1
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Rahbani N, de Silva P, Baudrin E. Density Functional Theory-Based Protocol to Calculate the Redox Potentials of First-row Transition Metal Complexes for Aqueous Redox Targeting Flow Batteries. CHEMSUSCHEM 2023; 16:e202300482. [PMID: 37226715 DOI: 10.1002/cssc.202300482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 05/26/2023]
Abstract
Transition metal complexes are a promising class of redox mediators for targeting redox flow batteries due to the tunability of their electrochemical potentials. However, reliable time-efficient tools for the prediction of their reduction potentials are needed. In this work, we establish a suitable density functional theory protocol for their prediction using an initial experimental data set of aqueous iron complexes with bidentate ligands. The approach is then cross-validated using different complexes found in the redox-flow literature. We find that the solvation model affects the prediction accuracy more than the functional or basis set. The smallest errors are obtained using the COSMO-RS solvation model (mean average error (MAE)=0.24 V). With implicit solvation models, a general deviation from experimental results is observed. For a set of similar ligands, they can be corrected using simple linear regression (MAE=0.051 V for the initial set of iron complexes).
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Affiliation(s)
- Noura Rahbani
- Laboratoire de Réactivité et Chimie des Solides, CNRS UMR7314, Université de Picardie Jules Verne, 33 Rue St-Leu, 80039, Amiens, Cedex, France
| | - Piotr de Silva
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, 2800, Kongens Lyngby, Copenhagen, Denmark
| | - Emmanuel Baudrin
- Laboratoire de Réactivité et Chimie des Solides, CNRS UMR7314, Université de Picardie Jules Verne, 33 Rue St-Leu, 80039, Amiens, Cedex, France
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2
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Sundararajan M. Redox Potentials of Uranyl Ions in Macrocyclic Complexes: Quantifying the Role of Counter-Ions. ACS OMEGA 2023; 8:18041-18046. [PMID: 37251172 PMCID: PMC10210231 DOI: 10.1021/acsomega.3c01244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
Several uranyl ions strapped with Schiff-base ligands in the presence of redox-innocent metal ions are synthesized, and their reduction potentials are recently estimated. The change in Lewis acidity of the redox-innocent metal ions contributes to ∼60 mV/pKa unit quantified which is intriguing. Upon increasing the Lewis acidity of metal ions, the number of triflate molecules found near the metal ions also increases whose contributions toward the redox potentials remain poorly understood and not quantified until now. Most importantly, to ease the computational burden, triflate anions are often neglected in quantum chemical models due to their larger size and weak coordination to metal ions. Herein, we have quantified and dissected the individual contributions that arise alone from Lewis acid metal ions and from triflate anions with electronic structure calculations. The triflate anion contributions are large, in particular, for divalent and trivalent anions that cannot be neglected. It was presumed to be innocent, but we here show that they can contribute more than 50% to the predicted redox potentials, suggesting that their vital role in the overall reduction processes cannot be neglected.
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3
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Malcomson T, Repiščák P, Erhardt S, Paterson MJ. Protocols for Understanding the Redox Behavior of Copper-Containing Systems. ACS OMEGA 2022; 7:45057-45066. [PMID: 36530299 PMCID: PMC9753522 DOI: 10.1021/acsomega.2c05484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Suitability of single-reference density functional theory (DFT) methods for the calculation of redox potentials of copper-containing macrocycle complexes was confirmed by the use of T 1 diagnostics along with a verification of negligible spin contamination or wave function instability. When examining the effect of improvement in the cc-pVnZ basis set series on calculated redox potentials, the results readily converged at the cc-pVTZ level. The all-electron Def2-TZVPP basis set is shown to be a suitable choice of a basis set for the calculation of redox potentials when utilizing a cc-pVTZ geometry. The best-performing model chemistries are determined to be the M06/polarizable continuum model (PCM); therefore, a scheme for redox potential calculations of copper macrocycles using either M06/cc-pVTZ with PCM solvation is proposed to reliably reproduce experimental trends.
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Affiliation(s)
- Thomas Malcomson
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, ManchesterM13 9PL, U.K.
| | - Peter Repiščák
- Beatson
Institute for Cancer Research, University
of Glasgow, Garscube Estate Switchback Road, BearsdenG61 1QH, U.K.
| | - Stefan Erhardt
- School
of Applied Sciences, Edinburgh Napier University, EdinburghEH11 4BN, Scotland, U.K.
| | - Martin J. Paterson
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, EdinburghEH14 4AS, U.K.
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4
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Kanamaru Y, Matsui T. Factor analysis of error in oxidation potential calculation: A machine learning study. J Comput Chem 2022; 43:1504-1512. [PMID: 35762851 DOI: 10.1002/jcc.26953] [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: 04/15/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 11/11/2022]
Abstract
The conductor-like polarizable continuum model (C-PCM), which is a low-cost solvation model, cannot treat characteristic interactions between the solvent and substructure(s) of the solute. Moreover, the error in a charged system is significant. Using machine learning, we clarified that the systematic error of the oxidation potential calculated by the G3B3/C-PCM was correlated with the molecular size of a solute. The G3B3/C-PCM overestimated the Gibbs oxidation energy by averaging 6.94 kcal/mol. According to the performance of related methods reported in previous studies, this error is mainly due to the solvation energy of the charged solute. Additionally, we succeeded in reducing the error to 2.27 kcal/mol (32%)-3.2 kcal/mol (40%) by correction based on the substructure information of the solute. To modify the C-PCM, effects that correlate with the molecular size of the solute in the charged system should be incorporated.
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Affiliation(s)
- Yuki Kanamaru
- Department of Chemistry, Graduate School of Pure and Applied Science, University of Tsukuba, Tsukuba, Japan
| | - Toru Matsui
- Department of Chemistry, Graduate School of Pure and Applied Science, University of Tsukuba, Tsukuba, Japan
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5
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Park Y, Tian L, Kim S, Pabst TP, Kim J, Scholes GD, Chirik PJ. Visible-Light-Driven, Iridium-Catalyzed Hydrogen Atom Transfer: Mechanistic Studies, Identification of Intermediates, and Catalyst Improvements. JACS AU 2022; 2:407-418. [PMID: 35252990 PMCID: PMC8889617 DOI: 10.1021/jacsau.1c00460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 06/14/2023]
Abstract
The harvesting of visible light is a powerful strategy for the synthesis of weak chemical bonds involving hydrogen that are below the thermodynamic threshold for spontaneous H2 evolution. Piano-stool iridium hydride complexes are effective for the blue-light-driven hydrogenation of organic substrates and contra-thermodynamic dearomative isomerization. In this work, a combination of spectroscopic measurements, isotopic labeling, structure-reactivity relationships, and computational studies has been used to explore the mechanism of these stoichiometric and catalytic reactions. Photophysical measurements on the iridium hydride catalysts demonstrated the generation of long-lived excited states with principally metal-to-ligand charge transfer (MLCT) character. Transient absorption spectroscopic studies with a representative substrate, anthracene revealed a diffusion-controlled dynamic quenching of the MLCT state. The triplet state of anthracene was detected immediately after the quenching events, suggesting that triplet-triplet energy transfer initiated the photocatalytic process. The key role of triplet anthracene on the post-energy transfer step was further demonstrated by employing photocatalytic hydrogenation with a triplet photosensitizer and a HAT agent, hydroquinone. DFT calculations support a concerted hydrogen atom transfer mechanism in lieu of stepwise electron/proton or proton/electron transfer pathways. Kinetic monitoring of the deactivation channel established an inverse kinetic isotope effect, supporting reversible C(sp2)-H reductive coupling followed by rate-limiting ligand dissociation. Mechanistic insights enabled design of a piano-stool iridium hydride catalyst with a rationally modified supporting ligand that exhibited improved photostability under blue light irradiation. The complex also provided improved catalytic performance toward photoinduced hydrogenation with H2 and contra-thermodynamic isomerization.
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6
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Bhattacharjee S, Isegawa M, Garcia-Ratés M, Neese F, Pantazis DA. Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches. J Chem Theory Comput 2022; 18:1619-1632. [PMID: 35191695 PMCID: PMC8908766 DOI: 10.1021/acs.jctc.1c01267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Hydrated transition
metal ions are prototypical systems that can
be used to model properties of transition metals in complex chemical
environments. These seemingly simple systems present challenges for
computational chemistry and are thus crucial in evaluations of quantum
chemical methods for spin-state and redox energetics. In this work,
we explore the applicability of the domain-based pair natural orbital
implementation of coupled cluster (DLPNO-CC) theory to the calculation
of ionization energies and redox potentials for hydrated ions of all
first transition row (3d) metals in the 2+/3+ oxidation states, in
connection with various solvation approaches. In terms of model definition,
we investigate the construction of a minimally explicitly hydrated
quantum cluster with a first and second hydration layer. We report
on the convergence with respect to the coupled cluster expansion and
the PNO space, as well as on the role of perturbative triple excitations.
A recent implementation of the conductor-like polarizable continuum
model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent
redox potentials at the coupled cluster level. Our results establish
conditions for the convergence of DLPNO-CCSD(T) energetics and stress
the absolute necessity to explicitly consider the second solvation
sphere even when CPCM is used. The achievable accuracy for redox potentials
of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore,
multilayer approaches that combine a higher-level DLPNO-CCSD(T) description
of the first solvation sphere with a lower-level description of the
second solvation layer are investigated. The present work establishes
optimal and transferable methodological choices for employing DLPNO-based
coupled cluster theory, the associated CPCM implementation, and cost-efficient
multilayer derivatives of the approach for open-shell transition metal
systems in complex environments.
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Affiliation(s)
- Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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7
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Hruska E, Gale A, Liu F. Bridging the Experiment-Calculation Divide: Machine Learning Corrections to Redox Potential Calculations in Implicit and Explicit Solvent Models. J Chem Theory Comput 2022; 18:1096-1108. [PMID: 34991320 DOI: 10.1021/acs.jctc.1c01040] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Prediction of redox potentials is essential for catalysis and energy storage. Although density functional theory (DFT) calculations have enabled rapid redox potential predictions for numerous compounds, prominent errors persist compared to experimental measurements. In this work, we develop machine learning (ML) models to reduce the errors of redox potential calculations in both implicit and explicit solvent models. Training and testing of the ML correction models are based on the diverse ROP313 data set with experimental redox potentials measured for organic and organometallic compounds in a variety of solvents. For the implicit solvent approach, our ML models can reduce both the systematic bias and the number of outliers. ML corrected redox potentials also demonstrate less sensitivity to DFT functional choice. For the explicit solvent approach, we significantly reduce the computational costs by embedding the microsolvated cluster in implicit bulk solvent, obtaining converged redox potential results with a smaller solvation shell. This combined implicit-explicit solvent model, together with GPU-accelerated quantum chemistry methods, enabled rapid generation of a large data set of explicit-solvent-calculated redox potentials for 165 organic compounds, allowing detailed investigation of the error sources in explicit solvent redox potential calculations.
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Affiliation(s)
- Eugen Hruska
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ariel Gale
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Fang Liu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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8
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Pankov I, Skidanenko A, Tsaturyan A. Impact of substituent nature in diformylpyridyl Schiff base on photophysical and electrochemical properties of ruthenium- and iron-based complexes. NEW J CHEM 2022. [DOI: 10.1039/d2nj04050f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The effect of substituents on the optical properties, redox potential, and reorganization energy in a series of Ru and Fe based complexes was studied. All studied complexes respond to the requirements for a sensitizer as the main component of DSSC.
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Affiliation(s)
- Ilya Pankov
- Institute of Physical and Organic Chemistry, Southern Federal University, Stachki Av. 194/2, Rostov-on-Don, Russia
| | - Anna Skidanenko
- Institute of Physical and Organic Chemistry, Southern Federal University, Stachki Av. 194/2, Rostov-on-Don, Russia
| | - Arshak Tsaturyan
- Institute of Physical and Organic Chemistry, Southern Federal University, Stachki Av. 194/2, Rostov-on-Don, Russia
- Univ Lyon, UJM-Saint-Etienne, CNRS, IOGS, Laboratoire Hubert Curien UMR5516, F-42023 St-Etienne, France
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9
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Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming. Molecules 2021; 26:molecules26206129. [PMID: 34684710 PMCID: PMC8538827 DOI: 10.3390/molecules26206129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
The effect of hydrogen bonds around the active site of Anabaena [2Fe-2S] ferredoxin (Fd) on a vertical ionization potential of the reduced state (IP(red)) is examined based on the density functional theory (DFT) calculations. The results indicate that a single hydrogen bond increases the relative stability of the reduced state, and shifts IP(red) to a reductive side by 0.31–0.33 eV, regardless of the attached sulfur atoms. In addition, the IP(red) value can be changed by the number of hydrogen bonds around the active site. The results also suggest that the redox potential of [2Fe-2S] Fd is controlled by the number of hydrogen bonds because IP(red) is considered to be a major factor in the redox potential. Furthermore, there is a possibility that the redox potentials of artificial iron-sulfur clusters can be finely controlled by the number of the hydrogen bonds attached to the sulfur atoms of the cluster.
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10
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Nandy A, Duan C, Taylor MG, Liu F, Steeves AH, Kulik HJ. Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning. Chem Rev 2021; 121:9927-10000. [PMID: 34260198 DOI: 10.1021/acs.chemrev.1c00347] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transition-metal complexes are attractive targets for the design of catalysts and functional materials. The behavior of the metal-organic bond, while very tunable for achieving target properties, is challenging to predict and necessitates searching a wide and complex space to identify needles in haystacks for target applications. This review will focus on the techniques that make high-throughput search of transition-metal chemical space feasible for the discovery of complexes with desirable properties. The review will cover the development, promise, and limitations of "traditional" computational chemistry (i.e., force field, semiempirical, and density functional theory methods) as it pertains to data generation for inorganic molecular discovery. The review will also discuss the opportunities and limitations in leveraging experimental data sources. We will focus on how advances in statistical modeling, artificial intelligence, multiobjective optimization, and automation accelerate discovery of lead compounds and design rules. The overall objective of this review is to showcase how bringing together advances from diverse areas of computational chemistry and computer science have enabled the rapid uncovering of structure-property relationships in transition-metal chemistry. We aim to highlight how unique considerations in motifs of metal-organic bonding (e.g., variable spin and oxidation state, and bonding strength/nature) set them and their discovery apart from more commonly considered organic molecules. We will also highlight how uncertainty and relative data scarcity in transition-metal chemistry motivate specific developments in machine learning representations, model training, and in computational chemistry. Finally, we will conclude with an outlook of areas of opportunity for the accelerated discovery of transition-metal complexes.
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Affiliation(s)
- Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Takahashi T, Matsui T, Hengphasatporn K, Shigeta Y. A Practical Prediction of Log Po/w through Semiempirical Electronic Structure Calculations with Dielectric Continuum Model. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Teruyuki Takahashi
- Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Toru Matsui
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
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12
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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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13
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Liu Y, Han Z, Yang Y, Zhu R, Liu C, Zhang D. DFT study on synergetic Ir/Cu-metallaphotoredox catalyzed trifluoromethylation of aryl bromides. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2020.111294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Gryaznova TV, Khrizanforov MN, Levitskaya AI, Kh.Rizvanov I, Balakina MY, Ivshin KA, Kataeva ON, Budnikova YH. Electrochemically Driven and Acid-Driven Pyridine-Directed ortho-Phosphorylation of C(sp2)–H Bonds. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tatyana V. Gryaznova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Mikhail N. Khrizanforov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Alina I. Levitskaya
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Ildar Kh.Rizvanov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Marina Yu. Balakina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Kamil A. Ivshin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Olga N. Kataeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
| | - Yulia H. Budnikova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov-str., 8, Kazan 420088, Russian Federation
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15
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Miyagawa Y, Tsatsuryan A, Haraguchi T, Shcherbakov I, Akitsu T. Photochemical reduction of Cr( vi) compounds by amino acid Schiff base copper complexes with a hydroxyl group and titanium oxide composites in aqueous solutions. NEW J CHEM 2020. [DOI: 10.1039/d0nj02481c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-driven reduction reaction of Cr(vi) to Cr(iii) by Schiff base Cu(ii) complexes was studied in aqueous and methanol solutions. The Cr(vi) reduction ratio with the CuVDB–TiO2 system reached 91%.
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Affiliation(s)
- Yoshito Miyagawa
- Department of Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Arshak Tsatsuryan
- Institute of Physical and Organic Chemistry
- Southern Federal University
- Rostov-on-Don
- Russian Federation
- Department of Chemistry
| | - Tomoyuki Haraguchi
- Department of Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Igor Shcherbakov
- Department of Chemistry
- Southern Federal University
- Rostov-on-Don
- Russia
| | - Takashiro Akitsu
- Department of Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
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16
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A Density Functional Theory-Based Scheme to Compute the Redox Potential of a Transition Metal Complex: Applications to Heme Compound. Molecules 2019; 24:molecules24040819. [PMID: 30823577 PMCID: PMC6412623 DOI: 10.3390/molecules24040819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 12/23/2022] Open
Abstract
We estimated the redox potential of a model heme compound by using the combination of our density functionals with a computational scheme, which corrects the solvation energy to the normal solvent model. Among many density functionals, the LC-BOP12 functional gave the smallest mean absolute error of 0.16 V in the test molecular sets. The application of these methods revealed that the redox potential of a model heme can be controlled within 200 mV by changing the protonation state and even within 20 mV by the flipping of the ligand histidine. In addition, the redox potential depends on the inverse of the dielectric constant, which controls the surroundings. The computational results also imply that a system with a low dielectric constant avoids the charged molecule by controlling either the redox potential or the protonation system.
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17
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Nakagame R, Tsaturyan A, Haraguchi T, Pimonova Y, Lastovina T, Akitsu T, Shcherbakov I. Photochemical reaction of amino acid Schiff base derived Cu complexes with extended π-system and their titanium oxide composites. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Fujiki R, Kasai Y, Seno Y, Matsui T, Shigeta Y, Yoshida N, Nakano H. A computational scheme of pK a values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme. Phys Chem Chem Phys 2018; 20:27272-27279. [PMID: 30167611 DOI: 10.1039/c8cp04354j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A scheme for quantitatively computing the acid dissociation constant, pKa, of hydrated molecules is proposed. It is based on the three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) theory coupled with the linear fitting correction (LFC) scheme. In LFC/3D-RISM-SCF, pKa values of target molecules are evaluated using the Gibbs energy difference between the protonated and unprotonated states calculated by 3D-RISM-SCF and the parameters fitted by the LFC scheme to the experimental values of training set systems. The pKa values computed by LFC/3D-RISM-SCF show quantitative agreement with the experimental data.
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Affiliation(s)
- Ryo Fujiki
- Department of Chemistry, Graduate School of Science, Kyushu University, 744, Motooka, Nishiku, Fukuoka, 819-0395, Japan.
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Kanematsu Y, Kondo HX, Imada Y, Takano Y. Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Kurniawan I, Kawaguchi K, Shoji M, Matsui T, Shigeta Y, Nagao H. A Theoretical Study on Redox Potential and p Kaof [2Fe-2S] Cluster Model from Iron-Sulfur Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Isman Kurniawan
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- School of Computing, Telkom University, Terusan Buah Batu, Bandung, 40257 Indonesia
| | - Kazutomo Kawaguchi
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Toru Matsui
- College of Chemistry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hidemi Nagao
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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21
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Kurniawan I, Kawaguchi K, Sugimori K, Sakurai T, Nagao H. Quantum Chemical Study of Axial Ligand Effect on the Electronic Properties of Type I Copper Protein. CHEM LETT 2018. [DOI: 10.1246/cl.180521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isman Kurniawan
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- School of Computing, Telkom University, Jl. Telekomunikasi, Terusan Buah Batu, Bandung, Indonesia 40257
| | - Kazutomo Kawaguchi
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kimikazu Sugimori
- Division of Higher Education Research and Development, Institute of Liberal Arts and Science, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidemi Nagao
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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22
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Photo-induced reduction of Cr6+ by the hybrid systems “CuII complex with Schiff base and TiO2”: dependence on irradiation wavelength. Russ Chem Bull 2018. [DOI: 10.1007/s11172-017-1981-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Imada Y, Nakamura H, Takano Y. Density functional study of porphyrin distortion effects on redox potential of heme. J Comput Chem 2017; 39:143-150. [DOI: 10.1002/jcc.25058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/29/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Yasuhiro Imada
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Haruki Nakamura
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Yu Takano
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
- Department of Biomedical Information Sciences; Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku; Hiroshima 731-3194 Japan
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24
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Liang G, DeYonker NJ, Zhao X, Webster CE. Prediction of the reduction potential in transition‐metal containing complexes: How expensive? For what accuracy? J Comput Chem 2017; 38:2430-2438. [DOI: 10.1002/jcc.24894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/26/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Guangchao Liang
- Department of ChemistryMississippi State University, Mississippi StateMississippi39762‐9573
| | | | - Xuan Zhao
- Department of ChemistryThe University of MemphisMemphis Tennessee38152
| | - Charles Edwin Webster
- Department of ChemistryMississippi State University, Mississippi StateMississippi39762‐9573
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25
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Bím D, Rulíšek L, Srnec M. Accurate Prediction of One-Electron Reduction Potentials in Aqueous Solution by Variable-Temperature H-Atom Addition/Abstraction Methodology. J Phys Chem Lett 2016; 7:7-13. [PMID: 26647144 DOI: 10.1021/acs.jpclett.5b02452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A robust and efficient theoretical approach for calculation of the reduction potentials of charged species in aqueous solution is presented. Within this approach, the reduction potential of a charged complex (with a charge |n| ≥ 2) is probed by means of the reduction potential of its neutralized (protonated/deprotonated) cognate, employing one or several H-atom addition/abstraction thermodynamic cycles. This includes a separation of one-electron reduction from protonation/deprotonation through the temperature dependence. The accuracy of the method has been assessed for the set of 15 transition-metal complexes that are considered as highly challenging systems for computational electrochemistry. Unlike the standard computational protocol(s), the presented approach yields results that are in excellent agreement with experimental electrochemical data. Last but not least, the applicability and limitations of the approach are thoroughly discussed.
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Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3, 182 20 Praha 8, Czech Republic
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MATSUI T, KIYAN A, SHOJI M, SHIGETA Y. Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Toru MATSUI
- Graduate School of Pure and Applied Sciences, University of Tsukuba.Center for Computational Sciences, University of Tsukuba. 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akane KIYAN
- Graduate School of Pure and Applied Sciences, University of Tsukuba.Center for Computational Sciences, University of Tsukuba. 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuo SHOJI
- Graduate School of Pure and Applied Sciences, University of Tsukuba.Center for Computational Sciences, University of Tsukuba. 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru SHIGETA
- Graduate School of Pure and Applied Sciences, University of Tsukuba.Center for Computational Sciences, University of Tsukuba. 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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27
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Yan L, Lu Y, Li X. A density functional theory protocol for the calculation of redox potentials of copper complexes. Phys Chem Chem Phys 2016; 18:5529-36. [DOI: 10.1039/c5cp06638g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The calculated redox potentials of copper complexes agree nicely with their corresponding experimental redox potentials.
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Affiliation(s)
- Liuming Yan
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Yi Lu
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Xuejiao Li
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 200444
- China
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28
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Maekawa S, Matsui T, Hirao K, Shigeta Y. Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Toward Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase. J Phys Chem B 2015; 119:5392-403. [DOI: 10.1021/acs.jpcb.5b01356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shintaro Maekawa
- Computational
Science Group, Mitsui Chemicals, Inc., 580-32 Nagaura, Sodegaura, Chiba 299-0265, Japan
| | - Toru Matsui
- RIKEN, Advanced
Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Kimihiko Hirao
- RIKEN, Advanced
Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yasuteru Shigeta
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawagoe, Saitama 332-0012, Japan
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29
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Caballero-Jiménez J, Habib F, Ramírez-Rosales D, Grande-Aztatzi R, Merino G, Korobkov I, Singh MK, Rajaraman G, Reyes-Ortega Y, Murugesu M. Inducing magnetic communication in caged dinuclear Co(ii) systems. Dalton Trans 2015; 44:8649-59. [DOI: 10.1039/c5dt00497g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Magnetic interactions were probed for a series of mono and tri atomic bridged dinuclear Co(ii) azacryptand complexes. Magneto-structural correlations were established usingab initiocalculations.
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Affiliation(s)
| | - Fatemah Habib
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada K1N6N5
| | - Daniel Ramírez-Rosales
- Departamento de Física
- Escuela Superior de Física y Matemáticas
- I.P.N
- Av. Instituto Politécnico Nacional s/n San Pedro Zacatenco
- México 07738
| | - Rafael Grande-Aztatzi
- Departamento de Física Aplicada
- Centro de Investigación de Estudios Avanzados Unidad Mérida. km 6 Antigua carretera a Progreso
- Mérida
- México
| | - Gabriel Merino
- Departamento de Física Aplicada
- Centro de Investigación de Estudios Avanzados Unidad Mérida. km 6 Antigua carretera a Progreso
- Mérida
- México
| | - Ilia Korobkov
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada K1N6N5
| | | | - Gopalan Rajaraman
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
| | - Yasmi Reyes-Ortega
- Centro de Química
- Instituto de Ciencias
- Universidad Autónoma de Puebla
- 72000 Puebla
- México
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30
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Barrière F. Electrostatic Modeling of the Tunable Potential Difference between the Two Consecutive Oxidation Steps of Dinickel Bisfulvalene. Organometallics 2014. [DOI: 10.1021/om500248z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Frédéric Barrière
- Institut des Sciences Chimiques de Rennes,
Equipe MaCSE, Université de Rennes 1, CNRS UMR no. 6226, Rennes, France
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31
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Theoretical Predictions of Redox Potentials of Fischer-Type Chromium Aminocarbene Complexes. Organometallics 2014. [DOI: 10.1021/om500259u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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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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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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