{"title":"How the Extent of Protein Folding and Oligomerization Modulate Condensate Formation and Properties","authors":"Ilan Edelstein, Yaakov Levy","doi":"10.1021/acs.jpclett.5c02083","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c02083","url":null,"abstract":"Although proteins across the order–disorder continuum can undergo phase separation, it remains unclear how the structural states of the protein constituents influence the material properties of the resulting condensates. Here, using a coarse-grained model of a primordial peptide–RNA system, we investigate how condensates formed from ordered versus disordered peptides differ in their properties. By systematically varying the degree of foldedness and oligomerization of the peptide constituents, we find that stronger peptide–peptide interactions reduce diffusivity, whereas stronger peptide–RNA interactions destabilize the condensate. We further show that peptide conformational plasticity modulates the balance between these interactions, acting as a powerful lever for tuning the condensate properties. This work highlights how subtle changes in protein structure shape condensate architecture, dynamics, or stability and, together with experimental observations, provides a framework for understanding how the evolutionary shift from disordered to ordered peptides may have expanded the material repertoire of biomolecular condensates.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"1 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332019","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}
环境科学与技术Pub Date : 2025-10-21DOI: 10.1021/acs.est.5c12675
Kuldip Kumar,Jonathan S Grabowy,Federico Sinche Chele,Thaís Bremm Pluth,Levi L Straka,Joseph A Kozak,Dominic A Brose
{"title":"Case for Open-Source Process Control Algorithms in Wastewater Treatment to Mitigate Greenhouse Gas Emissions: A Call to Academia for Climate Action.","authors":"Kuldip Kumar,Jonathan S Grabowy,Federico Sinche Chele,Thaís Bremm Pluth,Levi L Straka,Joseph A Kozak,Dominic A Brose","doi":"10.1021/acs.est.5c12675","DOIUrl":"https://doi.org/10.1021/acs.est.5c12675","url":null,"abstract":"","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"1 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Investigation of Electrocatalytic CO2 Reduction on MXene Materials via First-Principles Simulations","authors":"Colton Lund, Jiayi Xu, Cong Liu","doi":"10.1021/acs.jpcc.5c03901","DOIUrl":"https://doi.org/10.1021/acs.jpcc.5c03901","url":null,"abstract":"Computational studies of CO<sub>2</sub> reduction to yield various products were carried out on the basal plane and edges of different MXene materials. The impact of vacancies upon Mo<sub>2</sub>TiC<sub>2</sub>T<sub><i>x</i></sub>, W<sub>2</sub>TiC<sub>2</sub>T<sub><i>x</i></sub>, and Ti<sub>3</sub>C<sub>2</sub>T<sub><i>x</i></sub> (T<sub><i>x</i></sub> = O and OH) was also examined for both edge and basal sites. Initial calibrations were carried out to generate surfaces with optimal oxide/hydroxide ratios and proper termination sites upon which various vacancy sites were explored to ensure an accurate model of the surfaces’ resting states. From this work, Mo<sub>2</sub>TiC<sub>2</sub>O was determined to exhibit the lowest theoretical overpotential for methane as determined by volcano plot analyses. At a large enough vacancy concentration, the CO<sub>2</sub> reduction reaction (CO<sub>2</sub>RR) is predicted to outcompete the hydrogen evolution reaction (HER) as the predominant reaction on the surface. When examining the edge of Mo<sub>2</sub>TiC<sub>2</sub>O, stronger CO<sub>2</sub> binding was exhibited to such an extent that the reaction was predicted to terminate after the generation of formate on the edge.","PeriodicalId":61,"journal":{"name":"The Journal of Physical Chemistry C","volume":"200 1","pages":""},"PeriodicalIF":4.126,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332020","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":"Halogenated Organic Pollutant Degradation Driven by Fe(II) Redox Chemistry.","authors":"Xuejie Zhang,Zhilin Ran,Guohuang Yao,Haizhu Guo,Rumian Zhong,Li-Zhi Huang","doi":"10.1021/acs.est.5c06123","DOIUrl":"https://doi.org/10.1021/acs.est.5c06123","url":null,"abstract":"Fe(II) species play an important role in the global biogeochemical cycles of many other elements and the degradation of organic and inorganic compounds. However, the degradation effect of Fe(II) alone on pollutants, especially on highly toxic and persistent halogenated organic pollutants (HOPs), is extremely limited. Moreover, for a long time in the past, research efforts were mainly focused on the reductive reactivity of Fe(II) under anoxic conditions. In recent years, significant breakthroughs have been achieved in the electron transfer mechanism, reactivity regulation, and application scenarios of Fe(II). The aim of this review is to summarize these latest advances and the application progress of Fe(II) in HOPs degradation. Emphasis is placed on summarizing the structure-activity relationship of Fe(II), the regulatory strategies for Fe(II) reactivity, the interaction mechanisms between Fe(II) with H2O and dissolved oxygen at the solid-liquid interface (especially the formation processes of H• and •OH), and the reduction-oxidation synergistic technologies for HOPs degradation. These research trends and significant breakthroughs regarding Fe(II) are of crucial importance for promoting Fe(II) application in diverse fields.","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"41 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Nonradiative Dynamics of [Au25(SCH3)18]− Nanoclusters: Many-Body versus Single-Particle Excited State Dynamics","authors":"Junping Xie, Wei Li, Yong Pei","doi":"10.1021/acs.jpclett.5c02926","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c02926","url":null,"abstract":"Thiolate-protected gold nanoclusters (Au NCs) have attracted significant attention for their potential in photovoltaics, photocatalysis, and photoluminescence. Realizing the full potential of these applications requires a detailed understanding of the photoinduced excited-state dynamics. Here, we investigate the nonradiative relaxation dynamics of photoexcited carriers in the prototypical [Au<sub>25</sub>(SCH<sub>3</sub>)<sub>18</sub>]<sup>−</sup> nanocluster using <i>ab initio</i> nonadiabatic molecular dynamics (NAMD) simulations, incorporating both single-particle (SP) and many-body (MB) treatments of electronic excited states. Our results reveal distinct and contrasting roles of MB effects in internal conversion and nonradiative recombination processes. In particular, MB effects accelerate the relaxation of high energy excited states to the subpicosecond time scale by enhancing nonadiabatic couplings relative to SP description. In contrast, MB treatment slows the electron–hole recombination of the lowest-lying excited states (431.8 ps vs 136.5 ps in SP), owing to the weakened nonadiabatic couplings with ground state and enhanced uphill transitions among degenerate lowest-lying excited states. Relaxation from higher-energy states involves both core-to-semiring and core-to-core transitions, whereas charge recombination predominantly proceeds via core-to-core pathways. Low-frequency vibrational modes associated with the Au(core)–Au(core) and Au(core)–Au(ring) interactions couple strongly to the nonradiative relaxation processes. Overall, inclusion of MB effects in NAMD simulations yields relaxation time scales better agreement with experiments. These findings highlight the importance of MB effects in modeling excited state dynamics of Au NCs and provide fundamental insights into relevant to their application in optoelectronic energy conversion devices.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"41 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332017","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":"Rational Design of a Metal-Free Organic Radical Cation Exhibiting Mid-IR π–π* Transition Based on the Exchange Interaction","authors":"Yuta Fujimoto, Daiki Shimizu, Kenji Matsuda","doi":"10.1021/acs.jpclett.5c02562","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c02562","url":null,"abstract":"Mid-IR (2.5–25 μm) responsive dyes, characterized by their ability to produce excitons across the electronic transition to the vibrational energy region, hold significant potential for various applications. However, the commonly used highly π-extended chromophores are inevitably too large for practical synthesis and handling. We herein demonstrate a novel molecular design strategy to control the optical band gap in the near- and mid-IR region based on small chromophores. Namely, the presented radical cation generated from a phenanthrene-based Blatter-type diradical less than 600 Da exhibits π–π* electronic transition reaching the mid-IR region to ca. 2000 cm<sup>–1</sup> (5000 nm). The mid-IR responsive chromophore was stable in solution under ambient conditions for 1 week without any observable degradation. The chromophore was designed through our “oxidation of diradical” strategy by taking advantage of a small interaction between two pseudodegenerated SOMOs of organic diradicals. EPR spectroscopy confirmed the delocalized charge and spin nature of the mid-IR responsive radical cation, supporting the assignments of the mid-IR band to a π–π* transition due to the delocalized SOMO and SUMO.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"41 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332018","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}
Katarzyna Gawlińska−Nęcek, Paweł Dąbczyński, Paweł Nuckowski, Zbigniew Starowicz, Małgorzata Kot, Piotr Panek, Jan Ingo Flege
{"title":"Crystallographic Changes Mediated by Copper Migration from Hole Transporting Layer into CsPbBr3 Perovskite","authors":"Katarzyna Gawlińska−Nęcek, Paweł Dąbczyński, Paweł Nuckowski, Zbigniew Starowicz, Małgorzata Kot, Piotr Panek, Jan Ingo Flege","doi":"10.1021/acs.jpcc.5c06144","DOIUrl":"https://doi.org/10.1021/acs.jpcc.5c06144","url":null,"abstract":"Copper oxides, due to their low cost and high ambient stability, are promising candidates for use as a hole-transporting layer (HTL) in perovskite solar cells. However, it has been found that they can be very unstable in contact with organic–inorganic FAPbI<sub>3</sub> perovskite, causing mutual chemical reactions and changing a photoactive to a nonphotoactive perovskite phase. To verify if the copper migration and the occurrence of chemical reactions are a matter of contact with a type of perovskite (organic–inorganic or fully inorganic) or the nature of copper oxides, in this work, the interface between cupric and cuprous oxides and a fully inorganic cesium lead bromide (CsPbBr<sub>3</sub>) perovskite is investigated. It is found that CsPbBr<sub>3</sub> is not robust against copper ion migration from HTL, similarly to organic–inorganic FAPbI<sub>3</sub>; however, contrary to the previous results, they do not cause chemical reactions. Instead, crystallographic lattice shrinkage of the CsPbBr<sub>3</sub> occurred along with the substitution of Pb<sup>2+</sup> by copper ions. The work explains the mechanism of this phenomenon and confirms the unreliability of copper(I) oxide and copper(II) oxide as HTLs in p-i-n perovskite solar cells based on both organic–inorganic and fully inorganic lead halide perovskites.","PeriodicalId":61,"journal":{"name":"The Journal of Physical Chemistry C","volume":"1 1","pages":""},"PeriodicalIF":4.126,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332028","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}
环境科学与技术Pub Date : 2025-10-21DOI: 10.1021/acs.est.5c07661
Liam Amery,John Tobiason,Emily Kumpel
{"title":"Methods and Uncertainty in Predictions of Arsenic Exposure and Health Outcomes for Private Well Users in Massachusetts.","authors":"Liam Amery,John Tobiason,Emily Kumpel","doi":"10.1021/acs.est.5c07661","DOIUrl":"https://doi.org/10.1021/acs.est.5c07661","url":null,"abstract":"In the United States, most people get their drinking water from public water systems, whose quality is regulated by the Safe Drinking Water Act; however, an estimated 40 million people rely on unregulated private wells. In Massachusetts ∼500,000 people are estimated to rely on private wells, but records are incomplete, and public data on private well water quality is limited. We systematically explore the uncertainty and variability in estimated statewide health outcomes resulting from using different methods for estimating the number of users of private wells, groundwater arsenic concentrations, and arsenic toxicity. We use reported water quality data to approximate arsenic concentrations for private well users in the state and compare these methods to machine learning-based groundwater prediction maps. We compare the estimated cancer cases and adverse health effects for the different methods for assigning arsenic concentrations to wells, estimating locations of wells in Massachusetts, and the updated arsenic toxicity research. We find that updated arsenic toxicity research and uncertainty in groundwater arsenic concentrations have the greatest estimated impact on the cumulative number of cancer and noncancer outcomes. In Massachusetts, private well users have potentially 3-4 times greater risk of negative health impacts from arsenic compared to community water system users, with uncertainty largely driven by lack of contaminant concentration while in community water systems driven by uncertainty in toxicity.","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"129 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander Kyrychenko,Mykyta V Prud,Kateryna O Lohachova,Oleg V Prezhdo,Oleg N Kalugin
{"title":"Native Folding Stability of the Main Protease of Coronavirus SARS-CoV-2 on a Gold Surface.","authors":"Alexander Kyrychenko,Mykyta V Prud,Kateryna O Lohachova,Oleg V Prezhdo,Oleg N Kalugin","doi":"10.1021/acs.jpclett.5c02743","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c02743","url":null,"abstract":"The main protease (Mpro) of coronavirus SARS-CoV-2 plays a critical role in viral processing and is one of the most promising targets for developing anti-COVID-19 therapeutics. Gold nanomaterials have shown essential roles in both virus detection and treatment; however, the molecular mechanisms behind their antiviral effects are not yet well understood. We provide computational insights into how enzyme-gold interactions may influence the catalytic activity of Mpro. We investigate the binding interactions and stability of the native structure of the protease after its adsorption onto a flat Au(001) surface through a series of molecular dynamics simulations. We examine three different adsorption modes of Mpro, bound to the gold surface via its domains I, II, and III, respectively. Our findings reveal that the structural changes in the native conformation of Mpro depend on the binding mode. However, unexpectedly, the structure of its active site and the three-dimensional mapping of crucial proteolytic residues His41 and Cys145 remain preserved. These insights enhance our understanding of the molecular behavior of viral proteins, demonstrating that gold-based nanomaterials can effectively target and capture important SARS-CoV-2 proteins, thereby promoting viral elimination. Additionally, our computational insights indicate that strong physical adsorption of key viral proteases onto inorganic surfaces does not necessarily lead to the distortion or unfolding of their native structures, which are essential for maintaining their biological activity.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"17 1","pages":"11222-11229"},"PeriodicalIF":6.475,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331591","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}
Rajendra Acharya,Naresh Duvva,Habtom B Gobeze,Kirk S Schanze
{"title":"Photophysical Properties of π-Conjugated Donor-Acceptor-Donor Systems: Influence of Acceptor Type and Donor Segment Length.","authors":"Rajendra Acharya,Naresh Duvva,Habtom B Gobeze,Kirk S Schanze","doi":"10.1021/acs.joc.5c02007","DOIUrl":"https://doi.org/10.1021/acs.joc.5c02007","url":null,"abstract":"We report a comparative photophysical study of thiophene-based, donor-acceptor-donor (DAD) π-conjugated oligomers incorporating thienopyrroledione (TPD), benzothiadiazole (BTD), and benzoselenadiazole (BSeD) as acceptor units. Using femtosecond and nanosecond transient absorption spectroscopy, along with steady-state optical and electrochemical measurements, we investigate how acceptor identity and conjugation length influence intersystem crossing (ISC), triplet state formation, and fluorescence behavior. The TPD series exhibit high triplet yields (up to 88%) and long triplet lifetimes (up to 185 μs), with increasing fluorescence quantum yield and lifetime as conjugation length increases. The latter trend is attributed to LUMO delocalization along the oligomer backbone, which reduces acceptor influence and suppresses ISC. In contrast, the singlet excited states of the BTD and BSeD oligomers display strong charge-transfer (CT) character, leading to significantly reduced triplet yields.","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":"17 1","pages":""},"PeriodicalIF":4.354,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331732","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}