Faraday Discussions最新文献

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NMR Crystallography 核磁共振晶体学
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-09-06 DOI: 10.1039/d4fd00151f
Lyndon Emsley
{"title":"NMR Crystallography","authors":"Lyndon Emsley","doi":"10.1039/d4fd00151f","DOIUrl":"https://doi.org/10.1039/d4fd00151f","url":null,"abstract":"Chemical function is directly related to the spatial arrangement of atoms. Consequently, the determination of atomic-level three-dimensional structures has transformed molecular and materials science over the past 60 years. In this context, solid-state NMR has emerged to become the method of choice for atomic-level characterization of complex materials in powder form. In the following we present an overview of current methods for chemical shift driven NMR crystallography, illustrated with applications to complex materials","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208830","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
Making the InChI FAIR and sustainable while moving to Inorganics 在转向无机物的同时,使 InChI 具有 FAIR 和可持续性
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-09-04 DOI: 10.1039/d4fd00145a
Gerd Blanke, Jan Brammer, Djordje Baljozovic, Nauman Khan, Frank Lange, Felix Bänsch, Clare A. Tovee, Ulrich Schatzschneider, Richard M Hartshorn, Sonja Herres-Pawlis
{"title":"Making the InChI FAIR and sustainable while moving to Inorganics","authors":"Gerd Blanke, Jan Brammer, Djordje Baljozovic, Nauman Khan, Frank Lange, Felix Bänsch, Clare A. Tovee, Ulrich Schatzschneider, Richard M Hartshorn, Sonja Herres-Pawlis","doi":"10.1039/d4fd00145a","DOIUrl":"https://doi.org/10.1039/d4fd00145a","url":null,"abstract":"The InChI (International Chemical Identifier) standard stands as a cornerstone in chemical informatics, facilitating the structure-based identification and exchange of chemical compounds across various platforms and databases. The InChI as a unique canonical line notation has made chemical structures searchable on the internet at a broad scale. The largest repositories working with InChIs contain more than 1 billion structures. Central to the functionality of the InChI is its codebase, which orchestrates a series of intricate steps to generate unique identifiers for chemical compounds. Up to now, these steps have been sparsely documented and the InChI algorithm had to be seen as a black box. For the new v1.07 release, the code has been analyzed and the major steps documented, more than 3000 bugs and security issues, as well as nearly 60 Google OSS-Fuzz issues have been fixed. New test systems have been implemented that allow users to directly test the code developments. The move to GitHub has not only made the development more transparent but will also enable external contributors to join the further development of the InChI code. Motivation for this modernisation was the urgency to treat molecular inorganic compounds by the InChI in a meaningful way. Until now, no classic string representation fulfills this need of molecular inorganic chemistry. The connection of metal bonds is by definition disconnected which makes most inorganic InChIs meaningless at the moment. Herein, we propose new routines to remedy this problem in the representation of molecular inorganic compounds by the InChI.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208832","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: Dense Ionic Fluids: Because Sometimes, More is More 结束语:致密离子液体:因为有时多多益善
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-09-02 DOI: 10.1039/d4fd00150h
Rob Atkin
{"title":"Concluding remarks: Dense Ionic Fluids: Because Sometimes, More is More","authors":"Rob Atkin","doi":"10.1039/d4fd00150h","DOIUrl":"https://doi.org/10.1039/d4fd00150h","url":null,"abstract":"It is a formidable challenge, and a distinct privilege, to provide the concluding remarks for this Faraday Discussion on Dense Ionic Fluids (DIFs). What follows is an inherently subjective distillation of the insights that have shaped our understanding of these complex systems over the last few days, with the goal of capture the essence of the Discussion and providing suggestions for future investigations in this rapidly evolving field. DIFs are a fascinating class of electrolyte systems characterized by high ion concentrations in correlated domains. The multiscale nature of DIFs, and the challenges in connecting nanoscale phenomena to bulk properties are discussed in the context of contemporary experimental and computational methods. Next, emerging trends are explored, and then the paper concludes by identifying promising future research directions.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208839","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
Introducing electron correlation in solid-state calculations for superconducting states. 在超导态的固态计算中引入电子相关。
IF 3.3 3区 化学
Faraday Discussions Pub Date : 2024-08-30 DOI: 10.1039/d4fd00073k
Wilver A Muriel, Trinidad Novoa, Carlos Cárdenas, Julia Contreras-García
{"title":"Introducing electron correlation in solid-state calculations for superconducting states.","authors":"Wilver A Muriel, Trinidad Novoa, Carlos Cárdenas, Julia Contreras-García","doi":"10.1039/d4fd00073k","DOIUrl":"https://doi.org/10.1039/d4fd00073k","url":null,"abstract":"<p><p>Analyzing the electronic localization of superconductors has been recently shown to be relevant for understanding their critical temperature [<i>Nature Communications</i>, <b>12</b>, 5381, (2021)]. However, these relationships have only been shown at the Kohn-Sham density functional theory (DFT) level, where the onset of strong correlation linked to the superconducting state is missing. In this contribution, we approximate the superconducting gap in order to reconstruct the superconducting the one-reduced density matrix (1RDM) from a DFT calculation. This allows us to analyse the electron density and localization in the strong correlation regime. The method is applied to two well-known superconductors. Electron localization features along the electron-phonon coupling directions and hydrogen cluster formations are observed for different solids. However, in both cases we see that the overall localization channels are not affected by the onset of superconductivity, explaining the ability of DFT localization channels to characterize the superconducting ones.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102305","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
Regulation of Transmembrane Current through Modulation of Biomimetic Lipid Membrane Composition 通过调节仿生脂质膜成分调节跨膜电流
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-08-23 DOI: 10.1039/d4fd00149d
Zhiwei Shang, Jing Zhao, Mengyu Yang, Yuling Xiao, Wenjing Chu, Yilin Cai, Xiaoqing Yi, Meihua Lin, Fan Xia
{"title":"Regulation of Transmembrane Current through Modulation of Biomimetic Lipid Membrane Composition","authors":"Zhiwei Shang, Jing Zhao, Mengyu Yang, Yuling Xiao, Wenjing Chu, Yilin Cai, Xiaoqing Yi, Meihua Lin, Fan Xia","doi":"10.1039/d4fd00149d","DOIUrl":"https://doi.org/10.1039/d4fd00149d","url":null,"abstract":"Ion transport through biological channels is influenced not only by the structural properties of the channels themselves but also by the composition of the phospholipid membrane, which acts as a scaffold for these nanochannels. Drawing inspiration from how lipid membrane composition modulates ion currents, as seen in the activation of the K+ channel in Streptomyces A (KcsA) by anionic lipids, we propose a biomimetic nanochannel system that integrates DNA nanotechnology with two-dimensional graphene oxide (GO) nanosheets. By modifying the length of the multibranched DNA nanowires generated through the hybridization chain reactions (HCR) and varying the concentration of the linker strands that integrate these DNA nanowire structures with the GO membrane, the composition of the membrane can be effectively adjusted, consequently impacting ion transport. This method provides a strategy for developing devices with highly efficient and tunable ion transport, suitable for applications in mass transport, environmental protection, biomimetic channels, and biosensors.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208841","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
Prediction rigidities for data-driven chemistry 数据驱动化学的预测刚性
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-08-23 DOI: 10.1039/d4fd00101j
Sanggyu Chong, Filippo Bigi, Federico Grasselli, Philip Loche, Matthias Kellner, Michele Ceriotti
{"title":"Prediction rigidities for data-driven chemistry","authors":"Sanggyu Chong, Filippo Bigi, Federico Grasselli, Philip Loche, Matthias Kellner, Michele Ceriotti","doi":"10.1039/d4fd00101j","DOIUrl":"https://doi.org/10.1039/d4fd00101j","url":null,"abstract":"The widespread application of machine learning (ML) to the chemical sciences is making it very important to understand how the ML models learn to correlate chemical structures with their properties, and what can be done to improve the training efficiency whilst guaranteeing interpretability and transferability. In this work, we demonstrate the wide utility of prediction rigidities, a faimily of metrics derived from the loss function, in understanding the robustness of ML model predictions. We show that the prediction rigidities allow the assessment of the model not only at the global level, but also on the local or the component-wise level at which the intermediate (e.g. atomic, body-ordered, or range-separated) predictions are made. We leverage these metrics to understand the learning behavior of different ML models, and to guide efficient dataset construction for model training. We finally implement the formalism for a ML model targeting a coarse-grained system to demonstrate the applicability of the prediction rigidities to an even broader class of atomistic modeling problems.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208831","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
CO adsorption on Pt(111) studied by periodic coupled cluster theory. 利用周期耦合团簇理论研究 CO 在 Pt(111) 上的吸附。
IF 3.3 3区 化学
Faraday Discussions Pub Date : 2024-08-22 DOI: 10.1039/d4fd00085d
Johanna P Carbone, Andreas Irmler, Alejandro Gallo, Tobias Schäfer, William Z Van Benschoten, James J Shepherd, Andreas Grüneis
{"title":"CO adsorption on Pt(111) studied by periodic coupled cluster theory.","authors":"Johanna P Carbone, Andreas Irmler, Alejandro Gallo, Tobias Schäfer, William Z Van Benschoten, James J Shepherd, Andreas Grüneis","doi":"10.1039/d4fd00085d","DOIUrl":"10.1039/d4fd00085d","url":null,"abstract":"<p><p>We present an application of periodic coupled-cluster theory to the calculation of CO adsorption energies on the Pt(111) surface for different adsorption sites. The calculations employ a range of recently developed theoretical and computational methods. In particular, we use a recently introduced coupled-cluster ansatz, denoted as CCSD(cT), to compute correlation energies of the metallic Pt surface with and without adsorbed CO molecules. The convergence of Hartree-Fock adsorption energy contributions with respect to randomly shifted <i>k</i>-meshes is discussed. Recently introduced basis set incompleteness error corrections make it possible to achieve well-converged correlation energy contributions to the adsorption energies. We show that CCSD(cT) theory predicts the correct order of adsorption energies for the considered adsorption sites. Furthermore, we find that binding of the CO molecule to the top and fcc site is dominated by Hartree-Fock and correlation energy contributions, respectively.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11339635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Charge induced deformation of scanning electrolyte before contact 接触前扫描电解质的电荷诱导变形
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-08-20 DOI: 10.1039/d4fd00147h
Liang Liu
{"title":"Charge induced deformation of scanning electrolyte before contact","authors":"Liang Liu","doi":"10.1039/d4fd00147h","DOIUrl":"https://doi.org/10.1039/d4fd00147h","url":null,"abstract":"The recent developments of scanning electrochemical probe techniques focus on the strategy of scanning electrolyte. For example, scanning electrochemical cell microscopy (SECCM) is based on holding the electrolyte in a glass capillary, while scanning gel electrochemical microscopy (SGECM) immobilizes the gel electrolyte on micro-disk electrodes or etched metal wires. In both SECCM and SGECM, the first and essential step is to approach the electrolyte probe to be in contact with the sample, which is very often achieved by current feedback with a constant applied potential between the probe and the sample. This work attempts to theoretically analyse the deformation of electrolyte during this approaching process. For liquid electrolyte in SECCM, surface tension is considered to counterbalance the gravity and electrostatic force in 2D cylindrical coordinates with axial symmetry. The deformation at equilibrium is solved under certain conditions. For gel electrolyte, a viscoelastic gel is analysed with simplified 1D geometry. Both equilibrium and dynamic approaching are considered. The results suggest that for both liquid and gel electrolytes, critical conditions exist for breaking the equilibrium. When applied potential is higher or the distance is lower than the threshold, the force will not equilibrate and the electrolyte will deform until contact. The critical condition depends on the properties (surface tension for liquid, elastic and viscous modulus for gel) and geometry (radius of capillary for liquid, thickness for gel) of electrolyte. Prospects of further extending the work closer to real experimental scenarios, especially SGECM, are also discussed.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208842","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
Specialising and Analysing Instruction-Tuned and Byte-Level Language Models for Organic Reaction Prediction 针对有机反应预测的指令调整和字节级语言模型的专业化与分析
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-08-19 DOI: 10.1039/d4fd00104d
Jiayun Pang, Ivan Vulić
{"title":"Specialising and Analysing Instruction-Tuned and Byte-Level Language Models for Organic Reaction Prediction","authors":"Jiayun Pang, Ivan Vulić","doi":"10.1039/d4fd00104d","DOIUrl":"https://doi.org/10.1039/d4fd00104d","url":null,"abstract":"Transformer-based encoder-decoder models have demonstrated impressive results in chemical reaction prediction tasks. However, these models typically rely on pretraining using tens of millions of unlabelled molecules, which can be time-consuming and GPU-intensive. One of the central questions we aim to answer in this work is: Can FlanT5 and ByT5, the encode-decoder models pretrained solely on language data, be effectively specialised for organic reaction prediction through task-specific fine-tuning? We conduct a systematic empirical study on several key issues of the process, including tokenisation, the impact of (SMILES-oriented) pretraining, fine-tuning sample efficiency, and decoding algorithms at inference. Our key findings indicate that although being pretrained only on language tasks, FlanT5 and ByT5 provide a solid foundation to fine-tune for reaction prediction, and thus become 'chemistry domain compatible' in the process. This suggests that GPU-intensive and expensive pretraining on a large dataset of unlabelled molecules may be useful yet not essential to leverage the power of language models for chemistry. All our models achieve comparable Top-1 and Top-5 accuracy although some variation across different models does exist. Notably, tokenisation and vocabulary trimming slightly affect final performance but can speed up training and inference; The most efficient greedy decoding strategy is very competitive while only marginal gains can be achieved from more sophisticated decoding algorithms. In summary, we evaluate FlanT5 and ByT5 across several dimensions and benchmark their impact on organic reaction prediction, which may guide more effective use of these state-of-the-art language models for chemistry-related tasks in the future.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208840","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
Nafion Coated Nanopore Electrode for Improving Electrochemical Aptamer-Based Biosensing Nafion 涂层纳米孔电极用于改进基于电化学色聚体的生物传感
IF 3.4 3区 化学
Faraday Discussions Pub Date : 2024-08-14 DOI: 10.1039/d4fd00144c
Grayson Huldin, Junming Huang, Julius Reitemeier, Kaiyu Fu
{"title":"Nafion Coated Nanopore Electrode for Improving Electrochemical Aptamer-Based Biosensing","authors":"Grayson Huldin, Junming Huang, Julius Reitemeier, Kaiyu Fu","doi":"10.1039/d4fd00144c","DOIUrl":"https://doi.org/10.1039/d4fd00144c","url":null,"abstract":"The transition to a personalized point-of-care model in medicine will fundamentally change the way medicine is practiced, leading to better patient care. Electrochemical biosensors based on structure-switching aptamers can contribute to this medical revolution due to the feasibility and convenience of selecting aptamers for specific targets. Recent studies have reported that nanostructured electrodes can enhance the signals of aptamer-based biosensors. However, miniaturized systems and body fluid environments pose challenges such as signal-to-noise ratio reduction and biofouling. To address these issues, researchers have proposed various electrode coating materials, including zwitterionic materials, biocompatible polymers, and hybrid membranes. Nafion, a commonly used ion exchange membrane, is known for its excellent permselectivity and anti-biofouling properties, making it a suitable choice for biosensor systems. However, the performance and mechanism of Nafion-coated aptamer-based biosensor systems have not been thoroughly studied. In this work, we present a Nafion-coated gold nanoporous electrode, which excludes Nafion from the nanoporous structures and allows the aptamers immobilized inside the nanopores to freely detect chosen targets. The nanopore electrode is formed by a sputtering and dealloying process, resulting in a pore size in tens of nanometers. The biosensor is optimized by adjusting the electrochemical measurement parameters, aptamer density, Nafion thickness, and nanopore size. Furthermore, we propose an explanation for the unusual signaling behavior of the aptamers confined within the nanoporous structures. This work provides a generalizable platform to investigate membrane-coated aptamer-based biosensors.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226558","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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