Chemphyschem最新文献_第4页

Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors. 针对 SARS-CoV-2 临床药物的计算评估：预见分子机制和强效 Mpro 抑制剂。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-27 DOI: 10.1002/cphc.202400814

Saroj Kumar Panda, Pratyush Pani, Parth Sarthi Sen Gupta, Nimai Mahanandia, Malay Kumar Rana

{"title":"Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors.","authors":"Saroj Kumar Panda, Pratyush Pani, Parth Sarthi Sen Gupta, Nimai Mahanandia, Malay Kumar Rana","doi":"10.1002/cphc.202400814","DOIUrl":"10.1002/cphc.202400814","url":null,"abstract":"The emergence of new SARS-CoV-2 variants of concern (VOC) is a propulsion for accelerated potential therapeutic discovery. SARS-CoV-2's main protease (Mpro), essential for host cell viral replication, is a pre-eminent druggable protein target. Here, we perform extensive drug re-profiling of the comprehensive Excelra database, which compiles various under-trial drug candidates for COVID-19 treatment. For mechanistic understanding, the most promising screened-out molecules with targets are subjected to molecular dynamics (MD) simulations. Post-MD analyses demonstrate Darunavir, Ponatinib, and Tomivosertib forming a stable complex with Mpro, characterized by less fluctuation of Cα atoms, smooth and stable root-mean-square deviation (RMSD), and robust contact with the active site residues. Likewise, they all have lower binding free energy with Mpro, demonstrating strong affinity. In free energy landscape profiles, the distances from His41 and Cys145 exhibit a single energy minima basin, implying their preponderance in proximity to Mpro's catalytic dyad. Overall, the computational assessment earmarks promising candidates from the Excelra database, emphasizing on carrying out exhaustive biochemical experiments along with clinical trials. The work lays the foundation for potential therapeutic interventions in treating COVID-19.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400814"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Conformational and Solvent Effects on the Photoinduced Electron Transfer Dynamics of a Zinc Phthalocyanine-Benzoperylenetriimide Conjugate: A Nonadiabatic Dynamics Simulation. 构象和溶剂对酞菁锌-苯并吡啶三亚胺共轭物光诱导电子转移动力学的影响：非绝热动力学模拟。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-11 DOI: 10.1002/cphc.202400631

Sha-Sha Liu, Xin Wei, Yan Zheng, Shuai Liu, Dong-Hui Xu, Laicai Li, Ganglong Cui, Xiang-Yang Liu

{"title":"Conformational and Solvent Effects on the Photoinduced Electron Transfer Dynamics of a Zinc Phthalocyanine-Benzoperylenetriimide Conjugate: A Nonadiabatic Dynamics Simulation.","authors":"Sha-Sha Liu, Xin Wei, Yan Zheng, Shuai Liu, Dong-Hui Xu, Laicai Li, Ganglong Cui, Xiang-Yang Liu","doi":"10.1002/cphc.202400631","DOIUrl":"10.1002/cphc.202400631","url":null,"abstract":"Herein, we employed a combination of static electronic structure calculations and nonadiabatic dynamics simulations at linear-response time dependent density functional theory (LR-TDDFT) level with the optimally tuned range-separated hybrid (OT-RSH) functional to explore the ultrafast photoinduced dynamics of a zinc phthalocyanine-benzoperylenetriimide (ZnPc-BPTI) conjugate. Due to the flexibility of the linker, we identified two major conformations: the stacked conformation (ZnPc-BPTI-1) and the extended conformation (ZnPc-BPTI-2). Since the charge transfer states are much lower than the lowest local excitation in ZnPc-BPTI-1, which is contrary to ZnPc-BPTI-2, the ultrafast electron transfer (~3.6 ps) is only observed in the nonadiabatic simulations of ZnPc-BPTI-1 upon local excitation around the absorption maximum of ZnPc. However, when considering the solvent effects in benzonitrile: the lowest S1 states are both charge transfer states from ZnPc to BPTI for different conformers. Subsequent nonadiabatic dynamics simulations indicate that both conformers experience ultrafast electron transfer in benzonitrile with two time constants of 90 [100] fs and 1.40 [1.43] ps. Our present work not only agrees well with previous experimental study, but also points out the important role of conformational changes and solvent effects in regulating the photodynamics of organic donor-acceptor conjugates.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400631"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Tunable Focusing Liquid Crystal Lenses: The Challenges and the Opportunities. 可调焦液晶透镜：挑战与机遇。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 DOI: 10.1002/cphc.202401113

Pemika Hirankittiwong, Huddad Laeim, Vandana Molahalli, Abdullah Alodhayb, Nattaporn Chattham, Gurumurthy Hegde

引用次数: 0

Factors Determining the Selectivity of NO Reduction Catalyzed by Copper-Vanadium Oxide Cluster Anions Cu₂VO_3-5^. 决定铜钒氧化物簇阴离子 Cu2VO3-5 催化氮氧化物还原选择性的因素。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-09 DOI: 10.1002/cphc.202400888

Si-Dun Wang, Yi Liu, Tong-Mei Ma, Xiao-Na Li, Sheng-Gui He

{"title":"Factors Determining the Selectivity of NO Reduction Catalyzed by Copper-Vanadium Oxide Cluster Anions Cu2VO3-5.","authors":"Si-Dun Wang, Yi Liu, Tong-Mei Ma, Xiao-Na Li, Sheng-Gui He","doi":"10.1002/cphc.202400888","DOIUrl":"10.1002/cphc.202400888","url":null,"abstract":"Catalytic NO reduction by CO is imperative to satisfy the increasingly rigorous emission regulations. Identifying the structural characteristic of crucial intermediate that governs the selectivity of NO reduction is pivotal to having a fundamental understanding on real-life catalysis. Herein, benefiting from the state-of-the-art mass spectrometry, we demonstrated experimentally that the Cu2VO3-5 - clusters can mediate the catalysis of NO reduction by CO, and two competitive channels to generate N2O and N2 can co-exist. Quantum-chemical calculations were performed to rationalize this selectivity. The formation of the ONNO unit on the Cu2 dimer was demonstrated to be a precursor from which two pathways of NO reduction start to emerge. In the pathway of N2O generation, only the Cu2 dimer was oxidized and the VO3 moiety functions as a \"support\", while both moieties have to contribute to anchor oxygen atoms from the ONNO unit and then N2 can be generated. This finding displays a clear picture to elucidate how and why the involvement of VO3 \"support\" can regulate the selectivity of NO reduction.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400888"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Energy Landscapes in Chemical Reactions and Transport. 化学反应和传输中的能量景观。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 DOI: 10.1002/cphc.202400877

Karl-Michael Weitzel

{"title":"Energy Landscapes in Chemical Reactions and Transport.","authors":"Karl-Michael Weitzel","doi":"10.1002/cphc.202400877","DOIUrl":"https://doi.org/10.1002/cphc.202400877","url":null,"abstract":"Both, molecular chemical reactions and transport of atoms in solid media are determined by the energy landscape in which the seemingly different processes take place. Chemical reactions can be described as cooperative translocation of two chemical entities on a common potential energy surface. Transport of atoms in a solid can be envisaged as the translocation of a single particle in the potential energy landscape of all other particles constituting the solid. The goal of this manuscript is to demonstrate common grounds but also distinct differences in the physico-chemical processes, their experimental quantification and their theoretical modelling. This work will span the range from the historical foundations all the way to the current challenges. While scientists at the beginning of the 20th century where commonly active in both fields, e. g., Wilhelm Jost has pioneered and shaped the field of transport in solids and reaction kinetics in Germany, the fields have drifted apart for the last 50 decades. It is now time to bring the fields together again. Ultimately, it is suggested that knowledge gained in the field of transport may in fact stimulate advancement in the field of molecular reactivity and vice versa. Here, the energy landscapes are pivotal for knowledge-based advancement.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400877"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Scanning Transmission Soft X-Ray Microscopy Probes Topical Drug Delivery of Rapamycin Facilitated by Microneedles. 扫描透射软 X 射线显微镜探测微针对雷帕霉素局部给药的促进作用

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-19 DOI: 10.1002/cphc.202400819

J A Laux, T Ohigashi, M R Bittermann, T Araki, H Yuzawa, F Rancan, A Vogt, E Rühl

{"title":"Scanning Transmission Soft X-Ray Microscopy Probes Topical Drug Delivery of Rapamycin Facilitated by Microneedles.","authors":"J A Laux, T Ohigashi, M R Bittermann, T Araki, H Yuzawa, F Rancan, A Vogt, E Rühl","doi":"10.1002/cphc.202400819","DOIUrl":"10.1002/cphc.202400819","url":null,"abstract":"Scanning Transmission X-ray microscopy (STXM) is a sensitive and selective probe for the penetration of rapamycin which is topically applied to human skin ex vivo and is facilitated by skin treatment with microneedles puncturing the skin. Inner-shell excitation serves as a selective probe for detecting rapamycin by changes in optical density as well as linear combination modeling using reference spectra of the most abundant species. The results indicate that mechanical damage induced by microneedles allows this drug to accumulate in the stratum corneum without reaching the viable skin layers. This is unlike intact skin which shows no drug penetration at all and underscores the mechanical impact of microneedle skin treatment. These results are compared to drug penetration profiles of other drugs highlighting the importance of skin barriers. High spatial resolution studies also indicate that the lipophilic drug rapamycin is observed in corneocytes. Attempts in data evaluation are reported to probe rapamycin also in the lipid layers between the corneocytes, which was not accomplished before. These results are compared to recent results on rapamycin uptake in skin where barrier impairment was induced by pre-treatment with the enzyme trypsin and drug formulations leading to occlusion.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400819"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11733402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational Study of Carbon Dioxide Capture by Tertiary Amines. 叔胺捕获二氧化碳的计算研究。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-11 DOI: 10.1002/cphc.202400754

Chalakon Pornjariyawatch, Varangkana Jitchum, Krit Assawatwikrai, Pakanan Leepakorn, Michael Probst, Bundet Boekfa, Thana Maihom, Jumras Limtrakul

{"title":"Computational Study of Carbon Dioxide Capture by Tertiary Amines.","authors":"Chalakon Pornjariyawatch, Varangkana Jitchum, Krit Assawatwikrai, Pakanan Leepakorn, Michael Probst, Bundet Boekfa, Thana Maihom, Jumras Limtrakul","doi":"10.1002/cphc.202400754","DOIUrl":"10.1002/cphc.202400754","url":null,"abstract":"The reaction mechanisms and corresponding structure-activity relationships of tertiary amines with respect to CO2 capture have been investigated using density functional theory (DFT) calculations. The reaction mechanism for CO2 capture via base-catalyzed hydration to form bicarbonate is proposed to proceed in a single step involving proton transfer and the formation of a carbon-oxygen bond. Based on the height of the reaction barriers, we suggest that amines containing side chains with the ethyl group, along with a single hydroxyl group, and cyclic structures, are especially active for CO2 capture. The activation barrier is shown to be a descriptor for predicting the experimental CO2 loading values. To enhance the prediction accuracy for CO2 loading, we employ the sure-independence screening and sparsifying operator (SISSO) method, which can scan a large pool of mathematical terms stemming from combining DFT-derived descriptors to select the superior ones. Thus, we can predict the CO2 loading with acceptable accuracy from the obtained mathematical expression. Since the computational workload of applying this expression is negligible, this facilitates high-throughput screening and accelerates the design of tertiary amines for CO2 capture.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400754"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Stoichiometric-Ratio-Controlled Fe and Ni Non-Noble Metal Catalysts Supported on γ-Al₂O₃ for Turquoise Hydrogen and Carbon Nanotubes Production. 用于生产绿松石氢和碳纳米管的以γ-Al2O3 为载体的铁和镍非贵金属催化剂的化学计量比控制。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-11 DOI: 10.1002/cphc.202400670

Aakash Rajpoot, Afaq Ahmad Khan, Indra Mohan, Siddhartha Sengupta, Ejaz Ahmad

{"title":"Stoichiometric-Ratio-Controlled Fe and Ni Non-Noble Metal Catalysts Supported on γ-Al2O3 for Turquoise Hydrogen and Carbon Nanotubes Production.","authors":"Aakash Rajpoot, Afaq Ahmad Khan, Indra Mohan, Siddhartha Sengupta, Ejaz Ahmad","doi":"10.1002/cphc.202400670","DOIUrl":"10.1002/cphc.202400670","url":null,"abstract":"Herein, we synthesized a series of catalysts comprising iron (Fe), and nickel (Ni) supported on γ-Al2O3 nano-powder (Fe-Ni/γ-Al2O3) by controlling the stoichiometric ratio of the metals through the facile co-precipitation method. The ratio of Fe and Ni on the γ-Al2O3 support varied from 0 to 70 weight percent (wt %). The freshly prepared catalysts phase, structure, and crystallinity exhibited variability as the Fe and Ni stoichiometric ratios were altered. The catalyst demonstrated effective performance in methane cracking, producing turquoise hydrogen and carbon nanotubes (CNTs) using a temperature-programmed reactor coupled with mass spectrometry. It was observed that the Fe3Ni4 catalyst, comprising 30 % Fe and 40 % Ni, exhibited a maximum methane conversion rate of 85 % and a hydrogen yield of 72.55 %. Moreover, the values of turnover frequency (2.38 min-1) indicated that the Fe3Ni4 had a better production rate and was consistent with the conversion process throughout the reaction. The structural attributes of the spent catalysts were examined, revealing variations in the lateral length, uniformity, and diameters (~33 to 56 nm) of the produced Carbon Nanotubes (CNTs) when transitioning from catalyst Fe0Ni7 to Fe7Ni0. The investigation underscored the significance of metal stoichiometrically controlled catalysts and their catalytic efficacy in methane cracking applications.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400670"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Halogen Substitution Strategy for Exploiting High-Performance Molecular Ferroelectrics. 开发高性能分子铁电的卤素置换策略。

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-14 DOI: 10.1002/cphc.202400801

Xingguang Chen, Haojie Xu, Wenjing Li, Junhua Luo, Zhihua Sun

引用次数: 0

Size Effects of Gold Nanoparticles on Surface Plasmon Resonance Assays for DNA Hybridization. 金纳米粒子对 DNA 杂交表面等离子共振检测的尺寸效应

IF 2.3 3区化学

Chemphyschem Pub Date : 2025-01-14 Epub Date: 2024-11-21 DOI: 10.1002/cphc.202400484

Zhen Li, Deming Yan, Tianbao Dong, Chaowei Han, Meng Jiang, Qing Kang, Pengcheng Wang, Yanhui Wang, Wenjuan Guo, Feimeng Zhou

{"title":"Size Effects of Gold Nanoparticles on Surface Plasmon Resonance Assays for DNA Hybridization.","authors":"Zhen Li, Deming Yan, Tianbao Dong, Chaowei Han, Meng Jiang, Qing Kang, Pengcheng Wang, Yanhui Wang, Wenjuan Guo, Feimeng Zhou","doi":"10.1002/cphc.202400484","DOIUrl":"10.1002/cphc.202400484","url":null,"abstract":"Recent advancements in signal amplifiers, such as biofunctionalized gold nanoparticles (AuNPs) have improved the surface plasmon resonance (SPR) performance. However, the correlation between the sizes of DNA-Au conjugates and the SPR chips remains elusive. We investigated how the size of AuNPs functioned with DNA detection probes (D-AuNPs) affect SPR signals in sandwich DNA hybridization assays. The effects of three sizes (5, 13, and 29 nm) of D-AuNPs with an equal surface probe density were systematically compared to delineate the relationship between signal amplification and steric hindrance. Sporadically adsorbed target DNA on sparse capture probe-coated chips led to a growth of signal amplification with larger D-AuNPs. In contrast, on dense capture probe-coated SPR chips, when the target DNA concentration was above 1.5 nM, the medium-sized 13 nm AuNPs displayed 1.7- and 1.3-fold enhancement factors than 5 nm and 29 nm ones, respectively. Our results indicate the steric hindrance disturbs the capture of D-AuNPs on dense target DNA-modified chips, rendering the surface density of captured D-AuNPs a determining factor of the sensor response. Alternatively, the sensor sensitivity to D-AuNP surface density is crucial on chips with sparse target DNA. These insights should stimulate and guide future research on surface functionalization toward SPR sensors and AuNPs.","PeriodicalId":9819,"journal":{"name":"Chemphyschem","volume":" ","pages":"e202400484"},"PeriodicalIF":2.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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