1
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Mudryk K, Lee C, Tomaník L, Malerz S, Trinter F, Hergenhahn U, Neumark DM, Slavíček P, Bradforth S, Winter B. How Does Mg 2+(aq) Interact with ATP (aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy. J Am Chem Soc 2024; 146:16062-16075. [PMID: 38802319 PMCID: PMC11177255 DOI: 10.1021/jacs.4c03174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Liquid-jet photoemission spectroscopy (LJ-PES) allows for a direct probing of electronic structure in aqueous solutions. We show the applicability of the approach to biomolecules in a complex environment, exploring site-specific information on the interaction of adenosine triphosphate in the aqueous phase (ATP(aq)) with magnesium (Mg2+(aq)), highlighting the synergy brought about by the simultaneous analysis of different regions in the photoelectron spectrum. In particular, we demonstrate intermolecular Coulombic decay (ICD) spectroscopy as a new and powerful addition to the arsenal of techniques for biomolecular structure investigation. We apply LJ-PES assisted by electronic-structure calculations to study ATP(aq) solutions with and without dissolved Mg2+. Valence photoelectron data reveal spectral changes in the phosphate and adenine features of ATP(aq) due to interactions with the divalent cation. Chemical shifts in Mg 2p, Mg 2s, P 2p, and P 2s core-level spectra as a function of the Mg2+/ATP concentration ratio are correlated to the formation of [Mg(ATP) 2]6-(aq), [MgATP]2-(aq), and [Mg2ATP](aq) complexes, demonstrating the element sensitivity of the technique to Mg2+-phosphate interactions. The most direct probe of the intermolecular interactions between ATP(aq) and Mg2+(aq) is delivered by the emerging ICD electrons following ionization of Mg 1s electrons. ICD spectra are shown to sensitively probe ligand exchange in the Mg2+-ATP(aq) coordination environment. In addition, we report and compare P 2s data from ATP(aq) and adenosine mono- and diphosphate (AMP(aq) and ADP(aq), respectively) solutions, probing the electronic structure of the phosphate chain and the local environment of individual phosphate units in ATP(aq). Our results provide a comprehensive view of the electronic structure of ATP(aq) and Mg2+-ATP(aq) complexes relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.
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Affiliation(s)
- Karen Mudryk
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Chin Lee
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Lukáš Tomaník
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Sebastian Malerz
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Florian Trinter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Institut
für Kernphysik, Goethe-Universität
Frankfurt, Max-von-Laue-Straße
1, 60438 Frankfurt
am Main, Germany
| | - Uwe Hergenhahn
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Daniel M. Neumark
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Stephen Bradforth
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Bernd Winter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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2
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Mattioli G, Schürmann R, Nicolafrancesco C, Giuliani A, Milosavljević AR. Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study. J Phys Chem Lett 2023; 14:10173-10180. [PMID: 37925744 PMCID: PMC10658619 DOI: 10.1021/acs.jpclett.3c01666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.
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Affiliation(s)
- Giuseppe Mattioli
- Istituto
di Struttura della Materia (ISM), Consiglio
Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, CP 10, 00016 Monterotondo Scalo, Italy
| | - Robin Schürmann
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- Institute
of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- INRAE,
UAR1008, Transform Department, Rue de la Géraudière, BP 71627, 44316 Nantes, France
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3
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Zhao Y, Gao J, Yang Z, Li L, Cui J, Zhang P, Hu C, Diao C, Choi W. Efficient Exciton Dissociation in Ionically Interacted Methyl Viologen and Polymeric Carbon Nitride for Superior H 2O 2 Photoproduction. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Yubao Zhao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Jingyu Gao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Zhenchun Yang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Lina Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Jiahao Cui
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Peng Zhang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Chun Hu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education & Institute of Environmental Research at Greater Bay, Guangzhou University, 510006 Guangzhou, P. R. China
| | - Caozheng Diao
- Singapore Synchrotron Light Source, National University of Singapore, 117603 Singapore, Singapore
| | - Wonyong Choi
- KENTECH Institute for Environmental and Climate Technology, Korea Institute of Energy Technology (KENTECH), 58330 Naju, Korea
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4
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Wang K, Chai H, Cao Y. Using Anion‐Exchange to Induce the Formation of Edge Defects in CoNx to Enhance ORR Activity. ChemCatChem 2022. [DOI: 10.1002/cctc.202200146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kun Wang
- Xinjiang University College of Chemistry CHINA
| | - Hui Chai
- Xinjiang University College of Chemistry CHINA
| | - Yali Cao
- Xinjiang University Institue of Applied Chemistry Shenli Road, No. 666 830046 Urumqi CHINA
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5
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Peng X, Liu HX, Zhang Y, Huang ZQ, Yang L, Jiang Y, Wang X, Zheng L, Chang C, Au CT, Jiang L, Li J. Highly efficient ammonia synthesis at low temperature over a Ru-Co catalyst with dual atomically dispersed active centers. Chem Sci 2021; 12:7125-7137. [PMID: 34123340 PMCID: PMC8153211 DOI: 10.1039/d1sc00304f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/07/2021] [Indexed: 01/01/2023] Open
Abstract
The desire for a carbon-free society and the continuously increasing demand for clean energy make it valuable to exploit green ammonia (NH3) synthesis that proceeds via the electrolysis driven Haber-Bosch (eHB) process. The key for successful operation is to develop advanced catalysts that can operate under mild conditions with efficacy. The main bottleneck of NH3 synthesis under mild conditions is the known scaling relation in which the feasibility of N2 dissociative adsorption of a catalyst is inversely related to that of the desorption of surface N-containing intermediate species, which leads to the dilemma that NH3 synthesis could not be catalyzed effectively under mild conditions. The present work offers a new strategy via introducing atomically dispersed Ru onto a single Co atom coordinated with pyrrolic N, which forms RuCo dual single-atom active sites. In this system the d-band centers of Ru and Co were both regulated to decouple the scaling relation. Detailed experimental and theoretical investigations demonstrate that the d-bands of Ru and Co both become narrow, and there is a significant overlapping of t2g and eg orbitals as well as the formation of a nearly uniform Co 3d ligand field, making the electronic structure of the Co atom resemble that of a "free-atom". The "free-Co-atom" acts as a bridge to facilitate electron transfer from pyrrolic N to surface Ru single atoms, which enables the Ru atom to donate electrons to the antibonding π* orbitals of N2, thus resulting in promoted N2 adsorption and activation. Meanwhile, H2 adsorbs dissociatively on the Co center to form a hydride, which can transfer to the Ru site to cause the hydrogenation of the activated N2 to generate N2H x (x = 1-4) intermediates. The narrow d-band centers of this RuCo catalyst facilitate desorption of surface *NH3 intermediates even at 50 °C. The cooperativity of the RuCo system decouples the sites for the activation of N2 from those for the desorption of *NH3 and *N2H x intermediates, giving rise to a favorable pathway for efficient NH3 synthesis under mild conditions.
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Affiliation(s)
- Xuanbei Peng
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Han-Xuan Liu
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an 710049 China
| | - Yangyu Zhang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Zheng-Qing Huang
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an 710049 China
| | - Linlin Yang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Yafei Jiang
- Department of Chemistry, Southern University of Science and Technology Shenzhen China
| | - Xiuyun Wang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Lirong Zheng
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing China
| | - Chunran Chang
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an 710049 China
| | - Chak-Tong Au
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Lilong Jiang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Jun Li
- Department of Chemistry, Southern University of Science and Technology Shenzhen China
- Department of Chemistry, Tsinghua University Beijing China
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6
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Folkestad SD, Koch H. Equation-of-Motion MLCCSD and CCSD-in-HF Oscillator Strengths and Their Application to Core Excitations. J Chem Theory Comput 2020; 16:6869-6879. [PMID: 32955866 PMCID: PMC8011930 DOI: 10.1021/acs.jctc.0c00707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present an implementation of equation-of-motion oscillator strengths for the multilevel CCSD (MLCCSD) model where CCS is used as the lower level method (CCS/CCSD). In this model, the double excitations of the cluster operator are restricted to an active orbital space, whereas the single excitations are unrestricted. Calculated nitrogen K-edge spectra of adenosine, adenosine triphosphate (ATP), and an ATP-water system are used to demonstrate the performance of the model. Projected atomic orbitals (PAOs) are used to partition the virtual space into active and inactive orbital sets. Cholesky decomposition of the Hartree-Fock density is used to partition the occupied orbitals. This Cholesky-PAO partitioning is cheap, scaling as O(N3), and is suitable for the calculation of core excitations, which are localized in character. By restricting the single excitations of the cluster operator to the active space, as well as the double excitations, the CCSD-in-HF model is obtained. A comparison of the two models-MLCCSD and CCSD-in-HF-is presented for the core excitation spectra of the adenosine and ATP systems.
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Affiliation(s)
- Sarai Dery Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim N-7491, Norway.,Scuola Normale Superiore, Piazza dei Cavaleri 7, Pisa 56126, Italy
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7
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Wang XX, Prabhakaran V, He Y, Shao Y, Wu G. Iron-Free Cathode Catalysts for Proton-Exchange-Membrane Fuel Cells: Cobalt Catalysts and the Peroxide Mitigation Approach. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805126. [PMID: 30706548 DOI: 10.1002/adma.201805126] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/20/2018] [Indexed: 05/14/2023]
Abstract
High-performance and inexpensive platinum-group-metal (PGM)-free catalysts for the oxygen reduction reaction (ORR) in challenging acidic media are crucial for proton-exchange-membrane fuel cells (PEMFCs). Catalysts based on Fe and N codoped carbon (Fe-N-C) have demonstrated promising activity and stability. However, a serious concern is the Fenton reactions between Fe2+ and H2 O2 generating active free radicals, which likely cause degradation of the catalysts, organic ionomers within electrodes, and polymer membranes used in PEMFCs. Alternatively, Co-N-C catalysts with mitigated Fenton reactions have been explored as a promising replacement for Fe and PGM catalysts. Therefore, herein, the focus is on Co-N-C catalysts for the ORR relevant to PEMFC applications. Catalyst synthesis, structure/morphology, activity and stability improvement, and reaction mechanisms are discussed in detail. Combining experimental and theoretical understanding, the aim is to elucidate the structure-property correlations and provide guidance for rational design of advanced Co catalysts with a special emphasis on atomically dispersed single-metal-site catalysts. In the meantime, to reduce H2 O2 generation during the ORR on the Co catalysts, potential strategies are outlined to minimize the detrimental effect on fuel cell durability.
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Affiliation(s)
- Xiao Xia Wang
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | | | - Yanghua He
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Yuyan Shao
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gang Wu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
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8
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Gallagher N, Zhang H, Junghoefer T, Giangrisostomi E, Ovsyannikov R, Pink M, Rajca S, Casu MB, Rajca A. Thermally and Magnetically Robust Triplet Ground State Diradical. J Am Chem Soc 2019; 141:4764-4774. [PMID: 30816035 DOI: 10.1021/jacs.9b00558] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High spin ( S = 1) organic diradicals may offer enhanced properties with respect to several emerging technologies, but typically exhibit low singlet triplet energy gaps and possess limited thermal stability. We report triplet ground state diradical 2 with a large singlet-triplet energy gap, Δ EST ≥ 1.7 kcal mol-1, leading to nearly exclusive population of triplet ground state at room temperature, and good thermal stability with onset of decomposition at ∼160 °C under inert atmosphere. Magnetic properties of 2 and the previously prepared diradical 1 are characterized by SQUID magnetometry of polycrystalline powders, in polystyrene glass, and in other matrices. Polycrystalline diradical 2 forms a novel one-dimensional (1D) spin-1 ( S = 1) chain of organic radicals with intrachain antiferromagnetic coupling of J'/ k = -14 K, which is associated with the N···N and N···O intermolecular contacts. The intrachain antiferromagnetic coupling in 2 is by far strongest among all studied 1D S = 1 chains of organic radicals, which also makes 1D S = 1 chains of 2 most isotropic, and therefore an excellent system for studies of low-dimensional magnetism. In polystyrene glass and in frozen benzene or dibutyl phthalate solution, both 1 and 2 are monomeric. Diradical 2 is thermally robust and is evaporated under ultrahigh vacuum to form thin films of intact diradicals on silicon substrate, as demonstrated by X-ray photoelectron spectroscopy. Based on C-K NEXAFS spectra and AFM images of the ∼1.5 nm thick films, the diradical molecules form islands on the substrate with molecules stacked approximately along the crystallographic a-axis. The films are stable under ultrahigh vacuum for at least 60 h but show signs of decomposition when exposed to ambient conditions for 7 h.
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Affiliation(s)
- Nolan Gallagher
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Hui Zhang
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Tobias Junghoefer
- Institute of Physical and Theoretical Chemistry, University of Tübingen , 72076 Tübingen , Germany
| | - Erika Giangrisostomi
- Helmholtz-Zentrum Berlin für Materialien und Energie (HZB) , Albert-Einstein-Str 15 , 12489 Berlin , Germany
| | - Ruslan Ovsyannikov
- Helmholtz-Zentrum Berlin für Materialien und Energie (HZB) , Albert-Einstein-Str 15 , 12489 Berlin , Germany
| | - Maren Pink
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Suchada Rajca
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Maria Benedetta Casu
- Institute of Physical and Theoretical Chemistry, University of Tübingen , 72076 Tübingen , Germany
| | - Andrzej Rajca
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
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9
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Ekimova M, Kubin M, Ochmann M, Ludwig J, Huse N, Wernet P, Odelius M, Nibbering ETJ. Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs. J Phys Chem B 2018; 122:7737-7746. [PMID: 30024171 DOI: 10.1021/acs.jpcb.8b05424] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid-base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen 1s core electron excitations to elucidate the roles of N-H σ* and N-C σ* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases Et xNH3- x ( x = 0...3; Et- = C2H5-) and the conjugate positively charged ethylammonium cation acids Et yNH4- y+ ( y = 0...4; Et- = C2H5-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post-edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H σ* to N-C σ* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.
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Affiliation(s)
- Maria Ekimova
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max Born Strasse 2A , 12489 Berlin , Germany
| | - Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany
| | - Miguel Ochmann
- Institute for Nanostructure and Solid State Physics , Center for Free-Electron Laser Science , Luruper Chaussee 149 , 22761 Hamburg , Germany
| | - Jan Ludwig
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany
| | - Nils Huse
- Institute for Nanostructure and Solid State Physics , Center for Free-Electron Laser Science , Luruper Chaussee 149 , 22761 Hamburg , Germany
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany
| | - Michael Odelius
- Department of Physics, AlbaNova University Center , Stockholm University , 106 91 Stockholm , Sweden
| | - Erik T J Nibbering
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max Born Strasse 2A , 12489 Berlin , Germany
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10
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Hršak D, Nørby MS, Coriani S, Kongsted J. One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions. J Chem Theory Comput 2018; 14:2145-2154. [DOI: 10.1021/acs.jctc.8b00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten Steen Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kongens Lyngby, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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11
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Acres RG, Cheng X, Beranová K, Bercha S, Skála T, Matolín V, Xu Y, Prince KC, Tsud N. An experimental and theoretical study of adenine adsorption on Au(111). Phys Chem Chem Phys 2018; 20:4688-4698. [DOI: 10.1039/c7cp08102b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The parallel and upright adenine phases on Au(111) were studied by photoelectron and absorption spectroscopies in combination with density functional theory calculations.
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Affiliation(s)
| | - Xun Cheng
- Cain Department of Chemical Engineering
- Louisiana State University
- Baton Rouge
- USA
| | - Klára Beranová
- Elettra-Sincrotrone Trieste S.C.p.A
- Basovizza
- Italy
- Charles University
- Faculty of Mathematics and Physics
| | - Sofiia Bercha
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Tomáš Skála
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Vladimír Matolín
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Ye Xu
- Cain Department of Chemical Engineering
- Louisiana State University
- Baton Rouge
- USA
| | | | - Nataliya Tsud
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
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12
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Smith JW, Saykally RJ. Soft X-ray Absorption Spectroscopy of Liquids and Solutions. Chem Rev 2017; 117:13909-13934. [DOI: 10.1021/acs.chemrev.7b00213] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jacob W. Smith
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
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13
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Tsud N, Bercha S, Ševčíková K, Acres RG, Prince KC, Matolín V. Adenine adlayers on Cu(111): XPS and NEXAFS study. J Chem Phys 2015; 143:174704. [DOI: 10.1063/1.4935055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nataliya Tsud
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 18000 Prague 8, Czech Republic
| | - Sofiia Bercha
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 18000 Prague 8, Czech Republic
| | - Klára Ševčíková
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 18000 Prague 8, Czech Republic
| | - Robert G. Acres
- Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, 34149 Basovizza, Trieste, Italy
| | - Kevin C. Prince
- Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, 34149 Basovizza, Trieste, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, 34149 Basovizza, Trieste, Italy
| | - Vladimír Matolín
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 18000 Prague 8, Czech Republic
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14
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You B, Jiang N, Sheng M, Drisdell WS, Yano J, Sun Y. Bimetal–Organic Framework Self-Adjusted Synthesis of Support-Free Nonprecious Electrocatalysts for Efficient Oxygen Reduction. ACS Catal 2015. [DOI: 10.1021/acscatal.5b02325] [Citation(s) in RCA: 376] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo You
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
| | - Nan Jiang
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
| | - Meili Sheng
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
| | - Walter S. Drisdell
- Joint Center of Artificial Photosynthesis, Berkeley, California 94720, United States
| | - Junko Yano
- Joint Center of Artificial Photosynthesis, Berkeley, California 94720, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yujie Sun
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
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15
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Seidel R, Atak K, Thürmer S, Aziz EF, Winter B. Ti3+ Aqueous Solution: Hybridization and Electronic Relaxation Probed by State-Dependent Electron Spectroscopy. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b03337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Seidel
- Institute
of Methods for Material Development, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse
15, D-12489 Berlin, Germany
| | - Kaan Atak
- Institute
of Methods for Material Development, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse
15, D-12489 Berlin, Germany
| | - Stephan Thürmer
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Emad F. Aziz
- Institute
of Methods for Material Development, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse
15, D-12489 Berlin, Germany
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, D-14159 Berlin, Germany
| | - Bernd Winter
- Institute
of Methods for Material Development, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse
15, D-12489 Berlin, Germany
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16
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Lam RK, Shih O, Smith JW, Sheardy AT, Rizzuto AM, Prendergast D, Saykally RJ. Electrokinetic detection for X-ray spectra of weakly interacting liquids: n-decane and n-nonane. J Chem Phys 2014; 140:234202. [DOI: 10.1063/1.4882901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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17
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Shimada H, Fukao T, Minami H, Ukai M, Fujii K, Yokoya A, Fukuda Y, Saitoh Y. Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES). Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Kryzhevoi NV, Cederbaum LS. Exploring Protonation and Deprotonation Effects with Auger Electron Spectroscopy. J Phys Chem Lett 2012; 3:2733-2737. [PMID: 26295900 DOI: 10.1021/jz301130t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Auger electron spectroscopy is demonstrated to be a very efficient tool to probe alterations in local chemical environment due to changes in protonation states. We show that electronic and geometric structure changes induced by protonation or deprotonation are well reflected in Auger spectra through characteristic chemical shifts and spectral shape variations. We also present evidence that Auger spectra are sensitive to relative concentrations of compounds in different protonation states. Special attention is paid to the high kinetic energy spectral regions that exhibit remarkable features resulting from core ICD-like transitions in normal species and Auger transitions in deprotonated fragments. The latter contribution was so far ignored when explaining Auger spectra of species embedded in the environment. This contribution should be reconsidered, taking into account the recently discovered possibility of ultrafast dissociation of core-ionized hydrogen-bonded systems in media.
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Affiliation(s)
- Nikolai V Kryzhevoi
- Theoretical Chemistry, Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
| | - Lorenz S Cederbaum
- Theoretical Chemistry, Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
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19
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Milosavljević AR, Canon F, Nicolas C, Miron C, Nahon L, Giuliani A. Gas-Phase Protein Inner-Shell Spectroscopy by Coupling an Ion Trap with a Soft X-ray Beamline. J Phys Chem Lett 2012; 3:1191-1196. [PMID: 26288054 DOI: 10.1021/jz300324z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
C, N, and O near-edge ion yield spectroscopy of 8+ selected electrosprayed cations of cytochrome c protein (12 kDa) has been performed by coupling a linear quadrupole ion trap with a soft X-ray beamline. The photoactivation tandem mass spectra were recorded as a function of the photon energy. Photoionization of the precursor, accompanied by CO2 loss, is the dominant relaxation process, showing high photoion stability following direct or resonant photoionization. The partial ion yields extracted from recorded mass spectra show significantly different behaviors for single and double ionization channels, which can be qualitatively explained by different Auger decay mechanisms. However, the single ionization spectra reveal characteristic structures when compared to existing near-edge X-ray absorption fine structure (NEXAFS) spectra from thin films of peptides and proteins. Therefore, the present experiment opens up new avenues for near-edge X-ray spectroscopy of macromolecules in the gas phase, overcoming the radiation damage issue or the environmental effects as due to the surface, intermolecular interactions, and solvent.
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Affiliation(s)
| | - Francis Canon
- ‡Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Christophe Nicolas
- ‡Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Catalin Miron
- ‡Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Laurent Nahon
- ‡Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Alexandre Giuliani
- ‡Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
- §UAR 1008 Cepia, Institut National de la Recherche Agronomique (INRA), BP 71627, 44316 Nantes Cedex 3, France
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20
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Liang Y, Wang H, Zhou J, Li Y, Wang J, Regier T, Dai H. Covalent hybrid of spinel manganese-cobalt oxide and graphene as advanced oxygen reduction electrocatalysts. J Am Chem Soc 2012; 134:3517-23. [PMID: 22280461 DOI: 10.1021/ja210924t] [Citation(s) in RCA: 642] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Through direct nanoparticle nucleation and growth on nitrogen doped, reduced graphene oxide sheets and cation substitution of spinel Co(3)O(4) nanoparticles, a manganese-cobalt spinel MnCo(2)O(4)/graphene hybrid was developed as a highly efficient electrocatalyst for oxygen reduction reaction (ORR) in alkaline conditions. Electrochemical and X-ray near-edge structure (XANES) investigations revealed that the nucleation and growth method for forming inorganic-nanocarbon hybrids results in covalent coupling between spinel oxide nanoparticles and N-doped reduced graphene oxide (N-rmGO) sheets. Carbon K-edge and nitrogen K-edge XANES showed strongly perturbed C-O and C-N bonding in the N-rmGO sheet, suggesting the formation of C-O-metal and C-N-metal bonds between N-doped graphene oxide and spinel oxide nanoparticles. Co L-edge and Mn L-edge XANES suggested substitution of Co(3+) sites by Mn(3+), which increased the activity of the catalytic sites in the hybrid materials, further boosting the ORR activity compared with the pure cobalt oxide hybrid. The covalently bonded hybrid afforded much greater activity and durability than the physical mixture of nanoparticles and carbon materials including N-rmGO. At the same mass loading, the MnCo(2)O(4)/N-graphene hybrid can outperform Pt/C in ORR current density at medium overpotentials with stability superior to Pt/C in alkaline solutions.
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Affiliation(s)
- Yongye Liang
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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