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Kumar A, Islam MR, Zughaier SM, Chen X, Zhao Y. Precision classification and quantitative analysis of bacteria biomarkers via surface-enhanced Raman spectroscopy and machine learning. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124627. [PMID: 38880073 DOI: 10.1016/j.saa.2024.124627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/19/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
The SERS spectra of six bacterial biomarkers, 2,3-DHBA, 2,5-DHBA, Pyocyanin, lipoteichoic acid (LTA), Enterobactin, and β-carotene, of various concentrations, were obtained from silver nanorod array substrates, and the spectral peaks and the corresponding vibrational modes were identified to classify different spectra. The spectral variations in three different concentration regions due to various reasons have imposed a challenge to use classic calibration curve methods to quantify the concentration of biomarkers. Depending on baseline removal strategy, i.e., local or global baseline removal, the calibration curve differed significantly. With the aid of convolutional neural network (CNN), a two-step process was established to classify and quantify biomarker solutions based on SERS spectra: using a specific CNN model, a remarkable differentiation and classification accuracy of 99.99 % for all six biomarkers regardless of the concentration can be achieved. After classification, six regression CNN models were established to predict the concentration of biomarkers, with coefficient of determination R2 > 0.97 and mean absolute error (MAE) < 0.27. The feature of important calculations indicates the high classification and quantification accuracies were due to the intrinsic spectral features in SERS spectra. This study showcases the synergistic potential of SERS and advanced machine learning algorithms and holds significant promise for bacterial infection diagnostics.
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Affiliation(s)
- Amit Kumar
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA
| | - Md Redwan Islam
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Susu M Zughaier
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, P.O. Box 2731, Qatar
| | - Xianyan Chen
- Department of Statistics, The University of Georgia, Athens, GA 30602, USA
| | - Yiping Zhao
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA.
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2
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Kozisek J, Hrncirova J, Slouf M, Sloufova I. Plasmon-driven substitution of 4-mercaptophenylboronic acid to 4-nitrothiophenol monitored by surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124523. [PMID: 38820811 DOI: 10.1016/j.saa.2024.124523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Plasmon-driven reactions on plasmonic nanoparticles (NPs) occur under significantly different conditions from those of classical organic synthesis and provide a promising pathway for enhancing the efficiency of various chemical processes. However, these reactions can also have undesirable effects, such as 4-mercaptophenylboronic acid (MPBA) deboronation. MPBA chemisorbs well to Ag NPs through its thiol group and can subsequently bind to diols, enabling the detection of various biological structures by surface-enhanced Raman scattering (SERS), but not upon its deboronation. To avoid this reaction, we investigated the experimental conditions of MPBA deboronation on Ag NPs by SERS. Our results showed that the level of deboronation strongly depends on both the morphology of the system and the excitation laser wavelength and power. In addition, we detected not only the expected products, namely thiophenol and biphenyl-4,4-dithiol, but also 4-nitrothiophenol (NTP). The crucial reagent for NTP formation was an oxidation product of hydroxylamine hydrochloride, the reduction agent used in Ag NP synthesis. Ultimately, this reaction was replicated by adding NaNO2 to the system, and its progress was monitored as a function of the laser power, thereby identifying a new reaction of plasmon-driven -B(OH)2 substitution for -NO2.
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Affiliation(s)
- Jan Kozisek
- Charles University, Faculty of Science, Department of Physical and Macromolecular Chemistry, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Jana Hrncirova
- Charles University, Faculty of Science, Department of Physical and Macromolecular Chemistry, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Miroslav Slouf
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho nam. 2, 162 06 Prague 6, Czech Republic
| | - Ivana Sloufova
- Charles University, Faculty of Science, Department of Physical and Macromolecular Chemistry, Hlavova 2030, 128 40 Prague 2, Czech Republic.
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3
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Li J, Cupil-Garcia V, Wang HN, Strobbia P, Lai B, Hu J, Maiwald M, Sumpf B, Sun TP, Kemner KM, Vo-Dinh T. Plasmonics nanorod biosensor for in situ intracellular detection of gene expression biomarkers in intact plant systems. Biosens Bioelectron 2024; 261:116471. [PMID: 38878695 DOI: 10.1016/j.bios.2024.116471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
The intracellular developmental processes in plants, particularly concerning lignin polymer formation and biomass production are regulated by microRNAs (miRNAs). MiRNAs including miR397b are important for developing efficient and cost-effective biofuels. However, traditional methods of monitoring miRNA expression, like PCR, are time-consuming, require sample extraction, and lack spatial and temporal resolution, especially in real-world conditions. We present a novel approach using plasmonics nanosensing to monitor miRNA activity within living plant cells without sample extraction. Plasmonic biosensors using surface-enhanced Raman scattering (SERS) detection offer high sensitivity and precise molecular information. We used the Inverse Molecular Sentinel (iMS) biosensor on unique silver-coated gold nanorods (AuNR@Ag) with a high-aspect ratio to penetrate plant cell walls for detecting miR397b within intact living plant cells. MiR397b overexpression has shown promise in reducing lignin content. Thus, monitoring miR397b is essential for cost-effective biofuel generation. This study demonstrates the infiltration of nanorod iMS biosensors and detection of non-native miRNA 397b within plant cells for the first time. The investigation successfully demonstrates the localization of nanorod iMS biosensors through TEM and XRF-based elemental mapping for miRNA detection within plant cells of Nicotiana benthamiana. The study integrates shifted-excitation Raman difference spectroscopy (SERDS) to decrease background interference and enhance target signal extraction. In vivo SERDS testing confirms the dynamic detection of miR397b in Arabidopsis thaliana leaves after infiltration with iMS nanorods and miR397b target. This proof-of-concept study is an important stepping stone towards spatially resolved, intracellular miRNA mapping to monitor biomarkers and biological pathways for developing efficient renewable biofuel sources.
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Affiliation(s)
- Joy Li
- Department of Biomedical Engineering, Duke University, Durham, NC, 27706, USA
| | | | - Hsin-Neng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27706, USA; Fitzpatrick Institute for Photonics, Durham, NC, 27706, USA
| | - Pietro Strobbia
- Department of Biomedical Engineering, Duke University, Durham, NC, 27706, USA
| | - Barry Lai
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Martin Maiwald
- Laser Sensors Lab, Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Gustav-Kirchhoff-Str. 4, D-12489, Berlin, Germany
| | - Bernd Sumpf
- Laser Sensors Lab, Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Gustav-Kirchhoff-Str. 4, D-12489, Berlin, Germany
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Tuan Vo-Dinh
- Department of Biomedical Engineering, Duke University, Durham, NC, 27706, USA; Department of Chemistry, Duke University, Durham, NC, 27706, USA; Fitzpatrick Institute for Photonics, Durham, NC, 27706, USA.
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4
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O'Neale CV, Tran MH, Schey KL. Aquaporin-0-protein interactions elucidated by crosslinking mass spectrometry. Biochem Biophys Res Commun 2024; 727:150320. [PMID: 38963984 DOI: 10.1016/j.bbrc.2024.150320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
Aquaporin-0 (AQP0) constitutes 50 % of the lens membrane proteome and plays important roles in lens fiber cell adhesion, water permeability, and lens transparency. Previous work has shown that specific proteins, such as calmodulin (CaM), interact with AQP0 to modulate its water permeability; however, these studies often used AQP0 peptides, rather than full-length protein, to probe these interactions. Furthermore, the specific regions of interaction of several known AQP0 interacting partners, i.e. αA and αB-crystallins, and phakinin (CP49) remain unknown. The purpose of this study was to use crosslinking mass spectrometry (XL-MS) to identify interacting proteins with full-length AQP0 in crude lens cortical membrane fractions and to determine the specific protein regions of interaction. Our results demonstrate, for the first time, that the AQP0 N-terminus can engage in protein interactions. Specific regions of interaction are elucidated for several AQP0 interacting partners including phakinin, α-crystallin, connexin-46, and connexin-50. In addition, two new interacting partners, vimentin and connexin-46, were identified.
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Affiliation(s)
- Carla Vt O'Neale
- Department of Biochemistry, Vanderbilt University, 465 21(ST), Ave, So. MRB III, Suite 9160, Nashville, TN, 37240, USA
| | - Minh H Tran
- Chemical and Physical Biology Program, 465 21(ST), Ave, So. MRB III, Suite 9160, Vanderbilt University, Nashville, TN, 37240, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, 465 21(ST), Ave, So. MRB III, Suite 9160, Nashville, TN, 37240, USA.
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Bolonova EI, Melnik TN, Potekhin SA. Inside of the burst-phase intermediate of a protein folding. Hydration of hydrophobic groups. Biophys Chem 2024; 312:107268. [PMID: 38843749 DOI: 10.1016/j.bpc.2024.107268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/07/2024] [Accepted: 05/20/2024] [Indexed: 07/22/2024]
Abstract
The thermal effect of the formation of the "burst-phase" folding intermediate has been studied using a titration calorimeter. It is shown that, unlike the total thermal effect of native structure formation, it can be both positive and negative depending on the temperature. The reasons for this paradoxical behavior are analyzed. A conclusion is drawn about the leading role of dehydration of non-polar groups in the first stage of folding.
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Affiliation(s)
- Elena I Bolonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergey A Potekhin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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Chen M, Lai X, Su B, Jiang X, Xu J, Fu F, Lin Z, Dong Y. Rapid detection of tebuconazole based on hydrogel SERS chips. Talanta 2024; 277:126309. [PMID: 38795591 DOI: 10.1016/j.talanta.2024.126309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Tebuconazole is one of the most commonly used fungicides in agricultural production, that has the merits of highly effectiveness, broad spectrum and systemic function. Excessive tebuconazole may pose a great threat to human and animal health. Traditional detection techniques for tebuconazole usually have limitations such as expensive equipment, poor antibody stability, and time-consuming procedures. Herein, a sensitive sensor is developed for the rapid detection of tebuconazole based on hydrogel surface-enhanced Raman scattering (SERS) chips. Aggregated Ag nanoparticles (a-AgNPs) with tunable localized surface plasmon resonance (LSPR) wavelength are in-situ synthesized in polyvinyl alcohol (PVA) solution for preparing hydrogel SERS chips. Three hydrogel SERS chips are obtained to match the three commonly used laser wavelengths. On the basis, a match laser wavelength is selected according to the energy levels of tebuconazole and the Fermi level of a-AgNPs to gain a strong chemical enhancement. At the same time, the chip with a corresponding LSPR wavelength to the laser is applied to obtain a strong electromagnetic enhancement. Thus, highly sensitive SERS signal of tebuconazole is obtained. Furthermore, the obtained hydrogel SERS chips have good repeatability, outstanding reproducibility and strong anti-interference ability, and show outstanding reliability in practical applications. As a result, the SERS chips offer a reliable and convenient platform for the quick detection of tebuconazole in foods. The detection limit is as low as 1 ppb, and the recoveries is distributed in the range of 94.66-106.70 %. This work would promote greatly the application of SERS in small molecule detection.
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Affiliation(s)
- Mingming Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Xiaojing Lai
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Bihang Su
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Xiancai Jiang
- College of Chemical Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jinhua Xu
- Fujian Inspection and Research Institute for Product Quality, National Center of Processed Foods Quality Supervision and Inspection, Fuzhou, 350002, China
| | - Fengfu Fu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
| | - Zhenyu Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yongqing Dong
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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7
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Le Ster M, Pawłowski S, Lutsyk I, Kowalczyk PJ. Fourier transform-based post-processing drift compensation and calibration method for scanning probe microscopy. Ultramicroscopy 2024; 263:113984. [PMID: 38744124 DOI: 10.1016/j.ultramic.2024.113984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Scanning probe microscopy (SPM) is ubiquitous in nanoscale science allowing the observation of features in real space down to the angstrom resolution. The scanning nature of SPM, wherein a sharp tip rasters the surface during which a physical setpoint is maintained via a control feedback loop, often implies that the image is subject to drift effects, leading to distortion of the resulting image. While there are in-operando methods to compensate for the drift, correcting the residual linear drift in obtained images is often neglected. In this paper, we present a reciprocal space-based technique to compensate the linear drift in atomically-resolved scanning probe microscopy images without distinction of the fast and slow scanning directions; furthermore this method does not require the set of SPM images obtained for the different scanning directions. Instead, the compensation is made possible by the a priori knowledge of the lattice parameters. The method can also be used to characterize and calibrate the SPM instrument.
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Affiliation(s)
- M Le Ster
- University of Lodz, Faculty of Physics and Applied Informatics, Department of Solid-State Physics, Pomorska 149/153, Lodz, 90-236, Poland.
| | - S Pawłowski
- University of Lodz, Faculty of Physics and Applied Informatics, Department of Solid-State Physics, Pomorska 149/153, Lodz, 90-236, Poland
| | - I Lutsyk
- University of Lodz, Faculty of Physics and Applied Informatics, Department of Solid-State Physics, Pomorska 149/153, Lodz, 90-236, Poland
| | - P J Kowalczyk
- University of Lodz, Faculty of Physics and Applied Informatics, Department of Solid-State Physics, Pomorska 149/153, Lodz, 90-236, Poland.
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8
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Dai Z, Ben-Younis A, Vlachaki A, Raleigh D, Thalassinos K. Understanding the structural dynamics of human islet amyloid polypeptide: Advancements in and applications of ion-mobility mass spectrometry. Biophys Chem 2024; 312:107285. [PMID: 38941872 PMCID: PMC11260546 DOI: 10.1016/j.bpc.2024.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/30/2024] [Accepted: 06/23/2024] [Indexed: 06/30/2024]
Abstract
Human islet amyloid polypeptide (hIAPP) forms amyloid deposits that contribute to β-cell death in pancreatic islets and are considered a hallmark of Type II diabetes Mellitus (T2DM). Evidence suggests that the early oligomers of hIAPP formed during the aggregation process are the primary pathological agent in islet amyloid induced β-cell death. The self-assembly mechanism of hIAPP, however, remains elusive, largely due to limitations in conventional biophysical techniques for probing the distribution or capturing detailed structures of the early, structurally dynamic oligomers. The advent of Ion-mobility Mass Spectrometry (IM-MS) has enabled the characterisation of hIAPP early oligomers in the gas phase, paving the way towards a deeper understanding of the oligomerisation mechanism and the correlation of structural information with the cytotoxicity of the oligomers. The sensitivity and the rapid structural characterisation provided by IM-MS also show promise in screening hIAPP inhibitors, categorising their modes of inhibition through "spectral fingerprints". This review delves into the application of IM-MS to the dissection of the complex steps of hIAPP oligomerisation, examining the inhibitory influence of metal ions, and exploring the characterisation of hetero-oligomerisation with different hIAPP variants. We highlight the potential of IM-MS as a tool for the high-throughput screening of hIAPP inhibitors, and for providing insights into their modes of action. Finally, we discuss advances afforded by recent advancements in tandem IM-MS and the combination of gas phase spectroscopy with IM-MS, which promise to deliver a more sensitive and higher-resolution structural portrait of hIAPP oligomers. Such information may help facilitate a new era of targeted therapeutic strategies for islet amyloidosis in T2DM.
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Affiliation(s)
- Zijie Dai
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Aisha Ben-Younis
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Anna Vlachaki
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK
| | - Daniel Raleigh
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States.
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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9
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Zheng J, Zhang W, Gong Y, Liang W, Leng Y. A novel near-infrared polymethine dye biosensor for rapid and selective detection of lithocholic acid. Biosens Bioelectron 2024; 259:116383. [PMID: 38749286 DOI: 10.1016/j.bios.2024.116383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
Lithocholic acid (LCA), a secondary bile acid, has emerged as a potential early diagnostic biomarker for various liver diseases. In this study, we introduce a novel near-infrared (NIR) polymethine dye-based biosensor, capable of sensitive and selective detection of LCA in phosphate buffer and artificial urine (AU) solutions. The detection mechanism relies on the formation of J-aggregates resulting from the interplay of 3,3-Diethylthiatricarbocyanine iodide (DiSC2(7)) dye molecules and LCA, which induces a distinctive red shift in both absorption and fluorescence spectra. The biosensor demonstrates a detection limit for LCA of 70 μM in PBS solution (pH 7.4), while in AU solution, it responds to an LCA concentration as low as ∼60 μM. Notably, the proposed biosensor exhibits outstanding selectivity for LCA, effectively distinguishing it from common interferents such as uric acid, ascorbic acid, and glucose. This rapid, straightforward, and cost-effective spectrometer-based method underscores its potential for early diagnosis of liver diseases by monitoring LCA concentrations.
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Affiliation(s)
- Jianlu Zheng
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-Ku, Tokyo, 153-8505, Japan
| | - Wencui Zhang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Equipe Chimie des Polymères, Institut Parisien de Chimie Moléculaire (UMR-CNRS 8232), Sorbonne Université, 75252, Paris, France
| | - Yanli Gong
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Wenlang Liang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yongxiang Leng
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China; Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
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Yuan D, Qi Y, Ma C, Fu P, Volmer DA. Selective molecular characterization of organic aerosols using in situ laser desorption ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9847. [PMID: 38890224 DOI: 10.1002/rcm.9847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
RATIONALE The sources and chemical compositions of organic aerosol (OA) exert a significant influence on both regional and global atmospheric conditions, thereby having far-reaching implications on environmental chemistry. However, existing mass spectrometry (MS) methods have limitations in characterizing the detailed composition of OA due to selective ionization as well as fractionation during cold-water extraction and solid-phase extraction (SPE). METHODS A comprehensive MS study was conducted using aerosol samples collected on dusty, clean, and polluted days. To supplement the data obtained from electrospray ionization (ESI), a strategy for analyzing OAs collected using the quartz fiber filter directly utilizing laser desorption ionization (LDI) was employed. Additionally, the ESI method was conducted to explore suitable approaches for determining various OA compositions from samples collected on dusty, clean, and polluted days. RESULTS In situ LDI has the advantages of significantly reducing the sample volume, simplifying sample preparation, and overcoming the problem of overestimating sulfur-containing compounds usually encountered in ESI. It is suitable for the characterization of highly unsaturated and hydrophobic aerosols, such as brown carbon-type compounds with low volatility and high stability, which is supplementary to ESI. CONCLUSIONS Compared with other ionization methods, in situ LDI helps provide a complementary description of the molecular compositions of OAs, especially for analyzing OAs in polluted day samples. This method may contribute to a more comprehensive MS analysis of the elusive compositions and sources of OA in the atmosphere.
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Affiliation(s)
- Daohe Yuan
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Yulin Qi
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
- Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, China
| | - Chao Ma
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
- Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, China
| | - Dietrich A Volmer
- Bioanalytical Chemistry, Department of Chemistry, Humboldt University Berlin, Berlin, Germany
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Liu T, Wang P, Chen Y, Sun B, Li Q, Wan H, Yang W, Ma P, Zhang D, Dong G, Chen S, Chen Q, Ma W, Sun W. LC-MS and MALDI-MSI-based metabolomic approaches provide insights into the spatial-temporal metabolite profiles of Tartary buckwheat achene development. Food Chem 2024; 449:139183. [PMID: 38604028 DOI: 10.1016/j.foodchem.2024.139183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Tartary buckwheat, celebrated as the "king of grains" for its flavonoid and phenolic acid richness, has health-promoting properties. Despite significant morphological and metabolic variations in mature achenes, research on their developmental process is limited. Utilizing Liquid chromatography-mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry imaging, we conducted spatial-temporal metabolomics on two cultivars during achene development. Metabolic profiles including 17 phenolic acids and 83 flavonoids are influenced by both varietal distinctions and developmental intricacies. Notably, flavonols, as major flavonoids, accumulated with achene ripening and showed a tissue-specific distribution. Specifically, flavonol glycosides and aglycones concentrated in the embryo, while methylated flavonols and procyanidins in the hull. Black achenes at the green achene stage have higher bioactive compounds and enhanced antioxidant capacity. These findings provide insights into spatial and temporal characteristics of metabolites in Tartary buckwheat achenes and serve as a theoretical guide for selecting optimal resources for food production.
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Affiliation(s)
- Tingxia Liu
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Peng Wang
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Yiling Chen
- Amway (China) Botanical R&D Centre, Wuxi 214115, China
| | - Boshi Sun
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Qing Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huihua Wan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Pengda Ma
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Dong Zhang
- College of Agriculture, South China Agricultural University, Guangzhou Laboratory for Lingnan Modern Agriculture Science and Technology, Guangzhou 510642, China
| | | | - Shilin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu15 116, Guiyang 550001, China
| | - Wei Ma
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Wei Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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12
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Cernatic F, Fromager E. Extended N-centered ensemble density functional theory of double electronic excitations. J Comput Chem 2024; 45:1945-1962. [PMID: 38700389 DOI: 10.1002/jcc.27387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
A recent work (arXiv:2401.04685) has merged N-centered ensembles of neutral and charged electronic ground states with ensembles of neutral ground and excited states, thus providing a general and in-principle exact (so-called extended N-centered) ensemble density functional theory of neutral and charged electronic excitations. This formalism made it possible to revisit the concept of density-functional derivative discontinuity, in the particular case of single excitations from the highest occupied Kohn-Sham (KS) molecular orbital, without invoking the usual "asymptotic behavior of the density" argument. In this work, we address a broader class of excitations, with a particular focus on double excitations. An exact implementation of the theory is presented for the two-electron Hubbard dimer model. A thorough comparison of the true physical ground- and excited-state electronic structures with that of the fictitious ensemble density-functional KS system is also presented. Depending on the choice of the density-functional ensemble as well as the asymmetry of the dimer and the correlation strength, an inversion of states can be observed. In some other cases, the strong mixture of KS states within the true physical system makes the assignment "single excitation" or "double excitation" irrelevant.
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Affiliation(s)
- Filip Cernatic
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, Strasbourg, France
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, Strasbourg, France
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13
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Fang J, Zhu YN, Long X, Li XB, Zhang Q, Yang G, Du S, Liu Z, Liu Z, Peng F. Theoretical calculations and experimental verification of carbon dioxide reduction electrocatalyzed by metalloporphyrin. J Colloid Interface Sci 2024; 668:366-374. [PMID: 38678891 DOI: 10.1016/j.jcis.2024.04.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Metal-functionalized porphyrin-like graphene structures are promising electrocatalysts for carbon dioxide reduction reaction (CO2RR) as their metal centers can modulate activity. Yet, the role of metal center of metalloporphyrins (MTPPs) in CO2 reaction activity is still lacking deep understanding. Here, CO2RR mechanism on MTPPs with five different metal centers (M = Fe, Co, Cu, Zn and Ni) are examined by first-principles calculations. The *COOH formation is the rate determined step on the five MTPP structures, and the CoTPP exhibits the best CO2RR activity while ZnTPP and NiTPP are the worst, which is also verified by our experiment. The CO2RR activity is controlled by adsorption states of intermediates (*CO, *COOH), i.e., chemisorption (e.g., on CoTPP) and physisorption (on ZnTPP and NiTPP) of intermediates will lead to good and poor activity, respectively. The deeper the d-band center of the porphyrin ring complexed metal atom, the weaker bonding of MTPP with CO and COOH. Theoretical calculations and experimental results indicate that MTPPs with Co and Fe centers lead to a reduction in the energy barriers for the two uphill reaction steps in the electrocatalytic CO2 reduction process, thereby enhancing CO2 reduction electrocatalytic activity. Faradaic efficiency of CO is correlated with the reaction energy barrier of the first proton-coupled electron reduction process, displaying a strong linear correlation. This work provides a fundamental understanding of MTPPs used as electrocatalysts for CO2RR.
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Affiliation(s)
- Jun Fang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Ya-Nan Zhu
- Institute of Semiconductors, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Xuemei Long
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xi-Bo Li
- Department of Physics, Jinan University, Guangzhou 510632, China
| | - Qiao Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Guangxing Yang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Shengjun Du
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zhting Liu
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zhuming Liu
- Institute of Semiconductors, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Feng Peng
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China.
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14
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Sun Z, Wang X, An H, Liang S, Li N. A review on intelligence of cellulose based materials. Carbohydr Polym 2024; 338:122219. [PMID: 38763716 DOI: 10.1016/j.carbpol.2024.122219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Cellulose based materials are widely used in various fields such as papermaking, packaging, composite materials, textiles and clothing due to their diverse types, environmental friendliness, natural degradation, high specific strength, and low cost. The intelligence of cellulose based materials will further expand their application fields. This article first gives an in-depth analyzation on the intelligent structural design of these materials according to the two major categories of isotropic and anisotropic, then lists the main preparation methods of cellulose based intelligent materials. Subsequently, this article systematically summarizes the recent intelligent response methods and characteristics of cellulose based materials, and extensively elaborates on the intelligent application of these materials. Finally, the prospects for the intelligence of cellulose based materials are discussed.
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Affiliation(s)
- Zhanying Sun
- Hebei Key Laboratory of Flexible Functional Materials, School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China..
| | - Xin Wang
- Hebei Key Laboratory of Flexible Functional Materials, School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China..
| | - Haoran An
- Hebei Key Laboratory of Flexible Functional Materials, School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China..
| | - Shuang Liang
- Hebei Key Laboratory of Flexible Functional Materials, School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China..
| | - Na Li
- Hebei Key Laboratory of Flexible Functional Materials, School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China..
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15
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Berge E, Ulimoen M, Dobler A, Kashparov VA, Klein H, Lind OC. A study of particle dry deposition parameterizations in an atmospheric radioactive preparedness model: Application to the Chernobyl case. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134638. [PMID: 38838529 DOI: 10.1016/j.jhazmat.2024.134638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Parameterization of dry deposition is key for modelling of atmospheric transport and deposition of radioactive particles. Still, very simple parameterizations are often encountered in radioactive preparedness models such as the SNAP model (SNAP=Severe Nuclear Accident Program) of the Norwegian Meteorological Institute. In SNAP a constant dry deposition velocity (=0.2 cm/s) neglecting aerodynamic and surface resistances, is presently used. Therefore, two new dry depositions schemes (the Emerson scheme and the EMEP (European Monitoring and Evaluation Programme) scheme) have been implemented in SNAP to evaluate the benefits of including aerodynamic and surface resistances codes with respect to model prediction skills. The three dry deposition schemes are evaluated using 137Cs total deposition from soil sample data (n = 540) for a 60 km radial zone out from the Chernobyl Nuclear Power Plant (ChNPP) collected during the months after the accident. The present study capitalizes on high resolution meteorological data (2.5 km horizontal resolution), a detailed land-use data set with 273 sub-classes and the hitherto most comprehensive source term description for the Chernobyl accident. Based on our findings it is recommended to replace the present simple SNAP scheme with the Emerson or EMEP dry deposition scheme.
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Affiliation(s)
- Erik Berge
- The Norwegian Meteorological Institute, Oslo, Norway.
| | | | | | - Valery Alexandrovich Kashparov
- Ukrainian Institute of Agricultural Radiology (UIAR) of National University of Life and Environment Sciences of Ukraine, Kyiv, Ukraine
| | - Heiko Klein
- The Norwegian Meteorological Institute, Oslo, Norway
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16
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Voss J. Machine learning for accuracy in density functional approximations. J Comput Chem 2024; 45:1829-1845. [PMID: 38668453 DOI: 10.1002/jcc.27366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 07/21/2024]
Abstract
Machine learning techniques have found their way into computational chemistry as indispensable tools to accelerate atomistic simulations and materials design. In addition, machine learning approaches hold the potential to boost the predictive power of computationally efficient electronic structure methods, such as density functional theory, to chemical accuracy and to correct for fundamental errors in density functional approaches. Here, recent progress in applying machine learning to improve the accuracy of density functional and related approximations is reviewed. Promises and challenges in devising machine learning models transferable between different chemistries and materials classes are discussed with the help of examples applying promising models to systems far outside their training sets.
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Affiliation(s)
- Johannes Voss
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California, USA
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17
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Fazel K, Karimitari N, Shah T, Sutton C, Sundararaman R. Improving the reliability of machine learned potentials for modeling inhomogeneous liquids. J Comput Chem 2024; 45:1821-1828. [PMID: 38662330 DOI: 10.1002/jcc.27353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids-including the density response, surface tension and size-dependent cavitation free energies-for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.
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Affiliation(s)
- Kamron Fazel
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Nima Karimitari
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Tanooj Shah
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Christopher Sutton
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
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18
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Upadhyay S, Kumar A, Srivastava M, Srivastava A, Dwivedi A, Singh RK, Srivastava SK. Recent advancements of smartphone-based sensing technology for diagnosis, food safety analysis, and environmental monitoring. Talanta 2024; 275:126080. [PMID: 38615454 DOI: 10.1016/j.talanta.2024.126080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/16/2024]
Abstract
The emergence of computationally powerful smartphones, relatively affordable high-resolution camera, drones, and robotic sensors have ushered in a new age of advanced sensible monitoring tools. The present review article investigates the burgeoning smartphone-based sensing paradigms, including surface plasmon resonance (SPR) biosensors, electrochemical biosensors, colorimetric biosensors, and other innovations for modern healthcare. Despite the significant advancements, there are still scarcity of commercially available smart biosensors and hence need to accelerate the rates of technology transfer, application, and user acceptability. The application/necessity of smartphone-based biosensors for Point of Care (POC) testing, such as prognosis, self-diagnosis, monitoring, and treatment selection, have brought remarkable innovations which eventually eliminate sample transportation, sample processing time, and result in rapid findings. Additionally, it articulates recent advances in various smartphone-based multiplexed bio sensors as affordable and portable sensing platforms for point-of-care devices, together with statistics for point-of-care health monitoring and their prospective commercial viability.
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Affiliation(s)
- Satyam Upadhyay
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Anil Kumar
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Monika Srivastava
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Amit Srivastava
- Department of Physics TDPG College, VBS Purvanchal University, Jaunpur, 222001, India
| | - Arpita Dwivedi
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Rajesh Kumar Singh
- School of Physical and Material Sciences, Central University of Himachal Pradesh, Dharamshala, Kangra, 176215, India
| | - S K Srivastava
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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19
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Cvekl A, Vijg J. Aging of the eye: Lessons from cataracts and age-related macular degeneration. Ageing Res Rev 2024; 99:102407. [PMID: 38977082 DOI: 10.1016/j.arr.2024.102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Aging is the greatest risk factor for chronic human diseases, including many eye diseases. Geroscience aims to understand the effects of the aging process on these diseases, including the genetic, molecular, and cellular mechanisms that underlie the increased risk of disease over the lifetime. Understanding of the aging eye increases general knowledge of the cellular physiology impacted by aging processes at various biological extremes. Two major diseases, age-related cataract and age-related macular degeneration (AMD) are caused by dysfunction of the lens and retina, respectively. Lens transparency and light refraction are mediated by lens fiber cells lacking nuclei and other organelles, which provides a unique opportunity to study a single aging hallmark, i.e., loss of proteostasis, within an environment of limited metabolism. In AMD, local dysfunction of the photoreceptors/retinal pigmented epithelium/Bruch's membrane/choriocapillaris complex in the macula leads to the loss of photoreceptors and eventually loss of central vision, and is driven by nearly all the hallmarks of aging and shares features with Alzheimer's disease, Parkinson's disease, cardiovascular disease, and diabetes. The aging eye can function as a model for studying basic mechanisms of aging and, vice versa, well-defined hallmarks of aging can be used as tools to understand age-related eye disease.
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Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Jan Vijg
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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20
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Rai A, Jha NS, Sharma P, Tiwari S, Subramanian R. Curcumin-derivatives as fluorescence-electrochemical dual probe for ultrasensitive detections of picric acid in aqueous media. Talanta 2024; 275:126113. [PMID: 38669958 DOI: 10.1016/j.talanta.2024.126113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]
Abstract
We are reporting the two curcumin derivatives, ferrocenyl curcumin (Fc-cur) and 4-nitro-benzylidene curcumin (NBC), as a probe through dual modalities, i.e., fluorescence and electrochemical methods, for the detection of nitro-analytes, such as picric acid (PA). The probes exhibited aggregation-induced enhanced emission (AIEE), and the addition of picric acid (PA) demonstrated good and specific fluorimetric identification of PA in the aggregated state. By using density functional theory (DFT), the mechanism of picric acid's (PA) interactions with the probes was further investigated. DFT studies shows evidence of charge transfer from curcumin derivatives probe to picric acid resulting into the formation of an adduct. The reduction of trinitrophenol (PA) to 2, 4, 6-trinitrosophenol was investigated utilizing a probe-modified glassy carbon electrode (GCE) with a good detection limit of 9.63 ± 0.001 pM and 41.01 ± 0.002 pM, respectively, for Fc-cur@GCE and NBC@GCE, taking into account the redox behavior of the probe. The applicability of the designed sensor has been utilized for real-time application in the estimation of picric acid in several water samples collected from the different source.
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Affiliation(s)
- Anupama Rai
- Department of Chemistry, National Institute of Technology, Ashok Rajpath, Patna, 800005, Bihar, India
| | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology, Ashok Rajpath, Patna, 800005, Bihar, India.
| | - Padma Sharma
- Department of Chemistry, National Institute of Technology, Ashok Rajpath, Patna, 800005, Bihar, India
| | - Suresh Tiwari
- Department of Chemistry, Indian Institute of Technology, Patna, 801106, Bihar, India
| | - Ranga Subramanian
- Department of Chemistry, Indian Institute of Technology, Patna, 801106, Bihar, India
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21
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Mohammed Ameen SS, Omer KM. Temperature-resilient and sustainable Mn-MOF oxidase-like nanozyme (UoZ-4) for total antioxidant capacity sensing in some citrus fruits: Breaking the temperature barrier. Food Chem 2024; 448:139170. [PMID: 38579558 DOI: 10.1016/j.foodchem.2024.139170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/04/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
Current nanozyme applications rely heavily on peroxidase-like nanozymes and are limited to a specific temperature range, despite notable advancements in nanozyme development. In this work, we designed novel Mn-based metal organic frameworks (UoZ-4), with excellent oxidase mimic activity towards common substrates. UoZ-4 showed excellent oxidase-like activity (with Km 0.072 mM) in a wide range of temperature, from 10 °C to 100 °C with almost no activity loss, making it a very strong candidate for psychrophilic and thermophilic applications. Ascorbic acid, cysteine, and glutathione could quench the appearance of the blue color of oxTMB, led us to design a visual-based sensing platform for detection of total antioxidant capacity (TAC) in cold, mild and hot conditions. The visual mode successfully assessed TAC in citrus fruits with satisfactory recovery and precisions. Cold/hot adapted and magnetic property will broaden the horizon of nanozyme applications and breaks the notion of the temperature limitation of enzymes.
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Affiliation(s)
| | - Khalid M Omer
- Department of Chemistry, College of Science, University of Sulaimani, Qliasan St., 46002 Sulaymaniyah, Kurdistan region, Iraq..
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22
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Lei H, Wang H, Wang X, Xiao Z, Tian T, Cui K. Surface-enhanced Raman scattering-based identification of breast cancer progression using extracellular vesicles-derived integrin α6β4. Talanta 2024; 275:126092. [PMID: 38615459 DOI: 10.1016/j.talanta.2024.126092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Detection of progression is of great importance to breast cancer treatment and can benefit patients. Limited by current detection technologies and biomarkers, early breast cancer progression diagnosis remains challenging. Researchers have found blood extracellular vesicles (EVs)-derived integrin α6β4 directly facilitate progression in breast cancer, enabling cancer detection. However, EVs size and heterogeneity hinder protein detection, masked by abundant background EVs. Hence, novel tools for efficient detection of EVs with high selectivity and low interference are significantly desired. Here, a new silver-coated gold nanorods SERS probe, termed as Au@Ag@IDA-B/4MSTP, based on DNA aptamer was established for the detection of integrin α6β4 derived from EVs. Validation of the Au@Ag@IDA-B/4MSTP probes using cell-culture-derived EVs revealed a LOD of 23 particles/μL for EVs detection. This tool was further confirmed to mimic the real state of cancer with subcutaneous tumor model and lung metastasis model in mice. With 10 μL of blood plasma and simple Raman analysis process, the test achieved 85.7 % sensitivity and 83.3 % specificity. Moreover, our method achieves a simplified approach that expedites the detection process. These results demonstrate the good detection performance of Au@Ag@IDA-B/4MSTP probes for EVs integrin α6β4, and suggest that this non-invasive approach could be a promising tool for early detection of breast cancer progression.
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Affiliation(s)
- Haozhi Lei
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Shanghai, 200127, China
| | - Haoze Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China; College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
| | - Xiqiu Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zeyu Xiao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Tian Tian
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Kai Cui
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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23
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Liistro E, Battistuzzi M, Cocola L, Claudi R, Poletto L, La Rocca N. Synechococcus sp. PCC7335 responses to far-red enriched spectra and anoxic/microoxic atmospheres: Potential for astrobiotechnological applications. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108793. [PMID: 38870681 DOI: 10.1016/j.plaphy.2024.108793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Recently, cyanobacteria have gained attention in space exploration to support long-term crewed missions via Bioregenerative Life Support Systems. In this frame, cyanobacteria would provide biomass and profitable biomolecules through oxygenic photosynthesis, uptaking CO2, and releasing breathable O2. Their growth potential and organic matter production will depend on their ability to photoacclimate to different light intensities and spectra, maximizing incident light harvesting. Studying cyanobacteria responses to different light regimes will also benefit the broader field of astrobiology, providing data on the possibility of oxygenic photosynthetic life on planets orbiting stars with emission spectra different than the Sun. Here, we tested the acclimation and productivity of Synechococcus sp. PCC7335 (hereafter PCC7335), capable of Far-Red Light Photoacclimation (FaRLiP) and type III chromatic acclimation (CA3), in an anoxic, CO2-enriched atmosphere and under a spectrum simulating the low energetic light regime of an M-dwarf star, also comparable to a subsuperficial environment. When exposed to the light spectrum, with few photons in the visible (VIS) and rich in far-red (FR), PCC7335 did not activate FaRLiP but acclimated only via CA3, achieving a biomass productivity higher than expected, considering the low VIS light availability, and a higher production of phycocyanin, a valuable pigment, with respect to solar light. Its growth or physiological responses of PCC7335 were not affected by the anoxic atmosphere. In these conditions, PCC7335 efficiently produced O2 and scavenged CO2. Results highlight the photosynthetic plasticity of PCC7335, its suitability for astrobiotechnological applications, and the importance to investigate biodiversity of oxygenic photosynthesis for searching life beyond Earth.
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Affiliation(s)
| | - Mariano Battistuzzi
- Department of Biology, University of Padua, Padua, Italy; CNR-IFN, Padua, Italy; Giuseppe Colombo University Center for Studies and Activities, University of Padua, Padua, Italy
| | | | - Riccardo Claudi
- National Institute for Astrophysics, Astronomical Observatory of Padua (INAF-OAPD), Padua, Italy; Department of Mathematics and Physics, University Roma Tre, Rome, Italy
| | | | - Nicoletta La Rocca
- Department of Biology, University of Padua, Padua, Italy; Giuseppe Colombo University Center for Studies and Activities, University of Padua, Padua, Italy.
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24
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Zhou Y, Cui X, Wu B, Wang Z, Liu Y, Ren T, Xia S, Rittmann BE. Microalgal extracellular polymeric substances (EPS) and their roles in cultivation, biomass harvesting, and bioproducts extraction. BIORESOURCE TECHNOLOGY 2024; 406:131054. [PMID: 38944317 DOI: 10.1016/j.biortech.2024.131054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Microalgae extracellular polymeric substances (EPS) are complex high-molecular-weight polymers and the physicochemical properties of EPS strongly affect the core features of microalgae cultivation and resource utilization. Revealing the key roles of EPS in microalgae life-cycle processes in an interesting and novelty topic to achieve energy-efficient practical application of microalgae. This review found that EPS showed positive effect in non-gas uptake, extracellular electron transfer, toxicity resistance and heterotrophic symbiosis, but negative impact in gas transfer and light utilization during microalgae cultivation. For biomass harvesting, EPS favored biomass flocculation and large-size cell self-flocculation, but unfavored small size microalgae self-flocculation, membrane filtration, charge neutralization and biomass dewatering. During bioproducts extraction, EPS exhibited positive impact in extractant uptake, but the opposite effect in cellular membrane permeability and cell rupture. Future research on microalgal EPS were also identified, which offer suggestions for comprehensive understanding of microalgal EPS roles in various scenarios.
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Affiliation(s)
- Yun Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaocai Cui
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Beibei Wu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziqi Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Ren
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5701, United States of America
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25
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Ami D, Franco AR, Artusa V, Romerio A, Shaik MM, Italia A, Anguita J, Pasco S, Mereghetti P, Peri F, Natalello A. Vibrational spectroscopy coupled with machine learning sheds light on the cellular effects induced by rationally designed TLR4 agonists. Talanta 2024; 275:126104. [PMID: 38677166 DOI: 10.1016/j.talanta.2024.126104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
In this work, we present the potential of Fourier transform infrared (FTIR) microspectroscopy to compare on whole cells, in an unbiased and untargeted way, the capacity of bacterial lipopolysaccharide (LPS) and two rationally designed molecules (FP20 and FP20Rha) to activate molecular circuits of innate immunity. These compounds are important drug hits in the development of vaccine adjuvants and tumor immunotherapeutics. The biological assays indicated that FP20Rha was more potent than FP20 in inducing cytokine production in cells and in stimulating IgG antibody production post-vaccination in mice. Accordingly, the overall significant IR spectral changes induced by the treatment with LPS and FP20Rha were similar, lipids and glycans signals being the most diagnostic, while the effect of the less potent molecule FP20 on cells resulted to be closer to control untreated cells. We propose here the use of FTIR spectroscopy supported by artificial intelligence (AI) to achieve a more holistic understanding of the cell response to new drug candidates while screening them in cells.
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Affiliation(s)
- Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Ana Rita Franco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Valentina Artusa
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Alessio Romerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Mohammed Monsoor Shaik
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Alice Italia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Juan Anguita
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Samuel Pasco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | | | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy.
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26
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Hameed S, Sharif S, Ovais M, Xiong H. Emerging trends and future challenges of advanced 2D nanomaterials for combating bacterial resistance. Bioact Mater 2024; 38:225-257. [PMID: 38745587 PMCID: PMC11090881 DOI: 10.1016/j.bioactmat.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
The number of multi-drug-resistant bacteria has increased over the last few decades, which has caused a detrimental impact on public health worldwide. In resolving antibiotic resistance development among different bacterial communities, new antimicrobial agents and nanoparticle-based strategies need to be designed foreseeing the slow discovery of new functioning antibiotics. Advanced research studies have revealed the significant disinfection potential of two-dimensional nanomaterials (2D NMs) to be severed as effective antibacterial agents due to their unique physicochemical properties. This review covers the current research progress of 2D NMs-based antibacterial strategies based on an inclusive explanation of 2D NMs' impact as antibacterial agents, including a detailed introduction to each possible well-known antibacterial mechanism. The impact of the physicochemical properties of 2D NMs on their antibacterial activities has been deliberated while explaining the toxic effects of 2D NMs and discussing their biomedical significance, dysbiosis, and cellular nanotoxicity. Adding to the challenges, we also discussed the major issues regarding the current quality and availability of nanotoxicity data. However, smart advancements are required to fabricate biocompatible 2D antibacterial NMs and exploit their potential to combat bacterial resistance clinically.
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Affiliation(s)
- Saima Hameed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
- School of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Sumaira Sharif
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ovais
- BGI Genomics, BGI Shenzhen, Shenzhen, 518083, Guangdong, PR China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
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27
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Borkar S, Baumli P, Vance T, Sharma E, Shi X, Wu JY, Yao G, Myung D, Fuller GG. Elucidating the roles of electrolytes and hydrogen bonding in the dewetting dynamics of the tear film. Proc Natl Acad Sci U S A 2024; 121:e2407501121. [PMID: 39042697 DOI: 10.1073/pnas.2407501121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
This study explores the impact of electrostatic interactions and hydrogen bonding on tear film stability, a crucial factor for ocular surface health. While mucosal and meibomian layers have been extensively studied, the role of electrolytes in the aqueous phase remains unclear. Dry eye syndrome, characterized by insufficient tear quantity or quality, is associated with hyperosmolality, making electrolyte composition an important factor that might impact tear stability. Using a model buffer solution on a silica glass dome, we simulated physiologically relevant tear film conditions. Sodium chloride alone induced premature dewetting through salt crystal nucleation. In contrast, trace amounts of solutes with hydroxyl groups (sodium phosphate dibasic, potassium phosphate monobasic, and glucose) exhibited intriguing phenomena: quasi-stable films, solutal Marangoni-driven fluid influx increasing film thickness, and viscous fingering due to Saffman-Taylor instability. These observations are rationalized by the association of salt solutions with increased surface tension and the propensity of hydroxyl-group-containing solutes to engage in significant hydrogen bonding, altering local viscosity. This creates a viscosity contrast between the bulk buffer solution and the film region. Moreover, these solutes shield the glass dome, counteracting sodium chloride crystallization. These insights not only advance our understanding of tear film mechanics but also pave the way for predictive diagnostics in dry eye syndrome, offering a robust platform for personalized medical interventions based on individual tear film composition.
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Affiliation(s)
- Suraj Borkar
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Philipp Baumli
- Alcon Research, Limited Liability Company, Fort Worth, TX 76134
| | - Travis Vance
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Ekta Sharma
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Xinfeng Shi
- Alcon Research, Limited Liability Company, Fort Worth, TX 76134
| | - James Y Wu
- Alcon Research, Limited Liability Company, Fort Worth, TX 76134
| | - George Yao
- Alcon Research, Limited Liability Company, Fort Worth, TX 76134
| | - David Myung
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Spencer Center for Vision Research, Byers Eye Institute, Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94303
| | - Gerald G Fuller
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
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28
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Ward JS, Vezzoli A, Wells C, Bailey S, Jarvis SP, Lambert CJ, Robertson C, Nichols RJ, Higgins SJ. A Systematic Study of Methyl Carbodithioate Esters as Effective Gold Contact Groups for Single-Molecule Electronics. Angew Chem Int Ed Engl 2024; 63:e202403577. [PMID: 38770763 DOI: 10.1002/anie.202403577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
There are several binding groups used within molecular electronics for anchoring molecules to metal electrodes (e.g., R-SMe, R-NH2, R-CS2 -, R-S-). However, some anchoring groups that bind strongly to electrodes have poor/unknown stability, some have weak electrode coupling, while for some their binding motifs are not well defined. Further binding groups are required to aid molecular design and to achieve a suitable balance in performance across a range of properties. We present an in-depth investigation into the use of carbodithioate esters as contact groups for single-molecule conductance measurements, using scanning tunnelling microscopy break junction measurements (STM-BJ) and detailed surface spectroscopic analysis. We demonstrate that the methyl carbodithioate ester acts as an effective contact for gold electrodes in STM-BJ measurements. Surface enhanced Raman measurements demonstrate that the C=S functionality remains intact when adsorbed on to gold nanoparticles. A gold(I) complex was also synthesised showing a stable C=S→AuI interaction from the ester. Comparison with a benzyl thiomethyl ether demonstrates that the C=S moiety significantly contributes to charge transport in single-molecule junctions. The overall performance of the CS2Me group demonstrates it should be used more extensively and has strong potential for the fabrication of larger area devices with long-term stability.
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Affiliation(s)
- Jonathan S Ward
- Department of Chemistry, University of Liverpool, Crown St., Liverpool, L69 7ZD, UK
- Chemistry Department, Lancaster University, Bailrigg, Lancaster, LA1 4YB, UK
| | - Andrea Vezzoli
- Department of Chemistry, University of Liverpool, Crown St., Liverpool, L69 7ZD, UK
| | - Charlie Wells
- Physics Department, Lancaster University, Bailrigg, Lancaster, LA1 4YW, UK
| | - Steven Bailey
- Physics Department, Lancaster University, Bailrigg, Lancaster, LA1 4YW, UK
| | - Samuel P Jarvis
- Physics Department, Lancaster University, Bailrigg, Lancaster, LA1 4YW, UK
| | - Colin J Lambert
- Physics Department, Lancaster University, Bailrigg, Lancaster, LA1 4YW, UK
| | - Craig Robertson
- Department of Chemistry, University of Liverpool, Crown St., Liverpool, L69 7ZD, UK
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool, Crown St., Liverpool, L69 7ZD, UK
| | - Simon J Higgins
- Department of Chemistry, University of Liverpool, Crown St., Liverpool, L69 7ZD, UK
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29
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Dall'Osto G, Corni S. Time-dependent surface-enhanced Raman scattering: A theoretical approach. J Chem Phys 2024; 161:044103. [PMID: 39037131 DOI: 10.1063/5.0214564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
A new procedure for computing the time-dependent Raman scattering of molecules in the proximity of plasmonic nanoparticles (NPs) is proposed, drawing inspiration from the pioneering Lee and Heller's theory. This strategy is based on a preliminary simulation of the molecular vibronic wavefunction in the presence of a plasmonic nanostructure and an incident light pulse. Subsequently, the Raman signal is evaluated through an inverse Fourier Transform of the coefficients' dynamics. Employing a multiscale approach, the system is treated by coupling the quantum mechanical description of the molecule with the polarizable continuum model for the NP. This method offers a unique advantage by providing insights into the time evolution of the plasmon-enhanced Raman signal, tracking the dynamics of the incident electric field. It not only provides for the total Raman signal at the process's conclusion but also gives transient information. Importantly, the flexibility of this approach allows for the simulation of various incident electric field profiles, enabling a closer alignment with experimental setups. This adaptability ensures that the method is relevant and applicable to diverse real-world scenarios.
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Affiliation(s)
- Giulia Dall'Osto
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova 35100, Italy
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova 35100, Italy
- CNR Institute of Nanoscience, via Campi 213/A, Modena 41100, Italy
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30
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Fixot B, Louaas E, Bonhommeau DA. Collision of rare-gas atoms on helium nanodroplets: Theoretical evidence for an efficient coagulation of heavy rare-gas atoms. J Chem Phys 2024; 161:044307. [PMID: 39051833 DOI: 10.1063/5.0220027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
The coagulation of rare-gas atoms (RG = Ne, Ar, Kr, Xe, and Rn) in helium nanodroplets (HNDs) composed of 1000 atoms is investigated by zero-point averaged dynamics where a He-He pseudopotential is used to make the droplet liquid with proper energies. This method reproduces the qualitative abundances of embedded Arn+1 structures obtained by Time-Dependent Density Functional Theory and Ring Polymer Molecular Dynamics for Ar + ArnHe1000 collisions at realistic projectile speeds and impact parameters. More generally, coagulation is found to be much more efficient for heavy rare-gases (Xe and Rn) than for light ones (Ne and Ar), a behavior mainly attributed to a slower energy dissipation of the projectile in the HND. When coagulation does not occur, the projectile maintains a speed of 10-30 m s-1 within the HND, but its velocity vector is rarely oriented toward the dopant, and the projectile roams in a limited region of the droplet. The structure of embedded RGn+1 clusters does not systematically match their gas-phase global minimum structure, and more than 30% of RGn-RG unbound structures are due to one He atom located in between the projectile and a dopant atom.
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Affiliation(s)
- Brendan Fixot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, Evry-Courcouronnes 91025, France
| | - Elsa Louaas
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, Evry-Courcouronnes 91025, France
| | - David A Bonhommeau
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, Evry-Courcouronnes 91025, France
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31
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Boulougouris GC. Event horizon kinetic Monte Carlo. J Chem Phys 2024; 161:044109. [PMID: 39046345 DOI: 10.1063/5.0220945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/05/2024] [Indexed: 07/25/2024] Open
Abstract
In this study, we present a novel approach for modeling the dynamics of stochastic processes. The fundamental concept involves constructing a stochastic Markov chain comprising states separated by more than one stochastic event. Initially, the method explores the network of neighboring states connected by stochastic events. This exploration results in a "horizon" of events leading to a set of "boundary" states at the periphery of each local network. Subsequently, the next member in the Markov chain is selected from the "boundary" states based on the probability of reaching each of the "boundary" states for the first time. Meanwhile, the simulation clock is updated according to the time required to reach the boundary for the first time. This can be achieved using an analytical approach, where the probability of reaching each boundary state for the first time is estimated using absorbing conditions for all boundary states in the analytical solution of a master equation describing the local network of states around each current state. The proposed method is demonstrated in modeling the dynamics in networks of stochastic reactions but can be easily applied in any stochastic system whose dynamics can be expressed via the solution of a master equation. It is expected to enhance the efficiency of event-driven Monte Carlo simulations, originally introduced by Gillespie and widely regarded as the gold standard in the field, especially in cases where the presence of events is characterized by different timescales.
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Affiliation(s)
- Georgios C Boulougouris
- Laboratory of Computational Physical Chemistry, Department of Molecular Biology and Genetics, University of Thrace, GR-68100 Alexandroupoulis, Greece
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32
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Giri SK, Schatz GC. Laser pulse induced second- and third-harmonic generation of gold nanorods with real-time time-dependent density functional tight binding (RT-TDDFTB) method. J Chem Phys 2024; 161:044703. [PMID: 39041878 DOI: 10.1063/5.0216887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
In this study, we investigate second- and third-harmonic generation processes in Au nanorod systems using the real-time time-dependent density functional tight binding method. Our study focuses on the computation of nonlinear signals based on the time dependent dipole response induced by linearly polarized laser pulses interacting with nanoparticles. We systematically explore the influence of various laser parameters, including pump intensity, duration, frequency, and polarization directions, on harmonic generation. We demonstrate all the results using Au nanorod dimer systems arranged in end-to-end configurations, and disrupting the spatial symmetry of regular single nanorod systems is crucial for second-harmonic generation processes. Furthermore, we study the impact of nanorod lengths, which lead to variable plasmon energies, on harmonic generation, and estimates of polarizabilities and hyper-polarizabilities are provided.
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Affiliation(s)
- Sajal Kumar Giri
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - George C Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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33
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Accordino SR, Alarcón LM, Loubet NA, Appignanesi GA. Water at the nanoscale: From filling or dewetting hydrophobic pores and carbon nanotubes to "sliding" on graphene. J Chem Phys 2024; 161:044504. [PMID: 39037145 DOI: 10.1063/5.0215579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
In this work, we study the effect of nanoconfinement on the hydration properties of model hydrophobic pores and carbon nanotubes, determining their wetting propensity and the conditions for geometrically induced dehydration. By employing a recently introduced water structural index, we aim at two main goals: (1) to accurately quantify the local hydrophobicity and predict the drying transitions in such systems, and (2) to provide a molecular rationalization of the wetting process. In this sense, we will further discuss the number and strength of the interactions required by the water molecules to promote wetting. In the case of graphene-like surfaces, an explanation for their unexpectedly significant hydrophilicity will also be provided. On the one hand, the structural index will show that the net attraction to the dense carbon network that a water molecule experiences through several simultaneous weak interactions is sufficient to give rise to hydrophilic behavior. On the other hand, we will show that an additional effect is also at play: the hydrating water molecule is retained on the surface by a smooth exchange of such simultaneous weak interactions, as if "sliding" on graphene.
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Affiliation(s)
- Sebastián R Accordino
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Laureano M Alarcón
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Nicolás A Loubet
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
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34
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France-Lanord A, Menon S, Lam J. Harvesting nucleating structures in nanoparticle crystallization: The example of gold, silver, and iron. J Chem Phys 2024; 161:044108. [PMID: 39046348 DOI: 10.1063/5.0200850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
The thermodynamics and kinetics of nanoparticle crystallization, as opposed to bulk phases, may be influenced by surface and size effects. We investigate the importance of such factors in the crystallization process of gold, silver, and iron nanodroplets using numerical simulations in the form of molecular dynamics combined with path sampling. This modeling strategy is targeted at obtaining representative ensembles of structures located at the transition state of the crystallization process. A structural analysis of the transition state ensembles reveals that both the average size and location of the critical nucleation cluster are influenced by surface and nanoscale size effects. Furthermore, we also show that transition state structures in smaller nanodroplets exhibit a more ordered liquid phase, and differentiating between a well-ordered critical cluster and its surrounding disordered liquid phase becomes less evident. All in all, these findings demonstrate that crystallization mechanisms in nanoparticles go beyond the assumptions of classical nucleation theory.
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Affiliation(s)
- Arthur France-Lanord
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, F-75005 Paris, France
| | - Sarath Menon
- Max-Planck-Institut für Eisenforschung GmbH, D-40237 Düsseldorf, Germany
| | - Julien Lam
- Univ. Lille, CNRS, INRA, ENSCL, UMR 8207, UMET, Unité Matériaux et Transformations, F 59000 Lille, France
- Centre d'élaboration des Matériaux et d'Etudes Structurales, CNRS (UPR 8011), 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France
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35
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Schwarting M, Seifert NA, Davis MJ, Blaiszik B, Foster I, Prozument K. Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule? J Chem Phys 2024; 161:044309. [PMID: 39051838 DOI: 10.1063/5.0212632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.
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Affiliation(s)
- Marcus Schwarting
- Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Nathan A Seifert
- Department of Chemistry and Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, USA
| | - Michael J Davis
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ben Blaiszik
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ian Foster
- Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Kirill Prozument
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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36
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Guo J, Šindelka M, Moiseyev N. Oscillating direct electric current formed by a resonant tunneling diode inside a cavity with periodically oscillating mirrors. J Chem Phys 2024; 161:044308. [PMID: 39051832 DOI: 10.1063/5.0205463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
A novel phenomenon is described that enables the control of the flux of free electrons through a resonance tunneling diode (RTD) via coupling the RTD to a quantized electromagnetic mode in a dark cavity. As the control parameter, one uses here the distance between the two cavity mirrors (which are set to oscillate in time). The effect is illustrated by carrying out standard scattering calculations of the electron flux. However, the only efficient way to rationalize the phenomenon and to be able to select the proper distance between the two cavity mirrors is to employ non-Hermitian quantum mechanics and the language of discrete resonance poles of the scattering matrix. The demonstrated ability to control the flux of free electrons by using a dark cavity might open a new field of research and development of controllable RTD devices.
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Affiliation(s)
- Jiene Guo
- Department of Physics, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China, and Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Milan Šindelka
- Institute of Plasma Physics of the Czech Academy of Sciences, Za Slovankou 1782/3, 18200 Prague 8, Czech Republic, and Helen Diller Quantum Center, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry and Faculty of Physics and Solid State Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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37
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Wei YC, Hsu LY. Wide-Dynamic-Range Control of Quantum-Electrodynamic Electron Transfer Reactions in the Weak Coupling Regime. J Phys Chem Lett 2024; 15:7403-7410. [PMID: 38995883 DOI: 10.1021/acs.jpclett.4c01265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Catalyzing reactions effectively by vacuum fluctuations of electromagnetic fields is a significant challenge within the realm of chemistry. As opposed to most studies based on vibrational strong coupling, we introduce an innovative catalytic mechanism driven by weakly coupled polaritonic fields. Through the amalgamation of macroscopic quantum electrodynamics (QED) principles with Marcus electron transfer (ET) theory, we predict that ET reaction rates can be precisely modulated across a wide dynamic range by controlling the size and structure of nanocavities. Compared to QED-driven radiative ET rates in free space, plasmonic cavities induce substantial rate enhancements spanning the range from 103- to 10-fold. By contrast, Fabry-Perot cavities engender rate suppression spanning the range from 10-2- to 10-1-fold. This work overcomes the necessity of using strong light-matter interactions in QED chemistry, opening up a new era of manipulating QED-based chemical reactions in a wide dynamic range.
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Affiliation(s)
- Yu-Chen Wei
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
| | - Liang-Yan Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
- National Center for Theoretical Sciences, Taipei 106, Taiwan
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38
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Domanska M, Setny P. Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields. J Phys Chem B 2024; 128:7160-7171. [PMID: 38990314 DOI: 10.1021/acs.jpcb.4c02310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Curvature emerges as a fundamental membrane characteristic crucial for diverse biological processes, including vesicle formation, cell signaling, and membrane trafficking. Increasingly valuable insights into atomistic details governing curvature-dependent membrane properties are provided by computer simulations. Nevertheless, the underlying force field models are conventionally calibrated and tested in relation to experimentally derived parameters of planar bilayers, thereby leaving uncertainties concerning their consistency in reproducing curved lipid systems. In this study we compare the depiction of buckled phosphatidylcholine (POPC) and POPC-cholesterol membranes by four popular force field models. Aside from agreement with respect to general trends in curvature dependence of a number of parameters, we observe a few qualitative differences. Among the most prominent ones is the difference between atomistic and coarse grained force fields in their representation of relative compressibility of the polar headgroup region and hydrophobic lipid core. Through a number of downstream effects, this discrepancy can influence the way in which curvature modulates the behavior of membrane bound proteins depending on the adopted simulation model.
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Affiliation(s)
- Maria Domanska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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39
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Einsele R, Mitrić R. Nonadiabatic Exciton Dynamics and Energy Gradients in the Framework of FMO-LC-TDDFTB. J Chem Theory Comput 2024. [PMID: 39051619 DOI: 10.1021/acs.jctc.4c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We introduce a novel methodology for simulating the excited-state dynamics of extensive molecular aggregates in the framework of the long-range corrected time-dependent density-functional tight-binding fragment molecular orbital method (FMO-LC-TDDFTB) combined with the mean-field Ehrenfest method. The electronic structure of the system is described in a quasi-diabatic basis composed of locally excited and charge-transfer states of all fragments. In order to carry out nonadiabatic molecular dynamics simulations, we derive and implement the excited-state gradients of the locally excited and charge-transfer states. Subsequently, the accuracy of the analytical excited-state gradients is evaluated. The applicability to the simulation of exciton transport in organic semiconductors is illustrated on a large cluster of anthracene molecules. Additionally, nonadiabatic molecular dynamics simulations of a model system of benzothieno-benzothiophene molecules highlight the method's utility in studying charge-transfer dynamics in organic materials. Our new methodology will facilitate the investigation of excitonic transfer in extensive biological systems, nanomaterials, and other complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
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40
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Titov E. The Role of Double Excitations in Exciton Dynamics of Multiazobenzenes: Trisazobenzenophane as a Test Case. J Phys Chem Lett 2024; 15:7482-7488. [PMID: 39011968 DOI: 10.1021/acs.jpclett.4c01608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Molecular exciton dynamics underlie energy and charge transfer processes in organic multichromophoric systems. A particularly interesting class of the latter is multiphotochromic systems made of molecules capable of photochemical transformations. Exciton dynamics in assemblies of photoswitches have been recently investigated using either the molecular exciton model or supermolecular configuration interaction (CI) singles, both approaches being based on a semiempirical Hamiltonian and combined with surface hopping molecular dynamics. Here, we study how inclusion of double excitations in nonadiabatic dynamics simulations affects exciton dynamics of multiazobenzenes, using trisazobenzenophane as an example. We find that both CI singles and CI singles and doubles yield virtually the same time scale of dynamical exciton localization, ∼50 fs for the studied multiazobenzene. However, inclusion of double excitations considerably affects the excited state lifetimes and isomerization quantum yields.
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Affiliation(s)
- Evgenii Titov
- University of Potsdam, Institute of Chemistry, Theoretical Chemistry, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
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41
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Holtzapple E, Zhou G, Luo H, Tang D, Arazkhani N, Hansen C, Telmer CA, Miskov-Zivanov N. The BioRECIPE Knowledge Representation Format. ACS Synth Biol 2024. [PMID: 39051984 DOI: 10.1021/acssynbio.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
The BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution) knowledge representation format was introduced to standardize and facilitate human-machine interaction while creating, verifying, evaluating, curating, and expanding executable models of intra- and intercellular signaling. This format allows a human user to easily preview and modify any model component, while it is at the same time readable by machines and can be processed by a suite of model development and analysis tools. The BioRECIPE format is compatible with multiple representation formats, natural language processing tools, modeling tools, and databases that are used by the systems and synthetic biology communities.
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Affiliation(s)
| | | | | | | | | | | | - Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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42
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Malenfant-Thuot O, Ryczko K, Tamblyn I, Côté M. Efficient determination of Born-effective charges, LO-TO splitting, and Raman tensors of solids with a real-space atom-centered deep learning approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:425901. [PMID: 39019077 DOI: 10.1088/1361-648x/ad64a2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/17/2024] [Indexed: 07/19/2024]
Abstract
We introduce a deep neural network (DNN) framework called theReal-spaceAtomicDecompositionNETwork (radnet), which is capable of making accurate predictions of polarization and of electronic dielectric permittivity tensors in solids and aims to address limitations of previously available machine learning models for Raman predictions in periodic systems. This framework builds on previous, atom-centered approaches while utilizing deep convolutional neural networks. We report excellent accuracies on direct predictions for two prototypical examples: GaAs and BN. We then use automatic differentiation to efficiently calculate the Born-effective charges, longitudinal optical-transverse optical (LO-TO) splitting frequencies, and Raman tensors of these materials. We compute the Raman spectra, and find agreement withab initioresults. Lastly, we explore ways to generalize the predictions of polarization while taking into account periodic boundary conditions and symmetries.
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Affiliation(s)
- Olivier Malenfant-Thuot
- Département de physique et Institut Courtois, Université de Montréal, Montréal, Québec, Canada
| | - Kevin Ryczko
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
- SandboxAQ, Palo Alto, CA, United States of America
| | - Isaac Tamblyn
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Michel Côté
- Département de physique et Institut Courtois, Université de Montréal, Montréal, Québec, Canada
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43
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Pandey P, Durga Prasad M. Time-Dependent Multireference Coupled-Cluster Method (TDMRCCM) for the Bath-Dynamics in System-Bath Approach to Nonadiabatic Dynamics. J Phys Chem A 2024; 128:5990-5998. [PMID: 39012785 DOI: 10.1021/acs.jpca.4c01432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The time-dependent multireference coupled-cluster method (TDMRCCM) fits well in the scheme of the system-bath separation used to study the nonadiabatic dynamics. In TDMRCCM, a projection operator is defined as one that projects the full Hilbert space onto the space spanned by the collection of system degrees of freedom, called the model space. The inverse of this projection operator is a wave operator that acts on the model space and takes its projection back to the full wave function. This wave operator is defined as an exponential of the excitation terms and, hence, can be expanded into a Taylor series, which we have truncated in this work at the second-order of excitations. The attraction of using TDMRCCM for describing the bath dynamics is due to the exponential nature of the ansatz used in the method, which makes it possible for the higher-order excitations to be absorbed by the lower-order terms, even upon truncating the series. This improves the accuracy of the numerical calculations using TDMRCCM as an approximation for the bath-mode dynamics in the system-bath framework for nonadiabatic dynamics. We present the theoretical details of TDMRCCM and the numerical results for implementing this method to study the dynamics in the butatriene cation.
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Affiliation(s)
- Prachi Pandey
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - M Durga Prasad
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
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44
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Ozeki M, Orito M, Ishikawa H. Observation of the Infrared-Induced Structural Change in the Microscopic Hydrogen Bond Network of Phenol-Methanol Cluster Cations in a Cold-Ion Trap. J Phys Chem A 2024; 128:5873-5882. [PMID: 38996183 DOI: 10.1021/acs.jpca.4c01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
To gain insight into microscopic hydrogen bond networks, we measured ultraviolet photodissociation (UVPD) spectra of the phenol-methanol 1:3 cluster cation, [PhOH(MeOH)3]+ trapped in a variable temperature ion trap. At low temperatures, an isomer with a ring-type hydrogen bond structure dominates, whereas at higher temperatures the chain-type isomers become dominant due to the flexibility of their hydrogen bond structures. We also found a clear temperature dependence of the spectral features, such as band position and width. In addition to the above measurement, we observed the infrared (IR) induced isomerization of [PhOH(MeOH)3]+ to study the dynamical aspects of hydrogen bond networks. We succeeded in observing IR-induced isomerization from the ring to chain forms of [PhOH(MeOH)3]+ at low temperature. The isomerization was clearly identified as a change in the UVPD spectra. The time evolution of the UVPD spectra after IR excitation indicated that the IR-induced isomerization occurs within a nanosecond. The chain-type isomers produced by the IR-induced isomerization are then converted back to the ring-type form by collisions with cold He buffer gas in the trap. This backward isomerization proceeds with a time constant of 100 μs under our experimental conditions. In this study, we evaluated the temperatures of the chain isomers during the backward isomerization on the basis of the spectral features.
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Affiliation(s)
- Masayoshi Ozeki
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Masataka Orito
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
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45
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Šímová I, Chrupková P, Gardiner AT, Koblížek M, Kloz M, Polívka T. Femtosecond Stimulated Raman Spectroscopy of Linear Carotenoids. J Phys Chem Lett 2024; 15:7466-7472. [PMID: 39008850 DOI: 10.1021/acs.jpclett.4c01272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption data measured in a single experiment are used to determine the vibronic properties of the S1 state of linear carotenoids with different conjugation lengths. The Raman band corresponding to the C═C stretching mode in the S1 state peaks at 1799 cm-1 (neurosporene), 1802 cm-1 (spheroidene), and 1791 cm-1 (lycopene). Contrary to the ground state C═C mode, variation of the C═C stretching mode in the S1 state is small and does not follow a linear dependence on N. The lifetime of the Raman band matches the S1 decays obtained from transient absorption, confirming its S1 state origin. Direct comparison of transient absorption and FSRS signals allowed us to assign Raman signatures of nonrelaxed S1 and S0 states. For lycopene, FSRS data identified a component associated with a downshifted ground state C═C mode, which matches the dynamics of the S* signal observed in transient absorption data.
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Affiliation(s)
- Ivana Šímová
- Department of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Petra Chrupková
- Department of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
- The Extreme Light Infrastructure ERIC, ELI Beamlines Facility, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, ELI Beamlines Facility, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic
| | - Tomáš Polívka
- Department of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
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46
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Cristiano N, Cabayé A, Brabet I, Glatthar R, Tora A, Goudet C, Bertrand HO, Goupil-Lamy A, Flor PJ, Pin JP, McCort-Tranchepain I, Acher FC. Novel Inhibitory Site Revealed by XAP044 Mode of Action on the Metabotropic Glutamate 7 Receptor Venus Flytrap Domain. J Med Chem 2024; 67:11662-11687. [PMID: 38691510 DOI: 10.1021/acs.jmedchem.3c01924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Metabotropic glutamate (mGlu) receptors play a key role in modulating most synapses in the brain. The mGlu7 receptors inhibit presynaptic neurotransmitter release and offer therapeutic possibilities for post-traumatic stress disorders or epilepsy. Screening campaigns provided mGlu7-specific allosteric modulators as the inhibitor XAP044 (Gee et al. J. Biol. Chem. 2014). In contrast to other mGlu receptor allosteric modulators, XAP044 does not bind in the transmembrane domain but to the extracellular domain of the mGlu7 receptor and not at the orthosteric site. Here, we identified the mode of action of XAP044, combining synthesis of derivatives, modeling and docking experiments, and mutagenesis. We propose a unique mode of action of these inhibitors, preventing the closure of the Venus flytrap agonist binding domain. While acting as a noncompetitive antagonist of L-AP4, XAP044 and derivatives act as apparent competitive antagonists of LSP4-2022. These data revealed more potent XAP044 analogues and new possibilities to target mGluRs.
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Affiliation(s)
- Nunzia Cristiano
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
| | - Alexandre Cabayé
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
- BIOVIA Dassault Systèmes, F-78140 Vélizy-Villacoublay Cedex, France
| | - Isabelle Brabet
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Ralf Glatthar
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Amelie Tora
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Cyril Goudet
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | | | - Anne Goupil-Lamy
- BIOVIA Dassault Systèmes, F-78140 Vélizy-Villacoublay Cedex, France
| | - Peter J Flor
- Laboratory of Molecular and Cellular Neurobiology, Faculty of Biology and Preclinical Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Jean-Philippe Pin
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Isabelle McCort-Tranchepain
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
| | - Francine C Acher
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, CNRS UMR 8003, 75006 Paris, France
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47
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Nishi H, Higashi Y, Saito M. Active control of plasmon coupling via simple electrochemical surface oxidation/reduction of Au nanoparticle agglomerates. Chem Commun (Camb) 2024; 60:7870-7873. [PMID: 38912669 DOI: 10.1039/d4cc02024c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Reversible tuning of plasmon coupling of Au nanoparticle (AuNP) agglomerates containing dimers as the main component was achieved via electrochemical surface oxidation/reduction of the AuNP surface. The system required no reactant except for water and was almost finished within a unit second, which leads to novel active plasmonic devices.
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Affiliation(s)
- Hiroyasu Nishi
- Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
- Department of Chemistry, School of Science, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Yuki Higashi
- Department of Chemistry, School of Science, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Manaka Saito
- Department of Chemistry, School of Science, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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48
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Yang Y, Su W, Wang H, Bao X, Liu X, Bo Z, Zhang W. Promotion of Fast and Efficient Singlet Fission Process of PDI Dimers by Selenium Substitution. J Phys Chem B 2024; 128:7219-7226. [PMID: 39007639 DOI: 10.1021/acs.jpcb.4c01744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Singlet fission (SF) is a triplet generation mechanism capable of turning a singlet exciton into two triplet excitons. It has the potential to enhance the power conversion efficiency of single-junction solar cells. Perylene diimides (PDIs) are a class of dye molecules with photovoltaic properties and are beginning to receive more and more attention due to their potential for SF. Here, we report a selenium-substituted PDI dimer, Se-PDI-II, and we studied its SF mechanism by using steady-state, transient absorption, and time-resolved photoluminescence spectroscopy. Compared with the unsubstituted dimer PDI-II, we found that the introduction of selenium atoms can suppress excimer emission during the SF process, showing much higher SF efficiency and triplet yield.
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Affiliation(s)
- Yubo Yang
- School of Physics and Astronomy, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Wenli Su
- School of Physics and Astronomy, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Hang Wang
- College of Textiles & Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Xiaotian Bao
- School of Physics and Astronomy, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xinfeng Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhishan Bo
- College of Textiles & Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Wenkai Zhang
- School of Physics and Astronomy, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Multiscale Spin Physics, Ministry of Education, Beijing Normal University, Beijing 100875, China
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49
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Yan S, Zhang R, Ning C. Precision Measurement of the Electron Affinity of Chlorine via High-Resolution Photoelectron Spectroscopy. J Phys Chem Lett 2024:7735-7739. [PMID: 39046310 DOI: 10.1021/acs.jpclett.4c01821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Chlorine (Cl2) is a diatomic molecule used as an important industrial gas. However, the electron affinity (EA) of Cl2, a fundamental parameter for understanding chemical reactions, has no accurate experimental result available. The latest result of the EA value of Cl2 is 2.50(20) eV reported in 1983. In the present work, we report the precision measurement of the EA of Cl2 with the successive difference method via the high-resolution photoelectron spectroscopy of cryogenically cold chlorine anions Cl2-. The EA of Cl2 is determined to be 19432(9) cm-1 or 2.4093(11) eV.
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Affiliation(s)
- Shuaiting Yan
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, Beijing 100084, China
| | - Rui Zhang
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, Beijing 100084, China
| | - Chuangang Ning
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, Beijing 100084, China
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50
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Niblo JK, Swartley JR, Zhang Z, DuBay KH. 2D capsid formation within an oscillatory energy landscape: orderly self-assembly depends on the interplay between a dynamic potential and intrinsic relaxation times. SOFT MATTER 2024. [PMID: 39046256 DOI: 10.1039/d4sm00455h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but investigations thus far have focused on systems of simple colloids or their binary mixtures. In this work, we expand our understanding of the effect of temporally oscillating interactions to a two-dimensional coarse-grained viral capsid-like model that undergoes a self-limited assembly. This model includes multiple intrinsic relaxation times due to the internal structure of the capsid subunits and, under certain interaction regimes, proceeds via a two-step nucleation mechanism. We find that oscillations much faster than the local intrinsic relaxation times can be described via a time averaged inter-particle potential across a wide range of interaction strengths, while oscillations much slower than these relaxation times result in structures that adapt to the attraction strength of the current half-cycle. Interestingly, oscillation periods similar to these relaxation times shift the interaction window over which orderly assembly occurs by enabling error correction during the half-cycles with weaker attractions. Our results provide fundamental insights to non-equilibrium self-assembly on temporally variant energy landscapes.
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Affiliation(s)
- Jessica K Niblo
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Jacob R Swartley
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Zhongmin Zhang
- Department of Chemistry, University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Kateri H DuBay
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
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