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Unjaroen D, Duijnstee DR, Mancini MDB, Chen J, Hage R, Swart M, Browne WR. Role of non-redox innocent ligand units in the oxidation of alcohols with H 2O 2 catalyzed by μ-oxido-diiron(III) bis-phenolato polypyridyl complexes. J Inorg Biochem 2024; 260:112698. [PMID: 39178736 DOI: 10.1016/j.jinorgbio.2024.112698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
Redox non-innocent ligands hold the potential to expand the redox chemistry and activity of transition metal catalysts. The impact of the additional redox chemistry of phenol ligands in oxidation catalysis is explored here in the complex μ-oxido-diiron(III) polypyridyl (1) [(L)Fe(III)(μ-O)Fe(III)(L)](ClO4)2 (where HL is 2-(((di(pyridin-2-yl)methyl) (pyridin-2-ylmethyl) amino)methyl)phenol) and its tert-butyl substituted analog 2, in which each of the Fe(III) centers is coordinated to a phenolato moiety of the ligand. Complex 1 was shown earlier to catalyse the oxidation of benzyl alcohols to aldehydes with H2O2. In particular acid was found to accelerate the reactions by removal of a lag period before catalysis initiated. Here, we use reaction monitoring with resonance Raman, UV/vis absorption and EPR spectroscopy to show that under catalytic conditions, i.e. with excess H2O2, rapid (< 5 s) loss of the phenolato moiety occurs, resulting in the formation of an N4 ligated Fe(III) complex. This N4 coordinated complex forms a Fe(III)-OOH species, which is responsible for alcohol oxidation and over time a relatively stable oxido-bridged dinuclear Fe(III) complex forms as a resting state in the catalytic system. The main role of acid in the catalysis is shown to be to facilitate the initial coordination of H2O2 by driving the formation of mononuclear complexes from 1 and 2. The data show that although the phenolato moiety imparts interesting redox properties on complex 1, it does not contribute directly to the oxidation catalysis observed with H2O2.
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Affiliation(s)
- Duenpen Unjaroen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Daniël R Duijnstee
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Marika Di Berto Mancini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Juan Chen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Ronald Hage
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Marcel Swart
- IQCC & Dept. Quıímica, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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2
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Miller SA, Jeanne Dit Fouque K, Mebel AM, Chandler KB, Fernandez-Lima F. Gas-Phase Structures of Fucosylated Oligosaccharides: Alkali Metal and Halogen Influences. J Phys Chem B 2024; 128:8869-8877. [PMID: 39226480 PMCID: PMC11421426 DOI: 10.1021/acs.jpcb.4c02696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Fucosylated carbohydrate antigens play critical roles in physiology and pathology with function linked to their structural details. However, the separation and structural characterization of isomeric fucosylated epitopes remain challenging analytically. Here, we report for the first time the influence of alkali metal cations (Li+, Na+, K+, Rb+, and Cs+) and halogen anions (Cl-, Br-, and I-) on the gas-phase conformational landscapes of common fucosylated trisaccharides (Lewis A, X, and H types 1 and 2) and tetrasaccharides (Lewis B and Y) using trapped ion mobility spectrometry coupled to mass spectrometry and theoretical calculations. Inspection of the mobility profiles of individual standards showed a dependence on the number of mobility bands with the oligosaccharide and the alkali metal and halogen; collision cross sections are reported for all of the observed species. Results showed that trisaccharides (Lewis A, X, and H types 1 and 2) can be best mobility resolved in the positive mode using the [M + Li]+ molecular ion form (baseline resolution r ≈ 2.88 between Lewis X and A); tetrasaccharides can be best mobility resolved in the negative mode using the [M + I]- molecular ion form (baseline separation r ≈ 1.35 between Lewis B and Y). The correlation between the number of oligosaccharide conformers as a function of the molecular ion adduct was studied using density functional theory. Theoretical calculations revealed that smaller cations can form more stable structures based on the number of coordinations, while larger cations induced greater oligosaccharide reorganizations; candidate structures are proposed to better understand the gas-phase oligosaccharide rearrangement trends. Inspection of the candidate structures suggests that the interplay between ion size/charge density and molecular structure dictated the conformational preferences and, consequently, the number of mobility bands and the mobility separation across isomers. This work provides a fundamental understanding of the gas-phase structural dynamics of fucosylated oligosaccharides and their interaction with alkali metals and halogens.
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Affiliation(s)
- Samuel A Miller
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Alexander M Mebel
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kevin Brown Chandler
- Translational Glycobiology Institute, Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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3
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Katoch A, Mandal D. Impact of carboxylate ligation on the C-H activation reactivity of a non-heme Fe(IV)O complex: a computational investigation. Dalton Trans 2024; 53:15264-15272. [PMID: 39222036 DOI: 10.1039/d4dt02139h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A comprehensive DFT investigation has been presented to predict how a carboxylate-rich macrocycle would affect the reactivity of a non-heme Fe(IV)O complex towards C-H activation. The popular non-heme iron oxo complex [FeIV(O)(N4Py)]2+, (N4Py = N,N-(bis(2-pyridyl)methyl)N-bis(2-pyridylmethyl)amine) (1), has been selected here as the primary compound. It is transformed to the compound [FeIV(O)(nBu-P2DA)], where nBu-P2DA = N-(1',1'-bis(2-pyridyl)pentyl)iminodiacetate (2) after the replacement of two pyridine donors of N4Py with carboxylate groups. Two other complexes, namely 3 and 4, have been predicted sequentially substituting nitrogen with the carboxylate groups. Ethylbenzene and dihydrotoluene were chosen as substrates. In terms of C-H activation reactivity, an interesting pattern emerges: as the carboxylate group becomes more equatorially enriched, the reactivity increases, following the trend 1 < 2 < 3 < 4. This also aligns with available experimental reports related to complexes 1 and 2. Fe(IV)O complexes exhibit two-state reactivity (triplet and quintet), whereas the quintet state is more favourable due to the stabilization of the transition states through exchange interactions involving a greater number of unpaired electrons. A detailed analysis of the factors influencing reactivity has been performed, including distortion energy (which decreases for the transition state with the addition of carboxylate groups), the triplet-quintet oxidant energy gap (which consistently decreases as carboxylate group enrichment increases), steric factors, and quantum mechanical tunneling. This investigation provides a detailed explanation of the observed outcomes and predicts the higher reactivity of carboxylate-enriched Fe(IV)O complexes. After potential experimental verification, this could lead to the development of new, optimal catalysts for C-H activation.
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Affiliation(s)
- Akanksha Katoch
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
| | - Debasish Mandal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
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4
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Norwine EE, Kiernicki JJ, Zeller M, Szymczak NK. Additive Effects in Metal/Lewis Acid Cooperativity Assessed in a Tetrahedral Copper Hydrazine Complex Featuring an Appended Borane. Inorg Chem 2024. [PMID: 39287153 DOI: 10.1021/acs.inorgchem.4c02865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Within metal/ligand cooperative systems employing acidic groups, studies that empirically assess distance relationships are needed to maximize cooperative interactions with substrates. We report the formation of two Cu(I)-N2H4 complexes using 1,4,7-triazacyclononane ligand frameworks bearing two tert-butyl groups and either a Lewis acidic trialkylborane or an inert alkyl group. Metal/Lewis acid cooperativity imparts heightened acidification of the hydrazine substrate and plays a key role in the release of substrate to a competitive Lewis acidic group.
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Affiliation(s)
- Emily E Norwine
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John J Kiernicki
- Department of Chemistry, Drury University, Springfield, Missouri 65802, United States
| | - Matthias Zeller
- H. C. Brown Laboratory, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nathaniel K Szymczak
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Dai Y, Zhou Z, Yu W, Ma Y, Kim K, Rivera N, Mohammed J, Lantelme E, Hsu-Kim H, Chilkoti A, You L. Biomolecular condensates regulate cellular electrochemical equilibria. Cell 2024:S0092-8674(24)00909-7. [PMID: 39260373 DOI: 10.1016/j.cell.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024]
Abstract
Control of the electrochemical environment in living cells is typically attributed to ion channels. Here, we show that the formation of biomolecular condensates can modulate the electrochemical environment in bacterial cells, which affects cellular processes globally. Condensate formation generates an electric potential gradient, which directly affects the electrochemical properties of a cell, including cytoplasmic pH and membrane potential. Condensate formation also amplifies cell-cell variability of their electrochemical properties due to passive environmental effect. The modulation of the electrochemical equilibria further controls cell-environment interactions, thus directly influencing bacterial survival under antibiotic stress. The condensate-mediated shift in intracellular electrochemical equilibria drives a change of the global gene expression profile. Our work reveals the biochemical functions of condensates, which extend beyond the functions of biomolecules driving and participating in condensate formation, and uncovers a role of condensates in regulating global cellular physiology.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Zhengqing Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Wen Yu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Yuefeng Ma
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Nelson Rivera
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC 27705, USA
| | - Erica Lantelme
- Department of Pathology and Immunology, Washington University in St. Louis, Saint Louis, MO 63110, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Immunology, Duke University, Durham, NC 27705, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Immunology, Duke University, Durham, NC 27705, USA; Center for Quantitative Biodesign, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
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6
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Majorek KA, Gucwa M, Murzyn K, Minor W. Metal ions in biomedically relevant macromolecular structures. Front Chem 2024; 12:1426211. [PMID: 39246722 PMCID: PMC11378719 DOI: 10.3389/fchem.2024.1426211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/28/2024] [Indexed: 09/10/2024] Open
Abstract
Understanding the functions of metal ions in biological systems is crucial for many aspects of research, including deciphering their roles in diseases and potential therapeutic use. Structural information about the molecular or atomic details of these interactions, generated by methods like X-ray crystallography, cryo-electron microscopy, or nucleic magnetic resonance, frequently provides details that no other method can. As with any experimental method, they have inherent limitations that sometimes lead to an erroneous interpretation. This manuscript highlights different aspects of structural data available for metal-protein complexes. We examine the quality of modeling metal ion binding sites across different structure determination methods, where different kinds of errors stem from, and how they can impact correct interpretations and conclusions.
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Affiliation(s)
- Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
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7
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Song M, Alavi A, Li Manni G. Permutation symmetry in spin-adapted many-body wave functions. Faraday Discuss 2024. [PMID: 39158096 DOI: 10.1039/d4fd00061g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
In the domain of exchange-coupled polynuclear transition-metal (PNTM) clusters, local emergent symmetries exist which can be exploited to greatly increase the sparsity of the configuration interaction (CI) eigensolutions of such systems. Sparsity of the CI secular problem is revealed by exploring the site permutation space within spin-adapted many-body bases, and highly compressed wave functions may arise by finding optimal site orderings. However, the factorial cost of searching through the permutation space remains a bottleneck for clusters with a large number of metal centers. In this work, we explore ways to reduce the factorial scaling, by combining permutation and point group symmetry arguments, and using commutation relations between cumulative partial spin and the Hamiltonian operators, . Certain site orderings lead to commuting operators, from which more sparse wave functions arise. Two graphical strategies will be discussed, one to rapidly evaluate the commutators of interest, and one in the form of a tree search algorithm to predict how many and which distinct site permutations are to be analyzed, eliminating redundancies in the permutation space. Particularly interesting is the case of the singlet spin states for which an additional reversal symmetry can be utilized to further reduce the number of distinct site permutations.
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Affiliation(s)
- Maru Song
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
| | - Ali Alavi
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giovanni Li Manni
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
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8
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Vana F, Szabo Z, Masarik M, Kratochvilova M. The interplay of transition metals in ferroptosis and pyroptosis. Cell Div 2024; 19:24. [PMID: 39097717 PMCID: PMC11297737 DOI: 10.1186/s13008-024-00127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/08/2024] [Indexed: 08/05/2024] Open
Abstract
Cell death is one of the most important mechanisms of maintaining homeostasis in our body. Ferroptosis and pyroptosis are forms of necrosis-like cell death. These cell death modalities play key roles in the pathophysiology of cancer, cardiovascular, neurological diseases, and other pathologies. Transition metals are abundant group of elements in all living organisms. This paper presents a summary of ferroptosis and pyroptosis pathways and their connection to significant transition metals, namely zinc (Zn), copper (Cu), molybdenum (Mo), lead (Pb), cobalt (Co), iron (Fe), cadmium (Cd), nickel (Ni), mercury (Hg), uranium (U), platinum (Pt), and one crucial element, selenium (Se). Authors aim to summarize the up-to-date knowledge of this topic.In this review, there are categorized and highlighted the most common patterns in the alterations of ferroptosis and pyroptosis by transition metals. Special attention is given to zinc since collected data support its dual nature of action in both ferroptosis and pyroptosis. All findings are presented together with a brief description of major biochemical pathways involving mentioned metals and are visualized in attached comprehensive figures.This work concludes that the majority of disruptions in the studied metals' homeostasis impacts cell fate, influencing both death and survival of cells in the complex system of altered pathways. Therefore, this summary opens up the space for further research.
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Affiliation(s)
- Frantisek Vana
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Zoltan Szabo
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno, 656 53, Czech Republic
| | - Michal Masarik
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- First Faculty of Medicine, BIOCEV, Charles University, Prumyslova 595, Vestec, CZ-252 50, Czech Republic
| | - Monika Kratochvilova
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic.
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9
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Diaz-Pier S, Carloni P. Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives. Curr Opin Struct Biol 2024; 87:102817. [PMID: 38795562 DOI: 10.1016/j.sbi.2024.102817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/27/2024] [Indexed: 05/28/2024]
Abstract
New high-performance computing architectures are becoming operative, in addition to exascale computers. Quantum computers (QC) solve optimization problems with unprecedented efficiency and speed, while neuromorphic hardware (NMH) simulates neural network dynamics. Albeit, at the moment, both find no practical use in all atom biomolecular simulations, QC might be exploited in the not-too-far future to simulate systems for which electronic degrees of freedom play a key and intricate role for biological function, whereas NMH might accelerate molecular dynamics simulations with low energy consumption. Machine learning and artificial intelligence algorithms running on NMH and QC could assist in the analysis of data and speed up research. If these implementations are successful, modular supercomputing could further dramatically enhance the overall computing capacity by combining highly optimized software tools into workflows, linking these architectures to exascale computers.
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Affiliation(s)
- Sandra Diaz-Pier
- Simulation & Data Lab Neuroscience, Institute for Advanced Simulations IAS-5, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, JARA, 52428 Jülich, Germany.
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, JARA, 52428 Jülich, Germany
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10
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Ren Z, Zhang F, Kang W, Wang C, Shin H, Zeng X, Gunawardana S, Bowatte K, Krauß N, Lamparter T, Yang X. Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction. Chem 2024; 10:2103-2130. [PMID: 39170732 PMCID: PMC11335340 DOI: 10.1016/j.chempr.2024.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes. The prokaryotic DNA repair photolyase PhrB carries a four-iron-four-sulfur cluster ([4Fe4S]) in addition to the catalytic flavin adenine dinucleotide (FAD) and a second cofactor ribolumazine. Our recent study suggested that the [4Fe4S] cluster functions as an electron cache to coordinate two interdependent photoreactions of the FAD and ribolumazine. Here we report the crystallography observations of light-induced responses in PhrB using the cryo-trapping method and in situ serial Laue diffraction at room temperature. We capture strong signals that depict electron density changes arising from quantized electronic movements in the [4Fe4S] cluster. Our data reveal the mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light-induced redox changes. The quantum effects imaged by decomposition of electron density changes have shed light on the emerging roles of metal clusters in proteins.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
- Lead contact
| | - Fan Zhang
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Weijia Kang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiaoli Zeng
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Semini Gunawardana
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Kalinga Bowatte
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois Chicago, Chicago, IL 60607, USA
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11
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Sharma S, Pandey B, Rajaraman G. The interplay of covalency, cooperativity, and coupling strength in governing C-H bond activation in Ni 2E 2 (E = O, S, Se, Te) complexes. Chem Sci 2024; 15:10529-10540. [PMID: 38994414 PMCID: PMC11234824 DOI: 10.1039/d4sc02882a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
Dinickel dichalcogenide complexes hold vital multifaceted significance across catalysis, electron transfer, magnetism, materials science, and energy conversion. Understanding their structure, bonding, and reactivity is crucial for all aforementioned applications. These complexes are classified as dichalcogenide, subchalcogenide, or chalcogenide based on metal oxidation and coordinated chalcogen, and due to the associated complex electronic structure, ambiguity often lingers about their classification. In this work, using DFT, CASSCF/NEVPT2, and DLPNO-CCSD(T) methods, we have studied in detail [(NiL)2(E2)] (L = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane; E = O, S, Se and Te) complexes and explored their reactivity towards C-H bond activation for the first time. Through a comprehensive analysis of the structure, bonding, and reactivity of a series of [(NiL)2(E2)] complexes with E = O, S, Se, and Te, our computational findings suggest that {Ni2O2} and {Ni2S2} are best categorised as dichalcogenide-type complexes. In contrast, {Ni2Se2} and {Ni2Te2} display tendencies consistent with the subchalcogenide classification, and this aligns with the earlier structural correlation proposed (Berry and co-workers, J. Am. Chem. Soc. 2015, 137, 4993) reports on the importance of the E-E bond strength. Our study suggests the reactivity order of {Ni2O2} > {Ni2S2} > {Ni2Se2} > {Ni2Te2} for C-H bond activation, and the origin of the difference in reactivity was attributed to the difference in the Ni-E bond covalency, and electronic cooperativity between two Ni centres that switch among the classification during the reaction. Further non-adiabatic analysis at the C-H bond activation step demonstrates a decrease in coupling strength as we progress down the group, indicating a correlation with metal-ligand covalency. Notably, the reactivity trend is found to be correlated to the strength of the antiferromagnetic exchange coupling constant J via developing a magneto-structural-barrier map - offering a hitherto unknown route to fine-tune the reactivity of this important class of compound.
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Affiliation(s)
- Sunita Sharma
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
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12
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Bonastre-Sabater I, Lopera A, Martínez-Camarena Á, Blasco S, Doménech-Carbó A, Jiménez HR, Verdejo B, García-España E, Clares MP. Exo- or endo-1 H-pyrazole metal coordination modulated by the polyamine chain length in [1 + 1] condensation azamacrocycles. Binuclear complexes with remarkable SOD activity. Dalton Trans 2024. [PMID: 38973348 DOI: 10.1039/d4dt01236d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
The Cu2+ complexes of three [1 + 1] azacyclophane macrocycles having the 1H-pyrazole ring as the spacer and the pentaamine 1,5,8,11,15-pentaazadecane (L1) or hexaamines 1,5,8,12,15,19-hexaazanonadecane (L2) and 1,5,9,13,17,21-hexaazaheneicosane (L3) as bridges show endo- coordination of the pyrazolate bridge giving rise to discrete monomeric species. Previously reported pyrazolacyclophanes evidenced, however, exo-coordination with the formation of dimeric species of 2 : 2, 3 : 2 or even 4 : 2 Cu2+ : L stoichiometry. The complexes have been characterized in solution using potentiometric studies, UV-Vis spectroscopy, paramagnetic NMR, cyclic voltammetry and mass spectrometry. The measurements show that all three ligands have as many protonation steps in water as secondary amines are in the bridge, while they are able to form both mono- and binuclear Cu2+ species. The crystal structures of the complexes [Cu(HL1)Br]Br(1+x)(ClO4)(1-x)·yH2O (1) and [Cu2(H-1L2)Cl(ClO4)](ClO4)·H2O·C2H5OH (2) have been solved by X-ray diffraction studies. In 1 the metal ion lies at one side of the macrocyclic cavity being coordinated by one nitrogen of the pyrazolate moiety and the three consecutive nitrogen atoms of the polyamine bridge. The other nitrogen of the pyrazole ring is hydrogen-bonded to an amine group. In 2 the two metal ions are interconnected by a pyrazolate bis(monodentate) moiety and complete their coordination spheres with three amines and either a bromide or a perchlorate anion, which occupy the axial positions of distorted square pyramid geometries. Paramagnetic NMR studies of the binuclear complexes confirm the coordination pattern observed in the crystal structures. Cyclic voltamperommetry data show potentials within the adequate range to exhibit superoxide dismutase (SOD) activity. The IC50 values calculated by McCord-Fridovich enzymatic assays show that the binuclear Cu2+ complexes of L2 and L3 have SOD activities that rank amongst the highest ones reported so far.
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Affiliation(s)
- Irene Bonastre-Sabater
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Alberto Lopera
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Álvaro Martínez-Camarena
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, avda. Complutense s/n, 28040 Madrid, Spain
| | - Salvador Blasco
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Antonio Doménech-Carbó
- Departamento de Química Analítica, Universidad de Valencia, Calle Dr Moliner s/n, 46100 Burjassot, Valencia, Spain
| | - Hermas R Jiménez
- Departamento de Química Inorgánica, Universidad de Valencia, Calle Doctor Moliner s/n, 46100 Burjasot, Valencia, Spain
| | - Begoña Verdejo
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Enrique García-España
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - M Paz Clares
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular. Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
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13
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Jørgensen FK, Delcey MG, Hedegård ED. Perspective: multi-configurational methods in bio-inorganic chemistry. Phys Chem Chem Phys 2024; 26:17443-17455. [PMID: 38868993 DOI: 10.1039/d4cp01297f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the electronic structure and properties of metalloproteins poses significant challenges due to the complex nature of their electronic configurations and strong correlation effects. Multiconfigurational quantum chemistry methods are, in principle, the most appropriate tools for addressing these challenges, offering the capability to capture the inherent multi-reference character and strong electron correlation present in bio-inorganic systems. Yet their computational cost has long hindered wider adoption, making methods such as density functional theory (DFT) the method of choice. However, advancements over the past decade have substantially alleviated this limitation, rendering multiconfigurational quantum chemistry methods more accessible and applicable to a wider range of bio-inorganic systems. In this perspective, we discuss some of these developments and how they have already been used to answer some of the most important questions in bio-inorganic chemistry. We also comment on ongoing developments in the field and how the future of the field may evolve.
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Affiliation(s)
- Frederik K Jørgensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Mickaël G Delcey
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Erik D Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
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14
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Tran P, Wang Y, Dzikovski B, Lahm ME, Xie Y, Wei P, Klepov VV, Schaefer HF, Robinson GH. A Stable Aluminum Tris(dithiolene) Triradical. J Am Chem Soc 2024; 146:16340-16347. [PMID: 38820231 PMCID: PMC11177253 DOI: 10.1021/jacs.4c05631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
A stable aluminum tris(dithiolene) triradical (3) was experimentally realized through a low-temperature reaction of the sterically demanding lithium dithiolene radical (2) with aluminum iodide. Compound 3 was characterized by single-crystal X-ray diffraction, UV-vis and EPR spectroscopy, SQUID magnetometry, and theoretical computations. The quartet ground state of triradical 3 has been unambiguously confirmed by variable-temperature continuous wave EPR experiments and SQUID magnetometry. Both SQUID magnetometry and broken-symmetry DFT computations reveal a small doublet-quartet energy gap [ΔEDQ = 0.18 kcal mol-1 (SQUID); ΔEDQ = 0.14 kcal mol-1 (DFT)]. The pulsed EPR experiment (electron spin echo envelop modulation) provides further evidence for the interaction of these dithiolene-based radicals with the central aluminum nucleus of 3.
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Affiliation(s)
- Phuong
M. Tran
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Yuzhong Wang
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Boris Dzikovski
- Department
of Chemistry and Chemical Biology, and ACERT, National Biomedical
Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Mitchell E. Lahm
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Yaoming Xie
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Pingrong Wei
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Vladislav V. Klepov
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Henry F. Schaefer
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
| | - Gregory H. Robinson
- Department
of Chemistry and the Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602-2556, United States
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15
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Depenbrock F, Limpke T, Stammler A, Oldengott J, Bögge H, Glaser T. Increasing the electron donation in a dinucleating ligand family: molecular and electronic structures in a series of Co IICo II complexes. Dalton Trans 2024; 53:9554-9567. [PMID: 38771300 DOI: 10.1039/d4dt00877d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
We have developed a family of dinucleating ligands with varying terminal donors to generate dinuclear peroxo and high-valent complexes and to correlate their stabilities and reactivities with their molecular and electronic structures as a function of the terminal donors. It appears that the electron-donating ability of the terminal donors is an important handle for controlling these stabilities and reactivities. Here, we present the synthesis of a new dinucleating ligand with potentially strong donating terminal imidazole donors. As CoII ions are sensitive to variations in donor strength in terms of coordination number, magnetism, UV-Vis-NIR spectra, redox potentials, we probe the electron donation ability of this new ligand in CoIICoII complexes in comparison to the parent CoIICoII complexes with terminal pyridine donors and we synthesize the analogous CoIICoII complexes with terminal 6-methylpyridines and methoxy-substituted pyridines. The molecular structures show indeed strong variations in coordination numbers and bond lengths. These differences in the molecular structures are reflected in the magnetic properties and in the d-d transitions demonstrating that the molecular structures remain intact upon dissolution. The redox potentials are analyzed with respect to the electron donation ability and are the only handle to observe an effect of the methoxy-substituted pyridines. All data taken together show the following order of electron donating ability for the terminal donors: 6-methylpyridines ≪ pyridines < methoxy-substituted pyridines ≪ imidazoles.
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Affiliation(s)
- Felix Depenbrock
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| | - Thomas Limpke
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| | - Anja Stammler
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| | - Jan Oldengott
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| | - Hartmut Bögge
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
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16
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Juda CE, Handford RC, Bartholomew AK, Powers TM, Gu NX, Meyer E, Roth N, Chen YS, Zheng SL, Betley TA. Cluster dynamics of heterometallic trinuclear clusters during ligand substitution, redox chemistry, and group transfer processes. Chem Sci 2024; 15:8242-8248. [PMID: 38817579 PMCID: PMC11134326 DOI: 10.1039/d3sc03606e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/04/2024] [Indexed: 06/01/2024] Open
Abstract
Stepwise metalation of the hexadentate ligand tbsLH6 (tbsLH6 = 1,3,5-C6H9(NHC6H4-o-NHSiMe2tBu)3) affords bimetallic trinuclear clusters (tbsL)Fe2Zn(thf) and (tbsL)Fe2Zn(py). Reactivity studies were pursued to understand metal atom lability as the clusters undergo ligand substitution, redox chemistry, and group transfer processes. Chloride addition to (tbsL)Fe2Zn(thf) resulted in a mixture of species including both all-zinc and all-iron products. Addition of ArN3 (Ar = Ph, 3,5-(CF3)2C6H3) to (tbsL)Fe2Zn(py) yielded a mixture of two trinuclear products: (tbsL)Fe3(μ3-NAr) and (tbsL)Fe2Zn(μ3-NAr)(py). The two imido species were separated via crystallization, and outer sphere reduction of (tbsL)Fe2Zn(μ3-NAr)(py) resulted in the formation of a single product, [2,2,2-crypt(K)][(tbsL)Fe2Zn(μ3-NAr)]. These results provide insight into the relationship between heterometallic cluster structure and substitutional lability and could help inform both future catalyst design and our understanding of metal atom lability in bioinorganic systems.
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Affiliation(s)
- Cristin E Juda
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Rex C Handford
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | | | - Tamara M Powers
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Nina X Gu
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Elisabeth Meyer
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Nikolaj Roth
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Yu-Sheng Chen
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Theodore A Betley
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
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17
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Dobrautz W, Sokolov IO, Liao K, Ríos PL, Rahm M, Alavi A, Tavernelli I. Toward Real Chemical Accuracy on Current Quantum Hardware Through the Transcorrelated Method. J Chem Theory Comput 2024; 20:4146-4160. [PMID: 38723159 PMCID: PMC11137825 DOI: 10.1021/acs.jctc.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024]
Abstract
Quantum computing is emerging as a new computational paradigm with the potential to transform several research fields including quantum chemistry. However, current hardware limitations (including limited coherence times, gate infidelities, and connectivity) hamper the implementation of most quantum algorithms and call for more noise-resilient solutions. We propose an explicitly correlated Ansatz based on the transcorrelated (TC) approach to target these major roadblocks directly. This method transfers, without any approximation, correlations from the wave function directly into the Hamiltonian, thus reducing the resources needed to achieve accurate results with noisy quantum devices. We show that the TC approach allows for shallower circuits and improves the convergence toward the complete basis set limit, providing energies within chemical accuracy to experiment with smaller basis sets and, thus, fewer qubits. We demonstrate our method by computing bond lengths, dissociation energies, and vibrational frequencies close to experimental results for the hydrogen dimer and lithium hydride using two and four qubits, respectively. To demonstrate our approach's current and near-term potential, we perform hardware experiments, where our results confirm that the TC method paves the way toward accurate quantum chemistry calculations already on today's quantum hardware.
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Affiliation(s)
- Werner Dobrautz
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
| | - Igor O. Sokolov
- IBM
Quantum, IBM Research Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Ke Liao
- Max
Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany
| | - Pablo López Ríos
- Max
Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany
| | - Martin Rahm
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
| | - Ali Alavi
- Max
Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, U.K.
| | - Ivano Tavernelli
- IBM
Quantum, IBM Research Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
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18
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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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19
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Antolini C, Sosa Alfaro V, Reinhard M, Chatterjee G, Ribson R, Sokaras D, Gee L, Sato T, Kramer PL, Raj SL, Hayes B, Schleissner P, Garcia-Esparza AT, Lim J, Babicz JT, Follmer AH, Nelson S, Chollet M, Alonso-Mori R, van Driel TB. The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source. Molecules 2024; 29:2323. [PMID: 38792184 PMCID: PMC11124266 DOI: 10.3390/molecules29102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump-probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.
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Affiliation(s)
- Cali Antolini
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Victor Sosa Alfaro
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Marco Reinhard
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Gourab Chatterjee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Ryan Ribson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Dimosthenis Sokaras
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Leland Gee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Takahiro Sato
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Patrick L. Kramer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Sumana Laxmi Raj
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Brandon Hayes
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Pamela Schleissner
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Angel T. Garcia-Esparza
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Jinkyu Lim
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
- Department of Energy and Environmental Engineering, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Jeffrey T. Babicz
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Alec H. Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA;
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Matthieu Chollet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Tim B. van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
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20
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Bakhtiar D, Vorechovsky I. Copper-binding proteins and exonic splicing enhancers and silencers. Metallomics 2024; 16:mfae023. [PMID: 38692844 PMCID: PMC11097207 DOI: 10.1093/mtomcs/mfae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/21/2024] [Indexed: 05/03/2024]
Abstract
Eukaryotic DNA codes not only for proteins but contains a wealth of information required for accurate splicing of messenger RNA precursors and inclusion of constitutively or alternatively spliced exons in mature transcripts. This "auxiliary" splicing code has been characterized as exonic splicing enhancers and silencers (ESE and ESS). The exact interplay between protein and splicing codes is, however, poorly understood. Here, we show that exons encoding copper-coordinating amino acids in human cuproproteins lack ESEs and/or have an excess of ESSs, yet RNA sequencing and expressed sequence tags data show that they are more efficiently included in mature transcripts by the splicing machinery than average exons. Their largely constitutive inclusion in messenger RNA is facilitated by stronger splice sites, including polypyrimidine tracts, consistent with an important role of the surrounding intron architecture in ensuring high expression of metal-binding residues during evolution. ESE/ESS profiles of codons and entire exons that code for copper-coordinating residues were very similar to those encoding residues that coordinate zinc but markedly different from those that coordinate calcium. Together, these results reveal how the traditional and auxiliary splicing motifs responded to constraints of metal coordination in proteins.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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21
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- 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
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- 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
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22
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Zhao L, Lei T, Chen R, Tian Z, Bian B, Graham NJD, Yang Z. Bioinspired stormwater control measure for the enhanced removal of truly dissolved polycyclic aromatic hydrocarbons and heavy metals from urban runoff. WATER RESEARCH 2024; 254:121355. [PMID: 38430755 DOI: 10.1016/j.watres.2024.121355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Stormwater harvesting (SWH) addresses the UN's Sustainable Development Goals (SDGs). Conventional stormwater control measures (SCMs) effectively remove particulate and colloidal contaminants from urban runoff; however, they fail to retain dissolved contaminants, particularly substances of concern like polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs), thereby hindering the SWH applicability. Here, inspired by protein folding in nature, we reported a novel biomimetic SCM for the efficient removal of dissolved PAHs and HMs from urban runoff. Lab-scale tests were conducted together with a more mechanistic investigation on how the contaminants were removed. By integrating hydrophobic organic chains with low-cost hydrophilic flocculant matrixes, our biomimetic flocculants achieved a 1.4-9.5 times removal of all detected dissolved PAHs and HMs, while enhancing the removal of a wide-spectrum of particulate and colloidal contaminants, compared to existing SCMs. Ecotoxicity, as indicated by newborn Daphnia magna as experimental organisms, was reduced from "acute toxicity" of the original runoff sample (toxic unit of ∼2.6) to "non-toxicity" (toxic unit < 0.4) of the treated water. The improved performance is attributed to the protein-folding-like features of the bioinspired flocculants providing: (i) stronger binding to PAHs (via hydrophobic association) and HMs (via coordination), and (ii) the ability of spontaneous aggregation. The bio-inspired approach in this work holds strong promise as an alternative or supplementary component in SCM systems, and is expected to contribute to sustainable water management practices in relation to SDGs.
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Affiliation(s)
- Lina Zhao
- School of Chemistry and Materials Science, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Tao Lei
- School of Chemistry and Materials Science, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Ruhui Chen
- School of Chemistry and Materials Science, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Ziqi Tian
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, Ningbo 315000, China
| | - Bo Bian
- School of Chemistry and Materials Science, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, SW7 2AZ, UK
| | - Zhen Yang
- School of Chemistry and Materials Science, School of Environment, Nanjing Normal University, Nanjing 210023, China.
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23
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Maity S, Bhunia S, Drew MGB, Gomila RM, Frontera A, Chattopadhyay S. Formation of H-bonding networks in the solid state structure of a trinuclear cobalt(iii/ii/iii) complex with N 2O 2 donor Schiff base ligand and glutaric acid as bridging co-ligand: synthesis, structure and DFT study. RSC Adv 2024; 14:13200-13208. [PMID: 38655483 PMCID: PMC11037027 DOI: 10.1039/d3ra07697k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
A trinuclear linear mixed-valence centrosymmetric cobalt(iii)-cobalt(ii)-cobalt(iii) complex, [CoII{(μ-L)(μ-Hglu)CoIII(OH2)}2](ClO4)2·6H2O has been synthesized during tetradentate N2O2 donor 'Schiff base' ligand, H2L {N,N'-bis(salicylidene)-1,3-diaminopropane} and glutaric acid (H2glu) as anionic co-ligand. The complex has been characterized by spectroscopic measurements and its solid state structure has been determined by single crystal X-ray diffraction analysis. The supra-molecular assembly formed by the hydrogen bonding interactions in the solid state of the complex has been analysed using DFT calculations.
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Affiliation(s)
- Sovana Maity
- Department of Chemistry, Jadavpur University Kolkata 700032 West Bengal India
| | - Sudip Bhunia
- Department of Chemistry, Jadavpur University Kolkata 700032 West Bengal India
| | - Michael G B Drew
- School of Chemistry, The University of Reading P.O. Box 224 Whiteknights Reading RG6 6AD UK
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears Crta de valldemossa km 7.7 07122 Palma de Mallorca (Baleares) Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears Crta de valldemossa km 7.7 07122 Palma de Mallorca (Baleares) Spain
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24
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Zheng H, Zhang H, Zhong J, Gucwa M, Zhang Y, Ma H, Deng L, Mao L, Minor W, Wang N. PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules. RESEARCH SQUARE 2024:rs.3.rs-3908734. [PMID: 38463967 PMCID: PMC10925427 DOI: 10.21203/rs.3.rs-3908734/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures. Compared to other predictors, PMM excels in predicting regulatory sites (median deviation of 0.34 Å), demonstrating superior accuracy in locating catalytic sites (median deviation of 0.27 Å) and structural sites (median deviation of 0.14 Å). PMM assigns a certainty score to each predicted site based on local structural and physicochemical features independent of homolog presence. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validates diverse functional zinc sites from different structure sources (predicted structures, cryo-EM and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top. While currently trained on zinc, the PMM workflow can easily adapt to other metals through expanded training data.
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Affiliation(s)
| | | | | | | | | | | | - Lei Deng
- Hunan University College of Biology
| | | | | | - Nasui Wang
- Division of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College
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25
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Shisler KA, Kincannon WM, Mattice JR, Larson J, Valaydon-Pillay A, Mus F, Flusche T, Kumar Nath A, Stoian SA, Raugei S, Bothner B, DuBois JL, Peters JW. Homologous acetone carboxylases select Fe(II) or Mn(II) as the catalytic cofactor. mBio 2024; 15:e0298723. [PMID: 38126751 PMCID: PMC10865871 DOI: 10.1128/mbio.02987-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Acetone carboxylases (ACs) catalyze the metal- and ATP-dependent conversion of acetone and bicarbonate to form acetoacetate. Interestingly, two homologous ACs that have been biochemically characterized have been reported to have different metal complements, implicating different metal dependencies in catalysis. ACs from proteobacteria Xanthobacter autotrophicus and Aromatoleum aromaticum share 68% sequence identity but have been proposed to have different catalytic metals. In this work, the two ACs were expressed under the same conditions in Escherichia coli and were subjected to parallel chelation and reconstitution experiments with Mn(II) or Fe(II). Electron paramagnetic and Mössbauer spectroscopies identified signatures, respectively, of Mn(II) or Fe(II) bound at the active site. These experiments showed that the respective ACs, without the assistance of chaperones, second metal sites, or post-translational modifications facilitate correct metal incorporation, and despite the expected thermodynamic preference for Fe(II), each preferred a distinct metal. Catalysis was likewise associated uniquely with the cognate metal, though either could potentially serve the proposed Lewis acidic role. Subtle differences in the protein structure are implicated in serving as a selectivity filter for Mn(II) or Fe(II).IMPORTANCEThe Irving-Williams series refers to the predicted stabilities of transition metal complexes where the observed general stability for divalent first-row transition metal complexes increase across the row. Acetone carboxylases (ACs) use a coordinated divalent metal at their active site in the catalytic conversion of bicarbonate and acetone to form acetoacetate. Highly homologous ACs discriminate among different divalent metals at their active sites such that variations of the enzyme prefer Mn(II) over Fe(II), defying Irving-Williams-predicted behavior. Defining the determinants that promote metal discrimination within the first-row transition metals is of broad fundamental importance in understanding metal-mediated catalysis and metal catalyst design.
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Affiliation(s)
- Krista A. Shisler
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - William M. Kincannon
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jenna R. Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - James Larson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Tamara Flusche
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Arnab Kumar Nath
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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26
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Katti SS, Igumenova TI. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565546. [PMID: 38405767 PMCID: PMC10888879 DOI: 10.1101/2023.11.03.565546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca 2+ and Zn 2+ . The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd 2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn 2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd 2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α 3 DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
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27
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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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28
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Huang XL, Harmer JR, Schenk G, Southam G. Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology. Front Chem 2024; 12:1349020. [PMID: 38389729 PMCID: PMC10881703 DOI: 10.3389/fchem.2024.1349020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.
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Affiliation(s)
- Xiao-Lan Huang
- NYS Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Jeffrey R Harmer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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29
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Yao J, Shao L, Kang X, Zhu M, Huo X, Wang X. Direct α-Arylation of Benzo[ b]furans Catalyzed by a Pd 3 Cluster. J Org Chem 2024; 89:1719-1726. [PMID: 38204281 DOI: 10.1021/acs.joc.3c02428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
As an interim paradigm for the catalysts between those based on more conventional mononuclear molecular Pd complexes and Pdn nanoparticles widely used in organic synthesis, polynuclear palladium clusters have attracted great attention for their unique reactivity and electronic properties. However, the development of Pd cluster catalysts for organic transformations and mechanistic investigations is still largely unexploited. Herein, we disclose the use of trinuclear palladium (Pd3Cl) species as an active catalyst for the direct C-H α-arylation of benzo[b]furans with aryl iodides to afford 2-arylbenzofurans in good yields under mild conditions. With this method, broad substrate adaptability was observed, and several drug intermediates were synthesized in high yields. Mechanistic studies indicated that the Pd3 core most likely remained intact throughout the reaction course.
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Affiliation(s)
- Jian Yao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Lili Shao
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xi Kang
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials, Anhui University, Hefei 230601, China
| | - Manzhou Zhu
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials, Anhui University, Hefei 230601, China
| | - Xiaohong Huo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaoming Wang
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
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30
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Zhai Y, Tian W, Chen K, Lan L, Kan J, Shi H. Flagella-mediated adhesion of Escherichia coli O157:H7 to surface of stainless steel, glass and fresh produces during sublethal injury and recovery. Food Microbiol 2024; 117:104383. [PMID: 37918998 DOI: 10.1016/j.fm.2023.104383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 11/04/2023]
Abstract
E. coli O157:H7 can be induced into sublethally injured (SI) state by lactic acid (LA) and regain activity in nutrient environments. This research clarified the role of flagella-related genes (fliD, fliS, cheA and motA) in adhesion of E. coli O157:H7 onto stainless steel, glass, lettuce, spinach, red cabbage and cucumber during LA-induced SI and recovery by plate counting. Results of adhesion showed improper flagellar rotation caused by the deletion of motA resulting in the decreased adhesion. Motility of wildtype determined by diameter of motility halo decreased in SI state and repaired with recovery time increasing, lagging behind changes in expression of flagella-related genes. Flagellar function-impaired strains all exhibited non-motile property. Thus, we speculated that flagella-mediated motility is critical in early stage of adhesion. We also found the effects of Fe2+, Ca2+ and Mn2+ on adhesion or motility of wildtype was independent of bacterial states. However, the addition of Ca2+ and Mn2+ did not affect motility of flagellar function-impaired strains as they did on wildtype. This research provides new insights to understand the role of flagella and cations in bacterial adhesion, which will aid in development of anti-adhesion agents to reduce bio-contamination in food processing.
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Affiliation(s)
- Yujun Zhai
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Weina Tian
- College of Bioengineering, Beijing Polytechnic, Beijing, 100176, China
| | - Kewei Chen
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Linshu Lan
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Jianquan Kan
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Hui Shi
- College of Food Science, Southwest University, Chongqing, 400715, China.
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Gulyaeva ES, Osipova ES, Kovalenko SA, Filippov OA, Belkova NV, Vendier L, Canac Y, Shubina ES, Valyaev DA. Two active species from a single metal halide precursor: a case study of highly productive Mn-catalyzed dehydrogenation of amine-boranes via intermolecular bimetallic cooperation. Chem Sci 2024; 15:1409-1417. [PMID: 38274083 PMCID: PMC10806649 DOI: 10.1039/d3sc05356c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024] Open
Abstract
Metal-metal cooperation for inert bond activation is a ubiquitous concept in coordination chemistry and catalysis. While the great majority of such transformations proceed via intramolecular mode in binuclear complexes, to date only a few examples of intermolecular small molecule activation using usually bimetallic frustrated Lewis pairs (Mδ+⋯M'δ-) have been reported. We introduce herein an alternative approach for the intermolecular bimetallic cooperativity observed in the catalytic dehydrogenation of amine-boranes, in which the concomitant activation of N-H and B-H bonds of the substrate via the synergetic action of Lewis acidic (M+) and basic hydride (M-H) metal species derived from the same mononuclear complex (M-Br). It was also demonstrated that this system generated in situ from the air-stable Mn(i) complex fac-[(CO)3(bis(NHC))MnBr] and NaBPh4 shows high activity for H2 production from several substrates (Me2NHBH3, tBuNH2BH3, MeNH2BH3, NH3BH3) at low catalyst loading (0.1% to 50 ppm), providing outstanding efficiency for Me2NHBH3 (TON up to 18 200) that is largely superior to all known 3d-, s-, p-, f-block metal derivatives and frustrated Lewis pairs (FLPs). These results represent a step forward towards more extensive use of intermolecular bimetallic cooperation concepts in modern homogeneous catalysis.
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Affiliation(s)
- Ekaterina S Gulyaeva
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 Route de Narbonne 31077 Toulouse Cedex 4 France
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Elena S Osipova
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Sergey A Kovalenko
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Oleg A Filippov
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Natalia V Belkova
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Laure Vendier
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 Route de Narbonne 31077 Toulouse Cedex 4 France
| | - Yves Canac
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 Route de Narbonne 31077 Toulouse Cedex 4 France
| | - Elena S Shubina
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences 28/1 Vavilov Str., GSP-1, B-334 Moscow 119334 Russia
| | - Dmitry A Valyaev
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 Route de Narbonne 31077 Toulouse Cedex 4 France
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Michael S, Jeyaraman P, Marimuthu B, Rajamanikam R, Thanasamy R, Arunsunai Kumar K, Mitu L, Raman N. Pharmaceutical manifestation of Knoevenagel condensed metal (II) complexes through virtual, in vitro and in vivo assessments. J Biomol Struct Dyn 2024:1-15. [PMID: 38189286 DOI: 10.1080/07391102.2023.2301059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
Sulphur containing compounds possess a great deal of interest due to wide range of beneficial activities towards biotic species. This work also deals with the study of biological examination of newly synthesized sulphur containing Cu(II) and Zn(II) complexes derived from (E)-4-(phenylimino)-3-((E)-1-(phenylimino)ethyl)pent-2-ene-1-thiol Schiff bases. Moreover, the DNA nuclease efficiency of the synthesized metal complexes is studied by UV absorption studies, Fluorescence studies, Viscosity and CV titrations which confirm the intercalative mode of binding. Pharmacokinetic studies and drug like activity of these compounds are screened with the help of SWISS ADME online freeware. Their morphological nature is corroborated by various spectral techniques. Optimized geometry and biologically accessible nature of the synthesized compounds are investigated by Gaussian 09 W software. Interestingly, molecular docking studies are carried out against cancer DNA and 6J10 cancer cell. Anti-inflammatory and in vitro antioxidant activities have been studied to validate the theoretical prediction. Based on these preliminary pharmacological activities, the in vitro cytotoxicity and in vivo antitumor activities are examined using MCF-7, HeLa, Hep-2, HepG-2 and Ehrlich ascites carcinoma (EAC) cell lines. All the above examinations reveal that the nitro substituted transition metal complexes possess higher biological bustle.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samuel Michael
- Research Department of Chemistry, VHNSN College, Virudhungar, India
- Department of Chemistry, PSR Engineering College, Sivakasi, India
| | - Porkodi Jeyaraman
- Post Graduate and Research Department of Chemistry, The Standard Fireworks Rajaratnam College for Women (Autonomous), Sivakasi, India
| | | | | | - Radha Thanasamy
- Department of Chemistry, Saiva Bhanu Kshatriya College, Aruppukottai, India
| | | | - Liviu Mitu
- Department of Chemistry, University of Pitesti, Pitesti, Romania
| | - Natarajan Raman
- Research Department of Chemistry, VHNSN College, Virudhungar, India
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Jeong D, Kim K, Lee Y, Cho J. Synthetic Advances for Mechanistic Insights: Metal-Oxygen Intermediates with a Macrocyclic Pyridinophane System. Acc Chem Res 2024; 57:120-130. [PMID: 38110355 DOI: 10.1021/acs.accounts.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
ConspectusMetalloenzymes, which are proteins containing earth-abundant transition-metal ions as cofactors in the active site, generate various metal-oxygen intermediates via activating a dioxygen molecule (O2) to mediate vital metabolic functions, such as the oxidative metabolism of xenobiotics and the biotransformation of naturally occurring molecules. By replicating the active sites of metalloenzymes, many bioinorganic chemists have studied the geometric and electronic properties and reactivities of model complexes to understand the nature of enzymatic intermediates and develop bioinspired metal catalysts. Among the reported model complexes, nonporphyrinic macrocyclic ligands are the predominant coordination system widely used in stabilizing and isolating diverse metal-oxygen intermediates, which allows us to extensively investigate the physicochemical characteristics of the analogs of reactive intermediates of metalloenzymes. In particular, it has been reported that the ring size of the macrocyclic ligands, defined by the number of atoms in the macrocyclic ring, drastically affects the identity of the metal-oxygen intermediate. Thus, systematic modification of the macrocyclic ligands has been a great subject being examined in various inorganic fields.In this Account, we describe synthetic advances of a macrocyclic ligand system by introducing pyridine donors into a 12-membered tetraazamacrocyclic ligand (12-TMC) that initially has 4 amine donors. Interestingly, the backbone of the pyridinophane ligand with 2 pyridine and 2 amine donors in a 12-membered ring is shown to be much more folded than in other macrocyclic ligands, thereby allowing the axial and equatorial donors to separately control the electronic structure of metal complexes. Then, we looked over independent electronic and steric effects on metal-oxygen species with thorough physicochemical analysis. The NiIII-peroxo complexes exhibit nucleophilic reactivity dependent on the steric hindrance of the second coordination sphere. Furthermore, the C-H bond strength of the second coordination sphere has also been an important factor in determining the stability of MnIV-bis(hydroxo) intermediates. Electronic tuning on CoIII-hydroperoxo intermediates results in a trend between the electron-donating abilities of para-substituents on pyridine in the pyridinophane ligand and electrophilic reactivities, from which mechanistic insights into the metal-hydroperoxo species have been gained. Importantly, the metal-oxygen intermediates supported by the pyridinophane ligand system have revealed quite challenging chemical reactions, including dioxygenase-like nitrile activation by CoIII-peroxo intermediates and the oxidation of aldehyde and aromatic compounds by manganese-oxygen intermediates. Based on the fine substitution of donors, we have addressed that those novel reactions originated from the unique framework of the pyridinophane system incorporating spin-crossover behavior and high redox potentials of the metal-oxygen intermediates. These results will be valuable for the structure-activity relationship of metal-oxygen intermediates, giving a better understanding on the enzymatic coordination system where amino acid ligands vary for specific chemical reactions.
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Affiliation(s)
- Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungmin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yujeong Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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Kour M, Taborosi A, Boyd ES, Szilagyi RK. Development of molecular cluster models to probe pyrite surface reactivity. J Comput Chem 2023; 44:2486-2500. [PMID: 37650712 DOI: 10.1002/jcc.27213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic-scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n(FeS2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe(II) sites that are connected via a range of persulfide (S2 2- ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS2 units, we established guidelines for obtaining low-energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano-reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron-transfer reactions can occur.
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Affiliation(s)
- Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Attila Taborosi
- Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, Nagano, Japan
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Robert K Szilagyi
- Department of Chemistry, The University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
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Chatterjee S, Jain CK, Saha T, Roychoudhury S, Majumder HK, Das S. Utilizing coordination chemistry through formation of a Cu II-quinalizarin complex to manipulate cell biology: An in vitro, in silico approach. J Inorg Biochem 2023; 249:112369. [PMID: 37776829 DOI: 10.1016/j.jinorgbio.2023.112369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/02/2023]
Abstract
Quinalizarin, an analogue of anthracycline anticancer agents, is an anticancer agent itself. A CuII complex was prepared and characterized by elemental analysis, UV-Vis & IR spectroscopy, mass spectrometry, EPR and DFT. The intention behind the preparation of the complex was to increase cellular uptake, compare its binding with DNA against that of quinalizarin, modulation of semiquinone formation, realization of human DNA topoisomerase I & human DNA topoisomerase II inhibition and observation of anticancer activity. While the first two attributes of complex formation lead to increased efficacy, decrease in semiquinone generation could results in a compromise with efficacy. Inhibition of human DNA topoisomerase makes up this envisaged compromise in free radical activity since the complex shows remarkable ability to disrupt activities of human DNA topoisomerase I and II. The complex unlike quinalizarin, does not catalyze flow of electrons from NADH to O2 to the extent known for quinalizarin. Hence, decrease in semiquinone or superoxide radical anion could make modified quinalizarin [as CuII complex] less efficient in free radical pathway. However, it would be less cardiotoxic and that would be advantageous to qualify it as a better anticancer agent. Although binding to calf thymus DNA was comparable to quinalizarin, it was weaker than anthracyclines. Low cost of quinalizarin could justify consideration as a substitute for anthracyclines but the study revealed IC50 of quinalizarin/CuII-quinalizarin was much higher than anthracyclines or their complexes. Even then, there is a possibility that CuII-quinalizarin could be an improved and less costly form of quinalizarin as anticancer agent.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India; Department of Chemistry, Vijaygarh Jyotish Ray College, Kolkata 700 032, India
| | - Chetan Kumar Jain
- Cancer Biology & Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata 700 032, India; Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Tanmoy Saha
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India
| | - Susanta Roychoudhury
- Cancer Biology & Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta Kumar Majumder
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Saurabh Das
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India.
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Saini A, Das C, Rai S, Guha A, Dolui D, Majumder P, Dutta A. A homogeneous cobalt complex mediated electro and photocatalytic O 2/H 2O interconversion in neutral water. iScience 2023; 26:108189. [PMID: 37920669 PMCID: PMC10618691 DOI: 10.1016/j.isci.2023.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/25/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
The O2/H2O redox couple is vital in various renewable energy conversion strategies. This work delves into the Co(L-histidine)2 complex, a functional mimic of oxygen-carrying metalloproteins, and its electrochemical behavior driving the bidirectional oxygen reduction (ORR) and oxygen evolution (OER) activity in neutral water. This complex electrocatalyzes O2 via two distinct pathways: a two-electron O2/H2O2 reduction (catalytic rate = 250 s-1) and a four-electron O2 to H2O production (catalytic rate = 66 s-1). The formation of the key trans-μ-1,2-Co(III)-peroxo intermediate expedites this process. Additionally, this complex effectively oxidizes water to O2 (catalytic rate = 15606 s-1) at anodic potentials via a Co(IV)-oxo species. Additionally, this complex executes the ORR and OER under photocatalytic conditions in neutral water in the presence of appropriate photosensitizer (Eosin-Y) and redox mediators (triethanolamine/ORR and Na2S2O8/OER) at an appreciable rate. These results highlight one of the early examples of both electro- and photoactive bidirectional ORR/OER catalysts operational in neutral water.
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Affiliation(s)
- Abhishek Saini
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chandan Das
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Surabhi Rai
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- National Center of Excellence in CCU, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Aritra Guha
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Dependu Dolui
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Piyali Majumder
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Arnab Dutta
- Chemistry Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Interdisciplinary Program in Climate Studies, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- National Center of Excellence in CCU, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Forero N, Liu C, Sabbah SG, Loewen MC, Yang TC. Assay Development for Metal-Dependent Enzymes-Influence of Reaction Buffers on Activities and Kinetic Characteristics. ACS OMEGA 2023; 8:40119-40127. [PMID: 37929113 PMCID: PMC10620931 DOI: 10.1021/acsomega.3c02835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023]
Abstract
Buffers are often thought of as innocuous components of a reaction, with the sole task of maintaining the pH of a system. However, studies had shown that this is not always the case. Common buffers used in biochemical research, such as Tris (hydroxymethyl) aminomethane hydrochloride (Tris-HCl), can chelate metal ions and may thus affect the activity of metalloenzymes, which are enzymes that require metal ions for enhanced catalysis. To determine whether enzyme activity is influenced by buffer identity, the activity of three enzymes (BLC23O, Ro1,2-CTD, and trypsin) was comparatively characterized in N-2- hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES), Tris-HCl, and sodium phosphate buffer. The pH and temperature optima of BLC23O, a Mn2+-dependent dioxygenase, were first identified, and then the metal ion dissociation constant (Kd) was determined in the three buffer systems. It was observed that BLC23O exhibited different Kd values depending on the buffer, with the lowest (1.49 ± 0.05 μM) recorded in HEPES under the optimal set of conditions (pH 7.6 and 32.5 °C). Likewise, the kinetic parameters obtained varied depending on the buffer, with HEPES (pH 7.6) yielding overall the greatest catalytic efficiency and turnover number (kcat = 0.45 ± 0.01 s-1; kcat/Km = 0.84 ± 0.02 mM-1 s-1). To corroborate findings, the characterization of Fe3+-dependent Ro1,2-CTD was performed, resulting in different kinetic constants depending on the buffer (Km (HEPES, Tris-HCl, and Na-phosphate) = 1.80, 6.93, and 3.64 μM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 0.64, 1.14, and 1.01 s-1; kcat/Km(HEPES, Tris-HCl, and Na-phosphate)= 0.36, 0.17, and 0.28 μM-1 s-1). In order to determine whether buffer identity influenced the enzymatic activity of nonmetalloenzymes alike, the characterization of trypsin was also carried out. Contrary to the previous results, trypsin yielded comparable kinetic parameters independent of the buffer (Km (HEPES, Tris-HCl, and Na-Phosphate) = 3.14, 3.07, and 2.91 mM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 1.51, 1.47, and 1.53 s-1; kcat/Km (HEPES, Tris-HCl, and Na-phosphate) = 0.48, 0.48, and 0.52 mM-1 s-1). These results showed that the activity of tested metalloenzymes was impacted by different buffers. While selected buffers did not influence the tested nonmetalloenzyme activity, other research had shown impacts of buffers on other enzyme activities. As a result, we suggest that buffer selection be optimized for any new enzymes such that the results from one lab to another can be accurately compared.
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Affiliation(s)
- Natalia Forero
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Chengsong Liu
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
| | | | - Michele C. Loewen
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
| | - Trent Chunzhong Yang
- Aquatic
and Crop Resource Development Research Centre, National Research Council, Ottawa K1A 0R6, Canada
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Dai Y, Zhou Z, Kim K, Rivera N, Mohammed J, Hsu-Kim H, Chilkoti A, You L. Global control of cellular physiology by biomolecular condensates through modulation of electrochemical equilibria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563018. [PMID: 37904914 PMCID: PMC10614965 DOI: 10.1101/2023.10.19.563018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Control of the electrochemical environment in living cells is typically attributed to ion channels. Here we show that the formation of biomolecular condensates can modulate the electrochemical environment in cells, which affects processes globally within the cell and interactions of the cell with its environment. Condensate formation results in the depletion or enrichment of certain ions, generating intracellular ion gradients. These gradients directly affect the electrochemical properties of a cell, including the cytoplasmic pH and hyperpolarization of the membrane potential. The modulation of the electrochemical equilibria between the intra- and extra-cellular environments by biomolecular condensates governs charge-dependent uptake of small molecules by cells, and thereby directly influences bacterial survival under antibiotic stress. The shift of the intracellular electrochemical equilibria by condensate formation also drives a global change of the gene expression profile. The control of the cytoplasmic environment by condensates is correlated with their volume fraction, which can be highly variable between cells due to the stochastic nature of gene expression at the single cell level. Thus, condensate formation can amplify cell-cell variability of the environmental effects induced by the shift of cellular electrochemical equilibria. Our work reveals new biochemical functions of condensates, which extend beyond the biomolecules driving and participating in condensate formation, and uncovers a new role of biomolecular condensates in cellular regulation.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, 63130
| | - Zhengqing Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
| | - Nelson Rivera
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC, 27705
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Center for Quantitative Biodesign, Duke University, Durham, NC 27708
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Center for Quantitative Biodesign, Duke University, Durham, NC 27708
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
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Chatterjee A, Mondal P, Chakraborty P, Kumar B, Mandal S, Rizzoli C, Saha R, Adhikary B, Dey SK. Strategic Synthesis of Heptacoordinated Fe III Bifunctional Complexes for Efficient Water Electrolysis. Angew Chem Int Ed Engl 2023; 62:e202307832. [PMID: 37477221 DOI: 10.1002/anie.202307832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023]
Abstract
In this research, highly efficient heterogeneous bifunctional (BF) electrocatalysts (ECs) have been strategically designed by Fe coordination (CR ) complexes, [Fe2 L2 (H2 O)2 Cl2 ] (C1) and [Fe2 L2 (H2 O)2 (SO4 )].2(CH4 O) (C2) where the high seven CR number synergistically modifies the electronic environment of the Fe centre for facilitation of H2 O electrolysis. The electronic status of Fe and its adjacent atomic sites have been further modified by the replacement of -Cl- in C1 by -SO4 2- in C2. Interestingly, compared to C1, the O-S-O bridged C2 reveals superior BF activity with extremely low overpotential (η) at 10 mA cm-2 (140 mVOER , 62 mVHER ) and small Tafel slope (120.9 mV dec-1 OER , 45.8 mV dec-1 HER ). Additionally, C2 also facilitates a high-performance alkaline H2 O electrolyzer with cell voltage of 1.54 V at 10 mA cm-2 and exhibits remarkable long-term stability. Thus, exploration of the intrinsic properties of metal-organic framework (MOF)-based ECs opens up a new approach to the rational design of a wide range of molecular catalysts.
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Affiliation(s)
| | - Papri Mondal
- Department of Chemistry, Indian Institution of Engineering Science and Technology, 711103, Shibpur, Howrah, India
| | - Priyanka Chakraborty
- Department of Chemistry, Sidho-Kanho-Birsha University, 723104, Purulia, WB, India
| | - Bidyapati Kumar
- Department of Chemistry, Sidho-Kanho-Birsha University, 723104, Purulia, WB, India
| | - Sourav Mandal
- Department of Chemistry, Sidho-Kanho-Birsha University, 723104, Purulia, WB, India
| | - Corrado Rizzoli
- Dipartimento S.C.V.S.A., Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Rajat Saha
- Department of Chemistry, Kazi Nazrul University, 713340, Asansol, WB, India
| | - Bibhutosh Adhikary
- Department of Chemistry, Indian Institution of Engineering Science and Technology, 711103, Shibpur, Howrah, India
| | - Subrata K Dey
- Department of Chemistry, Sidho-Kanho-Birsha University, 723104, Purulia, WB, India
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Kähler S, Cebreiro-Gallardo A, Pokhilko P, Casanova D, Krylov AI. State-Interaction Approach for Evaluating g-Tensors within EOM-CC and RAS-CI Frameworks: Theory and Benchmarks. J Phys Chem A 2023; 127:8459-8472. [PMID: 37774315 DOI: 10.1021/acs.jpca.3c04134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Among various techniques designed for studying open-shell species, electron paramagnetic resonance (EPR) spectroscopy plays an important role. The key quantity measured by EPR is the g-tensor, describing the coupling between an external magnetic field and molecular electronic spin. One theoretical framework for quantum chemistry calculations of g-tensors is based on response theory, which involves substantial developments that are specific to the underlying electronic structure models. A simplified and easier-to-implement approach is based on the state-interaction scheme, in which perturbation is included by considering a small number of states. We describe and benchmark the state-interaction approach using equation-of-motion coupled-cluster and restricted-active-space configuration interaction wave functions. The analysis confirms that this approach can deliver accurate results and highlights caveats of applying it, such as a choice of the reference state, convergence with respect to the number of states used in calculations, etc. The analysis also contributes toward a better understanding of challenges in calculations of higher-order properties using approximate wave functions.
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Affiliation(s)
- Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - David Casanova
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Euskadi, Spain
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Janisse SE, Fernandez RL, Heffern MC. Characterizing metal-biomolecule interactions by mass spectrometry. Trends Biochem Sci 2023; 48:815-825. [PMID: 37433704 DOI: 10.1016/j.tibs.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism's health. The labile nature of metal-biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal-biomolecule interactions.
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Affiliation(s)
- Samuel E Janisse
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Rebeca L Fernandez
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Marie C Heffern
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA.
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42
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Chen J, Calderone LA, Pan L, Quist T, Pandelia ME. The Fe and Zn cofactor dilemma. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140931. [PMID: 37353133 DOI: 10.1016/j.bbapap.2023.140931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
Fe and Zn ions are essential enzymatic cofactors across all domains of life. Fe is an electron donor/acceptor in redox enzymes, while Zn is typically a structural element or catalytic component in hydrolases. Interestingly, the presence of Zn in oxidoreductases and Fe in hydrolases challenge this apparent functional dichotomy. In hydrolases, Fe either substitutes for Zn or specifically catalyzes certain reactions. On the other hand, Zn can replace divalent Fe and substitute for more complex Fe assemblies, known as Fe-S clusters. Although many zinc-binding proteins interchangeably harbor Zn and Fe-S clusters, these cofactors are only sometimes functional proxies.
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Affiliation(s)
- Jiahua Chen
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Logan A Calderone
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Luying Pan
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Trent Quist
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
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43
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Kim B, Karlin KD. Ligand-Copper(I) Primary O 2-Adducts: Design, Characterization, and Biological Significance of Cupric-Superoxides. Acc Chem Res 2023; 56:2197-2212. [PMID: 37527056 PMCID: PMC11152209 DOI: 10.1021/acs.accounts.3c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
In this Account, we overview and highlight synthetic bioinorganic chemistry focused on initial adducts formed from the reaction of reduced ligand-copper(I) coordination complexes with molecular oxygen, reactions that produce ligand-CuII(O2•-) complexes (O2•- ≡ superoxide anion). We provide mostly a historical perspective, starting in the Karlin research group in the 1980s, emphasizing the ligand design and ligand effects, structure, and spectroscopy of these O2 adducts and subsequent further reactivity with substrates, including the interaction with a second ligand-CuI complex to form binuclear species. The Account emphasizes the approach, evolution, and results obtained in the Karlin group, a synthetic bioinorganic research program inspired by the state of knowledge and insights obtained on enzymes possessing copper ion active sites which process molecular oxygen. These constitute an important biochemistry for all levels/types of organisms, bacteria, fungi, insects, and mammals, including humans.Copper is earth abundant, and its redox properties in complexes allow for facile CuII/CuI interconversions. Simple salts or coordination complexes have been well known to serve as oxidants for the stoichiometric or catalytic oxidation or oxygenation (i.e., O-atom insertion) of organic substrates. Thus, copper dioxygen- or peroxide-centered synthetic bioinorganic studies provide strong relevance and potential application to synthesis or even the development of cathodic catalysts for dioxygen reduction to hydrogen peroxide or water, as in fuel cells. The Karlin group's focus however was primarily oriented toward bioinorganic chemistry with the goal to provide fundamental insights into the nature of copper-dioxygen adducts and further reduced and/or protonated derivatives, species likely occurring in enzyme turnover or related in one or more aspects of formation, structure, spectroscopic properties, and scope of reactivity toward organic/biochemical substrates.Prior to this time, the 1980s, O2 adducts of redox-active first-row transition-metal ions focused on iron, such as the porphyrinate-Fe centers occurring in the oxygen carrier proteins myoglobin and hemoglobin and that determined to occur in cytochrome P-450 monooxygenase turnover. Deoxy (i.e., reduced Fe(II)) heme proteins react with O2, giving FeIII-superoxo complexes (preferably referred to by traditional biochemists as ferrous-oxy species). And, it was in the 1970s that great strides were made by synthetic chemists in generating hemes capable of forming O2 adducts, their physiochemical characterization providing critical insights to enzyme (bio)chemistry and providing ideas and important goals leading to countless person years of future research.
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Affiliation(s)
- Bohee Kim
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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Hoffnagle AM, Tezcan FA. Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries. J Am Chem Soc 2023; 145:14208-14214. [PMID: 37352018 PMCID: PMC10439731 DOI: 10.1021/jacs.3c04047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
We report a new computational protein design method for the construction of oligomeric protein assemblies around metal centers with predefined coordination geometries. We apply this method to design two homotrimeric assemblies, Tet4 and TP1, with tetrahedral and trigonal-pyramidal tris(histidine) metal coordination geometries, respectively, and demonstrate that both assemblies form the targeted metal centers with ≤0.2 Å accuracy. Although Tet4 and TP1 are constructed from the same parent protein building block, they are distinct in terms of their overall architectures, the environment surrounding the metal centers, and their metal-based reactivities, illustrating the versatility of our approach.
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Affiliation(s)
- Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
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45
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Zhang L, Wang P, Zhou XQ, Bretin L, Zeng X, Husiev Y, Polanco EA, Zhao G, Wijaya LS, Biver T, Le Dévédec SE, Sun W, Bonnet S. Cyclic Ruthenium-Peptide Conjugates as Integrin-Targeting Phototherapeutic Prodrugs for the Treatment of Brain Tumors. J Am Chem Soc 2023. [PMID: 37379365 DOI: 10.1021/jacs.3c04855] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
To investigate the potential of tumor-targeting photoactivated chemotherapy, a chiral ruthenium-based anticancer warhead, Λ/Δ-[Ru(Ph2phen)2(OH2)2]2+, was conjugated to the RGD-containing Ac-MRGDH-NH2 peptide by direct coordination of the M and H residues to the metal. This design afforded two diastereoisomers of a cyclic metallopeptide, Λ-[1]Cl2 and Δ-[1]Cl2. In the dark, the ruthenium-chelating peptide had a triple action. First, it prevented other biomolecules from coordinating with the metal center. Second, its hydrophilicity made [1]Cl2 amphiphilic so that it self-assembled in culture medium into nanoparticles. Third, it acted as a tumor-targeting motif by strongly binding to the integrin (Kd = 0.061 μM for the binding of Λ-[1]Cl2 to αIIbβ3), which resulted in the receptor-mediated uptake of the conjugate in vitro. Phototoxicity studies in two-dimensional (2D) monolayers of A549, U87MG, and PC-3 human cancer cell lines and U87MG three-dimensional (3D) tumor spheroids showed that the two isomers of [1]Cl2 were strongly phototoxic, with photoindexes up to 17. Mechanistic studies indicated that such phototoxicity was due to a combination of photodynamic therapy (PDT) and photoactivated chemotherapy (PACT) effects, resulting from both reactive oxygen species generation and peptide photosubstitution. Finally, in vivo studies in a subcutaneous U87MG glioblastoma mice model showed that [1]Cl2 efficiently accumulated in the tumor 12 h after injection, where green light irradiation generated a stronger tumoricidal effect than a nontargeted analogue ruthenium complex [2]Cl2. Considering the absence of systemic toxicity for the treated mice, these results demonstrate the high potential of light-sensitive integrin-targeted ruthenium-based anticancer compounds for the treatment of brain cancer in vivo.
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Affiliation(s)
- Liyan Zhang
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Peiyuan Wang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
- Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, P. R. China
| | - Xue-Quan Zhou
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Ludovic Bretin
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Xiaolong Zeng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Yurii Husiev
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Ehider A Polanco
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Gangyin Zhao
- Leiden Institute of Biology, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Lukas S Wijaya
- Leiden Academic Centre for Drug Research, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Sylvia E Le Dévédec
- Leiden Academic Centre for Drug Research, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Universiteit Leiden, Einsteinweg 55, 2333 CC Leiden, Netherlands
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46
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Azhar BJ, Abbas S, Aman S, Yamburenko MV, Chen W, Müller L, Uzun B, Jewell DA, Dong J, Shakeel SN, Groth G, Binder BM, Grigoryan G, Schaller GE. Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2215195120. [PMID: 37253004 PMCID: PMC10266040 DOI: 10.1073/pnas.2215195120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
The gaseous hormone ethylene is perceived in plants by membrane-bound receptors, the best studied of these being ETR1 from Arabidopsis. Ethylene receptors can mediate a response to ethylene concentrations at less than one part per billion; however, the mechanistic basis for such high-affinity ligand binding has remained elusive. Here we identify an Asp residue within the ETR1 transmembrane domain that plays a critical role in ethylene binding. Site-directed mutation of the Asp to Asn results in a functional receptor that has a reduced affinity for ethylene, but still mediates ethylene responses in planta. The Asp residue is highly conserved among ethylene receptor-like proteins in plants and bacteria, but Asn variants exist, pointing to the physiological relevance of modulating ethylene-binding kinetics. Our results also support a bifunctional role for the Asp residue in forming a polar bridge to a conserved Lys residue in the receptor to mediate changes in signaling output. We propose a new structural model for the mechanism of ethylene binding and signal transduction, one with similarities to that found in a mammalian olfactory receptor.
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Affiliation(s)
- Beenish J. Azhar
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Safdar Abbas
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Sitwat Aman
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | | | - Wei Chen
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | - Lena Müller
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - Buket Uzun
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - David A. Jewell
- Department of Computer Science, Dartmouth College, Hanover, NH03755
| | - Jian Dong
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | - Samina N. Shakeel
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - Brad M. Binder
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN37996
| | - Gevorg Grigoryan
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Computer Science, Dartmouth College, Hanover, NH03755
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
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47
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Selyutina OY, Timoshnikov VA, Polyakov NE, Kontoghiorghes GJ. Metal Complexes of Omadine ( N-Hydroxypyridine-2-thione): Differences of Antioxidant and Pro-Oxidant Behavior in Light and Dark Conditions with Possible Toxicity Implications. Molecules 2023; 28:molecules28104210. [PMID: 37241949 DOI: 10.3390/molecules28104210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Omadine or N-hydroxypyridine-2-thione and its metal complexes are widely used in medicine and show bactericidal, fungicidal, anticancer, and photochemical activity. The redox activity of omadine complexes with iron, copper, and zinc on lipid peroxidation under light and dark conditions has been investigated. The monitoring of the oxidation of linoleic acid micelles, resembling a model of lipid membrane, was carried out using nuclear magnetic resonance (1H-NMR). It has been shown that the omadine-zinc complex can induce the oxidation of linoleic acid under light irradiation, whereas the complexes with iron and copper are photochemically stable. All the chelating complexes of omadine appear to be redox-inactive in the presence of hydrogen peroxide under dark conditions. These findings suggest that omadine can demonstrate antioxidant behavior in processes involving reactive oxygen species generation induced by transition metals (Fenton and photo-Fenton reactions). However, the omadine complex with zinc, which is widely used in shampoos and ointments, is photochemically active and may cause oxidative cell membrane damage when exposed to light, with possible implications to health.
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Affiliation(s)
- Olga Yu Selyutina
- Institute of Chemical Kinetics & Combustion, 630090 Novosibirsk, Russia
- Institute of Solid Chemistry and Mechanochemistry, 630090 Novosibirsk, Russia
| | | | - Nikolay E Polyakov
- Institute of Chemical Kinetics & Combustion, 630090 Novosibirsk, Russia
- Institute of Solid Chemistry and Mechanochemistry, 630090 Novosibirsk, Russia
| | - George J Kontoghiorghes
- Postgraduate Research Institute of Science, Technology, Environment and Medicine, CY-3021 Limassol, Cyprus
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48
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Liu T, Zhan S, Shen N, Wang L, Szabó Z, Yang H, Ahlquist MSG, Sun L. Bioinspired Active Site with a Coordination-Adaptive Organosulfonate Ligand for Catalytic Water Oxidation at Neutral pH. J Am Chem Soc 2023; 145:11818-11828. [PMID: 37196315 DOI: 10.1021/jacs.3c03415] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Many enzymes use adaptive frameworks to preorganize substrates, accommodate various structural and electronic demands of intermediates, and accelerate related catalysis. Inspired by biological systems, a Ru-based molecular water oxidation catalyst containing a configurationally labile ligand [2,2':6',2″-terpyridine]-6,6″-disulfonate was designed to mimic enzymatic framework, in which the sulfonate coordination is highly flexible and functions as both an electron donor to stabilize high-valent Ru and a proton acceptor to accelerate water dissociation, thus boosting the catalytic water oxidation performance thermodynamically and kinetically. The combination of single-crystal X-ray analysis, various temperature NMR, electrochemical techniques, and DFT calculations was utilized to investigate the fundamental role of the self-adaptive ligand, demonstrating that the on-demand configurational changes give rise to fast catalytic kinetics with a turnover frequency (TOF) over 2000 s-1, which is compared to oxygen-evolving complex (OEC) in natural photosynthesis.
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Affiliation(s)
- Tianqi Liu
- Department of Chemistry, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Shaoqi Zhan
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
| | - Nannan Shen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 215123 Suzhou, China
| | - Linqin Wang
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, 310024 Hangzhou, China
| | - Zoltán Szabó
- Department of Chemistry, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Hao Yang
- Department of Chemistry, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Mårten S G Ahlquist
- Department of Chemistry, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Licheng Sun
- Department of Chemistry, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, 310024 Hangzhou, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology (DUT), Dalian 116024, China
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49
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Kircheva N, Angelova S, Dobrev S, Petkova V, Nikolova V, Dudev T. Cu +/Ag + Competition in Type I Copper Proteins (T1Cu). Biomolecules 2023; 13:biom13040681. [PMID: 37189429 DOI: 10.3390/biom13040681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Vladislava Petkova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
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50
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Jeong D, Selverstone Valentine J, Cho J. Bio-inspired mononuclear nonheme metal peroxo complexes: Synthesis, structures and mechanistic studies toward understanding enzymatic reactions. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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