Johanna P. Carbone, Andreas Irmler, Alejandro Gallo, Tobias Schäfer, William Z. Van Benschoten, James J. Shepherd and 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 and Andreas Grüneis","doi":"10.1039/D4FD00085D","DOIUrl":"10.1039/D4FD00085D","url":null,"abstract":"<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 <em>k</em>-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":49075,"journal":{"name":"Faraday Discussions","volume":"254 ","pages":" 586-597"},"PeriodicalIF":3.4,"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}
Magdalena Abramiuk, Carlos Acevedo-Rocha, Abdulrahman Alogaidi, Fraser Armstrong, Amulyasai Bakshi, Uwe T. Bornscheuer, Dominic J. Campopiano, Pimchai Chaiyen, Friedrich Johannes Ehinger, Sabine Flitsch, Jeremy N. Harvey, Donald Hilvert, Amanda G. Jarvis, Rhiannon E. H. Jones, Bruce R. Lichtenstein, Louis Y. P. Luk, Tara C. Lurshay, Thomas Malcomson, E. Neil G. Marsh, Neil R. McFarlane, Alexander McKenzie, Clare F. Megarity, Vicent Moliner, Adrian J. Mulholland, Ben Orton, Joelle N. Pelletier, Agata Raczyńska, Per-Olof Syrén, Sean Adeoti Thompson, Nicholas Turner, Francesca Valetti, Lu Shin Wong and Cathleen Zeymer
{"title":"Biocatalytic pathways, cascades, cells and systems: general discussion","authors":"Magdalena Abramiuk, Carlos Acevedo-Rocha, Abdulrahman Alogaidi, Fraser Armstrong, Amulyasai Bakshi, Uwe T. Bornscheuer, Dominic J. Campopiano, Pimchai Chaiyen, Friedrich Johannes Ehinger, Sabine Flitsch, Jeremy N. Harvey, Donald Hilvert, Amanda G. Jarvis, Rhiannon E. H. Jones, Bruce R. Lichtenstein, Louis Y. P. Luk, Tara C. Lurshay, Thomas Malcomson, E. Neil G. Marsh, Neil R. McFarlane, Alexander McKenzie, Clare F. Megarity, Vicent Moliner, Adrian J. Mulholland, Ben Orton, Joelle N. Pelletier, Agata Raczyńska, Per-Olof Syrén, Sean Adeoti Thompson, Nicholas Turner, Francesca Valetti, Lu Shin Wong and Cathleen Zeymer","doi":"10.1039/D4FD90023E","DOIUrl":"10.1039/D4FD90023E","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"252 ","pages":" 241-261"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015640","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}
{"title":"Charge-induced deformation of scanning electrolyte before contact","authors":"Liang Liu","doi":"10.1039/D4FD00147H","DOIUrl":"10.1039/D4FD00147H","url":null,"abstract":"<p >The recent developments in scanning electrochemical probe techniques focus on the strategy of scanning the 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 bring the electrolyte probe into 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 the electrolyte during this approaching process. For a 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 a gel electrolyte, a viscoelastic gel is analysed with a 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 the 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 a liquid, elastic and viscous moduli for a gel) and geometry (radius of the capillary for a liquid, thickness for a gel) of the electrolyte. Prospects of further extending the work closer to real experimental scenarios, especially SGECM, are also discussed.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"257 ","pages":" 240-253"},"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}
{"title":"Specialising and analysing instruction-tuned and byte-level language models for organic reaction prediction†","authors":"Jiayun Pang and Ivan Vulić","doi":"10.1039/D4FD00104D","DOIUrl":"10.1039/D4FD00104D","url":null,"abstract":"<p >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 encoder–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.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"256 ","pages":" 413-433"},"PeriodicalIF":3.4,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00104d?page=search","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Grayson F. Huldin, Junming Huang, Julius Reitemeier and Kaiyu X. Fu
{"title":"Nafion coated nanopore electrode for improving electrochemical aptamer-based biosensing†","authors":"Grayson F. Huldin, Junming Huang, Julius Reitemeier and Kaiyu X. Fu","doi":"10.1039/D4FD00144C","DOIUrl":"10.1039/D4FD00144C","url":null,"abstract":"<p >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.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"257 ","pages":" 316-332"},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00144c?page=search","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gil Alexandrowicz, Dmitri Babikov, Mark Brouard, Alexander Butler, Helen Chadwick, David W. Chandler, Michal Fárník, Jan Fingerhut, Hua Guo, Tibor Győri, Christian T. Haakansson, Dan J. Harding, Dwayne Heard, Brianna R. Heazlewood, David Heathcote, Nils Hertl, Pablo G. Jambrina, Geert-Jan Kroes, Olivia A. Krohn, Paul D. Lane, Viet Le Duc, Heather J. Lewandowski, Jérôme Loreau, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert M. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Nitish Pal, Eva Pluhařová, Christopher Reilly, Patrick Robertson, Steven J. Sibener, Chris Sparling, Vimala Sridurai, Ajeet Srivastav, Matt Strutton, Arthur G. Suits, Joshua Wagner, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec. M. Wodtke and Bum Suk Zhao
{"title":"Scattering in extreme environments: general discussion","authors":"Gil Alexandrowicz, Dmitri Babikov, Mark Brouard, Alexander Butler, Helen Chadwick, David W. Chandler, Michal Fárník, Jan Fingerhut, Hua Guo, Tibor Győri, Christian T. Haakansson, Dan J. Harding, Dwayne Heard, Brianna R. Heazlewood, David Heathcote, Nils Hertl, Pablo G. Jambrina, Geert-Jan Kroes, Olivia A. Krohn, Paul D. Lane, Viet Le Duc, Heather J. Lewandowski, Jérôme Loreau, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert M. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Nitish Pal, Eva Pluhařová, Christopher Reilly, Patrick Robertson, Steven J. Sibener, Chris Sparling, Vimala Sridurai, Ajeet Srivastav, Matt Strutton, Arthur G. Suits, Joshua Wagner, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec. M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90018A","DOIUrl":"10.1039/D4FD90018A","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 171-204"},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970078","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}
{"title":"A critical reflection on attempts to machine-learn materials synthesis insights from text-mined literature recipes","authors":"Wenhao Sun and Nicholas David","doi":"10.1039/D4FD00112E","DOIUrl":"10.1039/D4FD00112E","url":null,"abstract":"<p >Synthesis of predicted materials is the key and final step needed to realize a vision of computationally accelerated materials discovery. Because so many materials have been previously synthesized, one would anticipate that text-mining synthesis recipes from the literature would yield a valuable dataset to train machine-learning models that can predict synthesis recipes for new materials. Between 2016 and 2019, the corresponding author (Wenhao Sun) participated in efforts to text-mine 31 782 solid-state synthesis recipes and 35 675 solution-based synthesis recipes from the literature. Here, we characterize these datasets and show that they do not satisfy the “4 Vs” of data-science—that is: volume, variety, veracity and velocity. For this reason, we believe that machine-learned regression or classification models built from these datasets will have limited utility in guiding the predictive synthesis of novel materials. On the other hand, these large datasets provided an opportunity to identify anomalous synthesis recipes—which in fact did inspire new hypotheses on how materials form, which we later validated by experiment. Our case study here urges a re-evaluation on how to extract the most value from large historical materials-science datasets.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"256 ","pages":" 614-638"},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00112e?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208843","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}
Daniel J. Auerbach, Dmitri Babikov, Alexander Butler, David W. Chandler, Jan Fingerhut, Hua Guo, Dan J. Harding, David Heathcote, Nils Hertl, Bin Jiang, Geert-Jan Kroes, Paul D. Lane, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Daniel R. Moon, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, George C. Schatz, Steven J. Sibener, Ajeet Srivastav, Claire Vallance, Robert A. B. van Bree, Joshua Wagner, Gilbert C. Walker, Peter D. Watson, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao
{"title":"Scattering at condensed-phase surfaces: general discussion","authors":"Daniel J. Auerbach, Dmitri Babikov, Alexander Butler, David W. Chandler, Jan Fingerhut, Hua Guo, Dan J. Harding, David Heathcote, Nils Hertl, Bin Jiang, Geert-Jan Kroes, Paul D. Lane, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Daniel R. Moon, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, George C. Schatz, Steven J. Sibener, Ajeet Srivastav, Claire Vallance, Robert A. B. van Bree, Joshua Wagner, Gilbert C. Walker, Peter D. Watson, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90020K","DOIUrl":"10.1039/D4FD90020K","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 471-508"},"PeriodicalIF":3.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915508","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}
F. Javier Aoiz, Nadia Balucani, Astrid Bergeat, Alexander Butler, David W. Chandler, Gábor Czakó, Tibor Győri, Dwayne E. Heard, David Heathcote, Brianna R. Heazlewood, Nils Hertl, Pablo G. Jambrina, Ralf I. Kaiser, Olivia A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Jennifer Meyer, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, Christopher Reilly, Patrick Robertson, George C. Schatz, Steven J. Sibener, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao
{"title":"Scattering of larger molecules – part 2: general discussion","authors":"F. Javier Aoiz, Nadia Balucani, Astrid Bergeat, Alexander Butler, David W. Chandler, Gábor Czakó, Tibor Győri, Dwayne E. Heard, David Heathcote, Brianna R. Heazlewood, Nils Hertl, Pablo G. Jambrina, Ralf I. Kaiser, Olivia A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Jennifer Meyer, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, Christopher Reilly, Patrick Robertson, George C. Schatz, Steven J. Sibener, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90021A","DOIUrl":"10.1039/D4FD90021A","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 622-665"},"PeriodicalIF":3.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905063","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}
Harveen Kaur, Flaviano Della Pia, Ilyes Batatia, Xavier R. Advincula, Benjamin X. Shi, Jinggang Lan, Gábor Csányi, Angelos Michaelides and Venkat Kapil
{"title":"Data-efficient fine-tuning of foundational models for first-principles quality sublimation enthalpies","authors":"Harveen Kaur, Flaviano Della Pia, Ilyes Batatia, Xavier R. Advincula, Benjamin X. Shi, Jinggang Lan, Gábor Csányi, Angelos Michaelides and Venkat Kapil","doi":"10.1039/D4FD00107A","DOIUrl":"10.1039/D4FD00107A","url":null,"abstract":"<p >Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy – even with the aid of machine learning potentials – is a challenge that requires sub-kJ mol<small><sup>−1</sup></small> accuracy in the potential energy surface and finite-temperature sampling. We present an accurate and data-efficient protocol for training machine learning interatomic potentials by fine-tuning the foundational MACE-MP-0 model and showcase its capabilities on sublimation enthalpies and physical properties of ice polymorphs. Our approach requires only a few tens of training structures to achieve sub-kJ mol<small><sup>−1</sup></small> accuracy in the sublimation enthalpies and sub-1% error in densities at finite temperature and pressure. Exploiting this data efficiency, we perform preliminary <em>NPT</em> simulations of hexagonal ice at the random phase approximation level and demonstrate a good agreement with experiments. Our results show promise for finite-temperature modelling of molecular crystals with the accuracy of correlated electronic structure theory methods.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"256 ","pages":" 120-138"},"PeriodicalIF":3.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00107a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945613","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}
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
