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De Santis E, Alleva S, Minicozzi V, Morante S, Stellato F. Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders. Chempluschem 2024; 89:e202300712. [PMID: 38526934 DOI: 10.1002/cplu.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.
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Affiliation(s)
- Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Stefania Alleva
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Velia Minicozzi
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Silvia Morante
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Francesco Stellato
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
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2
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Ciccone L, Camodeca C, Tonali N, Barlettani L, Rossello A, Fruchart Gaillard C, Kaffy J, Petrarolo G, La Motta C, Nencetti S, Orlandini E. New Hybrid Compounds Incorporating Natural Products as Multifunctional Agents against Alzheimer's Disease. Pharmaceutics 2023; 15:2369. [PMID: 37896129 PMCID: PMC10610016 DOI: 10.3390/pharmaceutics15102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 10/29/2023] Open
Abstract
A series of new hybrid derivatives 1a-c, 2a-c, 3a-c, 4a-c, 5a-c, inspired by nature, were synthesized and studied as multifunctional agents for the treatment of Alzheimer's disease (AD). These compounds were designed to merge together the trifluoromethyl benzyloxyaminic bioactive moiety, previously identified, with different acids available in nature. The ability of the synthesized compounds to chelate biometals, such as Cu2+, Zn2+ and Fe2+, was studied by UV-Vis spectrometer, and through a preliminary screening their antioxidant activity was evaluated by DPPH. Then, selected compounds were tested by in vitro ABTS free radical method and ex vivo rat brain TBARS assay. Compounds 2a-c, combining the strongest antioxidant and biometal chelators activities, were studied for their ability to contrast Aβ1-40 fibrillization process. Finally, starting from the promising profile obtained for compound 2a, we evaluated if it could be able to induce a positive cross-interaction between transthyretin (TTR) and Aβ in presence and in absence of Cu2+.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Caterina Camodeca
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Nicolò Tonali
- CNRS, BioCIS, Bâtiment Henri Moissan, Université Paris-Saclay, 17 Av. des Sciences, 91400 Orsay, France; (N.T.); (J.K.)
| | - Lucia Barlettani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Armando Rossello
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
- Research Center “E. Piaggio”, University of Pisa, 56122 Pisa, Italy;
| | - Carole Fruchart Gaillard
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris Saclay, 91191 Gif-sur-Yvette, France;
| | - Julia Kaffy
- CNRS, BioCIS, Bâtiment Henri Moissan, Université Paris-Saclay, 17 Av. des Sciences, 91400 Orsay, France; (N.T.); (J.K.)
| | - Giovanni Petrarolo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Concettina La Motta
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (C.C.); (L.B.); (A.R.); (G.P.); (C.L.M.)
| | - Elisabetta Orlandini
- Research Center “E. Piaggio”, University of Pisa, 56122 Pisa, Italy;
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53, 56126 Pisa, Italy
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3
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Ghosh S, Mukamel S, Govind N. A Combined Wave Function and Density Functional Approach for K-Edge X-ray Absorption Near-Edge Spectroscopy: A Case Study of Hydrated First-Row Transition Metal Ions. J Phys Chem Lett 2023:5203-5209. [PMID: 37257001 DOI: 10.1021/acs.jpclett.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The prediction of X-ray absorption spectra (XAS) of transition metal complexes has important and broad application areas in chemistry and biology. In this letter, we have investigated the predictive ability of multiconfiguration pair-density functional theory (MC-PDFT) for X-ray absorption spectra by calculating the metal K pre-edge features of aquated 3d transition metal ions in common oxidation states. MC-PDFT results were compared with experimentally measured spectra as well as analyzed against results from restricted active-space second-order perturbation theory (RASPT2) and time-dependent density functional theory (TDDFT). As expected, TDDFT performs well for excited states that can be accurately represented by singly excited configurations but fails for excited states where higher order excitations become important. On the other hand, both RASPT2 and MC-PDFT provide quantitatively accurate results for all excited states irrespective of their character. While core-level spectroscopy with RASPT2 is accurate, it is computationally expensive. Our results show that MC-PDFT performs equally well with significantly lower computational cost and is an encouraging alternate approach for X-ray spectroscopies.
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Affiliation(s)
- Soumen Ghosh
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Shaul Mukamel
- Department of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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4
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McElhany SJ, Summers TJ, Shiery RC, Cantu DC. Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions. J Chem Inf Model 2023; 63:2699-2706. [PMID: 37083437 DOI: 10.1021/acs.jcim.3c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Rapid and accurate approaches to characterizing the coordination structure of an ion are important for designing ligands and quantifying structure-property trends. Here, we introduce AFICS (Analysis of the First Ion Coordination Sphere), a tool written in Python 3 for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. The principal feature of AFICS is its ability to quantify the distortion a coordination geometry undergoes compared to uniform polyhedra. This work applies the toolkit to analyze molecular dynamics simulations of the well-defined coordination structure of aqueous Cr3+ along with the more ambiguous structure of aqueous Eu3+ chelated to ethylenediaminetetraacetic acid. The tool is targeted for analyzing ions with fluxional or irregular coordination structures (e.g., solution structures of f-block elements) but is generalized such that it may be applied to other systems.
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Affiliation(s)
- Stuart J McElhany
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Thomas J Summers
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Richard C Shiery
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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5
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Ghosh S, Agarwal H, Galib M, Tran B, Balasubramanian M, Singh N, Fulton JL, Govind N. Near-Quantitative Predictions of the First-Shell Coordination Structure of Hydrated First-Row Transition Metal Ions Using K-Edge X-ray Absorption Near-Edge Spectroscopy. J Phys Chem Lett 2022; 13:6323-6330. [PMID: 35793526 DOI: 10.1021/acs.jpclett.2c01532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The solvation structure of transition metal ions is important for applications in geochemistry, biochemistry, energy storage, and environmental chemistry. We study the X-ray absorption pre-edge and near-edge spectra at the K-edge of a nearly complete series of hydrated first-row transition metal ions with d orbital occupancy from d2 to d10. We optimize all of the structures at the density functional theory (DFT) level with explicit solvation and then compute the pre-edge X-ray absorption spectra with time-dependent DFT (TDDFT) and restricted active space second-order perturbation theory (RASPT2). TDDFT provides accurate results for spectra that are dominated by single excitations, while RASPT2 correctly distinguishes between singly and doubly excited states with quantitative accuracy compared with experiment. We analyze the pre-edge features for each metal ion to reveal the impact of the variations in d orbital occupancy on the first-shell coordination environment. We also report the lowest-energy ligand field d-d transitions using complete active space second-order perturbation theory.
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Affiliation(s)
- Soumen Ghosh
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Harsh Agarwal
- Department of Chemical Engineering and Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mirza Galib
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ba Tran
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - Nirala Singh
- Department of Chemical Engineering and Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John L Fulton
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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6
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Leung K, Greathouse JA. Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces. Commun Chem 2022; 5:76. [PMID: 36697693 PMCID: PMC9814296 DOI: 10.1038/s42004-022-00688-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/30/2022] [Indexed: 01/28/2023] Open
Abstract
Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu2+-OH- bonds, yielding three local minima in the free energy profiles associated with 0-2 OH- bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH- hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu2+ dimer formation on silica surfaces over monomer adsorption.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, NM, USA.
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7
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Morante S, Botticelli S, Chiaraluce R, Consalvi V, La Penna G, Novak L, Pasquo A, Petrosino M, Proux O, Rossi G, Salina G, Stellato F. Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study. Front Mol Biosci 2022; 9:878017. [PMID: 35712353 PMCID: PMC9195147 DOI: 10.3389/fmolb.2022.878017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal.
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Affiliation(s)
- S. Morante
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- *Correspondence: S. Morante ,
| | - S. Botticelli
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - R. Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - V. Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - G. La Penna
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- CNR—Istituto di Chimica dei Composti Organometallici, Firenze, Italy
| | - L. Novak
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - A. Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory FSN-TECFIS-DIM, Frascati, Italy
| | - M. Petrosino
- Chair of Pharmacology, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - O. Proux
- Observatoire des Sciences de L’Univers de Grenoble, UAR 832 CNRS, Université Grenoble Alpes, Grenoble, France
| | - G. Rossi
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Roma, Italy
| | - G. Salina
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - F. Stellato
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
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8
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Lakey-Beitia J, Burillo AM, Penna GL, Hegde ML, Rao K. Polyphenols as Potential Metal Chelation Compounds Against Alzheimer's Disease. J Alzheimers Dis 2021; 82:S335-S357. [PMID: 32568200 PMCID: PMC7809605 DOI: 10.3233/jad-200185] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease affecting more than 50 million people worldwide. The pathology of this multifactorial disease is primarily characterized by the formation of amyloid-β (Aβ) aggregates; however, other etiological factors including metal dyshomeostasis, specifically copper (Cu), zinc (Zn), and iron (Fe), play critical role in disease progression. Because these transition metal ions are important for cellular function, their imbalance can cause oxidative stress that leads to cellular death and eventual cognitive decay. Importantly, these transition metal ions can interact with the amyloid-β protein precursor (AβPP) and Aβ42 peptide, affecting Aβ aggregation and increasing its neurotoxicity. Considering how metal dyshomeostasis may substantially contribute to AD, this review discusses polyphenols and the underlying chemical principles that may enable them to act as natural chelators. Furthermore, polyphenols have various therapeutic effects, including antioxidant activity, metal chelation, mitochondrial function, and anti-amyloidogenic activity. These combined therapeutic effects of polyphenols make them strong candidates for a moderate chelation-based therapy for AD.
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Affiliation(s)
- Johant Lakey-Beitia
- Centre for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
| | - Andrea M. Burillo
- Centre for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
| | - Giovanni La Penna
- National Research Council, Institute of Chemistry of Organometallic Compounds, Sesto Fiorentino (FI), Italy
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, USA
- Weill Medical College of Cornell University, New York, NY, USA
| | - K.S. Rao
- Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
- Zhongke Jianlan Medical Institute, Hangzhou, Republic of China
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9
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Zhang C, Liu L, Jia H. An Atomic-Scale Understanding of the Solution Chemistry of Antimony(V): Insights from First-Principles Molecular Dynamics Simulation. Inorg Chem 2020; 59:15741-15750. [PMID: 33040536 DOI: 10.1021/acs.inorgchem.0c02162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the structure, hydrolysis, and complexation of Sb(V) in aqueous solution has been elucidated by using first-principles molecular dynamics (FPMD) simulations. The results show that both antimonic acid and its deprotonated form have an octahedral configuration, with average Sb-OH2 and Sb-OH distances of 2.25 and 2.05 Å, respectively. The computed pKa of [Sb(OH)5(OH2)] is 1.8, while [Sb(OH)6]- has an extremely high pKa. Consequently, [Sb(OH)6]- is the most dominant species of Sb(V) under common environmental conditions. A stable aqueous complex can form between [Sb(OH)6]- and common cations, and an Sb-Al bidentate complex has the largest dissociation free energy, followed by a Sb-Mg bidentate complex, indicating that they have significantly higher stabilities. For Na+ and Ca2+, their respective monodentate and bidentate complexes have similar dissociation free energies, indicating very close possibilities. These findings provide a comprehensive understanding of the solution chemistry of Sb(V) from a quantitative and microscopic perspective.
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, People's Republic of China
| | - Libin Liu
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, People's Republic of China
| | - Hanzhong Jia
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, People's Republic of China
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10
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Nazmutdinov R, Quaino P, Colombo E, Santos E, Schmickler W. A model for the effect of ion pairing on an outer sphere electron transfer. Phys Chem Chem Phys 2020; 22:13923-13929. [PMID: 32542301 DOI: 10.1039/d0cp01915a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion pairing can strongly affect the rates of electron transfer reactions. To explain this effect, we propose a model Hamiltonian that describes the interactions between the pairing ion and the reactant, solvent and inner sphere reorganization, and bond breaking. Explicit expressions for the energies of the initial and final states, and for the energy of activation are derived in the weak adiabatic limit. The model is applied to the reduction of Cu(ii) in the presence of chloride ions. For this purpose, the pertinent system parameters are obtained from density functional theory. Our model explains why the chloride ion enhances the rate of the first electron transfer in copper deposition.
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Affiliation(s)
- Renat Nazmutdinov
- Kazan National Research Technological University, 420015 Kazan, Republic of Tatarstan, Russian Federation
| | - Paola Quaino
- Instituto de Química Aplicada del Litoral, IQAL (UNL-CONICET), Santa Fe, Argentina
| | - Estefania Colombo
- Instituto de Química Aplicada del Litoral, IQAL (UNL-CONICET), Santa Fe, Argentina
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11
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Yang C, Watanabe Y, Yoshida N, Nakano H. Three-Dimensional Reference Interaction Site Model Self-Consistent Field Study on the Coordination Structure and Excitation Spectra of Cu(II)–Water Complexes in Aqueous Solution. J Phys Chem A 2019; 123:3344-3354. [DOI: 10.1021/acs.jpca.9b01364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chen Yang
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihiro Watanabe
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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12
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Abstract
A proposal for building a Free Electron Laser, EuPRAXIA@SPARC_LAB, at the Laboratori Nazionali di Frascati, is at present under consideration. This FEL facility will provide a unique combination of a high brightness GeV-range electron beam generated in a X-band RF linac, a 0.5 PW-class laser system and the first FEL source driven by a plasma accelerator. The FEL will produce ultra-bright pulses, with up to 10 12 photons/pulse, femtosecond timescale and wavelength down to 3 nm, which lies in the so called “water window”. The experimental activity will be focused on the realization of a plasma driven short wavelength FEL able to provide high-quality photons for a user beamline. In this paper, we describe the main classes of experiments that will be performed at the facility, including coherent diffraction imaging, soft X-ray absorption spectroscopy, Raman spectroscopy, Resonant Inelastic X-ray Scattering and photofragmentation measurements. These techniques will allow studying a variety of samples, both biological and inorganic, providing information about their structure and dynamical behavior. In this context, the possibility of inducing changes in samples via pump pulses leading to the stimulation of chemical reactions or the generation of coherent excitations would tremendously benefit from pulses in the soft X-ray region. High power synchronized optical lasers and a TeraHertz radiation source will indeed be made available for THz and pump–probe experiments and a split-and-delay station will allow performing XUV-XUV pump–probe experiments.
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13
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X-Ray Absorption Spectroscopy Measurements of Cu-ProIAPP Complexes at Physiological Concentrations. CONDENSED MATTER 2019. [DOI: 10.3390/condmat4010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The amyloidogenic islet amyloid polypeptide (IAPP) and the associated pro-peptide ProIAPP1–48 are involved in cell death in type 2 diabetes mellitus. It has been observed that interactions of this peptide with metal ions have an impact on the cytotoxicity of the peptides as well as on their deposition in the form of amyloid fibrils. In particular, Cu(II) seems to inhibit amyloid fibril formation, thus suggesting that Cu homeostasis imbalance may be involved in the pathogenesis of type 2 diabetes mellitus. We performed X-ray Absorption Spectroscopy (XAS) measurements of Cu(II)-ProIAPP complexes under near-physiological (10 μM), equimolar concentrations of Cu(II) and peptide. Such low concentrations were made accessible to XAS measurements owing to the use of the High Energy Resolved Fluorescence Detection XAS facility recently installed at the ESRF beamline BM16 (FAME-UHD). Our preliminary data show that XAS measurements at micromolar concentrations are feasible and confirm that ProIAPP1–48-Cu(II) binding at near-physiological conditions can be detected.
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14
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Frank P, Benfatto M, Qayyum M. [Cu(aq)] 2+ is structurally plastic and the axially elongated octahedron goes missing. J Chem Phys 2018; 148:204302. [PMID: 29865827 DOI: 10.1063/1.5024693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High resolution (k = 18 Å-1 or k = 17 Å-1) copper K-edge EXAFS and MXAN (Minuit X-ray Absorption Near Edge) analyses have been used to investigate the structure of dissolved [Cu(aq)]2+ in 1,3-propanediol (1,3-P) or 1,5-pentanediol (1,5-P) aqueous frozen glasses. EXAFS analysis invariably found a single axially asymmetric 6-coordinate (CN6) site, with 4×Oeq = 1.97 Å, Oax1 = 2.22 Å, and Oax2 = 2.34 Å, plus a second-shell of 4×Owater = 3.6 Å. However, MXAN analysis revealed that [Cu(aq)]2+ occupies both square pyramidal (CN5) and axially asymmetric CN6 structures. The square pyramid included 4×H2O = 1.95 Å and 1×H2O = 2.23 Å. The CN6 sites included either a capped, near perfect, square pyramid with 5×H2O = 1.94 ± 0.04 Å and H2Oax = 2.22 Å (in 1,3-P) or a split axial configuration with 4×H2O = 1.94, H2Oax1 = 2.14 Å, and H2Oax2 = 2.28 Å (in 1,5-P). The CN6 sites also included an 8-H2O second-shell near 3.7 Å, which was undetectable about the strictly pyramidal sites. Equatorial angles averaging 94° ± 5° indicated significant departures from tetragonal planarity. MXAN assessment of the solution structure of [Cu(aq)]2+ in 1,5-P prior to freezing revealed the same structures as previously found in aqueous 1M HClO4, which have become axially compressed in the frozen glasses. [Cu(aq)]2+ in liquid and frozen solutions is dominated by a 5-coordinate square pyramid, but with split axial CN6 appearing in the frozen glasses. Among these phases, the Cu-O axial distances vary across 1 Å, and the equatorial angles depart significantly from the square plane. Although all these structures remove the dx2-y2 , dz2 degeneracy, no structure can be described as a Jahn-Teller (JT) axially elongated octahedron. The JT-octahedral description for dissolved [Cu(aq)]2+ should thus be abandoned in favor of square pyramidal [Cu(H2O)5]2+. The revised ligand environments have bearing on questions of the Cu(i)/Cu(ii) self-exchange rate and on the mechanism for ligand exchange with bulk water. The plasticity of dissolved Cu(ii) complex ions falsifies the foundational assumption of the rack-induced bonding theory of blue copper proteins and obviates any need for a thermodynamically implausible protein constraint.
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Affiliation(s)
- Patrick Frank
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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15
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La Penna G, Li MS. Towards High-Throughput Modelling of Copper Reactivity Induced by Structural Disorder in Amyloid Peptides. Chemistry 2018; 24:5259-5270. [DOI: 10.1002/chem.201704654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Giovanni La Penna
- National Research Council (CNR); Institute for Chemistry of Organometallic Compounds (ICCOM); via Madonna del Piano 10 50019 Sesto Fiorentino, Firenze Italy
| | - Mai Suan Li
- Polish Academy of Sciences; Institute of Physics; al. Lotników 32/46 02-668 Warsaw Poland
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12; Ho Chi Minh City Vietnam
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16
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Stellato F, Calandra M, D'Acapito F, De Santis E, La Penna G, Rossi G, Morante S. Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(ii) in water. Phys Chem Chem Phys 2018; 20:24775-24782. [DOI: 10.1039/c8cp04355h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems.
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Affiliation(s)
| | - Matteo Calandra
- Sorbonne Université
- CNRS, Institut des Nanosciences de Paris
- UMR7588
- Paris
- France
| | - Francesco D'Acapito
- CNR-IOM-OGG c/o European Synchrotron Radiation Facility
- F-38043 Grenoble
- France
| | - Emiliano De Santis
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
- Italy
| | - Giovanni La Penna
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- CNR – Institute for Chemistry of Organometallic Compounds
- Sesto Fiorentino
| | - Giancarlo Rossi
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
| | - Silvia Morante
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
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17
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Achilli E, Vertova A, Visibile A, Locatelli C, Minguzzi A, Rondinini S, Ghigna P. Structure and Stability of a Copper(II) Lactate Complex in Alkaline Solution: a Case Study by Energy-Dispersive X-ray Absorption Spectroscopy. Inorg Chem 2017; 56:6982-6989. [PMID: 28558207 DOI: 10.1021/acs.inorgchem.7b00553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Energy-dispersive X-ray absorption spectroscopy was applied, aimed at solving the problem of the structure and stability of a copper(II) lactate complex in alkaline solution, used as a precursor for the electrodeposition of Cu2O. The application of multiple scattering calculations to the simulation of the X-ray absorption near-edge structure part of the spectra allowed an accurate resolution of the structure: the copper(II) cation is surrounded by four lactate ions in a distorted tetrahedral environment, with the lactate anions acting as monodentate ligands. This results in an atomic arrangement where copper is surrounded by four oxygen atoms located at quite a short distance (ca. 1.87 Å) and four oxygen atoms located quite far apart (ca. 3.1-3.2 Å). The complex was finally found to be stable in a wide range of applied potentials.
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Affiliation(s)
- Elisabetta Achilli
- Dipartimento di Chimica, Università degli Studi di Pavia and Unita di Ricerca INSTM di Pavia , Viale Taramelli 16, 27100, Pavia, Italy
| | - Alberto Vertova
- Dipartimento di Chimica, Università degli Studi di Milano and Unita di Ricerca INSTM di Milano , Via Golgi 19, 20133, Milan, Italy
| | - Alberto Visibile
- Dipartimento di Chimica, Università degli Studi di Milano and Unita di Ricerca INSTM di Milano , Via Golgi 19, 20133, Milan, Italy
| | - Cristina Locatelli
- Dipartimento di Chimica, Università degli Studi di Milano and Unita di Ricerca INSTM di Milano , Via Golgi 19, 20133, Milan, Italy
| | - Alessandro Minguzzi
- Dipartimento di Chimica, Università degli Studi di Milano and Unita di Ricerca INSTM di Milano , Via Golgi 19, 20133, Milan, Italy
| | - Sandra Rondinini
- Dipartimento di Chimica, Università degli Studi di Milano and Unita di Ricerca INSTM di Milano , Via Golgi 19, 20133, Milan, Italy
| | - Paolo Ghigna
- Dipartimento di Chimica, Università degli Studi di Pavia and Unita di Ricerca INSTM di Pavia , Viale Taramelli 16, 27100, Pavia, Italy
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18
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Morales N, Galbis E, Martínez JM, Pappalardo RR, Sánchez Marcos E. Identifying Coordination Geometries of Metal Aquaions in Water: Application to the Case of Lanthanoid and Actinoid Hydrates. J Phys Chem Lett 2016; 7:4275-4280. [PMID: 27732784 DOI: 10.1021/acs.jpclett.6b02067] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The angular distribution function (ADF) associated with the oxygen-metal ion-oxygen angle (OMO) of several trivalent lanthanoid and actinoid aquaions has been used to identify the most probable coordination geometry of these aquaions in aqueous solutions. The ADFs extracted from the molecular dynamics trajectories have been compared with continuous distribution functions corresponding to the geometry of a reference polyhedron pattern. The procedure incorporates specific quantum-mechanical information on the aquaion under study. The new method is applied to the analysis of four M(H2O)n3+ aquaions in water, M = Lu and Cf for n = 8, and M = La and Ac for n = 9. For those that are 8-coordinated, the square antiprism (SA) coordination geometry is preferred. For the 9-fold coordination, the simulation ADFs are more similar to the continuous ADF derived from a Gyro-elongated-SA rather than to the usually proposed trigonal tricapped prism. Advantages of these continuous distributions with respect to the usually employed discrete distributions are emphasized as well as further applications are suggested.
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Affiliation(s)
- Noelia Morales
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - Elsa Galbis
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - José M Martínez
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - Rafael R Pappalardo
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
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Rossi G, d'Acapito F, Amidani L, Boscherini F, Pedio M. Local environment of metal ions in phthalocyanines: K-edge X-ray absorption spectra. Phys Chem Chem Phys 2016; 18:23686-94. [DOI: 10.1039/c6cp04022e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We describe a model for interpreting XAFS spectra of metal phthalocyanines. The near edge spectra are reproduced in a full potential approach.
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Affiliation(s)
- G. Rossi
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
| | - F. d'Acapito
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali – Operative Group in Grenoble
- c/o ESRF – The European Synchrotron
- CS 40220
- 38043 Grenoble Cedex 9
- France
| | - L. Amidani
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
| | - F. Boscherini
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali – Operative Group in Grenoble
| | - M. Pedio
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali
- Laboratorio TASC
- 34149 Trieste
- Italy
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