1
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Xie M, Shimogawa R, Liu Y, Zhang L, Foucher AC, Routh PK, Stach EA, Frenkel AI, Knecht MR. Biomimetic Control over Bimetallic Nanoparticle Structure and Activity via Peptide Capping Ligand Sequence. ACS NANO 2024; 18:3286-3294. [PMID: 38227802 DOI: 10.1021/acsnano.3c10016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The controlled design of bimetallic nanoparticles (BNPs) is a key goal in tailoring their catalytic properties. Recently, biomimetic pathways demonstrated potent control over the distribution of different metals within BNPs, but a direct understanding of the peptide effect on the compositional distribution at the interparticle and intraparticle levels remains lacking. We synthesized two sets of PtAu systems with two peptides and correlated their structure, composition, and distributions with the catalytic activity. Structural and compositional analyses were performed by a combined machine learning-assisted refinement of X-ray absorption spectra and Z-contrast measurements by scanning transmission electron microscopy. The difference in the catalytic activities between nanoparticles synthesized with different peptides was attributed to the details of interparticle distribution of Pt and Au across these markedly heterogeneous systems, comprising Pt-rich, Au-rich, and Au core/Pt shell nanoparticles. The total amount of Pt in the shells of the BNPs was proposed to be the key catalytic activity descriptor. This approach can be extended to other systems of metals and peptides to facilitate the targeted design of catalysts with the desired activity.
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Affiliation(s)
- Maichong Xie
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Ryuichi Shimogawa
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Mitsubishi Chemical Corporation, Science & Innovation Center, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Yang Liu
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Lihua Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Alexandre C Foucher
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Prahlad K Routh
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Eric A Stach
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
- Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, Florida 33136, United States
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2
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Wu D, Housel LM, King ST, Mansley ZR, Sadique N, Zhu Y, Ma L, Ehrlich SN, Zhong H, Takeuchi ES, Marschilok AC, Bock DC, Wang L, Takeuchi KJ. Simultaneous Elucidation of Solid and Solution Manganese Environments via Multiphase Operando Extended X-ray Absorption Fine Structure Spectroscopy in Aqueous Zn/MnO 2 Batteries. J Am Chem Soc 2022; 144:23405-23420. [PMID: 36513373 PMCID: PMC9801424 DOI: 10.1021/jacs.2c09477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aqueous Zn/MnO2 batteries (AZMOB) with mildly acidic electrolytes hold promise as potential green grid-level energy storage solutions for clean power generation. Mechanistic understanding is critical to advance capacity retention needed by the application but is complex due to the evolution of the cathode solid phases and the presence of dissolved manganese in the electrolyte due to a dissolution-deposition redox process. This work introduces operando multiphase extended X-ray absorption fine structure (EXAFS) analysis enabling simultaneous characterization of both aqueous and solid phases involved in the Mn redox reactions. The methodology was successfully conducted in multiple electrolytes (ZnSO4, Zn(CF3SO3)2, and Zn(CH3COO)2) revealing similar manganese coordination environments but quantitative differences in distribution of Mnn+ species in the solid and solution phases. Complementary Raman spectroscopy was utilized to identify the less crystalline Mn-containing products formed under charge at the cathodes. This was further augmented by transmission electron microscopy (TEM) to reveal the morphology and surface condition of the deposited solids. The results demonstrate an effective approach for bulk-level characterization of poorly crystalline multiphase solids while simultaneously gaining insight into the dissolved transition-metal species in solution. This work provides demonstration of a useful approach toward gaining insight into complex electrochemical mechanisms where both solid state and dissolved active materials are important contributors to redox activity.
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Affiliation(s)
- Daren Wu
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Materials Science and Chemical Engineering, Stony Brook University, Stony
Brook, New York 11794, United States
| | - Lisa M. Housel
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States
| | - Steven T. King
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Zachary R. Mansley
- Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States,Department
of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Nahian Sadique
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Yimei Zhu
- Department
of Materials Science and Chemical Engineering, Stony Brook University, Stony
Brook, New York 11794, United States,Department
of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Lu Ma
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Steven N. Ehrlich
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Hui Zhong
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Esther S. Takeuchi
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Materials Science and Chemical Engineering, Stony Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States,Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Amy C. Marschilok
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Materials Science and Chemical Engineering, Stony Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States,Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - David C. Bock
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States
| | - Lei Wang
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States
| | - Kenneth J. Takeuchi
- Institute
for Energy Sustainability and Equity, Stony
Brook University, Stony
Brook, New York 11794, United States,Department
of Materials Science and Chemical Engineering, Stony Brook University, Stony
Brook, New York 11794, United States,Interdisciplinary
Science Department, Brookhaven National
Laboratory, Upton, New York 11973, United States,Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States,
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3
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Liu Y, Halder A, Seifert S, Marcella N, Vajda S, Frenkel AI. Probing Active Sites in Cu xPd y Cluster Catalysts by Machine-Learning-Assisted X-ray Absorption Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:53363-53374. [PMID: 34255469 DOI: 10.1021/acsami.1c06714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Size-selected clusters are important model catalysts because of their narrow size and compositional distributions, as well as enhanced activity and selectivity in many reactions. Still, their structure-activity relationships are, in general, elusive. The main reason is the difficulty in identifying and quantitatively characterizing the catalytic active site in the clusters when it is confined within subnanometric dimensions and under the continuous structural changes the clusters can undergo in reaction conditions. Using machine learning approaches for analysis of the operando X-ray absorption near-edge structure spectra, we obtained accurate speciation of the CuxPdy cluster types during the propane oxidation reaction and the structural information about each type. As a result, we elucidated the information about active species and relative roles of Cu and Pd in the clusters.
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Affiliation(s)
- Yang Liu
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Avik Halder
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Soenke Seifert
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Nicholas Marcella
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Stefan Vajda
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
- Institute for Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
- Department of Nanocatalysis, J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 8 18223, Czech Republic
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
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4
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Halder A, Lenardi C, Timoshenko J, Mravak A, Yang B, Kolipaka LK, Piazzoni C, Seifert S, Bonačić-Koutecký V, Frenkel AI, Milani P, Vajda S. CO2 Methanation on Cu-Cluster Decorated Zirconia Supports with Different Morphology: A Combined Experimental In Situ GIXANES/GISAXS, Ex Situ XPS and Theoretical DFT Study. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Avik Halder
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Cristina Lenardi
- C.I. Ma.I.Na., Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, I-20133 Milano, Italy
| | - Janis Timoshenko
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794 United States
| | - Antonija Mravak
- Center of Excellence for Science and Technology - Integration of Mediterranean region (STIM), Faculty of Science, University of Split, Ruđera Boškovića 33, CR-21000 Split, Croatia
| | - Bing Yang
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lakshmi K Kolipaka
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Claudio Piazzoni
- C.I. Ma.I.Na., Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, I-20133 Milano, Italy
| | - Sönke Seifert
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Vlasta Bonačić-Koutecký
- Center of Excellence for Science and Technology - Integration of Mediterranean region (STIM), Faculty of Science, University of Split, Ruđera Boškovića 33, CR-21000 Split, Croatia
- Interdisciplinary Center for Advanced Science and Technology (ICAST) at University of Split, Meštrovićevo šetalište 45, CR-21000 Split, Croatia
- Chemistry Department, Humboldt University of Berlin, Brook-Taylor-Straße 2, D-12489 Berlin, Germany
| | - Anatoly I. Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794 United States
- Division of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Paolo Milani
- C.I. Ma.I.Na., Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, I-20133 Milano, Italy
| | - Stefan Vajda
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Nanocatalysis, J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-18223 Prague 8, Czech Republic
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5
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Nayak C, Abharana N, Modak B, Halankar K, Jha SN, Bhattacharyya D. Insight into the charging-discharging of magnetite electrodes: in situ XAS and DFT study. Phys Chem Chem Phys 2021; 23:6051-6061. [PMID: 33683228 DOI: 10.1039/d0cp05151a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The structural changes of Fe3O4 nanoparticle electrodes in Li ion batteries during charging-discharging cycles have been investigated using in situ X-ray absorption spectroscopy (XAS). Chemometric methods viz., Principal Component Analysis (PCA) and Multivariate Curve Resolution-Alternate Least Square (MCR-ALS) have been used for analysis of the in situ XANES data during the charge-discharge cycle, which help to identify the various species formed during the lithiation-delithiation of Fe3O4. The concentration variation of the different species has also been determined and the detailed intercalation-conversion mechanism of the Fe3O4 electrodes during the first discharge has been established. Subsequently, the first charge and second discharge cycles were also studied to apprehend the difference in redox reaction between the first discharge and subsequent cycles. The above studies clearly identify the four species involved in the whole intercalation-conversion process of Fe3O4 electrode of a Li ion battery and also indicate the irreversibility of the conversion reaction in subsequent cycles which may be one of the reasons for capacity fading of these electrodes. The above results have also been corroborated with density functional theory (DFT)based ab inito calculations.
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Affiliation(s)
- C Nayak
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
| | - N Abharana
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
| | - B Modak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - K Halankar
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - S N Jha
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
| | - D Bhattacharyya
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
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6
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Timoshenko J, Roldan Cuenya B. In Situ/ Operando Electrocatalyst Characterization by X-ray Absorption Spectroscopy. Chem Rev 2021; 121:882-961. [PMID: 32986414 PMCID: PMC7844833 DOI: 10.1021/acs.chemrev.0c00396] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/18/2022]
Abstract
During the last decades, X-ray absorption spectroscopy (XAS) has become an indispensable method for probing the structure and composition of heterogeneous catalysts, revealing the nature of the active sites and establishing links between structural motifs in a catalyst, local electronic structure, and catalytic properties. Here we discuss the fundamental principles of the XAS method and describe the progress in the instrumentation and data analysis approaches undertaken for deciphering X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra. Recent usages of XAS in the field of heterogeneous catalysis, with emphasis on examples concerning electrocatalysis, will be presented. The latter is a rapidly developing field with immense industrial applications but also unique challenges in terms of the experimental characterization restrictions and advanced modeling approaches required. This review will highlight the new insight that can be gained with XAS on complex real-world electrocatalysts including their working mechanisms and the dynamic processes taking place in the course of a chemical reaction. More specifically, we will discuss applications of in situ and operando XAS to probe the catalyst's interactions with the environment (support, electrolyte, ligands, adsorbates, reaction products, and intermediates) and its structural, chemical, and electronic transformations as it adapts to the reaction conditions.
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Affiliation(s)
- Janis Timoshenko
- Department of Interface Science, Fritz-Haber Institute of the Max-Planck Society, 14195 Berlin, Germany
| | - Beatriz Roldan Cuenya
- Department of Interface Science, Fritz-Haber Institute of the Max-Planck Society, 14195 Berlin, Germany
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7
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Tavani F, Capocasa G, Martini A, Sessa F, Di Stefano S, Lanzalunga O, D'Angelo P. Direct structural and mechanistic insights into fast bimolecular chemical reactions in solution through a coupled XAS/UV–Vis multivariate statistical analysis. Dalton Trans 2021; 50:131-142. [DOI: 10.1039/d0dt03083j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined multivariate and theoretical analysis of coupled XAS/UV–Vis data was proven to be an innovative method to obtain direct structural and mechanistic evidence for bimolecular reactions in solution involving organic substrates.
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Affiliation(s)
- Francesco Tavani
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Giorgio Capocasa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Andrea Martini
- Dipartimento di Chimica
- Università degli Studi di Torino
- 10125 Torino
- Italy
- The Smart Materials Research Institute
| | - Francesco Sessa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | | | | | - Paola D'Angelo
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
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8
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Tavani F, Fracchia M, Pianta N, Ghigna P, Quartarone E, D’Angelo P. Multivariate curve resolution analysis of operando XAS data for the investigation of the lithiation mechanisms in high entropy oxides. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137968] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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9
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Spectral Decomposition of X-ray Absorption Spectroscopy Datasets: Methods and Applications. CRYSTALS 2020. [DOI: 10.3390/cryst10080664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
X-ray absorption spectroscopy (XAS) today represents a widespread and powerful technique, able to monitor complex systems under in situ and operando conditions, while external variables, such us sampling time, sample temperature or even beam position over the analysed sample, are varied. X-ray absorption spectroscopy is an element-selective but bulk-averaging technique. Each measured XAS spectrum can be seen as an average signal arising from all the absorber-containing species/configurations present in the sample under study. The acquired XAS data are thus represented by a spectroscopic mixture composed of superimposed spectral profiles associated to well-defined components, characterised by concentration values evolving in the course of the experiment. The decomposition of an experimental XAS dataset in a set of pure spectral and concentration values is a typical example of an inverse problem and it goes, usually, under the name of multivariate curve resolution (MCR). In the present work, we present an overview on the major techniques developed to realize the MCR decomposition together with a selection of related results, with an emphasis on applications in catalysis. Therein, we will highlight the great potential of these methods which are imposing as an essential tool for quantitative analysis of large XAS datasets as well as the directions for further development in synergy with the continuous instrumental progresses at synchrotron sources.
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10
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Timoshenko J, Frenkel AI. “Inverting” X-ray Absorption Spectra of Catalysts by Machine Learning in Search for Activity Descriptors. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03599] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Janis Timoshenko
- Department of Interface Science, Fritz-Haber-Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Anatoly I. Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
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11
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Bachmann R, Shakiba N, Fischer M, Hackl T. Assessment of Mixtures by Spectral Superposition. An Approach in the Field of Metabolomics. J Proteome Res 2019; 18:2458-2466. [DOI: 10.1021/acs.jproteome.8b00985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- René Bachmann
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Navid Shakiba
- Hamburg School of Food Science—Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science—Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Thomas Hackl
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Hamburg School of Food Science—Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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12
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Huang P, Huang J, Pantovich SA, Carl AD, Fenton TG, Caputo CA, Grimm RL, Frenkel AI, Li G. Selective CO2 Reduction Catalyzed by Single Cobalt Sites on Carbon Nitride under Visible-Light Irradiation. J Am Chem Soc 2018; 140:16042-16047. [DOI: 10.1021/jacs.8b10380] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Peipei Huang
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03857, United States
| | - Jiahao Huang
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sebastian A. Pantovich
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03857, United States
| | - Alexander D. Carl
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Thomas G. Fenton
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03857, United States
| | - Christine A. Caputo
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03857, United States
| | - Ronald L. Grimm
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Anatoly I. Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Division of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Gonghu Li
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03857, United States
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13
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Nayak C, Bhattacharyya D, Jha SN, Sahoo NK. In Situ XAS Study on Growth of PVP-Stabilized Cu Nanoparticles. ChemistrySelect 2018. [DOI: 10.1002/slct.201801358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chandrani Nayak
- Atomic & Molecular Physics Division; Bhabha Atomic Research Centre; Mumbai - 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai- 400096 India
| | - Dibyendu Bhattacharyya
- Atomic & Molecular Physics Division; Bhabha Atomic Research Centre; Mumbai - 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai- 400096 India
| | - Shambhu N. Jha
- Atomic & Molecular Physics Division; Bhabha Atomic Research Centre; Mumbai - 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai- 400096 India
| | - Naba K. Sahoo
- Atomic & Molecular Physics Division; Bhabha Atomic Research Centre; Mumbai - 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai- 400096 India
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14
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Timoshenko J, Anspoks A, Cintins A, Kuzmin A, Purans J, Frenkel AI. Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy. PHYSICAL REVIEW LETTERS 2018; 120:225502. [PMID: 29906159 DOI: 10.1103/physrevlett.120.225502] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Indexed: 06/08/2023]
Abstract
The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.
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Affiliation(s)
- Janis Timoshenko
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Andris Anspoks
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, Riga, LV-1063, Latvia
| | - Arturs Cintins
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, Riga, LV-1063, Latvia
| | - Alexei Kuzmin
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, Riga, LV-1063, Latvia
| | - Juris Purans
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, Riga, LV-1063, Latvia
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
- Division of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, USA
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15
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Sun X, Sun F, Sun Z, Chen J, Du X, Wang J, Jiang Z, Huang Y. Disorder effects on EXAFS modeling for catalysts working at elevated temperatures. Radiat Phys Chem Oxf Engl 1993 2017. [DOI: 10.1016/j.radphyschem.2016.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Timoshenko J, Shivhare A, Scott RWJ, Lu D, Frenkel AI. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure. Phys Chem Chem Phys 2016; 18:19621-30. [DOI: 10.1039/c6cp04030f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
XANES analysis guided by ab initio modeling is proposed for refinement of local environments around metal impurities in heterogeneous catalysts.
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Affiliation(s)
| | - Atal Shivhare
- Department of Chemistry
- University of Saskatchewan
- Saskatoon
- Canada
| | | | - Deyu Lu
- Center for Functional Nanomaterials
- Brookhaven National Laboratory
- Upton
- USA
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17
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18
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Udi Y, Grossman M, Solomonov I, Dym O, Rozenberg H, Moreno V, Cuniasse P, Dive V, Arroyo A, Sagi I. Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational Antibody. Structure 2015; 23:104-115. [DOI: 10.1016/j.str.2014.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/25/2022]
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19
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Manceau A, Marcus M, Lenoir T. Estimating the number of pure chemical components in a mixture by X-ray absorption spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1140-1147. [PMID: 25178004 DOI: 10.1107/s1600577514013526] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
Principal component analysis (PCA) is a multivariate data analysis approach commonly used in X-ray absorption spectroscopy to estimate the number of pure compounds in multicomponent mixtures. This approach seeks to describe a large number of multicomponent spectra as weighted sums of a smaller number of component spectra. These component spectra are in turn considered to be linear combinations of the spectra from the actual species present in the system from which the experimental spectra were taken. The dimension of the experimental dataset is given by the number of meaningful abstract components, as estimated by the cascade or variance of the eigenvalues (EVs), the factor indicator function (IND), or the F-test on reduced EVs. It is shown on synthetic and real spectral mixtures that the performance of the IND and F-test critically depends on the amount of noise in the data, and may result in considerable underestimation or overestimation of the number of components even for a signal-to-noise (s/n) ratio of the order of 80 (σ = 20) in a XANES dataset. For a given s/n ratio, the accuracy of the component recovery from a random mixture depends on the size of the dataset and number of components, which is not known in advance, and deteriorates for larger datasets because the analysis picks up more noise components. The scree plot of the EVs for the components yields one or two values close to the significant number of components, but the result can be ambiguous and its uncertainty is unknown. A new estimator, NSS-stat, which includes the experimental error to XANES data analysis, is introduced and tested. It is shown that NSS-stat produces superior results compared with the three traditional forms of PCA-based component-number estimation. A graphical user-friendly interface for the calculation of EVs, IND, F-test and NSS-stat from a XANES dataset has been developed under LabVIEW for Windows and is supplied in the supporting information. Its possible application to EXAFS data is discussed, and several XANES and EXAFS datasets are also included for download.
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Affiliation(s)
- Alain Manceau
- ISTerre, Université Grenoble Alpes and CNRS, F-38000 Grenoble, France
| | - Matthew Marcus
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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20
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Wu LB, Wu LH, Yang WM, Frenkel AI. Study of the local structure and oxidation state of iron in complex oxide catalysts for propylene ammoxidation. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00197d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of X-ray absorption, Raman and UV-visible spectroscopy reveals the competing redox reactions during the deactivation of Fe-based complex catalysts.
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Affiliation(s)
- Li-bin Wu
- Shanghai Research Institute of Petrochemical Technology
- Shanghai 201208, China
- Physics Department
- Yeshiva University
- New York, USA
| | - Liang-hua Wu
- Shanghai Research Institute of Petrochemical Technology
- Shanghai 201208, China
| | - Wei-min Yang
- Shanghai Research Institute of Petrochemical Technology
- Shanghai 201208, China
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21
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Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I. Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases. J Mol Biol 2013; 425:2330-46. [DOI: 10.1016/j.jmb.2013.04.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 01/26/2023]
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22
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Bordiga S, Groppo E, Agostini G, van Bokhoven JA, Lamberti C. Reactivity of Surface Species in Heterogeneous Catalysts Probed by In Situ X-ray Absorption Techniques. Chem Rev 2013; 113:1736-850. [DOI: 10.1021/cr2000898] [Citation(s) in RCA: 488] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Bordiga
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Elena Groppo
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Giovanni Agostini
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Jeroen A. van Bokhoven
- ETH Zurich, Institute for Chemical and Bioengineering, HCI E127 8093 Zurich, Switzerland
- Laboratory for Catalysis and Sustainable Chemistry (LSK) Swiss Light Source, Paul Scherrer Instituteaul Scherrer Institute, Villigen, Switzerland
| | - Carlo Lamberti
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
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23
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Stötzel J, Lützenkirchen-Hecht D, Grunwaldt JD, Frahm R. T-REX: new software for advanced QEXAFS data analysis. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:920-929. [PMID: 23093750 DOI: 10.1107/s0909049512038599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
New approaches to analyze the data generated by modern time-resolved X-ray absorption spectroscopy instrumentation are presented as part of a new analysis software to handle files containing typically a few thousand EXAFS spectra. Various filter techniques to remove high-frequency noise and run-away values are discussed as well as advanced analysis tools like linear combination fitting, EXAFS fitting, principal component analysis and phase-sensitive detection. These techniques were implemented in a user-friendly graphical user interface to analyse huge data files where it is not possible to treat each spectrum separately. New ideas to exploit existent tools more efficiently for time-resolved EXAFS data analysis are discussed theoretically as well as applied to real measurements, especially in situ catalytic experiments and surface-sensitive reflection-mode X-ray absorption studies of thin film growth.
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Affiliation(s)
- Jan Stötzel
- Fachbereich C-Physik, Universität Wuppertal, Wuppertal, Germany.
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24
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Frenkel AI, Rodriguez JA, Chen JG. Synchrotron Techniques for In Situ Catalytic Studies: Capabilities, Challenges, and Opportunities. ACS Catal 2012. [DOI: 10.1021/cs3004006] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anatoly I. Frenkel
- Department of Physics, Yeshiva University, New York, New York 10016, United
States
| | - Jose A. Rodriguez
- Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973,
United States
| | - Jingguang G. Chen
- Department
of Chemical Engineering, University of Delaware, Newark, Delaware 19716, United
States
- Department of Chemical
Engineering, Columbia University, New York,
New York 10027, United
States
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25
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Bardelli F, Barone G, Crupi V, Longo F, Maisano G, Majolino D, Mazzoleni P, Venuti V. Iron speciation in ancient Attic pottery pigments: a non-destructive SR-XAS investigation. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:782-788. [PMID: 22898958 DOI: 10.1107/s0909049512023990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/25/2012] [Indexed: 06/01/2023]
Abstract
The present work reports a detailed investigation on the speciation of iron in the pigments of decorated pottery fragments of cultural heritage relevance. The fragments come from the Gioiosa Guardia archaeological site in the area of the `Strait of Messina' (Sicily, Southern Italy), and date back to VI-V century BC. The purpose of this study is to characterize the main pigmenting agents responsible for the dark-red coloration of the specimens using non-destructive analytical techniques such as synchrotron radiation X-ray absorption spectroscopy (SR-XAS), a well established technique for cultural heritage and environmental subjects. Absorption spectra were collected at the Fe K-edge on the Italian beamline for absorption and diffraction (BM8-GILDA) at the European Synchrotron Radiation Facility in Grenoble (France). In order to determine the speciation of Fe in the samples, principal component analysis and least-squares fitting procedures were applied to the near-edge part of the absorption spectra (XANES). Details on the local structure around the Fe sites were obtained by analyzing the extended part of the spectra (EXAFS). Furthermore, an accurate determination of the average Fe oxidation state was carried out through analysis of the pre-edge peaks of the absorption spectra. Samples resulted composed of an admixture of Fe(2)O(3) (hematite or maghemite) and magnetite (Fe(3)O(4)), occurring in different relative abundance in the dark- and light-colored areas of the specimens. The results obtained are complementary to information previously obtained by means of instrumental neutron activation analysis, Fourier transform infrared absorbance and time-of-flight neutron diffraction.
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Affiliation(s)
- Fabrizio Bardelli
- Institut des Sciences de la Terre (ISTerre), Maison de Geosciences, 1381 rue de la Piscine, 38400 Grenoble, France
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26
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Yan W, Vasic R, Frenkel AI, Koel BE. Intraparticle reduction of arsenite (As(III)) by nanoscale zerovalent iron (nZVI) investigated with In Situ X-ray absorption spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:7018-7026. [PMID: 22296302 DOI: 10.1021/es2039695] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
While a high efficiency of contaminant removal by nanoscale zerovalent iron (nZVI) has often been reported for several contaminants of great concern, including aqueous arsenic species, the transformations and translocation of contaminants at and within the nanoparticles are not clearly understood. By analysis using in situ time-dependent X-ray absorption spectroscopy (XAS) of the arsenic core level for nZVI in anoxic As(III) solutions, we have observed that As(III) species underwent two stages of transformation upon adsorption at the nZVI surface. The first stage corresponds to breaking of As-O bonds at the particle surface, and the second stage involves further reduction and diffusion of arsenic across the thin oxide layer enclosing the nanoparticles, which results in arsenic forming an intermetallic phase with the Fe(0) core. Extended X-ray absorption fine-structure (EXAFS) data from experiments conducted at different iron/arsenic ratios indicate that the reduced arsenic species tend to be enriched at the surface of the Fe(0) core region and had limited mobility into the interior of the metal core within the experimental time frame (up to 22 h). Therefore, there was an accumulation of partially reduced arsenic at the Fe(0)/oxide interface when a relatively large arsenic content was present in the solid phase. These results illuminate the role of intraparticle diffusion and reduction in affecting the chemical state and spatial distribution of arsenic in nZVI materials.
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Affiliation(s)
- Weile Yan
- Department of Civil and Environmental Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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27
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Frenkel AI. Applications of extended X-ray absorption fine-structure spectroscopy to studies of bimetallic nanoparticle catalysts. Chem Soc Rev 2012; 41:8163-78. [DOI: 10.1039/c2cs35174a] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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Grossman M, Born B, Heyden M, Tworowski D, Fields GB, Sagi I, Havenith M. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site. Nat Struct Mol Biol 2011; 18:1102-8. [PMID: 21926991 DOI: 10.1038/nsmb.2120] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 07/07/2011] [Indexed: 01/16/2023]
Abstract
Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme-inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.
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Affiliation(s)
- Moran Grossman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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29
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Marinkovic NS, Wang Q, Frenkel AI. In situ diffuse reflectance IR spectroscopy and X-ray absorption spectroscopy for fast catalytic processes. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:447-455. [PMID: 21525654 DOI: 10.1107/s0909049511005802] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/16/2011] [Indexed: 05/30/2023]
Abstract
A new instrument for synchronous in situ investigations of catalytic materials by IR and X-ray absorption spectroscopies was designed and built at the X18A beamline of the National Synchrotron Light Source of Brookhaven National Laboratory. It provides analytical tools for solving structural, electronic and kinetic problems in catalysis science by two complementary methods. Among the features attractive for catalysis research are the broad range of catalytically active elements that can be investigated (starting with Ni and beyond), the wide range of reaction conditions (temperatures up to 873 K, various reactive gases) and time scales (starting from tens of seconds). The results of several representative experiments that illustrate the attractive capabilities of the new set-up are discussed.
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Affiliation(s)
- Nebojsa S Marinkovic
- Synchrotron Catalysis Consortium, University of Delaware, 150 Academy St, Newark, DE 19716, USA.
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30
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Collins RN, Bakkaus E, Carrière M, Khodja H, Proux O, Morel JL, Gouget B. Uptake, localization, and speciation of cobalt in Triticum aestivum L. (wheat) and Lycopersicon esculentum M. (tomato). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:2904-2910. [PMID: 20345097 DOI: 10.1021/es903485h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The root-to-shoot transfer, localization, and chemical speciation of Co were investigated in a monocotyledon (Triticum aestivum L., wheat) and a dicotyledon (Lycopersicon esculentum M., tomato) plant species grown in nutrient solution at low (5 muM) and high (20 muM) Co(II) concentrations. Cobalt was measured in the roots and shoots by inductively coupled plasma-mass spectrometry. X-ray absorption spectroscopy measurements were used to identify the chemical structure of Co within the plants and Co distribution in the leaves was determined by micro-PIXE (particle induced X-ray emission). Although the root-to-shoot transport was higher for tomato plants exposed to excess Co, both plants appeared as excluders. The oxidation state of Co(II) was not transformed by either plant in the roots or shoots and Co appeared to be present as Co(II) in a complex with carboxylate containing organic acids. Cobalt was also essentially located in the vascular system of both plant species indicating that neither responded to Co toxicity via sequestration in epidermal or trichome tissues as has been observed for other metals in metal hyperaccumulating plants.
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Affiliation(s)
- Richard N Collins
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
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31
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Gaur A, Shrivastava BD, Joshi SK. Copper K-edge XANES of Cu(I) and Cu(II) oxide mixtures. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/190/1/012084] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Abstract
We discuss methods of Extended X-ray Absorption Fine-Structure (EXAFS) analysis that provide three-dimensional structural characterization of metal nanoparticles, both mono- and bi-metallic. For the bimetallic alloys, we use short range order measurements to discriminate between random and non-random inter-particle distributions of atoms. We also discuss the application of EXAFS to heterogeneous nanoparticle systems.
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33
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Suess E, Scheinost AC, Bostick BC, Merkel BJ, Wallschlaeger D, Planer-Friedrich B. Discrimination of Thioarsenites and Thioarsenates by X-ray Absorption Spectroscopy. Anal Chem 2009; 81:8318-26. [DOI: 10.1021/ac901094b] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elke Suess
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
| | - Andreas C. Scheinost
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
| | - Benjamin C. Bostick
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
| | - Broder J. Merkel
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
| | - Dirk Wallschlaeger
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
| | - Britta Planer-Friedrich
- Environmental Geochemistry, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany, Institute for Geology, Chair of Hydrogeology, TU Bergakademie Freiberg, Gustav-Zeuner-Strasse 12, 09596 Freiberg, Germany, Molecular Structure Division, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf (FZD), Bautzner Landstrasse 128, 01314 Dresden, Germany, Rossendorf Beamline at European Synchrotron Radiation Facility (ESRF), BP220, 38043 Grenoble, France, Department of Earth Sciences,
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34
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Smolentsev G, Guilera G, Tromp M, Pascarelli S, Soldatov AV. Local structure of reaction intermediates probed by time-resolved x-ray absorption near edge structure spectroscopy. J Chem Phys 2009; 130:174508. [DOI: 10.1063/1.3125940] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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35
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Bare SR, Ressler T. Chapter 6 Characterization of Catalysts in Reactive Atmospheres by X‐ray Absorption Spectroscopy. ADVANCES IN CATALYSIS 2009. [DOI: 10.1016/s0360-0564(08)00006-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Wang Q, Hanson JC, Frenkel AI. Solving the structure of reaction intermediates by time-resolved synchrotron x-ray absorption spectroscopy. J Chem Phys 2008; 129:234502. [DOI: 10.1063/1.3040271] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Noy D, Solomonov I, Sinkevich O, Arad T, Kjaer K, Sagi I. Zinc-amyloid beta interactions on a millisecond time-scale stabilize non-fibrillar Alzheimer-related species. J Am Chem Soc 2008; 130:1376-83. [PMID: 18179213 DOI: 10.1021/ja076282l] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of zinc, an essential element for normal brain function, in the pathology of Alzheimer's disease (AD) is poorly understood. On one hand, physiological and genetic evidence from transgenic mouse models supports its pathogenic role in promoting the deposition of the amyloid beta-protein (Abeta) in senile plaques. On the other hand, levels of extracellular ("free") zinc in the brain, as inferred by the levels of zinc in cerebrospinal fluid, were found to be too low for inducing Abeta aggregation. Remarkably, the release of transient high local concentrations of zinc during rapid synaptic events was reported. The role of such free zinc pulses in promoting Abeta aggregation has never been established. Using a range of time-resolved structural and spectroscopic techniques, we found that zinc, when introduced in millisecond pulses of micromolar concentrations, immediately interacts with Abeta 1-40 and promotes its aggregation. These interactions specifically stabilize non-fibrillar pathogenic related aggregate forms and prevent the formation of Abeta fibrils (more benign species) presumably by interfering with the self-assembly process of Abeta. These in vitro results strongly suggest a significant role for zinc pulses in Abeta pathology. We further propose that by interfering with Abeta self-assembly, which leads to insoluble, non-pathological fibrillar forms, zinc stabilizes transient, harmful amyloid forms. This report argues that zinc represents a class of molecular pathogens that effectively perturb the self-assembly of benign Abeta fibrils, and stabilize harmful non-fibrillar forms.
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Affiliation(s)
- Dror Noy
- Structural Biology Department and Electron Microscopy Unit, Weizmann Institute of Science, Rehovot 76100, Israel
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38
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Rosenblum G, Meroueh S, Toth M, Fisher JF, Fridman R, Mobashery S, Sagi I. Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: challenging the cysteine switch dogma. J Am Chem Soc 2007; 129:13566-74. [PMID: 17929919 DOI: 10.1021/ja073941l] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.
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Affiliation(s)
- Gabriel Rosenblum
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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Warner J, Rowson J. Technical Report:In-situMonitoring and Validation of a Uranium Mill Tailings Management Facility Design Using X-ray Absorption Near Edge Structure (XANES) Spectroscopy. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/08940880701401128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Solomon A, Akabayov B, Frenkel A, Milla ME, Sagi I. Key feature of the catalytic cycle of TNF-alpha converting enzyme involves communication between distal protein sites and the enzyme catalytic core. Proc Natl Acad Sci U S A 2007; 104:4931-6. [PMID: 17360351 PMCID: PMC1829242 DOI: 10.1073/pnas.0700066104] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their key roles in many normal and pathological processes, the molecular details by which zinc-dependent proteases hydrolyze their physiological substrates remain elusive. Advanced theoretical analyses have suggested reaction models for which there is limited and controversial experimental evidence. Here we report the structure, chemistry and lifetime of transient metal-protein reaction intermediates evolving during the substrate turnover reaction of a metalloproteinase, the tumor necrosis factor-alpha converting enzyme (TACE). TACE controls multiple signal transduction pathways through the proteolytic release of the extracellular domain of a host of membrane-bound factors and receptors. Using stopped-flow x-ray spectroscopy methods together with transient kinetic analyses, we demonstrate that TACE's catalytic zinc ion undergoes dynamic charge transitions before substrate binding to the metal ion. This indicates previously undescribed communication pathways taking place between distal protein sites and the enzyme catalytic core. The observed charge transitions are synchronized with distinct phases in the reaction kinetics and changes in metal coordination chemistry mediated by the binding of the peptide substrate to the catalytic metal ion and product release. Here we report key local charge transitions critical for proteolysis as well as long sought evidence for the proposed reaction model of peptide hydrolysis. This study provides a general approach for gaining critical insights into the molecular basis of substrate recognition and turnover by zinc metalloproteinases that may be used for drug design.
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Affiliation(s)
- Ariel Solomon
- *Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Barak Akabayov
- *Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anatoly Frenkel
- Department of Physics, Yeshiva University, New York, NY 10033
| | - Marcos E. Milla
- Department of Biochemical Pharmacology, Roche Pharmaceuticals, Palo Alto, CA 94304; and
| | - Irit Sagi
- *Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- To whom correspondence should be addressed. E-mail:
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Ruggles JL, Foran GJ, Tanida H, Nagatani H, Jimura Y, Watanabe I, Gentle IR. Interfacial behavior of tetrapyridylporphyrin monolayer arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:681-6. [PMID: 16401117 DOI: 10.1021/la051474k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The behavior of monolayer films of free base 5,10,15,20-tetrapyridylporphinato (TPyP) and 5,10,15,20-tetrapyridylporphinato zinc(II) (ZnTPyP) on pure water, 0.1 M CdCl2, and 0.1 M CuCl2 subphases was investigated by surface pressure-area isotherms, specular X-ray reflectometry, and polarized total reflection X-ray absorption spectroscopy (PTRXAS). Surface pressure-area isotherms showed significant differences in the area per molecule on pure water compared to that on salt subphases, with a marked increase in the area observed on the salt solutions. This behavior was noted for both forms of the porphyrin and both salts investigated. Modeling of specular X-ray reflectometry data indicated that thinner and more electron dense layers on salt subphases best fit the observed profiles. These data suggest that the porphyrin macrocycle is oriented parallel to the interface on salt subphases and takes on a tilted conformation on pure water. In the case of ZnTPyP, PTRXAS was used to determine the orientation of the porphyrin moiety relative to the surface and to probe the coordination of the central Zn ion. In agreement with the pressure-area isotherms and reflectometry, the PTRXAS data indicate a change in orientation on the salt subphases.
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Affiliation(s)
- Jeremy L Ruggles
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Australia 4072
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Nagatani H, Tanida H, Ozeki T, Watanabe I. Zinc(II) porphyrins at the air-water interface as studied by polarized total-reflection X-ray absorption fine structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:209-12. [PMID: 16378422 DOI: 10.1021/la0519204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The polarized total-reflection X-ray absorption fine structure method was applied to characterize zinc porphyrins at the air-water interface. The X-ray absorption near edge structure exhibited a significant difference depending on the polarization of the X-ray. A shoulder peak of the Zn K-edge corresponding to the 1s-4p(z) transition for a square planar metal complex without axial coordination(s) was observed at 9662 eV, which indicates that the axial coordination sites of zinc porphyrin molecules examined are not fully hydrated at the air-water interface. The molecular orientation of zinc porphyrins was determined by analyzing the polarization dependence of the transition peak intensity. The meso-substituted porphyrin derivative 5,10,15,20-tetraphenylporphyrinatozinc(II) (ZnTPP) orients rather parallel to the solution surface. In contrast to ZnTPP, the zinc(II) protoporphyrin IX (ZnPP) with hydrophilic carboxyl groups at one side of the molecule stands up with respect to the solution surface, and the average tilting angle of the porphyrin plane to the surface was evaluated to be between 57 degrees and 43 degrees. In addition, the axial coordination of ZnPP is modified depending on the surface concentration, in which the axial hydration to the zinc center is effectively inhibited in the compressed surface layer.
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Affiliation(s)
- Hirohisa Nagatani
- Department of Natural Sciences, Hyogo University of Teacher Education, Yashiro, Hyogo 673-1494, Japan.
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Wang X, Hanson JC, Frenkel AI, Kim JY, Rodriguez JA. Time-resolved Studies for the Mechanism of Reduction of Copper Oxides with Carbon Monoxide: Complex Behavior of Lattice Oxygen and the Formation of Suboxides. J Phys Chem B 2004. [DOI: 10.1021/jp040366o] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xianqin Wang
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, 11973, Physics Department, Yeshiva University, New York, New York 10016, and Beamline Division, Pohang Accelerator Laboratory, Pohang, 790−784, South Korea
| | - Jonathan C. Hanson
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, 11973, Physics Department, Yeshiva University, New York, New York 10016, and Beamline Division, Pohang Accelerator Laboratory, Pohang, 790−784, South Korea
| | - Anatoly I. Frenkel
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, 11973, Physics Department, Yeshiva University, New York, New York 10016, and Beamline Division, Pohang Accelerator Laboratory, Pohang, 790−784, South Korea
| | - Jaw-Yong Kim
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, 11973, Physics Department, Yeshiva University, New York, New York 10016, and Beamline Division, Pohang Accelerator Laboratory, Pohang, 790−784, South Korea
| | - José A. Rodriguez
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, 11973, Physics Department, Yeshiva University, New York, New York 10016, and Beamline Division, Pohang Accelerator Laboratory, Pohang, 790−784, South Korea
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Solomon A, Rosenblum G, Gonzales PE, Leonard JD, Mobashery S, Milla ME, Sagi I. Pronounced diversity in electronic and chemical properties between the catalytic zinc sites of tumor necrosis factor-alpha-converting enzyme and matrix metalloproteinases despite their high structural similarity. J Biol Chem 2004; 279:31646-54. [PMID: 15102849 DOI: 10.1074/jbc.m401310200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The metalloproteinase tumor necrosis factor-alpha-converting enzyme (TACE) is involved in the regulation of several key physiological and pathological processes. Therefore, potent and selective synthetic inhibitors are highly sought for the study of the physiological roles of TACE as well as for therapeutic purposes. Because of the high structural similarities between the active site of TACE and those of other related zinc endopeptidases such as disintegrin (ADAMs) and matrix metalloproteinases (MMPs), the design of such tailor-made inhibitors is not trivial. To obtain new insights into this problem, we have used a selective MMP inhibitor as a probe to examine the structural and kinetic effects occurring at the active site of TACE upon inhibition. Specifically, we used the selective MMP mechanism-based inhibitor SB-3CT to characterize the fine structural and electronic differences between the catalytic zinc ions within the active sites of TACE and MMP-2. We show that SB-3CT directly binds the metal ion of TACE as observed before with MMP-2. However, in contrast to MMP-2, the binding mode of SB-3CT to the catalytic zinc ion of TACE is different in the length of the Zn-S(SB-3CT) bond distance and the total effective charge of the catalytic zinc ion. In addition, SB-3CT inhibits TACE in a non-competitive fashion by inducing significant conformational changes in the structure. For MMP-2, SB-3CT behaved as a competitive inhibitor and no significant conformational changes were observed. An examination of the second shell amino acids surrounding the catalytic zinc ion of these enzymes indicated that the active site of TACE is more polar than that of MMP-2 and of other MMPs. On the basis of these results, we propose that although there is a seemingly high structural similarity between TACE and MMP-2, these enzymes are significantly diverse in the electronic and chemical properties within their active sites.
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Affiliation(s)
- Ariel Solomon
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
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Kim JY, Rodriguez JA, Hanson JC, Frenkel AI, Lee PL. Reduction of CuO and Cu2O with H2: H embedding and kinetic effects in the formation of suboxides. J Am Chem Soc 2003; 125:10684-92. [PMID: 12940754 DOI: 10.1021/ja0301673] [Citation(s) in RCA: 202] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved X-ray diffraction, X-ray absorption fine structure, and first-principles density functional calculations were used to investigate the reaction of CuO and Cu(2)O with H(2) in detail. The mechanism for the reduction of CuO is complex, involving an induction period and the embedding of H into the bulk of the oxide. The in-situ experiments show that, under a normal supply of hydrogen, CuO reduces directly to metallic Cu without formation of an intermediate or suboxide (i.e., no Cu(4)O(3) or Cu(2)O). The reduction of CuO is easier than the reduction of Cu(2)O. The apparent activation energy for the reduction of CuO is about 14.5 kcal/mol, while the value is 27.4 kcal/mol for Cu(2)O. During the reduction of CuO, the system can reach metastable states (MS) and react with hydrogen instead of forming Cu(2)O. To see the formation of Cu(2)O, one has to limit the flow of hydrogen, slowing the rate of reduction to allow a MS --> Cu(2)O transformation. These results show the importance of kinetic effects for the formation of well-defined suboxides during a reduction process and the activation of oxide catalysts.
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Affiliation(s)
- Jae Y Kim
- Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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Tanida H, Nagatani H, Watanabe I. Polarized total-reflection x-ray absorption fine structure for self-assembled monolayer of zinc porphyrin at air–water interface. J Chem Phys 2003. [DOI: 10.1063/1.1580095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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