化学•材料最新文献

{"title":"The influence of membrane curvature on insulin aggregation","authors":"Xiaoqi Ye ,&nbsp;Jillian Madine ,&nbsp;Heike Arnolds","doi":"10.1016/j.colsurfb.2025.114914","DOIUrl":"10.1016/j.colsurfb.2025.114914","url":null,"abstract":"<div><div>Insulin can form fibrils at the injection site in diabetic patients and is often used as a model for understanding protein aggregation properties, particularly the role of membranes. Here, we employ a range of spectroscopies and molecular dynamics simulations to understand differences in aggregation speed and structure of fibrils formed in the absence and presence of lipid vesicles, and influence of membrane curvature. We show that human insulin aggregation is accelerated in the presence of phosphatidylcholine vesicles, with small unilamellar vesicles accelerating aggregation more than large vesicles. Insulin fibrils formed in the presence of lipid vesicles have a more ordered β-sheet structure than those formed from bulk solution, which is not influenced by vesicle curvature as shown by vibrational spectroscopy. Changes in hydrogen bonding of the lipid phosphate and glycerol bonds within the lipid vesicles indicate that native insulin becomes embedded within the lipid headgroups. Molecular dynamics simulations confirm an increased residence time of insulin with increasing number of lipid packing defects and reveal the presence of three insulin adsorption states with different orientations. Our results suggest that a reduction in membrane damage can reduce insulin amyloid formation.</div></div>","PeriodicalId":279,"journal":{"name":"Colloids and Surfaces B: Biointerfaces","volume":"255 ","pages":"Article 114914"},"PeriodicalIF":5.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144501266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine Learning and Large Language Models for Modeling Complex Toxicity Pathways and Predicting Steroidogenesis.","authors":"Thomas R Lane, Patricia A Vignaux, Joshua S Harris, Scott H Snyder, Fabio Urbina, Sean Ekins","doi":"10.1021/acs.est.5c04054","DOIUrl":"https://doi.org/10.1021/acs.est.5c04054","url":null,"abstract":"<p><p>High-throughput screening and computational models have been effective in predicting chemical interactions with estrogen and androgen receptors, but similar approaches for steroidogenesis remain limited. To address this gap, we developed general steroidogenesis modulation models using data from ∼1,800 chemicals screened in H295R human adrenocortical carcinoma cells. A random forest model was validated using a prospective test set of 20 compounds (14 predicted active, 6 inactive), achieving 80% accuracy with conformal prediction adjustments. In parallel, we built classification and regression models based on IC₅₀ data from ChEMBL for key steroidogenic enzymes, including CYP17A1, CYP21A2, CYP11B1, CYP11B2, 17β-HSD (1/2/3/5), 5α-reductase (1/2), and CYP19A1 (126-9,327 compounds per target). These models enable predictions of both general steroidogenesis inhibition and potential molecular targets. Additionally, we developed a transformer-based model (MolBART) to predict all end points simultaneously and validated this performance. Combined, these models may offer a rapid and scalable system for assessing chemical impacts on steroidogenesis, supporting chemical risk assessment, product stewardship, and regulatory decision-making.</p>","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504056","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":"Near Infrared Light-Triggered Small Molecule Chemical Reactions in Biocompatible Systems.","authors":"Jie Zhong, Yuhang Li, Xiaotong Li, Feng Liang, Ran Tao, Shan Qian, Xinyuan Fan","doi":"10.1021/acs.bioconjchem.5c00293","DOIUrl":"https://doi.org/10.1021/acs.bioconjchem.5c00293","url":null,"abstract":"<p><p>Near-infrared (NIR) light, within the 700-1000 nm therapeutic optical window, offers deep tissue penetration, low photocytotoxicity, and minimal side effects, making it ideal for remote control of biocompatible reactions in vivo. This review explores recent advances in NIR-triggered reactions, focusing on direct and indirect activation strategies. Direct approaches utilize NIR-responsive protecting groups, while indirect methods employ upconversion materials and photocatalysis to overcome NIR's energy limitations. These innovations expand noninvasive in vivo control capabilities. Applications include NIR-mediated drug delivery, biological molecule activation, and proximity labeling for protein interaction studies. Such reactions enable precise modulation of biological events under native conditions. The review highlights the potential of integrating advanced nanomaterials and optimizing indirect activation techniques to enhance reaction efficiency. It also emphasizes the requirement for interdisciplinary collaboration to refine NIR-responsive systems and facilitate clinical translation. By showcasing state-of-the-art NIR-controlled chemistry and identifying key areas for future research, this work aims to inspire advancements in biomedical research and therapeutics. Addressing the challenges of in vivo chemical control, this review positions NIR chemistry as a critical component in the evolution of biocompatible reaction methodologies.</p>","PeriodicalId":29,"journal":{"name":"Bioconjugate Chemistry","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504142","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":"Two-Photon Circular Dichroism in the Algebraic Diagrammatic Construction Framework.","authors":"Antonia Papapostolou, Friederike Schneider, Dirk R Rehn, Andreas Dreuw","doi":"10.1021/acs.jpca.5c02108","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c02108","url":null,"abstract":"<p><p>We present the calculation of the rotatory strengths of two-photon circular dichroism (TPCD) in the framework of algebraic diagrammatic construction (ADC) using the intermediate state representation (ISR). First, the differences between the length-gauge formulation of TPCD and three gauge-origin invariant approaches are investigated depending on the order of perturbation theory and the basis set. Subsequently, our ADC/ISR results are compared with results of corresponding coupled cluster methods from the literature. The calculations were performed with the recently published Python package responsefun and show that the user can calculate arbitrary sum-over-states expressions without requiring knowledge of ADC theory. The treatment of response properties with the ADC/ISR approach is computationally feasible up to the third order of perturbation theory, and thus this methodology represents a valuable addition to highly accurate <i>ab initio</i> benchmark methods.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504224","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":"Approximation of Anisotropic Pair Potentials Using Multivariate Interpolation.","authors":"Mohammadreza Fakhraei, Chris A Kieslich, Michael P Howard","doi":"10.1021/acs.jpcb.5c01451","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01451","url":null,"abstract":"<p><p>The interaction between two particles with shape or interaction anisotropy can be modeled by using a pairwise potential energy function that depends on their relative position and orientation; however, this function is often challenging to mathematically formulate. Data-driven approaches for approximating anisotropic pair potentials have gained significant interest due to their flexibility and generality but often require large sets of training data, potentially limiting their feasibility when training data are computationally demanding to collect. Here, we investigate the use of multivariate polynomial interpolation to approximate anisotropic pair potentials from a limited set of prescribed particle configurations. We consider both standard Chebyshev polynomial interpolation and mixed-basis polynomial interpolation that uses trigonometric polynomials for coordinates along which the pair potential is known to be periodic. We exploit mathematical reasoning and physical knowledge to refine the interpolation domain and to design our interpolants. We test our approach on two-dimensional and three-dimensional model anisotropic nanoparticles, finding that satisfactory approximations can be constructed in all cases.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504225","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":"Cation-π Interactions in Biomolecular Contexts by Neutron Scattering and Molecular Dynamics: A Case Study of the Tetramethylammonium Cation.","authors":"Matej Cervenka, Brennon L Shanks, Philip E Mason, Pavel Jungwirth","doi":"10.1021/acs.jpcb.5c02001","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02001","url":null,"abstract":"<p><p>Cation-π interactions involving the tetramethylammonium motif are prevalent in biological systems, playing crucial roles in membrane protein function, DNA expression regulation, and protein folding. However, accurately modeling cation-π interactions where electronic polarization plays a critical role is computationally challenging, especially in large biomolecular systems. This study implements a physically justified electronic continuum correction (ECC) to the CHARMM36 force field, scaling ionic charges by a factor of 0.75 to effectively account for electronic polarization without additional computational overhead. This approach, while not specifically designed for cation-π interactions, is shown here to significantly improve predictions of the structure of an aqueous tetramethylammonium-pyridine complex as compared to neutron diffraction data. This result, together with computational predictions for the structure of the aqueous tetramethylammonium-phenol complex, underscores the potential of ECC as a versatile method to improve the description of cation-π interactions in biomolecular simulations.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504226","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":"Reactions of <i>N</i>,<i>O</i>- and <i>N</i>,<i>S</i>-Azoles and -Azolines with Ozone: Kinetics and Mechanisms.","authors":"Simon A Rath, Valentin Rougé, Julie Tolu, Daniel Rentsch, Maria Lia Halder, Urs von Gunten","doi":"10.1021/acs.est.5c01323","DOIUrl":"https://doi.org/10.1021/acs.est.5c01323","url":null,"abstract":"<p><p><i>N</i>,<i>O</i>- and <i>N</i>,<i>S</i>-azoles and -azolines are common functional groups in pharmaceuticals, agrochemicals and natural products. Their fate during ozone-based water treatment processes is unknown due to a lack of kinetic and mechanistic information on their reactions with ozone. Apparent second-order rate constants <i>k</i>_O₃ of 12 model compounds were determined at pH 7: oxazoles react 2 orders of magnitude faster (<i>k</i>_O₃ = 9 × 10²-5 × 10⁴ M^-1s^-1, depending on their substituents) than thiazoles (<i>k</i>_O₃ = 1 × 10¹-2 × 10³ M^-1s^-1). The low <i>k</i>_O₃ of thiazoles limits their degradability during ozonation. Only small yields of reactive oxygen species (^•OH, H₂O₂, and ¹O₂) were observed during ozonation of oxazoles, suggesting that all oxygen atoms from ozone are incorporated into the products. Oxazoles and thiazoles react initially by a Criegee-type reaction at the C=C double bond, followed by two reaction branches, leading to two observed product groups: (1) carboxylates and cyanate; (2) formate, amide and CO₂. For thiazoles, thiocarboxylic acids were identified as intermediates, reacting further to sulfate and carboxylic acids, forming ¹O₂. The nonaromatic 2-methyloxazoline is unreactive toward ozone. 2-Methylthiazoline reacts fast (<i>k</i>_O₃ = 2 × 10⁴ M^-1s^-1), forming ¹O₂, leading to ring-opening and formation of dimerization products which react further to <i>N</i>-acetyltaurine. These results enhance the understanding of the ozone reactivity of heterocycles and help predict transformation product formation.</p>","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511277","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":"Stereoselective Synthesis of Functionalized Indenes <i>via</i> Regioselective Cascade Iodoalkylation of Alkynes.","authors":"Muskan, Sushmita, Deepika Thakur, Nidhi, Akhilesh K Verma","doi":"10.1021/acs.joc.5c01020","DOIUrl":"https://doi.org/10.1021/acs.joc.5c01020","url":null,"abstract":"<p><p>Herein, an unprecedented and modular strategy for the stereoselective construction of functionalized indene scaffolds has been developed <i>via</i> a base-promoted, regioselective cascade iodoalkylation of alkynes. Michael addition of methanol to the carbon-carbon double bond initiated the consecutive formation of C-O, C-C, and C-I bonds in a single operation. The product features an exocyclic double bond and versatile functional groups (-CN, -COOEt, -I, -OMe), offering scope for transformation into biologically active pharmacophores. Notably, postfunctionalization of the resulting indene <i>via</i> decarboxylative protodeiodination in the presence of N-centered nucleophiles demonstrates the broad synthetic applicability of this protocol, enabling the metal-free construction of challenging C-N bonds and access to amine- and indole-substituted benzofulvenes.</p>","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511327","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":"Relative Thermodynamic Stability of α and β PVDF Crystal Phases: A Molecular Simulation Methodology.","authors":"Shubham Mireja, Devang V Khakhar","doi":"10.1021/acs.jpcb.5c01058","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01058","url":null,"abstract":"<p><p>Poly(vinylidene fluoride) (PVDF) is a piezoelectric polymer, with the crystalline β-phase having the highest polarity among all its phases. A multistage transformation process is developed, using molecular dynamics simulations, to compute the free energy difference between α- and β-phases of PVDF. Methods of free energy perturbation and Jarzynski's equality were used to determine Helmholtz free energy change, Δ<i>F</i>, for the individual stages, from which the Gibbs free energy difference, Δ<i>G</i>, between the α- and β-phases was calculated. Infinitely large crystals modeled using periodic boundaries with 36 chains and 12 monomers in each chain were used for the study. All-atom simulations were performed with the force fields previously developed for PVDF. In concurrence with experimental observations, the α-phase was found to be thermodynamically more stable at normal temperature and pressure conditions. The β-phase was found to be more stable at high and low temperatures and high pressure.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511330","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":"","authors":"Hongping Jiang,&nbsp;Xirong Liu,&nbsp;Chunling Zeng,&nbsp;Jie Tang* and Guofang Jiang*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":"90 25","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.joc.5c00709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488901","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}