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Sitek P, Lodowski P, Jaworska M. Mechanism of Methyl Transfer Reaction between CH 3Co(dmgBF 2) 2py and PPh 3Ni(Triphos). Molecules 2024; 29:3335. [PMID: 39064913 PMCID: PMC11280430 DOI: 10.3390/molecules29143335] [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: 04/23/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.
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Affiliation(s)
| | | | - Maria Jaworska
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, 40-006 Katowice, Poland (P.L.)
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2
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Biswas S, Chowdhury SN, Lepcha P, Sutradhar S, Das A, Paine TK, Paul S, Biswas AN. Electrochemical generation of high-valent oxo-manganese complexes featuring an anionic N5 ligand and their role in O-O bond formation. Dalton Trans 2023; 52:16616-16630. [PMID: 37882084 DOI: 10.1039/d3dt02740f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Generation of high-valent oxomanganese complexes through controlled removal of protons and electrons from low-valent congeners is a crucial step toward the synthesis of functional analogues of the native oxygen evolving complex (OEC). In-depth studies of the water oxidation activity of such biomimetic compounds help in understanding the mechanism of O-O bond formation presumably occurring in the last step of the photosynthetic cycle. Scarce reports of reactive high-valent oxomanganese complexes underscore the impetus for the present work, wherein we report the electrochemical generation of the non-heme oxomanganese(IV) species [(dpaq)MnIV(O)]+ (2) through a proton-coupled electron transfer (PCET) process from the hydroxomanganese complex [(dpaq)MnIII(OH)]ClO4 (1). Controlled potential spectroelectrochemical studies of 1 in wet acetonitrile at 1.45 V vs. NHE revealed quantitative formation of 2 within 10 min. The high-valent oxomanganese(IV) transient exhibited remarkable stability and could be reverted to the starting complex (1) by switching the potential to 0.25 V vs. NHE. The formation of 2via PCET oxidation of 1 demonstrates an alternate pathway for the generation of the oxomanganese(IV) transient (2) without the requirement of redox-inactive metal ions or acid additives as proposed earlier. Theoretical studies predict that one-electron oxidation of [(dpaq)MnIV(O)]+ (2) forms a manganese(V)-oxo (3) species, which can be oxidized further by one electron to a formal manganese(VI)-oxo transient (4). Theoretical analyses suggest that the first oxidation event (2 to 3) takes place at the metal-based d-orbital, whereas, in the second oxidation process (3 to 4), the electron eliminates from an orbital composed of equitable contribution from the metal and the ligand, leaving a single electron in the quinoline-dominant orbital in the doublet ground spin state of the manganese(VI)-oxo species (4). This mixed metal-ligand (quinoline)-based oxidation is proposed to generate a formal Mn(VI) species (4), a non-heme analogue of the species 'compound I', formed in the catalytic cycle of cytochrome P-450. We propose that the highly electrophilic species 4 catches water during cyclic voltammetry experiments and results in O-O bond formation leading to electrocatalytic oxidation of water to hydrogen peroxide.
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Affiliation(s)
- Sachidulal Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, Sikkim 737139, India.
| | - Srijan Narayan Chowdhury
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, Sikkim 737139, India.
| | - Panjo Lepcha
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, Sikkim 737139, India.
| | - Subhankar Sutradhar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Abhishek Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapan Kanti Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Satadal Paul
- Department of Chemistry, Bangabasi Morning College, 19, Rajkumar Chakraborty Sarani, Kolkata-700009, India
| | - Achintesh N Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, Sikkim 737139, India.
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3
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Reid AG, Moberg ME, Koellner CA, Machan CW, Thornton DA, Dickenson JC, Stober JJ, Turner DA, Tarring TJ, Brown CA, Harrison DP. Sterically attenuated electronic communication in cobalt complexes of meridional isoquinoline-derived ligands for applications in electrocatalysis. J Chem Phys 2023; 159:194306. [PMID: 37982482 DOI: 10.1063/5.0174177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023] Open
Abstract
The ability to synthetically tune the ligand frameworks of redox-active molecules is of critical importance to the economy of solar fuels because manipulating their redox properties can afford control over the operating potentials of sustained electrocatalytic or photoelectrocatalytic processes. The electronic and steric properties of 2,2':6',2″-terpyridine (Terpy) ligand frameworks can be tuned by functional group substitution on ligand backbones, and these correlate strongly to their Hammett parameters. The synthesis of a new series of tridentate meridional ligands of 2,4,6-trisubstituted pyridines that engineers the ability to finely tune the redox potentials of cobalt complexes to more positive potentials than that of their Terpy analogs is achieved by aryl-functionalizing at the four-position and by including isoquinoline at the two- and six-positions of pyridine (Aryl-DiQ). Their cobalt complex syntheses, their electronic properties, and their catalytic activity for carbon dioxide (CO2) reduction are reported and compared to their Terpy analogs. The cobalt derivatives generally experience a positive shift in their redox features relative to the Terpy-based analogs, covering a complementary potential range. Although those evaluated fail to produce any quantifiable products for the reduction of CO2 and suffer from long-term instability, these results suggest possible alternate strategies for stabilizing these compounds during catalysis. We speculate that lower equilibrium association constants to the cobalt center are intrinsic to these ligands, which originate from a steric interaction between protons on the pyridine and isoquinoline moieties. Nevertheless, the new Aryl-DiQ ligand framework has been engineered to selectively tune homoleptic cobalt complexes' redox potentials.
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Affiliation(s)
- Amelia G Reid
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, USA
| | - Megan E Moberg
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, USA
| | - Connor A Koellner
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, USA
| | - Charles W Machan
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, USA
| | - Diana A Thornton
- Virginia Tech, Department of Chemistry, Blacksburg, Virginia 24060, USA
| | - John C Dickenson
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
| | - Jeffry J Stober
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
| | - David A Turner
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
| | - Travis J Tarring
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
| | - Caleb A Brown
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
| | - Daniel P Harrison
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, USA
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4
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Thomas J, Goldberg DP. Factors controlling the reactivity of synthetic compound-I Analogs. J PORPHYR PHTHALOCYA 2023; 27:1489-1501. [PMID: 39132380 PMCID: PMC11308481 DOI: 10.1142/s1088424623300136] [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] [Indexed: 08/13/2024]
Abstract
A high-valent iron(IV)-oxo porphyrin radical cation (FeIV(O)(porph+•) serves as a key, reactive intermediate for a range of heme enzymes, including cytochrome P450 (CYP), horseradish peroxidase (HRP), and catalase (CAT). Synthetic analogs of this intermediate, known as Compound-I (Cpd-I) in the heme enzyme literature, have been generated with different tetrapyrrolic, macrocyclic ligands, including porphyrin derivatives, and the closely related ring-contracted macrocycles, corroles and corrolazines. These synthetic analogs have been useful for assigning and understanding structural and spectroscopic features and examining the reactivity of Cpd-I-like species in controlled and well-defined environments. This review focuses on summarizing recent developments in the synthesis and reactivity of high-valent iron-oxo porphyrinoid complexes in two main classes of reactions, proton-coupled electron transfer (PCET) and oxygen atom transfer (OAT). The relationship between the structure of the complexes and their reactivity is emphasized, including the influence of axial ligation and peripheral macrocyclic substitution, as well as the effects of solvent and secondary coordination spheres on the reactivity of the Cpd-I analogs. In bringing together the latest findings on Cpd-I analogs, this review intends to broaden our current understanding of the factors that control the stability and reactivity of Cpd-I species. This new knowledge should, in turn, point toward new synthetic strategies for constructing catalysts that rely on Cpd-I-like reactive intermediates.
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Affiliation(s)
- Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400N. Charles Street, Baltimore, Maryland 21218, USA
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400N. Charles Street, Baltimore, Maryland 21218, USA
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5
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Zhao H, Pan Y, Lau KC. Ferrocene/ferrocenium, cobaltocene/cobaltocenium and nickelocene/nickelocenium: from gas phase ionization energy to one-electron reduction potential in solvated medium. Phys Chem Chem Phys 2023. [PMID: 37325896 DOI: 10.1039/d3cp01904g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We propose a theoretical procedure for accurate determination of reduction potentials for three metallocene couples, Cp2M+/Cp2M, where M = Fe, Co and Ni. This procedure first computes the gas phase ionization energy (IE) using the explicitly correlated CCSD(T)-F12 method and includes the zero-point energy correction, core-valence electronic correlation, and relativistic and spin-orbit coupling effects. By means of Born-Haber thermochemical cycle, the one-electron reduction potential is obtained as the sum of the gas phase IE and the corresponding Gibbs free energies of solvation (ΔGsolv) for both the neutral and cationic species. Among the three solvent models (PCM, SMD and uESE) investigated here, it turns out that only the SMD model (computed at the DFT level) gives the best estimation of the value for "ΔGsolv(cation) - ΔGsolv(neutral)" and thus, combining with the accurate IE values, the theoretical protocol is capable of yielding reliable values (in V) for , and . These predictions compare favorably with the available experimental data (in V): , , and . We show that our theoretical procedure is reliable for accurate reduction potential predictions of Cp2Fe+/Cp2Fe, Cp2Co+/Cp2Co and Cp2Ni+/Cp2Ni redox couples in aqueous and non-aqueous media; the maximum absolute deviation is as small as ≈120 mV, which outperforms those of the existing theoretical methods.
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Affiliation(s)
- Hongyan Zhao
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
| | - Yi Pan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
| | - Kai-Chung Lau
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
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6
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Raßpe-Lange L, Hoffmann A, Gertig C, Heck J, Leonhard K, Herres-Pawlis S. Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III). J Comput Chem 2023; 44:319-328. [PMID: 35640228 DOI: 10.1002/jcc.26927] [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: 02/16/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 01/03/2023]
Abstract
Copper guanidine-quinoline complexes are an important class of bioinorganic complexes that find utilization in electron and atom transfer processes. By substitution of functional groups on the quinoline moiety the electron transfer abilities of these complexes can be tuned. In order to explore the full substitution space by simulations, the accurate theoretical description of the effect of functional groups is essential. In this study, we compare three different methods for the theoretical description of the structures. We use the semi-empirical tight-binding method GFN2-xTB, the density functional TPSSh and the double-hybrid functional B2PLYP. We evaluate the methods on five different complex pairs (Cu(I) and Cu(II) complexes), and compare how well calculated energies can predict the redox potentials. We find even though B2PLYP and TPSSh yield better accordance with the experimental structures. GFN2-xTB performs surprisingly well in the geometry optimization at a fraction of the computational cost. TPSSh offers a good compromise between computational cost and accuracy of the redox potential for real-life complexes.
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Affiliation(s)
- Lukas Raßpe-Lange
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany
| | - Alexander Hoffmann
- Institute of Inorganic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Christoph Gertig
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany.,Pharmaplan AG, Basel, Switzerland
| | - Joshua Heck
- Institute of Inorganic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany
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7
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Holubowitch NE, Nguyen G. Dimerization of [Fe III(bpy) 3] 3+ in Aqueous Solutions: Elucidating a Mechanism Based on Historical Proposals, Electrochemical Data, and Computational Free Energy Analysis. Inorg Chem 2022; 61:9541-9556. [PMID: 35699660 DOI: 10.1021/acs.inorgchem.2c00640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron(II) tris-bipyridine, [FeII(bpy)3]2+, is a historically significant organometallic coordination complex with attractive redox and photophysical properties. With respect to energy storage, it is a low-cost, high-redox potential complex and thus attractive for use as a catholyte in aqueous redox flow batteries. Despite these favorable characteristics, its oxidized Fe(III) form undergoes dimerization to form μ-O-[FeIII(bpy)2(H2O)]24+, leading to a dramatic ∼0.7 V decrease during battery discharge. To date, the energetics and complete mechanism of this slow, sequential electrochemical-chemical (EC) process, which includes electron transfer, nucleophilic attack, ligand cleavage, μ-oxo bond formation, and spin state transition, have not been elucidated. Using cyclic voltammetry, redox flow battery data, and density functional theory calculations guided by previously proposed mechanisms, we modeled more than 100 complexes and performed more than 50 geometry scans to resolve the key steps dictating these complex chemical processes. Quantitative free energy surfaces are developed to model the mechanism of dimerization accounting for the spins and identities of any possible Fe(II), Fe(III), or Fe(IV) intermediates. Electrochemical reduction of the dimer regenerates [FeII(bpy)3]2+ in an overall reversible process. Computational electrochemistry interrogates the influence of spin state, coordination environment, and molecular conformation at the electrode-electrolyte interface through a proposed stepwise dimer reduction process. Experimentally, we show that the considerable overpotential associated with this event can be catalytically mitigated with disparate materials, including platinum, copper hexacyanoferrate, and activated carbon. The findings are of fundamental and applied significance and could elevate [FeII(bpy)3]2+ and its derivatives to play a vital role in the burgeoning renewable energy economy.
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Affiliation(s)
- Nicolas E Holubowitch
- Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, Texas 78412, United States
| | - Giang Nguyen
- Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, Texas 78412, United States
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8
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Borges-Martínez M, Montenegro-Pohlhammer N, Zhang X, Galvez-Aranda DE, Ponce V, Seminario JM, Cárdenas-Jirón G. Fullerene binding effects in Al(III)/Zn(II) Porphyrin/Phthalocyanine photophysical properties and charge transport. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120740. [PMID: 34968837 DOI: 10.1016/j.saa.2021.120740] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
We evaluate the fullerene C60 binding effect; through the metal (Al) and through the ligand (Pc,TPP), on the photophysical and charge transport properties of M-porphyrin(TPP)/phthalocyanine(Pc) (M = Al(III), Zn(II)). We perform density functional theory (DFT) and time-dependent DFT calculations for the macrocycle-C60 dyads, showing that all systems studied are thermodynamically favorable. The C60 binding effect on the absorption spectrum is a red-shift of the Q and Soret (B) bands of TPPs and Pcs. The Pc-dyads show longer λ for Q bands (673 nm) than those with TPP (568 nm). AlTPP-C60 and ZnTPP-C60 show a more favorable electron injection to TiO2 than the analogs Pcs, and the regeneration of the dye is preferred in AlTPP-C60 and AlPc-C60. Zero-bias conductance is computed (10-4-10-7 G0) for the dyads using molecular junctions with Au(111)-based electrodes. When a bias voltage of around 0.6 V up to 1 V is applied, an increase in current is obtained for AlTPP-C60 (10-7 A), ZnTPP-C60 (10-7 A), and AlPc-C60 (10-8 A). Although there is not a unique trend in the behavior of the dyads, Pcs have better photophysical properties than TPPs and the latter are better in the charge transport. We conclude that AlTPP(ZnTPP)-C60 dyads are an excellent alternative for designing new materials for dye-sensitized solar cells or optoelectronic devices.
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Affiliation(s)
- Merlys Borges-Martínez
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
| | - Nicolás Montenegro-Pohlhammer
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
| | - Xiance Zhang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Diego E Galvez-Aranda
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Victor Ponce
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Jorge M Seminario
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A.
| | - Gloria Cárdenas-Jirón
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
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9
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Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism. Catalysts 2022. [DOI: 10.3390/catal12020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.
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10
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Zeng J, Li Z, Jiang H, Wang X. Progress on photocatalytic semiconductor hybrids for bacterial inactivation. MATERIALS HORIZONS 2021; 8:2964-3008. [PMID: 34609391 DOI: 10.1039/d1mh00773d] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Due to its use of green and renewable energy and negligible bacterial resistance, photocatalytic bacterial inactivation is to be considered a promising sterilization process. Herein, we explore the relevant mechanisms of the photoinduced process on the active sites of semiconductors with an emphasis on the active sites of semiconductors, the photoexcited electron transfer, ROS-induced toxicity and interactions between semiconductors and bacteria. Pristine semiconductors such as metal oxides (TiO2 and ZnO) have been widely reported; however, they suffer some drawbacks such as narrow optical response and high photogenerated carrier recombination. Herein, some typical modification strategies will be discussed including noble metal doping, ion doping, hybrid heterojunctions and dye sensitization. Besides, the biosafety and biocompatibility issues of semiconductor materials are also considered for the evaluation of their potential for further biomedical applications. Furthermore, 2D materials have become promising candidates in recent years due to their wide optical response to NIR light, superior antibacterial activity and favorable biocompatibility. Besides, the current research limitations and challenges are illustrated to introduce the appealing directions and design considerations for the future development of photocatalytic semiconductors for antibacterial applications.
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Affiliation(s)
- Jiayu Zeng
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Ziming Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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11
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Dickenson JC, Haley ME, Hyde JT, Reid ZM, Tarring TJ, Iovan DA, Harrison DP. Fine-Tuning Metal and Ligand-Centered Redox Potentials of Homoleptic Bis-Terpyridine Complexes with 4'-Aryl Substituents. Inorg Chem 2021; 60:9956-9969. [PMID: 34160216 DOI: 10.1021/acs.inorgchem.1c01233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Homoleptic transition-metal complexes of 2,2':6',2″-terpyridine (terpy) and substituted derivatives of the form [M(R-terpy)2]2+ display a wide range of redox potentials that correlate well to the Hammett parameter of the terpy substituents. Less is known about the impact of incorporating a phenyl spacer between the functional group responsible for controlling the electron density of terpy and how that translates to metal complexes of the form [M(4'-aryl-terpy)2]2+, where M = Mn, Fe, Co, Ni, and Zn. Herein, we report our studies on these complexes revealed a good correlation of redox potentials of both metal- and ligand-centered events with the Hammett parameters of the aryl substituents, regardless of aryl-substitution pattern (i.e., the presence of multiple functional groups, combinations of withdrawing and donating functional groups). The phenyl spacer results in 60-80% attenuation of electron density as compared to the 4'-substituted terpy analogue, depending on the metal and redox couple analyzed. Density functional theory calculations performed on a simple model system revealed a strong correlation between the Hammett parameters and lowest unoccupied molecular orbital energies of the corresponding substituted pyridine models, thus serving as an inexpensive predictive tool when coupled with electrochemical data. Overall, these data suggest that such ligand modifications may be used in combination with previous approaches to further fine-tune the redox potentials of homoleptic transition-metal complexes, which may have applications in photochemical and electrochemical catalytic processes.
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Affiliation(s)
- John C Dickenson
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
| | - MacKenzie E Haley
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
| | - Jacob T Hyde
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
| | - Zachary M Reid
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
| | - Travis J Tarring
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
| | - Diana A Iovan
- Virginia Tech, Department of Chemistry, Blacksburg, Virginia 24060, United States
| | - Daniel P Harrison
- Virginia Military Institute, Department of Chemistry, Lexington, Virginia 24450, United States
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12
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Beerhues J, Neubrand M, Sobottka S, Neuman NI, Aberhan H, Chandra S, Sarkar B. Directed Design of a Au I Complex with a Reduced Mesoionic Carbene Radical Ligand: Insights from 1,2,3-Triazolylidene Selenium Adducts and Extensive Electrochemical Investigations. Chemistry 2021; 27:6557-6568. [PMID: 33502818 PMCID: PMC8252451 DOI: 10.1002/chem.202100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 11/07/2022]
Abstract
Carbene-based radicals are important for both fundamental and applied chemical research. Herein, extensive electrochemical investigations of nine different 1,2,3-triazolylidene selenium adducts are reported. It is found that the half-wave potentials of the first reduction of the selones correlate with their calculated LUMO levels and the LUMO levels of the corresponding triazolylidene-based mesoionic carbenes (MICs). Furthermore, unexpected quasi-reversibility of the reduction of two triazoline selones, exhibiting comparable reduction potentials, was discovered. Through UV/Vis/NIR and EPR spectroelectrochemical investigations supported by DFT calculations, the radical anion was unambiguously assigned to be triazoline centered. This electrochemical behavior was transferred to a triazolylidene-type MIC-gold phenyl complex resulting in a MIC-radical coordinated AuI species. Apart from UV-Vis-NIR and EPR spectroelectrochemical investigations of the reduction, the reduced gold-coordinated MIC radical complex was also formed in situ in the bulk through chemical reduction. This is the first report of a monodentate triazolylidene-based MIC ligand that can be reduced to its anion radical in a metal complex. The results presented here provide design principles for stabilizing radicals based on MICs.
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Affiliation(s)
- Julia Beerhues
- Lehrstuhl für Anorganische KoordinationschemieInstitut für Anorganische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
- Institut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 34–3614195BerlinGermany
| | - Maren Neubrand
- Lehrstuhl für Anorganische KoordinationschemieInstitut für Anorganische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Sebastian Sobottka
- Institut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 34–3614195BerlinGermany
| | - Nicolás I. Neuman
- Lehrstuhl für Anorganische KoordinationschemieInstitut für Anorganische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Hannes Aberhan
- Institut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 34–3614195BerlinGermany
| | - Shubhadeep Chandra
- Lehrstuhl für Anorganische KoordinationschemieInstitut für Anorganische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Biprajit Sarkar
- Lehrstuhl für Anorganische KoordinationschemieInstitut für Anorganische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
- Institut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 34–3614195BerlinGermany
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13
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Cheng C, Hayashi S. Ab Initio Evaluation of the Redox Potential of Cytochrome c. J Chem Theory Comput 2021; 17:1194-1207. [PMID: 33459006 DOI: 10.1021/acs.jctc.0c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various biochemical activities of metabolism and biosynthesis are fulfilled by redox processes with explicit electron exchange, which furnish redox enzymes with high chemical reactivity. However, theoretical investigation of a redox process, which simultaneously involves a complex electronic change at a redox metal center and conformational reorganization of the surrounding protein environment coupled to the electronic change, requires computationally conflicting approaches, highly accurate quantum chemical calculations, and long-time molecular dynamics (MD) simulations, limiting the physicochemical understanding of biological redox processes. Here, we theoretically examined a redox process of cytochrome c by means of a hybrid molecular simulation technique, which enables one to consistently treat the redox center at the ab initio quantum chemistry level of theory and the protein reorganization with long-time MD simulations on the microsecond timescale. The calculations successfully evaluated a large absolute redox potential, 4.34 eV, with errors of only 0.03 to 0.34 eV to the experimental ones without any problem-specific empirical parameters. Through the long-time MD sampling, large and nonlinear reorganization of the protein environment was unveiled and the molecular determinants for the redox potential were identified. The present ab initio approach significantly expands the applicability of theoretical investigation to biological redox systems with more electronically complicated redox centers such as polynuclear transition metal complexes.
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Affiliation(s)
- Cheng Cheng
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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14
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Borges-Martínez M, Montenegro-Pohlhammer N, Cárdenas-Jirón G. The bimetallic and the anchoring group effects on both optical and charge transport properties of hexaphyrin amethyrin. NEW J CHEM 2021. [DOI: 10.1039/d1nj00091h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bimetallic Cu(ii)-hexaphyrin amethyrin proposed as a molecular switch operated by the application of an external magnetic field.
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Affiliation(s)
- Merlys Borges-Martínez
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
| | - Nicolás Montenegro-Pohlhammer
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
| | - Gloria Cárdenas-Jirón
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
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15
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Wang D, Gardinier JR. The Electronic Properties of Ni(PNN) Pincer Complexes Modulate Activity in Catalytic Hydrodehalogenation Reactions. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Denan Wang
- Department of Chemistry Marquette University Milwaukee WI 53201‐1881 USA
| | - James R. Gardinier
- Department of Chemistry Marquette University Milwaukee WI 53201‐1881 USA
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16
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Neugebauer H, Bohle F, Bursch M, Hansen A, Grimme S. Benchmark Study of Electrochemical Redox Potentials Calculated with Semiempirical and DFT Methods. J Phys Chem A 2020; 124:7166-7176. [DOI: 10.1021/acs.jpca.0c05052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hagen Neugebauer
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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17
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Radzhabov MR, Sheremetev AB, Pivina TS. Oxidative ability of organic iodine(iii) reagents: a theoretical assessment. NEW J CHEM 2020. [DOI: 10.1039/d0nj00837k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational prediction of the oxidative ability of hypervalent iodine reagents was performed based on redox potentials, calculated at the B3LYP/6-311+G(d,p) level of theory with the SDD ECP46MDF pseudopotential for the iodine atom.
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Affiliation(s)
- Maxim R. Radzhabov
- N. D. Zelinsky Institute of Organic Chemistry
- Russian Academy of Sciences
- Moscow
- Russian Federation
| | - Aleksei B. Sheremetev
- N. D. Zelinsky Institute of Organic Chemistry
- Russian Academy of Sciences
- Moscow
- Russian Federation
| | - Tatyana S. Pivina
- N. D. Zelinsky Institute of Organic Chemistry
- Russian Academy of Sciences
- Moscow
- Russian Federation
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18
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Kim MJ, Kang YK. Predicting Potential Inversion Behavior of Ru–aqua Complexes via Using Cost Effective DFT Calculations. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Moon Ju Kim
- Department of ChemistrySangmyung University Seoul 03016 Korea
| | - Youn K. Kang
- Department of ChemistrySangmyung University Seoul 03016 Korea
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19
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Kuo JL, Gunasekara T, Hansen A, Vibbert HB, Bohle F, Norton JR, Grimme S, Quinlivan PJ. Thermodynamics of H+/H•/H–/e– Transfer from [CpV(CO)3H]−: Comparisons to the Isoelectronic CpCr(CO)3H. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan L. Kuo
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Thilina Gunasekara
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Hunter B. Vibbert
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jack R. Norton
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Patrick J. Quinlivan
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
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20
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Sitek P, Chmielowska A, Jaworska M, Lodowski P, Szczepańska M. Theoretical study of cobalt and nickel complexes involved in methyl transfer reactions: structures, redox potentials and methyl binding energies. Struct Chem 2019. [DOI: 10.1007/s11224-019-01384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Computational DFT study on nickel symmetric bis(thiosemicarbazone) complexes: Electronic absorption and redox potentials. Polyhedron 2019. [DOI: 10.1016/j.poly.2018.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Computational electrochemistry of a novel ferrocene derivative. J Mol Graph Model 2018; 85:84-90. [PMID: 30125780 DOI: 10.1016/j.jmgm.2018.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/23/2022]
Abstract
In this study, the structural and redox properties of a novel ferrocene derivative in dichlomethane solvent were investigated. For this aim, various exchange-correlation functionals and basis sets in gas phase with different continuum solvation models and cavities in liquid phase were applied. The results indicated that UM06/6-31++G(d,p)/SDD level of theory successfully calculated bond lengths and angles with MADs = 0.02 Å and 0.78 deg., respectively. Also, its combination with CPCM-Pauling-UHF/6-31+G(d)/SDD level of theory in liquid phase effectively computed the redox potential with 0.06 V deviation from the experimental value. Moreover, transferability of the proposed method was studied through ferrocene molecule and its new synthesized derivative.
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23
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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24
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Accurate Ionization Energies for Mononuclear Copper Complexes Remain a Challenge for Density Functional Theory. Chemphyschem 2018; 19:959-966. [DOI: 10.1002/cphc.201701334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/21/2022]
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25
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Burnea FKB, Shi H, Ko KC, Lee JY. Reduction potential tuning of first row transition metal MIII/MII (M = Cr, Mn, Fe, Co, Ni) hexadentate complexes for viable aqueous redox flow battery catholytes: A DFT study. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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27
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Götze JP, Bühl M. Laccase Redox Potentials: pH Dependence and Mutants, a QM/MM Study. J Phys Chem B 2016; 120:9265-76. [DOI: 10.1021/acs.jpcb.6b04978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jan P. Götze
- EastChem School of Chemistry, University of St Andrews, North
Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Michael Bühl
- EastChem School of Chemistry, University of St Andrews, North
Haugh, St Andrews, Fife KY16 9ST, U.K
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28
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Johnston RC, Zhou J, Smith JC, Parks JM. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin. J Phys Chem B 2016; 120:7307-18. [PMID: 27391132 DOI: 10.1021/acs.jpcb.6b02701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and Kon/off values. These findings demonstrate the effectiveness of the present approach for computing electrochemical and thermodynamic properties of a complex transition metal-containing cofactor.
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Affiliation(s)
- Ryne C Johnston
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | | | | | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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29
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Isegawa M, Neese F, Pantazis DA. Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches. J Chem Theory Comput 2016; 12:2272-84. [PMID: 27065224 DOI: 10.1021/acs.jctc.6b00252] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree-Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.
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Affiliation(s)
- Miho Isegawa
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
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30
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Abstract
In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.
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31
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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32
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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33
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Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces. MINERALS 2014. [DOI: 10.3390/min4020345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Fihey A, Maurel F, Perrier A. A DFT study of a new class of gold nanocluster-photochrome multi-functional switches. Phys Chem Chem Phys 2014; 16:26240-51. [DOI: 10.1039/c4cp03287j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural and electronic properties of dithienylethene photochromic molecules grafted onto a Au25 nanocluster are reviewed and electron/energy transfers are discussed with the help of (TD-)DFT calculations.
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Affiliation(s)
- Arnaud Fihey
- Laboratoire Interfaces
- Traitements
- Organisation et Dynamique des Systèmes (ITODYS)
- CNRS UMR 7086
- Université Paris 7 - Paris Diderot
| | - François Maurel
- Laboratoire Interfaces
- Traitements
- Organisation et Dynamique des Systèmes (ITODYS)
- CNRS UMR 7086
- Université Paris 7 - Paris Diderot
| | - Aurélie Perrier
- Laboratoire Interfaces
- Traitements
- Organisation et Dynamique des Systèmes (ITODYS)
- CNRS UMR 7086
- Université Paris 7 - Paris Diderot
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