{"title":"Coherent Electron Transfer in Cytochrome Nanowires at 300 K.","authors":"William W Parson,Peter J Dahl,Nikhil S Malvankar","doi":"10.1021/acs.jpclett.5c01339","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01339","url":null,"abstract":"Electron transfer in cytochrome OmcZ and OmcS \"nanowires\" is explored computationally by integrating the quantum-mechanical stochastic Liouville equation with fluctuating energies and interaction matrix elements obtained from molecular-dynamics simulations and including a detailed treatment of vibronic coupling. Electron density oscillates between adjacent hemes very rapidly relative to thermal equilibration. These oscillations last for about 1.5 ns, which is long enough for a coherent wave of electron density to travel ∼60 Å, more than the length of the proteins' subunits. The calculated rates of electron flow underestimate the measured rates but reproduce the finding that long-range diffusion of electrons is significantly faster in OmcZ than in OmcS.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"68 1","pages":"8037-8045"},"PeriodicalIF":6.475,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bingxu Wang,Bin Feng,Linpeng Lv,Shunning Li,Feng Pan
{"title":"Structural Feature Extraction via Topological Data Analysis.","authors":"Bingxu Wang,Bin Feng,Linpeng Lv,Shunning Li,Feng Pan","doi":"10.1021/acs.jpclett.5c01831","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01831","url":null,"abstract":"With the advancement of artificial intelligence models, the development of scientifically grounded and structurally appropriate feature extraction methods has become critical for machine learning-based structure prediction and materials design. In recent years, there has been growing dissatisfaction with inefficient empirical descriptors and black-box feature extraction processes that require extensive training. This article introduces a topological data analysis-based framework for extracting structural features of materials, offering an informative perspective on structure-property relationships and predictive strategies. Emphasis is placed on the predictive power and interpretability of topological features, highlighting their advantages in uncovering structure-property correlations and providing physical insights into material behavior. This approach establishes a mathematically rigorous and computationally efficient paradigm for the discovery and design of advanced materials, achieving up to 55% reduction in prediction error for defect-sensitive properties and a notable improvement in MOF gas uptake prediction accuracy (e.g., R2 from 0.74 to 0.85), thus demonstrating both theoretical clarity and practical performance.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"719 1","pages":"8056-8067"},"PeriodicalIF":6.475,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Enes Suyabatmaz, Gustavo J R Aroeira, Raphael F Ribeiro
{"title":"Polaritonic Control of Blackbody Infrared Radiative Dissociation.","authors":"Enes Suyabatmaz, Gustavo J R Aroeira, Raphael F Ribeiro","doi":"10.1021/acs.jpclett.5c01475","DOIUrl":"10.1021/acs.jpclett.5c01475","url":null,"abstract":"<p><p>Vibrational strong light-matter coupling offers a promising approach for controlling chemical reactivity with infrared microcavities. While recent research has examined potential mechanisms for this phenomenon, many important questions remain, including what type of reactions can be modified and to what extent this modification can be achieved. In this study, we explore the dynamics of Blackbody Infrared Radiative Dissociation (BIRD) in microcavities under weak and strong light-matter interaction regimes. Using a Master equation approach, we simulate the effects of infrared field confinement and polariton formation on BIRD rates for diatomic molecules weakly coupled to the radiation field. We present a framework explaining how infrared microcavities influence BIRD kinetics, highlighting the importance of overtone transitions in the process. Our findings outline conditions under which significant enhancement or mild suppression of BIRD rates can be achieved, offering insights into practical limitations and new strategies for controlling chemistry within infrared resonators.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"7530-7539"},"PeriodicalIF":4.6,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andre Pointner, Daniela Thalheim, Sarah Belasi, Lukas Heinen, Cristian Bonato, Tobias Luehmann, Jan Meijer, Rainer Tietze, Christoph Alexiou, Regine Schneider-Stock, Roland Nagy
{"title":"Optimizing SPION Labeling for Single-Cell Magnetic Microscopy.","authors":"Andre Pointner, Daniela Thalheim, Sarah Belasi, Lukas Heinen, Cristian Bonato, Tobias Luehmann, Jan Meijer, Rainer Tietze, Christoph Alexiou, Regine Schneider-Stock, Roland Nagy","doi":"10.1021/acs.jpclett.5c01446","DOIUrl":"10.1021/acs.jpclett.5c01446","url":null,"abstract":"<p><p>This study explores the correlation between the iron mass on cell surfaces and the resultant magnetic field. Human colorectal cancer cells (HT29 line) were labeled with varying concentrations of superparamagnetic iron oxide nanoparticles (SPIONs) and imaged via an NV center widefield magnetic microscope. To assess the labeling efficacy, a convolutional neural network trained on simulated magnetic dipole data was utilized to reconstruct key labeling parameters on a cell-by-cell basis, including cell diameter, sensor proximity, and the iron mass associated with surface-bound SPIONs. Our analysis provided quantitative metrics for these parameters across a range of labeling concentrations. The findings indicated that increasing the SPION concentration enhances both the cell-surface iron mass and magnetic field strength, demonstrating a saturation effect. This methodology offers a coherent framework for the quantitative, high-throughput characterization of magnetically labeled cells, presenting significant implications for the fields of cell biology and magnetic sensing applications.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"7584-7590"},"PeriodicalIF":4.6,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reaction Exploration Reveals Strong Kinetic Filtering in Li-Ion Battery Electrolyte Degradation.","authors":"Hsuan-Hao Hsu, Tianfan Jin, Brett M Savoie","doi":"10.1021/acs.jpclett.5c01123","DOIUrl":"10.1021/acs.jpclett.5c01123","url":null,"abstract":"<p><p>A solid electrolyte interphase (SEI) forms spontaneously during the first few recharging cycles of a lithium-ion battery (LIB) due to electrolyte degradation at the electrodes. The properties of the SEI critically affect the lifespan and stability of LIBs, but the degradation reactions governing SEI formation are challenging to resolve, and broadly applicable computational methods for prediction remain limited. In this study, we demonstrate that automated reaction exploration methods can predict major degradation products of common electrolytes without relying on experimental data, revealing how kinetic barriers create strong filtering effects that constrain the observable degradation chemistry from a multitude of theoretically possible pathways. The degradation chemistry of a traditional LIB electrolyte, consisting of ethylene carbonate (EC) and lithium hexafluorophosphate (LiPF<sub>6</sub>), is analyzed out to a depth of five reactions as a benchmark. Despite the multitude of theoretically possible reaction pathways, our computational chemical reaction network (CRN) reveals strong kinetic selectivity toward lithium ethylene monocarbonate (LEMC) and lithium ethylene dicarbonate (LEDC), including several previously unreported routes to these key SEI organic species. The resulting network provides a unified explanation for how reaction barriers and kinetics drive the competing formation of LEMC and LEDC and clarifies the influence of moisture on SEI aging. Generated entirely on the basis of computational transition state searches, this comprehensive CRN demonstrates the potential of reaction exploration methods to uncover mechanistic insights governed by kinetic filtering and enable rational electrolyte design.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"7685-7694"},"PeriodicalIF":4.6,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yutong Wu,Maxim Zhelyabovskiy,Zhitao Chen,Karam Eeso,Alexandros Filippas,Haochen Yang,Guang Yang,Nian Liu
{"title":"Complexing Agent-Assisted Membraneless Zinc-Iodine Aqueous Batteries.","authors":"Yutong Wu,Maxim Zhelyabovskiy,Zhitao Chen,Karam Eeso,Alexandros Filippas,Haochen Yang,Guang Yang,Nian Liu","doi":"10.1021/acs.jpclett.5c01959","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01959","url":null,"abstract":"A membrane is required for conventional zinc-iodine aqueous batteries, since soluble polyiodides cross over to the anode side and react with zinc metal spontaneously. Making the battery membraneless increases ion transport and reduces its cost and overall footprint. In this paper, a membraneless Zn-I2 aqueous battery is demonstrated, employing a complexing agent, 1-butyl-1-methylpyrrolidinium iodide (MBPI), to promote the formation of I5--containing, phase-separated polyiodides upon charging, to minimize self-discharge and suppress Zn dendrite growth. With an additional 0.3 M MBPI in 4 M ZnI2 electrolyte, the membraneless battery achieved 65 cycles with >85% Coulombic efficiency, whereas the MBPI-free control failed immediately. Additionally, a volumetric capacity of 14.3 Ah L-1 was achieved, surpassing those of most membraneless batteries reported to date regardless of redox chemistry, and underscores the potential of complexing agents in simplifying the architecture of conventional Zn-I2 flow batteries.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"208 1","pages":"8024-8028"},"PeriodicalIF":6.475,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Margareth S. Baidun, Alexander A. Kolganov, Anastassia N. Alexandrova and Evgeny A. Pidko*,
{"title":"","authors":"Margareth S. Baidun, Alexander A. Kolganov, Anastassia N. Alexandrova and Evgeny A. Pidko*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"16 30","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":4.6,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.5c01571","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737878","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}