1
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Da-yang TE, Lai CH. Potential energy surfaces of the Cu2+(NH3)n=1−10 clusters in solvent phase: A DFT study. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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2
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Structures, Binding and Clustering Energies of Cu2+(MeOH)n=1-8 Clusters and Temperature Effects : A DFT Study. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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3
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Cu(Proline) 2 Complex: A Model of Bio-Copper Structural Ambivalence. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27185846. [PMID: 36144582 PMCID: PMC9502899 DOI: 10.3390/molecules27185846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/17/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
Complexes of Cu2+(d9) with proline may be considered a simple model to address the structural flexibility and electronic properties of copper metalloproteins. To discuss optical electronic spectra and infrared spectral responses, we use quantum chemistry applied to model systems prepared under different geometries and degree of hydration. A comparison of experimental data with calculations indicates that first explicit neighbor water clustering next to the Cu2+(d9) complex is critical for a correct description of the electronic properties of this system. We deduce that the moderately hydrated trans conformer is the main structural form of the complex in water. Further, we suggest that the antisymmetric stretching mode of the carbonyl moieties of the conformer is dominant in the spectrally broadened infrared resonance at 1605 cm−1, where inhomogeneity of the transition at the blue side can be ascribed to a continuum of less optimal interactions with the solvent. Extracted structural properties and hydration features provide information on the structural flexibility/plasticity specific to Cu2+(d9) systems in correlation with the electronic behavior upon photoexcitation. We discuss the role and the nature of the axial ligand in bio-copper structural ambivalence and reactivity.
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4
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Da-yang TE, Fifen JJ, Conradie J, Conradie MM. Structures, temperature effect, binding and clustering energies of Cu2+(MeOH)n=1-8 clusters and extrapolations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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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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6
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Castellini E, Bernini F, Sebastianelli L, Bighi B, Ignacio Sainz‐Díaz C, Mucci A, Malferrari D, Ranieri A, Gorni G, Marini C, Franca Brigatti M, Borsari M. The Copper Chemical Garden as a Low Cost and Efficient Material for Breaking Down Air Pollution by Gaseous Ammonia. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elena Castellini
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Fabrizio Bernini
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Lorenzo Sebastianelli
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Beatrice Bighi
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Claro Ignacio Sainz‐Díaz
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR) Av. de las Palmeras, 4 18100 Armilla, Granada Spain
| | - Adele Mucci
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Daniele Malferrari
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Antonio Ranieri
- Department of Life Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Giulio Gorni
- ALBA Synchrotron Light Source Crta. BP 1413, Km. 3.3 08290, Cerdanyola Del Vallès Barcelona Spain
| | - Carlo Marini
- ALBA Synchrotron Light Source Crta. BP 1413, Km. 3.3 08290, Cerdanyola Del Vallès Barcelona Spain
| | - Maria Franca Brigatti
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
| | - Marco Borsari
- Department of Chemical and Geological Sciences University of Modena and Reggio Emilia Via Campi 103 I-41125 Modena Italy
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7
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Miyake R, Suganuma E, Kimura S, Mori H, Okabayashi J, Kusamoto T. Cyclic Heterometallic Interactions formed from a Flexible Tripeptide Complex Showing Effective Antiferromagnetic Spin Coupling. Angew Chem Int Ed Engl 2021; 60:5179-5183. [PMID: 33207016 DOI: 10.1002/anie.202013373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 11/09/2022]
Abstract
Developing tunable motifs for heterometallic interactions should be beneficial for fabricating functional materials based on cooperative electronic communications between metal centers. Reported here is the efficient formation of cyclic heterometallic interactions from a complex containing an artificial tripeptide with metal binding sites on its main chain and side chains. X-ray structural analysis and X-ray absorption spectroscopy revealed that the cyclic metal-metal arrangements arise from the amide groups connecting four square-planar CuII centers and four octahedral NiII centers in a cyclic manner. UV/Vis spectral studies suggested that this efficient formation was achieved by the selective formation of the square-planar CuII centers and a crystallization process. Magnetic measurements using SQUID clarified that the cyclic complex represented the S=2 spin state at low temperatures due to effective antiferromagnetic interactions between the NiII and CuII centers.
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Affiliation(s)
- Ryosuke Miyake
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.,JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Eri Suganuma
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Shun Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Hirotoshi Mori
- Department of Applied Chemistry, Faculty of Science & Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-Ku, Tokyo, 112-8551, Japan
| | - Jun Okabayashi
- Research Center for Spectrochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tetsuro Kusamoto
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
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8
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Miyake R, Suganuma E, Kimura S, Mori H, Okabayashi J, Kusamoto T. Cyclic Heterometallic Interactions formed from a Flexible Tripeptide Complex Showing Effective Antiferromagnetic Spin Coupling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ryosuke Miyake
- Department of Chemistry and Biochemistry Graduate School of Humanities and Sciences Ochanomizu University 2-1-1, Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- JST-PRESTO 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Eri Suganuma
- Department of Chemistry and Biochemistry Graduate School of Humanities and Sciences Ochanomizu University 2-1-1, Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Shun Kimura
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Department of Life and Coordination-Complex Molecular Science Institute for Molecular Science 5-1 Higashiyama Myodaiji, Okazaki 444-8787 Japan
| | - Hirotoshi Mori
- Department of Applied Chemistry, Faculty of Science & Engineering Chuo University 1-13-27 Kasuga, Bunkyo-Ku Tokyo 112-8551 Japan
| | - Jun Okabayashi
- Research Center for Spectrochemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuro Kusamoto
- Department of Life and Coordination-Complex Molecular Science Institute for Molecular Science 5-1 Higashiyama Myodaiji, Okazaki 444-8787 Japan
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9
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Da-yang TE, Fifen JJ, Malloum A, Lahmar S, Nsangou M, Conradie J. Structures of the solvated copper(ii) ion in ammonia at various temperatures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05169d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu2+(NH3)n, n = 1–10.
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Affiliation(s)
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Souad Lahmar
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Mama Nsangou
- University of Maroua
- Maroua
- Cameroon
- Department of Physics
- Faculty of Science
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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10
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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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11
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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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12
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Mizrahi A, Maimon E, Cohen H, Kornweitz H, Zilbermann I, Meyerstein D. Mechanistic Studies on the Role of [Cu II (CO 3 ) n ] 2-2n as a Water Oxidation Catalyst: Carbonate as a Non-Innocent Ligand. Chemistry 2017; 24:1088-1096. [PMID: 28921692 DOI: 10.1002/chem.201703742] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 11/05/2022]
Abstract
Recently it was reported that copper bicarbonate/carbonate complexes are good electro-catalysts for water oxidation. However, the results did not enable a decision whether the active oxidant is a CuIII or a CuIV complex. Kinetic analysis of pulse radiolysis measurements coupled with DFT calculations point out that CuIII (CO3 )n3-2n complexes are the active intermediates in the electrolysis of CuII (CO3 )n2-2n solution. The results enable the evaluation of E°[(CuIII/II (CO3 )n )aq ]≈1.42 V versus NHE at pH 8.4. This redox potential is in accord with the electrochemical report. As opposed to literature suggestions for water oxidation, the present results rule out single-electron transfer from CuIII (CO3 )n3-2n to yield hydroxyl radicals. Significant charge transfer from the coordinated carbonate to CuIII results in the formation of C2 O62- by means of a second-order reaction of CuIII (CO3 )n3-2n . The results point out that carbonate stabilizes transition-metal cations at high oxidation states, not only as a good sigma donor, but also as a non-innocent ligand.
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Affiliation(s)
- Amir Mizrahi
- Chemistry Department, Nuclear Research Centre Negev Beer-Sheva, Israel
| | - Eric Maimon
- Chemistry Department, Nuclear Research Centre Negev Beer-Sheva, Israel.,Chemistry Department, Ben-Gurion University of the Negev Beer-Sheva, 84105, Israel
| | - Haim Cohen
- Chemical Sciences Department and the Schlesinger Family Center for, Compact Accelerators Radiation Sources and Applications, Ariel University, Ariel, Israel
| | - Haya Kornweitz
- Chemical Sciences Department, Ariel University, Ariel, Israel
| | - Israel Zilbermann
- Chemistry Department, Nuclear Research Centre Negev Beer-Sheva, Israel.,Chemistry Department, Ben-Gurion University of the Negev Beer-Sheva, 84105, Israel
| | - Dan Meyerstein
- Chemical Sciences Department and the Schlesinger Family Center for, Compact Accelerators Radiation Sources and Applications, Ariel University, Ariel, Israel.,Chemistry Department, Ben-Gurion University of the Negev Beer-Sheva, 84105, Israel
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13
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Gaisin Z, Gellerman G, Meyerstein D. Penta-glycine copper(II) complexes in slightly alkaline solutions. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.05.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Gorla L, Martí-Centelles V, Freimuth L, Altava B, Burguete MI, Luis SV. Cu(2+), Zn(2+), and Ni(2+) Complexes of C2-Symmetric Pseudopeptides with an Aromatic Central Spacer. Inorg Chem 2016; 55:7617-29. [PMID: 27438410 DOI: 10.1021/acs.inorgchem.6b01066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Two new tetradentate C2-symmetric pseudopeptidic ligands derived from Val and Phe containing two amino and two amido groups and a central o-substituted aromatic spacer have been prepared. Their complexes with Cu(2+), Zn(2+), and Ni(2+) have been studied by potentiometry, UV-vis spectrophotometry, FT-IR, and ESI-MS. The presence of the aromatic spacer provides Cu(2+) complexes with stability constants several orders of magnitude higher than those observed for related ligands containing aliphatic central spacers. Besides, the formation of [MH-2L] complex species is favored. Crystal structures for the corresponding Cu(2+) and Ni(2+) have been obtained, revealing the metal atom in an essentially square-planar geometry, although, in several instances, the oxygen atom of an amide carbonyl of a second complex species can act as a fifth coordination site. In the case of Zn(2+), the only crystal structure obtained displays a square-pyramidal arrangement of the metal center. Finally, preliminary experiments show the catalytic activity of some of these complexes, in particular, Zn(2+) complexes, for epoxide ring-opening with using aniline as the nucleophile in a ligand accelerated process.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Vicente Martí-Centelles
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Lena Freimuth
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Belén Altava
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - M Isabel Burguete
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Santiago V Luis
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
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15
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Antalek M, Pace E, Hedman B, Hodgson KO, Chillemi G, Benfatto M, Sarangi R, Frank P. Solvation structure of the halides from x-ray absorption spectroscopy. J Chem Phys 2016; 145:044318. [PMID: 27475372 PMCID: PMC4967075 DOI: 10.1063/1.4959589] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/11/2016] [Indexed: 11/14/2022] Open
Abstract
Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, and a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (-0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.
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Affiliation(s)
- Matthew Antalek
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Elisabetta Pace
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - 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
| | - Giovanni Chillemi
- CINECA, SCAI-SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Patrick Frank
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
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16
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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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17
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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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18
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D’Angelo P, Migliorati V. Solvation Structure of Zn2+ and Cu2+ Ions in Acetonitrile: A Combined EXAFS and XANES Study. J Phys Chem B 2015; 119:4061-7. [DOI: 10.1021/acs.jpcb.5b01634] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paola D’Angelo
- Dipartimento
di Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
| | - Valentina Migliorati
- Dipartimento
di Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
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19
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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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20
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Picco AS, Knoll W, Ceolín M, Azzaroni O. Mesophase Transformation in Amphiphilic Hyperbranched Polymers Induced by Transition Metal Ion Complexation. Creating Well-Defined Metallo-Supramolecular Assemblies from "Ill-Defined" Building Blocks. ACS Macro Lett 2015; 4:94-100. [PMID: 35596380 DOI: 10.1021/mz500688r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-organized metallo-supramolecular heterostructures have potential applications that include molecular electronics, photovoltaics, and magnetic devices, among other examples. The main challenge that scientists typically face when designing advanced supramolecular materials is to achieve structurally defined assemblies by resolving conflicting demands on the topological and/or chemical features of the constituting building blocks. Accordingly, the formation of well-defined metallo-supramolecular arrays using ill-defined, highly polydisperse, self-assemblable starting compounds marks a profound departure from traditional supramolecular paradigms. The present work describes the first observation of spontaneous mesophase transformation of well-defined metallo-supramolecular assemblies in solution as a result of the complexation of transition metal ions into the ionophilic domains of highly branched unimolecular micelles constituted of N-acylated hyperbranched polyethylenimine. Experimental results based on a combination of different synchrotron-based techniques provide unprecedented experimental evidence revealing that ion-induced self-assembly of amphiphilic hyperbranched polymers can be used to achieve highly ordered metallo-supramolecular structures not only in solution but also on solid surfaces. We believe that this emerging conceptual framework can open extremely interesting new synthetic and technological opportunities in the area of self-assembly of well-defined metallo-supramolecular architectures obtained from building blocks with poor structural regularity but easily provided in large quantities by simple and inexpensive preparative chemistries.
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Affiliation(s)
- Agustín S. Picco
- Instituto de Investigaciones
Fisicoquímicas
Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata, CONICET, CC 16 − Suc. 4, 1900 La
Plata, Argentina
| | - Wolfgang Knoll
- Austrian Institute of Technology (AIT), Donau-City-Strasse
1, 1220 Vienna, Austria
| | - Marcelo Ceolín
- Instituto de Investigaciones
Fisicoquímicas
Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata, CONICET, CC 16 − Suc. 4, 1900 La
Plata, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones
Fisicoquímicas
Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata, CONICET, CC 16 − Suc. 4, 1900 La
Plata, Argentina
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21
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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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22
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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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23
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Penfold TJ, Karlsson S, Capano G, Lima FA, Rittmann J, Reinhard M, Rittmann-Frank MH, Braem O, Baranoff E, Abela R, Tavernelli I, Rothlisberger U, Milne CJ, Chergui M. Solvent-induced luminescence quenching: static and time-resolved X-ray absorption spectroscopy of a copper(I) phenanthroline complex. J Phys Chem A 2013; 117:4591-601. [PMID: 23617226 DOI: 10.1021/jp403751m] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) ([Cu(dmp)2](+); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photoluminescence spectra in dichloromethane and acetonitrile are also presented and show a shift to longer wavelengths for the latter, which points to a stronger stabilization of the excited complex. The fine structure features of the static and transient X-ray spectra allow an unambiguous assignment of the electronic and geometric structure of the molecule in both its ground and excited (3)MLCT states. Importantly, the transient spectra are remarkably similar for both solvents, and the spectral changes can be rationalized using the optimized ground- and excited-state structures of the complex. The proposed assignment of the lifetime shortening of the excited state in donor solvents (acetonitrile) to a metal-centered exciplex is not corroborated here. Molecular dynamics simulations confirm the lack of complexation; however, in both solvents the molecules come close to the metal but undergo rapid exchange with the bulk. The shortening of the lifetime of the title complex and nine additional related complexes can be rationalized by the decrease in the (3)MLCT energy. Deviations from this trend may be explained by means of the effects of the dihedral angle between the ligand planes, the solvent, and the (3)MLCT-(1)MLCT energy gap.
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Affiliation(s)
- T J Penfold
- Laboratoire De Spectroscopie Ultrarapide, École Polytechnique Fédérale De Lausanne, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
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24
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Sarangi R, Frank P, Benfatto M, Morante S, Minicozzi V, Hedman B, Hodgson KO. The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine. J Chem Phys 2013. [PMID: 23206038 DOI: 10.1063/1.4767350] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The environment of sulfur in dissolved aqueous L-cysteine has been examined using K-edge x-ray absorption spectroscopy (XAS), extended continuum multiple scattering (ECMS) theory, and density functional theory (DFT). For the first time, bound-state and continuum transitions representing the entire XAS spectrum of L-cysteine sulfur are accurately reproduced by theory. Sulfur K-edge absorption features at 2473.3 eV and 2474.2 eV represent transitions to LUMOs that are mixtures of S-C and S-H σ∗ orbitals significantly delocalized over the entire L-cysteine molecule. Continuum features at 2479, 2489, and 2530 eV were successfully reproduced using extended continuum theory. The full L-cysteine sulfur K-edge XAS spectrum could not be reproduced without addition of a water-sulfur hydrogen bond. Density functional theory analysis shows that although the Cys(H)S⋯H-OH hydrogen bond is weak (∼2 kcal) the atomic charge on sulfur is significantly affected by this water. MXAN analysis of hydrogen-bonding structures for L-cysteine and water yielded a best fit model featuring a tandem of two water molecules, 2.9 Å and 5.8 Å from sulfur. The model included a S(cys)⋯H-O(w1)H hydrogen-bond of 2.19 Å and of 2.16 Å for H(2)O(w1)⋯H-O(w2)H. One hydrogen-bonding water-sulfur interaction alone was insufficient to fully describe the continuum XAS spectrum. However, density functional theoretical results are convincing that the water-sulfur interaction is weak and should be only transient in water solution. The durable water-sulfur hydrogen bond in aqueous L-cysteine reported here therefore represents a break with theoretical studies indicating its absence. Reconciling the apparent disparity between theory and result remains the continuing challenge.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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25
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Zitolo A, Chillemi G, D’Angelo P. X-ray Absorption Study of the Solvation Structure of Cu2+ in Methanol and Dimethyl Sulfoxide. Inorg Chem 2012; 51:8827-33. [DOI: 10.1021/ic3006647] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Zitolo
- Dipartimento di
Chimica, Universit̀a di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Giovanni Chillemi
- CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii
6b, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di
Chimica, Universit̀a di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
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26
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Sarangi R. X-ray absorption near-edge spectroscopy in bioinorganic chemistry: Application to M-O 2 systems. Coord Chem Rev 2012; 257:459-472. [PMID: 23525635 DOI: 10.1016/j.ccr.2012.06.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metal K-edge X-ray absorption spectroscopy (XAS) has been extensively applied to bioinorganic chemistry to obtain geometric structure information on metalloprotein and biomimetic model complex active sites by analyzing the higher energy extended X-ray absorption fine structure (EXAFS) region of the spectrum. In recent years, focus has been on developing methodologies to interpret the lower energy K-pre-edge and rising-edge regions (XANES) and using it for electronic structure determination in complex bioinorganic systems. In this review, the evolution and progress of 3d-transition metal K-pre-edge and rising-edge methodology development is presented with particular focus on applications to bioinorganic systems. Applications to biomimetic transition metal-O2 intermediates (M = Fe, Co, Ni and Cu) are reviewed, which demonstrate the power of the method as an electronic structure determination technique and its impact in understanding the role of supporting ligands in tuning the electronic configuration of transition metal-O2 systems.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, Stanford National Accelerator Laboratory, MS 69, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
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27
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Frank P, Benfatto M, Hedman B, Hodgson KO. The X-ray absorption spectroscopic model of the copper(II) imidazole complex ion in liquid aqueous solution: a strongly solvated square pyramid. Inorg Chem 2012; 51:2086-96. [PMID: 22316238 PMCID: PMC3328689 DOI: 10.1021/ic2017819] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cu K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near-edge structure (MXAN) analyses were combined to evaluate the structure of the copper(II) imidazole complex ion in liquid aqueous solution. Both methods converged to the same square-pyramidal inner coordination sphere [Cu(Im)(4)L(ax)](2+) (L(ax) indeterminate) with four equatorial nitrogen atoms at EXAFS, 2.02 ± 0.01 Å, and MXAN, 1.99 ± 0.03 Å. A short-axial N/O scatterer (L(ax)) was found at 2.12 ± 0.02 Å (EXAFS) or 2.14 ± 0.06 Å (MXAN). A second but very weak axial Cu-N/O interaction was found at 2.9 ± 0.1 Å (EXAFS) or 3.0 ± 0.1 Å (MXAN). In the MXAN fits, only a square-pyramidal structural model successfully reproduced the doubled maximum of the rising K-edge X-ray absorption spectrum, specifically excluding an octahedral model. Both EXAFS and MXAN also found eight outlying oxygen scatterers at 4.2 ± 0.3 Å that contributed significant intensity over the entire spectral energy range. Two prominent rising K-edge shoulders at 8987.1 and 8990.5 eV were found to reflect multiple scattering from the 3.0 Å axial scatterer and the imidazole rings, respectively. In the MXAN fits, the imidazole rings took in-plane rotationally staggered positions about copper. The combined (EXAFS and MXAN) model for the unconstrained cupric imidazole complex ion in liquid aqueous solution is an axially elongated square-pyramidal core, with a weak nonbonded interaction at the second axial coordination position and a solvation shell of eight nearest-neighbor water molecules. This core square-pyramidal motif has persisted through [Cu(H(2)O)(5)](2+), [Cu(NH(3))(4)(NH(3),H(2)O)](2+), (1, 2) and now [Cu(Im)(4)L(ax))](2+) and appears to be the geometry preferred by unconstrained aqueous-phase copper(II) complex ions.
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Affiliation(s)
- Patrick Frank
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.
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28
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29
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X-ray and Solution Structures of CuIIGHK and CuIIDAHK Complexes: Influence on Their Redox Properties. Chemistry 2011; 17:10151-60. [DOI: 10.1002/chem.201100751] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 12/24/2022]
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30
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Sarangi R, Cho J, Nam W, Solomon EI. XAS and DFT investigation of mononuclear cobalt(III) peroxo complexes: electronic control of the geometric structure in CoO2 versus NiO2 systems. Inorg Chem 2010; 50:614-20. [PMID: 21142119 DOI: 10.1021/ic101730r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometric and electronic structures of two mononuclear [(L)CoO2](+) complexes, [(12-TMC)CoO2](ClO4) (1) and [(14-TMC)CoO2](ClO4) (2), have been evaluated using Co K-edge X-ray absorption spectroscopy (XAS) and extended X-ray absorption fine structure (EXAFS) and correlated with density functional theory (DFT) calculations to evaluate the differences in the geometric and electronic structures due to changes in the TMC chelate ring size. Co K-edge XAS shows that both 1 and 2 are Co(III) species. Co K-edge EXAFS data show that both 1 and 2 are side-on O2-bound cobalt(III) peroxide complexes. A combination of EXAFS and DFT calculations reveals that while the constrained 12-TMC ring in 1 allows for side-on O2 binding to the Co center with ease, the 14-TMC chelate in 2 has to undergo significant distortion of the ring to overcome steric hindrance posed by the four cis-methyl groups of the chelate to allow side-on O2 binding to the Co center. The Ni analogue of 2, [(14-TMC)NiO2](+), has been shown to form an end-on-bound nickel(II) superoxide species. The electronic and geometric factors that determine the different electronic structures of 2 and [(14-TMC)NiO2](+) are evaluated using DFT calculations. The results show that while the sterics of the cis-14-TMC chelate contribute to the geometry of O2 binding and result in an end-on-bound Ni(II)O2(-) complex in [(14-TMC)NiO2](+), the higher thermodynamic driving force for oxidation of Co(II) overcomes this steric constraint, resulting in stabilization of a side-on-bound Co(III)O2(2-) electronic structure in 2.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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31
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Femoni C, Iapalucci MC, Longoni G, Lovato T, Stagni S, Zacchini S. Self-assembly of [Pt(3n)(CO)(6n)]2- (n = 4-8) carbonyl clusters: from molecules to conducting molecular metal wires. Inorg Chem 2010; 49:5992-6004. [PMID: 20536247 DOI: 10.1021/ic100547j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A comprehensive study discussing the different parameters that influence the self-assembly of [Pt(3n)(CO)(6n)](2-) (n = 4-8) clusters with miscellaneous mono- and dications into 0-D, 1-D, 2-D, and 3-D materials is herein reported. As an unexpected bonus, the use of Ru(II) dications allowed the first structural characterization of the previously unknown [Pt(21)(CO)(42)](2-) dianion. 0-D structures, which contain isolated ions, are electrical insulators in solid form. Conversely, as soon as infinite chains of clusters are formed, the electrical resistivity, measured in pressed pellets, decreases to 10(5)-10(6), 10(4), and 10(2) ohms cm for discontinuous, semicontinuous, and continuous chains, respectively. Therefore, the resemblance of these materials to molecular metal wires is not only morphological but also functional. Preliminary results of possible self-assembly phenomena in a solution of [Pt(15)(CO)(30)](2-) and [Pt(18)(CO)(36)](2-) according to dynamic light scattering experiments are also reported.
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Affiliation(s)
- Cristina Femoni
- Dipartimento di Chimica Fisica e Inorganica, Università di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
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32
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Burg A, Meyerstein D. Is it always correct to use the Marcus cross relation for calculations of electron self-exchange rates? Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2009.11.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Borghi E, Casella L. X-Ray absorption spectroscopy quantitative analysis of biomimetic copper(II) complexes with tridentate nitrogen ligands mimicking the tris(imidazole) array of protein centres. Phys Chem Chem Phys 2010; 12:1525-34. [PMID: 20126765 DOI: 10.1039/b921769j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study copper(ii) complexes with the tridentate nitrogen ligand bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB) are considered as model compounds for the Cu-tris(imidazole) array found in several copper proteins. 2-BB chelates copper(ii) forming two six-membered rings and the complexes contain methanol, nitrite, azide and water as ancillary ligands; both the coordination numbers and stereochemistries differ in these complexes. Their key structural features were investigated by using full multiple-scattering theoretical analysis of the copper K-edge X-ray absorption spectrum with the MXAN code. We showed that using cluster sizes large enough to include all atoms of the ligand, the analysis of the XANES region can give both a structural model of the metal centre and map the structure of the 2-BB complexes. Complex [Cu(2-BB)(N(3))](+) provided a critical test through the comparison of the XANES simulation results with crystallographic data, thus permitting the extension of the method to the complex [Cu(2-BB)(H(2)O)(n)](+) (n = 1 or 2), for which crystallographic data are not available but is expected to bear a five-coordinated Cu(3N)(2O) core (n = 2). The structural data of [Cu(2-BB)(MeOH)(ClO(4))](+) and [Cu(2-BB)(NO(2))](+), both with a Cu(3N)(2O) core but with a different stereochemistry, were used as the starting parameters for two independent simulations of the XANES region of the [Cu(2-BB)(H(2)O)(2)](+) cation. The two structural models generated by simulation converge towards a structure for the aqua-cation with a lower coordination number. New calculations, where four-coordinated Cu(3N)(O) cores were considered as the starting structures, validated that the structure of the aqua-complex in the powder state has a copper(ii) centre with a four-coordinated Cu(3N)(O) core and a molecular formula [Cu(2-BB)(H(2)O)](ClO(4)).(H(2)O). A water solvation molecule, presumed to be disordered from the simulations with the two Cu(3N)(2O) cores, is present. The successful treatment of this Cu-2-BB complex system allows the extension of the method to other biomimetic compounds when a structural characterization is lacking.
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Affiliation(s)
- Elena Borghi
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy.
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Frank P, Benfatto M, Hedman B, Hodgson KO. The XAS model of dissolved Cu(II) and its significance to biological electron transfer. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/190/1/012059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sarangi R, Dey M, Ragsdale SW. Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase. Biochemistry 2009; 48:3146-56. [PMID: 19243132 PMCID: PMC2667316 DOI: 10.1021/bi900087w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni−F430 cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state (MCRred1) on Me-SCoM to form a NiIII−methyl intermediate, while computational studies indicate that the first step involves the attack of NiI on the sulfur of Me-SCoM, forming a CH3• radical and a NiII−thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the NiI (MCRred1), NiII (MCRred1−silent), and NiIII−methyl (MCRMe) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCRred1. Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni−C bond (∼2.04 Å) in the NiIII−methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni−C bond length suggests a homolytic cleavage of the NiIII−methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F430 cofactor in tuning the stability of the different redox states of MCR.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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The structure of the amyloid-beta peptide high-affinity copper II binding site in Alzheimer disease. Biophys J 2008; 95:3447-56. [PMID: 18599641 DOI: 10.1529/biophysj.108.134429] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurodegeneration observed in Alzheimer disease (AD) is believed to be related to the toxicity from reactive oxygen species (ROS) produced in the brain by the amyloid-beta (Abeta) protein bound primarily to copper ions. The evidence for an oxidative stress role of Abeta-Cu redox chemistry is still incomplete. Details of the copper binding site in Abeta may be critical to the etiology of AD. Here we present the structure determined by combining x-ray absorption spectroscopy (XAS) and density functional theory analysis of Abeta peptides complexed with Cu(2+) in solution under a range of buffer conditions. Phosphate-buffered saline buffer salt (NaCl) concentration does not affect the high-affinity copper binding mode but alters the second coordination sphere. The XAS spectra for truncated and full-length Abeta-Cu(2+) peptides are similar. The novel distorted six-coordinated (3N3O) geometry around copper in the Abeta-Cu(2+) complexes include three histidines: glutamic, or/and aspartic acid, and axial water. The structure of the high-affinity Cu(2+) binding site is consistent with the hypothesis that the redox activity of the metal ion bound to Abeta can lead to the formation of dityrosine-linked dimers found in AD.
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