化学•材料最新文献

{"title":"From MM-PBSA to H-MMGB: Multiscale Modeling for Biomolecular Structure and Drug Discovery.","authors":"Matthew R Lee","doi":"10.1021/acs.jpcb.5c05744","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05744","url":null,"abstract":"<p><p>From early efforts to predict protein structure from simplified models, computational biophysics has progressed toward increasingly physics-based approaches for evaluating biomolecular structure, molecular interactions, and energetics. The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method provided one of the first broadly accessible ways to evaluate binding and folding energetics from molecular dynamics (MD) trajectories, with applications ranging from protein structure prediction benchmarks to protein-ligand affinity ranking. Building on this foundation, the hierarchical Molecular Mechanics Generalized Born (H-MMGB) approach was developed to provide MMGB-based binding free energy estimates more efficiently, employing the Generalized Born model in contrast to the Poisson-Boltzmann framework of MM-PBSA and thereby enabling prospective applications to ligand design. Case studies illustrate how these methods, ranging from protein folding assessment to intact-ligand modeling and to a deconstruction-reconstruction strategy using picofragments, enable hypothesis generation in the absence of experimental structures and in challenging protein-protein interaction targets. Together, these developments support a guiding principle: gradual incorporation of more physics into modeling workflows increases the probability of successfully meeting objectives across diverse computational simulation problems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327923","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":"Nuclear Quantum Effects in OH*/OD* Formation Kinetics on Pd(332): A Ring-Polymer Molecular Dynamics Study.","authors":"Liang Zhang,Chen Li,Michael Schwarzer,Dmitriy Borodin,Alec M Wodtke,Hua Guo","doi":"10.1021/acs.jpclett.5c02891","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c02891","url":null,"abstract":"A complete understanding of kinetics of heterogeneous catalysis requires accurate calculations of reaction rates for surface reactions, which is coverage-dependent. In this letter, a ring-polymer molecular dynamics investigation is carried out for a key step in the Pd-catalyzed hydrogen oxidation, namely, the formation of OH from adsorbed H and O species at both high and low coverages on Pd(332). It is found that the calculated rate coefficients agree with the recently reported experimental data. In addition, significant nuclear quantum effects are found even at relatively high temperatures.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"41 1","pages":"11175-11182"},"PeriodicalIF":6.475,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319100","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":"IITRS: A Promiscuous Enzyme Synchronizing β-Lactamase with Esterase.","authors":"Abirlal Mukherjee, Jyoti Barman, Rajsekhar Adhikary, Kunal Dhankhar, Sourya Bhattacharya, Niteesh Kumar Pandey, Ayushi Singh, Saugata Hazra","doi":"10.1021/acs.biochem.5c00384","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00384","url":null,"abstract":"<p><p>This study reveals dual catalytic activities (β-lactamase and esterase) in a new penicillin-recognizing protein (IITRS), found in two closely related species, <i>Enterococcus faecium</i> and <i>Enterococcus lactis</i>. IITRS is distinct from other β-lactamase classes, showing only limited structural and functional similarity to class C β-lactamases. The conserved KTG motif, which helps in substrate recognition in class C, is not present in this enzyme. The enzyme is different from class C in terms of different conserved loops, such as R₂ and Ω loops, which are involved in the recognition, specificity, and hydrolysis of β-lactams. Nevertheless, the involvement of Ser64 and Tyr150 residues in β-lactam hydrolysis as found in class C enzymes has been demonstrated by site-directed mutagenesis. The study also highlights Tyr150 from the catalytic triad Tyr-Asp-Lys as being responsible for the esterase activity. This dual functionality confers catalytic promiscuity, enabling IITRS to function through two different mechanisms. The enzyme exhibits hydrolysis of <i>p</i>-NP esters (acetate, butyrate, hexanoate, decanoate, and laurate) displaying progressively higher activity with increasing alkyl chain lengths. Since Tyr150 has been found as a common ligand-binding residue for both of the activities, the β-lactamase inhibition by diisopropyl fluorophosphate (DFP), a reported inhibitor of bacterial esterase, also has been demonstrated. This promising albeit unexplored biocatalyst also might be used in the production of chiral compounds, investigating its enantioselective nature similar to other bacterial esterases. Overall, this research upholds a new promiscuous enzyme and proposes a distinct active site, narrower than that of a β-lactamase and wider than that of an esterase.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formation of Distinct Isomers via Chemical Reaction in a Supersonic Jet: The Reaction of Sulfur Trioxide and Thioacetic Acid Studied by Rotational Spectroscopy.","authors":"Aaron J Reynolds, Kenneth J Koziol, Victor Drewanz, Luis R Padilla, Kenneth R Leopold","doi":"10.1021/acs.jpca.5c06025","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c06025","url":null,"abstract":"<p><p>The reaction between sulfur trioxide (SO₃) and thioacetic acid (thiol form, CH₃COSH) is studied by microwave spectroscopy in a supersonic jet. With multiple isotopic substitutions, and supported by MP2 and density functional theory calculations, the spectra unambiguously establish the formation of two distinct isomers. The first, denoted the O-S isomer, is CH₃C(=S)OSO₂OH and involves a new bond between the oxygen of the thioacetic acid and the sulfur of the SO₃. The second, denoted the S-S isomer, CH₃C(=O)SSO₂OH, involves the new bond between the sulfur of the acid and the sulfur of the SO₃. The O-S isomer is entirely analogous to the product identified in previous studies of the RCOOH + SO₃ and C₆H₅COSH + SO₃ reactions, but the formation of the S-S isomer is new. Calculations place the S-S isomer ∼8 kcal/mol lower in energy than the O-S form, suggesting that the latter is a kinetically controlled product. The mechanism by which the S-S isomer forms is unclear but may involve either a set of independent pathways or initial formation of the O-S isomer, followed by rapid rearrangement. Participation by a third body is likely. Without input from an external energy source, the formation of two isomers in a supersonic expansion is unusual.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327884","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":"Influence of Silicon Content on the Thermal/Mechanical Performance of Urea–Formaldehyde Fibers","authors":"Kai Yang,&nbsp;Jinbiao Ding,&nbsp;Muen Yang,&nbsp;Jiarui Cao,&nbsp;Yang Liu,&nbsp;Pengyu Li,&nbsp;Mingli Jiao","doi":"10.1134/S1560090425600883","DOIUrl":"10.1134/S1560090425600883","url":null,"abstract":"<p>Silicon-modified urea–formaldehyde fibers (SiUFF) were prepared by adding different proportions of phenyltriethoxysilane to urea–formaldehyde resin, which were then subjected to dry-spinning and curing treatment. The SiUFF were characterized by Fourier infrared spectroscopy, micro-infrared analysis and ¹³C nuclear magnetic resonance analysis (¹³C NMR). It was found that the element silicon existed in the form of Si–O bond in the SiUFF, and the hydroxymethyl group cross-linked with the amino group to form methylene at the curing stage, while internal thermal conduction caused surface crosslinking density to exceed that of the fiber core. Optimal performance of SiUFF was achieved with 4 wt % Si-modifier addition, cured at 190°C for 30 min, exhibiting an elongation at break of 7.1%, a tensile strength reaching 389 MPa and a char yield of 30.01% at 1000°C, which represented significant improvements of 96, 92, and 14.2%, respectively compared to the unmodified urea–formaldehyde fiber.</p>","PeriodicalId":739,"journal":{"name":"Polymer Science, Series B","volume":"67 2","pages":""},"PeriodicalIF":1.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Quantitative Environmental Risk Assessment for Microplastics in Sewage Sludge Applied to Land.","authors":"Paul Boisseaux,Marie Laure Delignette-Muller,Tamara Galloway","doi":"10.1021/acs.est.5c08026","DOIUrl":"https://doi.org/10.1021/acs.est.5c08026","url":null,"abstract":"The application of sewage sludge to land delivers high levels of microplastics (MPs), contributing to soil contamination and chronic effects on soil biota. Despite this, the quantitative chronic risk assessment of MPs in sludge-amended soils (SAS) to soil biota has not been thoroughly addressed, and none has been done directly on sludge samples. Here, we combined environmental exposure and species sensitivity distributions, built on published data, with two-dimensional Monte Carlo simulations to characterize the risk from MPs in sludge samples and in SAS, testing worst-case and realistic case scenarios of sludge behavior in soil. Contamination with MPs frequently exceeded the concentration likely to affect more than 5% of the species. Risk characterization showed that the worst-case MP scenario affects 39% of species, while the realistic scenario affects 15-18% of soil species, implying that the current state of sludge application fails to protect 95% of soil biota. The percentage of species affected by MPs approximately doubled in SAS. Our conservative results suggest that regulatory limits on MPs in sludge being applied to land should be urgently considered.","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"15 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319296","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":"Electrochemical Synthesis of 3,5-Disubstituted Pyrazoles from Ynone Hydrazones via Diselenide-Catalyzed Cyclization Strategy.","authors":"Zhouting Zeng,Feng Zhao,Huimei Zhong,Zi Yang,Huaixin Wei,Songwen Ji,Mingming Yu,Jinhui Cai","doi":"10.1021/acs.joc.5c02108","DOIUrl":"https://doi.org/10.1021/acs.joc.5c02108","url":null,"abstract":"Given the existing limitations of traditional methods for the synthesis of pyrazole derivatives, developing new, mild, and efficient approach toward pyrazole skeletons is necessary. Herein, we report an electrochemically driven diselenide-catalyzed cyclization of 1,3-disubstituted prop-2-yn-1-one hydrazones that realize the rapid synthesis of 3,5-disubstituted pyrazoles under metal-free, oxidant-free, and base-free conditions. The practical utility of this method is underscored by its wide substrate scope, high tolerance toward various functional groups, high efficiency, mild conditions, gram-scale synthesis, and diverse derivatizations. Furthermore, the preliminary mechanistic experiments indicate that this reaction possibly proceeds via a cationic pathway.","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":"95 1","pages":""},"PeriodicalIF":4.354,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319174","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":"Synthesis and Properties of Covalently Crosslinked Hydrogels Based on Arabinogalactan Polyaldehyde and Tartaric and Glutaric Dihydrazides","authors":"R. Kh. Mudarisova,&nbsp;L. A. Badykova,&nbsp;G. R. Mingaleeva,&nbsp;V. Z. Mingaleev","doi":"10.1134/S1560090425600810","DOIUrl":"10.1134/S1560090425600810","url":null,"abstract":"<p>New hydrogels based on arabinogalactan polyaldehyde and glutaric and tartaric dihydrazides have been synthesized. Arabinogalactan polyaldehyde was synthesized via periodate oxidation and characterized by NMR, IR, and UV spectroscopy. The synthesis of hydrogels is based on a click reaction between the aldehyde groups of oxidized arabinogalactan and the amino groups of crosslinking agents, yielding Schiff bases in crosslinks. The effect of hydroxyl groups of the crosslinking agent on the properties of the resulting hydrogels was investigated. It was found that the hydrogels formed using glutaric dihydrazide, which does not contain hydroxyl groups, exhibit a lower elastic response in the frequency rheology test and lower shear modulus compared to hydrogels crosslinked with tartaric dihydrazide. The use of hydroxyl-containing tartaric dihydrazide as a crosslinking agent allows the synthesis of hydrogels with good mechanical properties and high hydrolytic stability in both neutral and acidic media. A distinctive feature of the hydrogels obtained is their resistance to swelling at various pH values, which decreases slightly after hydrogels treatment with sodium borohydride. The effect of arabinogalactan oxidation conditions on the properties of the hydrogels is also discussed.</p>","PeriodicalId":739,"journal":{"name":"Polymer Science, Series B","volume":"67 2","pages":""},"PeriodicalIF":1.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic Insights into Chemoselectivity in Nickel-Catalyzed Arylation of Competitive Nucleophilic Systems: A DFT Perspective.","authors":"Chao Shan, Zhiqiang Zhang, Wanli Cheng, Xuexiang Ma, Ranran Li","doi":"10.1021/acs.jpca.5c04513","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04513","url":null,"abstract":"<p><p>Nickel-catalyzed cross-coupling of alcohols or amines with aryl electrophiles enables the selective arylation of complex substrates bearing competing nucleophilic groups without resorting to protective groups. In this study, the mechanisms underlying such competitive arylation reactions are investigated using DFT calculations to elucidate the origins of chemoselectivity. The results identify reductive elimination as the rate-limiting step, with chemoselectivity primarily governed by kinetic control. The dominant factor influencing the selectivity in various contending alcohols is the steric hindrance around the hydroxyl O atom. Diols exhibit selective primary <i>O</i>-arylation due to stronger d-p interactions between the alkoxide and the nickel-bisphosphine fragment in both reactant intermediates and transition states. Steric hindrance predominantly dictates <i>O</i>- versus <i>N</i>-arylation selectivity when alcohols and arylamines compete, whereas both steric and electronic effects collectively determine the preference for <i>N</i>-arylation when alcohols compete with alkylamines. Moreover, the selective <i>O</i>-arylation of amino alcohols is attributed to stronger noncovalent interactions between C and O. These mechanistic insights facilitate developing selective arylation methodologies for competitive nucleophilic systems.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327858","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":"Ethylene Polymerization and Copolymerization Reactions with a Catalyst Based on the Ti(IV) Complex with a Diolate Ligand","authors":"L. A. Rishina,&nbsp;Y. V. Kissin,&nbsp;S. S. Lalayan,&nbsp;V. G. Krasheninnikov,&nbsp;S. S. Gusarov,&nbsp;A. S. Zabolotnov,&nbsp;A. A. Gulin,&nbsp;V. A. Tuskaev,&nbsp;S. Ch. Gagieva,&nbsp;B. M. Bulychev","doi":"10.1134/S1560090425600871","DOIUrl":"10.1134/S1560090425600871","url":null,"abstract":"<p>A novel catalyst system containing a complex of Ti(IV) with a bidentate diolate ligand and a binary Al(C₂H₅)₂Cl/Mg(C₄H₉)₂ activator at a molar [Al]/[Mg] ratio of ~3 affords the synthesis of high-molecular weight polyethylene and ethylene copolymers with 1-hexene, 1-octene and 1-decene. Kinetic analysis shows that the catalyst contains two families of active centers, unstable and stable. The unstable centers, which dominate at the early stages of the polymerization reactions, produce polymers of high molecular weight and narrow molecular weight distribution (<i>M</i>_w/<i>M</i>_n ~ 2.5), similarly to alkene polymers prepared with several soluble metallocene and post-metallocene catalysts. The stable active centers produce polymers of lower molecular weight and broad molecular weight distribution, which is more typical for polymers produced with heterogeneous catalysts.</p>","PeriodicalId":739,"journal":{"name":"Polymer Science, Series B","volume":"67 2","pages":""},"PeriodicalIF":1.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145327522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}