1
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Kalvoda T, Martinek T, Jungwirth P, Rulíšek L. Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods. J Chem Phys 2024; 160:084308. [PMID: 38421065 DOI: 10.1063/5.0192024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca2+, Cd2+, Cu2+, Fe2+, Hg2+, Mg2+, Ni2+, Pb2+, and Zn2+, we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M(H2O)2]2+ aqua complexes to [M(H2O)9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M(H2O)n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion-water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data.
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Affiliation(s)
- Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Tomas Martinek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
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2
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Christensen EG, Steele RP. Structural, Thermodynamic, and Spectroscopic Evolution in the Hydration of Copper(II) Ions, Cu 2+(H 2O) 2-8. J Phys Chem A 2023; 127:6660-6676. [PMID: 37552878 DOI: 10.1021/acs.jpca.3c03719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Gas-phase clusters of the hydrated Cu(II) cation with 2-8 water molecules were investigated using ab initio quantum chemistry. Isomer structures, energies, and vibrational spectra were computed across this size range, yielding a qualitative picture of this ion as an intact Cu2+ hydrate that also partially oxidizes the surrounding water network at equilibrium. At sufficient cluster sizes, these ion hydrates also become thermodynamically preferred over competitive Cu(II) hydroxide hydrates. Competitive coordination environments were found to exist at some cluster sizes, due to both hydrogen-bonding and d-orbital chemical effects, and the dominant coordination number was found in some cases to be temperature-dependent. Clear spectral signatures of the ion's coordination environment were computed to exist at each cluster size, which should make experimental verification of these computational predictions straightforward. Through comparison to recent studies of hydrated CuOH+, the effective charge on the metal center was shown to converge to approximately +1.5 in both cases, despite qualitatively different behavior of their radical spin densities. Therefore, nominally Cu(II) ions exhibit considerable electronic, chemical, and structural flexibility. The electronic origins of this flexibility─including key roles played by the water network itself─are investigated in this work and should provide a conceptual foundation for future studies of copper-based, water-oxidation catalysts.
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Affiliation(s)
- Elizabeth G Christensen
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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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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A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. Int J Mol Sci 2023; 24:ijms24065440. [PMID: 36982515 PMCID: PMC10055966 DOI: 10.3390/ijms24065440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S2) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S2 and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites.
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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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Frank P, Benfatto M. Symmetry Breaking in Solution-Phase [Cu(tsc) 2(H 2O) 2] 2+: Emergent Asymmetry in Cu-S Distances and in Covalence. J Phys Chem B 2021; 125:10779-10795. [PMID: 34546762 DOI: 10.1021/acs.jpcb.1c05022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of aqueous Cu(II)-bis-thiosemicarbazide, [Cu(tsc)2]2+, is reported following EXAFS and MXAN analyses of the copper K-edge X-ray absorption (XAS) spectrum. The rising K-edge feature at 8987.1 eV is higher energy than those of crystalline models, implying unique electronic and structural solution states. EXAFS analysis (k = 2-13 Å-1; 2 × Cu-N = 2.02 ± 0.01 Å; 2 × Cu-S = 2.27 ± 0.01 Å; Cu-Oax = 2.41 ± 0.04 Å) could not resolve 5- versus 6-coordinate models. However, MXAN fits converged to an asymmetric broken symmetry 6-coordinate model with cis-disposed TSC ligands (Cu-Oax = 2.07 and 2.54 Å; Cu-N = 1.94 Å, 1.98 Å; Cu-S = 2.20 Å, 2.41 Å). Transition dipole integral evaluation of the sulfur K-edge XAS 1s → 3p valence transition feature at 2470.7 eV yielded a Cu-S covalence of 0.66 e-, indicating Cu1.34+. The high Cu-S covalence and short Cu-S bond in aqueous [Cu(tsc)2(H2O)2]2+ again contradict the need for a protein rack to explain the unique structure of the blue copper active site. MXAN models of dissolved Cu(II) complex ions have invariably featured broken centrosymmetry. The potential energy ground state for dissolved Cu(II) evidently includes the extended solvation field, providing a target for improved physical theory. A revised solvation model for aqueous Cu(II), |[Cu(H2O)5]·14H2O|2+, is presented.
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Affiliation(s)
- Patrick Frank
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, United States.,Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
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7
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Mergelsberg ST, Prange M, Song D, Bylaska EJ, Saslow SA, Catalano JG, Ilton ES. Resolving Configurational Disorder for Impurities in a Low-Entropy Phase. J Phys Chem Lett 2021; 12:5689-5694. [PMID: 34115494 DOI: 10.1021/acs.jpclett.1c01218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hematite (α-Fe2O3) exerts a strong control over the transport of minor but critical metals in the environment and is used in multiple industrial applications; the photocatalysis community has explored the properties of hematite nanoparticles over a wide range of transition metal dopants. Nonetheless, simplistic assumptions are used to rationalize the local coordination environment of impurities in hematite. Here, we use ab initio molecular dynamics (AIMD)-guided structural analysis to model the extended X-ray absorption fine structure (EXAFS) of Cu2+- and Zn2+-doped hematite nanoparticles. Specific defect-impurity associations were identified, and the local coordination environments of Cu and Zn both displayed considerable configurational disorder that, in aggregate, approached Jahn-Teller-like distortion for Cu but, in contrast, maintained hematite-like symmetry for Zn. This study highlights the role of defects in accommodating impurities in a nominally low-entropy phase and the limits to traditional shell-by-shell fitting of EXAFS for dopants/impurities in unprecedented bonding environments.
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Affiliation(s)
| | - Micah Prange
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Duo Song
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric J Bylaska
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah A Saslow
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jeffrey G Catalano
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri 63130, United States
| | - Eugene S Ilton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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8
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Zhang N, Tang J, Ma Y, Liang M, Zeng D, Hefter G. A spectroscopic study of solvent effects on the formation of Cu(ii)-chloride complexes in aqueous solution. Phys Chem Chem Phys 2021; 23:6807-6814. [PMID: 33724283 DOI: 10.1039/d0cp05243d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A combination of electronic (UV-vis) and X-ray absorption (EXAFS, XANES) spectroscopies has been used to investigate the formation of copper(ii)/chloride complexes in concentrated aqueous solutions. It is established that lowering the water activity by the addition of Mg(ClO4)2 at a constant Cl-/Cu(ii) ratio results in the replacement of water molecules by Cl- ions in the primary coordination shell of Cu(ii). This behavior closely parallels the effect of increasing the Cl-/Cu(ii) ratio and demonstrates that full understanding of the stoichiometry and structures of the complexes formed in concentrated metal-ion chloride solutions requires explicit consideration of the role of the solvent.
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Affiliation(s)
- Ning Zhang
- College of Science, Central South University of Forestry and Technology, Changsha 410004, Hunan, P. R. China.
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9
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Ohyama J, Hirayama A, Kondou N, Yoshida H, Machida M, Nishimura S, Hirai K, Miyazato I, Takahashi K. Data science assisted investigation of catalytically active copper hydrate in zeolites for direct oxidation of methane to methanol using H 2O 2. Sci Rep 2021; 11:2067. [PMID: 33483547 PMCID: PMC7822835 DOI: 10.1038/s41598-021-81403-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/06/2021] [Indexed: 11/25/2022] Open
Abstract
Dozens of Cu zeolites with MOR, FAU, BEA, FER, CHA and MFI frameworks are tested for direct oxidation of CH4 to CH3OH using H2O2 as oxidant. To investigate the active structures of the Cu zeolites, 15 structural variables, which describe the features of the zeolite framework and reflect the composition, the surface area and the local structure of the Cu zeolite active site, are collected from the Database of Zeolite Structures of the International Zeolite Association (IZA). Also analytical studies based on inductively coupled plasma-optical emission spectrometry (ICP-OES), X-ray fluorescence (XRF), N2 adsorption specific surface area measurement and X-ray absorption fine structure (XAFS) spectral measurement are performed. The relationships between catalytic activity and the structural variables are subsequently revealed by data science techniques, specifically, classification using unsupervised and supervised machine learning and data visualization using pairwise correlation. Based on the unveiled relationships and a detailed analysis of the XAFS spectra, the local structures of the Cu zeolites with high activity are proposed.
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Affiliation(s)
- Junya Ohyama
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan.
| | - Airi Hirayama
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Nahoko Kondou
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Hiroshi Yoshida
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Masato Machida
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Shun Nishimura
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Kenji Hirai
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-Ward, Sapporo, 001-0020, Japan
| | - Itsuki Miyazato
- Department of Chemistry, Hokkaido University, N-15 W-8, Sapporo, 060-0815, Japan
| | - Keisuke Takahashi
- Department of Chemistry, Hokkaido University, N-15 W-8, Sapporo, 060-0815, Japan
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10
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Shin U, Kim J, Lee J, Park D, Lee C, Jung HC, Park J, Lee K, Lee MW, Kim SW, Seo J. Development of 64Cu-loaded Perfluoropentane Nanodroplet: A Potential Tumor Theragnostic Nano-carrier and Dual-Modality PET-Ultrasound Imaging Agents. ULTRASOUND IN MEDICINE & BIOLOGY 2020; 46:2775-2784. [PMID: 32653208 DOI: 10.1016/j.ultrasmedbio.2020.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/24/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
The purpose of this study was to develop and preliminarily evaluate phospholipid-shelled nanodroplets (NDs) encapsulating perfluoropentane (PFP) and radioactive 64Cu as a hybrid positron emission tomography (PET)-ultrasound (US) probe. PFP NDs were fabricated by mixing liquid-phase PFP with a phospholipid solution. The 64Cu was encapsulated into the NDs in a size-controlled manner by exploiting the hydrophobicity of 64Cu-diacetyl-bis(N4-methylthiosemicarbazone) (64Cu-ATSM) using a vial mixer and an extruder. The fabricated 64Cu-loaded PFP NDs (64Cu-PFP NDs) were evaluated using in vitro/in vivo PET-computed tomography (PET-CT), US imaging and transmission electron microscopy. In the in vitro PET images, the 64Cu-PFP NDs were observed as a hot spot in the lower section of the test tube. In the acquired US images, the mean region of interest brightness values of 64Cu-PFP NDs were revealed by their strong echo image. In a tumor-bearing mouse animal model, tumor uptake of the 64Cu-PFP NDs was low, that is, approximately 65%, compared with that of only free 64Cu, as determined by PET-delayed imaging analysis. The dual-function concept of the NDs is expected to contribute to the prognosis and effectiveness of therapy by fusing the science and technology of nuclear medicine and US.
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Affiliation(s)
- Unchol Shin
- Department of Biomedical Engineering, College of Health Sciences, Yonsei University, Seoul, Republic of Korea; College of Health Sciences, Institute of Health Science, Korea University, Seoul, Republic of Korea
| | - Jungyoung Kim
- Department of Molecular Imaging Research Center, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Jiwoong Lee
- College of Health Sciences, Institute of Health Science, Korea University, Seoul, Republic of Korea
| | - Donghee Park
- Bioinfra Inc., Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Changmoon Lee
- Department of Biomedical Engineering, College of Engineering, Chonnam National University, Gwangju, Republic of Korea
| | - Hyon Chel Jung
- College of Health Sciences, Institute of Health Science, Korea University, Seoul, Republic of Korea
| | - Jiae Park
- Department of Molecular Imaging Research Center, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Kyochul Lee
- Department of Molecular Imaging Research Center, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Min Woo Lee
- College of Health Sciences, Institute of Health Science, Korea University, Seoul, Republic of Korea
| | - Suhng Wook Kim
- College of Health Sciences, Institute of Health Science, Korea University, Seoul, Republic of Korea
| | - Jongbum Seo
- Department of Biomedical Engineering, College of Health Sciences, Yonsei University, Seoul, Republic of Korea.
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11
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Persson I, Lundberg D, Bajnóczi ÉG, Klementiev K, Just J, Sigfridsson Clauss KGV. EXAFS Study on the Coordination Chemistry of the Solvated Copper(II) Ion in a Series of Oxygen Donor Solvents. Inorg Chem 2020; 59:9538-9550. [PMID: 32614569 PMCID: PMC7467664 DOI: 10.1021/acs.inorgchem.0c00403] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
structures of the solvated copper(II) ion in water and nine organic
oxygen donor solvents with similar electron-pair donor ability, but
with different space-demanding properties at coordination, have been
studied by EXAFS. N,N′-Dimethylpropyleneurea
and N,N,N′,N′-tetramethylurea are sufficiently
space demanding at coordination to make the axial positions not accessible,
resulting in square-planar copper(II) solvate complexes with an intense
green color. The mean Cu–O bond distances in these two solvate
complexes are 1.939(3) and 1.935(3) Å, respectively. The best
fits of the remaining solvates, which are light blue in different
hues, are obtained with a Jahn–Teller distorted-octahedral
model consisting of four strongly bound solvent molecules in the equatorial
positions at 1.96(2) Å and two in the axial positions but with
different Cu–Oax bond distances: ca. 2.15 and 2.32
Å. This is in agreement with observations in solid-state structures
of compounds containing hexaaquacopper(II) complexes crystallizing
in noncentrosymmetric space groups and all reported crystal structures
containing a [Cu(H2O)5(O-ligand)] complex with
Jahn–Teller distortion. Such a structure is in agreement with
previous EPR and EXAFS studies proving the hydrated copper(II) ion
to be a noncentrosymmetric complex in aqueous solution. The refinements
of the EXAFS data of the solids [Cu(H2O)6](ClO4)2, [Cu(H2O)6](BrO3)2, [Cu(H2O)6]SiF6, Cu(NO3)2·2.5H2O, and CuSO4·5H2O gave Cu–O bond distances significantly
different from those reported in the crystallographic studies but
similar to the configuration and bond distances in the hydrated copper(II)
ion in aqueous solution. This may depend on whether the orientation
of the axial positions is random in one or three dimensions, giving
a mean structure of the solid with symmetry higher than that of the
individual complexes. This study presents the very first experimental
data from the new X-ray absorption spectroscopy beamline Balder at
the MAX IV synchrotron radiation facility in Lund, Sweden, as well
as the utilized properties of the beamline. The coordination chemistry of the solvated copper(II) ion
has been studied in 10 solvents, including water. The copper(II) ion
has a noncentrosymmetric Jahn−Teller distorted-octahedral geometry
with the axial Cu−O bond distances differing by ca. 0.2 Å.
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Affiliation(s)
- Ingmar Persson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Daniel Lundberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Éva G Bajnóczi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | | | - Justus Just
- MAX IV Laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
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12
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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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13
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Tada S, Oshima K, Noda Y, Kikuchi R, Sohmiya M, Honma T, Satokawa S. Effects of Cu Precursor Types on the Catalytic Activity of Cu/ZrO2 toward Methanol Synthesis via CO2 Hydrogenation. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03627] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Shohei Tada
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazumasa Oshima
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan
| | - Yoshihiro Noda
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan
| | - Ryuji Kikuchi
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Minoru Sohmiya
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan
| | - Tetsuo Honma
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeo Satokawa
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan
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14
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15
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Sala D, Musiani F, Rosato A. Application of Molecular Dynamics to the Investigation of Metalloproteins Involved in Metal Homeostasis. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Viale Giuseppe Fanin 40, I 40127 Bologna Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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16
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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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17
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Sahu P, Ali SM, Shenoy KT, Mohan S. Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu-Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations. J Phys Chem B 2018; 122:4115-4130. [PMID: 29569915 DOI: 10.1021/acs.jpcb.8b01650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu+:H2O:Cl- and 1:6:0 for Cu2+:H2O:Cl-. The presence of the anionic Cu complex, [Cu+Cl2]-·2H2O, [Cu+Cl2]-·3H2O, [Cu2+Cl3]-·H2O, and [Cu2+Cl3]-·2H2O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.
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Affiliation(s)
- Pooja Sahu
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India.,Department of Chemical Science , Homi Bhabha National Institute , Mumbai , Maharashtra 400094 , India
| | - Sk Musharaf Ali
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India.,Department of Chemical Science , Homi Bhabha National Institute , Mumbai , Maharashtra 400094 , India
| | - K T Shenoy
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India
| | - S Mohan
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India
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18
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Bukharov MS, Shtyrlin VG, Gilyazetdinov EM, Serov NY, Madzhidov TI. Hydration of copper(II) amino acids complexes. J Comput Chem 2017; 39:821-826. [DOI: 10.1002/jcc.25154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Mikhail S. Bukharov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Valery G. Shtyrlin
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Edward M. Gilyazetdinov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Nikita Yu. Serov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Timur I. Madzhidov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
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19
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Migliorati V, Filipponi A, Di Cicco A, De Panfilis S, D’Angelo P. Structure of Water in Zn2+ Aqueous Solutions from Ambient Conditions up to the Gigapascal Pressure Range: A XANES and Molecular Dynamics Study. Inorg Chem 2017; 56:14013-14022. [DOI: 10.1021/acs.inorgchem.7b02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
| | - Adriano Filipponi
- Dipartimento di Scienze
Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy
| | - Andrea Di Cicco
- Sezione di Fisica,
Scuola di Scienze e Tecnologie, Università di Camerino, 62032 Camerino (MC), Italy
| | - Simone De Panfilis
- Centre
for Life Nano Science - IIT@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Rome, Italy
| | - Paola D’Angelo
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
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20
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Das AK, Meuwly M. Hydration Control Through Intramolecular Degrees of Freedom: Molecular Dynamics of [Cu(II)(Imidazole)4]. J Phys Chem B 2017; 121:9024-9031. [DOI: 10.1021/acs.jpcb.7b05949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akshaya K. Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4001 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4001 Basel, Switzerland
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21
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Martini A, Borfecchia E, Lomachenko KA, Pankin IA, Negri C, Berlier G, Beato P, Falsig H, Bordiga S, Lamberti C. Composition-driven Cu-speciation and reducibility in Cu-CHA zeolite catalysts: a multivariate XAS/FTIR approach to complexity. Chem Sci 2017; 8:6836-6851. [PMID: 29147509 PMCID: PMC5644121 DOI: 10.1039/c7sc02266b] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/23/2017] [Indexed: 12/21/2022] Open
Abstract
The small pore Cu-CHA zeolite is attracting increasing attention as a versatile platform to design novel single-site catalysts for deNO x applications and for the direct conversion of methane to methanol. Understanding at the atomic scale how the catalyst composition influences the Cu-species formed during thermal activation is a key step to unveil the relevant composition-activity relationships. Herein, we explore by in situ XAS the impact of Cu-CHA catalyst composition on temperature-dependent Cu-speciation and reducibility. Advanced multivariate analysis of in situ XANES in combination with DFT-assisted simulation of XANES spectra and multi-component EXAFS fits as well as in situ FTIR spectroscopy of adsorbed N2 allow us to obtain unprecedented quantitative structural information on the complex dynamics during the speciation of Cu-sites inside the framework of the CHA zeolite.
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Affiliation(s)
- A Martini
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy .
| | - E Borfecchia
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy . .,Haldor Topsøe A/S , Haldor Topsøes Allé 1 , Kgs. Lyngby , 2800 Denmark
| | - K A Lomachenko
- European Synchrotron Radiation Facility , 71 avenue des Martyrs, CS 40220 , Grenoble Cedex 9 , 38043 France.,IRC "Smart Materials" , Southern Federal University , Zorge str. 5 , Rostov-on-Don , 344090 Russia
| | - I A Pankin
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy . .,IRC "Smart Materials" , Southern Federal University , Zorge str. 5 , Rostov-on-Don , 344090 Russia
| | - C Negri
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy .
| | - G Berlier
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy .
| | - P Beato
- Haldor Topsøe A/S , Haldor Topsøes Allé 1 , Kgs. Lyngby , 2800 Denmark
| | - H Falsig
- Haldor Topsøe A/S , Haldor Topsøes Allé 1 , Kgs. Lyngby , 2800 Denmark
| | - S Bordiga
- Department of Chemistry , NIS Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy .
| | - C Lamberti
- IRC "Smart Materials" , Southern Federal University , Zorge str. 5 , Rostov-on-Don , 344090 Russia.,Department of Chemistry , CrisDi Centre and INSTM Reference Center , University of Turin , Via P. Giuria 7 , Turin , 10125 Italy
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22
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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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23
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Zhang N, Wang W, Brugger J, Zhang G, Zeng D. Species fine structure of transition metal Cu(II) in aqueous chloride-bearing solutions: Insights from X-ray absorption spectroscopy and ab initio XANES calculations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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25
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Galván-García EA, Agacino-Valdés E, Franco-Pérez M, Gómez-Balderas R. [Cu(H2O) n ]2+ (n = 1–6) complexes in solution phase: a DFT hierarchical study. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2056-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Vilhena FS, Felcman J, Szpoganicz B, Miranda FS. Potentiometric and DFT studies of Cu(II) complexes with glycylglycine and methionine of interest for the brain chemistry. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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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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28
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Affiliation(s)
- Inbal Tuvi-Arad
- Department of Natural Sciences; The Open University of Israel; 1 University Road Raanana 4353701 (Israel)
| | - András Stirling
- Institute of Organic Chemistry; Research Center for Natural Sciences; P.O.B. 286 Budapest 1519 (Hungary)
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29
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Jin H, Goyal P, Das AK, Gaus M, Meuwly M, Cui Q. Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations. J Phys Chem B 2015; 120:1894-910. [PMID: 26624804 DOI: 10.1021/acs.jpcb.5b09656] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable.
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Affiliation(s)
- Haiyun Jin
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Puja Goyal
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Akshaya Kumar Das
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Michael Gaus
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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30
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Bukharov MS, Shtyrlin VG, Mamin GV, Stapf S, Mattea C, Mukhtarov AS, Serov NY, Gilyazetdinov EM. Structure and Dynamics of Solvation Shells of Copper(II) Complexes with N,O-Containing Ligands. Inorg Chem 2015; 54:9777-84. [DOI: 10.1021/acs.inorgchem.5b01467] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikhail S. Bukharov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Valery G. Shtyrlin
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Georgy V. Mamin
- Institute of Physics, Kazan Federal University, Kremlevskaya St. 18, 420008 Kazan, Russian Federation
| | - Siegfried Stapf
- Fachgebiet Technische Physik II/Polymerphysik,
Institute of Physics, Technische Universität Ilmenau, P.O. Box 100 565, 98684 Ilmenau, Germany
| | - Carlos Mattea
- Fachgebiet Technische Physik II/Polymerphysik,
Institute of Physics, Technische Universität Ilmenau, P.O. Box 100 565, 98684 Ilmenau, Germany
| | - Anvar Sh. Mukhtarov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Nikita Yu. Serov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Edward M. Gilyazetdinov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
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31
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Calculations of hyperfine coupling constant of copper(II) in aqueous environment. Finite temperature molecular dynamics and relativistic effects. J Mol Model 2015; 21:237. [DOI: 10.1007/s00894-015-2752-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
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32
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Meyer A, Schnakenburg G, Glaum R, Schiemann O. (Bis(terpyridine))copper(II) Tetraphenylborate: A Complex Example for the Jahn–Teller Effect. Inorg Chem 2015; 54:8456-64. [DOI: 10.1021/acs.inorgchem.5b01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas Meyer
- Institute
of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr.
12, Bonn, Germany
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Str.
1, Bonn, Germany
| | - Robert Glaum
- Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Str.
1, Bonn, Germany
| | - Olav Schiemann
- Institute
of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr.
12, Bonn, Germany
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33
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Glassy carbon electrodes modified with supramolecular assemblies generated by π-stacking of Cobalt (II) octaethylporphyrins. A 4 electrons-dioxygen reduction reaction occurring at positive potentials. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.05.124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Migliorati V, D’Angelo P. Unraveling the perturbation induced by Zn2+ and Hg2+ ions on the hydrogen bond patterns of liquid methanol. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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Frank P, Benfatto M, Qayyam M, Hedman B, Hodgson KO. A high-resolution XAS study of aqueous Cu(II) in liquid and frozen solutions: pyramidal, polymorphic, and non-centrosymmetric. J Chem Phys 2015; 142:084310. [PMID: 25725734 PMCID: PMC4349298 DOI: 10.1063/1.4908266] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/04/2015] [Indexed: 11/15/2022] Open
Abstract
High-resolution EXAFS (k = 18 Å(-1)) and MXAN XAS analyses show that axially elongated square pyramidal [Cu(H2O)5](2+) dominates the structure of Cu(II) in aqueous solution, rather than 6-coordinate JT-octahedral [Cu(H2O)6](2+). Freezing produced a shoulder at 8989.6 eV on the rising XAS edge and an altered EXAFS spectrum, while 1s → 3d transitions remained invariant in energy position and intensity. Core square pyramidal [Cu(H2O)5](2+) also dominates frozen solution. Solvation shells were found at ∼3.6 Å (EXAFS) or ∼3.8 Å (MXAN) in both liquid and frozen phases. However, MXAN analysis revealed that about half the time in liquid solution, [Cu(H2O)5](2+) associates with an axially non-bonding 2.9 Å water molecule. This distant water apparently organizes the solvation shell. When the 2.9 Å water molecule is absent, the second shell is undetectable to MXAN. The two structural arrangements may represent energetic minima of fluxional dissolved aqueous [Cu(H2O)5](2+). The 2.9 Å trans-axial water resolves an apparent conflict of the [Cu(H2O)5](2+) core model with a dissociational exchange mechanism. In frozen solution, [Cu(H2O)5](2+) is associated with either a 3.0 Å axial non-bonded water molecule or an axial ClO4(-) at 3.2 Å. Both structures are again of approximately equal presence. When the axial ClO4(-) is present, Cu(II) is ∼0.5 Å above the mean O4 plane. This study establishes [Cu(H2O)5](2+) as the dominant core structure for Cu(II) in water solution, and is the first to both empirically resolve multiple extended solution structures for fluxional [Cu(H2O)5](2+) and to provide direct evidence for second shell dynamics.
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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 Qayyam
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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36
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Qiu SR, Wood BC, Ehrmann PR, Demos SG, Miller PE, Schaffers KI, Suratwala TI, Brow RK. Origins of optical absorption characteristics of Cu2+complexes in aqueous solutions. Phys Chem Chem Phys 2015; 17:18913-23. [DOI: 10.1039/c5cp01688f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectrometry is combined with first-principles simulations of solvated Cu2+complexes to elucidate the roles of ligand coordination, d-orbital fine structure, complex geometry, and solvation environment in determining optical absorption profiles.
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Affiliation(s)
- S. Roger Qiu
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | | | | | | | | | | | | | - Richard K. Brow
- Materials Science & Engineering
- Missouri University of Science and Technology
- Rolla
- USA
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37
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Borfecchia E, Lomachenko KA, Giordanino F, Falsig H, Beato P, Soldatov AV, Bordiga S, Lamberti C. Revisiting the nature of Cu sites in the activated Cu-SSZ-13 catalyst for SCR reaction. Chem Sci 2015; 6:548-563. [PMID: 28936309 PMCID: PMC5588737 DOI: 10.1039/c4sc02907k] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/13/2014] [Indexed: 12/23/2022] Open
Abstract
Cu-SSZ-13 is a highly active NH3-SCR catalyst for the abatement of harmful nitrogen oxides (NO x , x = 1, 2) from the exhausts of lean-burn engines. The study of Cu-speciation occurring upon thermal dehydration is a key step for the understanding of the enhanced catalytic properties of this material and for identifying the SCR active sites and their redox capability. Herein, we combined FTIR, X-ray absorption (XAS) and emission (XES) spectroscopies with DFT computational analysis to elucidate the nature and location of the most abundant Cu sites in the activated catalyst. Different Cu species have been found to be dominant as a function of the dehydration temperature and conditions. Data analysis revealed that the dehydration process of Cu cations is essentially completed at 250 °C, with the formation of dehydrated [CuOH]+ species hosted in close proximity to 1-Al sites in both d6r and 8r units of the SSZ-13 matrix. These species persist at higher temperatures only if a certain amount of O2 is present in the gas feed, while under inert conditions they undergo virtually total "self-reduction" as a consequence of an OH extra-ligand loss, resulting in bi-coordinated bare Cu+ cations. Synchrotron characterization supported by computational analysis allowed an unprecedented quantitative refinement of the local environment and structural parameters of these Cu(ii) and Cu(i) species.
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Affiliation(s)
- E Borfecchia
- Department of Chemistry and INSTM Reference Center , University of Turin , via P. Giuria 7 , 10125 Turin , Italy .
- NIS Centre of Excellence , University of Turin , Italy
| | - K A Lomachenko
- Department of Chemistry and INSTM Reference Center , University of Turin , via P. Giuria 7 , 10125 Turin , Italy .
- Southern Federal University , Zorge street 5 , 344090 Rostov-on-Don , Russia
| | - F Giordanino
- Department of Chemistry and INSTM Reference Center , University of Turin , via P. Giuria 7 , 10125 Turin , Italy .
- NIS Centre of Excellence , University of Turin , Italy
| | - H Falsig
- Haldor Topsøe A/S , Nymøllevej 55, 2800 Kgs. , Lyngby , Denmark
| | - P Beato
- Haldor Topsøe A/S , Nymøllevej 55, 2800 Kgs. , Lyngby , Denmark
| | - A V Soldatov
- Southern Federal University , Zorge street 5 , 344090 Rostov-on-Don , Russia
| | - S Bordiga
- Department of Chemistry and INSTM Reference Center , University of Turin , via P. Giuria 7 , 10125 Turin , Italy .
- NIS Centre of Excellence , University of Turin , Italy
| | - C Lamberti
- Department of Chemistry and INSTM Reference Center , University of Turin , via P. Giuria 7 , 10125 Turin , Italy .
- CrisDI Center of Crystallography , University of Turin , Italy
- Southern Federal University , Zorge street 5 , 344090 Rostov-on-Don , Russia
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38
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Kato Y, Fujiwara T, Komeiji Y, Nakano T, Mori H, Okiyama Y, Mochizuki Y. Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion. CHEM-BIO INFORMATICS JOURNAL 2014. [DOI: 10.1273/cbij.14.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yuji Kato
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
| | - Takayuki Fujiwara
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
| | - Yuto Komeiji
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tatsuya Nakano
- Division of Medicinal Safety Science, National Institute of Health Sciences
| | - Hirotoshi Mori
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University
| | - Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
- Institute of Industrial Science, The University of Tokyo
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39
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Zitolo A, Migliorati V, Aquilanti G, D’Angelo P. On the possibility of using XANES to investigate bromide-based ionic liquids. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.10.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Bukharov MS, Shtyrlin VG, Mukhtarov AS, Mamin GV, Stapf S, Mattea C, Krutikov AA, Il'in AN, Serov NY. Study of structural and dynamic characteristics of copper(ii) amino acid complexes in solutions by combined EPR and NMR relaxation methods. Phys Chem Chem Phys 2014; 16:9411-21. [DOI: 10.1039/c4cp00255e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Xiang JY, Ponder JW. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field. J Chem Theory Comput 2014; 10:298-311. [PMID: 25045338 PMCID: PMC4102146 DOI: 10.1021/ct400778h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.
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Affiliation(s)
- Jin Yu Xiang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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42
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Bowron DT, Moreno SD. The structure of water in solutions containing di- and trivalent cations by empirical potential structure refinement. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:454213. [PMID: 24141281 DOI: 10.1088/0953-8984/25/45/454213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Empirical potential structure refinement (EPSR) has been used to build experimentally consistent models of a range of electrolyte solutions containing di- and trivalent cations: Cu(ClO4)2 at concentrations of 0.5 and 2.0 m, and Cr(NO3)3, YCl3 and LaCl3 at a concentration of 1.0 m. The resulting models are used to investigate the perturbation of these electrolytes on the pair distribution and triplet angle correlations between solvent water molecules, compared with those found in the pure solvent. The results elucidate the differences that derive from the reflected range of highly structured local cation environments and provide a complementary viewpoint on the hydration shell geometries.
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Affiliation(s)
- Daniel T Bowron
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell - Oxford, Didcot, OX11 0QX, UK
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43
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Hu J, Chen Q, Hu H, Jiang Z, Wang D, Wang S, Li Y. Microscopic Insights into Extraction Mechanism of Copper(II) in Ammoniacal Solutions Studied by X-ray Absorption Spectroscopy and Density Functional Theory Calculation. J Phys Chem A 2013; 117:12280-7. [DOI: 10.1021/jp404768e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiugang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Key Laboratory of Resources Chemistry of Nonferrous Metals,
Ministry of Education, Central South University, Changsha 410083, China
| | - Qiyuan Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Key Laboratory of Resources Chemistry of Nonferrous Metals,
Ministry of Education, Central South University, Changsha 410083, China
| | - Huiping Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Key Laboratory of Resources Chemistry of Nonferrous Metals,
Ministry of Education, Central South University, Changsha 410083, China
| | - Zheng Jiang
- Shanghai Synchrotron Radiation Facility,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Duo Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Shubin Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yaomin Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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44
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Beloglazkina EK, Majouga AG, Mironov AV, Yudina AV, Moiseeva AA, Lebedeva MA, Khlobystov AN, Zyk NV. Synthesis, X-ray crystallography and electrochemistry of three novel copper complexes with imidazole-containing hydantoin and thiohydantoins. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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45
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Ganesan A, Dreyer J, Wang F, Akola J, Larrucea J. Density functional study of Cu2+-phenylalanine complex under micro-solvation environment. J Mol Graph Model 2013; 45:180-91. [DOI: 10.1016/j.jmgm.2013.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/15/2013] [Accepted: 08/17/2013] [Indexed: 10/26/2022]
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46
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Moin ST, Hofer TS, Weiss AKH, Rode BM. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region. J Chem Phys 2013; 139:014503. [DOI: 10.1063/1.4811114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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47
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Migliorati V, D'Angelo P. A quantum mechanics, molecular dynamics and EXAFS investigation into the Hg2+ ion solvation properties in methanol solution. RSC Adv 2013. [DOI: 10.1039/c3ra43412e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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Bowron DT, Amboage M, Boada R, Freeman A, Hayama S, Díaz-Moreno S. The hydration structure of Cu2+: more tetrahedral than octahedral? RSC Adv 2013. [DOI: 10.1039/c3ra42400f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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49
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Gómez-Salces S, Aguado F, Valiente R, Rodríguez F. Unraveling the Coordination Geometry of Copper(II) Ions in Aqueous Solution through Absorption Intensity. Angew Chem Int Ed Engl 2012; 51:9335-8. [DOI: 10.1002/anie.201202033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 07/13/2012] [Indexed: 11/08/2022]
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50
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Gómez-Salces S, Aguado F, Valiente R, Rodríguez F. Unraveling the Coordination Geometry of Copper(II) Ions in Aqueous Solution through Absorption Intensity. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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