ACS Publications最新文献_第4页

Lysozyme in Mixtures of Hydrogen Bond Acceptor Solvents with Water: Enthalpies and Entropies of Preferential Solvation. 氢键受体溶剂与水的混合物中的溶菌酶：优先溶剂化的焓和熵。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-06-05 Epub Date: 2025-05-21 DOI: 10.1021/acs.jpcb.5c00304

Vladimir A Sirotkin

{"title":"Lysozyme in Mixtures of Hydrogen Bond Acceptor Solvents with Water: Enthalpies and Entropies of Preferential Solvation.","authors":"Vladimir A Sirotkin","doi":"10.1021/acs.jpcb.5c00304","DOIUrl":"10.1021/acs.jpcb.5c00304","url":null,"abstract":"The main focus of this work is to clarify how enzyme macromolecules become solvated in water-organic mixtures and to estimate the enthalpies and entropies of this solvation process. Isothermal calorimetry and water/organic solvent adsorption measurements were used to investigate the preferential solvation of hen egg white lysozyme in hydrogen bond acceptor solvents at 298.15 K. Dimethyl sulfoxide, N,N-dimethylformamide, acetonitrile, 1,4-dioxane, and acetone were used as model organic cosolvents. Preferential solvation was described by analyzing the excess thermodynamic functions of the mixing. The novelty of this approach is that the enthalpies and entropies of protein, water, and organic solvents can be simultaneously investigated across the entire range of water content. There are three composition regimes in water-organic mixtures. Stabilization of the protein as a result of the preferential hydration of lysozyme was detected in the water-rich region. Protein stabilization is driven by the positive change in entropy. The residual enzyme activity values are close to 100%, compared with those for pure water. In the intermediate region, lysozyme has a higher affinity for organic solvent molecules than for water. The cosolvent-induced inactivation of lysozyme was detected at intermediate water content, and residual enzyme activity is close to zero. At the lowest water content, the cosolvent molecules are preferentially excluded from the protein surface, resulting in preferential hydration and nonzero residual enzyme activity. In the water-poor region, protein stabilization is driven by the exothermic enthalpy change. The present study clearly demonstrates that the preferential solvation thermodynamic quantities strongly depend on the acceptance strength of the cosolvent hydrogen bond.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5386-5399"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118349","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

Gut Microbiota and COVID-19: Unraveling the Gut-Lung Axis and Immunomodulatory Therapies. 肠道微生物群与COVID-19：解开肠-肺轴和免疫调节疗法。

IF 4 2区医学

ACS Infectious Diseases Pub Date : 2025-06-05 DOI: 10.1021/acsinfecdis.5c00250

Maria Cidinaria Silva Alves, Mireli Santana Rego, Ruana Carolina Cabral da Silva, Rousilândia de Araújo Silva, Igor Eduardo Silva Arruda, Sérgio de Sá Leitão Paiva-Júnior, Valdir de Queiroz Balbino

{"title":"Gut Microbiota and COVID-19: Unraveling the Gut-Lung Axis and Immunomodulatory Therapies.","authors":"Maria Cidinaria Silva Alves, Mireli Santana Rego, Ruana Carolina Cabral da Silva, Rousilândia de Araújo Silva, Igor Eduardo Silva Arruda, Sérgio de Sá Leitão Paiva-Júnior, Valdir de Queiroz Balbino","doi":"10.1021/acsinfecdis.5c00250","DOIUrl":"https://doi.org/10.1021/acsinfecdis.5c00250","url":null,"abstract":"The gut flora modulates immune responses and influences COVID-19 severity. SARS-CoV-2 disrupts the gut microbiota, causing dysbiosis, increased intestinal permeability, and systemic inflammation and worsening clinical outcomes. Dysbiosis correlates with elevated inflammatory markers, such as CRP and PCT, contributing to severe complications. Studies show that COVID-19 patients have reduced beneficial bacteria, such as Faecalibacterium prausnitzii and Bifidobacterium spp., alongside increased opportunistic pathogens. This review explores how gut microbiota impacts COVID-19 through predictive microbial signatures and immunomodulatory mechanisms. Therapeutic strategies, including probiotics, prebiotics, and fiber-rich diets, may restore microbial balance, reduce inflammation, and support recovery. Additionally, we examine the effects of antiviral and immunomodulatory therapies on the gut microbiota and their role in post-COVID-19 rehabilitation. Understanding the gut-lung axis in SARS-CoV-2 pathogenesis may reveal microbiota-targeted treatments to improve outcomes and prevent complications. As the host organ with the highest microbial diversity, the gut plays a crucial role in viral infections and warrants further research.","PeriodicalId":17,"journal":{"name":"ACS Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223702","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}

引用次数: 0

Transferability of Data Sets between Machine-Learned Interatomic Potential Algorithms. 机器学习原子间势算法之间数据集的可转移性。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-05 DOI: 10.1021/acs.jctc.5c00272

Samuel P Niblett, Panagiotis Kourtis, Ioan-Bogdan Magdău, Clare P Grey, Gábor Csányi

{"title":"Transferability of Data Sets between Machine-Learned Interatomic Potential Algorithms.","authors":"Samuel P Niblett, Panagiotis Kourtis, Ioan-Bogdan Magdău, Clare P Grey, Gábor Csányi","doi":"10.1021/acs.jctc.5c00272","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00272","url":null,"abstract":"The emergence of Foundational Machine Learning Interatomic Potential (FMLIP) models trained on extensive data sets motivates attempts to transfer data between different ML architectures. Using a common battery electrolyte solvent as a test case, we examine the extent to which training data optimized for one machine-learning method may be reused by a different learning algorithm, aiming to accelerate FMLIP fine-tuning and to reduce the need for costly iterative training. We consider several types of training configurations and compare the benefits they bring to feedforward neural networks (the Deep Potential model) and message-passing networks (MACE). We propose a simple metric to assess model performance and demonstrate that MACE models perform well with even the simplest training sets, whereas simpler architectures require further iterative training to describe the target liquids correctly. We find that configurations designed by human intuition to correct systematic deficiencies of a model often transfer well between algorithms, but that reusing configurations that were generated automatically by one MLIP does not necessarily benefit a different algorithm. We also compare the performance of these bespoke models against two pretrained FMLIPs, demonstrating that system-specific training data are usually necessary for realistic models. Finally, we examine how training data sets affect a model's ability to generalize to unseen molecules, finding that model stability is conserved for small changes in molecule shape but not changes in functional chemistry. Our results provide insight into how training set properties affect the behavior of an MLIP and principles to enhance training sets for molecular liquid models with minimal computational effort. These approaches may be used in tandem with FMLIPs to dramatically accelerate the rate at which new chemical systems can be simulated.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223736","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

Deciphering the Mechanism of the Nickel-Catalyzed Catalytic Transfer Hydrogenation of Furfural to Furfuryl Alcohol. 解读镍催化糠醛催化转移加氢制糠醇的机理。

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-06-05 Epub Date: 2025-05-23 DOI: 10.1021/acs.jpca.5c00853

Nova Pratiwi Indriyani, Nabil Khwarizmi Syuhada, Aditya Wibawa Sakti, Muhamad Abdulkadir Martoprawiro, Yessi Permana, I Made Arcana

引用次数: 0

Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications. 范围校正的MACE图神经网络的可转移性Δ-Machine学习潜力QM/MM应用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-06-05 Epub Date: 2025-05-26 DOI: 10.1021/acs.jpcb.5c02006

Timothy J Giese, Jinzhe Zeng, Darrin M York

{"title":"Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.","authors":"Timothy J Giese, Jinzhe Zeng, Darrin M York","doi":"10.1021/acs.jpcb.5c02006","DOIUrl":"10.1021/acs.jpcb.5c02006","url":null,"abstract":"We previously introduced a \"range corrected\" Δ-machine learning potential (ΔMLP) that used deep neural networks to improve the accuracy of combined quantum mechanical/molecular mechanical (QM/MM) simulations by correcting both the internal QM and QM/MM interaction energies and forces [J. Chem. Theory Comput. 2021, 17, 6993-7009]. The present work extends this approach to include graph neural networks. Specifically, the approach is applied to the MACE message passing neural network architecture, and a series of AM1/d + MACE models are trained to reproduce PBE0/6-31G* QM/MM energies and forces of model phosphoryl transesterification reactions. Several models are designed to test the transferability of AM1/d + MACE by varying the amount of training data and calculating free energy surfaces of reactions that were not included in the parameter refinement. The transferability is compared to AM1/d + DP models that use the DeepPot-SE (DP) deep neural network architecture. The AM1/d + MACE models are found to reproduce the target free energy surfaces even in instances where the AM1/d + DP models exhibit inaccuracies. We train \"end-state\" models that include data only from the reactant and product states of the 6 reactions. Unlike the uncorrected AM1/d profiles, the AM1/d + MACE method correctly reproduces a stable pentacoordinated phosphorus intermediate even though the training did not include structures with a similar bonding pattern. Furthermore, the message passing mechanism hyperparameters defining the MACE network are varied to explore their effect on the model's accuracy and performance. The AM1/d + MACE simulations are 28% slower than AM1/d QM/MM when the ΔMLP correction is performed on a graphics processing unit. Our results suggest that the MACE architecture may lead to ΔMLP models with improved transferability.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5477-5490"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140963","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

Interactions of Micro- and Nanoplastics with Biomolecules: From Public Health to Protein Corona Effect and Beyond. 微和纳米塑料与生物分子的相互作用：从公共卫生到蛋白质电晕效应及其他。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-06-05 Epub Date: 2025-05-25 DOI: 10.1021/acs.jpcb.5c00416

Tao Zhang, Zi Wang, Yue Wu, Sihao Zhu, Jiaye Su

{"title":"Interactions of Micro- and Nanoplastics with Biomolecules: From Public Health to Protein Corona Effect and Beyond.","authors":"Tao Zhang, Zi Wang, Yue Wu, Sihao Zhu, Jiaye Su","doi":"10.1021/acs.jpcb.5c00416","DOIUrl":"10.1021/acs.jpcb.5c00416","url":null,"abstract":"Micro- and nanoplastics (M/NPs), as ubiquitous global environmental pollutants, have garnered increasing attention due to their pervasive presence. These particles can interact with biological molecules through various mechanisms, subsequently inducing potential toxic effects on living organisms. This review investigates the hazards of M/NPs and their interactions with biological membranes and proteins, focusing on their interaction mechanisms and potential effects on biomolecular structure and function. Specifically, we summarize the exposure pathways and potential harms of M/NPs, which can enter the human body through ingestion, inhalation, and skin contact, potentially causing toxicity, inflammation responses, oxidative stress, and endocrine disruption. Additionally, we highlight the interaction between M/NPs and biological membranes, which can induce structural changes, including membrane thickening, increased fluidity, and pore formation, thereby compromising membrane integrity and affecting cellular health. Besides, we emphasize the interaction between M/NPs and proteins, suggesting that protein structural changes and corona formation can influence oxidative stress responses and cytotoxicity, thereby impacting cellular functions and viability. Ultimately, suggestions and outlooks for further research are proposed. Overall, this review systematically summarizes current research on the interactions between M/NPs and biomolecules, including their mechanisms and biological effects, providing researchers with a comprehensive understanding of the field.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5355-5374"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141021","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

Electron-Proton Resonance Propagates a Delocalized Proton Wavepacket─A Vibronic Understanding of Picosecond Oscillatory Spectra in Proton Transfer. 电子-质子共振传播离域质子波包─质子转移中皮秒振荡谱的振动学理解。

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-06-05 Epub Date: 2025-05-27 DOI: 10.1021/acs.jpca.4c07526

Luhao Zhang, Francesca Fassioli, Rong Li, Gregory D Scholes

{"title":"Electron-Proton Resonance Propagates a Delocalized Proton Wavepacket─A Vibronic Understanding of Picosecond Oscillatory Spectra in Proton Transfer.","authors":"Luhao Zhang, Francesca Fassioli, Rong Li, Gregory D Scholes","doi":"10.1021/acs.jpca.4c07526","DOIUrl":"10.1021/acs.jpca.4c07526","url":null,"abstract":"Ultrafast spectroscopy of excited-state intramolecular proton transfer (ESIPT) has revealed picosecond oscillatory dynamics that are usually attributed solely to vibrational coherence. This study explores the possibility that, instead, vibronic coherence among reactant and product electron-proton vibronic states underlies the oscillatory signal. We develop and apply a model for ESIPT to two different chromophores (HBT and HBQ), which is based on a vibronic Hamiltonian comprising four electronic states coupled to proton and skeleton coordinates, with dynamics simulated through a master equation of Lindblad form that accounts for quantum coherent evolution and dissipation on an equal footing. We find that, under conditions of resonance between the proton vibrational frequency and the reactant-product electronic energy gap, the reaction involves vibronic states delocalized on the reactant and product. The ensuing reactant and product electronic population dynamics, exhibiting quantum coherent oscillations, are shown to translate into the \"fast rise + oscillatory\" time-resolved fluorescence (TRF) signals. In our model, the low-frequency skeletal vibration acts as a perturbation of the coupled electron-proton dynamics.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"4844-4854"},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155210","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

Rational Enzyme Evolution by Facilitating Correlated Motion along the Reaction. 促进反应相关运动的合理酶进化。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-06-05 Epub Date: 2025-05-27 DOI: 10.1021/acs.jpcb.5c02133

Lianxin Wang, Yuanfei Xue, Jia-Ning Wang, Yan Mo, Ye Mei

引用次数: 0

Modulating the Structural Dynamics and Catalytic Properties of a Cu Cluster via CO-Mediated Spatial Confinement. 通过co介导的空间约束调节Cu簇的结构动力学和催化性能。

IF 4.8 2区化学

The Journal of Physical Chemistry Letters Pub Date : 2025-06-05 Epub Date: 2025-05-28 DOI: 10.1021/acs.jpclett.5c00949

Yurui Han, Feiyang Ren, Qiang Fu, Jinlong Yang

{"title":"Modulating the Structural Dynamics and Catalytic Properties of a Cu Cluster via CO-Mediated Spatial Confinement.","authors":"Yurui Han, Feiyang Ren, Qiang Fu, Jinlong Yang","doi":"10.1021/acs.jpclett.5c00949","DOIUrl":"10.1021/acs.jpclett.5c00949","url":null,"abstract":"Spatial confinement provides a powerful approach to tune the catalytic properties of metal clusters by creating unique nanoscale environments around them. However, the dynamic structural evolution of the confined clusters covered by high-coverage adsorbates and the consequent impact on the catalytic properties remain poorly understood. In this work, using density functional theory calculations and ab initio molecular dynamics simulations, we demonstrate that the CO molecules adsorbed on an encapsulated Cu18 cluster can mediate interactions between the (17, 0) zigzag carbon nanotube (CNT) inner wall and Cu18, which significantly regulates the structural dynamics and reactivity of the confined cluster. It is found that the Cu cluster in the CNT exhibits reduced Cu-Cu coordination numbers and recurrent multiadsorption structures of CO, both of which are absent in the corresponding cluster on the open space of graphene. The unique structural features of the encapsulated Cu cluster in the CNT can further promote a C-C coupling reaction. Our work provides a new adsorbate-assisted approach to tune the structural dynamics of confined clusters and may open up new opportunities to improve the performance of confined catalysts.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5553-5560"},"PeriodicalIF":4.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155281","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

Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations. 分子动力学模拟揭示MscL开口的不对称性质。

IF 5.6 2区化学

Journal of Chemical Information and Modeling Pub Date : 2025-06-05 DOI: 10.1021/acs.jcim.5c00307

Olga N Rogacheva, Wojciech Kopec

{"title":"Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations.","authors":"Olga N Rogacheva, Wojciech Kopec","doi":"10.1021/acs.jcim.5c00307","DOIUrl":"https://doi.org/10.1021/acs.jcim.5c00307","url":null,"abstract":"The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus offering an approach to study the mechanism of MscL gating. We employed all-atom molecular dynamics to simulate the L17A, V21A double mutant of MscL under a tension of 30 mN/m. Under these conditions, the closed state initially adopts a funnel-like conformation. Subsequently, five chains of MscL undergo sequential transitions into asymmetric states (S1, S2, etc.). Within its \"open\" fragment, the S1 state is similar to the expanded state of Methanosarcina acetivorans MscL and has a conductance 10 times lower than the open state. We applied committor analysis and a nonlinear regression model to construct a reaction coordinate for the transition between the closed and the S1 state as a linear combination of interatomic distances and contacts. The main contributions to the reaction coordinate are (1) the disruption of the \"cytoplasmic\" contact sites between the considered chain and two adjacent chains, (2) the delipidation of the lipid-binding pocket, formed by the I82, V86, and V22 residues, and (3) pulling the two neighboring chains apart via the tension sensors. The free energy profile along the reaction coordinate was calculated using the umbrella sampling approach. The S1 state is approximately 5 kJ/mol more favorable than the closed state under tension. The height of the free energy barrier for the transition toward the S1 state is approximately 10 kJ/mol, which is in reasonable agreement with the corresponding average transition time, estimated to be 133 ± 13 ns. The results and approach can be employed to elucidate the wild-type protein gating mechanism.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223713","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