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Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation. 靛蓝生产确定了细胞色素 P450 BM3 中芳香烃羟化多样化的热点。
IF 3.3 3区 化学
Faraday Discussions Pub Date : 2024-07-12 DOI: 10.1039/d4fd00017j
Douglas J Fansher, Jonathan N Besna, Joelle N Pelletier
{"title":"Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation.","authors":"Douglas J Fansher, Jonathan N Besna, Joelle N Pelletier","doi":"10.1039/d4fd00017j","DOIUrl":"https://doi.org/10.1039/d4fd00017j","url":null,"abstract":"<p><p>Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified <i>via</i> their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified <i>via</i> colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Seeing nanoscale electrocatalytic reactions at individual MoS2 particles under an optical microscope: probing sub-mM oxygen reduction reaction 在光学显微镜下观察单个 MoS2 颗粒的纳米级电催化反应:探测亚毫微米级的氧还原反应
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-10 DOI: 10.1039/d4fd00132j
Nikan Afsahi, Zhu Zhang, Sanli Faez, Jean-Marc Noël, Manas Ranjan Panda, Mainak Majumder, Naimeh Naseritaheri, Jean-François Lemineur, Frederic Kanoufi
{"title":"Seeing nanoscale electrocatalytic reactions at individual MoS2 particles under an optical microscope: probing sub-mM oxygen reduction reaction","authors":"Nikan Afsahi, Zhu Zhang, Sanli Faez, Jean-Marc Noël, Manas Ranjan Panda, Mainak Majumder, Naimeh Naseritaheri, Jean-François Lemineur, Frederic Kanoufi","doi":"10.1039/d4fd00132j","DOIUrl":"https://doi.org/10.1039/d4fd00132j","url":null,"abstract":"MoS2 is a promising electrocatalytic material for replacing noble metals. Nanoelectrochemistry studies, such as using nanoelectrochemical cell confinement, have particularly helped in demonstrating the preferential electrocatalytic activity of MoS2 edges. These findings have been accompanied by considerable research efforts to synthetize edge-abundant nanomaterials. However, to fully apprehend their electrocatalytic performance, at the single particle level, new instrumental developments are also needed. Here, we feature a highly sensitive refractive index optical microscopy technique, namely interferometric scattering microscopy (iSCAT), for monitoring local electrochemistry at single MoS2 petal-like sub-microparticles. This work focuses on the oxygen reduction reaction (ORR), which operates at low current densities and thus requires high-sensitivity imaging techniques. By employing a precipitation reaction to reveal the ORR activity and utilizing the high spatial resolution and contrast of iSCAT, we achieve the sensitivity required to evaluate the ORR activity at single MoS2 particles.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optical materials discovery and design via federated databases and machine learning 通过联合数据库和机器学习发现和设计光学材料
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-10 DOI: 10.1039/d4fd00092g
Victor Trinquet, Matthew Evans, Cameron Hargreaves, Pierre-Paul De Breuck, Gian-Marco Rignanese
{"title":"Optical materials discovery and design via federated databases and machine learning","authors":"Victor Trinquet, Matthew Evans, Cameron Hargreaves, Pierre-Paul De Breuck, Gian-Marco Rignanese","doi":"10.1039/d4fd00092g","DOIUrl":"https://doi.org/10.1039/d4fd00092g","url":null,"abstract":"Combinatorial and guided screening of materials space with density-functional theory and related approaches has provided a wealth of hypothetical inorganic materials, which are increasingly tabulated in open databases. The OPTIMADE API is a standardised format for representing crystal structures, their measured and computed properties, and the methods for querying and filtering them from remote resources. Currently, the OPTIMADE federation spans over 20 data providers, rendering over 30 million structures accessible in this way, many of which are novel and have only recently been suggested by machine learning-based approaches. In this work, we outline our approach to non-exhaustively screen this dynamic trove of structures for the next-generation of optical materials. By applying MODNet, a neural network-based model for property prediction that has been shown to perform especially well for small materials datasets, within a combined active learning and high-throughput computation framework, we isolate particular structures and chemistries that should be most fruitful for further theoretical calculations and for experimental study as high-refractive-index materials. By making explicit use of automated calculations, federated dataset curation and machine learning, and by releasing these publicly, the workflows presented here can be periodically re-assessed as new databases implement OPTIMADE, and new hypothetical materials are suggested.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141573174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Electrochemical Nucleation and Growth Kinetics: Insights from Single Particle Scanning Electrochemical Cell Microscopy Studies 电化学成核和生长动力学:单颗粒扫描电化学电池显微镜研究的启示
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-06 DOI: 10.1039/d4fd00131a
Kenneth Osoro, Caleb Hill
{"title":"Electrochemical Nucleation and Growth Kinetics: Insights from Single Particle Scanning Electrochemical Cell Microscopy Studies","authors":"Kenneth Osoro, Caleb Hill","doi":"10.1039/d4fd00131a","DOIUrl":"https://doi.org/10.1039/d4fd00131a","url":null,"abstract":"The kinetics of particle nucleation and growth are critical to a wide variety of electrochemical systems. While studies carried out at the single particle level are promising for improving our understanding of nucleation and growth processes, conventional analytical frameworks commonly employed in bulk studies may not be appropriate for single particle experiments. Here, we present scanning electrochemical cell microsocpy (SECCM) studies of Ag nucleation and growth on carbon and indium tin oxide (ITO) electrodes. Statistical analyses of the data from these experiments reveal significant discrepancies with traditional, quasi-equilibrium kinetic models commonly employed in the analysis of particle nucleation in electrochemical systems. Time-dependent kinetic models are presented capable of appropriately analysing the data generated via SECCM to extract meaningful chemical quantities such as surface energies and kinetic rate constants. These results demonstrate a powerful new approach to the analysis of single particle nucleation and growth data which could be leveraged in differentiating behavior within spatially heterogeneous systems.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141573175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Single-molecule electrochemical imaging of 'split waves' in the electrocatalytic (EC') mechanism 对电催化(EC)机制中的 "分裂波 "进行单分子电化学成像
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-06 DOI: 10.1039/d4fd00126e
Wandong Zhao, Jin Lu
{"title":"Single-molecule electrochemical imaging of 'split waves' in the electrocatalytic (EC') mechanism","authors":"Wandong Zhao, Jin Lu","doi":"10.1039/d4fd00126e","DOIUrl":"https://doi.org/10.1039/d4fd00126e","url":null,"abstract":"We describe a single-molecule electrochemical imaging strategy to study the electrocatalytic (EC') mechanism. Using the fluorescent molecule ATTO647N at extremely low concentrations as the substrate, we confirmed its catalytic reduction to a nonfluorescence form in the presence of the mediator phenazine methosulfate (PMS) by imaging and counting fluorescent molecules. Conventional electrochemical current in cyclic voltammetry would not have allowed us to infer the existence of an EC’ process or the PMS-mediated ATTO647N reduction. Additionally, we observed shifts in the catalytic reduction potential of ATTO647N at various mediator concentrations, which agree with the theoretical predictions by Savéant. Our work offers a new perspective on connecting single-molecule EC’ behaviors with the conventional ensemble EC’ mechanism, both practically and theoretically.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141573176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advanced Algorithm for Step Detection in Single-Entity Electrochemistry: A Comparative Study of Wavelet Transforms and Convolutional Neural Networks 单实体电化学中阶跃检测的先进算法:小波变换和卷积神经网络的比较研究
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-04 DOI: 10.1039/d4fd00130c
Ziwen Zhao, Arunava Naha, Nikolaos Kostopoulos, Alina Sekretareva
{"title":"Advanced Algorithm for Step Detection in Single-Entity Electrochemistry: A Comparative Study of Wavelet Transforms and Convolutional Neural Networks","authors":"Ziwen Zhao, Arunava Naha, Nikolaos Kostopoulos, Alina Sekretareva","doi":"10.1039/d4fd00130c","DOIUrl":"https://doi.org/10.1039/d4fd00130c","url":null,"abstract":"Single-entity electrochemistry (SEE) is an emerging field within electrochemistry focused on investigating individual entities such as nanoparticles, bacteria, cells, or single molecules. Accurate identification and analysis of SEE signals require effective data processing methods for unbiased and automated feature extraction. In this study, we apply and compare two approaches for step detection in SEE data: discrete wavelet transforms (DWT) and convolutional neural networks (CNN).","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141552191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Concluding remarks: biocatalysis. 结束语:生物催化。
IF 3.3 3区 化学
Faraday Discussions Pub Date : 2024-07-03 DOI: 10.1039/d4fd00127c
Uwe T Bornscheuer
{"title":"Concluding remarks: biocatalysis.","authors":"Uwe T Bornscheuer","doi":"10.1039/d4fd00127c","DOIUrl":"https://doi.org/10.1039/d4fd00127c","url":null,"abstract":"<p><p>Biocatalysis is a rapidly evolving field with increasing impact in organic synthesis, chemical manufacturing and medicine. The <i>Faraday Discussion</i> reflected the current state of biocatalysis, covering the design of <i>de novo</i> enzymatic activities, but especially methods for the improvement of enzymes targeting a broad range of applications (<i>i.e.</i>, hydroxylations by P450 monooxygenases, enzymatic deprotection of organic compounds under mild conditions, synthesis of chiral intermediates, plastic degradation, silicone polymer synthesis, and peptide synthesis). Central themes have been how to improve an enzyme using methods of rational design and directed evolution, informed by computer modelling and machine learning, and the incorporation of new catalytic functionalities to create hybrid and artificial enzymes.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated Scanning Electrochemical Cell Microscopy Platform with Local Electrochemical Impedance Spectroscopy using Preamplifier 利用前置放大器进行局部电化学阻抗光谱分析的集成扫描电化学细胞显微镜平台
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-02 DOI: 10.1039/d4fd00122b
Ancheng Wang, Rong Jin, Dechen Jiang
{"title":"Integrated Scanning Electrochemical Cell Microscopy Platform with Local Electrochemical Impedance Spectroscopy using Preamplifier","authors":"Ancheng Wang, Rong Jin, Dechen Jiang","doi":"10.1039/d4fd00122b","DOIUrl":"https://doi.org/10.1039/d4fd00122b","url":null,"abstract":"Local electrochemical impedance spectroscopy (LEIS) has emerged to characterize local electrochemical processes on heterogeneous surfaces. However, the current LEIS heavily relies on lock-in amplifier that has a poor gain effect for weak current, limiting the achievement of high-spatial imaging. Herein, an integrated scanning electrochemical cell microscopy is developed by directly collecting the alternating current (AC) current signal through a preamplifier. The recorded local current (sub nA-level) is compared with the initial excitation signal to get the parameters for Nyquist plotting. By integrating this method into a scanning electrochemical cell microscopy (SECCM), an image of LEIS at the Indium Tin Oxide/gold (ITO/Au) electrode is obtained with a spatial resolution of 180 nm. The established SECCM platform is integrated that could be positioned into the limited space (e.g. glove box) for real characterization of electrodes.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141501891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The electrochemical modulation of single molecule fluorescence 单分子荧光的电化学调制
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-02 DOI: 10.1039/d4fd00111g
Ying Yang, Yuanqing Ma, John Justin Gooding
{"title":"The electrochemical modulation of single molecule fluorescence","authors":"Ying Yang, Yuanqing Ma, John Justin Gooding","doi":"10.1039/d4fd00111g","DOIUrl":"https://doi.org/10.1039/d4fd00111g","url":null,"abstract":"Herein is presented our discovery of an electrochemical approach for modulating fluorophores between fluorescent bright states and dim states. We demonstrate how to effectively modulate the fluorescent intensity of organic dye-labelled cell samples on an indium tin oxide surface using electrochemistry with redox-active mediators present in an oxygen scavenger buffer. We showed the electrochemical fluorescence modulation is sensitive to the applied potential and the excitation laser intensity, indicating the possibility of coupled photochemical and electrochemical reactions occurring. We also compared the electrochemical fluorescence modulation of representative oxazine, rhodamine, and cyanine dyes using ATTO 655, Alexa Fluor 488, and Alexa Fluor 647. Different dyes with distinctly different structural core show fluorescence modulation to different extents. The electrochemical fluorescence modulation will be applicable in fluorescence imaging techniques as well as biosensing.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141527889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
High Throughput calculations and machine learning modeling of $^{17}text{O}$ NMR in non-magnetic oxides 非磁性氧化物中 $^{17}text{O}$ NMR 的高通量计算和机器学习建模
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-07-01 DOI: 10.1039/d4fd00128a
Zhiyuan Li, Bo Zhao, Hongbin Zhang, Yixuan Zhang
{"title":"High Throughput calculations and machine learning modeling of $^{17}text{O}$ NMR in non-magnetic oxides","authors":"Zhiyuan Li, Bo Zhao, Hongbin Zhang, Yixuan Zhang","doi":"10.1039/d4fd00128a","DOIUrl":"https://doi.org/10.1039/d4fd00128a","url":null,"abstract":"The only NMR active oxygen isotope, Oxygen-17($^{17}text{O}$ ), serves as a sensitive probe due to its large chemical shift range, the electric field gradient at the oxygen site, and the quadrupolar interaction. Consequently, $^{17}text{O}$ solid-state NMR offers unique insights into local structures and finds significant applications in the study of disorder, reactivity, and host-guest chemistry. Despite recent advances in sensitivity enhancement, isotopic labeling, and NMR crystallography, the application of $^{17}text{O}$ solid-state NMR is still hindered by low natural abundance, costly enrichment, and challenges in handling spectrum signals. Density functional theory calculations and machine learning techniques offer an alternative approach to mapping the local crystal structures to NMR parameters. However, the lack of high-quality data remains a challenge, despite the establishment of some datasets. In this study, we implement and execute a high-throughput workflow combining AiiDA and Castep to evaluate the NMR parameters. Focusing on non-magnetic oxides, we have collected over 7100 binary, ternary, and quaternary compounds from the Materials Project and performed calculations. Furthermore, using various descriptors for the local crystalline environments, we model the $^{17}text{O}$ NMR using machine learning techniques, further enhancing our ability to predict and understand $^{17}text{O}$ NMR parameters in oxide crystals.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141527890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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