Faraday Discussions最新文献_第2页

IF 3.4 3区化学

Faraday Discussions Pub Date : 2024-09-06 DOI: 10.1039/d4fd00151f

Lyndon Emsley

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

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

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

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

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

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