaiser","doi":"10.1038/s42004-025-01444-y","DOIUrl":"10.1038/s42004-025-01444-y","url":null,"abstract":"<p><p>RNA modifications are essential for the regulation of cellular processes and have a key role in diseases such as cancer and neurological disorders. A major challenge in the analysis of RNA modification is the differentiation between isomers, including methylated nucleosides as well as uridine and pseudouridine. A solution is their differential chemical reactivity which enables isomer discrimination by mass spectrometry (MS) or sequencing. In this study, we systematically determine the chemical reactivity of hydrazine with RNA and its native modifications in an aniline-free environment. We optimize the conditions to achieve nearly full conversion of all uridines while avoiding RNA cleavage. We apply the conditions to native tRNA<sup>Phe</sup> which allows discrimination of pseudouridine and uridine by MALDI-MS. Furthermore, we determine the identity of the reaction product of hydrazine with various modified nucleosides using high resolution mass spectrometry and quantify the reaction yield in native tRNA from E. coli and human cells under various hydrazine conditions. Most modified nucleosides react quantitatively at lower hydrazine concentration while uridines do not decompose under these conditions. Thus, this study paves the way to exploit aniline-free hydrazine reactions in the detection of RNA modifications through MS and potentially even long-read RNA sequencing.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"48"},"PeriodicalIF":5.9,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Measurement of phospholipid lateral diffusion at high pressure by in situ magic-angle spinning NMR spectroscopy.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-14 DOI: 10.1038/s42004-025-01449-7
Thomas M Osborn Popp, Mithun Karthikeyan, Elias M Herman, Andrew C Dufur, Costantino Vetriani, Andrew J Nieuwkoop
{"title":"Measurement of phospholipid lateral diffusion at high pressure by in situ magic-angle spinning NMR spectroscopy.","authors":"Thomas M Osborn Popp, Mithun Karthikeyan, Elias M Herman, Andrew C Dufur, Costantino Vetriani, Andrew J Nieuwkoop","doi":"10.1038/s42004-025-01449-7","DOIUrl":"10.1038/s42004-025-01449-7","url":null,"abstract":"<p><p>The development of experimental methodologies that enable investigations of biochemistry at high pressure promises to yield significant advances in our understanding of life on Earth and its origins. Here, we introduce a method for studying lipid membranes at thermodynamic conditions relevant for life at deep sea hydrothermal vents. Using in situ high pressure magic-angle spinning solid state nuclear magnetic resonance spectroscopy (NMR), we measure changes in the fluidity of model microbial membranes at pressures up to 28 MPa. We find that the fluid-phase lateral diffusion of phospholipids at high pressure is significantly affected by the stoichiometric ratio of lipids in the membrane. Our results were facilitated by an accessible pressurization strategy that we have developed to enable routine preparation of solid state NMR rotors to pressures of 30 MPa or greater.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"49"},"PeriodicalIF":5.9,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11828890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Women in chemistry: Q&A with Dr Qi Hao.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-12 DOI: 10.1038/s42004-025-01430-4
{"title":"Women in chemistry: Q&A with Dr Qi Hao.","authors":"","doi":"10.1038/s42004-025-01430-4","DOIUrl":"10.1038/s42004-025-01430-4","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"46"},"PeriodicalIF":5.9,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spin-state effect on the efficiency of a post-synthetic modification reaction on a spin crossover complex.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-12 DOI: 10.1038/s42004-025-01425-1
Alejandro Enríquez-Cabrera, Yongjian Lai, Lionel Salmon, Lucie Routaboul, Azzedine Bousseksou
{"title":"Spin-state effect on the efficiency of a post-synthetic modification reaction on a spin crossover complex.","authors":"Alejandro Enríquez-Cabrera, Yongjian Lai, Lionel Salmon, Lucie Routaboul, Azzedine Bousseksou","doi":"10.1038/s42004-025-01425-1","DOIUrl":"10.1038/s42004-025-01425-1","url":null,"abstract":"<p><p>The spin state of a metal center significantly influences the catalytic activity of its complex, a phenomenon so crucial that it has led to the dedicated field of spin catalysis. Here we investigate the effect of the spin state of an iron-based metal complex on the organic reactivity of its ligands. Specifically, we examined the post-synthetic modification of the spin crossover (SCO) complex [Fe(NH<sub>2</sub>trz)<sub>3</sub>](NO<sub>3</sub>)<sub>2</sub> with p-anisaldehyde. A series of experiments were performed to study the transformation of the amino groups depending on the spin state of the metal. Owing to the wide thermal hysteresis loop of the SCO complex, both spin states were compared under identical conditions. The results revealed that the high-spin state led to the formation of 1.34 times more imine functional groups than the low-spin state, we propose that this arises from the different interactions between the solvent and the SCO at the different spin states.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"47"},"PeriodicalIF":5.9,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Women in chemistry: Q&A with Professor Mónica H. Pérez-Temprano.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-12 DOI: 10.1038/s42004-025-01431-3
{"title":"Women in chemistry: Q&A with Professor Mónica H. Pérez-Temprano.","authors":"","doi":"10.1038/s42004-025-01431-3","DOIUrl":"10.1038/s42004-025-01431-3","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"45"},"PeriodicalIF":5.9,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Women in chemistry. 化学界的女性
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-11 DOI: 10.1038/s42004-025-01441-1
{"title":"Women in chemistry.","authors":"","doi":"10.1038/s42004-025-01441-1","DOIUrl":"10.1038/s42004-025-01441-1","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"43"},"PeriodicalIF":5.9,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11814145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Women in chemistry: Q&A with Professor Valeska Ting.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-10 DOI: 10.1038/s42004-025-01429-x
{"title":"Women in chemistry: Q&A with Professor Valeska Ting.","authors":"","doi":"10.1038/s42004-025-01429-x","DOIUrl":"10.1038/s42004-025-01429-x","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"44"},"PeriodicalIF":5.9,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An active representation learning method for reaction yield prediction with small-scale data.
IF 5.9 2区 化学
Communications Chemistry Pub Date : 2025-02-10 DOI: 10.1038/s42004-025-01434-0
Peng-Xiang Hua, Zhen Huang, Zhe-Yuan Xu, Qiang Zhao, Chen-Yang Ye, Yi-Feng Wang, Yun-He Xu, Yao Fu, Hu Ding
{"title":"An active representation learning method for reaction yield prediction with small-scale data.","authors":"Peng-Xiang Hua, Zhen Huang, Zhe-Yuan Xu, Qiang Zhao, Chen-Yang Ye, Yi-Feng Wang, Yun-He Xu, Yao Fu, Hu Ding","doi":"10.1038/s42004-025-01434-0","DOIUrl":"10.1038/s42004-025-01434-0","url":null,"abstract":"<p><p>Reaction optimization plays an essential role in chemical research and industrial production. To explore a large reaction system, a practical issue is how to reduce the heavy experimental load for finding the high-yield conditions. In this paper, we present an efficient machine learning tool called \"RS-Coreset\", where the key idea is to take advantage of deep representation learning techniques to guide an interactive procedure for representing the full reaction space. Our proposed tool only uses small-scale data, say 2.5% to 5% of the instances, to predict the yields of the reaction space. We validate the performance on three public datasets and achieve state-of-the-art results. Moreover, we apply this tool to assist the realistic exploration of the Lewis base-boryl radicals enabled dechlorinative coupling reactions in our lab. The tool can help us to effectively predict the yields and even discover several feasible reaction combinations that were overlooked in previous articles.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"42"},"PeriodicalIF":5.9,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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