ACS Publications最新文献_第5页

Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-08 Epub Date: 2025-03-19 DOI: 10.1021/acs.jctc.5c00039

Yongxian Wu, Qiang Zhu, Zhen Huang, Piotr Cieplak, Yong Duan, Ray Luo

{"title":"Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.","authors":"Yongxian Wu, Qiang Zhu, Zhen Huang, Piotr Cieplak, Yong Duan, Ray Luo","doi":"10.1021/acs.jctc.5c00039","DOIUrl":"10.1021/acs.jctc.5c00039","url":null,"abstract":"The critical importance of water in sustaining life highlights the need for accurate water models in computer simulations, aiming to mimic biochemical processes experimentally. The polarizable Gaussian multipole (pGM) model, recently introduced for biomolecular simulations, improves the handling of complex biomolecular interactions. As an integral part of our initial exploration, we examined a minimalist fixed geometry three-center pGM water model using ab initio quantum mechanical calculations of water oligomers. However, our final model development was based on liquid-phase water properties, leveraging automated machine learning (AutoML) techniques for optimization. This allows the development of a framework to refine both van der Waals and electrostatic parameters of the pGM model, aiming to accurately reproduce specific properties such as the oxygen-oxygen radial distribution function, density, and dipole moment, all at 298 K and 1.0 bar pressure. The efficacy of the optimized three-center pGM water model, pGM3P-25, was assessed through simulations of a water box of 512 water molecules, showcasing marked enhancements in both accuracy and practical utility. Notably, the model accurately reproduces thermodynamic properties not explicitly included in training while significantly reducing the time and human effort required for optimization. It was found that pGM3P-25 can reproduce temperature-dependent properties such as density, self-diffusion constants, heat capacity, second virial coefficient, and dielectric constant, which are important in biomolecular simulations. This study underscores the potential of AutoML-driven frameworks to streamline parameter refinement for molecular dynamics simulations, paving the way for broader applications in computational chemistry and beyond.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"3563-3575"},"PeriodicalIF":5.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661665","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

Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-08 Epub Date: 2025-03-24 DOI: 10.1021/acs.jctc.4c01661

Runduo Liu, Yufen Yao, Wanyi Huang, Yilin Zhong, Hai-Bin Luo, Zhe Li

{"title":"Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling.","authors":"Runduo Liu, Yufen Yao, Wanyi Huang, Yilin Zhong, Hai-Bin Luo, Zhe Li","doi":"10.1021/acs.jctc.4c01661","DOIUrl":"10.1021/acs.jctc.4c01661","url":null,"abstract":"Free energy perturbation (FEP) is a promising method for accurately predicting molecular interactions, widely applied in fields such as drug design, materials science, and catalysis. However, FEP calculations, particularly those in aqueous environments, often suffer from convergence issues due to insufficient sampling of water molecules. These challenges are particularly critical in solvation-related free energy calculations, such as small molecule-protein binding, interface interactions, and molecular adsorption on surfaces. To address these limitations, we present the divide-and-conquer absolute binding free energy (DC-ABFE) method. By partitioning the ligand or molecule into atomic groups and sequentially decoupling their van der Waals interactions, DC-ABFE improves water re-entry sampling, enhances phase-space overlap, and significantly enhances the convergence of free energy calculations. Our benchmark demonstrates that DC-ABFE achieves more reproducible and reliable binding free energy predictions compared to traditional FEP methods. DC-ABFE is applicable to a range of free energy calculations involving solvation effects. Additionally, this method establishes a stronger foundation for precise drug screening, offering a more robust tool for predicting binding affinities in drug discovery.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"3712-3725"},"PeriodicalIF":5.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699101","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

Discovery of a Novel ADC for Multifunctional Theranostics: From Vascular Normalization to Synergistic Therapy.

IF 4 2区化学

Bioconjugate Chemistry Pub Date : 2025-04-08 DOI: 10.1021/acs.bioconjchem.5c00116

Yanchen Li, Jin Wang, Tingting Liu, Junyu Zhang, Yuanyuan Shan, Jie Zhang

{"title":"Discovery of a Novel ADC for Multifunctional Theranostics: From Vascular Normalization to Synergistic Therapy.","authors":"Yanchen Li, Jin Wang, Tingting Liu, Junyu Zhang, Yuanyuan Shan, Jie Zhang","doi":"10.1021/acs.bioconjchem.5c00116","DOIUrl":"https://doi.org/10.1021/acs.bioconjchem.5c00116","url":null,"abstract":"Previous studies have shown the potential of bevacizumab-based ADCs in tumor vascular normalization and chemotherapy synergies. Here, in order to improve the tumor treatment efficiency of ADC and further avoid drug resistance, we introduced the previously discovered photodynamic therapy group PDT into bevacizumab, which has high reactive oxygen generation efficiency and deep tissue penetration ability, and has surprising imaging effect on solid tumors. At the same time, doxorubicin, a chemotherapy drug molecule with strong cytotoxicity, has also been introduced to construct novel multifunctional integrated antibody-drug conjugates, Bevacizumab-DOX-PDT. It is proved that novel ADCs have the antigen-antibody binding ability similar to bevacizumab, while also possess strong antitumor activity and vascular normalization activity. In addition, it also showed great tracer ability for transplanted tumors. In summary, the novel ADC showed a surprising vascular normalization-chemotherapy-photodynamic synergistic therapeutic effect, which further enriched the expansion of vascular normalization in the field of new drug discovery.","PeriodicalId":29,"journal":{"name":"Bioconjugate Chemistry","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143801980","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

Nanoclusters Embedded in Phthalocyanine Covalent Organic Polymer Enhance the Cycloaddition Reaction of Carbon Dioxide.

IF 4.3 2区化学

Inorganic Chemistry Pub Date : 2025-04-08 DOI: 10.1021/acs.inorgchem.5c00363

Haiyun Gao, Longchao Du, Yongwang Wei

{"title":"Nanoclusters Embedded in Phthalocyanine Covalent Organic Polymer Enhance the Cycloaddition Reaction of Carbon Dioxide.","authors":"Haiyun Gao, Longchao Du, Yongwang Wei","doi":"10.1021/acs.inorgchem.5c00363","DOIUrl":"https://doi.org/10.1021/acs.inorgchem.5c00363","url":null,"abstract":"Photocatalytic cycloaddition of carbon dioxide and epoxides under mild conditions is important for green chemistry, while metal clusters loaded on a variety of carriers are widely used in energy and biology. However, under long-term illumination, the light stability of metal clusters at the carrier interface is poor, which usually leads to the loss of catalytic performance. Covalent organic polymers (COPs) with periodic and ultrasmall pore structures are ideal carriers for dispersing and stabilizing metal clusters. Through a simple nitrogen purge process, embedding Mn2Dy2 clusters on a hydroxy-containing COP was successfully achieved, which makes it an effective photocatalyst for CO2 cycloaddition. By introducing adjacent hydroxyl and imine bonds in the COP unit, periodic dispersed adsorption sites of metal clusters were constructed, generating a large number of active photogenerated electrons. The photoelectric measurement results indicate that the catalyst is excellent, with good charge separation efficiency. The Mn2Dy2 clusters widely presented on COP expose large active surfaces, greatly promoting electron transfer. The highest cycloaddition conversion rate at room temperature and normal pressure is 99%, and the TON value is 2352. This is of great significance for the study of novel photocatalytic cycloaddition of carbon dioxide.","PeriodicalId":40,"journal":{"name":"Inorganic Chemistry","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802008","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

High-Performance Temperature Sensors for Early Warning Utilizing Flexible All-Inorganic Thermoelectric Films.

IF 8.3 2区材料科学

ACS Applied Materials & Interfaces Pub Date : 2025-04-08 DOI: 10.1021/acsami.5c00610

Zongfu Cai, Bo Wu, Xinxing Zhou, Kerui Li, Chengyi Hou, Qinghong Zhang, Yaogang Li, Hongzhi Wang

{"title":"High-Performance Temperature Sensors for Early Warning Utilizing Flexible All-Inorganic Thermoelectric Films.","authors":"Zongfu Cai, Bo Wu, Xinxing Zhou, Kerui Li, Chengyi Hou, Qinghong Zhang, Yaogang Li, Hongzhi Wang","doi":"10.1021/acsami.5c00610","DOIUrl":"https://doi.org/10.1021/acsami.5c00610","url":null,"abstract":"The demand for highly sensitive temperature-response materials is critical for the advancement of intelligent temperature sensing and fire warning systems. Despite notable progress in thermoelectrical (TE) materials and devices, designing TE materials suitable for wide-range temperature monitoring across diverse scenarios remains a challenge. In this study, we introduce a TE temperature sensor for fire warnings and hot object recognition, utilizing an all-inorganic TE film composite of reduced graphene oxide (rGO)/Te nanowires (Te NWs). The resulting all-inorganic TE film, annealed at a high temperature, exhibits distinct response ratios to varying temperature changes, enabling consistently sensitive thermosensation. The robust linear relationship between open circuit voltage and temperature difference establishes it as an effective thermoreceptor for enhanced temperature alerts. Furthermore, we demonstrate that the assembled TE sensor provides rapid high-temperature warnings with adjustable threshold voltages (1-7 mV), achieving an ultrafast response time of approximately 4.8 s at 1 mV threshold voltage. Additionally, this TE sensor can be integrated with the gloves to monitor high-temperature objects in various scenarios, such as the brewed milk in daily life and heating reactors in industrial applications. These results offer perspectives for future innovations in intelligent temperature monitoring.","PeriodicalId":5,"journal":{"name":"ACS Applied Materials & Interfaces","volume":" ","pages":""},"PeriodicalIF":8.3,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810136","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

Water-Soluble Unconventional Hyperbranched Polyborosiloxane Derivatives for Temperature Sensing in Living Cells.

IF 5.5 2区化学

Biomacromolecules Pub Date : 2025-04-08 DOI: 10.1021/acs.biomac.5c00105

Yanyun He, Rui Wu, Zheng Li, Yekun Zhang, Wenyan Liu, Weixu Feng, Hongxia Yan

{"title":"Water-Soluble Unconventional Hyperbranched Polyborosiloxane Derivatives for Temperature Sensing in Living Cells.","authors":"Yanyun He, Rui Wu, Zheng Li, Yekun Zhang, Wenyan Liu, Weixu Feng, Hongxia Yan","doi":"10.1021/acs.biomac.5c00105","DOIUrl":"https://doi.org/10.1021/acs.biomac.5c00105","url":null,"abstract":"Fluorescent polymeric thermometers, despite their noninvasive detection and rapid response for intracellular temperature monitoring, face challenges in achieving excellent biocompatibility and high sensitivity. Herein, we synthesized a water-soluble unconventional temperature-sensitive fluorescent polymer (P2) through terminally grafting poly(N-vinylcaprolactam) (PNVCL) onto hyperbranched polyborosiloxane (P1). The P2 exhibited efficient red-light emission and good photostability. Particularly, when the temperature rises, the PNVCL units transform from hydrophilic to hydrophobic, resulting in the dislocation of local segments of P2, suppressing radiative transitions and simultaneously weakening its through-space conjugation, further reducing its fluorescence intensity, and endowing the P2 with a high temperature-sensing sensitivity of 10.06% °C-1. Finally, the real-time monitoring of intracellular temperature variation was further conducted. This work not only develops promising thermochromic materials for intracellular temperature sensing but also provides further insight into the temperature-sensing mechanism of unconventional fluorescent polymers.","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810229","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

Fundamental Trade-Offs in the Robustness of Biological Systems with Feedback Regulation.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-04-08 DOI: 10.1021/acssynbio.4c00704

Nguyen Hoai Nam Tran, An Nguyen, Tasfia Wasima Rahman, Ania-Ariadna Baetica

{"title":"Fundamental Trade-Offs in the Robustness of Biological Systems with Feedback Regulation.","authors":"Nguyen Hoai Nam Tran, An Nguyen, Tasfia Wasima Rahman, Ania-Ariadna Baetica","doi":"10.1021/acssynbio.4c00704","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00704","url":null,"abstract":"Natural biological systems use feedback regulation to effectively respond and adapt to their changing environment. Even though in engineered systems we understand how accurate feedback can be depending on the electronic or mechanical parts that it is implemented with, we largely lack a similar theoretical framework to study feedback regulation in biological systems. Specifically, it is not fully understood or quantified how accurate or robust the implementation of biological feedback actually is. In this paper, we study the sensitivity of biological feedback to variations in biochemical parameters using five example circuits: positive autoregulation, negative autoregulation, double-positive feedback, positive-negative feedback, and double-negative feedback (the toggle switch). We find that some of these examples of biological feedback are subjected to fundamental performance trade-offs, and we propose multi-objective optimization as a framework to study their properties. The impact of this work is to improve robust circuit design for synthetic biology and to improve our understanding of feedback for systems biology.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating Large Language Models into the Chemistry and Materials Science Laboratory Curricula

IF 7.2 2区材料科学

Chemistry of Materials Pub Date : 2025-04-08 DOI: 10.1021/acs.chemmater.5c0011110.1021/acs.chemmater.5c00111

Annalise E. Maughan*, Eric S. Toberer* and Alexandra Zevalkink*,

引用次数: 0

Hybrid Gauge Approach for Accurate Real-Time TDDFT Simulations with Numerical Atomic Orbitals.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-08 Epub Date: 2025-03-24 DOI: 10.1021/acs.jctc.5c00111

Haotian Zhao, Lixin He

{"title":"Hybrid Gauge Approach for Accurate Real-Time TDDFT Simulations with Numerical Atomic Orbitals.","authors":"Haotian Zhao, Lixin He","doi":"10.1021/acs.jctc.5c00111","DOIUrl":"10.1021/acs.jctc.5c00111","url":null,"abstract":"Ultrafast real-time dynamics are critical for understanding a broad range of physical processes. Real-time time-dependent density functional theory (rt-TDDFT) has emerged as a powerful computational tool for simulating these dynamics, offering insight into ultrafast processes and light-matter interactions. In periodic systems, the velocity gauge is essential because it preserves the system's periodicity under an external electric field. Numerical atomic orbitals (NAOs) are widely employed in rt-TDDFT codes due to their efficiency and localized nature. However, directly applying the velocity gauge within the NAO basis set neglects the position-dependent phase variations within atomic orbitals induced by the vector potential, leading to significant computational errors - particularly in current calculations. To resolve this issue, we develop a hybrid gauge that incorporates both the electric field and the vector potential, preserving the essential phase information in atomic orbitals and thereby eliminating these errors. Our benchmark results demonstrate that the hybrid gauge fully resolves the issues encountered with the velocity gauge in NAO-based calculations, providing accurate and reliable results. This algorithm offers a robust framework for future studies on ultrafast dynamics in periodic systems using NAO bases.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"3335-3341"},"PeriodicalIF":5.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699102","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

Correction to "Calculating Apparent pK_a Values of Ionizable Lipids in Lipid Nanoparticles".

IF 4.5 2区医学

Molecular Pharmaceutics Pub Date : 2025-04-08 DOI: 10.1021/acs.molpharmaceut.5c00402

Nicholas B Hamilton, Steve Arns, Mee Shelley, Irene Bechis, John C Shelley

引用次数: 0