ACS Publications最新文献_第5页

Effects of Pressure and Temperature on the Thermodynamics of α-Helices: Implications for Piezophilic Adaptation. 压力和温度对α-螺旋热力学的影响：对亲压适应的影响。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-11 Epub Date: 2025-08-30 DOI: 10.1021/acs.jpcb.5c04293

George I Makhatadze, Caitlyn Moustouka, Carleton Coffin, Franco O Tzul

{"title":"Effects of Pressure and Temperature on the Thermodynamics of α-Helices: Implications for Piezophilic Adaptation.","authors":"George I Makhatadze, Caitlyn Moustouka, Carleton Coffin, Franco O Tzul","doi":"10.1021/acs.jpcb.5c04293","DOIUrl":"10.1021/acs.jpcb.5c04293","url":null,"abstract":"In light of the recent realization that a significant fraction of microbial biomass lives under high hydrostatic pressure, there is a renewed interest in understanding the molecular details by which proteins in these organisms modulate their functional native state. The effects of pressure on protein stability are defined by the volume changes between the native and denatured states. The conformational ensemble of the denatured state can depend on several extrinsic variables, such as pH and ionic strength of the solvent, temperature, and pressure. The effect of the latter on the elements of the secondary structures, including α-helical structures, has been inconclusive. This has been mainly due to the inherent difficulties associated with high-pressure experiments. Here, we adapted the method of choice, circular dichroism spectroscopy, on a well-established series of model peptides to study helical structure formation while focusing on the pressure and temperature dependencies of the helix-coil transition. We find that at low temperatures, pressure stabilizes the helical structure, suggesting that the volume of the helix-coil transition is positive. However, at higher temperatures (>40 °C), the volume changes become negative, and pressure destabilizes the helical structure. The stabilizing effect of pressure on the helical structure at low temperature correlates with the increase in the fraction of high-helix-forming amino acid residues at the expense of low-helix forming residues in psychrophilic bacterial strains adapted to live at the bottom of the ocean.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"9113-9123"},"PeriodicalIF":2.9,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936461","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}

引用次数: 0

An Adaptive Force Matching Potential for Alanine Developed with Møller-Plesset Perturbation Theory and Smooth Fourier Transform Correction Map. 利用Møller-Plesset微扰理论和平滑傅立叶变换校正图建立了丙氨酸的自适应力匹配势。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-11 Epub Date: 2025-08-26 DOI: 10.1021/acs.jpcb.5c04529

Ying Yuan, Feng Wang

{"title":"An Adaptive Force Matching Potential for Alanine Developed with Møller-Plesset Perturbation Theory and Smooth Fourier Transform Correction Map.","authors":"Ying Yuan, Feng Wang","doi":"10.1021/acs.jpcb.5c04529","DOIUrl":"10.1021/acs.jpcb.5c04529","url":null,"abstract":"Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with Møller-Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods. The ALAMP2_25 model incorporates a new correction scheme, Smooth Fourier Transform-based φ, ψ correction map (SFT-CMAP), which efficiently describes φ, ψ coupling with reduced overfitting. Our model demonstrates good agreement with experimental J-coupling data for hydrated polyalanine and shows improved transferability to N-methylated cyclic alanine when compared to previously reported DFT based models. The developed framework provides a pathway for creating accurate force fields for a broader range of amino acids and biomolecules, enabling first-principles-based simulations of complex biological systems with applications in protein folding, ligand binding, and drug design.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"9165-9174"},"PeriodicalIF":2.9,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936474","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}

引用次数: 0

Broadband Fourier-Transform Optical Photothermal Infrared Spectroscopy and Imaging. 宽带傅里叶变换光学光热红外光谱与成像。

IF 6.7 1区化学

Analytical Chemistry Pub Date : 2025-09-11 DOI: 10.1021/acs.analchem.5c02493

Aleksandr Razumtcev, Gwendylan A Turner, Sergey Zayats, Ferenc Borondics, Aris Polyzos, Garth J Simpson, Hans A Bechtel

{"title":"Broadband Fourier-Transform Optical Photothermal Infrared Spectroscopy and Imaging.","authors":"Aleksandr Razumtcev, Gwendylan A Turner, Sergey Zayats, Ferenc Borondics, Aris Polyzos, Garth J Simpson, Hans A Bechtel","doi":"10.1021/acs.analchem.5c02493","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c02493","url":null,"abstract":"Infrared (IR) spectroscopy is a powerful method for mapping chemical heterogeneity on the microscale. Synchrotron IR radiation uniquely provides a high brightness and broad bandwidth to further extend the capabilities of IR spectroscopic imaging. However, the diffraction-limited spatial resolution of IR spectroscopy is insufficient for studies requiring submicrometer spatial differentiation. Optical photothermal IR (O-PTIR) microscopy is a powerful, emerging method that overcomes the IR diffraction limit in IR hyperspectral imaging by employing a modulated IR beam and a visible probe laser beam to detect local temperature-induced modulation at the visible diffraction limit. In this work, we extend the spectral range of photothermal infrared measurements by incorporating a synchrotron IR source, demonstrating a combined synchrotron-based O-PTIR modality that enables high spatial resolution far-field chemical imaging spanning the entire mid-IR range. Both optical- and fluorescence-detected photothermal modalities were performed using a step-scan interferometer, demonstrating improved spectral range (541-4000 cm-1) when compared to optical photothermal microscopy with commercial laser sources (800-1800 cm-1 for this particular source) and improved spatial resolution, when compared to synchrotron microspectroscopy measurements. Following these initial validation studies, synchrotron Fourier-transform fluorescence-detected photothermal IR spectroscopy in combination with synchrotron microspectroscopy measurements was used to differentiate cells in mouse brain tissue sections, which requires submicron spatial resolutions beyond those accessible by IR spectroscopy alone.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":" ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Subnanometric Control of Coupling between WS₂ Monolayers with a Molecular Spacer. 分子间隔剂对WS2单层膜间耦合的亚纳米控制。

IF 8.2 2区材料科学

ACS Applied Materials & Interfaces Pub Date : 2025-09-11 DOI: 10.1021/acsami.5c12764

Sara A Elrafei, Tom T C Sistermans, Alberto G Curto

{"title":"Subnanometric Control of Coupling between WS2 Monolayers with a Molecular Spacer.","authors":"Sara A Elrafei, Tom T C Sistermans, Alberto G Curto","doi":"10.1021/acsami.5c12764","DOIUrl":"https://doi.org/10.1021/acsami.5c12764","url":null,"abstract":"Stacking monolayer semiconductors into heterostructures allows for control of their optical and electronic properties, offering advantages for nanoscale electronics, optoelectronics, and photonics. Specifically, adding a thin spacer between monolayers can yield bulk materials that retain interesting monolayer properties, such as a direct bandgap and a high emission quantum efficiency. The interaction mechanisms between monolayers, including interlayer coupling, charge transfer, and energy transfer, might be tuned through subnanometric control over the spacer thickness. Traditional spacer materials like bulk oxides or other layered materials can suffer from poor material interfaces or inhomogeneous thickness over large areas. Here, we use a spin-cast organic molecular spacer to adjust interlayer coupling in WS2 monolayer stacks. We vary the molecular spacer thickness to tune the interlayer distance, significantly altering the optical properties of the resulting organic-inorganic heterostructures. Additionally, we demonstrate a dependence of the valence-band splitting on molecular spacer thickness manifested as a change in the energy difference between A and B excitons resulting from spin-orbit coupling and interlayer interactions. Our results illustrate the potential of molecular spacers to tailor the properties of monolayer heterostructures. This accessible approach opens routes to advancing atomically thin devices and could enable sensing technologies at the subnanometer scale.","PeriodicalId":5,"journal":{"name":"ACS Applied Materials & Interfaces","volume":" ","pages":""},"PeriodicalIF":8.2,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Practically Significant Method Comparison Protocols for Machine Learning in Small Molecule Drug Discovery. 小分子药物发现中机器学习的实际意义方法比较协议。

IF 5.3 2区化学

Journal of Chemical Information and Modeling Pub Date : 2025-09-11 DOI: 10.1021/acs.jcim.5c01609

Jeremy R Ash, Cas Wognum, Raquel Rodríguez-Pérez, Matteo Aldeghi, Alan C Cheng, Djork-Arné Clevert, Ola Engkvist, Cheng Fang, Daniel J Price, Jacqueline M Hughes-Oliver, W Patrick Walters

{"title":"Practically Significant Method Comparison Protocols for Machine Learning in Small Molecule Drug Discovery.","authors":"Jeremy R Ash, Cas Wognum, Raquel Rodríguez-Pérez, Matteo Aldeghi, Alan C Cheng, Djork-Arné Clevert, Ola Engkvist, Cheng Fang, Daniel J Price, Jacqueline M Hughes-Oliver, W Patrick Walters","doi":"10.1021/acs.jcim.5c01609","DOIUrl":"https://doi.org/10.1021/acs.jcim.5c01609","url":null,"abstract":"Machine Learning (ML) methods that relate molecular structure to properties are frequently proposed as in silico surrogates for expensive or time-consuming experiments. In small molecule drug discovery, such methods inform high-stakes decisions like compound synthesis and in vivo studies. This application lies at the intersection of multiple scientific disciplines. When comparing new ML methods to baseline or state-of-the-art approaches, statistically rigorous method comparison protocols and domain-appropriate performance metrics are essential to ensure replicability and ultimately the adoption of ML in small molecule drug discovery. This paper proposes a set of guidelines to incentivize rigorous and domain-appropriate techniques for method comparison tailored to small molecule property modeling. These guidelines, accompanied by annotated examples using open-source software tools, lay a foundation for robust ML benchmarking and thus the development of more impactful methods.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032455","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}

引用次数: 0

Deep Eutectic Solvent Interaction with Graphene Oxide: A Combined Experimental and Molecular Dynamics Characterization. 深共晶溶剂与氧化石墨烯的相互作用：结合实验和分子动力学表征。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-11 Epub Date: 2025-08-26 DOI: 10.1021/acs.jpcb.5c03461

Simone Di Muzio, Fabio Ramondo, Giulia Fioravanti

{"title":"Deep Eutectic Solvent Interaction with Graphene Oxide: A Combined Experimental and Molecular Dynamics Characterization.","authors":"Simone Di Muzio, Fabio Ramondo, Giulia Fioravanti","doi":"10.1021/acs.jpcb.5c03461","DOIUrl":"10.1021/acs.jpcb.5c03461","url":null,"abstract":"The interaction between graphene oxide (GO) and deep eutectic solvents (DESs) plays a crucial role in the design of functional materials for a wide range of applications. In this study, we present a combined experimental and computational investigation aimed at elucidating the structural and molecular organization of GO-DES systems using ethaline and reline as model deep eutectic solvents. These two DESs are among the most widely studied and well-characterized, making them ideal benchmarks for probing GO-liquid interactions. We synthesized GO and performed a detailed characterization via X-ray photoelectron spectroscopy (XPS), obtaining precise information about the type and distribution of oxygen-containing functional groups. Based on these experimental data, we developed a realistic molecular model of GO, providing a reliable and reproducible framework for atomistic simulations. Infrared and Raman spectroscopies reveal specific changes in vibrational modes upon GO-DES interaction, while differential scanning calorimetry (DSC) indicates modifications in thermal behavior. Classical molecular dynamics (MD) simulations show the formation of hydrogen-bond networks between the DES components and GO surface functionalities. Our results demonstrate a reciprocal structural influence between GO and DES at the molecular level and establish a validated computational protocol for the study of these hybrid systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"9206-9218"},"PeriodicalIF":2.9,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936420","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}

引用次数: 0

Recent Advances in Nanozymes and Their Composites for Antibiofilm Applications. 纳米酶及其复合材料在抗菌膜中的应用研究进展。

IF 4.7

ACS Applied Bio Materials Pub Date : 2025-09-11 DOI: 10.1021/acsabm.5c01274

Hui Cui, Yuanyuan Cui, Huanxiang Yuan, Ruilian Qi

{"title":"Recent Advances in Nanozymes and Their Composites for Antibiofilm Applications.","authors":"Hui Cui, Yuanyuan Cui, Huanxiang Yuan, Ruilian Qi","doi":"10.1021/acsabm.5c01274","DOIUrl":"https://doi.org/10.1021/acsabm.5c01274","url":null,"abstract":"Biofilm-associated infections caused by microbial communities have become a major threat to the global public health. Once formed, biofilms not only significantly enhance microbial resistance to antibiotics but also render infections extremely difficult to eradicate, often resulting in poor clinical outcomes and high mortality rates. Therefore, there is an urgent need to develop effective antibiofilm strategies to combat these persistent infections. Nanozymes, nanomaterials with intrinsic enzyme-like catalytic activities, have attracted increasing attention as promising tools for combating biofilm-related infections. As artificial enzyme mimics, nanozymes exhibit excellent catalytic efficiency, enabling them to rapidly generate large amounts of reactive oxygen species (ROS) or catalyze the hydrolysis of biomolecules within microbial cells and biofilms, thereby effectively preventing biofilm formation or eradicating established biofilm. Combined with their good biocompatibility and stability, nanozymes have made remarkable progress in antibiofilm applications over the past five years. In this review, we first provide a brief overview of biofilm infections, biofilm structure, and the mechanisms underlying their antibiotic resistance. Then, we summarize recent advances in the application of nanozymes and their composites to the prevention and disruption of microbial biofilms. Finally, we briefly summarize the present status of nanozymes in antibiofilm research, discuss existing challenges, and propose future prospects for nanozymes in combating biofilms.","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to "Target Engagement Assays in Early Drug Discovery". 对“早期药物发现中的目标接触分析”的更正。

IF 6.8 1区医学

Journal of Medicinal Chemistry Pub Date : 2025-09-11 Epub Date: 2025-09-03 DOI: 10.1021/acs.jmedchem.5c02336

Sahra St John-Campbell, Gurdip Bhalay

引用次数: 0

Computation of Auger Electron Spectra in Organic Molecules with Multiconfiguration Pair-Density Functional Theory. 用多组态对密度泛函理论计算有机分子中的俄歇电子能谱。

IF 2.8 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-09-11 Epub Date: 2025-08-29 DOI: 10.1021/acs.jpca.5c01789

Adam E A Fouda, Bhavnesh Jangid, Eetu Pelimanni, Stephen H Southworth, Phay J Ho, Laura Gagliardi, Linda Young

引用次数: 0

First-Principles Calculation of ortho-para Effects in the Second Virial Coefficients of H₂ and D₂ at Low Temperatures. 低温条件下H2和D2第二维里系数的正交对位效应的第一性原理计算。

IF 2.8 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-09-11 Epub Date: 2025-08-27 DOI: 10.1021/acs.jpca.5c04224

Giovanni Garberoglio, Allan H Harvey

引用次数: 0